SI1
PARM99 modified by Carlos Simmerling
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 0.135 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 0.465 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
SI2
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
SI3
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
SI4
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
SI5
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
SI6
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;
SI7
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)
SI8
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
SI9
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-ZC-X 3 0.00 0.0 1. Junmei et al, 1999
SI10
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 0.700 180.0 -1. carlos ala3 refit
N -CT-C -N 1 1.100 180.0 2. carlos ala3 refit
C -N -CT-C 1 1.000 0.000 1. carlos ala3 refit
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&gt 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&gt 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.
SI11
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.
SI12
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 N3 NT NP NO NY
C C* CA CB CC CN CM CK CQ CW CV CR CA CX CY CD 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
CD 1.9080 0.0860 sp2 atom in the middle of C=CD-CD=C
CT 1.9080 0.1094 Spellmeyer
CA 1.9080 0.0860 Spellmeyer
SI13
CM 1.9080 0.0860 Spellmeyer
CY 1.9080 0.0860 sp C in nitrile
CZ 1.9080 0.0860 cp C
C 1.9080 0.0860 OPLS
N 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