# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 19:07:05 2020
#   Inital geometry file: a 47 line input string
#   Ligand name: 1H-benzimidazol-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1[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
 AX7  AX7  '1H-benzimidazol-2-amine  '  ligand  17  10  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AX7
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
 AX7  NAF   N  NR15  0  -0.719   1.1214  -1.0523  -0.0254
 AX7  CAI   C  CR56  0   0.337  -0.2031  -0.6803  -0.0158
 AX7  CAD   C  CR16  0  -0.314  -1.3809  -1.4068   0.0101
 AX7  CAB   C  CR16  0  -0.289  -2.5677  -0.6821   0.0116
 AX7  CAC   C  CR16  0  -0.273  -2.5612   0.7149  -0.0116
 AX7  CAE   C  CR16  0  -0.348  -1.3724   1.4333  -0.0366
 AX7  CAJ   C  CR56  0   0.158  -0.1741   0.7264  -0.0380
 AX7  NAG   N  N     0  -0.523   1.1255   1.1780  -0.0555
 AX7  CAH   C  CR5   0   0.606   1.8590   0.0919  -0.0474
 AX7  NAA   N  NH2   0  -0.847   3.2122   0.0632  -0.1171
 AX7  HNAF  H  HNR5  0   0.416   1.4816  -1.9933  -0.0212
 AX7  HAD   H  HCR6  0   0.260  -1.3834  -2.4889   0.0274
 AX7  HAB   H  HCR6  0   0.248  -3.5110  -1.2122   0.0317
 AX7  HAC   H  HCR6  0   0.246  -3.5028   1.2491  -0.0096
 AX7  HAE   H  HCR6  0   0.246  -1.3769   2.5159  -0.0540
 AX7  HNAA  H  HNH2  0   0.399   3.6792  -0.7508   0.2491
 AX7  HNAB  H  HNH2  0   0.397   3.6693   0.9273   0.1249

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
 AX7  NAF  CAI   aromatic  1.376  0.020  1.376
 AX7  NAF  CAH   aromatic  1.362  0.020  1.362
 AX7  CAI  CAD   aromatic  1.384  0.020  1.384
 AX7  CAI  CAJ   aromatic  1.407  0.020  1.407
 AX7  CAD  CAB   aromatic  1.391  0.020  1.391
 AX7  CAB  CAC   aromatic  1.397  0.020  1.397
 AX7  CAC  CAE   aromatic  1.389  0.020  1.389
 AX7  CAE  CAJ   aromatic  1.391  0.020  1.391
 AX7  CAJ  NAG   aromatic  1.376  0.020  1.376
 AX7  NAG  CAH   aromatic  1.311  0.020  1.311
 AX7  CAH  NAA   single    1.355  0.020  1.355
 AX7  NAF  HNAF  single    0.860  0.020  1.020
 AX7  CAD  HAD   single    0.930  0.020  1.080
 AX7  CAB  HAB   single    0.930  0.020  1.080
 AX7  CAC  HAC   single    0.930  0.020  1.080
 AX7  CAE  HAE   single    0.930  0.020  1.080
 AX7  NAA  HNAA  single    0.890  0.020  1.040
 AX7  NAA  HNAB  single    0.890  0.020  1.040

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
 AX7  HNAF  NAF  CAH   126.24  3.000
 AX7  HNAF  NAF  CAI   126.63  3.000
 AX7  CAH   NAF  CAI   107.12  3.000
 AX7  CAJ   CAI  CAD   122.85  3.000
 AX7  CAJ   CAI  NAF   104.50  3.000
 AX7  CAD   CAI  NAF   132.65  3.000
 AX7  HAD   CAD  CAB   121.27  3.000
 AX7  HAD   CAD  CAI   121.81  3.000
 AX7  CAB   CAD  CAI   116.92  3.000
 AX7  HAB   CAB  CAC   119.61  3.000
 AX7  HAB   CAB  CAD   119.25  3.000
 AX7  CAC   CAB  CAD   121.14  3.000
 AX7  HAC   CAC  CAE   119.29  3.000
 AX7  HAC   CAC  CAB   119.29  3.000
 AX7  CAE   CAC  CAB   121.42  3.000
 AX7  HAE   CAE  CAJ   120.77  3.000
 AX7  HAE   CAE  CAC   120.92  3.000
 AX7  CAJ   CAE  CAC   118.31  3.000
 AX7  NAG   CAJ  CAE   130.30  3.000
 AX7  NAG   CAJ  CAI   110.35  3.000
 AX7  CAE   CAJ  CAI   119.35  3.000
 AX7  CAH   NAG  CAJ   104.87  3.000
 AX7  NAA   CAH  NAG   125.18  3.000
 AX7  NAA   CAH  NAF   121.59  3.000
 AX7  NAG   CAH  NAF   113.16  3.000
 AX7  HNAB  NAA  HNAA  113.30  3.000
 AX7  HNAB  NAA  CAH   115.00  3.000
 AX7  HNAA  NAA  CAH   117.47  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
 AX7  CONST_01  CAB   CAD  CAI  NAF  180.00  0.0  0
 AX7  CONST_02  CAE   CAJ  CAI  NAF  180.00  0.0  0
 AX7  CONST_03  NAG   CAJ  CAI  NAF    0.00  0.0  0
 AX7  CONST_04  CAJ   NAG  CAH  NAF    0.00  0.0  0
 AX7  CONST_05  NAG   CAH  NAF  CAI    0.00  0.0  0
 AX7  CONST_06  CAC   CAB  CAD  CAI    0.00  0.0  0
 AX7  CONST_07  CAC   CAE  CAJ  CAI    0.00  0.0  0
 AX7  CONST_08  CAH   NAG  CAJ  CAI    0.00  0.0  0
 AX7  CONST_09  CAH   NAF  CAI  CAD  180.00  0.0  0
 AX7  CONST_10  CAE   CAJ  CAI  CAD    0.00  0.0  0
 AX7  CONST_11  NAG   CAJ  CAI  CAD  180.00  0.0  0
 AX7  CONST_12  CAE   CAC  CAB  CAD    0.00  0.0  0
 AX7  CONST_13  CAJ   CAI  CAD  CAB    0.00  0.0  0
 AX7  CONST_14  CAJ   CAE  CAC  CAB    0.00  0.0  0
 AX7  CONST_15  NAG   CAJ  CAE  CAC  180.00  0.0  0
 AX7  CONST_16  CAH   NAG  CAJ  CAE  180.00  0.0  0
 AX7  CONST_17  CAH   NAF  CAI  CAJ    0.00  0.0  0
 AX7  CONST_18  NAA   CAH  NAF  CAI  180.00  0.0  0
 AX7  CONST_19  NAA   CAH  NAG  CAJ  180.00  0.0  0
 AX7  CONST_20  HAD   CAD  CAI  NAF    0.00  0.0  0
 AX7  CONST_21  HAB   CAB  CAD  CAI  180.00  0.0  0
 AX7  CONST_22  HAE   CAE  CAJ  CAI  180.00  0.0  0
 AX7  CONST_23  HNAF  NAF  CAI  CAD    0.00  0.0  0
 AX7  CONST_24  HAC   CAC  CAB  CAD  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
 AX7  plan-1  NAF   0.020
 AX7  plan-1  CAI   0.020
 AX7  plan-1  CAD   0.020
 AX7  plan-1  CAB   0.020
 AX7  plan-1  CAC   0.020
 AX7  plan-1  CAE   0.020
 AX7  plan-1  CAJ   0.020
 AX7  plan-1  NAG   0.020
 AX7  plan-1  CAH   0.020
 AX7  plan-1  NAA   0.020
 AX7  plan-1  HNAF  0.020
 AX7  plan-1  HAD   0.020
 AX7  plan-1  HAB   0.020
 AX7  plan-1  HAC   0.020
 AX7  plan-1  HAE   0.020
 AX7  plan-2  CAH   0.020
 AX7  plan-2  NAA   0.020
 AX7  plan-2  HNAA  0.020
 AX7  plan-2  HNAB  0.020

