/usr/share/pymol/data/chempy/tinker/parm94_rsm.dat is in pymol-data 1.8.4.0+dfsg-1.
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BR 79.90 ! bromine
C 12.01 sp2 C carbonyl group
CA 12.01 sp2 C pure aromatic (benzene)
CB 12.01 sp2 aromatic C, 5&6 membered ring junction
CC 12.01 sp2 aromatic C, 5 memb. ring HIS
CF 12.01 sp2 aromatic C, 5 memb. ring furan (RSM)
CK 12.01 sp2 C 5 memb.ring in purines
CM 12.01 sp2 C pyrimidines in pos. 5 & 6
CN 12.01 sp2 C aromatic 5&6 memb.ring junct.(TRP)
CQ 12.01 sp2 C in 5 mem.ring of purines between 2 N
CR 12.01 sp2 arom as CQ but in HIS
CT 12.01 sp3 aliphatic C
CV 12.01 sp2 arom. 5 memb.ring w/1 N and 1 H (HIS)
CW 12.01 sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS)
CY 12.01 general sp carbon (RSM)
CX 12.01 general sp2 carbon (RSM)
C5 12.01 general sp2 carbon in 5-mem ring (RSM)
C* 12.01 sp2 arom. 5 memb.ring w/1 subst. (TRP)
C0 40.08 calcium
Cl 35.45 Cl (aromatic)
F 19.00 fluorine
H 1.008 H bonded to nitrogen atoms
HC 1.008 H aliph. bond. to C without electrwd.group
H1 1.008 H aliph. bond. to C with 1 electrwd. group
H2 1.008 H aliph. bond. to C with 2 electrwd.groups
H3 1.008 H aliph. bond. to C with 3 eletrwd.groups
HA 1.008 H arom. bond. to C without elctrwd. groups
H4 1.008 H arom. bond. to C with 1 electrwd. group
H5 1.008 H arom. bond. to C with 2 electrwd. groups
HO 1.008 hydroxyl group
HS 1.008 hydrogen bonded to sulphur
HW 1.008 H in TIP3P water
HP 1.008 H bonded to C next to positively charged gr
I 126.9 iodine
IM 35.45 assumed to be Cl-
IP 22.99 assumed to be Na+
MG 24.305 magnesium
N 14.01 sp2 nitrogen in amide groups
NA 14.01 sp2 N in 5 memb.ring w/H atom (HIS)
NB 14.01 sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA)
NC 14.01 sp2 N in 6 memb.ring w/LP (ADE,GUA)
N2 14.01 sp2 N in amino groups
N3 14.01 sp3 N for charged amino groups (Lys, etc)
N* 14.01 sp2 N
NX 14.01 sp2 N (RSM)
NZ 14.01 sp2 N coordinated to Zinc (RSM)
O 16.00 carbonyl group oxygen
OW 16.00 oxygen in TIP3P water
OH 16.00 oxygen in hydroxyl group
OS 16.00 ether and ester oxygen
O2 16.00 carboxyl and phosphate group oxygen
OM 16.00 O- (sp3) coordinated to Zinc (RSM)
OZ 16.00 O- (sp2) coordinated to Zinc (RSM)
P 30.97 phosphate
S 32.06 sulphur in disulfide linkage
SO 32.06 sulphur in sulfone / sulfonamide
SX 32.06 sulphur in benzothiazole ring
SH 32.06 sulphur in cystine
CU 63.55 copper
FE 55.00 iron
Li 6.94 lithium
K 39.10 potassium
Rb 85.47 rubidium
Cs 132.91 cesium
Ca 40.08 calcium (OPLS)
X 1.00 dummy atom for tethering
Z0 65.38 Zn++, noncovalent (Karplus, PROTEINS,23,12)
Z4 65.38 Zn++, tetracoord (Ryde, PROTEINS,21,40)
Z5 65.38 Zn++, pentacoord (Ryde, PROTEINS,21,40)
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 469.0 1.500 RSM, based on CSD analysis
C -CA 469.0 1.409 JCC,7,(1986),230; 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* 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 -OZ 656.0 1.250 RSM, based on C-O2
C -OH 450.0 1.364 JCC,7,(1986),230; TYR
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-CT 317.0 1.510 JCC,7,(1986),230; PHE,TYR
CA-CY 469.0 1.440 RSM, based on CSD analysis
CA-CX 469.0 1.400 RSM, based on CA-CA
CA-Cl 427.0 1.720 RSM, based on CSD analysis
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-N 427.0 1.412 RSM, based on CSD analysis
C -N2 481.0 1.340 RSM, based on CA-N2
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-N* 424.0 1.366 RSM, based on para-anilino pyridine (protonated)
CA-NX 428.0 1.391 RSM, based on Xray analysis
CA-SO 427.0 1.761 RSM, based on Xray analysis
CA-SX 427.0 1.732 RSM, based on Xray analysis
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
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
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
CR-S 367.0 1.715 RSM, from xray analysis
CT-CT 310.0 1.526 JCC,7,(1986),230; AA, SUGARS
CT-CX 317.0 1.499 RSM, based on Xray analysis
CT-CY 317.0 1.474 RSM, based on CSD analysis
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-NA 337.0 1.475 RSM, adapted from CT-N*
CT-N2 337.0 1.463 JCC,7,(1986),230; ARG
CT-OH 320.0 1.410 JCC,7,(1986),230; SUGARS
CT-OM 320.0 1.430 RSM, based on Xray analysis (Delta + CSD)
CT-OS 320.0 1.410 JCC,7,(1986),230; NUCLEIC ACIDS
CW-S 367.0 1.715 RSM, from xray analysis
CX-NA 418.0 1.434 RSM, based on Xray analysis
CX-NX 428.0 1.298 RSM, based on Xray analysis
CX-SX 227.0 1.747 RSM, based on Xray analysis
CY-CY 469.0 1.188 RSM, based on CSD analysis
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
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
N3-SO 230.0 1.615 RSM, based on Xray analysis
O2-SO 525.0 1.430 RSM, based on Xray analysis
CT-P 230.0 1.825 RSM, based on Xray analysis
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
C*-HC 367.0 1.080 changed from 340. bsd on C6H6 nmodes, not needed AA
C*-C* 515.0 1.421 RSM, estimated from Xray data
C*-CF 515.0 1.332 RSM, estimated from Xray data
C*-H4 367.0 1.071 RSM, estimated
C -N 490.0 1.335 JCC,7,(1986),230; 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
CA-CN 469.0 1.400 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
CC-NZ 410.0 1.394 RSM, from CC-NB
CC-O 570.0 1.229 RSM, adapted from C-O
CC-OH 410.0 1.330 RSM, estimated from 6-31G*
CC-OS 410.0 1.370 RSM, estimated from 6-31G*
CF-CT 317.0 1.495 RSM, based on Xray data
CF-CY 428.0 1.425 RSM, based on Xray data
CF-OS 428.0 1.369 RSM, based on Xray data
CN-CN 447.0 1.371 RSM, based on Xray data
CN-NA 428.0 1.380 JCC,7,(1986),230; TRP
CN-NB 428.0 1.407 RSM, based on xray
CN-NZ 428.0 1.380 RSM, based on CN-NA
CN-OS 428.0 1.390 RSM, based on xray data (fc from CN-NA)
CR-CT 317.0 1.495 RSM, based on C*-CT
CR-H5 367.0 1.080 changed from 340. bsd on C6H6 nmodes;HIS
CR-N2 410.0 1.360 RSM, estimated from 6-31G*
CR-NA 477.0 1.343 JCC,7,(1986),230; HIS
CR-NB 488.0 1.335 JCC,7,(1986),230; HIS
CR-NZ 488.0 1.335 RSM, from CR-NB
CR-OS 410.0 1.360 RSM, estimated from 6-31G*
CT-N 337.0 1.449 JCC,7,(1986),230; AA
CT-N3 367.0 1.471 JCC,7,(1986),230; LYS
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
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
CV-NZ 410.0 1.394 RSM, from CV-NB
CW-H4 367.0 1.080 changed from 340. bsd on C6H6 nmodes;HIS(epsilon,+)
CW-HC 367.0 1.080 RSM, based on CW-H4
CW-CT 317.0 1.487 RSM, based on xray data (fc from C*-CT)
CW-NA 427.0 1.381 JCC,7,(1986),230; HIS,TRP
CW-NB 410.0 1.400 RSM, estimated from 6-31G*
CW-NZ 410.0 1.400 RSM, estimated from 6-31G*
CW-OS 427.0 1.387 RSM, based on xray data
H -N 434.0 1.010 JCC,7,(1986),230; AA
H -N3 434.0 1.010 JCC,7,(1986),230; LYS
HS-SH 274.0 1.336 JCC,7,(1986),230; CYS
S -S 166.0 2.038 JCC,7,(1986),230; CYX (SCHERAGA)
CT-F 367.0 1.380 JCC,13,(1992),963;CF4; R0=1.332 FOR CHF3
HW-OW-HW 100. 104.52 TIP3P water
HW-HW-OW 0. 127.74 (found in crystallographic water with 3 bonds)
CA-C -O 80.0 120.00 RSM, estimated
CA-C -N 80.0 120.00 RSM, estimated
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 -OZ 70.0 117.00 RSM, based on CT-C -O2
CT-C -OH 70.0 117.00
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
CT-C -N 70.0 116.60 AA general
N -C -O 80.0 122.90 AA general
O -C -O 80.0 126.00 AA COO- terminal residues
O2-C -O2 80.0 126.00 AA GLU (SCH JPC 79,2379)
O2-C -OZ 80.0 126.00 RSM, based on O2-C -O2
O -C -OH 80.0 126.00
CA-C -C 63.0 120.00 RSM, estimated
CA-C -CA 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes; AA tyr
CA-C -OH 70.0 120.00 AA tyr
C -CA-C 63.0 120.00 RSM, estimated
C -CA-CA 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes
C -CA-CT 63.0 120.00 RSM, estimated
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-CX 63.0 120.00 RSM, based on CA-CA-CA
CA-CA-CY 70.0 120.00 RSM, estimated
CA-CA-Cl 70.0 120.00 RSM, estimated
CA-CA-HA 35.0 120.00
CX-CA-HA 35.0 120.00 RSM, from CA-CA-HA
NA-CA-HA 35.0 120.00 RSM, estimated
NC-CA-HA 35.0 120.00 RSM, estimated
CA-CA-H4 35.0 120.00
CA-CA-N 70.0 120.00 RSM, estimated
CA-CA-N2 70.0 120.00 RSM, estimated
CA-C -N2 70.0 120.00 RSM, estimated
CA-CA-NC 70.0 120.00 RSM, estimated
CA-CA-NX 70.0 115.00 RSM, based on Xray analysis
CA-CA-NA 70.0 120.00 RSM, estimated
CA-CA-N* 70.0 120.00 RSM, estimated
CA-CA-SO 70.0 120.00 RSM, based on Xray analysis
CA-CA-SX 70.0 109.20 RSM, based on Xray analysis
CB-CA-HA 35.0 120.00
CB-CA-H4 35.0 120.00
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
CT-CA-NC 70.0 120.00 RSM, estimated
N2-CA-NA 70.0 116.00
N2-CA-NC 70.0 119.30
NA-CA-NC 70.0 123.30
C -CA-HA 35.0 120.00 AA tyr
N2-CA-N2 70.0 120.00 AA arg
N2-C -N2 70.0 120.00 RSM, based on N2-CA-N2
CN-CA-HA 35.0 120.00 AA trp
CA-CA-CN 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes; AA trp
C -CB-CB 63.0 119.20 changed from 85.0 bsd on C6H6 nmodes; NA gua
C -CB-NB 70.0 130.00
C -CB-NZ 70.0 130.00 RSM, from C -CB-NB
CA-CB-CB 63.0 117.30 changed from 85.0 bsd on C6H6 nmodes; NA ade
CA-CB-NB 70.0 132.40
CA-CB-NZ 70.0 132.40 RSM, from CA-CB-NB
CB-CB-N* 70.0 106.20
CB-CB-NB 70.0 110.40
CB-CB-NZ 70.0 110.40 RSM, from CB-CB-NB
CB-CB-NC 70.0 127.70
N*-CB-NC 70.0 126.20
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
C*-CF-CT 70.0 133.10 RSM, based on Xray analysis
C*-CF-CY 70.0 133.10 RSM, based on Xray analysis
C*-CF-OS 70.0 110.20 RSM, based on Xray analysis
CT-CF-OS 70.0 113.70 RSM, based on Xray analysis
CY-CF-OS 70.0 113.70 RSM, based on Xray analysis
H5-CK-N* 35.0 123.05
H5-CK-NB 35.0 123.05
H5-CK-NZ 35.0 123.05 RSM, from H5-CK-NB
N*-CK-NB 70.0 113.90
N*-CK-NZ 70.0 113.90 RSM, from N*-CK-NB
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 35.0 119.70
C -CM-H4 35.0 119.70
CA-CM-CM 63.0 117.00 changed from 85.0 bsd on C6H6 nmodes; NA cyt
CA-CM-HA 35.0 123.30
CA-CM-H4 35.0 123.30
CM-CM-CT 70.0 119.70
CM-CM-HA 35.0 119.70
CM-CM-H4 35.0 119.70
CM-CM-N* 70.0 121.20
H4-CM-N* 35.0 119.10
H5-CQ-NC 35.0 115.45
NC-CQ-NC 70.0 129.10
CM-CT-HC 50.0 109.50 changed based on NMA nmodes
CA-CT-CY 40.0 111.00 RSM, based on CSD analysis
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
CA-CT-OH 50.0 109.50 RSM, estimated
CT-CT-OH 50.0 109.50
CT-CT-OM 50.0 109.50 RSM, from CT-CT-OH
CT-CT-OS 50.0 109.50
CT-CT-P 50.0 109.50 RSM, estimated
CT-CT-CF 50.0 109.50 RSM, estimated
CY-CT-HC 35.0 109.50 RSM, estimated
CY-CT-CT 50.0 109.50 RSM, estimated
CF-CT-HC 35.0 109.50 RSM, estimated
HC-CT-HC 35.0 109.50
HC-CT-OH 35.0 109.50 RSM, estimated
HC-CT-P 35.0 109.50 RSM, estimated
H1-CT-H1 35.0 109.50
HP-CT-HP 35.0 109.50 AA lys, ch3nh4+
H2-CT-N* 50.0 109.50 changed based on NMA nmodes
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-OM 50.0 109.50 RSM, from H1-CT-OH
H1-CT-OS 50.0 109.50 changed based on NMA nmodes
H2-CT-OS 50.0 109.50 changed based on NMA nmodes
N*-CT-OS 50.0 109.50
H1-CT-N 50.0 109.50 AA general changed based on NMA nmodes
H1-CT-NA 50.0 109.50 RSM, from H1-CT-N
H1-CT-N3 50.0 109.50 RSM, estimated
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
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
CT-CT-S 50.0 114.70 AA cyx (SCHERAGA JPC 79,1428)
CT-CT-SH 50.0 108.60 AA cys
H2-CT-H2 35.0 109.50 AA lys
H1-CT-N2 50.0 109.50 AA arg changed based on NMA nmodes
HP-CT-N3 50.0 109.50 AA lys, ch3nh3+, changed based on NMA nmodes
CA-CT-CT 63.0 114.00 AA phe tyr (SCH JPC 79,2379)
C -CT-HC 50.0 109.50 AA gln changed based on NMA nmodes
C -CT-N 63.0 110.10 AA general
CA-CT-NA 63.0 110.10 RSM, based on C-CT-N
CC-CT-NA 63.0 101.60 RSM, based on xray structures
C -CT-OH 63.0 110.10 RSM, estimated
C*-CT-OH 63.0 110.10 RSM, estimated
CR-CT-OH 63.0 110.10 RSM, estimated
CT-CT-N2 80.0 111.20 AA arg (JCP 76, 1439)
CT-CT-NA 80.0 109.70 RSM, based on CT-CT-N
CT-CT-N 80.0 109.70 AA ala, general (JACS 94, 2657)
C -CT-CT 63.0 111.10 AA general
CA-CT-HC 50.0 109.50 AA tyr changed based on NMA nmodes
CA-CT-H1 50.0 109.50 RSM, based on CA-CT-HC
CT-CT-N3 80.0 111.20 AA lys (JCP 76, 1439)
CC-CT-CT 63.0 113.10 AA his
CC-CT-HC 50.0 109.50 AA his changed based on NMA nmodes
CC-CT-H1 50.0 109.50 RSM, based on CC-CT-HC
CR-CT-H1 50.0 109.50 RSM, based on CC-CT-HC
CR-CT-F 50.0 109.50 RSM, assumed
CR-CT-CR 50.0 109.50 RSM, assumed
CR-CT-CT 63.0 115.60 RSM, based on C*-CT-CT
CR-CT-HC 50.0 109.50 RSM, based on CC-CT-HC
CR-CT-H1 50.0 109.50 RSM, based on CC-CT-HC
CR-CT-S 50.0 109.30 RSM, from xray
C -CT-N3 80.0 111.20 AA amino terminal residues
C*-CT-CT 63.0 115.60 AA trp
CW-CT-CT 63.0 115.60 RSM, estimated
C*-CT-HC 50.0 109.50 AA trp changed based on NMA nmodes
CW-CT-HC 50.0 109.50 RSM, estimated
CX-CT-CT 63.0 109.50 RSM, estimated
CX-CT-HC 50.0 109.50 RSM, estimated
NA-CT-N2 50.0 109.50 RSM, estimated
OH-CT-S 50.0 108.7 RSM, from xray
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
CT-CC-NZ 70.0 120.00 RSM, from CT-CC-NB
CT-CC-O 70.0 126.50 RSM, from xray structures
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
CW-CC-NZ 70.0 120.00 RSM, from CW-CC-NB
CW-CC-OH 70.0 134.50 RSM, estimated
CW-CC-OS 70.0 108.00 RSM, estimated
CT-CC-CW 70.0 120.00 AA his
NA-CC-NA 70.0 104.00 RSM, from xray structures
NA-CC-O 70.0 128.00 RSM, from xray structures
OH-CC-OS 70.0 117.40 RSM, estimated
CT-CR-NA 70.0 120.00 RSM, based on CC-CR-NA
CT-CR-NB 70.0 120.00 RSM, based on CC-CR-NA
CT-CR-NZ 70.0 120.00 RSM, based on CC-CR-NA
CT-CR-OS 70.0 116.70 RSM, from xray
H5-CR-NA 35.0 120.00 AA his
H5-CR-NB 35.0 120.00 AA his
H5-CR-NZ 35.0 120.00 RSM, from H5-CR-NB
NA-CR-NA 70.0 120.00 AA his
NA-CR-NB 70.0 120.00 AA his
NA-CR-NZ 70.0 120.00 RSM, from NA-CR-NB
N2-CR-NB 70.0 128.30 RSM, estimated
N2-CR-NZ 70.0 128.30 RSM, estimated
N2-CR-OS 70.0 116.40 RSM, estimated
N2-CR-S 70.0 123.20 RSM, estimated
NB-CR-OS 70.0 114.60 RSM, from xray data
NB-CR-S 70.0 113.60 RSM, from xray data
NZ-CR-OS 70.0 115.20 RSM, estimated
CC-CV-H4 35.0 120.00 AA his
CC-CV-NB 70.0 120.00 AA his
CC-CV-NZ 70.0 120.00 RSM, from CC-CV-NB
H4-CV-NB 35.0 120.00 AA his
H4-CV-NZ 35.0 120.00 RSM, from H4-CV-NZ
CC-CW-H4 35.0 120.00 AA his
CC-CW-HC 35.0 120.00 RSM, based on CC-CW-H4
CC-CW-NA 70.0 120.00 AA his
CC-CW-NB 70.0 108.80 RSM, estimated
CC-CW-NZ 70.0 108.80 RSM, estimated
CC-CW-S 70.0 110.20 RSM, from xray data
CT-CW-OS 70.0 114.80 RSM, from xray data
H4-CW-NA 35.0 120.00 AA his
H4-CW-S 35.0 122.60 RSM, from xray data
HC-CW-NB 35.0 122.40 RSM, estimated
HC-CW-NZ 35.0 122.40 RSM, estimated
C*-CW-H4 35.0 120.00 AA trp
C*-CW-NA 70.0 108.70 AA trp
C*-CW-CT 70.0 132.63 RSM, estimated from xray data
C*-CW-OS 70.0 111.54 RSM, estimated from xray data
CA-CX-CA 63.0 120.00 RSM, based on CA-CA-CA
CA-CX-NA 63.0 120.00 RSM, based on CA-CA-CA
CT-CX-NX 70.0 124.20 RSM, estimated from xray data
CT-CX-SX 70.0 120.30 RSM, estimated from xray data
NX-CX-SX 70.0 115.50 RSM, estimated from xray data
CA-CY-CY 70.0 180.00 RSM, estimated
CF-CY-CY 70.0 180.00 RSM, estimated
CT-CY-CY 70.0 180.00 RSM, estimated
CT-C*-CW 70.0 125.00 AA trp
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
CB-C*-H4 35.0 127.63 RSM, estimated (fc from CA-CA-HA)
CW-C*-H4 35.0 126.14 RSM, estimated (fc from CA-CA-HA)
C*-C*-CF 70.0 107.10 RSM, estimated from xray data
CF-C*-H4 35.0 126.45 RSM, estimated from xray data
C*-C*-H4 35.0 126.45 RSM, estimated from xray data
CA-CN-NA 70.0 132.80 AA trp
CA-CN-NB 70.0 131.00 RSM, from xray data
CA-CN-NZ 70.0 132.80 RSM, estimated from CA-CN-NA
CB-CN-NA 70.0 104.40 AA trp
CA-CN-OS 70.0 127.50 RSM, estimated from xray data
CB-CN-OS 70.0 110.45 RSM, estimated from xray data
CA-CN-CB 63.0 122.70 changed from 85.0 bsd on C6H6 nmodes; AA trp
CA-CN-CN 63.0 122.70 RSM, estimated from CA-CN-CB
CN-CN-NA 70.0 104.40 RSM, estimated from CB-CN-NA
CN-CN-NB 70.0 107.50 RSM, from xray data
CN-CN-NZ 70.0 104.40 RSM, estimated from CB-CN-NA
CN-CN-OS 70.0 108.40 RSM, from xray data
C -N -CT 50.0 121.90 AA general
C -N -H 30.0 120.00 AA general, gln, asn,changed based on NMA nmodes
CA-N -C 70.0 122.00 RSM, based on CSD analysis
CA-N -H 30.0 116.60 RSM, based on CSD analysis
CT-N -H 30.0 118.04 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
CA-N*-CT 70.0 123.90 RSM, estimated
CT-N*-CT 70.0 111.60 RSM, estimated
C -N*-H 30.0 119.20 changed based on NMA nmodes
CB-N*-CK 70.0 105.40
CB-N*-CT 70.0 125.80
CB-N*-H 30.0 125.80 for unmethylated n.a. bases,chngd bsd NMA nmodes
CK-N*-CT 70.0 128.80
CK-N*-H 30.0 128.80 for unmethylated n.a. bases,chngd bsd NMA nmodes
CM-N*-CT 70.0 121.20
CM-N*-H 30.0 121.20 for unmethylated n.a. bases,chngd bsd NMA nmodes
CA-N2-H 35.0 120.00
C -N2-H 35.0 120.00 RSM, based on CA-N2-H
CR-N2-H 35.0 120.00 RSM, based on CA-N2-H
H -N2-H 35.0 120.00
CT-N2-H 35.0 118.40 AA arg
CA-N2-CT 50.0 123.20 AA arg
CA-N2-CR 50.0 123.20 RSM, estimated
CT-N3-H 50.0 109.50 AA lys, changed based on NMA nmodes
H -N3-H 35.0 109.50 AA lys, AA(end)
CT-N3-CT 50.0 109.50 AA pro/nt
CT-N3-SO 50.0 121.20 RSM, estimated from Xray data
H -N3-SO 30.0 115.43 RSM, estimated from Xray data
H -N3-H 30.0 115.00 RSM, estimated from Xray data
C -NA-C 70.0 126.40
C -NA-CA 70.0 125.20
CA-NA-CA 70.0 125.20 RSM, estimated
C -NA-H 30.0 116.80 changed based on NMA nmodes
CA-NA-H 30.0 118.00 changed based on NMA nmodes
CC-NA-CC 70.0 120.00 RSM, based on CC-NA-CR
CC-NA-CR 70.0 120.00 AA his
CC-NA-CT 70.0 120.00 RSM, estimated
CC-NA-CX 70.0 124.10 RSM, from CSD analysis
CT-NA-CT 70.0 120.00 RSM, estimated
CN-NA-CR 70.0 120.00 RSM, based on CC-NA-CR
CN-NA-CT 70.0 120.00 RSM, estimated
CR-NA-CT 70.0 120.00 RSM, estimated
CC-NA-H 30.0 120.00 AA his, changed based on NMA nmodes
CR-NA-CW 70.0 120.00 AA his
CR-NA-H 30.0 120.00 AA his, changed based on NMA nmodes
CW-NA-H 30.0 120.00 AA his, changed based on NMA nmodes
CN-NA-CW 70.0 111.60 AA trp
CC-OS-CR 70.0 104.10 RSM, estimated
CN-OS-CR 70.0 104.00 RSM, from xray data
CN-OS-CW 70.0 105.89 RSM, estimated from xray analysis
CF-OS-CF 70.0 106.30 RSM, estimated from xray analysis
CN-NA-H 30.0 123.10 AA trp, changed based on NMA nmodes
CB-NB-CK 70.0 103.80
CC-NB-CR 70.0 117.00 AA his
CN-NB-CR 70.0 105.40 RSM, from xray data
CR-NB-CV 70.0 117.00 AA his
CR-NB-CW 70.0 103.90 RSM, estimated
C -NC-CA 70.0 120.50
CA-NC-CA 70.0 120.80 RSM, estimated
CA-NC-CB 70.0 112.20
CA-NC-CQ 70.0 118.60
CB-NC-CQ 70.0 111.00
CA-NX-CX 70.0 110.90 RSM, estimated from xray data
CB-NZ-CK 70.0 103.80 RSM, from CB-NB-CK
CC-NZ-CR 70.0 117.00 RSM, from CC-NB-CR
CN-NZ-CR 70.0 117.00 RSM, based on CC-NB-CR
CR-NZ-CV 70.0 117.00 RSM, from CR-NB-CV
CR-NZ-CW 70.0 103.90 RSM, estimated
CA-SO-N3 62.0 107.10 RSM, estimated from xray data
CA-SO-O2 100.0 107.80 RSM, estimated from xray data
N3-SO-N3 100.0 106.80 RSM, estimated from xray data
N3-SO-O2 100.0 107.10 RSM, estimated from xray data
O2-SO-O2 140.0 119.70 RSM, estimated from xray data
CA-SX-CX 62.0 89.30 RSM, estimated from xray data
C -OH-CT 55.0 119.44 RSM based on CSD analysis.
C -OH-CC 55.0 120.40 RSM, estimated
C -OH-HO 35.0 113.00
CT-OH-HO 55.0 108.50
HO-OH-P 100.0 108.50 korig = 45.
CT-OS-CT 60.0 109.50
CT-OS-P 100.0 120.50
P -OS-P 100.0 120.50
CT-P -O2 100.0 108.00 RSM, from CSD analysis
CT-P -OH 100.0 104.80 RSM, from CSD analysis
O2-P -OH 100.0 108.23 korig = 45.
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
CR-S -CW 80.0 90.10 RSM, from xray
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
F -CT-F 77.0 109.10 JCC,13,(1992),963;
F -CT-H1 35.0 109.50 JCC,13,(1992),963;
X -C -C -X 4 3.00 180.0 2. RSM, estimated
X -C -CA-X 4 8.00 180.0 2. ** korig = 14.5 **
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 -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 -OH-X 2 1.80 180.0 2. JCC,7,(1986),230
X -C -CT-X 4 0.00 0.0 2. JCC,7,(1986),230
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-CT-X 6 0.00 0.0 2. JCC,7,(1986),230
X -CA-CX-X 4 14.50 180.0 2. RSM: X -CA-CA-X
X -CA-CY-X 2 0.00 0.0 2. RSM, estimated
X -CA-N2-X 4 9.60 180.0 2. reinterpolated 93'
X -C -N2-X 4 9.60 180.0 2. RSM: X -CA-N2-X
X -CA-NA-X 4 6.00 180.0 2. JCC,7,(1986),230
X -CA-N*-X 2 9.60 180.0 2. RSM, estimated
X -CA-NC-X 2 9.60 180.0 2. JCC,7,(1986),230
X -CA-NX-X 2 6.00 180.0 2. RSM, estimated
X -CA-SX-X 2 6.00 180.0 2. RSM, estimated
X -CB-CB-X 4 21.80 180.0 2. intrpol.bsd.on C6H6
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-NZ-X 2 5.10 180.0 2. from X -CB-NB-X
X -CB-NC-X 2 8.30 180.0 2. JCC,7,(1986),230
X -CC-OH-X 2 1.80 180.0 2. RSM, from -C-OH-
X -CC-OS-X 2 4.80 180.0 2. RSM, ring torsion
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 -CK-NZ-X 2 20.00 180.0 2. from X -CK-NB-X
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 -CQ-NC-X 2 13.60 180.0 2. JCC,7,(1986),230
X -CR-S -X 2 10.00 0.00 2. RSM, estimated
X -CT-CT-X 9 1.40 0.0 3. JCC,7,(1986),230
X -CT-CX-X 6 0.00 0.0 3. RSM, estimated
X -CT-CY-X 3 0.00 0.0 3. RSM, estimated
X -CT-N -X 6 0.00 0.0 2. JCC,7,(1986),230
X -CT-NA-X 6 0.00 0.0 2. RSM, estimated
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-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 -CW-S -X 2 10.00 0.00 2. RSM, estimated
X -CX-NA-X 4 1.40 180.0 2. RSM, estimated
X -CX-NX-X 2 6.00 180.0 2. RSM, estimated
X -CX-SX-X 2 6.00 180.0 2. RSM, estimated
X -CY-CY-X 1 0.00 0.0 2. RSM, estimated
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
X -CT-P -X 9 0.75 0.0 3. RSM, estimated
X -C -N -X 4 10.00 180.0 2. AA|check Wendy?&NMA
X -CA-N -X 4 4.80 180.0 2. RSM, estimated
X -CT-N3-X 9 1.40 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*-C*-X 4 6.70 180.0 2. RSM, estimated
X -C*-CT-X 6 0.00 0.0 2. JCC,7,(1986),230
X -CT-CW-X 6 0.00 0.0 2. RSM, estimated
X -C*-CW-X 4 26.10 180.0 2. intrpol.bsd.on C6H6
X -C*-CF-X 4 26.10 180.0 2. RSM, estimated
X -CA-CN-X 4 14.50 180.0 2. reinterpolated 93'
X -CB-CN-X 4 12.00 180.0 2. reinterpolated 93'
X -CN-CN-X 4 12.00 180.0 2. RSM: X -CB-CN-X
X -CC-CT-X 6 0.00 0.0 2. JCC,7,(1986),230
X -CR-CT-X 6 0.00 0.0 2. RSM: X -CC-CT-X
X -CF-CT-X 6 0.00 0.0 2. RSM, estimated
X -CF-CY-X 6 0.00 0.0 2. RSM, estimated
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 -CC-NZ-X 2 4.80 180.0 2. from X -CC-NB-X
X -CF-OS-X 4 6.00 180.0 2. RSM, estimated
X -CN-NA-X 4 6.10 180.0 2. reinterpolated 93'
X -CN-NB-X 4 6.10 180.0 2. RSM, X -CN-NA-X
X -CN-NZ-X 4 6.10 180.0 2. RSM, X -CN-NA-X
X -CN-OS-X 2 6.10 180.0 2. RSM, estimated
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 -CR-NZ-X 2 10.00 180.0 2. from X -CR-NB-X
X -CR-N2-X 2 4.80 180.0 2. RSM, estimated
X -CR-OS-X 2 4.80 180.0 2. RSM, ring torsion
X -CV-NB-X 2 4.80 180.0 2. JCC,7,(1986),230
X -CV-NZ-X 2 4.80 180.0 2. from X -CV-NB-X
X -CW-NA-X 4 6.00 180.0 2. JCC,7,(1986),230
X -CW-NB-X 4 6.00 180.0 2. RSM, from -CW-NA-
X -CW-NZ-X 4 6.00 180.0 2. RSM, from -CW-NA-
X -CW-OS-X 2 6.00 180.0 2. RSM, estimated
X -CA-SO-X 6 0.00 0.0 2. RSM, estimated
X -N3-SO-X 6 2.40 0.0 3. RSM, estimated
CT-CT-OS-CT 1 0.383 0.0 -3.
CT-CT-OS-CT 1 0.1 180.0 2.
C -N -CT-C 1 0.20 180.0 2.
N -CT-C -N 1 0.40 180.0 -4.
N -CT-C -N 1 1.35 180.0 -2.
N -CT-C -N 1 0.75 180.0 1.
CT-CT-N -C 1 0.50 180.0 -4.
CT-CT-N -C 1 0.15 180.0 -3.
CT-CT-N -C 1 0.53 0.0 1.
CT-CT-C -N 1 0.100 0.0 -4.
CT-CT-C -N 1 0.07 0.0 2.
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
OS-CT-CT-OS 1 0.144 0.0 -3. JCC,7,(1986),230
OS-CT-CT-OS 1 1.00 0.0 2. pucker anal (93')
OS-CT-CT-OH 1 0.144 0.0 -3. JCC,7,(1986),230
OS-CT-CT-OH 1 1.00 0.0 2. pucker anal (93')
OH-CT-CT-OH 1 0.144 0.0 -3. JCC,7,(1986),230
OH-CT-CT-OH 1 1.00 0.0 2. check glicolWC? puc
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
OS-CT-N*-CK 1 0.50 180.0 -2. sugar frag calc (PC)
OS-CT-N*-CK 1 2.50 0.0 1. sugar frag calc (PC)
OS-CT-N*-CM 1 0.50 180.0 -2. sugar frag calc (PC)
OS-CT-N*-CM 1 2.50 0.0 1. sugar frag calc (PC)
X -X -C -O 10.5 180. 2. JCC,7,(1986),230
X -X -CC-O 10.5 180. 2. RSM, estimated
X -O2-C -O2 10.5 180. 2. JCC,7,(1986),230
X -O2-C -OZ 10.5 180. 2. RSM, X -O2-C -O2
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 10.5 180. 2. RSM, korig = 1.0
X -X -NA-CT 10.5 180. 2. RSM, korig = 1.0
X -N2-CA-N2 10.5 180. 2. JCC,7,(1986),230
X -X -N*-CA 1.0 180. 2. RSM, estimated
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 -CA-NX 1.1 180. 2. RSM, estimated
X -X -CA-SX 1.1 180. 2. RSM, estimated
X -X -CF-H4 1.1 180. 2. RSM, estimated
X -X -CF-CT 1.1 180. 2. RSM, estimated
X -X -CF-CY 1.1 180. 2. RSM, estimated
X -X -CN-CA 10.5 180. 2. RSM, estimated
X -X -CW-H4 1.1 180. 2.
X -X -CX-NA 1.1 180. 2. RSM, estimated
X -X -CX-NX 1.1 180. 2. RSM, estimated
X -X -CX-SX 1.1 180. 2. RSM, estimated
X -X -C*-H4 1.1 180. 2. RSM, estimated
X -X -C*-CT 1.1 180. 2. RSM, estimated
X -X -CR-CT 10.5 180. 2. RSM, estimated
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.
NZ-CW-CC-CT 1.1 180. 2. from NB-CW-CC-CT
NA-CW-CC-CT 1.1 180. 2.
CW-CB-C*-CT 1.1 180. 2.
CA-CA-CA-CT 1.1 180. 2.
CA-CA-CA-CY 1.1 180. 2. RSM, estimated
N2-CM-CA-NC 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
C -CM-CM-CT 1.1 180. 2. dac guess, 9/94
CA-CA-C -OH 1.1 180. 2.
HW OW 0000. 0000. 4. flag for fast water
N NA N2 N* NC NB N3 NP NO NX
C C* CA CB CC CF CN CM CK CQ CW CV CR CA CX CY CD C5
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
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
OM 1.0000 0.1700 RSM, adaped from OPLS
OZ 1.0000 0.1700 RSM, adaped from OPLS
CT 1.9080 0.1094 Spellmeyer
CA 1.9080 0.0860 Spellmeyer
CM 1.9080 0.0860 Spellmeyer
C 1.9080 0.0860 OPLS
Cl 1.9082 0.3000 RSM, adapted from OPLS
N 1.8240 0.1700 OPLS
NZ 1.0000 0.1700 RSM
S 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's
SO 2.0000 0.2500 RSM
SX 2.0000 0.2500 RSM
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)
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)
Ca 1.2060 0.25236 Ca++ OPLS (RSM- adapted)
I 2.35 0.40 JCC,7,(1986),230;
F 1.75 0.061 Gough et al. JCC 13,(1992),963.
X 0.000 0.0000 RSM
Z0 1.850 0.2500 Zn++ from PROTEINS,23,12.(Ro=1.95)
Z4 2.620 0.2700 Zn++ from Ryde PROTEINS,21,40.
Z5 2.620 0.2700 Zn++ from Ryde PROTEINS,21,40.
END
END
# bromine
CHEMPY BR 35 1
# carbon
CHEMPY C 6 3
CHEMPY CA 6 3
CHEMPY CB 6 3
CHEMPY CC 6 3
CHEMPY CF 6 3
CHEMPY CK 6 3
CHEMPY CM 6 3
CHEMPY CN 6 3
CHEMPY CQ 6 3
CHEMPY CR 6 3
CHEMPY CT 6 4
CHEMPY CV 6 3
CHEMPY CW 6 3
CHEMPY CY 6 2
CHEMPY CX 6 2
CHEMPY C5 6 3
CHEMPY C* 6 3
# calcium
CHEMPY C0 20 3
# chloride
CHEMPY Cl 17 1
# fluorine
CHEMPY F 9 1
# hydrogen
CHEMPY H 1 1
CHEMPY H1 1 1
CHEMPY H2 1 1
CHEMPY H3 1 1
CHEMPY H4 1 1
CHEMPY H5 1 1
CHEMPY HA 1 1
CHEMPY HC 1 1
CHEMPY HO 1 1
CHEMPY HP 1 1
CHEMPY HS 1 1
CHEMPY HW 1 1
# iodine
CHEMPY I 53 1
# chloride anion
CHEMPY IM 17 0
# sodium cation
CHEMPY IP 11 0
# magnesium
CHEMPY MG 12 0
# nitrogen
CHEMPY N 7 3
CHEMPY N* 7 2
CHEMPY N2 7 3
CHEMPY N3 7 4
CHEMPY NA 7 3
CHEMPY NB 7 2
CHEMPY NC 7 2
CHEMPY NX 7 2
CHEMPY NZ 7 3
#
CHEMPY OW 8 2
CHEMPY OH 8 2
CHEMPY OS 8 2
CHEMPY O 8 1
CHEMPY O2 8 1
CHEMPY OM 8 1
CHEMPY OZ 8 1
CHEMPY P 15 4
CHEMPY S 16 2
CHEMPY SO 16 4
CHEMPY SX 16 2
CHEMPY SH 16 2
# copper
CHEMPY CU 29 0
# iron
CHEMPY FE 26 0
# lithium
CHEMPY Li 3 0
# potassium
CHEMPY K 19 0
# rubidium
CHEMPY Rb 37 0
# cesium
CHEMPY Cs 55 0
# calcium (alternate)
CHEMPY Ca 20 0
# dummy
CHEMPY X 6 1
# zinc
CHEMPY Z0 30 0
CHEMPY Z4 30 4
CHEMPY Z5 30 5
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