# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 20:21:31 2020
#   Inital geometry file: a 43 line input string
#   Ligand name: 1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [nH]1cnc2ccccc12
#
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
 BZI  BZI  '1H-benzimidazole         '  ligand  15  9  .  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_BZI
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
 BZI  N1   N  NR15  0  -0.659  -1.0312   0.0155   1.5764
 BZI  C2   C  CR15  0   0.103   0.1168   0.0327   2.2938
 BZI  N3   N  N     0  -0.463   1.1910   0.0240   1.5567
 BZI  C3A  C  CR56  0   0.129   0.7265  -0.0006   0.2614
 BZI  C4   C  CR16  0  -0.325   1.4263  -0.0186  -0.9457
 BZI  C5   C  CR16  0  -0.272   0.6957  -0.0411  -2.1194
 BZI  C6   C  CR16  0  -0.278  -0.7083  -0.0468  -2.1071
 BZI  C7   C  CR16  0  -0.302  -1.4218  -0.0295  -0.9221
 BZI  C7A  C  CR56  0   0.330  -0.6793  -0.0063   0.2538
 BZI  HN1  H  HNR5  0   0.422  -1.9646   0.0196   1.9558
 BZI  H2   H  HCR5  0   0.286   0.1021   0.0512   3.3734
 BZI  H4   H  HCR6  0   0.254   2.5087  -0.0146  -0.9594
 BZI  H5   H  HCR6  0   0.252   1.2138  -0.0554  -3.0696
 BZI  H6   H  HCR6  0   0.255  -1.2450  -0.0655  -3.0467
 BZI  H7   H  HCR6  0   0.267  -2.5038  -0.0340  -0.9148

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
 BZI  N1   C2   aromatic  1.354  0.020  1.354
 BZI  N1   C7A  aromatic  1.369  0.020  1.369
 BZI  N1   HN1  single    0.860  0.020  1.020
 BZI  C2   N3   aromatic  1.303  0.020  1.303
 BZI  C2   H2   single    0.930  0.020  1.080
 BZI  N3   C3A  aromatic  1.376  0.020  1.376
 BZI  C3A  C4   aromatic  1.395  0.020  1.395
 BZI  C3A  C7A  aromatic  1.406  0.020  1.406
 BZI  C4   C5   aromatic  1.383  0.020  1.383
 BZI  C4   H4   single    0.930  0.020  1.080
 BZI  C5   C6   aromatic  1.404  0.020  1.404
 BZI  C5   H5   single    0.930  0.020  1.080
 BZI  C6   C7   aromatic  1.383  0.020  1.383
 BZI  C6   H6   single    0.930  0.020  1.080
 BZI  C7   C7A  aromatic  1.391  0.020  1.391
 BZI  C7   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
 BZI  HN1  N1   C7A  127.02  3.000
 BZI  HN1  N1   C2   125.87  3.000
 BZI  C7A  N1   C2   107.11  3.000
 BZI  H2   C2   N3   125.23  3.000
 BZI  H2   C2   N1   121.23  3.000
 BZI  N3   C2   N1   113.53  3.000
 BZI  C3A  N3   C2   104.73  3.000
 BZI  C7A  C3A  C4   119.79  3.000
 BZI  C7A  C3A  N3   110.04  3.000
 BZI  C4   C3A  N3   130.17  3.000
 BZI  H4   C4   C5   121.17  3.000
 BZI  H4   C4   C3A  120.82  3.000
 BZI  C5   C4   C3A  118.00  3.000
 BZI  H5   C5   C6   119.09  3.000
 BZI  H5   C5   C4   119.51  3.000
 BZI  C6   C5   C4   121.40  3.000
 BZI  H6   C6   C7   119.21  3.000
 BZI  H6   C6   C5   119.24  3.000
 BZI  C7   C6   C5   121.55  3.000
 BZI  H7   C7   C7A  121.88  3.000
 BZI  H7   C7   C6   121.43  3.000
 BZI  C7A  C7   C6   116.68  3.000
 BZI  C7   C7A  C3A  122.58  3.000
 BZI  C7   C7A  N1   132.84  3.000
 BZI  C3A  C7A  N1   104.58  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
 BZI  CONST_01  C3A  N3   C2   N1     0.00  0.0  0
 BZI  CONST_02  N3   C3A  C7A  N1     0.00  0.0  0
 BZI  CONST_03  C4   C3A  C7A  N1   180.00  0.0  0
 BZI  CONST_04  C6   C7   C7A  N1   180.00  0.0  0
 BZI  CONST_05  C3A  C7A  N1   C2     0.00  0.0  0
 BZI  CONST_06  C7   C7A  N1   C2   180.00  0.0  0
 BZI  CONST_07  C4   C3A  N3   C2   180.00  0.0  0
 BZI  CONST_08  C7A  C3A  N3   C2     0.00  0.0  0
 BZI  CONST_09  C7A  N1   C2   N3     0.00  0.0  0
 BZI  CONST_10  C5   C4   C3A  N3   180.00  0.0  0
 BZI  CONST_11  C7   C7A  C3A  N3   180.00  0.0  0
 BZI  CONST_12  C6   C5   C4   C3A    0.00  0.0  0
 BZI  CONST_13  C6   C7   C7A  C3A    0.00  0.0  0
 BZI  CONST_14  C7   C7A  C3A  C4     0.00  0.0  0
 BZI  CONST_15  C7   C6   C5   C4     0.00  0.0  0
 BZI  CONST_16  C7A  C3A  C4   C5     0.00  0.0  0
 BZI  CONST_17  C7A  C7   C6   C5     0.00  0.0  0
 BZI  CONST_18  H7   C7   C7A  N1     0.00  0.0  0
 BZI  CONST_19  HN1  N1   C2   N3   180.00  0.0  0
 BZI  CONST_20  H4   C4   C3A  N3     0.00  0.0  0
 BZI  CONST_21  H2   C2   N3   C3A  180.00  0.0  0
 BZI  CONST_22  H5   C5   C4   C3A  180.00  0.0  0
 BZI  CONST_23  H6   C6   C5   C4   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
 BZI  plan-1  N1   0.020
 BZI  plan-1  C2   0.020
 BZI  plan-1  N3   0.020
 BZI  plan-1  C3A  0.020
 BZI  plan-1  C4   0.020
 BZI  plan-1  C5   0.020
 BZI  plan-1  C6   0.020
 BZI  plan-1  C7   0.020
 BZI  plan-1  C7A  0.020
 BZI  plan-1  HN1  0.020
 BZI  plan-1  H2   0.020
 BZI  plan-1  H4   0.020
 BZI  plan-1  H5   0.020
 BZI  plan-1  H6   0.020
 BZI  plan-1  H7   0.020

