# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 29 23:30:49 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: 1H-benzimidazole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1[nH]c2ccccc2n1
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 TRM  TRM  '1H-benzimidazole-2-carboxylic acid'  ligand  18  12  .  2022-07-22  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_TRM
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 TRM  NG    N  N     0  -0.436   1.1597  -0.0256   0.4432
 TRM  CD1   C  CR5   0   0.348   0.0605  -0.0038   1.1454
 TRM  NE1   N  NR15  0  -0.683  -1.0647   0.0214   0.3889
 TRM  CE2   C  CR56  0   0.346  -0.6655   0.0159  -0.9131
 TRM  CZ2   C  CR16  0  -0.300  -1.3683   0.0341  -2.1166
 TRM  CH2   C  CR16  0  -0.270  -0.6122   0.0213  -3.2705
 TRM  CZ3   C  CR16  0  -0.267   0.7955  -0.0086  -3.2356
 TRM  CE3   C  CR16  0  -0.325   1.4860  -0.0262  -2.0427
 TRM  CD2   C  CR56  0   0.136   0.7409  -0.0137  -0.8590
 TRM  C     C  C     0   0.472  -0.0375  -0.0056   2.6181
 TRM  O     O  O     0  -0.426  -1.0984   0.0116   3.1913
 TRM  OXT   O  OH1   0  -0.575   1.1450  -0.0269   3.1962
 TRM  HE11  H  HNR5  0   0.428  -2.0130   0.0434   0.7331
 TRM  HZ21  H  HCR6  0   0.273  -2.4493   0.0567  -2.1474
 TRM  HH21  H  HCR6  0   0.263  -1.1128   0.0350  -4.2297
 TRM  HZ31  H  HCR6  0   0.260   1.3426  -0.0179  -4.1691
 TRM  HE31  H  HCR6  0   0.262   2.5675  -0.0481  -2.0169
 TRM  HXT   H  HOH1  0   0.496   1.0434  -0.0275   4.1603

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 TRM  NG   CD1   aromatic  1.305  0.020  1.305
 TRM  NG   CD2   aromatic  1.368  0.020  1.368
 TRM  CD1  NE1   aromatic  1.356  0.020  1.356
 TRM  CD1  C     single    1.476  0.020  1.476
 TRM  NE1  CE2   aromatic  1.362  0.020  1.362
 TRM  NE1  HE11  single    0.860  0.020  1.020
 TRM  CE2  CZ2   aromatic  1.394  0.020  1.394
 TRM  CE2  CD2   aromatic  1.408  0.020  1.408
 TRM  CZ2  CH2   aromatic  1.380  0.020  1.380
 TRM  CZ2  HZ21  single    0.930  0.020  1.080
 TRM  CH2  CZ3   aromatic  1.408  0.020  1.408
 TRM  CH2  HH21  single    0.930  0.020  1.080
 TRM  CZ3  CE3   aromatic  1.379  0.020  1.379
 TRM  CZ3  HZ31  single    0.930  0.020  1.080
 TRM  CE3  CD2   aromatic  1.399  0.020  1.399
 TRM  CE3  HE31  single    0.930  0.020  1.080
 TRM  C    O     double    1.206  0.020  1.206
 TRM  C    OXT   single    1.316  0.020  1.316
 TRM  OXT  HXT   single    0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 TRM  CD2   NG   CD1  104.73  3.000
 TRM  C     CD1  NE1  120.10  3.000
 TRM  C     CD1  NG   126.37  3.000
 TRM  NE1   CD1  NG   113.52  3.000
 TRM  HE11  NE1  CE2  127.00  3.000
 TRM  HE11  NE1  CD1  126.14  3.000
 TRM  CE2   NE1  CD1  106.86  3.000
 TRM  CD2   CE2  CZ2  122.49  3.000
 TRM  CD2   CE2  NE1  104.85  3.000
 TRM  CZ2   CE2  NE1  132.66  3.000
 TRM  HZ21  CZ2  CH2  121.61  3.000
 TRM  HZ21  CZ2  CE2  121.92  3.000
 TRM  CH2   CZ2  CE2  116.47  3.000
 TRM  HH21  CH2  CZ3  118.99  3.000
 TRM  HH21  CH2  CZ2  119.19  3.000
 TRM  CZ3   CH2  CZ2  121.82  3.000
 TRM  HZ31  CZ3  CE3  119.55  3.000
 TRM  HZ31  CZ3  CH2  118.96  3.000
 TRM  CE3   CZ3  CH2  121.49  3.000
 TRM  HE31  CE3  CD2  120.83  3.000
 TRM  HE31  CE3  CZ3  121.43  3.000
 TRM  CD2   CE3  CZ3  117.73  3.000
 TRM  CE3   CD2  CE2  119.99  3.000
 TRM  CE3   CD2  NG   129.97  3.000
 TRM  CE2   CD2  NG   110.04  3.000
 TRM  OXT   C    O    125.57  3.000
 TRM  OXT   C    CD1  112.25  3.000
 TRM  O     C    CD1  122.19  3.000
 TRM  HXT   OXT  C    110.04  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 TRM  CONST_01  CE2   NE1  CD1  NG      0.00   0.0  0
 TRM  CONST_02  NE1   CE2  CD2  NG      0.00   0.0  0
 TRM  CONST_03  CZ2   CE2  CD2  NG    180.00   0.0  0
 TRM  CONST_04  CZ3   CE3  CD2  NG    180.00   0.0  0
 TRM  CONST_05  CE2   CD2  NG   CD1     0.00   0.0  0
 TRM  CONST_06  CE3   CD2  NG   CD1   180.00   0.0  0
 TRM  CONST_07  CZ2   CE2  NE1  CD1   180.00   0.0  0
 TRM  CONST_08  CD2   CE2  NE1  CD1     0.00   0.0  0
 TRM  CONST_09  CD2   NG   CD1  NE1     0.00   0.0  0
 TRM  CONST_10  CH2   CZ2  CE2  NE1   180.00   0.0  0
 TRM  CONST_11  CE3   CD2  CE2  NE1   180.00   0.0  0
 TRM  CONST_12  CZ3   CH2  CZ2  CE2     0.00   0.0  0
 TRM  CONST_13  CZ3   CE3  CD2  CE2     0.00   0.0  0
 TRM  CONST_14  CE3   CD2  CE2  CZ2     0.00   0.0  0
 TRM  CONST_15  CE3   CZ3  CH2  CZ2     0.00   0.0  0
 TRM  CONST_16  CD2   CE2  CZ2  CH2     0.00   0.0  0
 TRM  CONST_17  CD2   CE3  CZ3  CH2     0.00   0.0  0
 TRM  CONST_18  C     CD1  NE1  CE2   180.00   0.0  0
 TRM  CONST_19  C     CD1  NG   CD2   180.00   0.0  0
 TRM  CONST_20  HE11  NE1  CD1  NG    180.00   0.0  0
 TRM  CONST_21  HE31  CE3  CD2  NG      0.00   0.0  0
 TRM  CONST_22  HZ21  CZ2  CE2  NE1     0.00   0.0  0
 TRM  CONST_23  HH21  CH2  CZ2  CE2   180.00   0.0  0
 TRM  CONST_24  HZ31  CZ3  CH2  CZ2   180.00   0.0  0
 TRM  CONST_25  HXT   OXT  C    CD1   180.00   0.0  0
 TRM  Var_01    O     C    CD1  NG   -179.77  30.0  2

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 TRM  plan-1  NG    0.020
 TRM  plan-1  CD1   0.020
 TRM  plan-1  NE1   0.020
 TRM  plan-1  CE2   0.020
 TRM  plan-1  CZ2   0.020
 TRM  plan-1  CH2   0.020
 TRM  plan-1  CZ3   0.020
 TRM  plan-1  CE3   0.020
 TRM  plan-1  CD2   0.020
 TRM  plan-1  C     0.020
 TRM  plan-1  HE11  0.020
 TRM  plan-1  HZ21  0.020
 TRM  plan-1  HH21  0.020
 TRM  plan-1  HZ31  0.020
 TRM  plan-1  HE31  0.020
 TRM  plan-2  CD1   0.020
 TRM  plan-2  C     0.020
 TRM  plan-2  O     0.020
 TRM  plan-2  OXT   0.020
 TRM  plan-2  HXT   0.020

