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ener_one_lib.cif
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ener_one_lib.cif
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# ---------------------------------------------------
# ener_lib.cif 4-APR-95/31-MAY-00
# ---------------------------------------------------
#
data_energy
#
# ---------------------------------------------------
# _dictionary_name ciflibdic
# _dictionary_version 2.0
#
# ---------------------------------------------------
# ----------- Description of atom's type --------
#HEADER C Carbon PI
#ATOMTYPE CSP = with triple bond
#ATOMTYPE CSP1 = with triple bond and 1 hydrogen
#HEADER C Carbon SP2
#ATOMTYPE C = without hydrogen ( carbonyl C )
#ATOMTYPE C1 = connected to 1 hydrogen
#ATOMTYPE C2 = connected to 2 hydrogens
#ATOMTYPE CR1 = between two pyrrole units
#ATOMTYPE CR1H = CR1 connected to 1 hydrogen ( CHA of HEME )
#ATOMTYPE CR15 = connected to 1 hydrogen in 5 atoms ring ( CE1 of HIS)
#ATOMTYPE CR16 = connected to 1 hydrogen in 6 atoms ring ( CE1 of PHE)
#ATOMTYPE CR6 = without hydrogen in 6 atoms ring
#ATOMTYPE CR5 = without hydrogen in 5 atoms ring
#ATOMTYPE CR56 = between two atoms in 5-6 rings ( CD2 CE2 of TRP )
#ATOMTYPE CR55 = between two atoms in 5-5 rings
#ATOMTYPE CR66 = between two atoms in 6-6 rings
#HEADER C Carbon SP3
#ATOMTYPE CH1 = connected to 1 hydrogen ( CA of most amono acids )
#ATOMTYPE CH2 = connected to 2 hydrogens ( CB of most amono acids)
#ATOMTYPE CH3 = connected to 3 hydrogens ( CD1 CD2 of LEUCINE)
#ATOMTYPE CT = without hydrogen
#ATOMTYPE SI = tetragonal silicon
#ATOMTYPE SI1 = other silicons
#HEADER H Hydrogen
#ATOMTYPE HCH = hydrogen of aliphatic group
#ATOMTYPE HCR = hydrogen of aromatic group
#ATOMTYPE HNC1 = hydrogen connected to NC1
#ATOMTYPE HNC2 = hydrogen connected to NC2
#ATOMTYPE HNC3 = hydrogen connected to NC3
#ATOMTYPE HNH1 = hydrogen connected to NH1
#ATOMTYPE HNH2 = hydrogen connected to NH2
#ATOMTYPE HNR5 = hydrogen connected to NR15
#ATOMTYPE HNR6 = hydrogen connected to NR16
#ATOMTYPE HOH1 = hydrogen connected to OH1
#ATOMTYPE HOH2 = hydrogen of water
#ATOMTYPE HSH1 = hydrogen of sulphur
#HEADER N Nitrogen PI
#ATOMTYPE NS = without hydrogen ( triple bond )
#ATOMTYPE NS1 = connected to 1 hydrogen
#HEADER N Nitrogen SP2
#ATOMTYPE N = without hydrogen ( N of PRO )
#ATOMTYPE NC1 = connected to 1 hyd. in a charged group ( NE of ARG )
#ATOMTYPE NC2 = connected to 2 hyd. in a charged group ( NH2 of ARG )
#ATOMTYPE NH1 = connected to 1 hydrogen ( N of main chain )
#ATOMTYPE NH2 = connected to 2 hydrogen ( NE2 of GLU )
#ATOMTYPE NPA = without hydrogen ( NA and NC of HEME )
#ATOMTYPE NPB = without hydrogen ( NB and ND of HEME )
#ATOMTYPE NRD5 = without hydrogen but with electronic doublet in 5 atoms ring
#ATOMTYPE NRD6 = without hydrogen but with electronic doublet in 6 atoms ring
#ATOMTYPE NR15 = connected to 1 hyd. in 5 atoms ring ( ND1 of HIS )
#ATOMTYPE NR16 = connected to 1 hyd. in 6 atoms ring
#ATOMTYPE NR5 = connected to 3 atoms in 5 atoms ring ( N9 of ADE )
#ATOMTYPE NR6 = connected to 3 atoms in 6 atoms ring ( N1 of CYT )
#HEADER N Nitrogen SP3
#ATOMTYPE NT = without hydrogen
#ATOMTYPE NT1 = connected to 1 hydrogen
#ATOMTYPE NT2 = connected to 2 hydrogens
#ATOMTYPE NT3 = connected to 3 hydrogens
#ATOMTYPE P = tetragonal P with four bonds
#ATOMTYPE P1 = with three bonds. Planar?
#HEADER O Oxygen SP2
#ATOMTYPE O = without NET charge ( O of main chain )
#ATOMTYPE OC = with a NET charge ( OE1 OE2 of GLU )
#ATOMTYPE OP = with a NET charge connected to P (O1P of phosphate group )
#ATOMTYPE OS = with a NET charge connected to S ( O1 of sulphate group )
#ATOMTYPE OB = with a NET charge connected to B
#HEADER O Oxygen SP3
#ATOMTYPE O2 = connected to 2 atoms ( O4' of ribose )
#ATOMTYPE OC2 = with a NET charge connected to 2 ATOMS ( O3' of ribose )
#ATOMTYPE OH1 = oxygen of alcohol groups ( OG1 of THR )
#ATOMTYPE OH2 = oxygen of water
#ATOMTYPE OHA = oxygen of water in MO6
#ATOMTYPE OHB = oxygen of water in MO6
#ATOMTYPE OHC = oxygen of water in MO6
#HEADER S Sulphur
#ATOMTYPE S = sulphur without hydrogen
#ATOMTYPE SH1 = sulphur with a hydrogen ( SG of CYS )
#ATOMTYPE S3 = sulphur with 3 bonds (sulphoxide)
#ATOMTYPE S2 = sulphur with 2 bonds (methionine)
#ATOMTYPE S1 = sulphur with 1 double bond
#HEADER Fe
#ATOMTYPE FE = iron
#HEADER P
#ATOMTYPE P = phosphorus
#HEADER Zn
#ATOMTYPE ZN = zinc
#END
# ---------------------------------------------------
#
# --- ATOM ---
#
loop_
_lib_atom.type
_lib_atom.weight
_lib_atom.hb_type
_lib_atom.vdw_radius
_lib_atom.vdwh_radius
_lib_atom.ion_radius
_lib_atom.element
_lib_atom.valency
_lib_atom.sp
#
# _type atomic chemical type
# _weight atomic weight
# _hb_type donnor/acceptor's type:
# N=neither
# D=donnor
# A=acceptor
# B=both
# H=hydrogen candidate to hydrogen bonding
# _vdw_radius Van-Der-Waals radius
# _vdwh_radius Van-Der-Waals radius for atom+H
# Ionic radii for most of the atoms without hydrogens are
# http://www.webelements.com/webelements/elements/text/radii/N.html
#
# or
# Chemstry of the elements by Greenwood and Earnshaw
# VDW radii of carbon atoms with hydrogen have been taken from paper
# Li and Nussinov, Proteins, 32 111-127 (1998)
#
CSP 12.01150 N 1.700 1.700 . C 4 1
CSP1 12.01150 N 1.700 1.700 . C 4 1
C 12.01150 N 1.700 1.750 . C 4 2
C1 12.01150 N 1.700 1.820 . C 4 2
C2 12.01150 N 1.700 1.800 . C 4 2
CR1 12.01150 N 1.700 1.800 . C 4 2
CR2 12.01150 N 1.700 1.800 . C 4 2
CR1H 12.01150 N 1.700 1.800 . C 4 2
CR15 12.01150 N 1.700 1.740 . C 4 2
CR5 12.01150 N 1.700 1.740 . C 4 2
CR56 12.01150 N 1.700 1.740 . C 4 2
CR55 12.01150 N 1.700 1.740 . C 4 2
CR16 12.01150 N 1.700 1.820 . C 4 2
CR6 12.01150 N 1.700 1.740 . C 4 2
CR66 12.01150 N 1.700 1.740 . C 4 2
CH1 12.01150 N 1.700 1.950 . C 4 3
CH2 12.01150 N 1.700 1.920 . C 4 3
CH3 12.01150 N 1.700 1.940 . C 4 3
CT 12.01150 N 1.700 1.850 . C 4 3
#
NS 14.00670 N 1.550 1.600 1.32 N 3 1
N 14.00670 N 1.550 1.600 1.32 N 3 2
NC1 14.00670 D 1.550 1.600 1.32 N 3 2
NH1 14.00670 D 1.550 1.600 1.32 N 3 2
NC2 14.00670 D 1.550 1.600 1.32 N 3 2
NH2 14.00670 D 1.550 1.600 1.32 N 3 2
NC3 14.00670 D 1.550 1.600 1.32 N 3 2
NT 14.00670 D 1.550 1.600 1.32 N 3 3
NT1 14.00670 D 1.550 1.600 1.32 N 3 3
NT2 14.00670 D 1.550 1.600 1.32 N 3 3
NT3 14.00670 D 1.550 1.600 1.32 N 3 3
NPA 14.00670 A 1.550 1.600 1.32 N 3 2
NPB 14.00670 A 1.550 1.600 1.32 N 3 2
NR5 14.00670 N 1.550 1.600 1.32 N 3 2
NR15 14.00670 D 1.550 1.600 1.32 N 3 2
NRD5 14.00670 A 1.550 1.600 1.32 N 3 2
NR56 14.00670 A 1.550 1.600 1.32 N 3 2
NR55 14.00670 A 1.550 1.600 1.32 N 3 2
NR6 14.00670 N 1.550 1.600 1.32 N 3 2
NR66 14.00670 N 1.550 1.600 1.32 N 3 2
NR16 14.00670 D 1.550 1.600 1.32 N 3 2
NRD6 14.00670 A 1.550 1.600 1.32 N 3 2
#
OS 15.99940 A 1.520 1.520 1.28 O 2 2
O 15.99940 A 1.520 1.520 1.28 O 2 2
O2 15.99940 A 1.520 1.520 1.28 O 2 3
OH1 15.99940 B 1.520 1.520 1.28 O 2 3
OH2 15.99940 B 1.520 1.520 1.28 O 2 3
OHA 15.99940 B 1.520 1.680 1.28 O 2 3
OHB 15.99940 B 1.520 1.680 1.28 O 2 3
OHC 15.99940 B 1.520 1.680 1.28 O 2 3
OC2 15.99940 A 1.520 1.520 1.28 O 2 2
OC 15.99940 A 1.520 1.520 1.28 O 2 2
OP 15.99940 A 1.520 1.520 1.28 O 2 2
OB 15.99940 A 1.520 1.520 1.28 O 2 2
#
P 30.97380 N 1.800 1.88 0.59 P 5 .
P1 30.97380 N 1.800 1.88 0.59 P 5 .
PS 30.97380 N 1.800 1.90 0.59 P 5 .
S 32.06400 A 1.800 1.88 0.4 S 2 .
S3 32.06400 A 1.800 1.88 0.4 S 4 .
S2 32.06400 A 1.800 1.88 0.4 S 2 .
S1 32.06400 A 1.800 1.88 0.4 S 2 .
ST 32.06400 A 1.800 1.88 0.4 S 6 3
SH1 32.06400 B 1.800 1.950 0.4 S 2 .
#
H 1.00800 N 1.200 . . H 1 .
HCH 1.00800 N 1.200 . . H 1 .
HCH1 1.00800 N 1.200 . . H 1 .
HCH2 1.00800 N 1.200 . . H 1 .
HCH3 1.00800 N 1.200 . . H 1 .
HCR1 1.00800 N 1.200 . . H 1 .
HC2 1.00800 N 1.200 . . H 1 .
HC1 1.00800 N 1.200 . . H 1 .
HC2 1.00800 N 1.200 . . H 1 .
HCR5 1.00800 N 1.200 . . H 1 .
HCR6 1.00800 N 1.200 . . H 1 .
HNC1 1.00800 H 1.200 . . H 1 .
HNC2 1.00800 H 1.200 . . H 1 .
HNH1 1.00800 H 1.200 . . H 1 .
HNH2 1.00800 H 1.200 . . H 1 .
HNR5 1.00800 H 1.200 . . H 1 .
HNR6 1.00800 H 1.200 . . H 1 .
HNT1 1.00800 H 1.200 . . H 1 .
HNT2 1.00800 H 1.200 . . H 1 .
HNT3 1.00800 H 1.200 . . H 1 .
HOH1 1.00800 H 1.200 . . H 1 .
HOH2 1.00800 H 1.200 . . H 1 .
HOHA 1.00800 H 1.200 . . H 1 .
HOHB 1.00800 H 1.200 . . H 1 .
HOHC 1.00800 H 1.200 . . H 1 .
HSH1 1.00800 H 1.200 . . H 1 .
#
# Sort out valencies of atoms
#
SI 28.0855 N 2.10 . 0.40 SI 4 3
SI1 28.0855 N 2.10 . 0.40 SI 4 .
GE 72.59 N 2.10 . 0.40 GE 1 .
GE1 72.59 N 2.10 . 0.40 GE 1 .
SN 118.69 N 2.17 . 0.69 SN 1 .
PB 207.2 N 2.02 . 0.79 PB 1 .
#
LI 6.941 N 1.82 . 0.73 LI 1 .
NA 22.990 N 2.27 . 1.13 NA 1 .
K 30.0983 N 2.75 . 1.51 K 1 .
RB 85.468 N 2.00 . 1.48 RB 1 .
CS 132.905 N 2.98 . 1.81 CS 1 .
FR 223.0 N . . 1.94 FR 1 .
#
BE 9.0123 N 1.12 . 0.41 BE 1 .
MG 24.30500 N 1.73 . 0.71 MG 1 .
CA 40.08000 N 1.94 . 1.14 CA 1 .
SR 87.62 N 2.19 . 1.32 SR 1 .
BA 137.33 N 2.53 . 1.49 BA 1 .
RA 226.025 N 2.15 . 1.62 RA 1 .
#
SC 44.9559 N 1.60 . 0.885 SC 1 .
Y 88.9059 N 1.80 . 1.04 Y 1 .
LA 138.9055 N 1.95 . 1.172 LA 1 .
CE 140.12 N 1.85 . 1.01 CE 1 .
PR 140.9077 N 1.85 . 0.99 PR 1 .
ND 144.24 N 1.85 . 1.123 ND 1 .
PM . N . . 1.11 PM 1 .
SM 150.36 N 1.85 . 1.098 SM 1 .
EU 151.96 N 1.85 . 1.087 EU 1 .
GD 157.25 N 1.80 . 1.078 GD 1 .
TB 158.9254 N 1.75 . 0.90 TB 1 .
DY 162.50 N 1.75 . 1.052 DY 1 .
HO 164.9304 N 1.75 . 1.041 HO 1 .
ER 167.26 N 1.75 . 1.03 ER 1 .
TM 168.9342 N 1.75 . 1.02 TM 1 .
YB 173.04 N 1.75 . 1.008 YB 1 .
LU 174.967 N 1.75 . 1.001 LU 1 .
#
AC 227.028 N 1.95 . 1.26 AC 1 .
TH 232.0 N 1.80 . 1.08 TH 1 .
PA 231.0 N 1.80 . 0.92 PA 1 .
U 238.0 N 1.86 . 0.66 U 1 .
NP 237.0 N 1.75 . 0.85 NP 1 .
PU 239.0 N 1.75 . 0.85 PU 1 .
AM 241.0 N 1.75 . 0.99 AM 1 .
CM 244.0 N . . 0.99 CM 1 .
BK 249.0 N . . 0.97 BK 1 .
CF 252.0 N . . 0.961 CF 1 .
ES 253.0 N . . . ES 1 .
FM 257.0 N . . . FM 1 .
MD 256.0 N . . . MD 1 .
NO 255.0 N . . . NO 1 .
LR 256.0 N . . . LR 1 .
#
TI 47.88 N 1.40 . 0.56 TI 1 .
ZR 91.22 N 1.55 . 0.73 ZR 1 .
HF 178.49 N 1.55 . 0.72 HF 1 .
RF . N . . . RF 1 .
#
V 50.9415 N 1.35 . 0.68 V 1 .
NB 92.9064 N 1.45 . 0.62 NB 1 .
TA 180.9479 N 1.45 . 0.78 TA 1 .
DB . N . . . DB 1 .
#
CR 51.996 N 1.40 . 0.53 CR 1 .
MO 95.94 N 1.45 . 0.55 MO 1 .
W 183.85 N 1.35 . 0.56 W 1 .
SG . N . . . SG 1 .
#
MN 54.938 N 1.40 . 0.46 MN 1 .
TC 98.906 N 1.35 . 0.51 TC 1 .
RE 186.207 N 1.35 . 0.52 RE 1 .
BH . N . . . BH 1 .
#
FE 55.847 N 1.40 . 0.68 FE 1 .
RU 101.07 N 1.30 . 0.52 RU 1 .
OSE 190.2 N 1.30 . 0.53 OS 1 .
HS . N . . . HS 1 .
#
CO 58.9332 N 1.35 . 0.54 CO 1 .
RH 102.9055 N 1.35 . 0.69 RH 1 .
IR 192.22 N 1.35 . 0.71 IR 1 .
MT . N . . . MT 1 .
#
NI 58.69 N 1.63 . 0.63 NI 1 .
PD 106.42 N 1.63 . 0.78 PD 1 .
PT 195.08 N 1.75 . 0.71 PT 1 .
#
CU 63.546 N 1.40 . 0.71 CU 1 .
AG 107.868 N 1.72 . 0.81 AG 1 .
AU 196.9665 N 1.66 . 0.71 AU 1 .
#
ZN 65.38 N 1.39 . 0.74 ZN 1 .
CD 112.41 N 1.58 . 0.92 CD 1 .
HG 200.59 N 1.55 . 1.10 HG 1 .
#
B 10.81 N 0.85 . 0.25 B 1 .
AL 26.98154 N 1.25 . 0.53 AL 1 .
GA 69.72 N 1.87 . 0.61 GA 1 .
IN 114.82 N 1.93 . 0.76 IN 1 .
TL 204.383 N 1.96 . 0.89 TL 1 .
#
AS 74.9216 N 1.85 . 0.475 AS 1 .
AS1 74.9216 N 1.85 . 0.475 AS 1 .
SB 121.75 N 1.8 . 0.90 SB 1 .
BI 208.9804 N 1.8 . 0.90 BI 1 .
#
SE 78.96 N 1.90 . 0.42 SE 1 .
TE 127.60 N 2.06 . 0.57 TE 1 .
PO 210.0 N 2.0 . 0.81 PO 1 .
#
F 18.998 B 1.47 . 1.19 F 1 .
CL 35.453 A 1.75 . 1.67 CL 1 .
BR 79.904 N 1.85 . 0.73 BR 1 .
I 126.9045 N 1.98 . 0.56 I 1 .
AT 210.0 N 1.80 . 0.76 AT 1 .
#
HE 4.0026 N 1.40 . . HE 1 .
NE 20.179 N 1.54 . 1.12 NE 1 .
AR 39.948 N 1.88 . 1.54 AR 1 .
KR 83.80 N 2.02 . 1.69 KR 1 .
XE 131.29 N 2.16 . 1.90 XE 1 .
RN 222.0 N 2.20 . 2.0 RN 1 .
DUM 16.0 N 0.6 0.6 0.6 O . .
. . . . . . . . .
#
# --- LIST OF SYNONYMS ---
#
loop_
_lib_synonym.atom_type
_lib_synonym.atom_alternative_type
#
NT3 NH3
#
# --- BONDS ---
#
loop_
_lib_bond.atom_type_1
_lib_bond.atom_type_2
_lib_bond.type
_lib_bond.const
_lib_bond.length
_lib_bond.value_esd
#
# _atom_type atomic chemical type
# _const constant KBOND
# _value equilibrium length of this bond BOND0
# BOND - actual bond length
#
# ENERGY = KBOND * ( BOND - BOND0 )**2
#
# Values for bond distances and sigmas are from (where it is possible):
# International tables for crystallography
# Volume C, 1992,
# Edited by AJC Wilson
# Published for IUCr by Kluwer Academic Publishers, Dordrecht/Boston/London
# For carbon-carbon etc
# Section: Typical Interatomic distances: Organic compounds
# Authors: FH Allen, O. Kennard, DG Watson, L Brammer, AG Orpen and R Taylor
# pages: 685-706
#
# For metal radii and distances.
# Section: Typical interatomic distances: Organometallic Compounds and
# Coordination complexes of the d- and f-block metals
# Authors: AG Orpen, L. Brammer, FH Allen, O Kennard, DG Watson and R Taylor
# pages: 707-791
#
C C single 420.0 1.460 0.025
C C double 420.0 1.330 0.020
C1 C single 420.000 1.475 0.020
C1 C double 420.000 1.340 0.020
C1 C1 single 420.000 1.460 0.015
C1 C1 double 420.000 1.330 0.014
C2 C double 420.000 1.320 0.030
C2 C1 double 420.000 1.320 0.030
C2 C2 double 420.000 1.320 0.030
C CR1 single 450.000 1.480 0.020
C1 CR1 single 450.000 1.480 0.020
C2 CR1 single 450.000 1.480 0.020
CR15 CR15 aromatic 450.000 1.380 0.020
CR5 C single 405.000 1.490 0.016
CR5 C1 single 405.000 1.483 0.015
CR5 C2 single 405.000 1.483 0.020
CR5 CR1 aromatic 450.000 1.455 0.020
CR5 CR1H aromatic 450.000 1.455 0.020
CR5 CR15 aromatic 450.000 1.387 0.020
CR55 CR15 aromatic 450.000 1.390 0.020
CR5 CR5 aromatic 450.000 1.390 0.020
CR5 CR5 single 450.000 1.490 0.015
CR55 CR5 aromatic 450.000 1.390 0.020
CR55 CR5 single . 1.490 0.020
CR56 CR5 aromatic 450.000 1.390 0.020
CR56 CR5 single 450.000 1.490 0.020
CR56 CR56 aromatic 450.000 1.390 0.020
CR56 CR56 single 450.000 1.490 0.020
CR16 CR56 aromatic 450.000 1.390 0.020
CR16 CR16 aromatic 450.000 1.390 0.020
CR6 C single 405.000 1.500 0.020
CR6 C1 single 405.000 1.480 0.020
CR6 C2 single 405.000 1.480 0.020
CR6 CR5 single 450.000 1.490 0.015
CR6 CR5 aromatic 450.000 1.390 0.015
CR6 CR56 aromatic 450.000 1.390 0.020
CR6 CR56 single 450.000 1.490 0.020
CR6 CR16 aromatic 450.000 1.390 0.020
CR6 CR6 aromatic 450.000 1.384 0.013
CR6 CR6 single 450.000 1.487 0.015
CR66 CR16 aromatic 450.000 1.390 0.015
CR66 CR6 aromatic 450.000 1.390 0.015
CR66 CR6 single 450.000 1.490 0.015
CR66 CR66 aromatic 450.000 1.390 0.015
CR66 CR66 single 450.000 1.490 0.015
CR15 . aromatic . 1.390 0.020
CR15 . single . 1.490 0.020
CR5 . aromatic . 1.390 0.020
CR5 . single . 1.490 0.020
CR55 . single . 1.490 0.020
CR55 . aromatic . 1.390 0.020
CR56 . single . 1.490 0.020
CR56 . aromatic . 1.390 0.020
CR16 . single . 1.490 0.020
CR16 . aromatic . 1.390 0.020
CR6 . single . 1.490 .
CR6 . aromatic . 1.390 .
CR66 . single . 1.490 .
CR66 . aromatic . 1.390 .
CR1 . single . 1.500 .
CR1H . single . 1.500 .
C . single . 1.460 .
C . double . 1.330 .
C1 . single . 1.480 .
C1 . double . 1.330 .
C2 . single . 1.480 .
C2 . double . 1.330 .
CH1 . single . 1.530 .
CH1 C single 405.000 1.500 0.020
CH1 C1 single 405.000 1.510 0.020
CH1 C2 single 405.000 1.510 0.020
CH1 CR1 single 405.000 1.500 .
CH1 CR5 single 405.000 1.480 0.020
CH1 CR6 single 405.000 1.480 0.020
CH1 CH1 single 200.000 1.524 0.020
CH1 CSP single 200.000 1.470 0.020
CH2 . single . 1.524 0.020
CH2 C single 405.000 1.510 0.020
CH2 C1 single 405.000 1.510 0.020
CH2 C2 single 405.000 1.510 0.020
CH2 CR1 single 405.000 1.500 0.020
CH2 CR5 single 405.000 1.510 0.020
CH2 CR6 single 405.000 1.511 0.020
CH2 CH1 single 200.000 1.524 0.020
CH2 CH2 single 200.000 1.524 0.020
CH2 CSP single 200.00 1.470 0.020
CH3 . single . 1.524 0.020
CH3 CSP single 405.000 1.470 0.020
CH3 C single 405.000 1.500 0.020
CH3 C1 single 405.000 1.510 0.020
CH3 CR1 single 405.000 1.500 0.020
CH3 CR5 single 405.000 1.506 0.020
CH3 CR6 single 405.000 1.506 0.020
CH3 CH1 single 200.000 1.524 0.020
CH3 CH2 single 200.000 1.513 0.014
CH3 CH3 single 200.000 1.530 0.014
CSP . single . 1.377 0.020
CSP CSP single 200.000 1.377 0.012
CSP . triple . 1.180 0.020
CSP1 . triple . 1.180 0.020
CSP1 . single . 1.377 0.020
CSP CSP triple 200.000 1.180 0.015
CT . single . 1.524 0.020
CT C single 200.000 1.507 0.020
CT C1 single 200.000 1.510 0.020
CT C2 single 200.000 1.520 0.020
CT CR5 single 200.000 1.500 0.020
CT CR56 single 200.000 1.500 0.020
CT CR6 single 405.000 1.500 0.020
CT CH1 single 200.000 1.524 0.020
CT CH2 single 200.000 1.524 0.020
CT CH3 single 200.000 1.524 0.020
CT CT single 200.000 1.524 0.020
CT CSP single 200.000 1.470 0.020
NS1 . triple . 1.170 .
NS1 . single . 1.350 . # ?
NS . triple . 1.170 .
NS . single . 1.350 . # ?
NS CSP triple . 1.158 .
NS CSP1 triple . 1.158 .
NS NS triple . 1.158 . # ?
N . single . 1.410 . # ?
N N single . 1.410 . # ?
N . deloc . 1.30 0.020
N N deloc . 1.30 0.020
N . double . 1.24 0.020
N N double . 1.24 0.020
N C double 471.000 1.260 .
N C aromat 471.000 1.330 .
N C1 double 471.000 1.260 .
N C2 double 471.000 1.260 .
N CR6 single 422.000 1.400 .
N CR6 aromatic 422.000 1.355 .
N CR16 single 422.000 1.400 .
N CR16 aromatic 422.000 1.355 .
N CH1 single 422.000 1.455 .
N CH2 single 422.000 1.455 .
N CH3 single 422.000 1.455 .
N CT single 422.000 1.455 .
NC1 . single 422.000 1.400 .
NC1 C deloc 471.000 1.339 .
NC1 C1 deloc 471.000 1.327 .
NC1 C2 deloc 471.000 1.327 .
NC1 CH2 single 422.000 1.457 .
NH1 . single 422.000 1.400 .
NH1 C deloc 471.000 1.330 .
NH1 C1 deloc 471.000 1.330 .
NH1 C2 deloc 471.000 1.330 .
NH1 CR6 deloc 471.000 1.350 .
NH1 CR5 deloc 422.000 1.350 .
NH1 CH1 single 422.000 1.450 .
NH1 CH2 single 422.000 1.450 .
NH1 CH3 single 422.000 1.450 .
NH1 CT single 422.000 1.450 .
NC2 . single . 1.400 .
NC2 C deloc 400.000 1.336 0.017
NC2 C1 deloc 400.000 1.336 0.017
NC2 C2 deloc 400.000 1.336 0.017
NC2 CR6 deloc 422.000 1.355 0.020
NC2 CH1 single 422.000 1.457 .
NC2 CH2 single 422.000 1.457 .
NC3 . single . 1.410 .
NC3 CH1 single 422.000 1.470 . # ?
NC3 CH2 single 422.000 1.470 . # ?
NH2 . single . 1.400 .
NH2 C deloc 471.000 1.332 0.020
NH2 C1 deloc 471.000 1.332 0.020
NH2 C2 deloc 471.000 1.332 0.020
NH2 CR5 deloc 422.000 1.355 0.020
NH2 CR6 deloc 471.000 1.355 0.020
NH2 CH1 single 422.000 1.450 0.020
NH2 CH2 single 422.000 1.450 0.020
NT3 . single . 1.420 .
NT3 CR6 single 422.000 1.488 .
NT3 CH1 single 422.000 1.488 0.020
NT3 CH2 single 422.000 1.488 0.020
NT3 CH3 single 422.000 1.488 0.020
NT3 CT single 422.000 1.488 0.020
NT3 C single 422.000 1.420 0.020
NT3 C1 single 422.000 1.420 0.020
NT3 C2 single 422.000 1.420 0.020
NT1 . single . 1.420 0.020
NT2 . single . 1.420 0.020
NT . single . 1.420 .
NT C single 422.000 1.416 0.020
NT C1 single 422.000 1.416 0.020
NT C2 single 422.000 1.416 0.020
NT CH1 single 422.000 1.469 0.020
NT CH2 single 422.000 1.469 0.020
NT CH3 single 422.000 1.469 0.020
NPA . aromatic . 1.31 .
NPA . single . 1.40 .
NPA CR5 aromatic 471.000 1.336 0.014
NPA CH1 single 422.000 1.450 . # ?
NPA CT single 422.000 1.450 . # ?
NPB . aromatic . 1.310 .
NPB . single . 1.400 .
NPB CR5 aromatic 471.000 1.336 0.014
NR5 . aromatic . 1.304 .
NR5 . single . 1.400 . # ?
NR5 CR15 aromatic 440.000 1.337 0.020
NR5 CR5 aromatic 471.000 1.337 0.020
NR5 CR56 aromatic 436.000 1.337 0.020
NR5 CR16 aromatic 471.000 1.337 0.020
NR5 CR6 aromatic 471.000 1.337 0.020
NR5 CH1 single 337.000 1.485 0.020
NR5 CH3 single 337.000 1.485 0.020
NR5 CT single 337.000 1.485 0.020
NR15 . aromatic . 1.304 .
NR15 . single . 1.400 .
NR15 NR15 aromatic 422.000 1.304 .
NR15 CR15 aromatic 471.000 1.350 .
NR15 CR5 aromatic 471.000 1.340 .
NR15 CR56 aromatic 471.000 1.340 .
NRD5 . aromatic . 1.304 .
NRD5 . single . 1.404 .
NRD5 CR15 aromatic 471.000 1.350 . #?
NRD5 CR5 aromatic 471.000 1.350 . #?
NRD5 CR56 aromatic 471.000 1.350 . #?
NRD5 CR56 aromatic 414.000 1.390 . #?
NRD5 CR56 aromatic 471.000 1.350 . #?
NR56 . aromatic . 1.304 .
NR56 . single . 1.400 . # ?
NR55 CR15 aromatic 450.000 1.390 0.020
NR55 CR5 aromatic 450.000 1.390 0.020
NR55 CR5 single . 1.490 0.020
NR55 . single . 1.400 . # ?
NR55 . aromatic . 1.390 0.020
NR56 CR5 aromatic 448.000 1.337 .
NR56 CR6 aromatic 448.000 1.337 .
NR56 CR56 aromatic 448.000 1.337 .
NR56 CR15 aromatic 448.000 1.337 .
NR56 CR16 aromatic 448.000 1.337 .
NR6 . aromatic . 1.304 .
NR6 . single . 1.400 .
NR6 CR16 aromatic 448.000 1.337 .
NR6 CR6 single 424.000 1.410 .
NR6 CR6 aromatic 424.000 1.337 .
NR6 CR66 single 424.000 1.410 .
NR6 CR66 aromatic 424.000 1.337 .
NR6 CH1 single 337.000 1.465 .
NR6 CH2 single 337.000 1.465 .
NR6 CH3 single 337.000 1.465 .
NR6 CT single 337.000 1.465 .
NR16 CR6 aromatic 422.000 1.337 .
NR16 . aromatic . 1.304 .
NR16 . single . 1.400 .
NR16 CR16 aromatic 422.000 1.337 .
NR16 CR66 aromatic 422.000 1.337 .
NR16 CR56 aromatic 461.000 1.337 .
NRD6 . aromatic . 1.330 .
NRD6 . single . 1.400 .
NRD6 CR56 aromatic 461.000 1.355 . #?
NR6 CR56 aromatic 461.000 1.337 .
NRD6 CR16 aromatic 471.000 1.337 . #?
NRD6 CR6 aromatic 470.000 1.350 . #?
NRD6 CR66 aromatic 470.000 1.350 . #?
O H single . 1.040 .
O . single . 1.269 .
O . double . 1.080 .
O C single 580.000 1.330 .
O C double 580.000 1.220 .
O C1 single 580.000 1.330 .
O C1 double 580.000 1.220 .
O C2 double 580.000 1.220 .
O CR15 single 580.000 1.370 .
O CR15 aromatic 580.000 1.250 .
O CR6 single 580.000 1.330 .
O CR6 aromatic 580.000 1.250 .
O CH1 single 400.000 1.420 .
O CH2 single 400.000 1.420 .
O CH3 single 400.000 1.413 0.018
O CT single 400.000 1.430 0.015
O N single 580.000 1.400 .
O N double . 1.220 0.020
O2 . single . 1.269 .
O2 C single 580.000 1.454 0.016
O2 C2 single 580.000 1.454 0.016
O2 C1 single 580.000 1.454 0.016
O2 CR5 aromatic 580.000 1.250 .
O2 CR5 single . 1.370 .
O2 CR6 aromatic 580.000 1.250 .
O2 CR6 single 580.000 1.370 .
O2 CR66 aromatic 580.000 1.250 .
O2 CR66 single . 1.370 0.020
O2 CH1 single 320.000 1.426 0.020
O2 CH2 single 320.000 1.426 0.020
O2 CH3 single 320.000 1.426 0.020
O2 CT single 320.000 1.426 0.020
O2 NR15 aromatic 580.000 1.400 0.020
OH1 . single . 1.469 .
OH1 C single 450.000 1.330 0.015
OH1 C1 single 450.000 1.330 0.015
OH1 C2 single 450.000 1.330 0.015
OH1 CR15 single 450.000 1.362 0.015 # ? impossible
OH1 CR6 single 450.000 1.362 0.015
OH1 CH1 single 320.000 1.432 0.020
OH1 CH2 single 320.000 1.432 0.020
OH1 CH3 single 320.000 1.413 0.020
OH1 CT single 320.000 1.432 0.020
OH1 N single 450.000 1.392 0.015
OH1 NH1 single 450.000 1.392 0.020
OH1 NT single 450.000 1.460 0.020
OH1 NT3 single 450.000 1.460 0.020
OC2 . single . 1.469 0.020
OC2 CR15 single 580.000 1.354 . #?
OC2 CR15 aromatic 580.000 1.254 . #?
OC2 CH1 single 320.000 1.410 .
OC2 CH2 single 320.000 1.410 .
OC2 CT single 320.000 1.410 .
OC . single . 1.150 . #? for OC single and double
OC . double . 1.150 . #? are equavalent
OC C deloc 580.000 1.250 . # bond should be delocalised
OC C1 deloc 580.000 1.250 .
OC C2 deloc 580.000 1.250 .
OC CH1 deloc 580.000 1.420 . #impossible ?
OP . single . 1.150 . # ?
OP . double . 1.150 . # single and double are equavalent
H . single . 0.667 0.020
HCH1 . single . 0.667 .
HCH1 CH1 single 300.000 1.099 0.010
HCH2 . single . 0.667 .
HCH2 CH2 single 300.000 1.092 0.013
HCH3 . single . 0.667 .
HCH3 CH3 single 300.000 1.059 0.030
HCR1 . single . 0.667 .
HCR1 CR1 single 350.000 1.077 0.012 # impossible
HCR1 CR1H single 350.000 1.077 0.012
HC2 . single . 0.667 .
HC2 C2 single 350.000 1.077 0.012
HC1 . single . 0.667 .
HC1 C1 single 350.000 1.077 0.012
HCR5 . single . 0.667 .
HCR5 CR15 single 350.000 1.083 0.011
HCR6 . single . 0.667 .
HCR6 CR16 single 350.000 1.083 0.011
HNC1 . single . 0.667 .
HNC1 NC1 single 405.000 1.009 0.020 #?
HNC2 . single . 0.667 .
HNC2 NC2 single 405.000 1.009 0.020 #?
HNT1 . single . 0.667 .
HNT1 NT1 single 405.000 1.033 0.022
HNT2 . single . 0.667 .
HNT2 NT2 single 405.000 1.033 0.022
HNT3 . single . 0.667 .
HNT3 NT3 single 405.000 1.033 0.022
HNH1 . single . 0.667 .
HNH1 NH1 single 405.000 1.010 0.020 #?
HNH2 . single . 0.667 .
HNH2 NH2 single 405.000 1.010 0.020
HNR5 . single . 0.667 .
HNR5 NR15 single 405.000 1.040 0.020 #?
HNR6 . single . 0.667 .
HNR6 NR16 single 405.000 1.040 0.020 #?
HOH1 . single . 0.667 .
HOH1 OH1 single 450.000 0.967 0.010
HOH2 . single . 0.667 .
HOH2 OH2 single 450.000 0.960 0.020 #?
HOHA . single . 0.667 .
HOHA OHA single 450.000 0.960 0.020 #?
HOHB . single . 0.667 .
HOHB OHB single 450.000 0.960 0.020 #?
HOHC . single . 0.667 .
HOHC OHC single 450.000 0.960 0.020 #?
P . single . 2.256 .
P . double . 2.050 .
P . deloc . 2.100 0.020
P1 . single . 2.200 0.020
P O double . 1.48 .
P O single . 1.61 .
P OH1 single . 1.61 .
P O2 single 230.000 1.610 .
P OC2 single 230.000 1.610 .
P OP deloc . 1.510 .
P OP double . 1.480 .
P OP single . 1.610 .
P OC single . 1.610 .
P OC2 single . 1.610 .
P P single . 2.214 0.022
P P double . 2.030 0.030
PS PS single . 2.214 0.022
PS PS double . 2.030 0.030
PS . single . 2.114 0.040
PS . double . 1.930 0.040
#
S . single . 2.050 .
S . double . 1.890 . # ?
S CH1 single 450.000 1.810 .
S CH2 single 450.000 1.810 .
S CH3 single 450.000 1.810 .
S OS single 525.000 1.577 .
S OS double 525.000 1.436 .
S OS deloc . 1.470 .
S O single 525.000 1.577 . # impossible
S O double 525.000 1.436 .
S3 O double . 1.480 .
S3 O single . 1.577 .
S3 . single . 2.050 .
S3 . double . 1.890 .
ST . single . 2.050 .
ST . double . 1.80 0.020
ST . deloc . 1.80 0.020
S2 . single . 2.00 0.020
S1 . double . 1.80 0.020
ST OS single 525.000 1.577 .
ST OS double 525.000 1.436 .
ST OS delocal 525.000 1.480 .
ST O single 525.000 1.575 .
ST O double 525.000 1.436 .
S S single 500.000 2.036 .
SH1 . single . 2.050 .
SH1 CSP single 450.000 1.680 .
SH1 CH2 single 450.000 1.810 .
SH1 HSH1 single 300.000 1.330 . # ?
FE . metal . 2.470 0.040 # ?
FE NPA metal 500.000 2.090 0.040 # ?
FE NPB metal 500.000 2.090 0.040 # ?
FE NR5 metal 500.000 2.090 0.040 # ?
FE NRD5 metal 500.000 1.980 0.040 # ?
FE O metal 500.000 2.040 0.040 # ?
FE S metal 500.000 2.300 0.040
MG . metal . 2.670 0.040
MG NPA metal 500.000 2.090 .
MG NPB metal 500.000 2.090 .
MG OHA metal 500.000 2.150 . # ?
MG OHB metal 500.000 2.150 . # ?
MG OHC metal 500.000 2.150 . # ?
MG O metal 500.000 2.180 . # ?
MG OC metal 500.000 2.180 . # ?
F . single . 1.300 . # ?
F CH1 single . 1.370 .
F CH2 single . 1.370 .
F CH3 single . 1.370 .
F CT single . 1.320 .
B . single . 1.600 . # ?
B CH1 single . 1.600 .
B CH2 single . 1.600 .
B CH3 single . 1.600 .
B CT single . 1.600 .
B CR6 single . 1.560 .
B CR5 single . 1.560 .
B OB single . 1.37 .
CA . metal . 3.25 0.050
CA OS metal . 2.32 0.050
CA O metal . 2.32 0.050
CA O2 metal . 2.32 0.050
CA OH1 metal . 2.32 0.050
CA OH2 metal . 2.32 0.050
CA OHA metal . 2.32 0.050
CA OHB metal . 2.32 0.050
CA OHC metal . 2.32 0.050
CA OC2 metal . 2.32 0.050
CA OC metal . 2.32 0.050
CA OP metal . 2.32 0.050
CL . single . 2.20 0.040
CL CH1 single . 1.790 0.020
CL CH2 single . 1.790 0.020
CL CH3 single . 1.790 0.020
CL CT single . 1.790 0.020
CO . metal . 2.380 0.050
CO C metal 65.000 1.980 .
CO C1 metal 65.000 1.980 .
CO C2 metal 65.000 1.980 .
CO CT metal 65.000 1.980 .
CO CH1 metal 65.000 1.980 .
CO CH2 metal 65.000 1.980 .
CO CH3 metal 65.000 1.980 .
CO NPA metal 500.000 1.980 .
CO NPB metal 500.000 1.980 .
CO NT3 metal 500.000 1.980 .
CO NRD5 metal 65.000 1.980 .
ZN . metal . 2.900 .
ZN NRD5 metal 65.000 2.150 .
I . single . 2.80 .
I CR6 single 65.000 2.090 .
BR . metal . 2.500 .
BR CR6 metal 65.000 1.890 .
#
NA . metal . 3.400 .
V . metal . 2.740 .
MN . metal . 2.700 .
CU . metal . 2.750 .
CD . metal . 3.250 .
PB . metal . 3.530 .
HG . metal . 3.200 0.070
U . metal . 3.400 0.070 # ?
W . metal . 3.000 0.070
Y . metal . 3.550 0.070
K . metal . 4.130 0.070
SI . single . 2.10 0.020
SI SI single . 2.35 0.020
SI1 . single . 2.10 0.030
AL . metal . 2.30 0.070
AL O double . 1.850 0.030
AL F single . 1.800 0.030
GD . metal . 3.570 0.070
NI . metal . 2.800 0.070
SM . metal . 2.450 0.070
SR . metal . 3.800 0.070
IN . metal . 3.400 0.070
HO . metal . 3.250 0.070
YB . metal . 3.350 0.070
TE . metal . 2.600 0.070
LI . metal . 2.400 0.070
RB . metal . 3.800 0.070
BA . metal . 4.350 0.070 # ?
CS . metal . 4.500 0.070
TL . metal . 3.400 0.070
PT . metal . 2.650 0.040
BE . metal . 2.230 0.040
SC . metal . . 0.04
TI . metal . . 0.04
CR . metal . . 0.04
GA . metal . . 0.04
GE . single . 2.35 0.02
GE . metal . 2.40 0.04
GE1 . metal . 2.40 0.04
GE1 . single . 2.35 0.02
SN . single . 2.75 0.03
SN . metal . 2.75 0.03
PB . metal . 2.90 0.04
# AS . metal . 2.46 0.04
AS . single . 2.40 0.03
AS1 . single . 2.46 0.03
SB . metal . . 0.04
BI . metal . 2.80 0.04
#
ZR . metal . . 0.04
NB . metal . . 0.04
TC . metal . . 0.04
RU . metal . . 0.04
RH . metal . . 0.04
PD . metal . . 0.04
AG . metal . . 0.04
SE CH1 single . 1.948 0.030
SE CH2 single . 1.948 0.030
SE CH3 single . 1.948 0.030
SE CT single . 1.948 0.030
SE . single . 2.340 0.040
SE . double . 1.750 0.040
SE O single . 1.974 0.030
SE O double . 1.597 0.030
MO . metal . 2.650 0.040
OSE . metal . 2.650 0.040
IR . metal . 2.650 0.040
#
DUM . . . 0.01 1.000
. . . . 2.4 0.100
#
# --- ANGLES ---
#
loop_
_lib_angle.atom_type_1
_lib_angle.atom_type_2
_lib_angle.atom_type_3
_lib_angle.const
_lib_angle.value
#
# _atom_type atomic chemical type
# _const constant KTHETA
# _value equilibrium value for the angle THETA0
# THETA - actual angle
#
# ENERGY = KTHETA * ( THETA - THETA0 )**2
#
NS CSP CH3 . 180.000
NS CSP SH1 . 180.000
C C C 45.000 120.000
CH1 C C 45.000 120.000
CH2 C C 45.000 120.000
CH3 C C 45.000 120.000
CT C C 45.000 120.000
C1 C C 45.000 120.000
C2 C C 45.000 120.000
C1 C C1 45.000 120.000
C2 C C1 45.000 120.000
CH1 C C1 45.000 120.000
CH2 C C1 45.000 120.000
CH3 C C1 45.000 120.000
CT C C1 45.000 120.000
C2 C C2 45.000 120.000
CH1 C C2 45.000 120.000
CH2 C C2 45.000 120.000
CH3 C C2 45.000 120.000
CT C C2 45.000 120.000
CH2 C CR5 45.000 116.500
CH3 C CR5 45.000 116.500
CH1 C CH3 45.000 120.000
CH1 C CH2 45.000 120.000
CH2 C CH3 45.000 120.000
CH3 C CH3 45.000 120.000
CT C CH1 45.000 120.000
CT C CH2 45.000 120.000
CT C CH3 45.000 120.000
N C C 20.000 116.500
N C C1 20.000 116.500
N C C2 20.000 116.500
N C CH1 20.000 116.500
N C CH2 20.000 116.500
N C CH3 20.000 116.500
N C CT 20.000 116.500