PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 C 12.01 0.616 ! sp2 C carbonyl group CA 12.01 0.360 sp2 C pure aromatic (benzene) CB 12.01 0.360 sp2 aromatic C, 5&6 membered ring junction CC 12.01 0.360 sp2 aromatic C, 5 memb. ring HIS CD 12.01 0.360 sp2 C atom in the middle of: C=CD-CD=C CK 12.01 0.360 sp2 C 5 memb.ring in purines CM 12.01 0.360 sp2 C pyrimidines in pos. 5 & 6 CN 12.01 0.360 sp2 C aromatic 5&6 memb.ring junct.(TRP) CQ 12.01 0.360 sp2 C in 5 mem.ring of purines between 2 N CR 12.01 0.360 sp2 arom as CQ but in HIS CT 12.01 0.878 sp3 aliphatic C CV 12.01 0.360 sp2 arom. 5 memb.ring w/1 N and 1 H (HIS) CW 12.01 0.360 sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS) C* 12.01 0.360 sp2 arom. 5 memb.ring w/1 subst. (TRP) CY 12.01 0.360 nitrile C (Howard et al.JCC,16,243,1995) CZ 12.01 0.360 sp C (Howard et al.JCC,16,243,1995) C0 40.08 calcium H 1.008 0.161 H bonded to nitrogen atoms HC 1.008 0.135 H aliph. bond. to C without electrwd.group H1 1.008 0.135 H aliph. bond. to C with 1 electrwd. group H2 1.008 0.135 H aliph. bond. to C with 2 electrwd.groups H3 1.008 0.135 H aliph. bond. to C with 3 eletrwd.groups HA 1.008 0.167 H arom. bond. to C without elctrwd. groups H4 1.008 0.167 H arom. bond. to C with 1 electrwd. group H5 1.008 0.167 H arom.at C with 2 elctrwd. gr,+HCOO group HO 1.008 0.135 hydroxyl group HS 1.008 0.135 hydrogen bonded to sulphur (pol?) HW 1.008 0.000 H in TIP3P water HP 1.008 0.135 H bonded to C next to positively charged gr HZ 1.008 0.161 H bond sp C (Howard et al.JCC,16,243,1995) F 19.00 0.320 fluorine Cl 35.45 1.910 chlorine (Applequist) Br 79.90 2.880 bromine (Applequist) I 126.9 4.690 iodine (Applequist) IM 35.45 3.235 assumed to be Cl- (ion minus) IB 131.0 'big ion w/ waters' for vacuum (Na+, 6H2O) MG 24.305 0.120 magnesium N 14.01 0.530 sp2 nitrogen in amide groups NA 14.01 0.530 sp2 N in 5 memb.ring w/H atom (HIS) NB 14.01 0.530 sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA) NC 14.01 0.530 sp2 N in 6 memb.ring w/LP (ADE,GUA) N2 14.01 0.530 sp2 N in amino groups N3 14.01 0.530 sp3 N for charged amino groups (Lys, etc) NT 14.01 0.530 sp3 N for amino groups amino groups N* 14.01 0.530 sp2 N NY 14.01 0.530 nitrile N (Howard et al.JCC,16,243,1995) O 16.00 0.434 carbonyl group oxygen O2 16.00 0.434 carboxyl and phosphate group oxygen OW 16.00 0.000 oxygen in TIP3P water OH 16.00 0.465 oxygen in hydroxyl group OS 16.00 0.465 ether and ester oxygen P 30.97 1.538 phosphate,pol:JACS,112,8543,90,K.J.Miller S 32.06 2.900 S in disulfide linkage,pol:JPC,102,2399,98 SH 32.06 2.900 S in cystine CU 63.55 copper FE 55.00 iron Li 6.94 0.029 lithium, ions pol:J.PhysC,11,1541,(1978) IP 22.99 0.250 assumed to be Na+ (ion plus) Na 22.99 0.250 Na+, ions pol:J.PhysC,11,1541,(1978) K 39.10 1.060 potassium Rb 85.47 rubidium Cs 132.91 cesium Zn 65.4 Zn2+ LP 3.00 0.000 lone pair C H HO N NA NB NC N2 NT N2 N3 N* O OH OS P O2 OW-HW 553.0 0.9572 ! TIP3P water HW-HW 553.0 1.5136 TIP3P water C -C 310.0 1.525 Junmei et al, 1999 C -CA 469.0 1.409 JCC,7,(1986),230; (not used any more in TYR) C -CB 447.0 1.419 JCC,7,(1986),230; GUA C -CM 410.0 1.444 JCC,7,(1986),230; THY,URA C -CT 317.0 1.522 JCC,7,(1986),230; AA C -N 490.0 1.335 JCC,7,(1986),230; AA C -N* 424.0 1.383 JCC,7,(1986),230; CYT,URA C -NA 418.0 1.388 JCC,7,(1986),230; GUA.URA C -NC 457.0 1.358 JCC,7,(1986),230; CYT C -O 570.0 1.229 JCC,7,(1986),230; AA,CYT,GUA,THY,URA C -O2 656.0 1.250 JCC,7,(1986),230; GLU,ASP C -OH 450.0 1.364 JCC,7,(1986),230; (not used any more for TYR) C -OS 450.0 1.323 Junmei et al, 1999 C -H4 367.0 1.080 Junmei et al, 1999 C -H5 367.0 1.080 Junmei et al, 1999 CA-CA 469.0 1.400 JCC,7,(1986),230; BENZENE,PHE,TRP,TYR CA-CB 469.0 1.404 JCC,7,(1986),230; ADE,TRP CA-CM 427.0 1.433 JCC,7,(1986),230; CYT CA-CN 469.0 1.400 JCC,7,(1986),230; TRP CA-CT 317.0 1.510 JCC,7,(1986),230; PHE,TYR CA-HA 367.0 1.080 changed from 340. bsd on C6H6 nmodes; PHE,TRP,TYR CA-H4 367.0 1.080 changed from 340. bsd on C6H6 nmodes; no assigned CA-N2 481.0 1.340 JCC,7,(1986),230; ARG,CYT,GUA CA-NA 427.0 1.381 JCC,7,(1986),230; GUA CA-NC 483.0 1.339 JCC,7,(1986),230; ADE,CYT,GUA CA-OH 450.0 1.364 substituted for C-OH in tyr CB-CB 520.0 1.370 JCC,7,(1986),230; ADE,GUA CB-N* 436.0 1.374 JCC,7,(1986),230; ADE,GUA CB-NB 414.0 1.391 JCC,7,(1986),230; ADE,GUA CB-NC 461.0 1.354 JCC,7,(1986),230; ADE,GUA CD-HA 367.0 1.080 Junmei et al, 1999 CD-CD 469.0 1.400 Junmei et al, 1999 CD-CM 549.0 1.350 Junmei et al, 1999 CD-CT 317.0 1.510 Junmei et al, 1999 CK-H5 367.0 1.080 changed from 340. bsd on C6H6 nmodes; ADE,GUA CK-N* 440.0 1.371 JCC,7,(1986),230; ADE,GUA CK-NB 529.0 1.304 JCC,7,(1986),230; ADE,GUA CM-CM 549.0 1.350 JCC,7,(1986),230; CYT,THY,URA CM-CT 317.0 1.510 JCC,7,(1986),230; THY CM-HA 367.0 1.080 changed from 340. bsd on C6H6 nmodes; CYT,URA CM-H4 367.0 1.080 changed from 340. bsd on C6H6 nmodes; CYT,URA CM-H5 367.0 1.080 changed from 340. bsd on C6H6 nmodes; not assigned CM-N* 448.0 1.365 JCC,7,(1986),230; CYT,THY,URA CM-OS 480.0 1.240 Junmei et al, 1999 CQ-H5 367.0 1.080 changed from 340. bsd on C6H6 nmodes; ADE CQ-NC 502.0 1.324 JCC,7,(1986),230; ADE CT-CT 310.0 1.526 JCC,7,(1986),230; AA, SUGARS CT-HC 340.0 1.090 changed from 331 bsd on NMA nmodes; AA, SUGARS CT-H1 340.0 1.090 changed from 331 bsd on NMA nmodes; AA, RIBOSE CT-H2 340.0 1.090 changed from 331 bsd on NMA nmodes; SUGARS CT-H3 340.0 1.090 changed from 331 bsd on NMA nmodes; not assigned CT-HP 340.0 1.090 changed from 331; AA-lysine, methyl ammonium cation CT-N* 337.0 1.475 JCC,7,(1986),230; ADE,CYT,GUA,THY,URA CT-N2 337.0 1.463 JCC,7,(1986),230; ARG CT-OH 320.0 1.410 JCC,7,(1986),230; SUGARS CT-OS 320.0 1.410 JCC,7,(1986),230; NUCLEIC ACIDS C*-HC 367.0 1.080 changed from 340. bsd on C6H6 nmodes, not needed AA C*-CB 388.0 1.459 JCC,7,(1986),230; TRP C*-CT 317.0 1.495 JCC,7,(1986),230; TRP C*-CW 546.0 1.352 JCC,7,(1986),230; TRP CB-CN 447.0 1.419 JCC,7,(1986),230; TRP CC-CT 317.0 1.504 JCC,7,(1986),230; HIS CC-CV 512.0 1.375 JCC,7,(1986),230; HIS(delta) CC-CW 518.0 1.371 JCC,7,(1986),230; HIS(epsilon) CC-NA 422.0 1.385 JCC,7,(1986),230; HIS CC-NB 410.0 1.394 JCC,7,(1986),230; HIS CN-NA 428.0 1.380 JCC,7,(1986),230; TRP CR-H5 367.0 1.080 changed from 340. bsd on C6H6 nmodes;HIS CR-NA 477.0 1.343 JCC,7,(1986),230; HIS CR-NB 488.0 1.335 JCC,7,(1986),230; HIS CT-N 337.0 1.449 JCC,7,(1986),230; AA CT-N3 367.0 1.471 JCC,7,(1986),230; LYS CT-NT 367.0 1.471 for neutral amines CT-S 227.0 1.810 changed from 222.0 based on dimethylS nmodes CT-SH 237.0 1.810 changed from 222.0 based on methanethiol nmodes CT-CY 400.0 1.458 Howard et al JCC.16,243,1995 CT-CZ 400.0 1.459 Howard et al JCC,16,243,1995 CV-H4 367.0 1.080 changed from 340. bsd on C6H6 nmodes; HIS CV-NB 410.0 1.394 JCC,7,(1986),230; HIS CW-H4 367.0 1.080 changed from 340. bsd on C6H6 nmodes;HIS(epsilon,+) CW-NA 427.0 1.381 JCC,7,(1986),230; HIS,TRP CY-NY 600.0 1.150 Howard et al JCC,16,243,1995 CZ-CZ 600.0 1.206 Howard et al JCC,16,243,1995 CZ-HZ 400.0 1.056 Howard et al JCC,16,243,1995 O2-P 525.0 1.480 JCC,7,(1986),230; NA PHOSPHATES OH-P 230.0 1.610 JCC,7,(1986),230; NA PHOSPHATES OS-P 230.0 1.610 JCC,7,(1986),230; NA PHOSPHATES H -N2 434.0 1.010 JCC,7,(1986),230; ADE,CYT,GUA,ARG H-N* 434.0 1.010 for plain unmethylated bases ADE,CYT,GUA,ARG H -NA 434.0 1.010 JCC,7,(1986),230; GUA,URA,HIS H -N 434.0 1.010 JCC,7,(1986),230; AA H -N3 434.0 1.010 JCC,7,(1986),230; LYS H -NT 434.0 1.010 for neutral amines HO-OH 553.0 0.960 JCC,7,(1986),230; SUGARS,SER,TYR HO-OS 553.0 0.960 JCC,7,(1986),230; NUCLEOTIDE ENDS HS-SH 274.0 1.336 JCC,7,(1986),230; CYS S -S 166.0 2.038 JCC,7,(1986),230; CYX (SCHERAGA) F -CT 367.0 1.380 JCC,13,(1992),963;CF4; R0=1.332 FOR CHF3 Cl-CT 232.0 1.766 6-31g* opt Br-CT 159.0 1.944 Junmei et al,99 I -CT 148.0 2.166 Junmei et al,99 F -CA 386.0 1.359 Junmei et al,99 Cl-CA 193.0 1.727 Junmei et al,99 I -CA 171.0 2.075 Junmei et al,99 Br-CA 172.0 1.890 Junmei et al,99 LP-O 600.0 0.200 or 0.35 LP-OH 600.0 0.200 or 0.35 LP-OS 600.0 0.200 or 0.35 LP-N3 600.0 0.200 or 0.35 LP-NT 600.0 0.200 or 0.35 LP-NB 600.0 0.200 or 0.35 histidines, nucleic acids LP-NC 600.0 0.200 or 0.35 nucleic acids LP-S 600.0 0.700 cys,cyx,met LP-SH 600.0 0.700 cys,cyx HW-OW-HW 100. 104.52 TIP3P water HW-HW-OW 0. 127.74 (found in crystallographic water with 3 bonds) C -C -O 80.0 120.00 Junmei et al, 1999 acrolein C -C -OH 80.0 120.00 Junmei et al, 1999 CA-C -CA 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes; AA CA-C -OH 70.0 120.00 AA (not used in tyr) CB-C -NA 70.0 111.30 NA CB-C -O 80.0 128.80 CM-C -NA 70.0 114.10 CM-C -O 80.0 125.30 CT-C -O 80.0 120.40 CT-C -O2 70.0 117.00 CT-C -N 70.0 116.60 AA general CT-C -CT 63.0 117.00 Junmei et al, 1999 CT-C -OS 80.0 115.00 Junmei et al, 1999 CT-C -OH 80.0 110.00 Junmei et al, 1999 N*-C -NA 70.0 115.40 N*-C -NC 70.0 118.60 N*-C -O 80.0 120.90 NA-C -O 80.0 120.60 NC-C -O 80.0 122.50 N -C -O 80.0 122.90 AA general O -C -O 80.0 126.00 AA COO- terminal residues O -C -OH 80.0 120.00 (check with Junmei for: theta0:120.0?) O -C -OS 80.0 125.00 Junmei et al, 1999 O2-C -O2 80.0 126.00 AA GLU (SCH JPC 79,2379) H4-C -C 50.0 120.00 Junmei et al, 1999 H4-C -CM 50.0 115.00 Junmei et al, 1999 H4-C -CT 50.0 115.00 Junmei et al, 1999 H4-C -O 50.0 120.00 Junmei et al, 1999 H4-C -OH 50.0 120.00 Junmei et al, 1999 H5-C -N 50.0 120.00 Junmei et al, 1999 H5-C -O 50.0 119.00 Junmei et al, 1999 H5-C -OH 50.0 107.00 Junmei et al, 1999 H5-C -OS 50.0 107.00 Junmei et al, 1999 C -CA-CA 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes C -CA-HA 50.0 120.00 AA (not used in tyr) CA-CA-CA 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes CA-CA-CB 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes CA-CA-CT 70.0 120.00 CA-CA-HA 50.0 120.00 CA-CA-H4 50.0 120.00 CA-CA-OH 70.0 120.00 replacement in tyr CA-CA-CN 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes; AA trp CB-CA-HA 50.0 120.00 CB-CA-H4 50.0 120.00 CB-CA-N2 70.0 123.50 CB-CA-NC 70.0 117.30 CM-CA-N2 70.0 120.10 CM-CA-NC 70.0 121.50 CN-CA-HA 50.0 120.00 AA trp NA-CA-NC 70.0 123.30 N2-CA-NA 70.0 116.00 N2-CA-NC 70.0 119.30 N2-CA-N2 70.0 120.00 AA arg F -CA-CA 70.0 121.00 Junmei et al,99 Cl-CA-CA 70.0 118.80 Junmei et al,99 Br-CA-CA 70.0 118.80 Junmei et al,99 I -CA-CA 70.0 118.80 Junmei et al,99 C -CB-CB 63.0 119.20 changed from 85.0 bsd on C6H6 nmodes; NA gua C -CB-NB 70.0 130.00 CA-CB-CB 63.0 117.30 changed from 85.0 bsd on C6H6 nmodes; NA ade CA-CB-NB 70.0 132.40 CB-CB-N* 70.0 106.20 CB-CB-NB 70.0 110.40 CB-CB-NC 70.0 127.70 C*-CB-CA 63.0 134.90 changed from 85.0 bsd on C6H6 nmodes; AA trp C*-CB-CN 63.0 108.80 changed from 85.0 bsd on C6H6 nmodes; AA trp CA-CB-CN 63.0 116.20 changed from 85.0 bsd on C6H6 nmodes; AA trp N*-CB-NC 70.0 126.20 CD-CD-CM 63.0 120.00 Junmei et al, 1999 CD-CD-CT 70.0 120.00 Junmei et al, 1999 CM-CD-CT 70.0 120.00 Junmei et al, 1999 HA-CD-HA 35.0 119.00 Junmei et al, 1999 HA-CD-CD 50.0 120.00 Junmei et al, 1999 HA-CD-CM 50.0 120.00 Junmei et al, 1999 H5-CK-N* 50.0 123.05 H5-CK-NB 50.0 123.05 N*-CK-NB 70.0 113.90 C -CM-CM 63.0 120.70 changed from 85.0 bsd on C6H6 nmodes; NA thy C -CM-CT 70.0 119.70 C -CM-HA 50.0 119.70 C -CM-H4 50.0 119.70 CA-CM-CM 63.0 117.00 changed from 85.0 bsd on C6H6 nmodes; NA cyt CA-CM-HA 50.0 123.30 CA-CM-H4 50.0 123.30 CM-CM-CT 70.0 119.70 CM-CM-HA 50.0 119.70 CM-CM-H4 50.0 119.70 CM-CM-N* 70.0 121.20 CM-CM-OS 80.0 125.00 Junmei et al, 1999 H4-CM-N* 50.0 119.10 H4-CM-OS 50.0 113.00 Junmei et al, 1999 HA-CM-HA 35.0 120.00 Junmei et al, 1999 HA-CM-CD 50.0 120.00 Junmei et al, 1999 HA-CM-CT 50.0 120.00 Junmei et al, 1999 NC-CQ-NC 70.0 129.10 H5-CQ-NC 50.0 115.45 H1-CT-H1 35.0 109.50 H1-CT-N* 50.0 109.50 changed based on NMA nmodes H1-CT-OH 50.0 109.50 changed based on NMA nmodes H1-CT-OS 50.0 109.50 changed based on NMA nmodes H1-CT-CM 50.0 109.50 Junmei et al, 1999 H1-CT-CY 50.0 110.00 Junmei et al, 1999 H1-CT-CZ 50.0 110.00 Junmei et al, 1999 H1-CT-N 50.0 109.50 AA general changed based on NMA nmodes H1-CT-S 50.0 109.50 AA cys changed based on NMA nmodes H1-CT-SH 50.0 109.50 AA cyx changed based on NMA nmodes H1-CT-N2 50.0 109.50 AA arg changed based on NMA nmodes H1-CT-NT 50.0 109.50 neutral amines H2-CT-H2 35.0 109.50 AA lys H2-CT-N* 50.0 109.50 changed based on NMA nmodes H2-CT-OS 50.0 109.50 changed based on NMA nmodes HP-CT-HP 35.0 109.50 AA lys, ch3nh4+ HP-CT-N3 50.0 109.50 AA lys, ch3nh3+, changed based on NMA nmodes HC-CT-HC 35.0 109.50 HC-CT-CM 50.0 109.50 changed based on NMA nmodes HC-CT-CD 50.0 109.50 Junmei et al, 1999 HC-CT-CZ 50.0 110.00 Junmei et al, 1999 C -CT-H1 50.0 109.50 AA general changed based on NMA nmodes C -CT-HP 50.0 109.50 AA zwitterion changed based on NMA nmodes C -CT-HC 50.0 109.50 AA gln changed based on NMA nmodes C -CT-N 63.0 110.10 AA general C -CT-N3 80.0 111.20 AA amino terminal residues C -CT-CT 63.0 111.10 AA general C -CT-OS 60.0 109.50 Junmei et al, 1999 CA-CT-HC 50.0 109.50 AA tyr changed based on NMA nmodes CC-CT-CT 63.0 113.10 AA his CC-CT-HC 50.0 109.50 AA his changed based on NMA nmodes CM-CT-CT 63.0 111.00 Junmei et al, 1999 (last change: Mar24,99) CM-CT-OS 50.0 109.50 Junmei et al, 1999 CT-CT-CT 40.0 109.50 CT-CT-HC 50.0 109.50 changed based on NMA nmodes CT-CT-H1 50.0 109.50 changed based on NMA nmodes CT-CT-H2 50.0 109.50 changed based on NMA nmodes CT-CT-HP 50.0 109.50 changed based on NMA nmodes CT-CT-N* 50.0 109.50 CT-CT-OH 50.0 109.50 CT-CT-OS 50.0 109.50 CT-CT-S 50.0 114.70 AA cyx (SCHERAGA JPC 79,1428) CT-CT-SH 50.0 108.60 AA cys CT-CT-CA 63.0 114.00 AA phe tyr (SCH JPC 79,2379) CT-CT-N2 80.0 111.20 AA arg (JCP 76, 1439) CT-CT-N 80.0 109.70 AA ala, general (JACS 94, 2657) CT-CT-N3 80.0 111.20 AA lys (JCP 76, 1439) CT-CT-NT 80.0 111.20 neutral amines CT-CT-CY 63.0 110.00 Junmei et al, 1999 CT-CT-CZ 63.0 110.00 Junmei et al, 1999 C*-CT-CT 63.0 115.60 AA trp C*-CT-HC 50.0 109.50 AA trp changed based on NMA nmodes OS-CT-OS 160.0 101.00 Junmei et al, 1999 OS-CT-CY 50.0 110.00 Junmei et al, 1999 OS-CT-CZ 50.0 110.00 Junmei et al, 1999 OS-CT-CZ 50.0 110.00 Junmei et al, 1999 OS-CT-CY 50.0 110.00 Junmei et al, 1999 OS-CT-N* 50.0 109.50 F -CT-F 77.0 109.10 JCC,13,(1992),963; F -CT-H1 50.0 109.50 JCC,13,(1992),963; F -CT-CT 50.0 109.00 F -CT-H2 50.0 109.50 Cl-CT-CT 50.0 108.50 (6-31g* opt value) Cl-CT-H1 50.0 108.50 (6-31g* opt value) Br-CT-CT 50.0 108.00 Junmei et al 99 Br-CT-H1 50.0 106.50 Junmei et al 99 I -CT-CT 50.0 106.00 Junmei et al,99 CT-CC-NA 70.0 120.00 AA his CT-CC-CV 70.0 120.00 AA his CT-CC-NB 70.0 120.00 AA his CV-CC-NA 70.0 120.00 AA his CW-CC-NA 70.0 120.00 AA his CW-CC-NB 70.0 120.00 AA his CT-CC-CW 70.0 120.00 AA his H5-CR-NA 50.0 120.00 AA his H5-CR-NB 50.0 120.00 AA his NA-CR-NA 70.0 120.00 AA his NA-CR-NB 70.0 120.00 AA his CC-CV-H4 50.0 120.00 AA his CC-CV-NB 70.0 120.00 AA his H4-CV-NB 50.0 120.00 AA his CC-CW-H4 50.0 120.00 AA his CC-CW-NA 70.0 120.00 AA his C*-CW-H4 50.0 120.00 AA trp C*-CW-NA 70.0 108.70 AA trp H4-CW-NA 50.0 120.00 AA his CB-C*-CT 70.0 128.60 AA trp CB-C*-CW 63.0 106.40 changed from 85.0 bsd on C6H6 nmodes; AA trp CT-C*-CW 70.0 125.00 AA trp CA-CN-CB 63.0 122.70 changed from 85.0 bsd on C6H6 nmodes; AA trp CA-CN-NA 70.0 132.80 AA trp CB-CN-NA 70.0 104.40 AA trp CT-CY-NY 80.0 180.00 Junmei et al, 1999 CT-CZ-CZ 80.0 180.00 Junmei et al, 1999 CZ-CZ-HZ 50.0 180.00 Junmei et al, 1999 C -N -CT 50.0 121.90 AA general C -N -H 50.0 120.00 AA general, gln, asn,changed based on NMA nmodes CT-N -H 50.0 118.04 AA general, changed based on NMA nmodes CT-N -CT 50.0 118.00 AA pro (DETAR JACS 99,1232) H -N -H 35.0 120.00 ade,cyt,gua,gln,asn ** C -N*-CM 70.0 121.60 C -N*-CT 70.0 117.60 C -N*-H 50.0 119.20 changed based on NMA nmodes CB-N*-CK 70.0 105.40 CB-N*-CT 70.0 125.80 CB-N*-H 50.0 125.80 for unmethylated n.a. bases,chngd bsd NMA nmodes CK-N*-CT 70.0 128.80 CK-N*-H 50.0 128.80 for unmethylated n.a. bases,chngd bsd NMA nmodes CM-N*-CT 70.0 121.20 CM-N*-H 50.0 121.20 for unmethylated n.a. bases,chngd bsd NMA nmodes CA-N2-H 50.0 120.00 CA-N2-CT 50.0 123.20 AA arg CT-N2-H 50.0 118.40 AA arg H -N2-H 35.0 120.00 CT-N3-H 50.0 109.50 AA lys, changed based on NMA nmodes CT-N3-CT 50.0 109.50 AA pro/nt H -N3-H 35.0 109.50 AA lys, AA(end) CT-NT-H 50.0 109.50 neutral amines CT-NT-CT 50.0 109.50 neutral amines H -NT-H 35.0 109.50 neutral amines C -NA-C 70.0 126.40 C -NA-CA 70.0 125.20 C -NA-H 50.0 116.80 changed based on NMA nmodes CA-NA-H 50.0 118.00 changed based on NMA nmodes CC-NA-CR 70.0 120.00 AA his CC-NA-H 50.0 120.00 AA his, changed based on NMA nmodes CR-NA-CW 70.0 120.00 AA his CR-NA-H 50.0 120.00 AA his, changed based on NMA nmodes CW-NA-H 50.0 120.00 AA his, changed based on NMA nmodes CN-NA-CW 70.0 111.60 AA trp CN-NA-H 50.0 123.10 AA trp, changed based on NMA nmodes CB-NB-CK 70.0 103.80 CC-NB-CR 70.0 117.00 AA his CR-NB-CV 70.0 117.00 AA his C -NC-CA 70.0 120.50 CA-NC-CB 70.0 112.20 CA-NC-CQ 70.0 118.60 CB-NC-CQ 70.0 111.00 C -OH-HO 50.0 113.00 (not used in tyr anymore) CA-OH-HO 50.0 113.00 replacement in tyr CT-OH-HO 55.0 108.50 HO-OH-P 45.0 108.50 C -OS-CT 60.0 117.00 Junmei et al, 1999 CM-OS-CT 60.0 117.00 Junmei et al, 1999 CT-OS-CT 60.0 109.50 CT-OS-P 100.0 120.50 P -OS-P 100.0 120.50 O2-P -OH 45.0 108.23 O2-P -O2 140.0 119.90 O2-P -OS 100.0 108.23 OH-P -OS 45.0 102.60 OS-P -OS 45.0 102.60 CT-S -CT 62.0 98.90 AA met CT-S -S 68.0 103.70 AA cyx (SCHERAGA JPC 79,1428) CT-SH-HS 43.0 96.00 changed from 44.0 based on methanethiol nmodes HS-SH-HS 35.0 92.07 AA cys CB-NB-LP 150.0 126.0 NA CC-NB-LP 150.0 126.0 his,NA CK-NB-LP 150.0 126.0 NA CR-NB-LP 150.0 126.0 his,NA CV-NB-LP 150.0 126.0 his,NA C -NC-LP 150.0 120.0 NA CA-NC-LP 150.0 120.0 NA CB-NC-LP 150.0 120.0 NA CQ-NC-LP 150.0 120.0 NA CT-N3-LP 150.0 109.5 in neutral lysine H -N3-LP 150.0 109.5 in neutral lysine CT-NT-LP 150.0 109.5 H -NT-LP 150.0 109.5 C -O -LP 150.0 120.0 LP-O -LP 150.0 120.0 C -OH-LP 150.0 120.0 CT-OH-LP 150.0 109.5 HO-OH-LP 150.0 109.5 LP-OH-LP 150.0 109.5 C -OS-LP 150.0 109.5 CM-OS-LP 150.0 109.5 methyl vinyl ether CT-OS-LP 150.0 109.5 LP-OS-LP 150.0 109.5 CT-S -LP 150.0 90.0 cys,cyx,met CT-SH-LP 150.0 90.0 cys,cyx,met P -OS-LP 150.0 109.5 NA LP-S -LP 150.0 180.0 cys,cyx,met LP-SH-LP 150.0 180.0 cys,cyx,met HS-SH-LP 150.0 90.0 cys X -C -C -X 4 14.50 180.0 2. Junmei et al, 1999 X -C -CA-X 4 14.50 180.0 2. intrpol.bsd.on C6H6 X -C -CB-X 4 12.00 180.0 2. intrpol.bsd.on C6H6 X -C -CM-X 4 8.70 180.0 2. intrpol.bsd.on C6H6 X -C -CT-X 6 0.00 0.0 2. JCC,7,(1986),230 X -C -N -X 4 10.00 180.0 2. AA,NMA X -C -N*-X 4 5.80 180.0 2. JCC,7,(1986),230 X -C -NA-X 4 5.40 180.0 2. JCC,7,(1986),230 X -C -NC-X 2 8.00 180.0 2. JCC,7,(1986),230 X -C -O -X 4 11.20 180.0 2. Junmei et al, 1999 X -C -OH-X 2 4.60 180.0 2. Junmei et al, 1999 X -C -OS-X 2 5.40 180.0 2. Junmei et al, 1999 X -CA-CA-X 4 14.50 180.0 2. intrpol.bsd.on C6H6 X -CA-CB-X 4 14.00 180.0 2. intrpol.bsd.on C6H6 X -CA-CM-X 4 10.20 180.0 2. intrpol.bsd.on C6H6 X -CA-CN-X 4 14.50 180.0 2. reinterpolated 93' X -CA-CT-X 6 0.00 0.0 2. JCC,7,(1986),230 X -CA-N2-X 4 9.60 180.0 2. reinterpolated 93' X -CA-NA-X 4 6.00 180.0 2. JCC,7,(1986),230 X -CA-NC-X 2 9.60 180.0 2. JCC,7,(1986),230 X -CA-OH-X 2 1.80 180.0 2. Junmei et al, 99 X -CB-CB-X 4 21.80 180.0 2. intrpol.bsd.on C6H6 X -CB-CN-X 4 12.00 180.0 2. reinterpolated 93' X -CB-N*-X 4 6.60 180.0 2. JCC,7,(1986),230 X -CB-NB-X 2 5.10 180.0 2. JCC,7,(1986),230 X -CB-NC-X 2 8.30 180.0 2. JCC,7,(1986),230 X -CC-CT-X 6 0.00 0.0 2. JCC,7,(1986),230 X -CC-CV-X 4 20.60 180.0 2. intrpol.bsd.on C6H6 X -CC-CW-X 4 21.50 180.0 2. intrpol.bsd.on C6H6 X -CC-NA-X 4 5.60 180.0 2. JCC,7,(1986),230 X -CC-NB-X 2 4.80 180.0 2. JCC,7,(1986),230 X -CD-CD-X 4 4.00 180.0 2. Junmei et al, 1999 X -CD-CT-X 6 0.00 0.0 2. Junmei et al, 1999 X -CD-CM-X 4 26.60 180.0 2. Junmei et al, 1999 X -CK-N*-X 4 6.80 180.0 2. JCC,7,(1986),230 X -CK-NB-X 2 20.00 180.0 2. JCC,7,(1986),230 X -CM-CM-X 4 26.60 180.0 2. intrpol.bsd.on C6H6 X -CM-CT-X 6 0.00 0.0 3. JCC,7,(1986),230 X -CM-N*-X 4 7.40 180.0 2. JCC,7,(1986),230 X -CM-OS-X 2 2.10 180.0 2. Junmei et al, 1999 X -CN-NA-X 4 6.10 180.0 2. reinterpolated 93' X -CQ-NC-X 2 13.60 180.0 2. JCC,7,(1986),230 X -CT-CT-X 9 1.40 0.0 3. JCC,7,(1986),230 X -CT-CY-X 3 0.00 0.0 1. Junmei et al, 1999 X -CT-CZ-X 3 0.00 0.0 1. Junmei et al, 1999 X -CT-N -X 6 0.00 0.0 2. JCC,7,(1986),230 X -CT-N*-X 6 0.00 0.0 2. JCC,7,(1986),230 X -CT-N2-X 6 0.00 0.0 3. JCC,7,(1986),230 X -CT-NT-X 6 1.80 0.0 3. Junmei et al, 1999 X -CT-N3-X 9 1.40 0.0 3. JCC,7,(1986),230 X -CT-OH-X 3 0.50 0.0 3. JCC,7,(1986),230 X -CT-OS-X 3 1.15 0.0 3. JCC,7,(1986),230 X -CT-S -X 3 1.00 0.0 3. JCC,7,(1986),230 X -CT-SH-X 3 0.75 0.0 3. JCC,7,(1986),230 X -C*-CB-X 4 6.70 180.0 2. intrpol.bsd.onC6H6aa X -C*-CT-X 6 0.00 0.0 2. JCC,7,(1986),230 X -C*-CW-X 4 26.10 180.0 2. intrpol.bsd.on C6H6 X -CR-NA-X 4 9.30 180.0 2. JCC,7,(1986),230 X -CR-NB-X 2 10.00 180.0 2. JCC,7,(1986),230 X -CV-NB-X 2 4.80 180.0 2. JCC,7,(1986),230 X -CW-NA-X 4 6.00 180.0 2. JCC,7,(1986),230 X -OH-P -X 3 0.75 0.0 3. JCC,7,(1986),230 X -OS-P -X 3 0.75 0.0 3. JCC,7,(1986),230 N -CT-C -N 1 1.700 180.000 -1. N -CT-C -N 1 2.000 180.000 2. C -N -CT-C 1 0.850 180.000 -2. C -N -CT-C 1 0.800 0.000 1. CT-CT-N -C 1 0.50 180.0 -4. phi,psi,parm94 CT-CT-N -C 1 0.15 180.0 -3. phi,psi,parm94 CT-CT-N -C 1 0.53 0.0 1. phi,psi,parm94 CT-CT-C -N 1 0.100 0.0 -4. phi,psi,parm94 CT-CT-C -N 1 0.07 0.0 2. phi,psi,parm94 H -N -C -O 1 2.50 180.0 -2. JCC,7,(1986),230 H -N -C -O 1 2.00 0.0 1. J.C.cistrans-NMA DE CT-S -S -CT 1 3.50 0.0 -2. JCC,7,(1986),230 CT-S -S -CT 1 0.60 0.0 3. JCC,7,(1986),230 OH-P -OS-CT 1 0.25 0.0 -3. JCC,7,(1986),230 OH-P -OS-CT 1 1.20 0.0 2. gg> ene.631g*/mp2 OS-P -OS-CT 1 0.25 0.0 -3. JCC,7,(1986),230 OS-P -OS-CT 1 1.20 0.0 2. gg> ene.631g*/mp2 H1-CT-C -O 1 0.80 0.0 -1. Junmei et al, 1999 H1-CT-C -O 1 0.08 180.0 3. Junmei et al, 1999 HC-CT-C -O 1 0.80 0.0 -1. Junmei et al, 1999 HC-CT-C -O 1 0.08 180.0 3. Junmei et al, 1999 HC-CT-CT-HC 1 0.15 0.0 3. Junmei et al, 1999 HC-CT-CT-CT 1 0.16 0.0 3. Junmei et al, 1999 HC-CT-CM-CM 1 0.38 180.0 -3. Junmei et al, 1999 HC-CT-CM-CM 1 1.15 0.0 1. Junmei et al, 1999 HO-OH-CT-CT 1 0.16 0.0 -3. Junmei et al, 1999 HO-OH-CT-CT 1 0.25 0.0 1. Junmei et al, 1999 HO-OH-C -O 1 2.30 180.0 -2. Junmei et al, 1999 HO-OH-C -O 1 1.90 0.0 1. Junmei et al, 1999 CM-CM-C -O 1 2.175 180.0 -2. Junmei et al, 1999 CM-CM-C -O 1 0.30 0.0 3. Junmei et al, 1999 CT-CM-CM-CT 1 6.65 180.0 -2. Junmei et al, 1999 CT-CM-CM-CT 1 1.90 180.0 1. Junmei et al, 1999 CT-CT-CT-CT 1 0.18 0.0 -3. Junmei et al, 1999 CT-CT-CT-CT 1 0.25 180.0 -2. Junmei et al, 1999 CT-CT-CT-CT 1 0.20 180.0 1. Junmei et al, 1999 CT-CT-NT-CT 1 0.30 0.0 -3. Junmei et al, 1999 CT-CT-NT-CT 1 0.48 180.0 2. Junmei et al, 1999 CT-CT-OS-CT 1 0.383 0.0 -3. CT-CT-OS-CT 1 0.1 180.0 2. CT-CT-OS-C 1 0.383 0.0 -3. Junmei et al, 1999 CT-CT-OS-C 1 0.80 180.0 1. Junmei et al, 1999 CT-OS-CT-OS 1 0.10 0.0 -3. Junmei et al, 1999 CT-OS-CT-OS 1 0.85 180.0 -2. Junmei et al, 1999 CT-OS-CT-OS 1 1.35 180.0 1. Junmei et al, 1999 CT-OS-CT-N* 1 0.383 0.0 -3. parm98.dat, TC,PC,PAK CT-OS-CT-N* 1 0.65 0.0 2. Piotr et al. CT-CZ-CZ-HZ 1 0.00 0.0 1. Junmei et al, 1999 O -C -OS-CT 1 2.70 180.0 -2. Junmei et al, 1999 O -C -OS-CT 1 1.40 180.0 1. Junmei et al, 1999 OS-CT-N*-CK 1 0.00 000.0 -2. parm98, TC,PC,PAK OS-CT-N*-CK 1 2.50 0.0 1. parm98, TC,PC,PAK OS-CT-N*-CM 1 0.00 000.0 -2. parm98, TC,PC,PAK OS-CT-N*-CM 1 2.50 0.0 1. parm98, TC,PC,PAK OS-CT-CT-OS 1 0.144 0.0 -3. parm98, TC,PC,PAK OS-CT-CT-OS 1 1.175 0.0 2. Piotr et al. OS-CT-CT-OH 1 0.144 0.0 -3. parm98, TC,PC,PAK OS-CT-CT-OH 1 1.175 0.0 2. parm98, TC,PC,PAK OH-CT-CT-OH 1 0.144 0.0 -3. parm98, TC,PC,PAK OH-CT-CT-OH 1 1.175 0.0 2. parm98, TC,PC,PAK F -CT-CT-F 1 1.20 180.0 1. Junmei et al, 1999 Cl-CT-CT-Cl 1 0.45 180.0 1. Junmei et al, 1999 Br-CT-CT-Br 1 0.00 180.0 1. Junmei et al, 1999 H1-CT-CT-OS 1 0.25 0.0 1. Junmei et al, 1999 H1-CT-CT-OH 1 0.25 0.0 1. Junmei et al, 1999 H1-CT-CT-F 1 0.19 0.0 1. Junmei et al, 1999 H1-CT-CT-Cl 1 0.25 0.0 1. Junmei et al, 1999 H1-CT-CT-Br 1 0.55 0.0 1. Junmei et al, 1999 HC-CT-CT-OS 1 0.25 0.0 1. Junmei et al, 1999 HC-CT-CT-OH 1 0.25 0.0 1. Junmei et al, 1999 HC-CT-CT-F 1 0.19 0.0 1. Junmei et al, 1999 HC-CT-CT-Cl 1 0.25 0.0 1. Junmei et al, 1999 HC-CT-CT-Br 1 0.55 0.0 1. Junmei et al, 1999 H1-CT-NT-LP 1 0.000 0.000 3.000 CT-CT-NT-LP 1 0.000 0.000 3.000 CT-C -N -LP 1 0.000 180.000 2.000 O -C -N -LP 1 0.000 180.000 2.000 H1-CT-OH-LP 1 0.000 0.000 3.000 CT-CT-OH-LP 1 0.000 0.000 3.000 H1-CT-OS-LP 1 0.000 0.000 3.000 H2-CT-OS-LP 1 0.000 0.000 3.000 CT-CT-OS-LP 1 0.000 0.000 3.000 CM-CM-OS-LP 1 0.000 180.000 2.000 HA-CM-OS-LP 1 0.000 180.000 2.000 H4-CM-OS-LP 1 0.000 180.000 2.000 X -X -C -O 10.5 180. 2. JCC,7,(1986),230 X -O2-C -O2 10.5 180. 2. JCC,7,(1986),230 X -X -N -H 1.0 180. 2. JCC,7,(1986),230 X -X -N2-H 1.0 180. 2. JCC,7,(1986),230 X -X -NA-H 1.0 180. 2. JCC,7,(1986),230 X -N2-CA-N2 10.5 180. 2. JCC,7,(1986),230 X -CT-N -CT 1.0 180. 2. JCC,7,(1986),230 X -X -CA-HA 1.1 180. 2. bsd.on C6H6 nmodes X -X -CW-H4 1.1 180. 2. X -X -CR-H5 1.1 180. 2. X -X -CV-H4 1.1 180. 2. X -X -CQ-H5 1.1 180. 2. X -X -CK-H5 1.1 180. 2. X -X -CM-H4 1.1 180. 2. X -X -CM-HA 1.1 180. 2. X -X -CA-H4 1.1 180. 2. bsd.on C6H6 nmodes X -X -CA-H5 1.1 180. 2. bsd.on C6H6 nmodes CK-CB-N*-CT 1.0 180. 2. CM-C -N*-CT 1.0 180. 2. dac guess, 9/94 CM-C -CM-CT 1.1 180. 2. CT-O -C -OH 10.5 180. 2. NA-CV-CC-CT 1.1 180. 2. NB-CW-CC-CT 1.1 180. 2. NA-CW-CC-CT 1.1 180. 2. CW-CB-C*-CT 1.1 180. 2. CA-CA-CA-CT 1.1 180. 2. C -CM-CM-CT 1.1 180. 2. dac guess, 9/94 NC-CM-CA-N2 1.1 180. 2. dac guess, 9/94 CB-NC-CA-N2 1.1 180. 2. dac, 10/94 NA-NC-CA-N2 1.1 180. 2. dac, 10/94 CA-CA-C -OH 1.1 180. 2. (not used in tyr!) CA-CA-CA-OH 1.1 180. 2. in tyr H5-O -C -OH 1.1 180. 2. Junmei et al.1999 H5-O -C -OS 1.1 180. 2. CM-CT-CM-HA 1.1 180. 2. Junmei et al.1999 CA-CA-CA-Br 1.1 180. 2. Junmei et al.1999 CM-H4-C -O 1.1 180. 2. Junmei et al.1999 C -CT-N -H 1.1 180. 2. Junmei et al.1999 C -CT-N -O 1.1 180. 2. Junmei et al.1999 HW OW 0000. 0000. 4. flag for fast water N NA N2 N* NC NB NT NP NO NY C* CA CB CC CD CK CM CN CQ CR CV CW CX CY CZ MOD4 RE H 0.6000 0.0157 !Ferguson base pair geom. HO 0.0000 0.0000 OPLS Jorgensen, JACS,110,(1988),1657 HS 0.6000 0.0157 W. Cornell CH3SH --> CH3OH FEP HC 1.4870 0.0157 OPLS H1 1.3870 0.0157 Veenstra et al JCC,8,(1992),963 H2 1.2870 0.0157 Veenstra et al JCC,8,(1992),963 H3 1.1870 0.0157 Veenstra et al JCC,8,(1992),963 HP 1.1000 0.0157 Veenstra et al JCC,8,(1992),963 HA 1.4590 0.0150 Spellmeyer H4 1.4090 0.0150 Spellmeyer, one electrowithdr. neighbor H5 1.3590 0.0150 Spellmeyer, two electrowithdr. neighbor HW 0.0000 0.0000 TIP3P water model HZ 1.4590 0.0150 H bonded to sp C (Howard et al JCC 16) O 1.6612 0.2100 OPLS O2 1.6612 0.2100 OPLS OW 1.7683 0.1520 TIP3P water model OH 1.7210 0.2104 OPLS OS 1.6837 0.1700 OPLS ether C* 1.9080 0.0860 Spellmeyer CT 1.9080 0.1094 Spellmeyer C 1.9080 0.0860 OPLS N 1.8240 0.1700 OPLS N3 1.8240 0.1700 OPLS NY 1.8240 0.1700 N in nitrile S 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's SH 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's P 2.1000 0.2000 JCC,7,(1986),230; IM 2.47 0.1 Cl- Smith & Dang, JCP 1994,100:5,3757 Li 1.1370 0.0183 Li+ Aqvist JPC 1990,94,8021. (adapted) IP 1.8680 0.00277 Na+ Aqvist JPC 1990,94,8021. (adapted) Na 1.8680 0.00277 Na+ Aqvist JPC 1990,94,8021. (adapted) K 2.6580 0.000328 K+ Aqvist JPC 1990,94,8021. (adapted) Rb 2.9560 0.00017 Rb+ Aqvist JPC 1990,94,8021. (adapted) Cs 3.3950 0.0000806 Cs+ Aqvist JPC 1990,94,8021. (adapted) MG 0.7926 0.8947 Mg2+ Aqvist JPC 1990,94,8021.(adapted) C0 1.7131 0.459789 Ca2+ Aqvist JPC 1990,94,8021.(adapted) Zn 1.10 0.0125 Zn2+, Merz,PAK, JACS,113,8262,(1991) F 1.75 0.061 Gough et al. JCC 13,(1992),963. Cl 1.948 0.265 Fox, JPCB,102,8070,(98),flex.mdl CHCl3 Br 2.22 0.320 Junmei(?) I 2.35 0.40 JCC,7,(1986),230; IB 5.0 0.1 solvated ion for vacuum approximation LP 0.00 0.0000 lone pair END #################################################### Polarizabilities: Mg2+ 0.120 F- 0.9743 additional parameters of LP H1-CT-NT-LP 1 0.000 0.000 3.000 CT-CT-NT-LP 1 0.000 0.000 3.000 CT-C -N -LP 1 0.000 180.000 2.000 O -C -N -LP 1 0.000 180.000 2.000 H1-CT-OH-LP 1 0.000 0.000 3.000 CT-CT-OH-LP 1 0.000 0.000 3.000 H1-CT-OS-LP 1 0.000 0.000 3.000 H2-CT-OS-LP 1 0.000 0.000 3.000 CT-CT-OS-LP 1 0.000 0.000 3.000 CM-CM-OS-LP 1 0.000 180.000 2.000 HA-CM-OS-LP 1 0.000 180.000 2.000 H4-CM-OS-LP 1 0.000 180.000 2.000