# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 01:40:16 2020
#   Inital geometry file: a 47 line input string
#   Ligand name: 1H-benzimidazol-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cccc2[nH]cnc12
#
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
 7WA  7WA  '1H-benzimidazol-4-amine  '  ligand  17  10  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7WA
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
 7WA  C10  C  CR56  0   0.071   0.1782   0.4617  -0.0295
 7WA  N01  N  NH2   0  -0.850  -1.6852   1.9907  -0.1412
 7WA  C02  C  CR6   0   0.230  -1.2065   0.7059  -0.0445
 7WA  C03  C  CR16  0  -0.366  -2.0299  -0.4173  -0.0142
 7WA  C04  C  CR16  0  -0.272  -1.5035  -1.7164   0.0227
 7WA  C05  C  CR16  0  -0.341  -0.1449  -1.9727   0.0356
 7WA  C06  C  CR56  0   0.342   0.6769  -0.8456   0.0111
 7WA  N07  N  NR15  0  -0.665   2.0369  -0.6856   0.0180
 7WA  C08  C  CR15  0   0.100   2.2900   0.6461  -0.0132
 7WA  N09  N  N     0  -0.457   1.2102   1.3720  -0.0437
 7WA  H1   H  HNH2  0   0.378  -1.0646   2.7087   0.1971
 7WA  H2   H  HNH2  0   0.379  -2.6336   2.1309   0.1672
 7WA  H3   H  HCR6  0   0.248  -3.1055  -0.2859  -0.0216
 7WA  H4   H  HCR6  0   0.249  -2.1970  -2.5476   0.0433
 7WA  H5   H  HCR6  0   0.254   0.2492  -2.9792   0.0653
 7WA  H6   H  HNR5  0   0.419   2.7302  -1.4154   0.0525
 7WA  H7   H  HCR5  0   0.283   3.3006   1.0262  -0.0124

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
 7WA  N01  C02  single    1.375  0.020  1.375
 7WA  C03  C02  aromatic  1.393  0.020  1.393
 7WA  C03  C04  aromatic  1.402  0.020  1.402
 7WA  C02  C10  aromatic  1.406  0.020  1.406
 7WA  C04  C05  aromatic  1.383  0.020  1.383
 7WA  C05  C06  aromatic  1.395  0.020  1.395
 7WA  C10  C06  aromatic  1.400  0.020  1.400
 7WA  C10  N09  aromatic  1.376  0.020  1.376
 7WA  C06  N07  aromatic  1.369  0.020  1.369
 7WA  N09  C08  aromatic  1.301  0.020  1.301
 7WA  N07  C08  aromatic  1.356  0.020  1.356
 7WA  N01  H1   single    0.890  0.020  1.040
 7WA  N01  H2   single    0.890  0.020  1.040
 7WA  C03  H3   single    0.930  0.020  1.080
 7WA  C04  H4   single    0.930  0.020  1.080
 7WA  C05  H5   single    0.930  0.020  1.080
 7WA  N07  H6   single    0.860  0.020  1.020
 7WA  C08  H7   single    0.930  0.020  1.080

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
 7WA  N09  C10  C06  110.54  3.000
 7WA  N09  C10  C02  128.57  3.000
 7WA  C06  C10  C02  120.89  3.000
 7WA  H2   N01  H1   112.22  3.000
 7WA  H2   N01  C02  115.88  3.000
 7WA  H1   N01  C02  115.34  3.000
 7WA  C03  C02  N01  123.32  3.000
 7WA  C03  C02  C10  116.22  3.000
 7WA  N01  C02  C10  120.40  3.000
 7WA  H3   C03  C04  119.03  3.000
 7WA  H3   C03  C02  119.26  3.000
 7WA  C04  C03  C02  121.71  3.000
 7WA  H4   C04  C05  119.14  3.000
 7WA  H4   C04  C03  118.12  3.000
 7WA  C05  C04  C03  122.75  3.000
 7WA  H5   C05  C06  122.54  3.000
 7WA  H5   C05  C04  122.06  3.000
 7WA  C06  C05  C04  115.40  3.000
 7WA  N07  C06  C05  132.79  3.000
 7WA  N07  C06  C10  104.17  3.000
 7WA  C05  C06  C10  123.03  3.000
 7WA  H6   N07  C08  125.73  3.000
 7WA  H6   N07  C06  126.81  3.000
 7WA  C08  N07  C06  107.46  3.000
 7WA  H7   C08  N09  125.47  3.000
 7WA  H7   C08  N07  121.36  3.000
 7WA  N09  C08  N07  113.17  3.000
 7WA  C08  N09  C10  104.65  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
 7WA  CONST_01  C04  C03  C02  C10    0.00  0.0  0
 7WA  CONST_02  C04  C05  C06  C10    0.00  0.0  0
 7WA  CONST_03  C08  N07  C06  C10    0.00  0.0  0
 7WA  CONST_04  N07  C08  N09  C10    0.00  0.0  0
 7WA  CONST_05  C05  C04  C03  C02    0.00  0.0  0
 7WA  CONST_06  C05  C06  C10  C02    0.00  0.0  0
 7WA  CONST_07  N07  C06  C10  C02  180.00  0.0  0
 7WA  CONST_08  C08  N09  C10  C02  180.00  0.0  0
 7WA  CONST_09  C06  C10  C02  C03    0.00  0.0  0
 7WA  CONST_10  N09  C10  C02  C03  180.00  0.0  0
 7WA  CONST_11  C06  C05  C04  C03    0.00  0.0  0
 7WA  CONST_12  N07  C06  C05  C04  180.00  0.0  0
 7WA  CONST_13  N09  C10  C06  C05  180.00  0.0  0
 7WA  CONST_14  C08  N07  C06  C05  180.00  0.0  0
 7WA  CONST_15  C08  N09  C10  C06    0.00  0.0  0
 7WA  CONST_16  N09  C08  N07  C06    0.00  0.0  0
 7WA  CONST_17  N09  C10  C06  N07    0.00  0.0  0
 7WA  CONST_18  C04  C03  C02  N01  180.00  0.0  0
 7WA  CONST_19  C06  C10  C02  N01  180.00  0.0  0
 7WA  CONST_20  N09  C10  C02  N01    0.00  0.0  0
 7WA  CONST_21  H3   C03  C02  C10  180.00  0.0  0
 7WA  CONST_22  H5   C05  C06  C10  180.00  0.0  0
 7WA  CONST_23  H6   N07  C06  C10  180.00  0.0  0
 7WA  CONST_24  H7   C08  N09  C10  180.00  0.0  0
 7WA  CONST_25  H4   C04  C03  C02  180.00  0.0  0

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
 7WA  plan-1  C10  0.020
 7WA  plan-1  N01  0.020
 7WA  plan-1  C02  0.020
 7WA  plan-1  C03  0.020
 7WA  plan-1  C04  0.020
 7WA  plan-1  C05  0.020
 7WA  plan-1  C06  0.020
 7WA  plan-1  N07  0.020
 7WA  plan-1  C08  0.020
 7WA  plan-1  N09  0.020
 7WA  plan-1  H3   0.020
 7WA  plan-1  H4   0.020
 7WA  plan-1  H5   0.020
 7WA  plan-1  H6   0.020
 7WA  plan-1  H7   0.020
 7WA  plan-2  N01  0.020
 7WA  plan-2  C02  0.020
 7WA  plan-2  H1   0.020
 7WA  plan-2  H2   0.020

