From 7a73717422d6f83d705cc5bba3631dae212e12fd Mon Sep 17 00:00:00 2001 From: toshinagata1964 Date: Sat, 2 Jul 2011 15:24:26 +0000 Subject: [PATCH] Gaff and parm99 parameters: the equilibrium bond lengths have now three significant digits after the decimal point. Ruby: AtomRef#exclusion method is implemented. MM/MD: minimization sometimes caused crash. Hopefully fixed. git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@66 a2be9bc6-48de-4e38-9406-05402d4bc13c --- Documents/src/doc_source.html | 4 +- Documents/src/molby_rb/AtomRef.html | 20 + Makefile_amber11 | 2 +- MolLib/Ruby_bind/ruby_bind.c | 37 +- README | 2 +- Scripts/gaff.par | 1516 +++++++++++++++++------------------ Scripts/md.rb | 82 ++ Scripts/parm99.par | 390 +++++---- Version | 2 +- amberparm2molby.pl | 3 +- msw-build/molby.iss | 2 +- wxSources/MyDocument.cpp | 4 +- wxSources/MyVersion.c | 2 +- xcode-build/Info.plist | 2 +- 14 files changed, 1093 insertions(+), 975 deletions(-) diff --git a/Documents/src/doc_source.html b/Documents/src/doc_source.html index 809a71d..a64e42c 100644 --- a/Documents/src/doc_source.html +++ b/Documents/src/doc_source.html @@ -13,13 +13,13 @@

Molby

An Interactive Molecular Modeling Software
with Integrated Ruby Interpreter

-

Version 0.5.5 build 20110426

+

Version 0.5.5 build 20110702

Toshi Nagata

Molby

対話型分子モデリングソフトウェア
（Ruby インタプリタ内蔵）

-

Version 0.5.5 build 20110426

+

Version 0.5.5 build 20110702

永田　央

diff --git a/Documents/src/molby_rb/AtomRef.html b/Documents/src/molby_rb/AtomRef.html index eedbfac..13c852d 100644 --- a/Documents/src/molby_rb/AtomRef.html +++ b/Documents/src/molby_rb/AtomRef.html @@ -186,6 +186,26 @@ Setting the chemical element also causes change of the + +
+ +exclusion → [[i1, i2, ...], [j1, j2, ...], [k1, k2, ...]]
+ +
+
+

+Get the exclusion table, which is used to "exclude" the pair of atoms from the calculation of the non-bonding interaction. [i1, i2, ...] are the atoms which are directly connected to this atom (1-2 exclusion). [j1, j2, ...] are the atoms (other than self) that are connected to [i1, i2, ...] and not in the 1-2 exclusion list (1-3 exclusion). [k1, k2, ...] are the atoms (other than self) that are connected to [j1, j2, ...] and not in the 1-2 nor 1-3 exclusion list. +

+

+This is a read-only attribute. +

+

+This method requires that the MDArena object for the parent molecule is already established and prepare'd. +

+
+ + +
diff --git a/Makefile_amber11 b/Makefile_amber11 index ba28b26..47dbeb7 100644 --- a/Makefile_amber11 +++ b/Makefile_amber11 @@ -13,5 +13,5 @@ amber11 : ../amber11/src/antechamber/*.[ch] ../amber11/src/sqm/*.f ../amber11/sr cp -p ../amber11/dat/leap/parm/{gaff,parm99}.dat amber11/dat/leap/parm cp -rp ../amber11/dat/antechamber amber11/dat mkdir -p amber11/bin - cp -r build/amber11-build/bin/{am1bcc,atomtype,parmchk,antechamber,bondtype,resp,respgen,sqm}* amber11/bin + cp -r build/amber11-build/bin/{am1bcc,atomtype,parmchk,antechamber,bondtype,resp,respgen,prepgen,sqm}* amber11/bin diff --git a/MolLib/Ruby_bind/ruby_bind.c b/MolLib/Ruby_bind/ruby_bind.c index 438189b..06750cd 100644 --- a/MolLib/Ruby_bind/ruby_bind.c +++ b/MolLib/Ruby_bind/ruby_bind.c @@ -58,7 +58,8 @@ static VALUE s_RSym, s_XSym, s_YSym, s_ZSym, s_FractRSym, s_FractXSym, s_FractYSym, s_FractZSym, s_VSym, s_FSym, s_OccupancySym, s_TempFactorSym, - s_AnisoSym, s_IntChargeSym, s_FixForceSym, s_FixPosSym; + s_AnisoSym, s_IntChargeSym, s_FixForceSym, s_FixPosSym, + s_ExclusionSym; /* Symbols for parameter attributes */ static VALUE @@ -3293,6 +3294,34 @@ static VALUE s_AtomRef_GetFixPos(VALUE self) { return ValueFromVector(&(s_AtomFromValue(self)->fix_pos)); } +static VALUE s_AtomRef_GetExclusion(VALUE self) { + Molecule *mol; + Atom *ap; + int idx, i; + MDExclusion *exinfo; + Int *exlist; + VALUE retval, aval; + idx = s_AtomIndexFromValue(self, &ap, &mol); + if (mol->arena == NULL || mol->arena->is_initialized == 0 || mol->needsMDRebuild) + rb_raise(rb_eMolbyError, "Molecular dynamics is not ready. Please consider doing 'minimize' by hand or 'mol.md_arena.prepare' from script."); + exinfo = mol->arena->exinfo + idx; + exlist = mol->arena->exlist; + retval = rb_ary_new(); + aval = rb_ary_new(); + for (i = exinfo->index1; i < exinfo->index2; i++) /* 1-2 exclusion */ + rb_ary_push(aval, INT2NUM(exlist[i])); + rb_ary_push(retval, aval); + aval = rb_ary_new(); + for (i = exinfo->index2; i < exinfo->index3; i++) /* 1-3 exclusion */ + rb_ary_push(aval, INT2NUM(exlist[i])); + rb_ary_push(retval, aval); + aval = rb_ary_new(); + for (i = exinfo->index3; i < (exinfo + 1)->index0; i++) /* 1-4 exclusion */ + rb_ary_push(aval, INT2NUM(exlist[i])); + rb_ary_push(retval, aval); + return retval; +} + static VALUE s_AtomRef_SetIndex(VALUE self, VALUE val) { rb_raise(rb_eMolbyError, "index cannot be directly set"); return Qnil; @@ -3608,6 +3637,11 @@ static VALUE s_AtomRef_SetFixPos(VALUE self, VALUE val) { return val; } +static VALUE s_AtomRef_SetExclusion(VALUE self, VALUE val) { + rb_raise(rb_eMolbyError, "exclusion table is read-only."); + return val; /* Not reached */ +} + static struct s_AtomAttrDef { char *name; VALUE *symref; /* Address of s_IndexSymbol etc. */ @@ -3643,6 +3677,7 @@ static struct s_AtomAttrDef { {"int_charge", &s_IntChargeSym, 0, s_AtomRef_GetIntCharge, s_AtomRef_SetIntCharge}, {"fix_force", &s_FixForceSym, 0, s_AtomRef_GetFixForce, s_AtomRef_SetFixForce}, {"fix_pos", &s_FixPosSym, 0, s_AtomRef_GetFixPos, s_AtomRef_SetFixPos}, + {"exclusion", &s_ExclusionSym, 0, s_AtomRef_GetExclusion, s_AtomRef_SetExclusion}, {NULL} /* Sentinel */ }; diff --git a/README b/README index d998003..359cc14 100644 --- a/README +++ b/README @@ -5,7 +5,7 @@ An Interactive Molecular Modeling Software with Integrated Ruby Interpreter - Version 0.5.5 build 20110426 + Version 0.5.5 build 20110702 Toshi Nagata diff --git a/Scripts/gaff.par b/Scripts/gaff.par index f02d018..8aa9f8d 100644 --- a/Scripts/gaff.par +++ b/Scripts/gaff.par @@ -5,7 +5,7 @@ ! Thanks to the AMBER development team, the force field parameters are in the public domain. Hereby I acknowledge their great scientific contribution, with references to the literature as below. ! 1. D.A. Case, T.E. Cheatham, III, T. Darden, H. Gohlke, R. Luo, K.M. Merz, Jr., A. Onufriev, C. Simmerling, B. Wang and R. Woods. The Amber biomolecular simulation programs. J. Computat. Chem. 26, 1668-1688 (2005). ! 2. J.W. Ponder and D.A. Case. Force fields for protein simulations. Adv. Prot. Chem. 66, 27-85 (2003). Similar information for nucleic acids is given by T.E. Cheatham, III and M.A. Young. Molecular dynamics simulation of nucleic acids: Successes, limitations and promise. Biopolymers 56, 232-256 (2001). -! 3. D.A. Case, T.A. Darden, T.E. Cheatham, III, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, M. Crowley, Ross C. Walker,W. Zhang, K.M. Merz, B.Wang, S. Hayik, A. Roitberg, G. Seabra, I. Kolossváry, K.F.Wong, F. Paesani, J. Vanicek, X.Wu, S.R. Brozell, T. Steinbrecher, H. Gohlke, L. Yang, C. Tan, J. Mongan, V. Hornak, G. Cui, D.H. Mathews, M.G. Seetin, C. Sagui, V. Babin, and P.A. Kollman (2008), AMBER 10, University of California, San Francisco. +! 3. D.A. Case, T.A. Darden, T.E. Cheatham, III, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, M. Crowley, Ross C. Walker,W. Zhang, K.M. Merz, B.Wang, S. Hayik, A. Roitberg, G. Seabra, I. Kolossvﾃ｡ry, K.F.Wong, F. Paesani, J. Vanicek, X.Wu, S.R. Brozell, T. Steinbrecher, H. Gohlke, L. Yang, C. Tan, J. Mongan, V. Hornak, G. Cui, D.H. Mathews, M.G. Seetin, C. Sagui, V. Babin, and P.A. Kollman (2008), AMBER 10, University of California, San Francisco. ! vdw h1 0.0157 1.3870 0.0157 1.3870 0 1.008 ! H bonded to aliphatic carbon with 1 electrwd. group vdw h2 0.0157 1.2870 0.0157 1.2870 0 1.008 ! H bonded to aliphatic carbon with 2 electrwd. group @@ -42,7 +42,6 @@ vdw cv 0.0860 1.9080 0.0860 1.9080 0 12.010 ! Sp2 carbons in square systems vdw cx 0.0860 1.9080 0.0860 1.9080 0 12.010 ! Sp3 carbons in triangle systems vdw cy 0.0860 1.9080 0.0860 1.9080 0 12.010 ! Sp3 carbons in square systems vdw n 0.1700 1.8240 0.1700 1.8240 0 14.010 ! Sp2 nitrogen in amide groups -vdw n 0.1700 1.8240 0.1700 1.8240 0 0.000 vdw n1 0.1700 1.8240 0.1700 1.8240 0 14.010 ! Sp N vdw n2 0.1700 1.8240 0.1700 1.8240 0 14.010 ! aliphatic Sp2 N with two connected atoms vdw n3 0.1700 1.8240 0.1700 1.8240 0 14.010 ! Sp3 N with three connected atoms @@ -75,753 +74,745 @@ vdw cl 0.2650 1.9480 0.2650 1.9480 0 35.450 ! Chlorine vdw br 0.3200 2.2200 0.3200 2.2200 0 79.900 ! Bromine vdw i 0.4000 2.3500 0.4000 2.3500 0 126.900 ! Iodine -bond ow hw 553.0 0.96 ! TIP3P water -bond br br 123.2 2.54 ! SOURCE1 4 0.0000 0.0000 -bond br c 240.3 1.95 ! SOURCE2 2 0.0285 0.0285 -bond br c1 352.7 1.79 ! SOURCE2 4 0.0022 0.0024 -bond br c2 278.7 1.88 ! SOURCE1 31 0.0000 0.0000 -bond br c3 229.5 1.97 ! SOURCE1 100 0.0000 0.0000 -bond br ca 269.6 1.90 ! SOURCE1 127 0.0028 0.0058 -bond br cx 261.4 1.91 ! SOURCE1 8 0.0000 0.0000 -bond br i 142.4 2.67 ! SOURCE1 2 0.0245 0.0245 -bond br n 320.2 1.87 ! SOURCE3 4 0.0037 0.0046 -bond br n1 330.4 1.86 ! SOURCE0 1 -bond br n2 219.0 2.04 ! SOURCE3 5 0.0956 0.1082 -bond br n3 265.9 1.95 ! SOURCE3 2 0.0000 0.0000 -bond br n4 282.4 1.93 ! SOURCE3 3 0.0012 0.0013 -bond br na 237.3 2.00 ! SOURCE3 7 0.1938 0.2156 -bond br nh 270.9 1.94 ! SOURCE3 1 0.0000 0.0000 -bond br no 191.0 2.10 ! SOURCE3 1 0.0000 0.0000 -bond br o 278.9 1.80 ! SOURCE0 1 -bond br oh 237.2 1.87 ! SOURCE3 1 0.0000 0.0000 -bond br os 225.6 1.89 ! SOURCE3 2 0.0000 0.0000 -bond br p2 174.3 2.21 ! SOURCE3 9 0.0470 0.0510 -bond br p3 167.0 2.23 ! SOURCE3 3 0.0096 0.0101 -bond br p4 188.8 2.17 ! SOURCE0 1 -bond br p5 179.3 2.20 ! SOURCE3 3 0.0094 0.0099 -bond br s 170.6 2.22 ! SOURCE0 1 -bond br s4 134.3 2.34 ! SOURCE3 1 0.0000 0.0000 -bond br s6 172.7 2.21 ! SOURCE3 3 0.0417 0.0443 -bond br sh 174.4 2.21 ! SOURCE3 1 0.0000 0.0000 -bond br ss 176.6 2.20 ! SOURCE3 3 0.0033 0.0035 -bond c c 290.1 1.55 ! SOURCE1 31 0.0080 0.0100 -bond c c1 379.8 1.46 ! SOURCE0 1 -bond c c2 449.9 1.41 ! SOURCE3 2 0.0370 0.0370 -bond c c3 328.3 1.51 ! SOURCE1 2949 0.0049 0.0060 -bond c ca 349.7 1.49 ! SOURCE1 480 0.0031 0.0055 -bond c cc 377.4 1.46 ! SOURCE3 132 0.0165 0.0210 -bond c cd 377.4 1.46 ! SOURCE3 132 0.0165 0.0210 -bond c ce 363.8 1.47 ! SOURCE1 601 0.0091 0.0105 -bond c cf 363.8 1.47 ! SOURCE1 601 0.0091 0.0105 -bond c cg 389.3 1.45 ! SOURCE3 2 0.0000 0.0000 -bond c ch 389.3 1.45 ! SOURCE3 2 same as c -cg -bond c cl 293.5 1.77 ! SOURCE3 6 0.0235 0.0250 -bond c cu 441.4 1.41 ! SOURCE2 1 0.0000 0.0000 -bond c cx 350.8 1.49 ! SOURCE1 105 0.0000 0.0000 -bond c cy 308.5 1.53 ! SOURCE1 18 0.0000 0.0000 -bond c f 387.9 1.32 ! SOURCE2 6 0.0140 0.0147 -bond c ha 325.1 1.10 ! SOURCE3 53 0.0078 0.0102 -bond c i 198.9 2.21 ! SOURCE3 4 0.0332 0.0365 -bond c n 478.2 1.34 ! SOURCE1 1235 0.0162 0.0215 -bond c n2 374.6 1.42 ! SOURCE0 1 -bond c n4 255.5 1.55 ! SOURCE3 4 0.0388 0.0388 -bond c nc 438.8 1.37 ! SOURCE3 2 0.0108 0.0108 -bond c nd 438.8 1.37 ! SOURCE3 2 same as c -nc -bond c ne 388.0 1.41 ! SOURCE3 3 0.0088 0.0094 -bond c nf 388.0 1.41 ! SOURCE3 3 same as c -ne -bond c no 260.1 1.54 ! SOURCE0 1 -bond c o 648.0 1.21 ! SOURCE1 3682 0.0134 0.0165 -bond c oh 466.4 1.31 ! SOURCE1 271 0.0026 0.0041 -bond c os 411.3 1.34 ! SOURCE1 1044 0.0114 0.0171 -bond c p2 210.3 1.90 ! SOURCE0 1 -bond c p3 219.0 1.88 ! SOURCE3 6 0.0094 0.0129 -bond c p4 220.6 1.88 ! SOURCE0 1 -bond c p5 225.9 1.87 ! SOURCE0 1 -bond c pe 204.9 1.91 ! SOURCE3 3 0.0023 0.0025 -bond c pf 204.9 1.91 ! SOURCE3 3 same as c -pe -bond c px 208.3 1.90 ! SOURCE3 1 0.0000 0.0000 -bond c py 227.6 1.87 ! SOURCE3 6 0.0141 0.0199 -bond c s 328.9 1.68 ! SOURCE1 401 0.0077 0.0128 -bond c s4 200.4 1.87 ! SOURCE0 1 -bond c s6 200.4 1.87 ! SOURCE0 1 -bond c sh 249.6 1.78 ! SOURCE3 6 0.0157 0.0171 -bond c ss 261.9 1.76 ! SOURCE1 20 0.0000 0.0000 -bond c sx 193.3 1.89 ! SOURCE3 5 0.0070 0.0088 -bond c sy 202.8 1.86 ! SOURCE3 5 0.0063 0.0085 -bond c1 c1 986.2 1.18 ! SOURCE1 265 0.0022 0.0031 -bond c1 c2 625.0 1.31 ! SOURCE1 18 0.0000 0.0000 -bond c1 c3 368.3 1.47 ! SOURCE1 215 0.0013 0.0017 -bond c1 ca 404.1 1.44 ! SOURCE0 1 -bond c1 cg 845.8 1.22 ! SOURCE3 22 0.0074 0.0101 -bond c1 ch 845.8 1.22 ! SOURCE3 22 same as c1-cg -bond c1 cl 419.7 1.63 ! SOURCE2 6 0.0046 0.0050 -bond c1 cx 399.1 1.44 ! SOURCE1 38 0.0000 0.0000 -bond c1 f 469.4 1.27 ! SOURCE2 2 0.0085 0.0085 -bond c1 ha 375.9 1.07 ! SOURCE3 63 0.0022 0.0035 -bond c1 hc 385.6 1.06 ! SOURCE0 1 -bond c1 i 318.8 1.99 ! SOURCE2 4 0.0025 0.0032 -bond c1 n 503.0 1.33 ! SOURCE0 1 -bond c1 n1 1014.5 1.14 ! SOURCE1 170 0.0038 0.0055 -bond c1 n2 769.8 1.21 ! SOURCE3 5 0.0089 0.0115 -bond c1 n3 409.8 1.39 ! SOURCE2 1 0.0000 0.0000 -bond c1 n4 378.2 1.42 ! SOURCE3 3 0.0030 0.0032 -bond c1 na 452.0 1.36 ! SOURCE3 8 0.0031 0.0034 -bond c1 ne 741.8 1.22 ! SOURCE3 1 0.0000 0.0000 -bond c1 nf 741.8 1.22 ! SOURCE3 1 same as c1-ne -bond c1 ng 465.7 1.35 ! SOURCE3 3 0.0025 0.0027 -bond c1 nh 465.7 1.35 ! SOURCE3 3 0.0025 0.0027 -bond c1 no 393.0 1.41 ! SOURCE3 3 0.0004 0.0005 -bond c1 o 777.0 1.17 ! SOURCE2 9 0.0044 0.0052 -bond c1 oh 435.6 1.33 ! SOURCE3 1 0.0000 0.0000 -bond c1 os 437.1 1.32 ! SOURCE3 3 0.0139 0.0148 -bond c1 p2 289.3 1.77 ! SOURCE0 1 -bond c1 p3 275.1 1.79 ! SOURCE0 1 -bond c1 p4 275.1 1.79 ! SOURCE0 1 -bond c1 p5 302.2 1.75 ! SOURCE3 2 0.0000 0.0000 -bond c1 s 371.8 1.63 ! SOURCE1 14 0.0000 0.0000 -bond c1 s2 410.0 1.59 ! SOURCE3 1 0.0000 0.0000 -bond c1 s4 272.9 1.75 ! SOURCE3 2 0.0000 0.0000 -bond c1 s6 290.4 1.72 ! SOURCE3 2 0.0000 0.0000 -bond c1 sh 324.5 1.68 ! SOURCE0 1 -bond c1 ss 325.4 1.68 ! SOURCE1 10 0.0000 0.0000 -bond c2 c2 589.7 1.32 ! SOURCE1 974 0.0048 0.0096 -bond c2 c3 328.3 1.51 ! SOURCE1 2536 0.0016 0.0021 -bond c2 ca 357.2 1.48 ! SOURCE0 1 -bond c2 cc 522.6 1.36 ! SOURCE1 771 0.0152 0.0185 -bond c2 cd 522.6 1.36 ! SOURCE1 771 0.0152 0.0185 -bond c2 ce 560.5 1.34 ! SOURCE3 62 0.0085 0.0128 -bond c2 cf 560.5 1.34 ! SOURCE3 62 same as c2-ce -bond c2 cl 328.8 1.72 ! SOURCE1 163 0.0093 0.0098 -bond c2 cu 573.9 1.33 ! SOURCE2 1 0.0000 0.0000 -bond c2 cx 333.3 1.50 ! SOURCE2 1 0.0000 0.0000 -bond c2 cy 309.4 1.53 ! SOURCE2 1 0.0000 0.0000 -bond c2 f 368.7 1.34 ! SOURCE1 34 0.0000 0.0000 -bond c2 h4 348.6 1.08 ! SOURCE3 40 0.0037 0.0058 -bond c2 h5 357.5 1.08 ! SOURCE3 3 0.0061 0.0067 -bond c2 ha 344.3 1.09 ! SOURCE3 797 0.0030 0.0046 -bond c2 hc 344.3 1.09 ! SOURCE3 789 0.0030 0.0046 -bond c2 hx 350.1 1.08 ! SOURCE3 3 0.0008 0.0008 -bond c2 i 223.2 2.15 ! SOURCE3 2 0.0000 0.0000 -bond c2 n 390.5 1.41 ! SOURCE3 9 0.0109 0.0124 -bond c2 n1 546.0 1.31 ! SOURCE3 4 0.0161 0.0161 -bond c2 n2 581.1 1.29 ! SOURCE1 103 0.0095 0.0100 -bond c2 n3 486.3 1.34 ! SOURCE0 1 -bond c2 n4 309.1 1.48 ! SOURCE3 5 0.0047 0.0064 -bond c2 na 411.1 1.39 ! SOURCE3 31 0.0271 0.0289 -bond c2 nc 533.0 1.31 ! SOURCE1 99 0.0065 0.0095 -bond c2 nd 533.0 1.31 ! SOURCE1 99 same as c2-nc -bond c2 ne 597.7 1.28 ! SOURCE3 37 0.0090 0.0110 -bond c2 nf 597.7 1.28 ! SOURCE3 37 same as c2-ne -bond c2 nh 462.6 1.35 ! SOURCE3 38 0.0385 0.0413 -bond c2 no 327.6 1.46 ! SOURCE3 4 0.0013 0.0013 -bond c2 o 546.2 1.26 ! SOURCE3 4 0.0144 0.0144 -bond c2 oh 425.4 1.33 ! SOURCE1 53 0.0000 0.0000 -bond c2 os 392.6 1.36 ! SOURCE1 315 0.0088 0.0097 -bond c2 p2 375.9 1.67 ! SOURCE3 62 0.0078 0.0147 -bond c2 p3 246.6 1.83 ! SOURCE3 5 0.0041 0.0042 -bond c2 p4 254.0 1.82 ! SOURCE0 1 -bond c2 p5 255.2 1.82 ! SOURCE0 1 -bond c2 pe 355.3 1.69 ! SOURCE3 52 0.0318 0.0542 -bond c2 pf 355.3 1.69 ! SOURCE3 52 same as c2-pe -bond c2 s 281.5 1.73 ! SOURCE3 4 0.0034 0.0034 -bond c2 s2 393.1 1.61 ! SOURCE2 1 0.0000 0.0000 -bond c2 s4 263.2 1.76 ! SOURCE0 1 -bond c2 s6 263.2 1.76 ! SOURCE0 1 -bond c2 sh 255.3 1.77 ! SOURCE3 3 0.0068 0.0072 -bond c2 ss 280.0 1.74 ! SOURCE1 209 0.0135 0.0155 -bond c3 c3 303.1 1.54 ! SOURCE1 14664 0.0043 0.0048 -bond c3 ca 323.5 1.51 ! SOURCE1 1813 0.0000 0.0000 -bond c3 cc 337.3 1.50 ! SOURCE3 50 0.0059 0.0096 -bond c3 cd 337.3 1.50 ! SOURCE3 50 0.0059 0.0096 -bond c3 ce 331.3 1.50 ! SOURCE3 9 0.0019 0.0024 -bond c3 cf 331.3 1.50 ! SOURCE3 9 same as c3-ce -bond c3 cl 279.0 1.79 ! SOURCE1 267 0.0151 0.0194 -bond c3 cu 359.4 1.48 ! SOURCE1 7 0.0000 0.0000 -bond c3 cv 347.6 1.49 ! SOURCE1 11 0.0000 0.0000 -bond c3 cx 322.5 1.51 ! SOURCE1 712 0.0044 0.0045 -bond c3 cy 308.5 1.53 ! SOURCE1 376 0.0000 0.0000 -bond c3 f 363.8 1.34 ! SOURCE1 617 0.0241 0.0281 -bond c3 h1 335.9 1.09 ! SOURCE3 2175 0.0045 0.0082 -bond c3 h2 326.4 1.10 ! SOURCE3 66 0.0110 0.0280 -bond c3 h3 335.9 1.09 ! SOURCE2 1 0.0000 0.0000 -bond c3 hc 337.3 1.09 ! SOURCE3 2815 0.0040 0.0059 -bond c3 hx 338.7 1.09 ! SOURCE3 146 0.0023 0.0066 -bond c3 i 219.1 2.16 ! SOURCE1 15 0.0000 0.0000 -bond c3 n 330.6 1.46 ! SOURCE1 187 0.0065 0.0079 -bond c3 n1 325.1 1.47 ! SOURCE3 -bond c3 n2 313.8 1.48 ! SOURCE1 129 0.0136 0.0138 -bond c3 n3 320.6 1.47 ! SOURCE1 1678 0.0013 0.0017 -bond c3 n4 293.6 1.50 ! SOURCE1 1370 0.0000 0.0000 -bond c3 na 334.7 1.46 ! SOURCE3 23 0.0096 0.0119 -bond c3 nc 334.7 1.46 ! SOURCE3 9 0.0091 0.0109 -bond c3 nd 334.7 1.46 ! SOURCE3 9 same as c3-nc -bond c3 nh 332.7 1.46 ! SOURCE3 27 0.0067 0.0085 -bond c3 no 265.4 1.53 ! SOURCE1 83 0.0163 0.0212 -bond c3 o 422.6 1.33 ! SOURCE3 4 0.0100 0.0100 -bond c3 oh 314.1 1.43 ! SOURCE1 914 0.0110 0.0129 -bond c3 os 301.5 1.44 ! SOURCE1 3123 0.0112 0.0126 -bond c3 p2 234.3 1.85 ! SOURCE3 9 0.0100 0.0125 -bond c3 p3 240.6 1.84 ! SOURCE3 109 0.0091 0.0107 -bond c3 p4 247.2 1.83 ! SOURCE3 29 0.0091 0.0138 -bond c3 p5 259.7 1.81 ! SOURCE1 84 0.0000 0.0000 -bond c3 px 252.7 1.82 ! SOURCE3 28 0.0079 0.0098 -bond c3 py 259.7 1.81 ! SOURCE3 13 0.0144 0.0163 -bond c3 s 212.9 1.84 ! SOURCE3 4 0.0185 0.0185 -bond c3 s4 233.8 1.81 ! SOURCE1 139 0.0022 0.0023 -bond c3 s6 254.0 1.77 ! SOURCE1 118 0.0080 0.0103 -bond c3 sh 225.3 1.82 ! SOURCE3 12 0.0042 0.0051 -bond c3 ss 225.8 1.82 ! SOURCE1 358 0.0049 0.0075 -bond c3 sx 232.6 1.81 ! SOURCE3 30 0.0050 0.0067 -bond c3 sy 248.9 1.78 ! SOURCE3 31 0.0034 0.0039 -bond ca ca 478.4 1.39 ! SOURCE1 6228 0.0096 0.0147 -bond ca cc 411.7 1.43 ! SOURCE1 80 0.0000 0.0000 -bond ca cd 411.7 1.43 ! SOURCE1 80 0.0000 0.0000 -bond ca ce 366.0 1.47 ! SOURCE1 71 0.0029 0.0030 -bond ca cf 366.0 1.47 ! SOURCE1 71 0.0029 0.0030 -bond ca cg 406.6 1.44 ! SOURCE1 71 0.0045 0.0045 -bond ca ch 406.6 1.44 ! SOURCE1 71 0.0045 0.0045 -bond ca cl 322.8 1.73 ! SOURCE1 704 0.0095 0.0095 -bond ca cp 466.1 1.40 ! SOURCE3 14 0.0098 0.0110 -bond ca cx 350.8 1.49 ! SOURCE1 98 0.0064 0.0118 -bond ca f 363.8 1.34 ! SOURCE1 205 0.0069 0.0089 -bond ca h4 342.9 1.09 ! SOURCE3 57 0.0016 0.0026 -bond ca h5 347.2 1.08 ! SOURCE3 15 0.0038 0.0048 -bond ca ha 344.3 1.09 ! SOURCE3 1496 0.0024 0.0045 -bond ca i 252.4 2.10 ! SOURCE1 51 0.0000 0.0000 -bond ca n 372.3 1.42 ! SOURCE3 9 0.0092 0.0098 -bond ca n1 398.1 1.40 ! SOURCE3 -bond ca n2 320.6 1.47 ! SOURCE2 1 0.0000 0.0000 -bond ca n4 325.6 1.47 ! SOURCE1 23 0.0000 0.0000 -bond ca na 470.3 1.35 ! SOURCE1 150 0.0091 0.0103 -bond ca nb 483.1 1.34 ! SOURCE3 104 0.0052 0.0076 -bond ca nc 492.9 1.34 ! SOURCE1 1826 0.0012 0.0020 -bond ca nd 492.9 1.34 ! SOURCE1 1826 0.0012 0.0020 -bond ca ne 361.8 1.43 ! SOURCE1 52 0.0000 0.0000 -bond ca nf 361.8 1.43 ! SOURCE1 52 0.0000 0.0000 -bond ca nh 449.0 1.36 ! SOURCE1 137 0.0084 0.0085 -bond ca no 322.6 1.47 ! SOURCE1 556 0.0000 0.0000 -bond ca o 519.7 1.27 ! SOURCE3 2 0.0000 0.0000 -bond ca oh 386.1 1.36 ! SOURCE1 551 0.0000 0.0000 -bond ca os 372.4 1.37 ! SOURCE1 1092 0.0048 0.0071 -bond ca p2 243.0 1.84 ! SOURCE0 1 -bond ca p3 252.7 1.82 ! SOURCE1 145 0.0171 0.0187 -bond ca p4 264.3 1.81 ! SOURCE0 1 -bond ca p5 271.6 1.79 ! SOURCE1 571 0.0020 0.0028 -bond ca pe 249.6 1.83 ! SOURCE3 10 0.0034 0.0042 -bond ca pf 249.6 1.83 ! SOURCE3 10 0.0034 0.0042 -bond ca px 252.1 1.82 ! SOURCE3 5 0.0153 0.0168 -bond ca py 268.3 1.80 ! SOURCE3 3 0.0051 0.0054 -bond ca s 277.9 1.74 ! SOURCE3 2 0.0000 0.0000 -bond ca s4 245.2 1.79 ! SOURCE1 51 0.0038 0.0048 -bond ca s6 263.9 1.76 ! SOURCE1 229 0.0030 0.0036 -bond ca sh 245.8 1.79 ! SOURCE3 2 0.0055 0.0055 -bond ca ss 256.6 1.77 ! SOURCE1 297 0.0034 0.0041 -bond ca sx 233.8 1.81 ! SOURCE3 3 0.0015 0.0016 -bond ca sy 247.7 1.78 ! SOURCE3 13 0.0068 0.0094 -bond cc cc 418.3 1.43 ! SOURCE1 740 0.0058 0.0069 -bond cc cd 504.0 1.37 ! SOURCE3 523 0.0156 0.0217 -bond cc cf 519.2 1.36 ! SOURCE3 1 0.0000 0.0000 -bond cc cg 420.9 1.43 ! SOURCE1 560 0.0000 0.0000 -bond cc ch 420.9 1.43 ! SOURCE1 560 0.0000 0.0000 -bond cc cl 348.3 1.70 ! SOURCE3 1 0.0000 0.0000 -bond cc h4 350.1 1.08 ! SOURCE3 599 0.0028 0.0037 -bond cc h5 356.0 1.08 ! SOURCE3 40 0.0040 0.0051 -bond cc ha 347.2 1.08 ! SOURCE3 740 0.0029 0.0039 -bond cc n 426.0 1.38 ! SOURCE3 56 0.0075 0.0109 -bond cc n2 561.3 1.30 ! SOURCE3 4 0.0096 0.0096 -bond cc na 438.8 1.37 ! SOURCE3 440 0.0107 0.0144 -bond cc nc 431.6 1.38 ! SOURCE1 88 0.0000 0.0000 -bond cc nd 494.6 1.33 ! SOURCE3 203 0.0171 0.0239 -bond cc nh 449.0 1.36 ! SOURCE3 6 0.0038 0.0040 -bond cc oh 405.9 1.35 ! SOURCE3 3 0.0077 0.0077 -bond cc os 376.1 1.37 ! SOURCE3 86 0.0139 0.0192 -bond cc pd 318.2 1.73 ! SOURCE3 84 same as cd-pc -bond cc ss 279.3 1.74 ! SOURCE3 52 0.0162 0.0194 -!bond cd cd 418.3 1.43 ! SOURCE1 740 0.0058 0.0069 -bond cd cd 504.0 1.37 ! SOURCE3 523 same as cc-cd -bond cd ce 519.2 1.36 ! SOURCE3 1 same as cc-cf -bond cd cg 420.9 1.43 ! SOURCE1 560 0.0000 0.0000 -bond cd ch 420.9 1.43 ! SOURCE1 560 0.0000 0.0000 -bond cd cl 348.3 1.70 ! SOURCE3 1 same as cc-cl -bond cd h4 350.1 1.08 ! SOURCE3 599 0.0028 0.0037 -bond cd h5 356.0 1.08 ! SOURCE3 40 0.0040 0.0051 -bond cd ha 347.2 1.08 ! SOURCE3 740 0.0029 0.0039 -bond cd n 426.0 1.38 ! SOURCE3 56 0.0075 0.0109 -bond cd n2 561.3 1.30 ! SOURCE3 4 0.0096 0.0096 -bond cd na 438.8 1.37 ! SOURCE3 440 0.0107 0.0144 -bond cd nc 494.6 1.33 ! SOURCE3 203 0.0171 0.0239 -bond cd nd 431.6 1.38 ! SOURCE1 88 0.0000 0.0000 -bond cd nh 449.0 1.36 ! SOURCE3 6 0.0038 0.0040 -bond cd oh 405.9 1.35 ! SOURCE3 3 0.0077 0.0077 -bond cd os 376.1 1.37 ! SOURCE3 86 0.0139 0.0192 -bond cd pc 318.2 1.73 ! SOURCE3 84 0.0088 0.0161 -bond cd ss 279.3 1.74 ! SOURCE3 52 0.0162 0.0194 -bond ce ce 390.5 1.45 ! SOURCE1 66 0.0060 0.0060 -bond ce cf 562.4 1.34 ! SOURCE1 543 0.0035 0.0045 -bond ce cg 415.6 1.43 ! SOURCE1 22 0.0000 0.0000 -bond ce ch 415.6 1.43 ! SOURCE1 22 0.0000 0.0000 -bond ce ha 341.5 1.09 ! SOURCE3 55 0.0030 0.0056 -bond ce n1 522.2 1.32 ! SOURCE3 3 0.0121 0.0121 -bond ce n2 599.8 1.28 ! SOURCE1 75 0.0000 0.0000 -bond ce ne 381.8 1.41 ! SOURCE3 7 0.0093 0.0103 -bond ce nh 484.7 1.34 ! SOURCE3 1 0.0000 0.0000 -bond ce p2 259.1 1.81 ! SOURCE0 1 -bond ce pe 256.5 1.82 ! SOURCE3 8 0.0090 0.0108 -bond ce px 254.6 1.82 ! SOURCE3 6 0.0034 0.0046 -bond ce py 272.3 1.79 ! SOURCE3 5 0.0034 0.0045 -bond ce s 324.5 1.68 ! SOURCE0 1 -bond ce sx 239.7 1.80 ! SOURCE3 5 0.0080 0.0082 -bond ce sy 248.9 1.78 ! SOURCE3 5 0.0105 0.0114 -!bond cf cf 390.5 1.45 ! SOURCE1 66 0.0060 0.0060 -bond cf cf 562.4 1.34 ! SOURCE1 543 same as ce-cf -bond cf cg 415.6 1.43 ! SOURCE1 22 0.0000 0.0000 -bond cf ch 415.6 1.43 ! SOURCE1 22 0.0000 0.0000 -bond cf ha 341.5 1.09 ! SOURCE3 55 0.0030 0.0056 -bond cf n1 522.2 1.32 ! SOURCE3 3 0.0121 0.0121 -bond cf n2 599.8 1.28 ! SOURCE1 75 same as ce-n2 -bond cf nf 381.8 1.41 ! SOURCE3 7 same as ce-ne -bond cf nh 484.7 1.34 ! SOURCE3 1 same as ce-nh -bond cf p2 259.1 1.81 ! SOURCE0 1 same as ce-p2 -bond cf pf 256.5 1.82 ! SOURCE3 8 same as ce-pe -bond cf px 254.6 1.82 ! SOURCE3 6 same as ce-px -bond cf py 272.3 1.79 ! SOURCE3 5 same as ce-py -bond cf s 324.5 1.68 ! SOURCE0 1 same as ce- s -bond cf sx 239.7 1.80 ! SOURCE3 5 same as ce-sx -bond cf sy 248.9 1.78 ! SOURCE3 5 same as ce-sy -bond cg cg 494.2 1.38 ! SOURCE1 42 0.0000 0.0000 -bond cg ch 949.5 1.19 ! SOURCE1 80 0.0015 0.0015 -bond cg n1 994.7 1.14 ! SOURCE1 316 0.0011 0.0018 -bond cg ne 450.5 1.36 ! SOURCE3 4 0.0189 0.0204 -bond cg pe 429.8 1.62 ! SOURCE3 11 0.1928 0.2008 -!bond ch ch 494.2 1.38 ! SOURCE1 42 0.0000 0.0000 -bond ch ch 949.5 1.19 ! SOURCE1 80 same as cg-ch -bond ch n1 994.7 1.14 ! SOURCE1 316 0.0011 0.0018 -bond ch nf 450.5 1.36 ! SOURCE3 4 same as cg-ne -bond ch pf 429.8 1.62 ! SOURCE3 11 same as cg-pe -bond cl cl 143.3 2.27 ! SOURCE1 2 0.0395 0.0395 -bond cl cx 301.8 1.75 ! SOURCE1 64 0.0000 0.0000 -bond cl cy 292.0 1.77 ! SOURCE2 2 0.0070 0.0070 -bond cl f 298.6 1.65 ! SOURCE2 2 0.0500 0.0500 -bond cl i 163.5 2.55 ! SOURCE1 6 0.0605 0.0893 -bond cl n 331.8 1.73 ! SOURCE3 3 0.0107 0.0113 -bond cl n1 431.6 1.63 ! SOURCE0 1 -bond cl n2 263.4 1.82 ! SOURCE3 6 0.0784 0.1020 -bond cl n3 298.6 1.77 ! SOURCE3 4 0.0070 0.0095 -bond cl n4 311.1 1.75 ! SOURCE3 4 0.0085 0.0098 -bond cl na 253.2 1.83 ! SOURCE3 7 0.1858 0.2083 -bond cl nh 303.2 1.76 ! SOURCE3 1 0.0000 0.0000 -bond cl no 250.1 1.84 ! SOURCE2 1 0.0000 0.0000 -bond cl o 557.6 1.48 ! SOURCE3 4 0.0000 0.0000 -bond cl oh 309.7 1.69 ! SOURCE2 1 0.0000 0.0000 -bond cl os 278.8 1.73 ! SOURCE3 4 0.0000 0.0000 -bond cl p2 217.5 2.07 ! SOURCE3 6 0.0086 0.0108 -bond cl p3 249.4 2.01 ! SOURCE1 111 0.0000 0.0000 -bond cl p4 249.4 2.01 ! SOURCE1 111 0.0000 0.0000 -bond cl p5 249.4 2.01 ! SOURCE1 111 0.0000 0.0000 -bond cl pb 255.6 2.00 ! SOURCE1 46 0.0000 0.0000 -bond cl s 208.7 2.07 ! SOURCE1 6 0.0000 0.0000 -bond cl s2 172.7 2.16 ! SOURCE2 1 0.0000 0.0000 -bond cl s4 208.7 2.07 ! SOURCE1 6 0.0000 0.0000 -bond cl s6 208.7 2.07 ! SOURCE1 6 0.0000 0.0000 -bond cl sh 208.7 2.07 ! SOURCE1 6 0.0000 0.0000 -bond cl ss 208.7 2.07 ! SOURCE1 6 0.0000 0.0000 -bond cl sx 208.7 2.07 ! SOURCE1 6 0.0000 0.0000 -bond cl sy 208.7 2.07 ! SOURCE1 6 0.0000 0.0000 -bond cp cp 346.5 1.49 ! SOURCE1 242 0.0007 0.0010 -bond cp nb 470.3 1.35 ! SOURCE3 2 0.0000 0.0000 -bond cq cq 346.5 1.49 ! SOURCE1 242 0.0007 0.0010 -bond cu cu 653.7 1.29 ! SOURCE1 10 0.0000 0.0000 -bond cu cx 327.3 1.51 ! SOURCE1 20 0.0000 0.0000 -bond cu ha 353.0 1.08 ! SOURCE2 3 0.0104 0.0111 -bond cv cv 568.1 1.33 ! SOURCE1 25 0.0000 0.0000 -bond cv cy 323.5 1.51 ! SOURCE1 50 0.0000 0.0000 -bond cv ha 344.3 1.09 ! SOURCE3 2 0.0000 0.0000 -bond cx cv 328.3 1.51 ! SOURCE1 2536 Same as -bond cx cx 337.3 1.50 ! SOURCE1 1204 0.0159 0.0183 -bond cx cy 321.5 1.52 ! SOURCE3 2 0.0000 0.0000 -bond cx f 347.2 1.36 ! SOURCE2 3 0.0047 0.0050 -bond cx h1 344.3 1.09 ! SOURCE3 10 0.0013 0.0017 -bond cx h2 350.1 1.08 ! SOURCE3 2 0.0000 0.0000 -bond cx hc 345.8 1.09 ! SOURCE3 44 0.0009 0.0011 -bond cx n 315.7 1.48 ! SOURCE3 1 0.0000 0.0000 -bond cx n2 309.1 1.48 ! SOURCE3 2 0.0000 0.0000 -bond cx n3 318.7 1.47 ! SOURCE1 134 0.0000 0.0000 -bond cx oh 387.4 1.36 ! SOURCE3 3 0.0017 0.0018 -bond cx os 320.1 1.42 ! SOURCE3 7 0.0205 0.0222 -bond cx p3 227.6 1.87 ! SOURCE2 1 0.0000 0.0000 -bond cx s4 225.3 1.82 ! SOURCE2 1 0.0000 0.0000 -bond cx s6 283.7 1.73 ! SOURCE2 1 0.0000 0.0000 -bond cx ss 229.2 1.81 ! SOURCE2 1 0.0000 0.0000 -bond cy cy 286.8 1.55 ! SOURCE1 742 0.0013 0.0041 -bond cy h1 330.4 1.10 ! SOURCE3 17 0.0042 0.0058 -bond cy hc 334.5 1.09 ! SOURCE3 63 0.0012 0.0014 -bond cy n3 307.2 1.48 ! SOURCE1 21 0.0000 0.0000 -bond cy oh 325.2 1.42 ! SOURCE3 2 0.0000 0.0000 -bond cy os 280.7 1.46 ! SOURCE3 4 0.0101 0.0101 -bond f n 391.7 1.40 ! SOURCE3 3 0.0106 0.0112 -bond f n1 375.7 1.41 ! SOURCE0 1 -bond f n2 337.5 1.44 ! SOURCE3 5 0.0292 0.0377 -bond f n3 380.6 1.41 ! SOURCE1 9 0.0000 0.0000 -bond f n4 526.8 1.31 ! SOURCE3 2 0.0000 0.0000 -bond f na 374.5 1.41 ! SOURCE3 7 0.0537 0.0611 -bond f nh 357.1 1.43 ! SOURCE3 3 0.0080 0.0085 -bond f no 314.4 1.47 ! SOURCE2 1 0.0000 0.0000 -bond f o 442.2 1.33 ! SOURCE0 1 -bond f oh 305.4 1.44 ! SOURCE3 1 0.0000 0.0000 -bond f os 326.2 1.42 ! SOURCE3 2 0.0000 0.0000 -bond f p2 287.3 1.54 ! SOURCE3 7 0.1437 0.2054 -bond f p3 254.5 1.58 ! SOURCE2 8 0.0093 0.0103 -bond f p4 246.0 1.59 ! SOURCE0 1 -bond f p5 253.8 1.58 ! SOURCE1 72 0.0000 0.0000 -bond f s 233.3 1.66 ! SOURCE0 1 -bond f s2 244.4 1.64 ! SOURCE2 1 0.0000 0.0000 -bond f s4 282.4 1.59 ! SOURCE2 4 0.0065 0.0065 -bond f s6 312.1 1.56 ! SOURCE2 5 0.0163 0.0220 -bond f sh 240.4 1.65 ! SOURCE3 1 0.0000 0.0000 -bond f ss 250.5 1.63 ! SOURCE3 3 0.0147 0.0156 -bond hn n 410.2 1.01 ! SOURCE3 149 0.0089 0.0098 -bond hn n1 455.1 0.99 ! SOURCE2 1 0.0000 0.0000 -bond hn n2 375.5 1.03 ! SOURCE3 108 0.0070 0.0096 -bond hn n3 394.1 1.02 ! SOURCE3 157 0.0063 0.0086 -bond hn n4 369.0 1.03 ! SOURCE3 264 0.0054 0.0082 -bond hn na 406.6 1.01 ! SOURCE3 46 0.0076 0.0107 -bond hn nh 401.2 1.01 ! SOURCE3 209 0.0068 0.0091 -bond hn no 385.6 1.02 ! SOURCE3 1 0.0000 0.0000 -bond ho o 357.9 0.98 ! SOURCE3 1 0.0000 0.0000 -bond ho oh 369.6 0.97 ! SOURCE3 367 0.0069 0.0105 -bond hp p2 385.1 1.34 ! SOURCE3 87 0.1430 0.1706 -bond hp p3 303.1 1.41 ! SOURCE3 101 0.0170 0.0617 -bond hp p4 368.7 1.35 ! SOURCE3 17 0.1277 0.1577 -bond hp p5 305.0 1.41 ! SOURCE3 7 0.0049 0.0062 -bond hs s 286.4 1.35 ! SOURCE3 1 0.0000 0.0000 -bond hs s4 266.4 1.38 ! SOURCE3 5 0.0004 0.0004 -bond hs s6 280.8 1.36 ! SOURCE3 5 0.0012 0.0015 -bond hs sh 302.2 1.34 ! SOURCE3 98 0.0150 0.0486 -bond i i 109.2 2.92 ! SOURCE1 1 0.0000 0.0000 -bond i n 278.3 2.10 ! SOURCE3 5 0.0153 0.0156 -bond i n1 302.1 2.06 ! SOURCE0 1 -bond i n2 182.6 2.30 ! SOURCE3 6 0.1010 0.1186 -bond i n3 231.8 2.19 ! SOURCE3 3 0.0412 0.0437 -bond i n4 246.6 2.15 ! SOURCE3 3 0.0158 0.0168 -bond i na 260.5 2.13 ! SOURCE3 8 0.0838 0.1276 -bond i nh 249.2 2.15 ! SOURCE3 1 0.0000 0.0000 -bond i no 211.0 2.23 ! SOURCE3 1 0.0000 0.0000 -bond i o 323.8 1.98 ! SOURCE0 1 -bond i oh 247.9 2.10 ! SOURCE3 2 0.0000 0.0000 -bond i os 233.6 2.13 ! SOURCE3 3 0.0138 0.0146 -bond i p2 108.2 2.64 ! SOURCE3 6 0.0266 0.0297 -bond i p3 123.6 2.57 ! SOURCE3 3 0.0015 0.0016 -bond i p4 183.0 2.35 ! SOURCE3 4 0.2600 0.2600 -bond i p5 117.3 2.60 ! SOURCE3 3 0.0135 0.0143 -bond i s 175.1 2.43 ! SOURCE0 1 -bond i s4 82.8 2.87 ! SOURCE0 1 -bond i s6 82.8 2.87 ! SOURCE3 1 0.0000 0.0000 -bond i sh 138.5 2.56 ! SOURCE0 1 -bond i ss 135.9 2.57 ! SOURCE3 3 0.0061 0.0065 -bond n n 469.7 1.39 ! SOURCE3 5 0.0035 0.0038 -bond n n1 553.9 1.34 ! SOURCE0 1 -bond n n2 499.7 1.37 ! SOURCE3 9 0.0164 0.0200 -bond n n3 443.3 1.41 ! SOURCE3 5 0.0077 0.0087 -bond n n4 410.8 1.43 ! SOURCE3 5 0.0096 0.0098 -bond n na 486.8 1.38 ! SOURCE3 11 0.0052 0.0071 -bond n nc 532.1 1.35 ! SOURCE3 4 0.0055 0.0058 -bond n nd 532.1 1.35 ! SOURCE3 4 same as n -nc -bond n nh 437.7 1.41 ! SOURCE3 4 0.0035 0.0037 -bond n no 381.2 1.46 ! SOURCE3 4 0.0278 0.0327 -bond n o 646.6 1.26 ! SOURCE3 9 0.0336 0.0381 -bond n oh 395.4 1.41 ! SOURCE3 6 0.0078 0.0106 -bond n os 372.3 1.43 ! SOURCE3 7 0.0364 0.0528 -bond n p2 310.3 1.73 ! SOURCE3 8 0.0143 0.0217 -bond n p3 282.2 1.77 ! SOURCE3 9 0.0102 0.0118 -bond n p4 309.5 1.73 ! SOURCE3 1 0.0000 0.0000 -bond n p5 327.0 1.71 ! SOURCE3 4 0.0084 0.0109 -bond n pc 304.8 1.74 ! SOURCE3 3 0.0009 0.0010 -bond n pd 304.8 1.74 ! SOURCE3 3 same as n -pc -bond n s 247.5 1.77 ! SOURCE3 3 0.0011 0.0011 -bond n s4 238.2 1.78 ! SOURCE3 4 0.0154 0.0214 -bond n s6 270.8 1.73 ! SOURCE3 4 0.0177 0.0224 -bond n sh 273.6 1.73 ! SOURCE3 4 0.0108 0.0128 -bond n ss 281.6 1.72 ! SOURCE3 7 0.0120 0.0133 -!bond n1 n1 1221.7 1.12 ! SOURCE1 19 0.0000 0.0000 -bond n1 n1 1365.7 1.10 ! SOURCE3 -bond n1 n2 857.4 1.22 ! SOURCE1 19 0.0000 0.0000 -bond n1 n3 535.7 1.35 ! SOURCE0 1 -bond n1 n4 518.2 1.36 ! SOURCE0 1 -bond n1 na 535.7 1.35 ! SOURCE0 1 -bond n1 nc 857.4 1.22 ! SOURCE1 38 0.0000 0.0000 -bond n1 nd 857.4 1.22 ! SOURCE1 38 0.0000 0.0000 -bond n1 ne 751.9 1.25 ! SOURCE2 1 0.0000 0.0000 -bond n1 nf 751.9 1.25 ! SOURCE2 1 same as n1-ne -bond n1 nh 553.9 1.34 ! SOURCE0 1 -bond n1 no 454.8 1.40 ! SOURCE0 1 -bond n1 o 617.5 1.28 ! SOURCE3 5 0.0340 0.0438 -bond n1 oh 569.8 1.30 ! SOURCE0 1 -bond n1 os 550.5 1.31 ! SOURCE0 1 -bond n1 p2 358.8 1.68 ! SOURCE3 2 0.0282 0.0282 -bond n1 p3 376.7 1.66 ! SOURCE0 1 -bond n1 p4 353.0 1.68 ! SOURCE3 -bond n1 p5 482.7 1.57 ! SOURCE1 132 0.0000 0.0000 -bond n1 s 328.7 1.66 ! SOURCE3 6 0.0693 0.0789 -bond n1 s2 604.3 1.45 ! SOURCE2 2 0.0010 0.0010 -bond n1 s4 336.8 1.65 ! SOURCE0 1 -bond n1 s6 670.3 1.42 ! SOURCE2 2 0.0000 0.0000 -bond n1 sh 376.1 1.61 ! SOURCE0 1 -bond n1 ss 376.1 1.61 ! SOURCE0 1 -bond n2 n2 702.7 1.27 ! SOURCE3 27 0.0228 0.0347 -bond n2 n3 574.8 1.33 ! SOURCE2 1 0.0000 0.0000 -bond n2 n4 200.8 1.68 ! SOURCE3 7 0.2778 0.3138 -bond n2 na 450.4 1.40 ! SOURCE3 14 0.0399 0.0575 -bond n2 nc 743.9 1.25 ! SOURCE1 13 same as n2-nd -bond n2 nd 743.9 1.25 ! SOURCE1 13 0.0000 0.0000 -bond n2 ne 685.5 1.28 ! SOURCE3 30 0.0224 0.0302 -bond n2 nf 685.5 1.28 ! SOURCE3 30 same as n2-ne -bond n2 nh 525.1 1.36 ! SOURCE3 22 0.0218 0.0300 -bond n2 no 231.9 1.63 ! SOURCE3 4 0.1591 0.1933 -bond n2 o 789.9 1.21 ! SOURCE3 20 0.0284 0.0344 -bond n2 oh 416.2 1.39 ! SOURCE1 67 0.0000 0.0000 -bond n2 os 400.5 1.41 ! SOURCE3 10 0.0120 0.0147 -bond n2 p2 438.3 1.60 ! SOURCE3 35 0.0392 0.0737 -bond n2 p3 286.5 1.76 ! SOURCE3 7 0.0320 0.0374 -bond n2 p4 317.7 1.72 ! SOURCE0 1 -bond n2 p5 445.8 1.60 ! SOURCE1 7 0.0000 0.0000 -bond n2 pe 527.9 1.54 ! SOURCE3 20 0.1112 0.1392 -bond n2 pf 527.9 1.54 ! SOURCE3 20 same as n2-pe -bond n2 s 458.1 1.54 ! SOURCE1 37 0.0000 0.0000 -bond n2 s2 499.0 1.51 ! SOURCE2 1 0.0000 0.0000 -bond n2 s4 376.1 1.61 ! SOURCE0 1 -bond n2 s6 468.9 1.53 ! SOURCE3 3 0.0144 0.0144 -bond n2 sh 266.6 1.74 ! SOURCE3 5 0.0405 0.0511 -bond n2 ss 331.4 1.66 ! SOURCE1 36 0.0000 0.0000 -bond n3 n3 383.6 1.45 ! SOURCE1 44 0.0000 0.0000 -bond n3 n4 434.9 1.41 ! SOURCE1 13 0.0000 0.0000 -bond n3 na 426.7 1.42 ! SOURCE1 68 0.0000 0.0000 -bond n3 nh 426.7 1.42 ! SOURCE1 68 0.0000 0.0000 -bond n3 no 394.5 1.45 ! SOURCE3 3 0.0196 0.0208 -bond n3 o 564.0 1.30 ! SOURCE3 4 0.1197 0.1217 -bond n3 oh 413.5 1.40 ! SOURCE1 28 0.0000 0.0000 -bond n3 os 359.6 1.44 ! SOURCE1 34 0.0301 0.0315 -bond n3 p2 366.6 1.67 ! SOURCE0 1 -bond n3 p3 312.8 1.73 ! SOURCE1 40 0.0000 0.0000 -bond n3 p4 341.1 1.70 ! SOURCE1 88 0.0000 0.0000 -bond n3 p5 373.6 1.66 ! SOURCE1 501 0.0033 0.0086 -bond n3 s 232.3 1.79 ! SOURCE3 3 0.0168 0.0178 -bond n3 s4 251.3 1.76 ! SOURCE3 6 0.0563 0.0766 -bond n3 s6 353.8 1.63 ! SOURCE1 99 0.0090 0.0136 -bond n3 sh 265.9 1.74 ! SOURCE3 3 0.0145 0.0154 -bond n3 ss 277.9 1.72 ! SOURCE3 5 0.0172 0.0207 -bond n4 n4 349.9 1.48 ! SOURCE3 4 0.0089 0.0089 -bond n4 na 407.0 1.44 ! SOURCE3 9 0.0242 0.0390 -bond n4 nh 369.7 1.47 ! SOURCE3 5 0.0097 0.0108 -bond n4 no 354.2 1.48 ! SOURCE0 1 -bond n4 o 463.6 1.36 ! SOURCE3 3 0.0039 0.0041 -bond n4 oh 408.2 1.40 ! SOURCE3 3 0.0108 0.0115 -bond n4 os 381.8 1.42 ! SOURCE3 5 0.0225 0.0249 -bond n4 p2 185.9 1.94 ! SOURCE3 10 0.0514 0.0643 -bond n4 p3 215.1 1.88 ! SOURCE3 5 0.0143 0.0146 -bond n4 p4 187.6 1.94 ! SOURCE3 1 0.0000 0.0000 -bond n4 p5 242.9 1.83 ! SOURCE3 5 0.0082 0.0087 -bond n4 py 204.2 1.90 ! SOURCE3 4 0.0000 0.0000 -bond n4 s 210.3 1.83 ! SOURCE3 3 0.0004 0.0004 -bond n4 s4 151.0 1.97 ! SOURCE3 3 0.0187 0.0198 -bond n4 s6 172.7 1.91 ! SOURCE3 5 0.0414 0.0432 -bond n4 sh 221.5 1.81 ! SOURCE3 3 0.0025 0.0027 -bond n4 ss 221.0 1.81 ! SOURCE3 5 0.0061 0.0064 -bond na na 453.3 1.40 ! SOURCE1 40 0.0000 0.0000 -bond na nc 535.7 1.35 ! SOURCE3 152 0.0117 0.0180 -bond na nd 535.7 1.35 ! SOURCE3 152 0.0117 0.0180 -bond na nh 453.3 1.40 ! SOURCE1 40 0.0000 0.0000 -bond na no 401.9 1.44 ! SOURCE3 9 0.0241 0.0289 -bond na o 644.3 1.27 ! SOURCE1 25 0.0345 0.0347 -bond na oh 412.2 1.40 ! SOURCE3 9 0.0161 0.0217 -bond na os 355.2 1.44 ! SOURCE3 45 0.0349 0.0423 -bond na p2 297.8 1.75 ! SOURCE3 11 0.0164 0.0192 -bond na p3 288.0 1.76 ! SOURCE3 8 0.0101 0.0113 -bond na p4 492.4 1.56 ! SOURCE3 5 0.2116 0.2161 -bond na p5 325.3 1.71 ! SOURCE3 11 0.0197 0.0238 -bond na pc 311.1 1.73 ! SOURCE3 81 0.0124 0.0207 -bond na pd 311.1 1.73 ! SOURCE3 81 same as na-pc -bond na py 327.8 1.71 ! SOURCE3 2 0.0000 0.0000 -bond na s 248.7 1.77 ! SOURCE3 8 0.0083 0.0095 -bond na s4 231.7 1.79 ! SOURCE3 10 0.0316 0.0421 -bond na s6 274.3 1.73 ! SOURCE3 10 0.0169 0.0201 -bond na sh 278.6 1.72 ! SOURCE3 9 0.0101 0.0113 -bond na ss 270.1 1.73 ! SOURCE3 38 0.0280 0.0412 -bond na sy 274.3 1.73 ! SOURCE3 1 -bond nb nb 550.2 1.34 ! SOURCE1 15 0.0307 0.0314 -bond nb pb 461.1 1.59 ! SOURCE1 162 0.0076 0.0091 -bond nc nc 486.8 1.38 ! SOURCE3 9 0.0145 0.0164 -bond nc nd 602.9 1.31 ! SOURCE3 9 0.0205 0.0221 -bond nc os 414.9 1.40 ! SOURCE1 46 0.0163 0.0188 -bond nc ss 433.5 1.56 ! SOURCE1 74 0.0000 0.0000 -bond nc sy 439.8 1.56 ! SOURCE3 2 -!bond nd nd 486.8 1.38 ! SOURCE3 9 0.0145 0.0164 -bond nd nd 602.9 1.31 ! SOURCE3 9 same as nc-nd -bond nd os 414.9 1.40 ! SOURCE1 46 0.0163 0.0188 -bond nd ss 433.5 1.56 ! SOURCE1 74 0.0000 0.0000 -bond nd sy 439.8 1.56 ! SOURCE3 2 -bond ne ne 355.3 1.48 ! SOURCE3 19 0.0960 0.1705 -bond ne nf 738.6 1.26 ! SOURCE3 1 0.0000 0.0000 -bond ne o 736.4 1.23 ! SOURCE3 40 0.0207 0.0255 -bond ne p2 493.9 1.56 ! SOURCE3 14 0.0950 0.1325 -bond ne pe 327.8 1.71 ! SOURCE3 28 0.0848 0.1076 -bond ne px 336.6 1.70 ! SOURCE3 11 0.0578 0.0883 -bond ne py 320.2 1.72 ! SOURCE3 15 0.0497 0.0702 -bond ne s 463.5 1.54 ! SOURCE3 22 0.1396 0.1708 -bond ne sx 207.3 1.84 ! SOURCE3 7 0.0760 0.1060 -bond ne sy 257.1 1.75 ! SOURCE3 7 0.0640 0.0814 -!bond nf nf 355.3 1.48 ! SOURCE3 19 same as ne-ne -bond nf nf 738.6 1.26 ! SOURCE3 1 same as ne-nf -bond nf o 736.4 1.23 ! SOURCE3 40 same as ne- o -bond nf p2 493.9 1.56 ! SOURCE3 14 same as ne-p2 -bond nf pf 327.8 1.71 ! SOURCE3 28 same as ne-pe -bond nf px 336.6 1.70 ! SOURCE3 11 same as ne-px -bond nf py 320.2 1.72 ! SOURCE3 15 same as ne-py -bond nf s 463.5 1.54 ! SOURCE3 22 same as ne- s -bond nf sx 207.3 1.84 ! SOURCE3 7 same as ne-sx -bond nf sy 257.1 1.75 ! SOURCE3 7 same as ne-sy -bond nh nh 453.3 1.40 ! SOURCE1 40 0.0000 0.0000 -bond nh no 381.2 1.46 ! SOURCE3 4 0.0364 0.0370 -bond nh o 596.2 1.29 ! SOURCE3 3 0.0424 0.0450 -bond nh oh 359.6 1.44 ! SOURCE3 1 0.0000 0.0000 -bond nh os 358.5 1.44 ! SOURCE3 3 0.0029 0.0031 -bond nh p2 357.8 1.68 ! SOURCE3 17 0.0422 0.0872 -bond nh p3 312.8 1.73 ! SOURCE3 3 0.0015 0.0016 -bond nh p4 333.1 1.71 ! SOURCE3 3 0.0008 0.0008 -bond nh p5 365.6 1.67 ! SOURCE3 3 0.0007 0.0007 -bond nh s 237.0 1.78 ! SOURCE3 3 0.0072 0.0076 -bond nh s4 259.1 1.75 ! SOURCE3 3 0.0192 0.0203 -bond nh s6 300.0 1.69 ! SOURCE3 3 0.0036 0.0038 -bond nh sh 288.3 1.71 ! SOURCE3 1 0.0000 0.0000 -bond nh ss 288.3 1.71 ! SOURCE1 52 0.0015 0.0015 -bond nh sy 324.2 1.66 ! SOURCE3 1 0.0000 0.0000 -bond no no 138.3 1.82 ! SOURCE3 1 0.0000 0.0000 -bond no o 761.2 1.22 ! SOURCE1 1838 0.0023 0.0049 -bond no oh 400.5 1.41 ! SOURCE2 1 0.0000 0.0000 -bond no os 320.8 1.48 ! SOURCE3 4 0.0526 0.0532 -bond no p2 306.3 1.74 ! SOURCE3 10 0.2024 0.2231 -bond no p3 234.7 1.84 ! SOURCE3 3 0.0005 0.0005 -bond no p4 220.4 1.87 ! SOURCE3 3 0.0005 0.0006 -bond no p5 240.5 1.83 ! SOURCE3 4 0.0019 0.0020 -bond no s 263.8 1.74 ! SOURCE3 2 0.0000 0.0000 -bond no s4 143.0 2.00 ! SOURCE3 3 0.0295 0.0313 -bond no s6 149.6 1.98 ! SOURCE3 3 0.0490 0.0520 -bond no sh 225.4 1.80 ! SOURCE3 1 0.0000 0.0000 -bond no ss 212.4 1.83 ! SOURCE3 3 0.0230 0.0244 -bond o o 384.3 1.43 ! SOURCE3 2 0.0500 0.0500 -bond o oh 294.6 1.52 ! SOURCE3 2 0.0000 0.0000 -bond o os 306.3 1.50 ! SOURCE3 3 0.0110 0.0117 -bond o p2 449.7 1.51 ! SOURCE3 17 0.0167 0.0306 -bond o p3 440.4 1.52 ! SOURCE3 35 0.0214 0.0297 -bond o p4 456.4 1.50 ! SOURCE3 42 0.0343 0.0749 -bond o p5 487.7 1.48 ! SOURCE1 263 0.0180 0.0205 -bond o pe 432.6 1.52 ! SOURCE3 20 0.0138 0.0171 -bond o pf 432.6 1.52 ! SOURCE3 20 same as o -pe -bond o px 459.2 1.50 ! SOURCE3 37 0.0125 0.0160 -bond o py 477.5 1.49 ! SOURCE3 63 0.0063 0.0091 -bond o s 194.8 1.80 ! SOURCE3 2 0.0000 0.0000 -bond o s2 333.6 1.60 ! SOURCE3 3 0.0666 0.0707 -bond o s4 448.7 1.50 ! SOURCE1 90 0.0000 0.0000 -bond o s6 541.1 1.44 ! SOURCE1 1038 0.0072 0.0128 -bond o sh 328.0 1.60 ! SOURCE3 2 0.0000 0.0000 -bond o ss 398.5 1.54 ! SOURCE3 3 0.0434 0.0501 -bond o sx 434.2 1.51 ! SOURCE3 40 0.0083 0.0130 -bond o sy 493.0 1.47 ! SOURCE3 92 0.0077 0.0114 -bond oh oh 340.5 1.47 ! SOURCE3 1 0.0000 0.0000 -bond oh os 342.6 1.47 ! SOURCE3 3 0.0065 0.0072 -bond oh p2 316.8 1.63 ! SOURCE3 8 0.0600 0.0916 -bond oh p3 278.8 1.68 ! SOURCE3 3 0.0140 0.0148 -bond oh p4 307.4 1.64 ! SOURCE3 4 0.0092 0.0092 -bond oh p5 321.2 1.62 ! SOURCE3 92 0.0293 0.0451 -bond oh py 332.1 1.61 ! SOURCE3 79 0.0111 0.0138 -bond oh s 190.0 1.81 ! SOURCE3 2 0.0000 0.0000 -bond oh s4 274.3 1.67 ! SOURCE3 3 0.0173 0.0184 -bond oh s6 344.1 1.59 ! SOURCE3 13 0.0072 0.0091 -bond oh sh 258.6 1.69 ! SOURCE3 2 0.0003 0.0003 -bond oh ss 265.6 1.68 ! SOURCE3 4 0.0131 0.0131 -bond oh sy 302.6 1.63 ! SOURCE3 4 0.0153 0.0154 -bond os os 343.6 1.47 ! SOURCE1 20 0.0047 0.0067 -bond os p2 371.9 1.57 ! SOURCE1 16 0.0000 0.0000 -bond os p3 272.2 1.69 ! SOURCE3 6 0.0141 0.0201 -bond os p4 311.6 1.64 ! SOURCE3 4 0.0056 0.0057 -bond os p5 342.5 1.60 ! SOURCE1 248 0.0332 0.0400 -bond os py 328.5 1.62 ! SOURCE3 17 0.0082 0.0139 -bond os s 195.8 1.80 ! SOURCE3 3 0.0049 0.0052 -bond os s4 253.9 1.70 ! SOURCE3 8 0.0194 0.0223 -bond os s6 355.0 1.58 ! SOURCE1 75 0.0019 0.0030 -bond os sh 273.6 1.67 ! SOURCE3 3 0.0100 0.0106 -bond os ss 250.5 1.70 ! SOURCE3 9 0.0241 0.0277 -bond os sy 253.9 1.70 ! SOURCE3 1 0.0000 0.0000 -bond p2 p2 490.3 1.79 ! SOURCE3 25 0.3198 0.3488 -bond p2 p3 211.9 2.15 ! SOURCE3 9 0.1116 0.1777 -bond p2 p4 200.4 2.18 ! SOURCE0 1 -bond p2 p5 199.9 2.18 ! SOURCE0 1 -bond p2 pe 401.6 1.87 ! SOURCE3 16 0.3079 0.3571 -bond p2 pf 401.6 1.87 ! SOURCE3 16 same as p2-pe -bond p2 s 361.6 1.77 ! SOURCE3 26 0.2523 0.3014 -bond p2 s4 139.4 2.19 ! SOURCE0 1 -bond p2 s6 142.3 2.18 ! SOURCE0 1 -bond p2 sh 224.0 1.97 ! SOURCE3 10 0.2263 0.2829 -bond p2 ss 226.6 1.97 ! SOURCE3 10 0.2189 0.2739 -bond p3 p3 186.5 2.21 ! SOURCE1 41 0.0000 0.0000 -bond p3 p4 185.7 2.22 ! SOURCE3 3 0.0010 0.0011 -bond p3 p5 186.9 2.21 ! SOURCE3 9 0.0257 0.0265 -bond p3 s 179.7 2.07 ! SOURCE0 1 -bond p3 s4 173.2 2.09 ! SOURCE3 8 0.1935 0.2235 -bond p3 s6 176.9 2.08 ! SOURCE3 11 0.1085 0.1420 -bond p3 sh 157.3 2.13 ! SOURCE3 3 0.0073 0.0078 -bond p3 ss 161.0 2.12 ! SOURCE3 3 0.0056 0.0059 -bond p4 p4 273.1 2.03 ! SOURCE1 1 0.0000 0.0000 -bond p4 p5 178.0 2.24 ! SOURCE0 1 -bond p4 s 152.7 2.15 ! SOURCE3 5 0.0571 0.0601 -bond p4 s4 123.2 2.25 ! SOURCE0 1 -bond p4 s6 118.9 2.27 ! SOURCE0 1 -bond p4 sh 163.1 2.12 ! SOURCE3 4 0.0006 0.0008 -bond p4 ss 167.0 2.10 ! SOURCE3 4 0.0042 0.0044 -bond p5 p5 261.4 2.05 ! SOURCE1 1 0.0000 0.0000 -bond p5 s 250.8 1.92 ! SOURCE1 89 0.0097 0.0140 -bond p5 s4 191.9 2.04 ! SOURCE0 1 -bond p5 s6 191.9 2.04 ! SOURCE0 1 -bond p5 sh 175.0 2.08 ! SOURCE3 3 0.0033 0.0035 -bond p5 ss 164.8 2.11 ! SOURCE3 6 0.0379 0.0531 -bond pe pe 240.7 2.09 ! SOURCE3 7 0.1280 0.1369 -bond pe pf 260.8 2.06 ! SOURCE3 1 0.0000 0.0000 -bond pe px 291.4 2.00 ! SOURCE3 12 0.2364 0.2609 -bond pe py 278.6 2.02 ! SOURCE3 12 0.2453 0.2617 -bond pe s 374.7 1.76 ! SOURCE3 31 0.2925 0.3197 -bond pe sx 145.9 2.17 ! SOURCE3 9 0.1092 0.1743 -bond pe sy 133.0 2.21 ! SOURCE3 6 0.0106 0.0127 -!bond pf pf 240.7 2.09 ! SOURCE3 7 same as pe-pe -bond pf pf 260.8 2.06 ! SOURCE3 1 same as pe-pf -bond pf px 291.4 2.00 ! SOURCE3 12 same as pe-px -bond pf py 278.6 2.02 ! SOURCE3 12 same as pe-py -bond pf s 374.7 1.76 ! SOURCE3 31 same as pe- s -bond pf sx 145.9 2.17 ! SOURCE3 9 same as pe-sx -bond pf sy 133.0 2.21 ! SOURCE3 6 same as pe-sy -bond px py 192.3 2.20 ! SOURCE3 5 0.0221 0.0238 -bond px sx 125.4 2.24 ! SOURCE3 3 0.0112 0.0119 -bond px sy 123.7 2.25 ! SOURCE3 3 0.0256 0.0272 -bond py py 197.5 2.19 ! SOURCE3 8 0.0110 0.0132 -bond py sx 121.2 2.26 ! SOURCE3 7 0.0595 0.0603 -bond py sy 141.7 2.18 ! SOURCE3 5 0.0044 0.0047 -bond s s 169.0 2.03 ! SOURCE3 1 0.0000 0.0000 -bond s s2 229.2 1.90 ! SOURCE1 5 0.0000 0.0000 -bond s s4 152.8 2.08 ! SOURCE3 4 0.0345 0.0345 -bond s s6 166.0 2.04 ! SOURCE3 3 0.0293 0.0311 -bond s sh 142.0 2.11 ! SOURCE3 2 0.0000 0.0000 -bond s ss 148.5 2.09 ! SOURCE3 1 0.0000 0.0000 -bond s4 s4 151.5 2.08 ! SOURCE0 1 -bond s4 s6 151.5 2.08 ! SOURCE0 1 -bond s4 sh 125.7 2.17 ! SOURCE3 3 0.0214 0.0227 -bond s4 ss 126.2 2.17 ! SOURCE3 5 0.0241 0.0247 -bond s6 s6 151.5 2.08 ! SOURCE0 1 -bond s6 sh 142.6 2.11 ! SOURCE3 3 0.0136 0.0144 -bond s6 ss 139.6 2.12 ! SOURCE3 5 0.0198 0.0209 -bond sh sh 158.9 2.06 ! SOURCE2 1 0.0000 0.0000 -bond sh ss 155.8 2.07 ! SOURCE3 3 0.0027 0.0029 -bond ss ss 161.7 2.05 ! SOURCE1 225 0.0015 0.0015 -bond sx sx 80.9 2.39 ! SOURCE3 3 0.0174 0.0185 -bond sx sy 105.3 2.25 ! SOURCE3 5 0.0703 0.0737 -bond sy sy 106.4 2.25 ! SOURCE3 3 0.0272 0.0289 +bond ow hw 553.0 0.957 ! TIP3P water +bond br br 123.2 2.542 ! SOURCE1 4 0.0000 0.0000 +bond br c 240.3 1.946 ! SOURCE2 2 0.0285 0.0285 +bond br c1 352.7 1.787 ! SOURCE2 4 0.0022 0.0024 +bond br c2 278.7 1.883 ! SOURCE1 31 0.0000 0.0000 +bond br c3 229.5 1.966 ! SOURCE1 100 0.0000 0.0000 +bond br ca 269.6 1.897 ! SOURCE1 127 0.0028 0.0058 +bond br cx 261.4 1.910 ! SOURCE1 8 0.0000 0.0000 +bond br i 142.4 2.671 ! SOURCE1 2 0.0245 0.0245 +bond br n 320.2 1.873 ! SOURCE3 4 0.0037 0.0046 +bond br n1 330.4 1.860 ! SOURCE0 1 +bond br n2 219.0 2.038 ! SOURCE3 5 0.0956 0.1082 +bond br n3 265.9 1.952 ! SOURCE3 2 0.0000 0.0000 +bond br n4 282.4 1.926 ! SOURCE3 3 0.0012 0.0013 +bond br na 237.3 2.002 ! SOURCE3 7 0.1938 0.2156 +bond br nh 270.9 1.944 ! SOURCE3 1 0.0000 0.0000 +bond br no 191.0 2.101 ! SOURCE3 1 0.0000 0.0000 +bond br o 278.9 1.800 ! SOURCE0 1 +bond br oh 237.2 1.866 ! SOURCE3 1 0.0000 0.0000 +bond br os 225.6 1.887 ! SOURCE3 2 0.0000 0.0000 +bond br p2 174.3 2.210 ! SOURCE3 9 0.0470 0.0510 +bond br p3 167.0 2.231 ! SOURCE3 3 0.0096 0.0101 +bond br p4 188.8 2.171 ! SOURCE0 1 +bond br p5 179.3 2.196 ! SOURCE3 3 0.0094 0.0099 +bond br s 170.6 2.220 ! SOURCE0 1 +bond br s4 134.3 2.341 ! SOURCE3 1 0.0000 0.0000 +bond br s6 172.7 2.214 ! SOURCE3 3 0.0417 0.0443 +bond br sh 174.4 2.209 ! SOURCE3 1 0.0000 0.0000 +bond br ss 176.6 2.203 ! SOURCE3 3 0.0033 0.0035 +bond c c 290.1 1.550 ! SOURCE1 31 0.0080 0.0100 +bond c c1 379.8 1.460 ! SOURCE0 1 +bond c c2 449.9 1.406 ! SOURCE3 2 0.0370 0.0370 +bond c c3 328.3 1.508 ! SOURCE1 2949 0.0049 0.0060 +bond c ca 349.7 1.487 ! SOURCE1 480 0.0031 0.0055 +bond c cc 377.4 1.462 ! SOURCE3 132 0.0165 0.0210 +bond c cd 377.4 1.462 ! SOURCE3 132 0.0165 0.0210 +bond c ce 363.8 1.474 ! SOURCE1 601 0.0091 0.0105 +bond c cf 363.8 1.474 ! SOURCE1 601 0.0091 0.0105 +bond c cg 389.3 1.452 ! SOURCE3 2 0.0000 0.0000 +bond c ch 389.3 1.452 ! SOURCE3 2 same as c -cg +bond c cl 293.5 1.766 ! SOURCE3 6 0.0235 0.0250 +bond c cu 441.4 1.412 ! SOURCE2 1 0.0000 0.0000 +bond c cx 350.8 1.486 ! SOURCE1 105 0.0000 0.0000 +bond c cy 308.5 1.529 ! SOURCE1 18 0.0000 0.0000 +bond c f 387.9 1.325 ! SOURCE2 6 0.0140 0.0147 +bond c ha 325.1 1.101 ! SOURCE3 53 0.0078 0.0102 +bond c i 198.9 2.209 ! SOURCE3 4 0.0332 0.0365 +bond c n 478.2 1.345 ! SOURCE1 1235 0.0162 0.0215 +bond c n2 374.6 1.420 ! SOURCE0 1 +bond c n4 255.5 1.546 ! SOURCE3 4 0.0388 0.0388 +bond c nc 438.8 1.371 ! SOURCE3 2 0.0108 0.0108 +bond c nd 438.8 1.371 ! SOURCE3 2 same as c -nc +bond c ne 388.0 1.409 ! SOURCE3 3 0.0088 0.0094 +bond c nf 388.0 1.409 ! SOURCE3 3 same as c -ne +bond c no 260.1 1.540 ! SOURCE0 1 +bond c o 648.0 1.214 ! SOURCE1 3682 0.0134 0.0165 +bond c oh 466.4 1.306 ! SOURCE1 271 0.0026 0.0041 +bond c os 411.3 1.343 ! SOURCE1 1044 0.0114 0.0171 +bond c p2 210.3 1.900 ! SOURCE0 1 +bond c p3 219.0 1.883 ! SOURCE3 6 0.0094 0.0129 +bond c p4 220.6 1.880 ! SOURCE0 1 +bond c p5 225.9 1.870 ! SOURCE0 1 +bond c pe 204.9 1.911 ! SOURCE3 3 0.0023 0.0025 +bond c pf 204.9 1.911 ! SOURCE3 3 same as c -pe +bond c px 208.3 1.904 ! SOURCE3 1 0.0000 0.0000 +bond c py 227.6 1.867 ! SOURCE3 6 0.0141 0.0199 +bond c s 328.9 1.675 ! SOURCE1 401 0.0077 0.0128 +bond c s4 200.4 1.870 ! SOURCE0 1 +bond c s6 200.4 1.870 ! SOURCE0 1 +bond c sh 249.6 1.781 ! SOURCE3 6 0.0157 0.0171 +bond c ss 261.9 1.762 ! SOURCE1 20 0.0000 0.0000 +bond c sx 193.3 1.885 ! SOURCE3 5 0.0070 0.0088 +bond c sy 202.8 1.865 ! SOURCE3 5 0.0063 0.0085 +bond c1 c1 986.2 1.181 ! SOURCE1 265 0.0022 0.0031 +bond c1 c2 625.0 1.307 ! SOURCE1 18 0.0000 0.0000 +bond c1 c3 368.3 1.470 ! SOURCE1 215 0.0013 0.0017 +bond c1 ca 404.1 1.440 ! SOURCE0 1 +bond c1 cg 845.8 1.222 ! SOURCE3 22 0.0074 0.0101 +bond c1 ch 845.8 1.222 ! SOURCE3 22 same as c1-cg +bond c1 cl 419.7 1.631 ! SOURCE2 6 0.0046 0.0050 +bond c1 cx 399.1 1.444 ! SOURCE1 38 0.0000 0.0000 +bond c1 f 469.4 1.270 ! SOURCE2 2 0.0085 0.0085 +bond c1 ha 375.9 1.066 ! SOURCE3 63 0.0022 0.0035 +bond c1 hc 385.6 1.060 ! SOURCE0 1 +bond c1 i 318.8 1.989 ! SOURCE2 4 0.0025 0.0032 +bond c1 n 503.0 1.330 ! SOURCE0 1 +bond c1 n1 1014.5 1.138 ! SOURCE1 170 0.0038 0.0055 +bond c1 n2 769.8 1.210 ! SOURCE3 5 0.0089 0.0115 +bond c1 n3 409.8 1.392 ! SOURCE2 1 0.0000 0.0000 +bond c1 n4 378.2 1.417 ! SOURCE3 3 0.0030 0.0032 +bond c1 na 452.0 1.362 ! SOURCE3 8 0.0031 0.0034 +bond c1 ne 741.8 1.220 ! SOURCE3 1 0.0000 0.0000 +bond c1 nf 741.8 1.220 ! SOURCE3 1 same as c1-ne +bond c1 nh 465.7 1.353 ! SOURCE3 3 0.0025 0.0027 +bond c1 no 393.0 1.405 ! SOURCE3 3 0.0004 0.0005 +bond c1 o 777.0 1.166 ! SOURCE2 9 0.0044 0.0052 +bond c1 oh 435.6 1.326 ! SOURCE3 1 0.0000 0.0000 +bond c1 os 437.1 1.325 ! SOURCE3 3 0.0139 0.0148 +bond c1 p2 289.3 1.770 ! SOURCE0 1 +bond c1 p3 275.1 1.790 ! SOURCE0 1 +bond c1 p4 275.1 1.790 ! SOURCE0 1 +bond c1 p5 302.2 1.753 ! SOURCE3 2 0.0000 0.0000 +bond c1 s 371.8 1.630 ! SOURCE1 14 0.0000 0.0000 +bond c1 s2 410.0 1.595 ! SOURCE3 1 0.0000 0.0000 +bond c1 s4 272.9 1.746 ! SOURCE3 2 0.0000 0.0000 +bond c1 s6 290.4 1.722 ! SOURCE3 2 0.0000 0.0000 +bond c1 sh 324.5 1.680 ! SOURCE0 1 +bond c1 ss 325.4 1.679 ! SOURCE1 10 0.0000 0.0000 +bond c2 c2 589.7 1.324 ! SOURCE1 974 0.0048 0.0096 +bond c2 c3 328.3 1.508 ! SOURCE1 2536 0.0016 0.0021 +bond c2 ca 357.2 1.480 ! SOURCE0 1 +bond c2 cc 522.6 1.360 ! SOURCE1 771 0.0152 0.0185 +bond c2 cd 522.6 1.360 ! SOURCE1 771 0.0152 0.0185 +bond c2 ce 560.5 1.339 ! SOURCE3 62 0.0085 0.0128 +bond c2 cf 560.5 1.339 ! SOURCE3 62 same as c2-ce +bond c2 cl 328.8 1.722 ! SOURCE1 163 0.0093 0.0098 +bond c2 cu 573.9 1.332 ! SOURCE2 1 0.0000 0.0000 +bond c2 cx 333.3 1.503 ! SOURCE2 1 0.0000 0.0000 +bond c2 cy 309.4 1.528 ! SOURCE2 1 0.0000 0.0000 +bond c2 f 368.7 1.340 ! SOURCE1 34 0.0000 0.0000 +bond c2 h4 348.6 1.084 ! SOURCE3 40 0.0037 0.0058 +bond c2 h5 357.5 1.078 ! SOURCE3 3 0.0061 0.0067 +bond c2 ha 344.3 1.087 ! SOURCE3 797 0.0030 0.0046 +bond c2 hc 344.3 1.087 ! SOURCE3 789 0.0030 0.0046 +bond c2 hx 350.1 1.083 ! SOURCE3 3 0.0008 0.0008 +bond c2 i 223.2 2.153 ! SOURCE3 2 0.0000 0.0000 +bond c2 n 390.5 1.407 ! SOURCE3 9 0.0109 0.0124 +bond c2 n1 546.0 1.306 ! SOURCE3 4 0.0161 0.0161 +bond c2 n2 581.1 1.288 ! SOURCE1 103 0.0095 0.0100 +bond c2 n3 486.3 1.340 ! SOURCE0 1 +bond c2 n4 309.1 1.482 ! SOURCE3 5 0.0047 0.0064 +bond c2 na 411.1 1.391 ! SOURCE3 31 0.0271 0.0289 +bond c2 nc 533.0 1.313 ! SOURCE1 99 0.0065 0.0095 +bond c2 nd 533.0 1.313 ! SOURCE1 99 same as c2-nc +bond c2 ne 597.7 1.280 ! SOURCE3 37 0.0090 0.0110 +bond c2 nf 597.7 1.280 ! SOURCE3 37 same as c2-ne +bond c2 nh 462.6 1.355 ! SOURCE3 38 0.0385 0.0413 +bond c2 no 327.6 1.463 ! SOURCE3 4 0.0013 0.0013 +bond c2 o 546.2 1.261 ! SOURCE3 4 0.0144 0.0144 +bond c2 oh 425.4 1.333 ! SOURCE1 53 0.0000 0.0000 +bond c2 os 392.6 1.357 ! SOURCE1 315 0.0088 0.0097 +bond c2 p2 375.9 1.670 ! SOURCE3 62 0.0078 0.0147 +bond c2 p3 246.6 1.834 ! SOURCE3 5 0.0041 0.0042 +bond c2 p4 254.0 1.822 ! SOURCE0 1 +bond c2 p5 255.2 1.820 ! SOURCE0 1 +bond c2 pe 355.3 1.691 ! SOURCE3 52 0.0318 0.0542 +bond c2 pf 355.3 1.691 ! SOURCE3 52 same as c2-pe +bond c2 s 281.5 1.734 ! SOURCE3 4 0.0034 0.0034 +bond c2 s2 393.1 1.610 ! SOURCE2 1 0.0000 0.0000 +bond c2 s4 263.2 1.760 ! SOURCE0 1 +bond c2 s6 263.2 1.760 ! SOURCE0 1 +bond c2 sh 255.3 1.772 ! SOURCE3 3 0.0068 0.0072 +bond c2 ss 280.0 1.736 ! SOURCE1 209 0.0135 0.0155 +bond c3 c3 303.1 1.535 ! SOURCE1 14664 0.0043 0.0048 +bond c3 ca 323.5 1.513 ! SOURCE1 1813 0.0000 0.0000 +bond c3 cc 337.3 1.499 ! SOURCE3 50 0.0059 0.0096 +bond c3 cd 337.3 1.499 ! SOURCE3 50 0.0059 0.0096 +bond c3 ce 331.3 1.505 ! SOURCE3 9 0.0019 0.0024 +bond c3 cf 331.3 1.505 ! SOURCE3 9 same as c3-ce +bond c3 cl 279.0 1.786 ! SOURCE1 267 0.0151 0.0194 +bond c3 cu 359.4 1.478 ! SOURCE1 7 0.0000 0.0000 +bond c3 cv 347.6 1.489 ! SOURCE1 11 0.0000 0.0000 +bond c3 cx 322.5 1.514 ! SOURCE1 712 0.0044 0.0045 +bond c3 cy 308.5 1.529 ! SOURCE1 376 0.0000 0.0000 +bond c3 f 363.8 1.344 ! SOURCE1 617 0.0241 0.0281 +bond c3 h1 335.9 1.093 ! SOURCE3 2175 0.0045 0.0082 +bond c3 h2 326.4 1.100 ! SOURCE3 66 0.0110 0.0280 +bond c3 h3 335.9 1.093 ! SOURCE2 1 0.0000 0.0000 +bond c3 hc 337.3 1.092 ! SOURCE3 2815 0.0040 0.0059 +bond c3 hx 338.7 1.091 ! SOURCE3 146 0.0023 0.0066 +bond c3 i 219.1 2.162 ! SOURCE1 15 0.0000 0.0000 +bond c3 n 330.6 1.460 ! SOURCE1 187 0.0065 0.0079 +bond c3 n1 325.1 1.470 ! SOURCE3 +bond c3 n2 313.8 1.477 ! SOURCE1 129 0.0136 0.0138 +bond c3 n3 320.6 1.470 ! SOURCE1 1678 0.0013 0.0017 +bond c3 n4 293.6 1.499 ! SOURCE1 1370 0.0000 0.0000 +bond c3 na 334.7 1.456 ! SOURCE3 23 0.0096 0.0119 +bond c3 nc 334.7 1.456 ! SOURCE3 9 0.0091 0.0109 +bond c3 nd 334.7 1.456 ! SOURCE3 9 same as c3-nc +bond c3 nh 332.7 1.458 ! SOURCE3 27 0.0067 0.0085 +bond c3 no 265.4 1.533 ! SOURCE1 83 0.0163 0.0212 +bond c3 o 422.6 1.335 ! SOURCE3 4 0.0100 0.0100 +bond c3 oh 314.1 1.426 ! SOURCE1 914 0.0110 0.0129 +bond c3 os 301.5 1.439 ! SOURCE1 3123 0.0112 0.0126 +bond c3 p2 234.3 1.855 ! SOURCE3 9 0.0100 0.0125 +bond c3 p3 240.6 1.844 ! SOURCE3 109 0.0091 0.0107 +bond c3 p4 247.2 1.833 ! SOURCE3 29 0.0091 0.0138 +bond c3 p5 259.7 1.813 ! SOURCE1 84 0.0000 0.0000 +bond c3 px 252.7 1.824 ! SOURCE3 28 0.0079 0.0098 +bond c3 py 259.7 1.813 ! SOURCE3 13 0.0144 0.0163 +bond c3 s 212.9 1.845 ! SOURCE3 4 0.0185 0.0185 +bond c3 s4 233.8 1.807 ! SOURCE1 139 0.0022 0.0023 +bond c3 s6 254.0 1.774 ! SOURCE1 118 0.0080 0.0103 +bond c3 sh 225.3 1.822 ! SOURCE3 12 0.0042 0.0051 +bond c3 ss 225.8 1.821 ! SOURCE1 358 0.0049 0.0075 +bond c3 sx 232.6 1.809 ! SOURCE3 30 0.0050 0.0067 +bond c3 sy 248.9 1.782 ! SOURCE3 31 0.0034 0.0039 +bond ca ca 478.4 1.387 ! SOURCE1 6228 0.0096 0.0147 +bond ca cc 411.7 1.434 ! SOURCE1 80 0.0000 0.0000 +bond ca cd 411.7 1.434 ! SOURCE1 80 0.0000 0.0000 +bond ca ce 366.0 1.472 ! SOURCE1 71 0.0029 0.0030 +bond ca cf 366.0 1.472 ! SOURCE1 71 0.0029 0.0030 +bond ca cg 406.6 1.438 ! SOURCE1 71 0.0045 0.0045 +bond ca ch 406.6 1.438 ! SOURCE1 71 0.0045 0.0045 +bond ca cl 322.8 1.729 ! SOURCE1 704 0.0095 0.0095 +bond ca cp 466.1 1.395 ! SOURCE3 14 0.0098 0.0110 +bond ca cx 350.8 1.486 ! SOURCE1 98 0.0064 0.0118 +bond ca f 363.8 1.344 ! SOURCE1 205 0.0069 0.0089 +bond ca h4 342.9 1.088 ! SOURCE3 57 0.0016 0.0026 +bond ca h5 347.2 1.085 ! SOURCE3 15 0.0038 0.0048 +bond ca ha 344.3 1.087 ! SOURCE3 1496 0.0024 0.0045 +bond ca i 252.4 2.095 ! SOURCE1 51 0.0000 0.0000 +bond ca n 372.3 1.422 ! SOURCE3 9 0.0092 0.0098 +bond ca n1 398.1 1.400 ! SOURCE3 +bond ca n2 320.6 1.470 ! SOURCE2 1 0.0000 0.0000 +bond ca n4 325.6 1.465 ! SOURCE1 23 0.0000 0.0000 +bond ca na 470.3 1.350 ! SOURCE1 150 0.0091 0.0103 +bond ca nb 483.1 1.342 ! SOURCE3 104 0.0052 0.0076 +bond ca nc 492.9 1.336 ! SOURCE1 1826 0.0012 0.0020 +bond ca nd 492.9 1.336 ! SOURCE1 1826 0.0012 0.0020 +bond ca ne 361.8 1.431 ! SOURCE1 52 0.0000 0.0000 +bond ca nf 361.8 1.431 ! SOURCE1 52 0.0000 0.0000 +bond ca nh 449.0 1.364 ! SOURCE1 137 0.0084 0.0085 +bond ca no 322.6 1.468 ! SOURCE1 556 0.0000 0.0000 +bond ca o 519.7 1.275 ! SOURCE3 2 0.0000 0.0000 +bond ca oh 386.1 1.362 ! SOURCE1 551 0.0000 0.0000 +bond ca os 372.4 1.373 ! SOURCE1 1092 0.0048 0.0071 +bond ca p2 243.0 1.840 ! SOURCE0 1 +bond ca p3 252.7 1.824 ! SOURCE1 145 0.0171 0.0187 +bond ca p4 264.3 1.806 ! SOURCE0 1 +bond ca p5 271.6 1.795 ! SOURCE1 571 0.0020 0.0028 +bond ca pe 249.6 1.829 ! SOURCE3 10 0.0034 0.0042 +bond ca pf 249.6 1.829 ! SOURCE3 10 0.0034 0.0042 +bond ca px 252.1 1.825 ! SOURCE3 5 0.0153 0.0168 +bond ca py 268.3 1.800 ! SOURCE3 3 0.0051 0.0054 +bond ca s 277.9 1.739 ! SOURCE3 2 0.0000 0.0000 +bond ca s4 245.2 1.788 ! SOURCE1 51 0.0038 0.0048 +bond ca s6 263.9 1.759 ! SOURCE1 229 0.0030 0.0036 +bond ca sh 245.8 1.787 ! SOURCE3 2 0.0055 0.0055 +bond ca ss 256.6 1.770 ! SOURCE1 297 0.0034 0.0041 +bond ca sx 233.8 1.807 ! SOURCE3 3 0.0015 0.0016 +bond ca sy 247.7 1.784 ! SOURCE3 13 0.0068 0.0094 +bond cc cc 418.3 1.429 ! SOURCE1 740 0.0058 0.0069 +bond cc cd 504.0 1.371 ! SOURCE3 523 0.0156 0.0217 +bond cc cf 519.2 1.362 ! SOURCE3 1 0.0000 0.0000 +bond cc cg 420.9 1.427 ! SOURCE1 560 0.0000 0.0000 +bond cc ch 420.9 1.427 ! SOURCE1 560 0.0000 0.0000 +bond cc cl 348.3 1.700 ! SOURCE3 1 0.0000 0.0000 +bond cc h4 350.1 1.083 ! SOURCE3 599 0.0028 0.0037 +bond cc h5 356.0 1.079 ! SOURCE3 40 0.0040 0.0051 +bond cc ha 347.2 1.085 ! SOURCE3 740 0.0029 0.0039 +bond cc n 426.0 1.380 ! SOURCE3 56 0.0075 0.0109 +bond cc n2 561.3 1.298 ! SOURCE3 4 0.0096 0.0096 +bond cc na 438.8 1.371 ! SOURCE3 440 0.0107 0.0144 +bond cc nc 431.6 1.376 ! SOURCE1 88 0.0000 0.0000 +bond cc nd 494.6 1.335 ! SOURCE3 203 0.0171 0.0239 +bond cc nh 449.0 1.364 ! SOURCE3 6 0.0038 0.0040 +bond cc oh 405.9 1.347 ! SOURCE3 3 0.0077 0.0077 +bond cc os 376.1 1.370 ! SOURCE3 86 0.0139 0.0192 +bond cc pd 318.2 1.733 ! SOURCE3 84 same as cd-pc +bond cc ss 279.3 1.737 ! SOURCE3 52 0.0162 0.0194 +bond cd cd 418.3 1.429 ! SOURCE1 740 0.0058 0.0069 +bond cd ce 519.2 1.362 ! SOURCE3 1 same as cc-cf +bond cd cg 420.9 1.427 ! SOURCE1 560 0.0000 0.0000 +bond cd ch 420.9 1.427 ! SOURCE1 560 0.0000 0.0000 +bond cd cl 348.3 1.700 ! SOURCE3 1 same as cc-cl +bond cd h4 350.1 1.083 ! SOURCE3 599 0.0028 0.0037 +bond cd h5 356.0 1.079 ! SOURCE3 40 0.0040 0.0051 +bond cd ha 347.2 1.085 ! SOURCE3 740 0.0029 0.0039 +bond cd n 426.0 1.380 ! SOURCE3 56 0.0075 0.0109 +bond cd n2 561.3 1.298 ! SOURCE3 4 0.0096 0.0096 +bond cd na 438.8 1.371 ! SOURCE3 440 0.0107 0.0144 +bond cd nc 494.6 1.335 ! SOURCE3 203 0.0171 0.0239 +bond cd nd 431.6 1.376 ! SOURCE1 88 0.0000 0.0000 +bond cd nh 449.0 1.364 ! SOURCE3 6 0.0038 0.0040 +bond cd oh 405.9 1.347 ! SOURCE3 3 0.0077 0.0077 +bond cd os 376.1 1.370 ! SOURCE3 86 0.0139 0.0192 +bond cd pc 318.2 1.733 ! SOURCE3 84 0.0088 0.0161 +bond cd ss 279.3 1.737 ! SOURCE3 52 0.0162 0.0194 +bond ce ce 390.5 1.451 ! SOURCE1 66 0.0060 0.0060 +bond ce cf 562.4 1.338 ! SOURCE1 543 0.0035 0.0045 +bond ce cg 415.6 1.431 ! SOURCE1 22 0.0000 0.0000 +bond ce ch 415.6 1.431 ! SOURCE1 22 0.0000 0.0000 +bond ce ha 341.5 1.089 ! SOURCE3 55 0.0030 0.0056 +bond ce n1 522.2 1.319 ! SOURCE3 3 0.0121 0.0121 +bond ce n2 599.8 1.279 ! SOURCE1 75 0.0000 0.0000 +bond ce ne 381.8 1.414 ! SOURCE3 7 0.0093 0.0103 +bond ce nh 484.7 1.341 ! SOURCE3 1 0.0000 0.0000 +bond ce p2 259.1 1.814 ! SOURCE0 1 +bond ce pe 256.5 1.818 ! SOURCE3 8 0.0090 0.0108 +bond ce px 254.6 1.821 ! SOURCE3 6 0.0034 0.0046 +bond ce py 272.3 1.794 ! SOURCE3 5 0.0034 0.0045 +bond ce s 324.5 1.680 ! SOURCE0 1 +bond ce sx 239.7 1.797 ! SOURCE3 5 0.0080 0.0082 +bond ce sy 248.9 1.782 ! SOURCE3 5 0.0105 0.0114 +bond cf cf 390.5 1.451 ! SOURCE1 66 0.0060 0.0060 +bond cf cg 415.6 1.431 ! SOURCE1 22 0.0000 0.0000 +bond cf ch 415.6 1.431 ! SOURCE1 22 0.0000 0.0000 +bond cf ha 341.5 1.089 ! SOURCE3 55 0.0030 0.0056 +bond cf n1 522.2 1.319 ! SOURCE3 3 0.0121 0.0121 +bond cf n2 599.8 1.279 ! SOURCE1 75 same as ce-n2 +bond cf nf 381.8 1.414 ! SOURCE3 7 same as ce-ne +bond cf nh 484.7 1.341 ! SOURCE3 1 same as ce-nh +bond cf p2 259.1 1.814 ! SOURCE0 1 same as ce-p2 +bond cf pf 256.5 1.818 ! SOURCE3 8 same as ce-pe +bond cf px 254.6 1.821 ! SOURCE3 6 same as ce-px +bond cf py 272.3 1.794 ! SOURCE3 5 same as ce-py +bond cf s 324.5 1.680 ! SOURCE0 1 same as ce- s +bond cf sx 239.7 1.797 ! SOURCE3 5 same as ce-sx +bond cf sy 248.9 1.782 ! SOURCE3 5 same as ce-sy +bond cg cg 494.2 1.377 ! SOURCE1 42 0.0000 0.0000 +bond cg ch 949.5 1.191 ! SOURCE1 80 0.0015 0.0015 +bond cg n1 994.7 1.143 ! SOURCE1 316 0.0011 0.0018 +bond cg ne 450.5 1.363 ! SOURCE3 4 0.0189 0.0204 +bond cg pe 429.8 1.621 ! SOURCE3 11 0.1928 0.2008 +bond ch ch 494.2 1.377 ! SOURCE1 42 0.0000 0.0000 +bond ch n1 994.7 1.143 ! SOURCE1 316 0.0011 0.0018 +bond ch nf 450.5 1.363 ! SOURCE3 4 same as cg-ne +bond ch pf 429.8 1.621 ! SOURCE3 11 same as cg-pe +bond cl cl 143.3 2.267 ! SOURCE1 2 0.0395 0.0395 +bond cl cx 301.8 1.755 ! SOURCE1 64 0.0000 0.0000 +bond cl cy 292.0 1.768 ! SOURCE2 2 0.0070 0.0070 +bond cl f 298.6 1.648 ! SOURCE2 2 0.0500 0.0500 +bond cl i 163.5 2.550 ! SOURCE1 6 0.0605 0.0893 +bond cl n 331.8 1.728 ! SOURCE3 3 0.0107 0.0113 +bond cl n1 431.6 1.630 ! SOURCE0 1 +bond cl n2 263.4 1.819 ! SOURCE3 6 0.0784 0.1020 +bond cl n3 298.6 1.769 ! SOURCE3 4 0.0070 0.0095 +bond cl n4 311.1 1.753 ! SOURCE3 4 0.0085 0.0098 +bond cl na 253.2 1.835 ! SOURCE3 7 0.1858 0.2083 +bond cl nh 303.2 1.763 ! SOURCE3 1 0.0000 0.0000 +bond cl no 250.1 1.840 ! SOURCE2 1 0.0000 0.0000 +bond cl o 557.6 1.483 ! SOURCE3 4 0.0000 0.0000 +bond cl oh 309.7 1.690 ! SOURCE2 1 0.0000 0.0000 +bond cl os 278.8 1.730 ! SOURCE3 4 0.0000 0.0000 +bond cl p2 217.5 2.070 ! SOURCE3 6 0.0086 0.0108 +bond cl p3 249.4 2.008 ! SOURCE1 111 0.0000 0.0000 +bond cl p4 249.4 2.008 ! SOURCE1 111 0.0000 0.0000 +bond cl p5 249.4 2.008 ! SOURCE1 111 0.0000 0.0000 +bond cl pb 255.6 1.997 ! SOURCE1 46 0.0000 0.0000 +bond cl s 208.7 2.072 ! SOURCE1 6 0.0000 0.0000 +bond cl s2 172.7 2.161 ! SOURCE2 1 0.0000 0.0000 +bond cl s4 208.7 2.072 ! SOURCE1 6 0.0000 0.0000 +bond cl s6 208.7 2.072 ! SOURCE1 6 0.0000 0.0000 +bond cl sh 208.7 2.072 ! SOURCE1 6 0.0000 0.0000 +bond cl ss 208.7 2.072 ! SOURCE1 6 0.0000 0.0000 +bond cl sx 208.7 2.072 ! SOURCE1 6 0.0000 0.0000 +bond cl sy 208.7 2.072 ! SOURCE1 6 0.0000 0.0000 +bond cp cp 346.5 1.490 ! SOURCE1 242 0.0007 0.0010 +bond cp nb 470.3 1.350 ! SOURCE3 2 0.0000 0.0000 +bond cq cq 346.5 1.490 ! SOURCE1 242 0.0007 0.0010 +bond cu cu 653.7 1.294 ! SOURCE1 10 0.0000 0.0000 +bond cu cx 327.3 1.509 ! SOURCE1 20 0.0000 0.0000 +bond cu ha 353.0 1.081 ! SOURCE2 3 0.0104 0.0111 +bond cv cv 568.1 1.335 ! SOURCE1 25 0.0000 0.0000 +bond cv cy 323.5 1.513 ! SOURCE1 50 0.0000 0.0000 +bond cv ha 344.3 1.087 ! SOURCE3 2 0.0000 0.0000 +bond cx cv 328.3 1.508 ! SOURCE1 2536 Same as +bond cx cx 337.3 1.499 ! SOURCE1 1204 0.0159 0.0183 +bond cx cy 321.5 1.515 ! SOURCE3 2 0.0000 0.0000 +bond cx f 347.2 1.358 ! SOURCE2 3 0.0047 0.0050 +bond cx h1 344.3 1.087 ! SOURCE3 10 0.0013 0.0017 +bond cx h2 350.1 1.083 ! SOURCE3 2 0.0000 0.0000 +bond cx hc 345.8 1.086 ! SOURCE3 44 0.0009 0.0011 +bond cx n 315.7 1.475 ! SOURCE3 1 0.0000 0.0000 +bond cx n2 309.1 1.482 ! SOURCE3 2 0.0000 0.0000 +bond cx n3 318.7 1.472 ! SOURCE1 134 0.0000 0.0000 +bond cx oh 387.4 1.361 ! SOURCE3 3 0.0017 0.0018 +bond cx os 320.1 1.420 ! SOURCE3 7 0.0205 0.0222 +bond cx p3 227.6 1.867 ! SOURCE2 1 0.0000 0.0000 +bond cx s4 225.3 1.822 ! SOURCE2 1 0.0000 0.0000 +bond cx s6 283.7 1.731 ! SOURCE2 1 0.0000 0.0000 +bond cx ss 229.2 1.815 ! SOURCE2 1 0.0000 0.0000 +bond cy cy 286.8 1.554 ! SOURCE1 742 0.0013 0.0041 +bond cy h1 330.4 1.097 ! SOURCE3 17 0.0042 0.0058 +bond cy hc 334.5 1.094 ! SOURCE3 63 0.0012 0.0014 +bond cy n3 307.2 1.484 ! SOURCE1 21 0.0000 0.0000 +bond cy oh 325.2 1.415 ! SOURCE3 2 0.0000 0.0000 +bond cy os 280.7 1.462 ! SOURCE3 4 0.0101 0.0101 +bond f n 391.7 1.397 ! SOURCE3 3 0.0106 0.0112 +bond f n1 375.7 1.410 ! SOURCE0 1 +bond f n2 337.5 1.444 ! SOURCE3 5 0.0292 0.0377 +bond f n3 380.6 1.406 ! SOURCE1 9 0.0000 0.0000 +bond f n4 526.8 1.308 ! SOURCE3 2 0.0000 0.0000 +bond f na 374.5 1.411 ! SOURCE3 7 0.0537 0.0611 +bond f nh 357.1 1.426 ! SOURCE3 3 0.0080 0.0085 +bond f no 314.4 1.467 ! SOURCE2 1 0.0000 0.0000 +bond f o 442.2 1.330 ! SOURCE0 1 +bond f oh 305.4 1.444 ! SOURCE3 1 0.0000 0.0000 +bond f os 326.2 1.423 ! SOURCE3 2 0.0000 0.0000 +bond f p2 287.3 1.536 ! SOURCE3 7 0.1437 0.2054 +bond f p3 254.5 1.578 ! SOURCE2 8 0.0093 0.0103 +bond f p4 246.0 1.590 ! SOURCE0 1 +bond f p5 253.8 1.579 ! SOURCE1 72 0.0000 0.0000 +bond f s 233.3 1.660 ! SOURCE0 1 +bond f s2 244.4 1.643 ! SOURCE2 1 0.0000 0.0000 +bond f s4 282.4 1.591 ! SOURCE2 4 0.0065 0.0065 +bond f s6 312.1 1.556 ! SOURCE2 5 0.0163 0.0220 +bond f sh 240.4 1.649 ! SOURCE3 1 0.0000 0.0000 +bond f ss 250.5 1.634 ! SOURCE3 3 0.0147 0.0156 +bond hn n 410.2 1.009 ! SOURCE3 149 0.0089 0.0098 +bond hn n1 455.1 0.986 ! SOURCE2 1 0.0000 0.0000 +bond hn n2 375.5 1.029 ! SOURCE3 108 0.0070 0.0096 +bond hn n3 394.1 1.018 ! SOURCE3 157 0.0063 0.0086 +bond hn n4 369.0 1.033 ! SOURCE3 264 0.0054 0.0082 +bond hn na 406.6 1.011 ! SOURCE3 46 0.0076 0.0107 +bond hn nh 401.2 1.014 ! SOURCE3 209 0.0068 0.0091 +bond hn no 385.6 1.023 ! SOURCE3 1 0.0000 0.0000 +bond ho o 357.9 0.981 ! SOURCE3 1 0.0000 0.0000 +bond ho oh 369.6 0.974 ! SOURCE3 367 0.0069 0.0105 +bond hp p2 385.1 1.336 ! SOURCE3 87 0.1430 0.1706 +bond hp p3 303.1 1.409 ! SOURCE3 101 0.0170 0.0617 +bond hp p4 368.7 1.349 ! SOURCE3 17 0.1277 0.1577 +bond hp p5 305.0 1.407 ! SOURCE3 7 0.0049 0.0062 +bond hs s 286.4 1.353 ! SOURCE3 1 0.0000 0.0000 +bond hs s4 266.4 1.375 ! SOURCE3 5 0.0004 0.0004 +bond hs s6 280.8 1.359 ! SOURCE3 5 0.0012 0.0015 +bond hs sh 302.2 1.337 ! SOURCE3 98 0.0150 0.0486 +bond i i 109.2 2.917 ! SOURCE1 1 0.0000 0.0000 +bond i n 278.3 2.098 ! SOURCE3 5 0.0153 0.0156 +bond i n1 302.1 2.060 ! SOURCE0 1 +bond i n2 182.6 2.304 ! SOURCE3 6 0.1010 0.1186 +bond i n3 231.8 2.185 ! SOURCE3 3 0.0412 0.0437 +bond i n4 246.6 2.155 ! SOURCE3 3 0.0158 0.0168 +bond i na 260.5 2.129 ! SOURCE3 8 0.0838 0.1276 +bond i nh 249.2 2.150 ! SOURCE3 1 0.0000 0.0000 +bond i no 211.0 2.231 ! SOURCE3 1 0.0000 0.0000 +bond i o 323.8 1.980 ! SOURCE0 1 +bond i oh 247.9 2.101 ! SOURCE3 2 0.0000 0.0000 +bond i os 233.6 2.129 ! SOURCE3 3 0.0138 0.0146 +bond i p2 108.2 2.643 ! SOURCE3 6 0.0266 0.0297 +bond i p3 123.6 2.566 ! SOURCE3 3 0.0015 0.0016 +bond i p4 183.0 2.352 ! SOURCE3 4 0.2600 0.2600 +bond i p5 117.3 2.596 ! SOURCE3 3 0.0135 0.0143 +bond i s 175.1 2.430 ! SOURCE0 1 +bond i s4 82.8 2.870 ! SOURCE0 1 +bond i s6 82.8 2.870 ! SOURCE3 1 0.0000 0.0000 +bond i sh 138.5 2.560 ! SOURCE0 1 +bond i ss 135.9 2.571 ! SOURCE3 3 0.0061 0.0065 +bond n n 469.7 1.390 ! SOURCE3 5 0.0035 0.0038 +bond n n1 553.9 1.340 ! SOURCE0 1 +bond n n2 499.7 1.371 ! SOURCE3 9 0.0164 0.0200 +bond n n3 443.3 1.408 ! SOURCE3 5 0.0077 0.0087 +bond n n4 410.8 1.432 ! SOURCE3 5 0.0096 0.0098 +bond n na 486.8 1.379 ! SOURCE3 11 0.0052 0.0071 +bond n nc 532.1 1.352 ! SOURCE3 4 0.0055 0.0058 +bond n nd 532.1 1.352 ! SOURCE3 4 same as n -nc +bond n nh 437.7 1.412 ! SOURCE3 4 0.0035 0.0037 +bond n no 381.2 1.456 ! SOURCE3 4 0.0278 0.0327 +bond n o 646.6 1.264 ! SOURCE3 9 0.0336 0.0381 +bond n oh 395.4 1.410 ! SOURCE3 6 0.0078 0.0106 +bond n os 372.3 1.429 ! SOURCE3 7 0.0364 0.0528 +bond n p2 310.3 1.733 ! SOURCE3 8 0.0143 0.0217 +bond n p3 282.2 1.770 ! SOURCE3 9 0.0102 0.0118 +bond n p4 309.5 1.734 ! SOURCE3 1 0.0000 0.0000 +bond n p5 327.0 1.713 ! SOURCE3 4 0.0084 0.0109 +bond n pc 304.8 1.740 ! SOURCE3 3 0.0009 0.0010 +bond n pd 304.8 1.740 ! SOURCE3 3 same as n -pc +bond n s 247.5 1.767 ! SOURCE3 3 0.0011 0.0011 +bond n s4 238.2 1.782 ! SOURCE3 4 0.0154 0.0214 +bond n s6 270.8 1.732 ! SOURCE3 4 0.0177 0.0224 +bond n sh 273.6 1.728 ! SOURCE3 4 0.0108 0.0128 +bond n ss 281.6 1.717 ! SOURCE3 7 0.0120 0.0133 +bond n1 n1 1221.7 1.124 ! SOURCE1 19 0.0000 0.0000 +bond n1 n2 857.4 1.216 ! SOURCE1 19 0.0000 0.0000 +bond n1 n3 535.7 1.350 ! SOURCE0 1 +bond n1 n4 518.2 1.360 ! SOURCE0 1 +bond n1 na 535.7 1.350 ! SOURCE0 1 +bond n1 nc 857.4 1.216 ! SOURCE1 38 0.0000 0.0000 +bond n1 nd 857.4 1.216 ! SOURCE1 38 0.0000 0.0000 +bond n1 ne 751.9 1.252 ! SOURCE2 1 0.0000 0.0000 +bond n1 nf 751.9 1.252 ! SOURCE2 1 same as n1-ne +bond n1 nh 553.9 1.340 ! SOURCE0 1 +bond n1 no 454.8 1.400 ! SOURCE0 1 +bond n1 o 617.5 1.277 ! SOURCE3 5 0.0340 0.0438 +bond n1 oh 569.8 1.300 ! SOURCE0 1 +bond n1 os 550.5 1.310 ! SOURCE0 1 +bond n1 p2 358.8 1.678 ! SOURCE3 2 0.0282 0.0282 +bond n1 p3 376.7 1.660 ! SOURCE0 1 +bond n1 p4 353.0 1.680 ! SOURCE3 +bond n1 p5 482.7 1.571 ! SOURCE1 132 0.0000 0.0000 +bond n1 s 328.7 1.659 ! SOURCE3 6 0.0693 0.0789 +bond n1 s2 604.3 1.449 ! SOURCE2 2 0.0010 0.0010 +bond n1 s4 336.8 1.650 ! SOURCE0 1 +bond n1 s6 670.3 1.416 ! SOURCE2 2 0.0000 0.0000 +bond n1 sh 376.1 1.610 ! SOURCE0 1 +bond n1 ss 376.1 1.610 ! SOURCE0 1 +bond n2 n2 702.7 1.271 ! SOURCE3 27 0.0228 0.0347 +bond n2 n3 574.8 1.329 ! SOURCE2 1 0.0000 0.0000 +bond n2 n4 200.8 1.679 ! SOURCE3 7 0.2778 0.3138 +bond n2 na 450.4 1.403 ! SOURCE3 14 0.0399 0.0575 +bond n2 nc 743.9 1.255 ! SOURCE1 13 same as n2-nd +bond n2 nd 743.9 1.255 ! SOURCE1 13 0.0000 0.0000 +bond n2 ne 685.5 1.278 ! SOURCE3 30 0.0224 0.0302 +bond n2 nf 685.5 1.278 ! SOURCE3 30 same as n2-ne +bond n2 nh 525.1 1.356 ! SOURCE3 22 0.0218 0.0300 +bond n2 no 231.9 1.626 ! SOURCE3 4 0.1591 0.1933 +bond n2 o 789.9 1.209 ! SOURCE3 20 0.0284 0.0344 +bond n2 oh 416.2 1.394 ! SOURCE1 67 0.0000 0.0000 +bond n2 os 400.5 1.406 ! SOURCE3 10 0.0120 0.0147 +bond n2 p2 438.3 1.605 ! SOURCE3 35 0.0392 0.0737 +bond n2 p3 286.5 1.764 ! SOURCE3 7 0.0320 0.0374 +bond n2 p4 317.7 1.724 ! SOURCE0 1 +bond n2 p5 445.8 1.599 ! SOURCE1 7 0.0000 0.0000 +bond n2 pe 527.9 1.540 ! SOURCE3 20 0.1112 0.1392 +bond n2 pf 527.9 1.540 ! SOURCE3 20 same as n2-pe +bond n2 s 458.1 1.541 ! SOURCE1 37 0.0000 0.0000 +bond n2 s2 499.0 1.512 ! SOURCE2 1 0.0000 0.0000 +bond n2 s4 376.1 1.610 ! SOURCE0 1 +bond n2 s6 468.9 1.533 ! SOURCE3 3 0.0144 0.0144 +bond n2 sh 266.6 1.738 ! SOURCE3 5 0.0405 0.0511 +bond n2 ss 331.4 1.656 ! SOURCE1 36 0.0000 0.0000 +bond n3 n3 383.6 1.454 ! SOURCE1 44 0.0000 0.0000 +bond n3 n4 434.9 1.414 ! SOURCE1 13 0.0000 0.0000 +bond n3 na 426.7 1.420 ! SOURCE1 68 0.0000 0.0000 +bond n3 nh 426.7 1.420 ! SOURCE1 68 0.0000 0.0000 +bond n3 no 394.5 1.445 ! SOURCE3 3 0.0196 0.0208 +bond n3 o 564.0 1.303 ! SOURCE3 4 0.1197 0.1217 +bond n3 oh 413.5 1.396 ! SOURCE1 28 0.0000 0.0000 +bond n3 os 359.6 1.440 ! SOURCE1 34 0.0301 0.0315 +bond n3 p2 366.6 1.670 ! SOURCE0 1 +bond n3 p3 312.8 1.730 ! SOURCE1 40 0.0000 0.0000 +bond n3 p4 341.1 1.697 ! SOURCE1 88 0.0000 0.0000 +bond n3 p5 373.6 1.663 ! SOURCE1 501 0.0033 0.0086 +bond n3 s 232.3 1.792 ! SOURCE3 3 0.0168 0.0178 +bond n3 s4 251.3 1.761 ! SOURCE3 6 0.0563 0.0766 +bond n3 s6 353.8 1.632 ! SOURCE1 99 0.0090 0.0136 +bond n3 sh 265.9 1.739 ! SOURCE3 3 0.0145 0.0154 +bond n3 ss 277.9 1.722 ! SOURCE3 5 0.0172 0.0207 +bond n4 n4 349.9 1.484 ! SOURCE3 4 0.0089 0.0089 +bond n4 na 407.0 1.435 ! SOURCE3 9 0.0242 0.0390 +bond n4 nh 369.7 1.466 ! SOURCE3 5 0.0097 0.0108 +bond n4 no 354.2 1.480 ! SOURCE0 1 +bond n4 o 463.6 1.361 ! SOURCE3 3 0.0039 0.0041 +bond n4 oh 408.2 1.400 ! SOURCE3 3 0.0108 0.0115 +bond n4 os 381.8 1.421 ! SOURCE3 5 0.0225 0.0249 +bond n4 p2 185.9 1.942 ! SOURCE3 10 0.0514 0.0643 +bond n4 p3 215.1 1.880 ! SOURCE3 5 0.0143 0.0146 +bond n4 p4 187.6 1.938 ! SOURCE3 1 0.0000 0.0000 +bond n4 p5 242.9 1.830 ! SOURCE3 5 0.0082 0.0087 +bond n4 py 204.2 1.902 ! SOURCE3 4 0.0000 0.0000 +bond n4 s 210.3 1.832 ! SOURCE3 3 0.0004 0.0004 +bond n4 s4 151.0 1.972 ! SOURCE3 3 0.0187 0.0198 +bond n4 s6 172.7 1.914 ! SOURCE3 5 0.0414 0.0432 +bond n4 sh 221.5 1.811 ! SOURCE3 3 0.0025 0.0027 +bond n4 ss 221.0 1.812 ! SOURCE3 5 0.0061 0.0064 +bond na na 453.3 1.401 ! SOURCE1 40 0.0000 0.0000 +bond na nc 535.7 1.350 ! SOURCE3 152 0.0117 0.0180 +bond na nd 535.7 1.350 ! SOURCE3 152 0.0117 0.0180 +bond na nh 453.3 1.401 ! SOURCE1 40 0.0000 0.0000 +bond na no 401.9 1.439 ! SOURCE3 9 0.0241 0.0289 +bond na o 644.3 1.265 ! SOURCE1 25 0.0345 0.0347 +bond na oh 412.2 1.397 ! SOURCE3 9 0.0161 0.0217 +bond na os 355.2 1.444 ! SOURCE3 45 0.0349 0.0423 +bond na p2 297.8 1.749 ! SOURCE3 11 0.0164 0.0192 +bond na p3 288.0 1.762 ! SOURCE3 8 0.0101 0.0113 +bond na p4 492.4 1.564 ! SOURCE3 5 0.2116 0.2161 +bond na p5 325.3 1.715 ! SOURCE3 11 0.0197 0.0238 +bond na pc 311.1 1.732 ! SOURCE3 81 0.0124 0.0207 +bond na pd 311.1 1.732 ! SOURCE3 81 same as na-pc +bond na py 327.8 1.712 ! SOURCE3 2 0.0000 0.0000 +bond na s 248.7 1.765 ! SOURCE3 8 0.0083 0.0095 +bond na s4 231.7 1.793 ! SOURCE3 10 0.0316 0.0421 +bond na s6 274.3 1.727 ! SOURCE3 10 0.0169 0.0201 +bond na sh 278.6 1.721 ! SOURCE3 9 0.0101 0.0113 +bond na ss 270.1 1.733 ! SOURCE3 38 0.0280 0.0412 +bond na sy 274.3 1.727 ! SOURCE3 1 +bond nb nb 550.2 1.342 ! SOURCE1 15 0.0307 0.0314 +bond nb pb 461.1 1.587 ! SOURCE1 162 0.0076 0.0091 +bond nc nc 486.8 1.379 ! SOURCE3 9 0.0145 0.0164 +bond nc nd 602.9 1.315 ! SOURCE3 9 0.0205 0.0221 +bond nc os 414.9 1.395 ! SOURCE1 46 0.0163 0.0188 +bond nc ss 433.5 1.560 ! SOURCE1 74 0.0000 0.0000 +bond nc sy 439.8 1.555 ! SOURCE3 2 +bond nd nd 486.8 1.379 ! SOURCE3 9 0.0145 0.0164 +bond nd os 414.9 1.395 ! SOURCE1 46 0.0163 0.0188 +bond nd ss 433.5 1.560 ! SOURCE1 74 0.0000 0.0000 +bond nd sy 439.8 1.555 ! SOURCE3 2 +bond ne ne 355.3 1.479 ! SOURCE3 19 0.0960 0.1705 +bond ne nf 738.6 1.257 ! SOURCE3 1 0.0000 0.0000 +bond ne o 736.4 1.228 ! SOURCE3 40 0.0207 0.0255 +bond ne p2 493.9 1.563 ! SOURCE3 14 0.0950 0.1325 +bond ne pe 327.8 1.712 ! SOURCE3 28 0.0848 0.1076 +bond ne px 336.6 1.702 ! SOURCE3 11 0.0578 0.0883 +bond ne py 320.2 1.721 ! SOURCE3 15 0.0497 0.0702 +bond ne s 463.5 1.537 ! SOURCE3 22 0.1396 0.1708 +bond ne sx 207.3 1.838 ! SOURCE3 7 0.0760 0.1060 +bond ne sy 257.1 1.752 ! SOURCE3 7 0.0640 0.0814 +bond nf nf 355.3 1.479 ! SOURCE3 19 same as ne-ne +bond nf o 736.4 1.228 ! SOURCE3 40 same as ne- o +bond nf p2 493.9 1.563 ! SOURCE3 14 same as ne-p2 +bond nf pf 327.8 1.712 ! SOURCE3 28 same as ne-pe +bond nf px 336.6 1.702 ! SOURCE3 11 same as ne-px +bond nf py 320.2 1.721 ! SOURCE3 15 same as ne-py +bond nf s 463.5 1.537 ! SOURCE3 22 same as ne- s +bond nf sx 207.3 1.838 ! SOURCE3 7 same as ne-sx +bond nf sy 257.1 1.752 ! SOURCE3 7 same as ne-sy +bond nh nh 453.3 1.401 ! SOURCE1 40 0.0000 0.0000 +bond nh no 381.2 1.456 ! SOURCE3 4 0.0364 0.0370 +bond nh o 596.2 1.287 ! SOURCE3 3 0.0424 0.0450 +bond nh oh 359.6 1.440 ! SOURCE3 1 0.0000 0.0000 +bond nh os 358.5 1.441 ! SOURCE3 3 0.0029 0.0031 +bond nh p2 357.8 1.679 ! SOURCE3 17 0.0422 0.0872 +bond nh p3 312.8 1.730 ! SOURCE3 3 0.0015 0.0016 +bond nh p4 333.1 1.706 ! SOURCE3 3 0.0008 0.0008 +bond nh p5 365.6 1.671 ! SOURCE3 3 0.0007 0.0007 +bond nh s 237.0 1.784 ! SOURCE3 3 0.0072 0.0076 +bond nh s4 259.1 1.749 ! SOURCE3 3 0.0192 0.0203 +bond nh s6 300.0 1.693 ! SOURCE3 3 0.0036 0.0038 +bond nh sh 288.3 1.708 ! SOURCE3 1 0.0000 0.0000 +bond nh ss 288.3 1.708 ! SOURCE1 52 0.0015 0.0015 +bond nh sy 324.2 1.664 ! SOURCE3 1 0.0000 0.0000 +bond no no 138.3 1.824 ! SOURCE3 1 0.0000 0.0000 +bond no o 761.2 1.219 ! SOURCE1 1838 0.0023 0.0049 +bond no oh 400.5 1.406 ! SOURCE2 1 0.0000 0.0000 +bond no os 320.8 1.477 ! SOURCE3 4 0.0526 0.0532 +bond no p2 306.3 1.738 ! SOURCE3 10 0.2024 0.2231 +bond no p3 234.7 1.844 ! SOURCE3 3 0.0005 0.0005 +bond no p4 220.4 1.870 ! SOURCE3 3 0.0005 0.0006 +bond no p5 240.5 1.834 ! SOURCE3 4 0.0019 0.0020 +bond no s 263.8 1.742 ! SOURCE3 2 0.0000 0.0000 +bond no s4 143.0 1.996 ! SOURCE3 3 0.0295 0.0313 +bond no s6 149.6 1.976 ! SOURCE3 3 0.0490 0.0520 +bond no sh 225.4 1.804 ! SOURCE3 1 0.0000 0.0000 +bond no ss 212.4 1.828 ! SOURCE3 3 0.0230 0.0244 +bond o o 384.3 1.430 ! SOURCE3 2 0.0500 0.0500 +bond o oh 294.6 1.517 ! SOURCE3 2 0.0000 0.0000 +bond o os 306.3 1.504 ! SOURCE3 3 0.0110 0.0117 +bond o p2 449.7 1.508 ! SOURCE3 17 0.0167 0.0306 +bond o p3 440.4 1.515 ! SOURCE3 35 0.0214 0.0297 +bond o p4 456.4 1.503 ! SOURCE3 42 0.0343 0.0749 +bond o p5 487.7 1.481 ! SOURCE1 263 0.0180 0.0205 +bond o pe 432.6 1.521 ! SOURCE3 20 0.0138 0.0171 +bond o pf 432.6 1.521 ! SOURCE3 20 same as o -pe +bond o px 459.2 1.501 ! SOURCE3 37 0.0125 0.0160 +bond o py 477.5 1.488 ! SOURCE3 63 0.0063 0.0091 +bond o s 194.8 1.802 ! SOURCE3 2 0.0000 0.0000 +bond o s2 333.6 1.599 ! SOURCE3 3 0.0666 0.0707 +bond o s4 448.7 1.497 ! SOURCE1 90 0.0000 0.0000 +bond o s6 541.1 1.436 ! SOURCE1 1038 0.0072 0.0128 +bond o sh 328.0 1.605 ! SOURCE3 2 0.0000 0.0000 +bond o ss 398.5 1.537 ! SOURCE3 3 0.0434 0.0501 +bond o sx 434.2 1.508 ! SOURCE3 40 0.0083 0.0130 +bond o sy 493.0 1.466 ! SOURCE3 92 0.0077 0.0114 +bond oh oh 340.5 1.469 ! SOURCE3 1 0.0000 0.0000 +bond oh os 342.6 1.467 ! SOURCE3 3 0.0065 0.0072 +bond oh p2 316.8 1.630 ! SOURCE3 8 0.0600 0.0916 +bond oh p3 278.8 1.677 ! SOURCE3 3 0.0140 0.0148 +bond oh p4 307.4 1.641 ! SOURCE3 4 0.0092 0.0092 +bond oh p5 321.2 1.625 ! SOURCE3 92 0.0293 0.0451 +bond oh py 332.1 1.613 ! SOURCE3 79 0.0111 0.0138 +bond oh s 190.0 1.812 ! SOURCE3 2 0.0000 0.0000 +bond oh s4 274.3 1.670 ! SOURCE3 3 0.0173 0.0184 +bond oh s6 344.1 1.588 ! SOURCE3 13 0.0072 0.0091 +bond oh sh 258.6 1.692 ! SOURCE3 2 0.0003 0.0003 +bond oh ss 265.6 1.682 ! SOURCE3 4 0.0131 0.0131 +bond oh sy 302.6 1.634 ! SOURCE3 4 0.0153 0.0154 +bond os os 343.6 1.466 ! SOURCE1 20 0.0047 0.0067 +bond os p2 371.9 1.573 ! SOURCE1 16 0.0000 0.0000 +bond os p3 272.2 1.686 ! SOURCE3 6 0.0141 0.0201 +bond os p4 311.6 1.636 ! SOURCE3 4 0.0056 0.0057 +bond os p5 342.5 1.602 ! SOURCE1 248 0.0332 0.0400 +bond os py 328.5 1.617 ! SOURCE3 17 0.0082 0.0139 +bond os s 195.8 1.800 ! SOURCE3 3 0.0049 0.0052 +bond os s4 253.9 1.699 ! SOURCE3 8 0.0194 0.0223 +bond os s6 355.0 1.577 ! SOURCE1 75 0.0019 0.0030 +bond os sh 273.6 1.671 ! SOURCE3 3 0.0100 0.0106 +bond os ss 250.5 1.704 ! SOURCE3 9 0.0241 0.0277 +bond os sy 253.9 1.699 ! SOURCE3 1 0.0000 0.0000 +bond p2 p2 490.3 1.786 ! SOURCE3 25 0.3198 0.3488 +bond p2 p3 211.9 2.152 ! SOURCE3 9 0.1116 0.1777 +bond p2 p4 200.4 2.179 ! SOURCE0 1 +bond p2 p5 199.9 2.180 ! SOURCE0 1 +bond p2 pe 401.6 1.867 ! SOURCE3 16 0.3079 0.3571 +bond p2 pf 401.6 1.867 ! SOURCE3 16 same as p2-pe +bond p2 s 361.6 1.772 ! SOURCE3 26 0.2523 0.3014 +bond p2 s4 139.4 2.190 ! SOURCE0 1 +bond p2 s6 142.3 2.180 ! SOURCE0 1 +bond p2 sh 224.0 1.971 ! SOURCE3 10 0.2263 0.2829 +bond p2 ss 226.6 1.966 ! SOURCE3 10 0.2189 0.2739 +bond p3 p3 186.5 2.214 ! SOURCE1 41 0.0000 0.0000 +bond p3 p4 185.7 2.216 ! SOURCE3 3 0.0010 0.0011 +bond p3 p5 186.9 2.213 ! SOURCE3 9 0.0257 0.0265 +bond p3 s 179.7 2.070 ! SOURCE0 1 +bond p3 s4 173.2 2.087 ! SOURCE3 8 0.1935 0.2235 +bond p3 s6 176.9 2.077 ! SOURCE3 11 0.1085 0.1420 +bond p3 sh 157.3 2.132 ! SOURCE3 3 0.0073 0.0078 +bond p3 ss 161.0 2.121 ! SOURCE3 3 0.0056 0.0059 +bond p4 p4 273.1 2.034 ! SOURCE1 1 0.0000 0.0000 +bond p4 p5 178.0 2.237 ! SOURCE0 1 +bond p4 s 152.7 2.146 ! SOURCE3 5 0.0571 0.0601 +bond p4 s4 123.2 2.251 ! SOURCE0 1 +bond p4 s6 118.9 2.269 ! SOURCE0 1 +bond p4 sh 163.1 2.115 ! SOURCE3 4 0.0006 0.0008 +bond p4 ss 167.0 2.104 ! SOURCE3 4 0.0042 0.0044 +bond p5 p5 261.4 2.054 ! SOURCE1 1 0.0000 0.0000 +bond p5 s 250.8 1.922 ! SOURCE1 89 0.0097 0.0140 +bond p5 s4 191.9 2.040 ! SOURCE0 1 +bond p5 s6 191.9 2.040 ! SOURCE0 1 +bond p5 sh 175.0 2.082 ! SOURCE3 3 0.0033 0.0035 +bond p5 ss 164.8 2.110 ! SOURCE3 6 0.0379 0.0531 +bond pe pe 240.7 2.092 ! SOURCE3 7 0.1280 0.1369 +bond pe pf 260.8 2.055 ! SOURCE3 1 0.0000 0.0000 +bond pe px 291.4 2.005 ! SOURCE3 12 0.2364 0.2609 +bond pe py 278.6 2.025 ! SOURCE3 12 0.2453 0.2617 +bond pe s 374.7 1.758 ! SOURCE3 31 0.2925 0.3197 +bond pe sx 145.9 2.168 ! SOURCE3 9 0.1092 0.1743 +bond pe sy 133.0 2.213 ! SOURCE3 6 0.0106 0.0127 +bond pf pf 240.7 2.092 ! SOURCE3 7 same as pe-pe +bond pf px 291.4 2.005 ! SOURCE3 12 same as pe-px +bond pf py 278.6 2.025 ! SOURCE3 12 same as pe-py +bond pf s 374.7 1.758 ! SOURCE3 31 same as pe- s +bond pf sx 145.9 2.168 ! SOURCE3 9 same as pe-sx +bond pf sy 133.0 2.213 ! SOURCE3 6 same as pe-sy +bond px py 192.3 2.199 ! SOURCE3 5 0.0221 0.0238 +bond px sx 125.4 2.242 ! SOURCE3 3 0.0112 0.0119 +bond px sy 123.7 2.249 ! SOURCE3 3 0.0256 0.0272 +bond py py 197.5 2.186 ! SOURCE3 8 0.0110 0.0132 +bond py sx 121.2 2.259 ! SOURCE3 7 0.0595 0.0603 +bond py sy 141.7 2.182 ! SOURCE3 5 0.0044 0.0047 +bond s s 169.0 2.030 ! SOURCE3 1 0.0000 0.0000 +bond s s2 229.2 1.897 ! SOURCE1 5 0.0000 0.0000 +bond s s4 152.8 2.076 ! SOURCE3 4 0.0345 0.0345 +bond s s6 166.0 2.038 ! SOURCE3 3 0.0293 0.0311 +bond s sh 142.0 2.110 ! SOURCE3 2 0.0000 0.0000 +bond s ss 148.5 2.089 ! SOURCE3 1 0.0000 0.0000 +bond s4 s4 151.5 2.080 ! SOURCE0 1 +bond s4 s6 151.5 2.080 ! SOURCE0 1 +bond s4 sh 125.7 2.168 ! SOURCE3 3 0.0214 0.0227 +bond s4 ss 126.2 2.166 ! SOURCE3 5 0.0241 0.0247 +bond s6 s6 151.5 2.080 ! SOURCE0 1 +bond s6 sh 142.6 2.108 ! SOURCE3 3 0.0136 0.0144 +bond s6 ss 139.6 2.118 ! SOURCE3 5 0.0198 0.0209 +bond sh sh 158.9 2.058 ! SOURCE2 1 0.0000 0.0000 +bond sh ss 155.8 2.067 ! SOURCE3 3 0.0027 0.0029 +bond ss ss 161.7 2.050 ! SOURCE1 225 0.0015 0.0015 +bond sx sx 80.9 2.391 ! SOURCE3 3 0.0174 0.0185 +bond sx sy 105.3 2.255 ! SOURCE3 5 0.0703 0.0737 +bond sy sy 106.4 2.250 ! SOURCE3 3 0.0272 0.0289 angle hw ow hw 100.0 104.52 ! TIP3P water angle hw hw ow 0.0 127.74 ! (found in crystallographic water with 3 bonds) @@ -1043,7 +1034,7 @@ angle c2 c1 s2 56.7 172.98 ! SOURCE3 1 0.0000 0.0000 angle c3 c1 n1 58.3 177.57 ! SOURCE2 3 2.3778 2.5773 angle cg c1 ha 44.0 177.41 ! SOURCE3 22 2.3752 2.4947 angle ch c1 ha 44.0 177.41 ! SOURCE3 22 same as cg-c1-ha -!angle n1 c1 n1 93.2 102.01 ! SOURCE0 1 +angle n1 c1 n1 93.2 102.01 ! SOURCE0 1 angle n1 c1 n3 63.7 169.70 ! SOURCE2 1 0.0000 0.0000 angle n1 c1 os 64.7 178.59 ! SOURCE3 1 0.0000 0.0000 angle n1 c1 p3 67.7 171.20 ! SOURCE2 1 0.0000 0.0000 @@ -2077,7 +2068,7 @@ angle cf n1 s 64.8 117.34 ! SOURCE3 1 0.0000 0.0000 angle ce n1 s 64.8 117.34 ! SOURCE3 1 same as cf-n1-s angle o n1 p2 84.7 116.05 ! SOURCE3 1 0.0000 0.0000 angle p2 n1 s 80.3 119.93 ! SOURCE3 1 0.0000 0.0000 -!angle n1 n1 s 54.6 180.00 ! SOURCE3 1 0.0000 0.0000 +angle n1 n1 s 54.6 180.00 ! SOURCE3 1 0.0000 0.0000 angle br n2 br 63.9 106.60 ! SOURCE0 1 angle br n2 c2 59.1 112.40 ! SOURCE3 1 0.0000 0.0000 angle br n2 n2 61.1 110.42 ! SOURCE3 1 0.0000 0.0000 @@ -4018,6 +4009,7 @@ angle sh s6 ss 60.4 102.64 ! SOURCE0 1 angle ss s6 ss 60.5 101.82 ! SOURCE3 1 0.0000 0.0000 angle br sh hs 43.5 95.64 ! SOURCE3 1 0.0000 0.0000 angle c sh hs 46.0 96.07 ! SOURCE3 6 0.9968 1.1164 +angle c1 sh hs 29.9 95.99 ! calculated based on C#C-SH angle c2 sh hs 46.2 95.94 ! SOURCE3 3 0.3373 0.3578 angle c3 sh hs 44.9 96.60 ! SOURCE3 12 0.6315 0.8009 angle ca sh hs 45.7 96.61 ! SOURCE3 2 0.2867 0.2867 @@ -4240,7 +4232,6 @@ angle c1 n1 s4 55.2 169.60 ! HF/6-31G* angle c1 n1 s6 61.8 175.92 ! HF/6-31G* angle c1 n1 sh 55.7 174.25 ! HF/6-31G* angle c1 n1 ss 55.4 176.06 ! HF/6-31G* -angle c1 ng ng 51.9 179.97 ! HF/6-31G* angle c2 c1 n1 63.1 180.00 ! HF/6-31G* angle c2 c2 n1 71.7 122.98 ! HF/6-31G* angle c2 n1 n1 61.6 180.00 ! HF/6-31G* @@ -4278,7 +4269,6 @@ angle n1 n1 oh 64.8 173.77 ! HF/6-31G* angle n1 n1 os 64.0 176.12 ! HF/6-31G* angle n1 n1 p2 69.4 174.71 ! HF/6-31G* angle n1 n1 p3 70.2 174.27 ! HF/6-31G* -angle n1 n1 s 54.6 179.96 ! HF/6-31G* angle n1 n1 sh 57.0 175.07 ! HF/6-31G* angle n1 n1 ss 56.9 175.61 ! HF/6-31G* angle n1 p4 o 49.7 114.59 ! HF/6-31G* @@ -4286,7 +4276,6 @@ angle n1 p5 o 44.7 113.78 ! HF/6-31G* angle n1 s2 o 73.1 108.46 ! HF/6-31G* angle n1 s4 o 70.2 110.09 ! HF/6-31G* angle n1 s6 o 78.8 107.52 ! HF/6-31G* -angle n1 c1 n1 70.2 180.00 ! HF/6-31G* angle n1 c2 n1 73.6 124.15 ! HF/6-31G* angle n1 c3 n1 80.0 105.07 ! HF/6-31G* angle n1 ca n1 75.8 117.03 ! HF/6-31G* @@ -4329,8 +4318,6 @@ angle n4 c1 n4 56.3 180.00 ! Guess angle nh c1 nh 59.0 180.00 ! Guess angle no c1 no 56.8 180.00 ! Guess angle na c1 na 58.6 180.00 ! Guess -angle na c1 na 58.6 180.00 ! Guess -angle na c1 na 58.6 180.00 ! Guess dihe X c c X 0.30 2 180.00 dihe X c c1 X 0.00 2 180.00 @@ -4357,7 +4344,6 @@ dihe X c na X 0.35 4 180.00 dihe X c no X 0.45 2 180.00 dihe X c oh X 2.30 2 180.00 ! Junmei et al, 1999 dihe X c os X 2.70 2 180.00 ! Junmei et al, 1999 -dihe X c pc X 2.00 2 180.00 ! estimated dihe X c p2 X 6.65 2 180.00 ! double bond, same as X-c2-p2-X dihe X c pc X 2.00 2 180.00 ! estimated dihe X c pd X 2.00 2 180.00 ! estimated @@ -4875,7 +4861,6 @@ dihe X p3 p5 X 1.83 2 180.00 dihe X p3 py X 1.83 2 180.00 dihe X p3 sh X 4.60 2 0.00 dihe X p3 ss X 1.15 3 0.00 -dihe X p3 ss X 1.15 3 0.00 dihe X p3 s4 X 3.85 2 0.00 dihe X p3 sx X 3.85 2 0.00 dihe X p3 s6 X 0.27 3 0.00 @@ -4927,12 +4912,12 @@ dihe n c3 c n 2.00 2 180.00 dihe c n c3 c 0.80 1 0.00 dihe c3 c3 n c 0.53 1 0.00 ! phi,psi,parm94 dihe c3 c3 c n 0.07 2 0.00 ! phi,psi,parm94 -dihe c2 ne p5 o 2.30 1 0.00 ! phi,psi,parm94 -dihe c2 nf p5 o 2.30 1 0.00 ! phi,psi,parm94 -dihe ce ne p5 o 2.30 1 0.00 ! phi,psi,parm94 -dihe ce nf p5 o 2.30 1 0.00 ! phi,psi,parm94 -dihe cf ne p5 o 2.30 1 0.00 ! phi,psi,parm94 -dihe cf nf p5 o 2.30 1 0.00 ! phi,psi,parm94 +dihe c2 ne p5 o 2.30 1 0.00 +dihe c2 nf p5 o 2.30 1 0.00 +dihe ce ne p5 o 2.30 1 0.00 +dihe ce nf p5 o 2.30 1 0.00 +dihe cf ne p5 o 2.30 1 0.00 +dihe cf nf p5 o 2.30 1 0.00 dihe hn n c o 2.00 1 0.00 ! J.C.cistrans-NMA DE dihe c3 ss ss c3 0.60 3 0.00 ! JCC,7,(1986),230 dihe c3 n3 nh ca 1.90 3 0.00 @@ -4988,7 +4973,6 @@ impr c c3 n hn 1.10 2 180.00 ! Junmei et al.1999 impr c c3 n o 1.10 2 180.00 ! Junmei et al.1999 impr c2 c2 na c3 1.10 2 180.00 impr c2 c c2 c3 1.10 2 180.00 -impr c3 o c oh 1.10 2 180.00 impr c2 c3 c2 hc 1.10 2 180.00 ! Junmei et al.1999 impr c2 c3 ca hc 1.10 2 180.00 ! Junmei et al.1999 impr c2 hc c o 1.10 2 180.00 ! Junmei et al.1999 @@ -5011,8 +4995,6 @@ impr ca n2 ca n2 1.10 2 180.00 ! dac, 10/94 impr hc o c oh 1.10 2 180.00 ! Junmei et al.1999 impr hc o c os 1.10 2 180.00 impr n2 c2 ca n2 1.10 2 180.00 ! dac guess, 9/94 -impr n2 ca ca c3 1.10 2 180.00 impr n2 ca ca n2 1.10 2 180.00 ! dac guess, 9/94 -impr na ca ca c3 1.10 2 180.00 impr na n2 ca n2 1.10 2 180.00 ! dac, 10/94 diff --git a/Scripts/md.rb b/Scripts/md.rb index f52725d..bed8209 100755 --- a/Scripts/md.rb +++ b/Scripts/md.rb @@ -583,6 +583,88 @@ class Molecule } end + def export_ac(acfile) + open(acfile, "w") { |fp| + charge = 0.0 + each_atom { |ap| + charge += ap.charge + } + fp.printf "CHARGE %6.3f\n", charge + form = [] + each_atom { |ap| + form[ap.atomic_number] = (form[ap.atomic_number] || 0) + 1 + } + fp.print "Formula: " + form.each_with_index { |n, i| + if n != nil + fp.print Parameter.builtin.elements[i].name + n.to_s + end + } + fp.print "\n" + each_atom { |ap| + fp.printf "ATOM %6d %-4s%3.3s 1 %8.3f%8.3f%8.3f%10.5f %-4s %s\n", ap.index + 1, ap.name, ap.res_name, ap.x, ap.y, ap.z, ap.charge, ap.atom_type, ap.name + } + bonds.each_with_index { |bd, i| + n1, n2 = bd + fp.printf "BOND%5d%5d%5d%5d %4s%4s\n", i + 1, n1 + 1, n2 + 1, 0, atoms[n1].name, atoms[n2].name + } + } + end + + def export_frcmod(frcfile) + p = self.parameter + open(frcfile, "w") { |fp| + fp.print "remark goes here\n" + fp.print "MASS\n" + p.vdws.each { |np| + if np.source != "gaff" && np.source != "parm99" + fp.printf "%s %10.5f %s\n", np.atom_type, np.weight, np.comment + end + } + fp.print "\n" + fp.print "BOND\n" + p.bonds.each { |bp| + if bp.source != "gaff" && bp.source != "parm99" + types = sprintf("%-2s-%-2s", bp.atom_types[0], bp.atom_types[1]) + fp.printf "%s %6.3f %7.3f %s\n", types, bp.k, bp.r0, bp.comment + end + } + fp.print "\n" + fp.print "ANGLE\n" + p.angles.each { |ap| + if ap.source != "gaff" && ap.source != "parm99" + types = sprintf("%-2s-%-2s-%-2s", ap.atom_types[0], ap.atom_types[1], ap.atom_types[2]) + fp.printf "%s %7.3f %7.3f %s\n", types, ap.k, ap.a0, ap.comment + end + } + fp.print "\n" + fp.print "DIHE\n" + p.dihedrals.each { |dp| + if dp.source != "gaff" && dp.source != "parm99" + types = sprintf("%-2s-%-2s-%-2s-%-2s", dp.atom_types[0], dp.atom_types[1], dp.atom_types[2], dp.atom_types[3]) + fp.printf "%s %d %6.3f %7.3f %6.3f %s\n", types, dp.mult, dp.k, dp.phi0, dp.period, dp.comment + end + } + fp.print "\n" + fp.print "IMPROPER\n" + p.impropers.each { |dp| + if dp.source != "gaff" && dp.source != "parm99" + types = sprintf("%-2s-%-2s-%-2s-%-2s", dp.atom_types[0], dp.atom_types[1], dp.atom_types[2], dp.atom_types[3]) + fp.printf "%s %6.2f %7.3f %6.2f %s\n", types, dp.k, dp.phi0, dp.period, dp.comment + end + } + fp.print "\n" + fp.print "NONBON\n" + p.vdws.each { |np| + if np.source != "gaff" && np.source != "parm99" + types = sprintf("%2s", np.atom_types[0]) + fp.printf "%s %10.5f %10.5f %s\n", np.atom_type, np.r_eq, np.eps, np.comment + end + } + fp.print "\n" + } + end + def count_elements elements = [] each_atom { |ap| diff --git a/Scripts/parm99.par b/Scripts/parm99.par index 737067b..ff127e2 100644 --- a/Scripts/parm99.par +++ b/Scripts/parm99.par @@ -5,124 +5,188 @@ ! Thanks to the AMBER development team, the force field parameters are in the public domain. Hereby I acknowledge their great scientific contribution, with references to the literature as below. ! 1. D.A. Case, T.E. Cheatham, III, T. Darden, H. Gohlke, R. Luo, K.M. Merz, Jr., A. Onufriev, C. Simmerling, B. Wang and R. Woods. The Amber biomolecular simulation programs. J. Computat. Chem. 26, 1668-1688 (2005). ! 2. J.W. Ponder and D.A. Case. Force fields for protein simulations. Adv. Prot. Chem. 66, 27-85 (2003). Similar information for nucleic acids is given by T.E. Cheatham, III and M.A. Young. Molecular dynamics simulation of nucleic acids: Successes, limitations and promise. Biopolymers 56, 232-256 (2001). -! 3. D.A. Case, T.A. Darden, T.E. Cheatham, III, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, M. Crowley, Ross C. Walker,W. Zhang, K.M. Merz, B.Wang, S. Hayik, A. Roitberg, G. Seabra, I. Kolossváry, K.F.Wong, F. Paesani, J. Vanicek, X.Wu, S.R. Brozell, T. Steinbrecher, H. Gohlke, L. Yang, C. Tan, J. Mongan, V. Hornak, G. Cui, D.H. Mathews, M.G. Seetin, C. Sagui, V. Babin, and P.A. Kollman (2008), AMBER 10, University of California, San Francisco. -! -bond OW HW 553.0 0.96 ! TIP3P water -bond HW HW 553.0 1.51 ! TIP3P water -bond C C 310.0 1.52 ! Junmei et al, 1999 -bond C CA 469.0 1.41 ! JCC,7,(1986),230; (not used any more in TYR) -bond C CB 447.0 1.42 ! JCC,7,(1986),230; GUA -bond C CM 410.0 1.44 ! JCC,7,(1986),230; THY,URA -bond C CT 317.0 1.52 ! JCC,7,(1986),230; AA -bond C N 490.0 1.33 ! JCC,7,(1986),230; AA -bond C N* 424.0 1.38 ! JCC,7,(1986),230; CYT,URA -bond C NA 418.0 1.39 ! JCC,7,(1986),230; GUA.URA -bond C NC 457.0 1.36 ! JCC,7,(1986),230; CYT -bond C O 570.0 1.23 ! JCC,7,(1986),230; AA,CYT,GUA,THY,URA -bond C O2 656.0 1.25 ! JCC,7,(1986),230; GLU,ASP -bond C OH 450.0 1.36 ! JCC,7,(1986),230; (not used any more for TYR) -bond C OS 450.0 1.32 ! Junmei et al, 1999 -bond C H4 367.0 1.08 ! Junmei et al, 1999 -bond C H5 367.0 1.08 ! Junmei et al, 1999 -bond CA CA 469.0 1.40 ! JCC,7,(1986),230; BENZENE,PHE,TRP,TYR -bond CA CB 469.0 1.40 ! JCC,7,(1986),230; ADE,TRP -bond CA CM 427.0 1.43 ! JCC,7,(1986),230; CYT -bond CA CN 469.0 1.40 ! JCC,7,(1986),230; TRP -bond CA CT 317.0 1.51 ! JCC,7,(1986),230; PHE,TYR -bond CA HA 367.0 1.08 ! changed from 340. bsd on C6H6 nmodes; PHE,TRP,TYR -bond CA H4 367.0 1.08 ! changed from 340. bsd on C6H6 nmodes; no assigned -bond CA N2 481.0 1.34 ! JCC,7,(1986),230; ARG,CYT,GUA -bond CA NA 427.0 1.38 ! JCC,7,(1986),230; GUA -bond CA NC 483.0 1.34 ! JCC,7,(1986),230; ADE,CYT,GUA -bond CA OH 450.0 1.36 ! substituted for C-OH in tyr -bond CB CB 520.0 1.37 ! JCC,7,(1986),230; ADE,GUA -bond CB N* 436.0 1.37 ! JCC,7,(1986),230; ADE,GUA -bond CB NB 414.0 1.39 ! JCC,7,(1986),230; ADE,GUA -bond CB NC 461.0 1.35 ! JCC,7,(1986),230; ADE,GUA -bond CD HA 367.0 1.08 ! Junmei et al, 1999 -bond CD CD 469.0 1.40 ! Junmei et al, 1999 -bond CD CM 549.0 1.35 ! Junmei et al, 1999 -bond CD CT 317.0 1.51 ! Junmei et al, 1999 -bond CK H5 367.0 1.08 ! changed from 340. bsd on C6H6 nmodes; ADE,GUA -bond CK N* 440.0 1.37 ! JCC,7,(1986),230; ADE,GUA -bond CK NB 529.0 1.30 ! JCC,7,(1986),230; ADE,GUA -bond CM CM 549.0 1.35 ! JCC,7,(1986),230; CYT,THY,URA -bond CM CT 317.0 1.51 ! JCC,7,(1986),230; THY -bond CM HA 367.0 1.08 ! changed from 340. bsd on C6H6 nmodes; CYT,URA -bond CM H4 367.0 1.08 ! changed from 340. bsd on C6H6 nmodes; CYT,URA -bond CM H5 367.0 1.08 ! changed from 340. bsd on C6H6 nmodes; not assigned -bond CM N* 448.0 1.36 ! JCC,7,(1986),230; CYT,THY,URA -bond CM OS 480.0 1.24 ! Junmei et al, 1999 -bond CQ H5 367.0 1.08 ! changed from 340. bsd on C6H6 nmodes; ADE -bond CQ NC 502.0 1.32 ! JCC,7,(1986),230; ADE -bond CT CT 310.0 1.53 ! JCC,7,(1986),230; AA, SUGARS -bond CT HC 340.0 1.09 ! changed from 331 bsd on NMA nmodes; AA, SUGARS -bond CT H1 340.0 1.09 ! changed from 331 bsd on NMA nmodes; AA, RIBOSE -bond CT H2 340.0 1.09 ! changed from 331 bsd on NMA nmodes; SUGARS -bond CT H3 340.0 1.09 ! changed from 331 bsd on NMA nmodes; not assigned -bond CT HP 340.0 1.09 ! changed from 331; AA-lysine, methyl ammonium cation -bond CT N* 337.0 1.48 ! JCC,7,(1986),230; ADE,CYT,GUA,THY,URA -bond CT N2 337.0 1.46 ! JCC,7,(1986),230; ARG -bond CT OH 320.0 1.41 ! JCC,7,(1986),230; SUGARS -bond CT OS 320.0 1.41 ! JCC,7,(1986),230; NUCLEIC ACIDS -bond C* HC 367.0 1.08 ! changed from 340. bsd on C6H6 nmodes, not needed AA -bond C* CB 388.0 1.46 ! JCC,7,(1986),230; TRP -bond C* CT 317.0 1.50 ! JCC,7,(1986),230; TRP -bond C* CW 546.0 1.35 ! JCC,7,(1986),230; TRP -bond CB CN 447.0 1.42 ! JCC,7,(1986),230; TRP -bond CC CT 317.0 1.50 ! JCC,7,(1986),230; HIS -bond CC CV 512.0 1.38 ! JCC,7,(1986),230; HIS(delta) -bond CC CW 518.0 1.37 ! JCC,7,(1986),230; HIS(epsilon) -bond CC NA 422.0 1.39 ! JCC,7,(1986),230; HIS -bond CC NB 410.0 1.39 ! JCC,7,(1986),230; HIS -bond CN NA 428.0 1.38 ! JCC,7,(1986),230; TRP -bond CR H5 367.0 1.08 ! changed from 340. bsd on C6H6 nmodes;HIS -bond CR NA 477.0 1.34 ! JCC,7,(1986),230; HIS -bond CR NB 488.0 1.33 ! JCC,7,(1986),230; HIS -bond CT N 337.0 1.45 ! JCC,7,(1986),230; AA -bond CT N3 367.0 1.47 ! JCC,7,(1986),230; LYS -bond CT NT 367.0 1.47 ! for neutral amines -bond CT S 227.0 1.81 ! changed from 222.0 based on dimethylS nmodes -bond CT SH 237.0 1.81 ! changed from 222.0 based on methanethiol nmodes -bond CT CY 400.0 1.46 ! Howard et al JCC.16,243,1995 -bond CT CZ 400.0 1.46 ! Howard et al JCC,16,243,1995 -bond CV H4 367.0 1.08 ! changed from 340. bsd on C6H6 nmodes; HIS -bond CV NB 410.0 1.39 ! JCC,7,(1986),230; HIS -bond CW H4 367.0 1.08 ! changed from 340. bsd on C6H6 nmodes;HIS(epsilon,+) -bond CW NA 427.0 1.38 ! JCC,7,(1986),230; HIS,TRP -bond CY NY 600.0 1.15 ! Howard et al JCC,16,243,1995 -bond CZ CZ 600.0 1.21 ! Howard et al JCC,16,243,1995 -bond CZ HZ 400.0 1.06 ! Howard et al JCC,16,243,1995 -bond O2 P 525.0 1.48 ! JCC,7,(1986),230; NA PHOSPHATES -bond OH P 230.0 1.61 ! JCC,7,(1986),230; NA PHOSPHATES -bond OS P 230.0 1.61 ! JCC,7,(1986),230; NA PHOSPHATES -bond H N2 434.0 1.01 ! JCC,7,(1986),230; ADE,CYT,GUA,ARG -bond H N* 434.0 1.01 ! for plain unmethylated bases ADE,CYT,GUA,ARG -bond H NA 434.0 1.01 ! JCC,7,(1986),230; GUA,URA,HIS -bond H N 434.0 1.01 ! JCC,7,(1986),230; AA -bond H N3 434.0 1.01 ! JCC,7,(1986),230; LYS -bond H NT 434.0 1.01 ! for neutral amines -bond HO OH 553.0 0.96 ! JCC,7,(1986),230; SUGARS,SER,TYR -bond HO OS 553.0 0.96 ! JCC,7,(1986),230; NUCLEOTIDE ENDS -bond HS SH 274.0 1.34 ! JCC,7,(1986),230; CYS -bond S S 166.0 2.04 ! JCC,7,(1986),230; CYX (SCHERAGA) -bond F CT 367.0 1.38 ! JCC,13,(1992),963;CF4; R0=1.332 FOR CHF3 -bond Cl CT 232.0 1.77 ! 6-31g* opt -bond Br CT 159.0 1.94 ! Junmei et al,99 -bond I CT 148.0 2.17 ! Junmei et al,99 -bond F CA 386.0 1.36 ! Junmei et al,99 -bond Cl CA 193.0 1.73 ! Junmei et al,99 -bond I CA 171.0 2.08 ! Junmei et al,99 -bond Br CA 172.0 1.89 ! Junmei et al,99 -bond LP O 600.0 0.20 ! or 0.35 -bond LP OH 600.0 0.20 ! or 0.35 -bond LP OS 600.0 0.20 ! or 0.35 -bond LP N3 600.0 0.20 ! or 0.35 -bond LP NT 600.0 0.20 ! or 0.35 -bond LP NB 600.0 0.20 ! or 0.35 histidines, nucleic acids -bond LP NC 600.0 0.20 ! or 0.35 nucleic acids -bond LP S 600.0 0.70 ! cys,cyx,met -bond LP SH 600.0 0.70 ! cys,cyx +! 3. D.A. Case, T.A. Darden, T.E. Cheatham, III, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, M. Crowley, Ross C. Walker,W. Zhang, K.M. Merz, B.Wang, S. Hayik, A. Roitberg, G. Seabra, I. Kolossvﾃ｡ry, K.F.Wong, F. Paesani, J. Vanicek, X.Wu, S.R. Brozell, T. Steinbrecher, H. Gohlke, L. Yang, C. Tan, J. Mongan, V. Hornak, G. Cui, D.H. Mathews, M.G. Seetin, C. Sagui, V. Babin, and P.A. Kollman (2008), AMBER 10, University of California, San Francisco. + +vdw H 0.0157 0.6000 0.0157 0.6000 0 1.008 ! H bonded to nitrogen atoms +vdw HO 0.0000 0.0000 0.0000 0.0000 0 1.008 ! hydroxyl group +vdw HS 0.0157 0.6000 0.0157 0.6000 0 1.008 ! hydrogen bonded to sulphur (pol?) +vdw HC 0.0157 1.4870 0.0157 1.4870 0 1.008 ! H aliph. bond. to C without electrwd.group +vdw H1 0.0157 1.3870 0.0157 1.3870 0 1.008 ! H aliph. bond. to C with 1 electrwd. group +vdw H2 0.0157 1.2870 0.0157 1.2870 0 1.008 ! H aliph. bond. to C with 2 electrwd.groups +vdw H3 0.0157 1.1870 0.0157 1.1870 0 1.008 ! H aliph. bond. to C with 3 eletrwd.groups +vdw HP 0.0157 1.1000 0.0157 1.1000 0 1.008 ! H bonded to C next to positively charged gr +vdw HA 0.0150 1.4590 0.0150 1.4590 0 1.008 ! H arom. bond. to C without elctrwd. groups +vdw H4 0.0150 1.4090 0.0150 1.4090 0 1.008 ! H arom. bond. to C with 1 electrwd. group +vdw H5 0.0150 1.3590 0.0150 1.3590 0 1.008 ! H arom.at C with 2 elctrwd. gr,+HCOO group +vdw HW 0.0000 0.0000 0.0000 0.0000 0 1.008 ! H in TIP3P water +vdw HZ 0.0150 1.4590 0.0150 1.4590 0 1.008 ! H bond sp C (Howard et al.JCC,16,243,1995) +vdw O 0.2100 1.6612 0.2100 1.6612 0 16.000 ! carbonyl group oxygen +vdw O2 0.2100 1.6612 0.2100 1.6612 0 16.000 ! carboxyl and phosphate group oxygen +vdw OW 0.1520 1.7683 0.1520 1.7683 0 16.000 ! oxygen in TIP3P water +vdw OH 0.2104 1.7210 0.2104 1.7210 0 16.000 ! oxygen in hydroxyl group +vdw OS 0.1700 1.6837 0.1700 1.6837 0 16.000 ! ether and ester oxygen +vdw C* 0.0860 1.9080 0.0860 1.9080 0 12.010 ! sp2 arom. 5 memb.ring w/1 subst. (TRP) +vdw CA 0.0860 1.9080 0.0860 1.9080 0 12.010 ! sp2 C pure aromatic (benzene) +vdw CB 0.0860 1.9080 0.0860 1.9080 0 12.010 ! sp2 aromatic C, 5&6 membered ring junction +vdw CC 0.0860 1.9080 0.0860 1.9080 0 12.010 ! sp2 aromatic C, 5 memb. ring HIS +vdw CD 0.0860 1.9080 0.0860 1.9080 0 12.010 ! sp2 C atom in the middle of: C=CD-CD=C +vdw CK 0.0860 1.9080 0.0860 1.9080 0 12.010 ! sp2 C 5 memb.ring in purines +vdw CM 0.0860 1.9080 0.0860 1.9080 0 12.010 ! sp2 C pyrimidines in pos. 5 & 6 +vdw CN 0.0860 1.9080 0.0860 1.9080 0 12.010 ! sp2 C aromatic 5&6 memb.ring junct.(TRP) +vdw CQ 0.0860 1.9080 0.0860 1.9080 0 12.010 ! sp2 C in 5 mem.ring of purines between 2 N +vdw CR 0.0860 1.9080 0.0860 1.9080 0 12.010 ! sp2 arom as CQ but in HIS +vdw CV 0.0860 1.9080 0.0860 1.9080 0 12.010 ! sp2 arom. 5 memb.ring w/1 N and 1 H (HIS) +vdw CW 0.0860 1.9080 0.0860 1.9080 0 12.010 ! sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS) +vdw CY 0.0860 1.9080 0.0860 1.9080 0 12.010 ! nitrile C (Howard et al.JCC,16,243,1995) +vdw CZ 0.0860 1.9080 0.0860 1.9080 0 12.010 ! sp C (Howard et al.JCC,16,243,1995) +vdw CT 0.1094 1.9080 0.1094 1.9080 0 12.010 ! sp3 aliphatic C +vdw C 0.0860 1.9080 0.0860 1.9080 0 12.010 ! sp2 C carbonyl group +vdw N 0.1700 1.8240 0.1700 1.8240 0 14.010 ! sp2 nitrogen in amide groups +vdw NA 0.1700 1.8240 0.1700 1.8240 0 14.010 ! sp2 N in 5 memb.ring w/H atom (HIS) +vdw N2 0.1700 1.8240 0.1700 1.8240 0 14.010 ! sp2 N in amino groups +vdw N* 0.1700 1.8240 0.1700 1.8240 0 14.010 ! sp2 N +vdw NC 0.1700 1.8240 0.1700 1.8240 0 14.010 ! sp2 N in 6 memb.ring w/LP (ADE,GUA) +vdw NB 0.1700 1.8240 0.1700 1.8240 0 14.010 ! sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA) +vdw NT 0.1700 1.8240 0.1700 1.8240 0 14.010 ! sp3 N for amino groups amino groups +vdw NY 0.1700 1.8240 0.1700 1.8240 0 14.010 ! nitrile N (Howard et al.JCC,16,243,1995) +vdw N3 0.1700 1.8240 0.1700 1.8240 0 14.010 ! sp3 N for charged amino groups (Lys, etc) +vdw NY 0.1700 1.8240 0.1700 1.8240 0 14.010 ! nitrile N (Howard et al.JCC,16,243,1995) +vdw S 0.2500 2.0000 0.2500 2.0000 0 32.060 ! S in disulfide linkage,pol:JPC,102,2399,98 +vdw SH 0.2500 2.0000 0.2500 2.0000 0 32.060 ! S in cystine +vdw P 0.2000 2.1000 0.2000 2.1000 0 30.970 ! phosphate,pol:JACS,112,8543,90,K.J.Miller +vdw IM 0.1000 2.4700 0.1000 2.4700 0 35.450 ! assumed to be Cl- (ion minus) +vdw Li 0.0183 1.1370 0.0183 1.1370 0 6.940 ! lithium, ions pol:J.PhysC,11,1541,(1978) +vdw IP 0.0028 1.8680 0.0028 1.8680 0 22.990 ! assumed to be Na+ (ion plus) +vdw Na 0.0028 1.8680 0.0028 1.8680 0 22.990 ! Na+, ions pol:J.PhysC,11,1541,(1978) +vdw K 0.0003 2.6580 0.0003 2.6580 0 39.100 ! potassium +vdw Rb 0.0002 2.9560 0.0002 2.9560 0 85.470 ! rubidium +vdw Cs 0.0001 3.3950 0.0001 3.3950 0 132.910 ! cesium +vdw MG 0.8947 0.7926 0.8947 0.7926 0 24.305 ! magnesium +vdw C0 0.4598 1.7131 0.4598 1.7131 0 40.080 ! calcium +vdw Zn 0.0125 1.1000 0.0125 1.1000 0 65.400 ! Zn2+ +vdw F 0.0610 1.7500 0.0610 1.7500 0 19.000 ! fluorine +vdw Cl 0.2650 1.9480 0.2650 1.9480 0 35.450 ! chlorine (Applequist) +vdw Br 0.3200 2.2200 0.3200 2.2200 0 79.900 ! bromine (Applequist) +vdw I 0.4000 2.3500 0.4000 2.3500 0 126.900 ! iodine (Applequist) +vdw IB 0.1000 5.0000 0.1000 5.0000 0 131.000 ! 'big ion w/ waters' for vacuum (Na+, 6H2O) +vdw LP 0.0000 0.0000 0.0000 0.0000 0 3.000 ! lone pair + +bond OW HW 553.0 0.957 ! TIP3P water +bond HW HW 553.0 1.514 ! TIP3P water +bond C C 310.0 1.525 ! Junmei et al, 1999 +bond C CA 469.0 1.409 ! JCC,7,(1986),230; (not used any more in TYR) +bond C CB 447.0 1.419 ! JCC,7,(1986),230; GUA +bond C CM 410.0 1.444 ! JCC,7,(1986),230; THY,URA +bond C CT 317.0 1.522 ! JCC,7,(1986),230; AA +bond C N 490.0 1.335 ! JCC,7,(1986),230; AA +bond C N* 424.0 1.383 ! JCC,7,(1986),230; CYT,URA +bond C NA 418.0 1.388 ! JCC,7,(1986),230; GUA.URA +bond C NC 457.0 1.358 ! JCC,7,(1986),230; CYT +bond C O 570.0 1.229 ! JCC,7,(1986),230; AA,CYT,GUA,THY,URA +bond C O2 656.0 1.250 ! JCC,7,(1986),230; GLU,ASP +bond C OH 450.0 1.364 ! JCC,7,(1986),230; (not used any more for TYR) +bond C OS 450.0 1.323 ! Junmei et al, 1999 +bond C H4 367.0 1.080 ! Junmei et al, 1999 +bond C H5 367.0 1.080 ! Junmei et al, 1999 +bond CA CA 469.0 1.400 ! JCC,7,(1986),230; BENZENE,PHE,TRP,TYR +bond CA CB 469.0 1.404 ! JCC,7,(1986),230; ADE,TRP +bond CA CM 427.0 1.433 ! JCC,7,(1986),230; CYT +bond CA CN 469.0 1.400 ! JCC,7,(1986),230; TRP +bond CA CT 317.0 1.510 ! JCC,7,(1986),230; PHE,TYR +bond CA HA 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; PHE,TRP,TYR +bond CA H4 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; no assigned +bond CA N2 481.0 1.340 ! JCC,7,(1986),230; ARG,CYT,GUA +bond CA NA 427.0 1.381 ! JCC,7,(1986),230; GUA +bond CA NC 483.0 1.339 ! JCC,7,(1986),230; ADE,CYT,GUA +bond CA OH 450.0 1.364 ! substituted for C-OH in tyr +bond CB CB 520.0 1.370 ! JCC,7,(1986),230; ADE,GUA +bond CB N* 436.0 1.374 ! JCC,7,(1986),230; ADE,GUA +bond CB NB 414.0 1.391 ! JCC,7,(1986),230; ADE,GUA +bond CB NC 461.0 1.354 ! JCC,7,(1986),230; ADE,GUA +bond CD HA 367.0 1.080 ! Junmei et al, 1999 +bond CD CD 469.0 1.400 ! Junmei et al, 1999 +bond CD CM 549.0 1.350 ! Junmei et al, 1999 +bond CD CT 317.0 1.510 ! Junmei et al, 1999 +bond CK H5 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; ADE,GUA +bond CK N* 440.0 1.371 ! JCC,7,(1986),230; ADE,GUA +bond CK NB 529.0 1.304 ! JCC,7,(1986),230; ADE,GUA +bond CM CM 549.0 1.350 ! JCC,7,(1986),230; CYT,THY,URA +bond CM CT 317.0 1.510 ! JCC,7,(1986),230; THY +bond CM HA 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; CYT,URA +bond CM H4 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; CYT,URA +bond CM H5 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; not assigned +bond CM N* 448.0 1.365 ! JCC,7,(1986),230; CYT,THY,URA +bond CM OS 480.0 1.240 ! Junmei et al, 1999 +bond CQ H5 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; ADE +bond CQ NC 502.0 1.324 ! JCC,7,(1986),230; ADE +bond CT CT 310.0 1.526 ! JCC,7,(1986),230; AA, SUGARS +bond CT HC 340.0 1.090 ! changed from 331 bsd on NMA nmodes; AA, SUGARS +bond CT H1 340.0 1.090 ! changed from 331 bsd on NMA nmodes; AA, RIBOSE +bond CT H2 340.0 1.090 ! changed from 331 bsd on NMA nmodes; SUGARS +bond CT H3 340.0 1.090 ! changed from 331 bsd on NMA nmodes; not assigned +bond CT HP 340.0 1.090 ! changed from 331; AA-lysine, methyl ammonium cation +bond CT N* 337.0 1.475 ! JCC,7,(1986),230; ADE,CYT,GUA,THY,URA +bond CT N2 337.0 1.463 ! JCC,7,(1986),230; ARG +bond CT OH 320.0 1.410 ! JCC,7,(1986),230; SUGARS +bond CT OS 320.0 1.410 ! JCC,7,(1986),230; NUCLEIC ACIDS +bond C* HC 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes, not needed AA +bond C* CB 388.0 1.459 ! JCC,7,(1986),230; TRP +bond C* CT 317.0 1.495 ! JCC,7,(1986),230; TRP +bond C* CW 546.0 1.352 ! JCC,7,(1986),230; TRP +bond CB CN 447.0 1.419 ! JCC,7,(1986),230; TRP +bond CC CT 317.0 1.504 ! JCC,7,(1986),230; HIS +bond CC CV 512.0 1.375 ! JCC,7,(1986),230; HIS(delta) +bond CC CW 518.0 1.371 ! JCC,7,(1986),230; HIS(epsilon) +bond CC NA 422.0 1.385 ! JCC,7,(1986),230; HIS +bond CC NB 410.0 1.394 ! JCC,7,(1986),230; HIS +bond CN NA 428.0 1.380 ! JCC,7,(1986),230; TRP +bond CR H5 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes;HIS +bond CR NA 477.0 1.343 ! JCC,7,(1986),230; HIS +bond CR NB 488.0 1.335 ! JCC,7,(1986),230; HIS +bond CT N 337.0 1.449 ! JCC,7,(1986),230; AA +bond CT N3 367.0 1.471 ! JCC,7,(1986),230; LYS +bond CT NT 367.0 1.471 ! for neutral amines +bond CT S 227.0 1.810 ! changed from 222.0 based on dimethylS nmodes +bond CT SH 237.0 1.810 ! changed from 222.0 based on methanethiol nmodes +bond CT CY 400.0 1.458 ! Howard et al JCC.16,243,1995 +bond CT CZ 400.0 1.459 ! Howard et al JCC,16,243,1995 +bond CV H4 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes; HIS +bond CV NB 410.0 1.394 ! JCC,7,(1986),230; HIS +bond CW H4 367.0 1.080 ! changed from 340. bsd on C6H6 nmodes;HIS(epsilon,+) +bond CW NA 427.0 1.381 ! JCC,7,(1986),230; HIS,TRP +bond CY NY 600.0 1.150 ! Howard et al JCC,16,243,1995 +bond CZ CZ 600.0 1.206 ! Howard et al JCC,16,243,1995 +bond CZ HZ 400.0 1.056 ! Howard et al JCC,16,243,1995 +bond O2 P 525.0 1.480 ! JCC,7,(1986),230; NA PHOSPHATES +bond OH P 230.0 1.610 ! JCC,7,(1986),230; NA PHOSPHATES +bond OS P 230.0 1.610 ! JCC,7,(1986),230; NA PHOSPHATES +bond H N2 434.0 1.010 ! JCC,7,(1986),230; ADE,CYT,GUA,ARG +bond H N* 434.0 1.010 ! for plain unmethylated bases ADE,CYT,GUA,ARG +bond H NA 434.0 1.010 ! JCC,7,(1986),230; GUA,URA,HIS +bond H N 434.0 1.010 ! JCC,7,(1986),230; AA +bond H N3 434.0 1.010 ! JCC,7,(1986),230; LYS +bond H NT 434.0 1.010 ! for neutral amines +bond HO OH 553.0 0.960 ! JCC,7,(1986),230; SUGARS,SER,TYR +bond HO OS 553.0 0.960 ! JCC,7,(1986),230; NUCLEOTIDE ENDS +bond HS SH 274.0 1.336 ! JCC,7,(1986),230; CYS +bond S S 166.0 2.038 ! JCC,7,(1986),230; CYX (SCHERAGA) +bond F CT 367.0 1.380 ! JCC,13,(1992),963;CF4; R0=1.332 FOR CHF3 +bond Cl CT 232.0 1.766 ! 6-31g* opt +bond Br CT 159.0 1.944 ! Junmei et al,99 +bond I CT 148.0 2.166 ! Junmei et al,99 +bond F CA 386.0 1.359 ! Junmei et al,99 +bond Cl CA 193.0 1.727 ! Junmei et al,99 +bond I CA 171.0 2.075 ! Junmei et al,99 +bond Br CA 172.0 1.890 ! Junmei et al,99 +bond LP O 600.0 0.200 ! or 0.35 +bond LP OH 600.0 0.200 ! or 0.35 +bond LP OS 600.0 0.200 ! or 0.35 +bond LP N3 600.0 0.200 ! or 0.35 +bond LP NT 600.0 0.200 ! or 0.35 +bond LP NB 600.0 0.200 ! or 0.35 histidines, nucleic acids +bond LP NC 600.0 0.200 ! or 0.35 nucleic acids +bond LP S 600.0 0.700 ! cys,cyx,met +bond LP SH 600.0 0.700 ! cys,cyx angle HW OW HW 100.0 104.52 ! TIP3P water angle HW HW OW 0.0 127.74 ! (found in crystallographic water with 3 bonds) @@ -277,8 +341,6 @@ angle C* CT HC 50.0 109.50 ! AA trp changed based on NMA nmodes angle OS CT OS 160.0 101.00 ! Junmei et al, 1999 angle OS CT CY 50.0 110.00 ! Junmei et al, 1999 angle OS CT CZ 50.0 110.00 ! Junmei et al, 1999 -angle OS CT CZ 50.0 110.00 ! Junmei et al, 1999 -angle OS CT CY 50.0 110.00 ! Junmei et al, 1999 angle OS CT N* 50.0 109.50 angle F CT F 77.0 109.10 ! JCC,13,(1992),963; angle F CT H1 50.0 109.50 ! JCC,13,(1992),963; @@ -544,93 +606,27 @@ impr X X CM H4 1.10 2 180.00 impr X X CM HA 1.10 2 180.00 impr X X CA H4 1.10 2 180.00 ! bsd.on C6H6 nmodes impr X X CA H5 1.10 2 180.00 ! bsd.on C6H6 nmodes -impr CK CB N* CT 1.00 2 180.00 -impr CM C N* CT 1.00 2 180.00 ! dac guess, 9/94 -impr CM C CM CT 1.10 2 180.00 +impr CB CK N* CT 1.00 2 180.00 +impr C CM N* CT 1.00 2 180.00 ! dac guess, 9/94 +impr C CM CM CT 1.10 2 180.00 impr CT O C OH 10.50 2 180.00 -impr NA CV CC CT 1.10 2 180.00 -impr NB CW CC CT 1.10 2 180.00 -impr NA CW CC CT 1.10 2 180.00 -impr CW CB C* CT 1.10 2 180.00 +impr CT CV CC NA 1.10 2 180.00 +impr CT CW CC NB 1.10 2 180.00 +impr CT CW CC NA 1.10 2 180.00 +impr CB CT C* CW 1.10 2 180.00 impr CA CA CA CT 1.10 2 180.00 impr C CM CM CT 1.10 2 180.00 ! dac guess, 9/94 -impr NC CM CA N2 1.10 2 180.00 ! dac guess, 9/94 -impr CB NC CA N2 1.10 2 180.00 ! dac, 10/94 -impr NA NC CA N2 1.10 2 180.00 ! dac, 10/94 +impr CM N2 CA NC 1.10 2 180.00 ! dac guess, 9/94 +impr CB N2 CA NC 1.10 2 180.00 ! dac, 10/94 +impr N2 NA CA NC 1.10 2 180.00 ! dac, 10/94 impr CA CA C OH 1.10 2 180.00 ! (not used in tyr!) impr CA CA CA OH 1.10 2 180.00 ! in tyr impr H5 O C OH 1.10 2 180.00 ! Junmei et al.1999 impr H5 O C OS 1.10 2 180.00 impr CM CT CM HA 1.10 2 180.00 ! Junmei et al.1999 -impr CA CA CA Br 1.10 2 180.00 ! Junmei et al.1999 +impr Br CA CA CA 1.10 2 180.00 ! Junmei et al.1999 impr CM H4 C O 1.10 2 180.00 ! Junmei et al.1999 impr C CT N H 1.10 2 180.00 ! Junmei et al.1999 impr C CT N O 1.10 2 180.00 ! Junmei et al.1999 -vdw H 0.0157 0.6000 0.0157 0.6000 0 1.008 ! H bonded to nitrogen atoms -vdw HO 0.0000 0.0000 0.0000 0.0000 0 1.008 ! hydroxyl group -vdw HS 0.0157 0.6000 0.0157 0.6000 0 1.008 ! hydrogen bonded to sulphur (pol?) -vdw HC 0.0157 1.4870 0.0157 1.4870 0 1.008 ! H aliph. bond. to C without electrwd.group -vdw H1 0.0157 1.3870 0.0157 1.3870 0 1.008 ! H aliph. bond. to C with 1 electrwd. group -vdw H2 0.0157 1.2870 0.0157 1.2870 0 1.008 ! H aliph. bond. to C with 2 electrwd.groups -vdw H3 0.0157 1.1870 0.0157 1.1870 0 1.008 ! H aliph. bond. to C with 3 eletrwd.groups -vdw HP 0.0157 1.1000 0.0157 1.1000 0 1.008 ! H bonded to C next to positively charged gr -vdw HA 0.0150 1.4590 0.0150 1.4590 0 1.008 ! H arom. bond. to C without elctrwd. groups -vdw H4 0.0150 1.4090 0.0150 1.4090 0 1.008 ! H arom. bond. to C with 1 electrwd. group -vdw H5 0.0150 1.3590 0.0150 1.3590 0 1.008 ! H arom.at C with 2 elctrwd. gr,+HCOO group -vdw HW 0.0000 0.0000 0.0000 0.0000 0 1.008 ! H in TIP3P water -vdw HZ 0.0150 1.4590 0.0150 1.4590 0 1.008 ! H bond sp C (Howard et al.JCC,16,243,1995) -vdw O 0.2100 1.6612 0.2100 1.6612 0 16.000 ! carbonyl group oxygen -vdw O2 0.2100 1.6612 0.2100 1.6612 0 16.000 ! carboxyl and phosphate group oxygen -vdw OW 0.1520 1.7683 0.1520 1.7683 0 16.000 ! oxygen in TIP3P water -vdw OH 0.2104 1.7210 0.2104 1.7210 0 16.000 ! oxygen in hydroxyl group -vdw OS 0.1700 1.6837 0.1700 1.6837 0 16.000 ! ether and ester oxygen -vdw C* 0.0860 1.9080 0.0860 1.9080 0 12.010 ! sp2 arom. 5 memb.ring w/1 subst. (TRP) -vdw CA 0.0860 1.9080 0.0860 1.9080 0 12.010 ! sp2 C pure aromatic (benzene) -vdw CB 0.0860 1.9080 0.0860 1.9080 0 12.010 ! sp2 aromatic C, 5&6 membered ring junction -vdw CC 0.0860 1.9080 0.0860 1.9080 0 12.010 ! sp2 aromatic C, 5 memb. ring HIS -vdw CD 0.0860 1.9080 0.0860 1.9080 0 12.010 ! sp2 C atom in the middle of: C=CD-CD=C -vdw CK 0.0860 1.9080 0.0860 1.9080 0 12.010 ! sp2 C 5 memb.ring in purines -vdw CM 0.0860 1.9080 0.0860 1.9080 0 12.010 ! sp2 C pyrimidines in pos. 5 & 6 -vdw CN 0.0860 1.9080 0.0860 1.9080 0 12.010 ! sp2 C aromatic 5&6 memb.ring junct.(TRP) -vdw CQ 0.0860 1.9080 0.0860 1.9080 0 12.010 ! sp2 C in 5 mem.ring of purines between 2 N -vdw CR 0.0860 1.9080 0.0860 1.9080 0 12.010 ! sp2 arom as CQ but in HIS -vdw CV 0.0860 1.9080 0.0860 1.9080 0 12.010 ! sp2 arom. 5 memb.ring w/1 N and 1 H (HIS) -vdw CW 0.0860 1.9080 0.0860 1.9080 0 12.010 ! sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS) -vdw CX 0.0860 1.9080 0.0860 1.9080 0 0.000 -vdw CY 0.0860 1.9080 0.0860 1.9080 0 12.010 ! nitrile C (Howard et al.JCC,16,243,1995) -vdw CZ 0.0860 1.9080 0.0860 1.9080 0 12.010 ! sp C (Howard et al.JCC,16,243,1995) -vdw CT 0.1094 1.9080 0.1094 1.9080 0 12.010 ! sp3 aliphatic C -vdw C 0.0860 1.9080 0.0860 1.9080 0 12.010 ! sp2 C carbonyl group -vdw N 0.1700 1.8240 0.1700 1.8240 0 14.010 ! sp2 nitrogen in amide groups -vdw NA 0.1700 1.8240 0.1700 1.8240 0 14.010 ! sp2 N in 5 memb.ring w/H atom (HIS) -vdw N2 0.1700 1.8240 0.1700 1.8240 0 14.010 ! sp2 N in amino groups -vdw N* 0.1700 1.8240 0.1700 1.8240 0 14.010 ! sp2 N -vdw NC 0.1700 1.8240 0.1700 1.8240 0 14.010 ! sp2 N in 6 memb.ring w/LP (ADE,GUA) -vdw NB 0.1700 1.8240 0.1700 1.8240 0 14.010 ! sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA) -vdw N3 0.1700 1.8240 0.1700 1.8240 0 14.010 ! sp3 N for charged amino groups (Lys, etc) -vdw NT 0.1700 1.8240 0.1700 1.8240 0 14.010 ! sp3 N for amino groups amino groups -vdw NP 0.1700 1.8240 0.1700 1.8240 0 0.000 -vdw NO 0.1700 1.8240 0.1700 1.8240 0 0.000 -vdw NY 0.1700 1.8240 0.1700 1.8240 0 14.010 ! nitrile N (Howard et al.JCC,16,243,1995) -vdw NY 0.1700 1.8240 0.1700 1.8240 0 14.010 ! nitrile N (Howard et al.JCC,16,243,1995) -vdw S 0.2500 2.0000 0.2500 2.0000 0 32.060 ! S in disulfide linkage,pol:JPC,102,2399,98 -vdw SH 0.2500 2.0000 0.2500 2.0000 0 32.060 ! S in cystine -vdw P 0.2000 2.1000 0.2000 2.1000 0 30.970 ! phosphate,pol:JACS,112,8543,90,K.J.Miller -vdw IM 0.1000 2.4700 0.1000 2.4700 0 35.450 ! assumed to be Cl- (ion minus) -vdw Li 0.0183 1.1370 0.0183 1.1370 0 6.940 ! lithium, ions pol:J.PhysC,11,1541,(1978) -vdw IP 0.0028 1.8680 0.0028 1.8680 0 22.990 ! assumed to be Na+ (ion plus) -vdw Na 0.0028 1.8680 0.0028 1.8680 0 22.990 ! Na+, ions pol:J.PhysC,11,1541,(1978) -vdw K 0.0003 2.6580 0.0003 2.6580 0 39.100 ! potassium -vdw Rb 0.0002 2.9560 0.0002 2.9560 0 85.470 ! rubidium -vdw Cs 0.0001 3.3950 0.0001 3.3950 0 132.910 ! cesium -vdw MG 0.8947 0.7926 0.8947 0.7926 0 24.305 ! magnesium -vdw C0 0.4598 1.7131 0.4598 1.7131 0 40.080 ! calcium -vdw Zn 0.0125 1.1000 0.0125 1.1000 0 65.400 ! Zn2+ -vdw F 0.0610 1.7500 0.0610 1.7500 0 19.000 ! fluorine -vdw Cl 0.2650 1.9480 0.2650 1.9480 0 35.450 ! chlorine (Applequist) -vdw Br 0.3200 2.2200 0.3200 2.2200 0 79.900 ! bromine (Applequist) -vdw I 0.4000 2.3500 0.4000 2.3500 0 126.900 ! iodine (Applequist) -vdw IB 0.1000 5.0000 0.1000 5.0000 0 131.000 ! 'big ion w/ waters' for vacuum (Na+, 6H2O) -vdw LP 0.0000 0.0000 0.0000 0.0000 0 3.000 ! lone pair diff --git a/Version b/Version index 93d4083..8256c77 100644 --- a/Version +++ b/Version @@ -1,2 +1,2 @@ version = "0.5.5" -date = "20110426" +date = "20110702" diff --git a/amberparm2molby.pl b/amberparm2molby.pl index a115cb0..2a632d3 100644 --- a/amberparm2molby.pl +++ b/amberparm2molby.pl @@ -4,6 +4,7 @@ # output (stdout): a Molby parm file # Written as amberparm2namd.pl by Toshi Nagata, Dec 2 2004 # Updated for Molby, Nov 13 2009 +# Revised Jul 2 2011 $title = <>; print "! ", $title; @@ -39,7 +40,7 @@ while (<>) { chomp; last if /^\s*$/; ($a1, $a2, $fc, $len, $com) = unpack("A2 x1 A2 A10 A10 A75", $_ . $blanks); - printf "bond %-2s %-2s %7.1f %5.2f%s\n", $a1, $a2, $fc, $len, format_com($com); + printf "bond %-2s %-2s %7.1f %5.3f%s\n", $a1, $a2, $fc, $len, format_com($com); } print "\n"; diff --git a/msw-build/molby.iss b/msw-build/molby.iss index c6b75c3..9e3d050 100755 --- a/msw-build/molby.iss +++ b/msw-build/molby.iss @@ -1,6 +1,6 @@ [Setup] AppName = Molby -AppVerName = Molby (v0.5.5 build 20110426) +AppVerName = Molby (v0.5.5 build 20110702) DefaultDirName = {pf}\Molby DefaultGroupName = Molby UninstallDisplayIcon = {app}\Molby.exe diff --git a/wxSources/MyDocument.cpp b/wxSources/MyDocument.cpp index e63613b..85aefe4 100755 --- a/wxSources/MyDocument.cpp +++ b/wxSources/MyDocument.cpp @@ -713,8 +713,10 @@ sDoMolecularDynamics(void *argptr, int argnum) md_copy_coordinates_from_internal(mol->arena); MoleculeUnlock(mol); */ - if (minimize && mol->arena->minimize_complete) + if (minimize && mol->arena->minimize_complete) { + r = -2; /* Minimization complete */ break; + } wxPostEvent(doc, insertFrameEvent); } } diff --git a/wxSources/MyVersion.c b/wxSources/MyVersion.c index 8570a14..549cbf5 100644 --- a/wxSources/MyVersion.c +++ b/wxSources/MyVersion.c @@ -15,5 +15,5 @@ GNU General Public License for more details. */ -const char *gVersionString = "v0.5.5 build 20110426"; +const char *gVersionString = "v0.5.5 build 20110702"; const char *gCopyrightString = "Copyright (c) 2008-2011 Toshi Nagata"; diff --git a/xcode-build/Info.plist b/xcode-build/Info.plist index ffef2cb..ef724ce 100755 --- a/xcode-build/Info.plist +++ b/xcode-build/Info.plist @@ -36,6 +36,6 @@ CFBundleSignature ???? CFBundleVersion - v0.5.5 build 20110426 + v0.5.5 build 20110702 -- 2.11.0