! PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 ! ! Original file was taken from the AMBER home page: http://ambermd.org/ (as of Nov 13, 2009) ! Converted for Molby by amberparm2molby.pl by Toshi Nagata. ! 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. 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) angle C C O 80.0 120.00 ! Junmei et al, 1999 acrolein angle C C OH 80.0 120.00 ! Junmei et al, 1999 angle CA C CA 63.0 120.00 ! changed from 85.0 bsd on C6H6 nmodes; AA angle CA C OH 70.0 120.00 ! AA (not used in tyr) angle CB C NA 70.0 111.30 ! NA angle CB C O 80.0 128.80 angle CM C NA 70.0 114.10 angle CM C O 80.0 125.30 angle CT C O 80.0 120.40 angle CT C O2 70.0 117.00 angle CT C N 70.0 116.60 ! AA general angle CT C CT 63.0 117.00 ! Junmei et al, 1999 angle CT C OS 80.0 115.00 ! Junmei et al, 1999 angle CT C OH 80.0 110.00 ! Junmei et al, 1999 angle N* C NA 70.0 115.40 angle N* C NC 70.0 118.60 angle N* C O 80.0 120.90 angle NA C O 80.0 120.60 angle NC C O 80.0 122.50 angle N C O 80.0 122.90 ! AA general angle O C O 80.0 126.00 ! AA COO- terminal residues angle O C OH 80.0 120.00 ! (check with Junmei for: theta0:120.0?) angle O C OS 80.0 125.00 ! Junmei et al, 1999 angle O2 C O2 80.0 126.00 ! AA GLU (SCH JPC 79,2379) angle H4 C C 50.0 120.00 ! Junmei et al, 1999 angle H4 C CM 50.0 115.00 ! Junmei et al, 1999 angle H4 C CT 50.0 115.00 ! Junmei et al, 1999 angle H4 C O 50.0 120.00 ! Junmei et al, 1999 angle H4 C OH 50.0 120.00 ! Junmei et al, 1999 angle H5 C N 50.0 120.00 ! Junmei et al, 1999 angle H5 C O 50.0 119.00 ! Junmei et al, 1999 angle H5 C OH 50.0 107.00 ! Junmei et al, 1999 angle H5 C OS 50.0 107.00 ! Junmei et al, 1999 angle C CA CA 63.0 120.00 ! changed from 85.0 bsd on C6H6 nmodes angle C CA HA 50.0 120.00 ! AA (not used in tyr) angle CA CA CA 63.0 120.00 ! changed from 85.0 bsd on C6H6 nmodes angle CA CA CB 63.0 120.00 ! changed from 85.0 bsd on C6H6 nmodes angle CA CA CT 70.0 120.00 angle CA CA HA 50.0 120.00 angle CA CA H4 50.0 120.00 angle CA CA OH 70.0 120.00 ! replacement in tyr angle CA CA CN 63.0 120.00 ! changed from 85.0 bsd on C6H6 nmodes; AA trp angle CB CA HA 50.0 120.00 angle CB CA H4 50.0 120.00 angle CB CA N2 70.0 123.50 angle CB CA NC 70.0 117.30 angle CM CA N2 70.0 120.10 angle CM CA NC 70.0 121.50 angle CN CA HA 50.0 120.00 ! AA trp angle NA CA NC 70.0 123.30 angle N2 CA NA 70.0 116.00 angle N2 CA NC 70.0 119.30 angle N2 CA N2 70.0 120.00 ! AA arg angle F CA CA 70.0 121.00 ! Junmei et al,99 angle Cl CA CA 70.0 118.80 ! Junmei et al,99 angle Br CA CA 70.0 118.80 ! Junmei et al,99 angle I CA CA 70.0 118.80 ! Junmei et al,99 angle C CB CB 63.0 119.20 ! changed from 85.0 bsd on C6H6 nmodes; NA gua angle C CB NB 70.0 130.00 angle CA CB CB 63.0 117.30 ! changed from 85.0 bsd on C6H6 nmodes; NA ade angle CA CB NB 70.0 132.40 angle CB CB N* 70.0 106.20 angle CB CB NB 70.0 110.40 angle CB CB NC 70.0 127.70 angle C* CB CA 63.0 134.90 ! changed from 85.0 bsd on C6H6 nmodes; AA trp angle C* CB CN 63.0 108.80 ! changed from 85.0 bsd on C6H6 nmodes; AA trp angle CA CB CN 63.0 116.20 ! changed from 85.0 bsd on C6H6 nmodes; AA trp angle N* CB NC 70.0 126.20 angle CD CD CM 63.0 120.00 ! Junmei et al, 1999 angle CD CD CT 70.0 120.00 ! Junmei et al, 1999 angle CM CD CT 70.0 120.00 ! Junmei et al, 1999 angle HA CD HA 35.0 119.00 ! Junmei et al, 1999 angle HA CD CD 50.0 120.00 ! Junmei et al, 1999 angle HA CD CM 50.0 120.00 ! Junmei et al, 1999 angle H5 CK N* 50.0 123.05 angle H5 CK NB 50.0 123.05 angle N* CK NB 70.0 113.90 angle C CM CM 63.0 120.70 ! changed from 85.0 bsd on C6H6 nmodes; NA thy angle C CM CT 70.0 119.70 angle C CM HA 50.0 119.70 angle C CM H4 50.0 119.70 angle CA CM CM 63.0 117.00 ! changed from 85.0 bsd on C6H6 nmodes; NA cyt angle CA CM HA 50.0 123.30 angle CA CM H4 50.0 123.30 angle CM CM CT 70.0 119.70 angle CM CM HA 50.0 119.70 angle CM CM H4 50.0 119.70 angle CM CM N* 70.0 121.20 angle CM CM OS 80.0 125.00 ! Junmei et al, 1999 angle H4 CM N* 50.0 119.10 angle H4 CM OS 50.0 113.00 ! Junmei et al, 1999 angle HA CM HA 35.0 120.00 ! Junmei et al, 1999 angle HA CM CD 50.0 120.00 ! Junmei et al, 1999 angle HA CM CT 50.0 120.00 ! Junmei et al, 1999 angle NC CQ NC 70.0 129.10 angle H5 CQ NC 50.0 115.45 angle H1 CT H1 35.0 109.50 angle H1 CT N* 50.0 109.50 ! changed based on NMA nmodes angle H1 CT OH 50.0 109.50 ! changed based on NMA nmodes angle H1 CT OS 50.0 109.50 ! changed based on NMA nmodes angle H1 CT CM 50.0 109.50 ! Junmei et al, 1999 angle H1 CT CY 50.0 110.00 ! Junmei et al, 1999 angle H1 CT CZ 50.0 110.00 ! Junmei et al, 1999 angle H1 CT N 50.0 109.50 ! AA general changed based on NMA nmodes angle H1 CT S 50.0 109.50 ! AA cys changed based on NMA nmodes angle H1 CT SH 50.0 109.50 ! AA cyx changed based on NMA nmodes angle H1 CT N2 50.0 109.50 ! AA arg changed based on NMA nmodes angle H1 CT NT 50.0 109.50 ! neutral amines angle H2 CT H2 35.0 109.50 ! AA lys angle H2 CT N* 50.0 109.50 ! changed based on NMA nmodes angle H2 CT OS 50.0 109.50 ! changed based on NMA nmodes angle HP CT HP 35.0 109.50 ! AA lys, ch3nh4+ angle HP CT N3 50.0 109.50 ! AA lys, ch3nh3+, changed based on NMA nmodes angle HC CT HC 35.0 109.50 angle HC CT CM 50.0 109.50 ! changed based on NMA nmodes angle HC CT CD 50.0 109.50 ! Junmei et al, 1999 angle HC CT CZ 50.0 110.00 ! Junmei et al, 1999 angle C CT H1 50.0 109.50 ! AA general changed based on NMA nmodes angle C CT HP 50.0 109.50 ! AA zwitterion changed based on NMA nmodes angle C CT HC 50.0 109.50 ! AA gln changed based on NMA nmodes angle C CT N 63.0 110.10 ! AA general angle C CT N3 80.0 111.20 ! AA amino terminal residues angle C CT CT 63.0 111.10 ! AA general angle C CT OS 60.0 109.50 ! Junmei et al, 1999 angle CA CT HC 50.0 109.50 ! AA tyr changed based on NMA nmodes angle CC CT CT 63.0 113.10 ! AA his angle CC CT HC 50.0 109.50 ! AA his changed based on NMA nmodes angle CM CT CT 63.0 111.00 ! Junmei et al, 1999 (last change: Mar24,99) angle CM CT OS 50.0 109.50 ! Junmei et al, 1999 angle CT CT CT 40.0 109.50 angle CT CT HC 50.0 109.50 ! changed based on NMA nmodes angle CT CT H1 50.0 109.50 ! changed based on NMA nmodes angle CT CT H2 50.0 109.50 ! changed based on NMA nmodes angle CT CT HP 50.0 109.50 ! changed based on NMA nmodes angle CT CT N* 50.0 109.50 angle CT CT OH 50.0 109.50 angle CT CT OS 50.0 109.50 angle CT CT S 50.0 114.70 ! AA cyx (SCHERAGA JPC 79,1428) angle CT CT SH 50.0 108.60 ! AA cys angle CT CT CA 63.0 114.00 ! AA phe tyr (SCH JPC 79,2379) angle CT CT N2 80.0 111.20 ! AA arg (JCP 76, 1439) angle CT CT N 80.0 109.70 ! AA ala, general (JACS 94, 2657) angle CT CT N3 80.0 111.20 ! AA lys (JCP 76, 1439) angle CT CT NT 80.0 111.20 ! neutral amines angle CT CT CY 63.0 110.00 ! Junmei et al, 1999 angle CT CT CZ 63.0 110.00 ! Junmei et al, 1999 angle C* CT CT 63.0 115.60 ! AA trp 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 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; angle F CT CT 50.0 109.00 angle F CT H2 50.0 109.50 angle Cl CT CT 50.0 108.50 ! (6-31g* opt value) angle Cl CT H1 50.0 108.50 ! (6-31g* opt value) angle Br CT CT 50.0 108.00 ! Junmei et al 99 angle Br CT H1 50.0 106.50 ! Junmei et al 99 angle I CT CT 50.0 106.00 ! Junmei et al,99 angle CT CC NA 70.0 120.00 ! AA his angle CT CC CV 70.0 120.00 ! AA his angle CT CC NB 70.0 120.00 ! AA his angle CV CC NA 70.0 120.00 ! AA his angle CW CC NA 70.0 120.00 ! AA his angle CW CC NB 70.0 120.00 ! AA his angle CT CC CW 70.0 120.00 ! AA his angle H5 CR NA 50.0 120.00 ! AA his angle H5 CR NB 50.0 120.00 ! AA his angle NA CR NA 70.0 120.00 ! AA his angle NA CR NB 70.0 120.00 ! AA his angle CC CV H4 50.0 120.00 ! AA his angle CC CV NB 70.0 120.00 ! AA his angle H4 CV NB 50.0 120.00 ! AA his angle CC CW H4 50.0 120.00 ! AA his angle CC CW NA 70.0 120.00 ! AA his angle C* CW H4 50.0 120.00 ! AA trp angle C* CW NA 70.0 108.70 ! AA trp angle H4 CW NA 50.0 120.00 ! AA his angle CB C* CT 70.0 128.60 ! AA trp angle CB C* CW 63.0 106.40 ! changed from 85.0 bsd on C6H6 nmodes; AA trp angle CT C* CW 70.0 125.00 ! AA trp angle CA CN CB 63.0 122.70 ! changed from 85.0 bsd on C6H6 nmodes; AA trp angle CA CN NA 70.0 132.80 ! AA trp angle CB CN NA 70.0 104.40 ! AA trp angle CT CY NY 80.0 180.00 ! Junmei et al, 1999 angle CT CZ CZ 80.0 180.00 ! Junmei et al, 1999 angle CZ CZ HZ 50.0 180.00 ! Junmei et al, 1999 angle C N CT 50.0 121.90 ! AA general angle C N H 50.0 120.00 ! AA general, gln, asn,changed based on NMA nmodes angle CT N H 50.0 118.04 ! AA general, changed based on NMA nmodes angle CT N CT 50.0 118.00 ! AA pro (DETAR JACS 99,1232) angle H N H 35.0 120.00 ! ade,cyt,gua,gln,asn ** angle C N* CM 70.0 121.60 angle C N* CT 70.0 117.60 angle C N* H 50.0 119.20 ! changed based on NMA nmodes angle CB N* CK 70.0 105.40 angle CB N* CT 70.0 125.80 angle CB N* H 50.0 125.80 ! for unmethylated n.a. bases,chngd bsd NMA nmodes angle CK N* CT 70.0 128.80 angle CK N* H 50.0 128.80 ! for unmethylated n.a. bases,chngd bsd NMA nmodes angle CM N* CT 70.0 121.20 angle CM N* H 50.0 121.20 ! for unmethylated n.a. bases,chngd bsd NMA nmodes angle CA N2 H 50.0 120.00 angle CA N2 CT 50.0 123.20 ! AA arg angle CT N2 H 50.0 118.40 ! AA arg angle H N2 H 35.0 120.00 angle CT N3 H 50.0 109.50 ! AA lys, changed based on NMA nmodes angle CT N3 CT 50.0 109.50 ! AA pro/nt angle H N3 H 35.0 109.50 ! AA lys, AA(end) angle CT NT H 50.0 109.50 ! neutral amines angle CT NT CT 50.0 109.50 ! neutral amines angle H NT H 35.0 109.50 ! neutral amines angle C NA C 70.0 126.40 angle C NA CA 70.0 125.20 angle C NA H 50.0 116.80 ! changed based on NMA nmodes angle CA NA H 50.0 118.00 ! changed based on NMA nmodes angle CC NA CR 70.0 120.00 ! AA his angle CC NA H 50.0 120.00 ! AA his, changed based on NMA nmodes angle CR NA CW 70.0 120.00 ! AA his angle CR NA H 50.0 120.00 ! AA his, changed based on NMA nmodes angle CW NA H 50.0 120.00 ! AA his, changed based on NMA nmodes angle CN NA CW 70.0 111.60 ! AA trp angle CN NA H 50.0 123.10 ! AA trp, changed based on NMA nmodes angle CB NB CK 70.0 103.80 angle CC NB CR 70.0 117.00 ! AA his angle CR NB CV 70.0 117.00 ! AA his angle C NC CA 70.0 120.50 angle CA NC CB 70.0 112.20 angle CA NC CQ 70.0 118.60 angle CB NC CQ 70.0 111.00 angle C OH HO 50.0 113.00 ! (not used in tyr anymore) angle CA OH HO 50.0 113.00 ! replacement in tyr angle CT OH HO 55.0 108.50 angle HO OH P 45.0 108.50 angle C OS CT 60.0 117.00 ! Junmei et al, 1999 angle CM OS CT 60.0 117.00 ! Junmei et al, 1999 angle CT OS CT 60.0 109.50 angle CT OS P 100.0 120.50 angle P OS P 100.0 120.50 angle O2 P OH 45.0 108.23 angle O2 P O2 140.0 119.90 angle O2 P OS 100.0 108.23 angle OH P OS 45.0 102.60 angle OS P OS 45.0 102.60 angle CT S CT 62.0 98.90 ! AA met angle CT S S 68.0 103.70 ! AA cyx (SCHERAGA JPC 79,1428) angle CT SH HS 43.0 96.00 ! changed from 44.0 based on methanethiol nmodes angle HS SH HS 35.0 92.07 ! AA cys angle CB NB LP 150.0 126.00 ! NA angle CC NB LP 150.0 126.00 ! his,NA angle CK NB LP 150.0 126.00 ! NA angle CR NB LP 150.0 126.00 ! his,NA angle CV NB LP 150.0 126.00 ! his,NA angle C NC LP 150.0 120.00 ! NA angle CA NC LP 150.0 120.00 ! NA angle CB NC LP 150.0 120.00 ! NA angle CQ NC LP 150.0 120.00 ! NA angle CT N3 LP 150.0 109.50 ! in neutral lysine angle H N3 LP 150.0 109.50 ! in neutral lysine angle CT NT LP 150.0 109.50 angle H NT LP 150.0 109.50 angle C O LP 150.0 120.00 angle LP O LP 150.0 120.00 angle C OH LP 150.0 120.00 angle CT OH LP 150.0 109.50 angle HO OH LP 150.0 109.50 angle LP OH LP 150.0 109.50 angle C OS LP 150.0 109.50 angle CM OS LP 150.0 109.50 ! methyl vinyl ether angle CT OS LP 150.0 109.50 angle LP OS LP 150.0 109.50 angle CT S LP 150.0 90.00 ! cys,cyx,met angle CT SH LP 150.0 90.00 ! cys,cyx,met angle P OS LP 150.0 109.50 ! NA angle LP S LP 150.0 180.00 ! cys,cyx,met angle LP SH LP 150.0 180.00 ! cys,cyx,met angle HS SH LP 150.0 90.00 ! cys dihe X C C X 3.62 2 180.00 ! Junmei et al, 1999 dihe X C CA X 3.62 2 180.00 ! intrpol.bsd.on C6H6 dihe X C CB X 3.00 2 180.00 ! intrpol.bsd.on C6H6 dihe X C CM X 2.17 2 180.00 ! intrpol.bsd.on C6H6 dihe X C CT X 0.00 2 0.00 ! JCC,7,(1986),230 dihe X C N X 2.50 2 180.00 ! AA,NMA dihe X C N* X 1.45 2 180.00 ! JCC,7,(1986),230 dihe X C NA X 1.35 2 180.00 ! JCC,7,(1986),230 dihe X C NC X 4.00 2 180.00 ! JCC,7,(1986),230 dihe X C O X 2.80 2 180.00 ! Junmei et al, 1999 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 CA CA X 3.62 2 180.00 ! intrpol.bsd.on C6H6 dihe X CA CB X 3.50 2 180.00 ! intrpol.bsd.on C6H6 dihe X CA CM X 2.55 2 180.00 ! intrpol.bsd.on C6H6 dihe X CA CN X 3.62 2 180.00 ! reinterpolated 93' dihe X CA CT X 0.00 2 0.00 ! JCC,7,(1986),230 dihe X CA N2 X 2.40 2 180.00 ! reinterpolated 93' dihe X CA NA X 1.50 2 180.00 ! JCC,7,(1986),230 dihe X CA NC X 4.80 2 180.00 ! JCC,7,(1986),230 dihe X CA OH X 0.90 2 180.00 ! Junmei et al, 99 dihe X CB CB X 5.45 2 180.00 ! intrpol.bsd.on C6H6 dihe X CB CN X 3.00 2 180.00 ! reinterpolated 93' dihe X CB N* X 1.65 2 180.00 ! JCC,7,(1986),230 dihe X CB NB X 2.55 2 180.00 ! JCC,7,(1986),230 dihe X CB NC X 4.15 2 180.00 ! JCC,7,(1986),230 dihe X CC CT X 0.00 2 0.00 ! JCC,7,(1986),230 dihe X CC CV X 5.15 2 180.00 ! intrpol.bsd.on C6H6 dihe X CC CW X 5.38 2 180.00 ! intrpol.bsd.on C6H6 dihe X CC NA X 1.40 2 180.00 ! JCC,7,(1986),230 dihe X CC NB X 2.40 2 180.00 ! JCC,7,(1986),230 dihe X CD CD X 1.00 2 180.00 ! Junmei et al, 1999 dihe X CD CT X 0.00 2 0.00 ! Junmei et al, 1999 dihe X CD CM X 6.65 2 180.00 ! Junmei et al, 1999 dihe X CK N* X 1.70 2 180.00 ! JCC,7,(1986),230 dihe X CK NB X 10.00 2 180.00 ! JCC,7,(1986),230 dihe X CM CM X 6.65 2 180.00 ! intrpol.bsd.on C6H6 dihe X CM CT X 0.00 3 0.00 ! JCC,7,(1986),230 dihe X CM N* X 1.85 2 180.00 ! JCC,7,(1986),230 dihe X CM OS X 1.05 2 180.00 ! Junmei et al, 1999 dihe X CN NA X 1.52 2 180.00 ! reinterpolated 93' dihe X CQ NC X 6.80 2 180.00 ! JCC,7,(1986),230 dihe X CT CT X 0.16 3 0.00 ! JCC,7,(1986),230 dihe X CT CY X 0.00 1 0.00 ! Junmei et al, 1999 dihe X CT CZ X 0.00 1 0.00 ! Junmei et al, 1999 dihe X CT N X 0.00 2 0.00 ! JCC,7,(1986),230 dihe X CT N* X 0.00 2 0.00 ! JCC,7,(1986),230 dihe X CT N2 X 0.00 3 0.00 ! JCC,7,(1986),230 dihe X CT NT X 0.30 3 0.00 ! Junmei et al, 1999 dihe X CT N3 X 0.16 3 0.00 ! JCC,7,(1986),230 dihe X CT OH X 0.17 3 0.00 ! JCC,7,(1986),230 dihe X CT OS X 0.38 3 0.00 ! JCC,7,(1986),230 dihe X CT S X 0.33 3 0.00 ! JCC,7,(1986),230 dihe X CT SH X 0.25 3 0.00 ! JCC,7,(1986),230 dihe X C* CB X 1.68 2 180.00 ! intrpol.bsd.onC6H6aa dihe X C* CT X 0.00 2 0.00 ! JCC,7,(1986),230 dihe X C* CW X 6.53 2 180.00 ! intrpol.bsd.on C6H6 dihe X CR NA X 2.33 2 180.00 ! JCC,7,(1986),230 dihe X CR NB X 5.00 2 180.00 ! JCC,7,(1986),230 dihe X CV NB X 2.40 2 180.00 ! JCC,7,(1986),230 dihe X CW NA X 1.50 2 180.00 ! JCC,7,(1986),230 dihe X OH P X 0.25 3 0.00 ! JCC,7,(1986),230 dihe X OS P X 0.25 3 0.00 ! JCC,7,(1986),230 dihe N CT C N 2.00 2 180.00 dihe C N CT C 0.80 1 0.00 dihe CT CT N C 0.53 1 0.00 ! phi,psi,parm94 dihe CT CT C N 0.07 2 0.00 ! phi,psi,parm94 dihe H N C O 2.00 1 0.00 ! J.C.cistrans-NMA DE dihe CT S S CT 0.60 3 0.00 ! JCC,7,(1986),230 dihe OH P OS CT 1.20 2 0.00 ! gg> ene.631g*/mp2 dihe OS P OS CT 1.20 2 0.00 ! gg> ene.631g*/mp2 dihe H1 CT C O 0.08 3 180.00 ! Junmei et al, 1999 dihe HC CT C O 0.08 3 180.00 ! Junmei et al, 1999 dihe HC CT CT HC 0.15 3 0.00 ! Junmei et al, 1999 dihe HC CT CT CT 0.16 3 0.00 ! Junmei et al, 1999 dihe HC CT CM CM 1.15 1 0.00 ! Junmei et al, 1999 dihe HO OH CT CT 0.25 1 0.00 ! Junmei et al, 1999 dihe HO OH C O 1.90 1 0.00 ! Junmei et al, 1999 dihe CM CM C O 0.30 3 0.00 ! Junmei et al, 1999 dihe CT CM CM CT 1.90 1 180.00 ! Junmei et al, 1999 dihe CT CT CT CT 0.20 1 180.00 ! Junmei et al, 1999 dihe CT CT NT CT 0.48 2 180.00 ! Junmei et al, 1999 dihe CT CT OS CT 0.10 2 180.00 dihe CT CT OS C 0.80 1 180.00 ! Junmei et al, 1999 dihe CT OS CT OS 1.35 1 180.00 ! Junmei et al, 1999 dihe CT OS CT N* 0.65 2 0.00 ! Piotr et al. dihe CT CZ CZ HZ 0.00 1 0.00 ! Junmei et al, 1999 dihe O C OS CT 1.40 1 180.00 ! Junmei et al, 1999 dihe OS CT N* CK 2.50 1 0.00 ! parm98, TC,PC,PAK dihe OS CT N* CM 2.50 1 0.00 ! parm98, TC,PC,PAK dihe OS CT CT OS 1.18 2 0.00 ! Piotr et al. dihe OS CT CT OH 1.18 2 0.00 ! parm98, TC,PC,PAK dihe OH CT CT OH 1.18 2 0.00 ! parm98, TC,PC,PAK dihe F CT CT F 1.20 1 180.00 ! Junmei et al, 1999 dihe Cl CT CT Cl 0.45 1 180.00 ! Junmei et al, 1999 dihe Br CT CT Br 0.00 1 180.00 ! Junmei et al, 1999 dihe H1 CT CT OS 0.25 1 0.00 ! Junmei et al, 1999 dihe H1 CT CT OH 0.25 1 0.00 ! Junmei et al, 1999 dihe H1 CT CT F 0.19 1 0.00 ! Junmei et al, 1999 dihe H1 CT CT Cl 0.25 1 0.00 ! Junmei et al, 1999 dihe H1 CT CT Br 0.55 1 0.00 ! Junmei et al, 1999 dihe HC CT CT OS 0.25 1 0.00 ! Junmei et al, 1999 dihe HC CT CT OH 0.25 1 0.00 ! Junmei et al, 1999 dihe HC CT CT F 0.19 1 0.00 ! Junmei et al, 1999 dihe HC CT CT Cl 0.25 1 0.00 ! Junmei et al, 1999 dihe HC CT CT Br 0.55 1 0.00 ! Junmei et al, 1999 dihe H1 CT NT LP 0.00 3 0.00 dihe CT CT NT LP 0.00 3 0.00 dihe CT C N LP 0.00 2 180.00 dihe O C N LP 0.00 2 180.00 dihe H1 CT OH LP 0.00 3 0.00 dihe CT CT OH LP 0.00 3 0.00 dihe H1 CT OS LP 0.00 3 0.00 dihe H2 CT OS LP 0.00 3 0.00 dihe CT CT OS LP 0.00 3 0.00 dihe CM CM OS LP 0.00 2 180.00 dihe HA CM OS LP 0.00 2 180.00 dihe H4 CM OS LP 0.00 2 180.00 impr X X C O 10.50 2 180.00 ! JCC,7,(1986),230 impr X O2 C O2 10.50 2 180.00 ! JCC,7,(1986),230 impr X X N H 1.00 2 180.00 ! JCC,7,(1986),230 impr X X N2 H 1.00 2 180.00 ! JCC,7,(1986),230 impr X X NA H 1.00 2 180.00 ! JCC,7,(1986),230 impr X N2 CA N2 10.50 2 180.00 ! JCC,7,(1986),230 impr X CT N CT 1.00 2 180.00 ! JCC,7,(1986),230 impr X X CA HA 1.10 2 180.00 ! bsd.on C6H6 nmodes impr X X CW H4 1.10 2 180.00 impr X X CR H5 1.10 2 180.00 impr X X CV H4 1.10 2 180.00 impr X X CQ H5 1.10 2 180.00 impr X X CK H5 1.10 2 180.00 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 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 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 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 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