# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 21:08:27 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: N-[3-(2H-tetrazol-5-yl)phenyl]-6-(trifluoromethyl)-1H-benzimidazole-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1cc2[nH]cnc2c(c1)C(=O)Nc3cccc(c3)c4n[nH]nn4
#
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
 3GK  3GK  N-[3-(2H-tetrazol-5-yl)phenyl]-6-(trifluoromethyl)-1H-benzimidazole-4-carboxamide  ligand  37  27  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3GK
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
 3GK  N1   N  NR15  0  -0.223   7.1651  -0.5417  -0.9142
 3GK  C6   C  CR6   0   0.067   4.1710   0.8877   0.0684
 3GK  C7   C  CR16  0  -0.364   2.8825   0.3663  -0.0330
 3GK  C8   C  CR6   0   0.415   1.8039   1.0872   0.4739
 3GK  C9   C  CR16  0  -0.349   2.0310   2.3304   1.0699
 3GK  C13  C  C     0   0.525  -0.0234  -0.5322  -0.0076
 3GK  C17  C  CR56  0   0.374  -3.5381  -1.9046   0.3979
 3GK  C18  C  CR16  0  -0.329  -4.3583  -0.8368   0.0687
 3GK  C22  C  CR15  0   0.117  -2.6363  -3.7952   1.0106
 3GK  F27  F  F     0  -0.301  -5.8289   1.3716  -0.5204
 3GK  F25  F  F     0  -0.314  -4.3157   1.8572  -1.9709
 3GK  F26  F  F     0  -0.313  -4.1706   2.6287   0.0275
 3GK  C19  C  CR6   0  -0.208  -3.7225   0.3411  -0.2780
 3GK  N23  N  NR15  0  -0.659  -3.8185  -3.1782   0.8025
 3GK  N21  N  N     0  -0.442  -1.6022  -3.0313   0.7825
 3GK  C16  C  CR56  0   0.137  -2.1338  -1.8331   0.3922
 3GK  C20  C  CR16  0  -0.332  -2.3228   0.4469  -0.2798
 3GK  C15  C  CR6   0  -0.107  -1.5111  -0.6233   0.0529
 3GK  O14  O  O     0  -0.446   0.6528  -1.4552  -0.4197
 3GK  N12  N  NH1   0  -0.758   0.4770   0.6523   0.4292
 3GK  C10  C  CR16  0  -0.226   3.3142   2.8363   1.1662
 3GK  C11  C  CR16  0  -0.307   4.3935   2.1220   0.6701
 3GK  C3   C  CR5   0   0.366   5.2927   0.1129  -0.4564
 3GK  N2   N  N     0  -0.266   6.5635   0.4259  -0.2805
 3GK  N4   N  N     0  -0.338   5.1690  -1.0160  -1.1796
 3GK  N5   N  N     0  -0.055   6.3676  -1.4103  -1.4540
 3GK  H1   H  HNR5  0   0.459   8.1722  -0.6161  -0.9804
 3GK  H2   H  HCR6  0   0.286   2.7310  -0.5905  -0.5043
 3GK  H3   H  HCR6  0   0.278   1.1974   2.8987   1.4652
 3GK  H4   H  HCR6  0   0.292  -5.4349  -0.9349   0.0823
 3GK  H5   H  HCR5  0   0.297  -2.5885  -4.8225   1.3386
 3GK  H6   H  HNR5  0   0.432  -4.7307  -3.5981   0.8939
 3GK  H8   H  HCR6  0   0.284  -1.8685   1.3834  -0.5801
 3GK  H9   H  HNH1  0   0.425  -0.1818   1.2857   0.8564
 3GK  H10  H  HCR6  0   0.269   3.4736   3.7983   1.6342
 3GK  H11  H  HCR6  0   0.262   5.3941   2.5245   0.7499
 3GK  C24  C  CT    0   1.054  -4.5142   1.5438  -0.6814

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
 3GK  N23  C22  aromatic  1.350  0.020  1.350
 3GK  N23  C17  aromatic  1.365  0.020  1.365
 3GK  C22  N21  aromatic  1.306  0.020  1.306
 3GK  C17  C18  aromatic  1.386  0.020  1.386
 3GK  C17  C16  aromatic  1.406  0.020  1.406
 3GK  N21  C16  aromatic  1.368  0.020  1.368
 3GK  C18  C19  aromatic  1.383  0.020  1.383
 3GK  C16  C15  aromatic  1.402  0.020  1.402
 3GK  F25  C24  single    1.342  0.020  1.342
 3GK  C19  C24  single    1.495  0.020  1.495
 3GK  C19  C20  aromatic  1.404  0.020  1.404
 3GK  C15  C20  aromatic  1.384  0.020  1.384
 3GK  C15  C13  single    1.492  0.020  1.492
 3GK  N2   N1   aromatic  1.304  0.020  1.304
 3GK  N2   C3   aromatic  1.321  0.020  1.321
 3GK  C24  F27  single    1.336  0.020  1.336
 3GK  C24  F26  single    1.341  0.020  1.341
 3GK  N1   N5   aromatic  1.297  0.020  1.297
 3GK  N12  C13  single    1.358  0.020  1.358
 3GK  N12  C8   single    1.397  0.020  1.397
 3GK  C7   C8   aromatic  1.393  0.020  1.393
 3GK  C7   C6   aromatic  1.394  0.020  1.394
 3GK  C13  O14  double    1.216  0.020  1.216
 3GK  C8   C9   aromatic  1.397  0.020  1.397
 3GK  C3   C6   single    1.461  0.020  1.461
 3GK  C3   N4   aromatic  1.346  0.020  1.346
 3GK  N5   N4   aromatic  1.291  0.020  1.291
 3GK  C6   C11  aromatic  1.391  0.020  1.391
 3GK  C9   C10  aromatic  1.383  0.020  1.383
 3GK  C11  C10  aromatic  1.386  0.020  1.386
 3GK  N1   H1   single    0.860  0.020  1.020
 3GK  C7   H2   single    0.930  0.020  1.080
 3GK  C9   H3   single    0.930  0.020  1.080
 3GK  C18  H4   single    0.930  0.020  1.080
 3GK  C22  H5   single    0.930  0.020  1.080
 3GK  N23  H6   single    0.860  0.020  1.020
 3GK  C20  H8   single    0.930  0.020  1.080
 3GK  N12  H9   single    0.860  0.020  1.020
 3GK  C10  H10  single    0.930  0.020  1.080
 3GK  C11  H11  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
 3GK  H1   N1   N5   122.38  3.000
 3GK  H1   N1   N2   123.06  3.000
 3GK  N5   N1   N2   114.56  3.000
 3GK  C3   C6   C11  120.21  3.000
 3GK  C11  C6   C7   120.75  3.000
 3GK  C3   C6   C7   119.04  3.000
 3GK  H2   C7   C8   120.66  3.000
 3GK  H2   C7   C6   119.61  3.000
 3GK  C8   C7   C6   119.73  3.000
 3GK  N12  C8   C9   116.42  3.000
 3GK  C9   C8   C7   119.33  3.000
 3GK  N12  C8   C7   124.24  3.000
 3GK  H3   C9   C10  119.78  3.000
 3GK  H3   C9   C8   119.81  3.000
 3GK  C10  C9   C8   120.40  3.000
 3GK  N12  C13  O14  124.48  3.000
 3GK  O14  C13  C15  121.46  3.000
 3GK  N12  C13  C15  114.07  3.000
 3GK  C16  C17  N23  104.70  3.000
 3GK  C16  C17  C18  123.42  3.000
 3GK  N23  C17  C18  131.87  3.000
 3GK  H4   C18  C19  122.57  3.000
 3GK  H4   C18  C17  121.08  3.000
 3GK  C19  C18  C17  116.34  3.000
 3GK  H5   C22  N21  125.09  3.000
 3GK  H5   C22  N23  121.37  3.000
 3GK  N21  C22  N23  113.54  3.000
 3GK  C20  C19  C24  117.83  3.000
 3GK  C20  C19  C18  121.54  3.000
 3GK  C24  C19  C18  120.62  3.000
 3GK  H6   N23  C22  126.02  3.000
 3GK  H6   N23  C17  126.95  3.000
 3GK  C22  N23  C17  106.99  3.000
 3GK  C16  N21  C22  104.75  3.000
 3GK  C15  C16  N21  130.71  3.000
 3GK  C15  C16  C17  119.23  3.000
 3GK  N21  C16  C17  110.02  3.000
 3GK  H8   C20  C15  119.29  3.000
 3GK  H8   C20  C19  118.93  3.000
 3GK  C15  C20  C19  121.75  3.000
 3GK  C20  C15  C16  117.71  3.000
 3GK  C20  C15  C13  121.87  3.000
 3GK  C16  C15  C13  120.36  3.000
 3GK  H9   N12  C13  116.30  3.000
 3GK  H9   N12  C8   114.28  3.000
 3GK  C13  N12  C8   129.19  3.000
 3GK  H10  C10  C11  119.90  3.000
 3GK  H10  C10  C9   119.49  3.000
 3GK  C11  C10  C9   120.61  3.000
 3GK  H11  C11  C10  120.15  3.000
 3GK  H11  C11  C6   120.67  3.000
 3GK  C10  C11  C6   119.18  3.000
 3GK  N4   C3   N2   111.02  3.000
 3GK  N4   C3   C6   124.55  3.000
 3GK  N2   C3   C6   124.43  3.000
 3GK  C3   N2   N1   101.73  3.000
 3GK  N5   N4   C3   106.56  3.000
 3GK  N4   N5   N1   106.12  3.000
 3GK  C19  C24  F26  111.87  3.000
 3GK  F26  C24  F25  106.33  3.000
 3GK  C19  C24  F25  111.64  3.000
 3GK  F26  C24  F27  107.03  3.000
 3GK  C19  C24  F27  112.64  3.000
 3GK  F25  C24  F27  106.95  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
 3GK  CONST_01  C6   C3   N2   N1    180.00   0.0  0
 3GK  CONST_02  N4   C3   N2   N1      0.00   0.0  0
 3GK  CONST_03  C3   N4   N5   N1      0.00   0.0  0
 3GK  CONST_04  C9   C8   C7   C6      0.00   0.0  0
 3GK  CONST_05  N5   N4   C3   C6    180.00   0.0  0
 3GK  CONST_06  C9   C10  C11  C6      0.00   0.0  0
 3GK  CONST_07  C10  C9   C8   C7      0.00   0.0  0
 3GK  CONST_08  N2   C3   C6   C7    180.00   0.0  0
 3GK  CONST_09  N4   C3   C6   C7      0.00   0.0  0
 3GK  CONST_10  C10  C11  C6   C7      0.00   0.0  0
 3GK  CONST_11  C3   C6   C7   C8    180.00   0.0  0
 3GK  CONST_12  C11  C6   C7   C8      0.00   0.0  0
 3GK  CONST_13  C11  C10  C9   C8      0.00   0.0  0
 3GK  CONST_14  N21  C22  N23  C17     0.00   0.0  0
 3GK  CONST_15  C20  C19  C18  C17     0.00   0.0  0
 3GK  CONST_16  C22  N21  C16  C17     0.00   0.0  0
 3GK  CONST_17  C20  C15  C16  C17     0.00   0.0  0
 3GK  CONST_18  C22  N23  C17  C18   180.00   0.0  0
 3GK  CONST_19  N21  C16  C17  C18   180.00   0.0  0
 3GK  CONST_20  C15  C16  C17  C18     0.00   0.0  0
 3GK  CONST_21  C15  C20  C19  C18     0.00   0.0  0
 3GK  CONST_22  C16  C17  N23  C22     0.00   0.0  0
 3GK  CONST_23  C15  C16  N21  C22   180.00   0.0  0
 3GK  CONST_24  N23  C17  C18  C19   180.00   0.0  0
 3GK  CONST_25  C16  C17  C18  C19     0.00   0.0  0
 3GK  CONST_26  C16  C15  C20  C19     0.00   0.0  0
 3GK  CONST_27  C16  N21  C22  N23     0.00   0.0  0
 3GK  CONST_28  N21  C16  C17  N23     0.00   0.0  0
 3GK  CONST_29  C15  C16  C17  N23   180.00   0.0  0
 3GK  CONST_30  C20  C15  C16  N21   180.00   0.0  0
 3GK  CONST_31  C3   C6   C11  C10   180.00   0.0  0
 3GK  CONST_32  N2   C3   C6   C11     0.00   0.0  0
 3GK  CONST_33  N4   C3   C6   C11   180.00   0.0  0
 3GK  CONST_34  N5   N1   N2   C3      0.00   0.0  0
 3GK  CONST_35  N4   N5   N1   N2      0.00   0.0  0
 3GK  CONST_36  N5   N4   C3   N2      0.00   0.0  0
 3GK  CONST_37  N12  C8   C7   C6    180.00   0.0  0
 3GK  CONST_38  C17  C16  C15  C13   180.00   0.0  0
 3GK  CONST_39  N21  C16  C15  C13     0.00   0.0  0
 3GK  CONST_40  C19  C20  C15  C13   180.00   0.0  0
 3GK  CONST_41  C24  C19  C18  C17   180.00   0.0  0
 3GK  CONST_42  C15  C20  C19  C24   180.00   0.0  0
 3GK  CONST_43  C10  C9   C8   N12   180.00   0.0  0
 3GK  CONST_44  H10  C10  C11  C6    180.00   0.0  0
 3GK  CONST_45  H3   C9   C8   C7    180.00   0.0  0
 3GK  CONST_46  H11  C11  C6   C7    180.00   0.0  0
 3GK  CONST_47  H2   C7   C8   C9    180.00   0.0  0
 3GK  CONST_48  H5   C22  N23  C17   180.00   0.0  0
 3GK  CONST_49  H6   N23  C17  C18     0.00   0.0  0
 3GK  CONST_50  H8   C20  C19  C18   180.00   0.0  0
 3GK  CONST_51  H4   C18  C17  N23     0.00   0.0  0
 3GK  CONST_52  H1   N1   N2   C3    180.00   0.0  0
 3GK  CONST_53  C15  C13  N12  C8    180.00   0.0  0
 3GK  CONST_54  C13  N12  C8   C7      0.00   0.0  0
 3GK  CONST_55  C13  N12  C8   C9    180.00   0.0  0
 3GK  CONST_56  H9   N12  C8   C7    180.00   0.0  0
 3GK  CONST_57  O14  C13  N12  C8      0.00   0.0  0
 3GK  Var_01    F25  C24  C19  C18  -113.59  30.0  2
 3GK  Var_02    N12  C13  C15  C16  -143.36  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
 3GK  plan-1  N1   0.020
 3GK  plan-1  C6   0.020
 3GK  plan-1  C3   0.020
 3GK  plan-1  N2   0.020
 3GK  plan-1  N4   0.020
 3GK  plan-1  N5   0.020
 3GK  plan-1  H1   0.020
 3GK  plan-2  C6   0.020
 3GK  plan-2  C7   0.020
 3GK  plan-2  C8   0.020
 3GK  plan-2  C9   0.020
 3GK  plan-2  N12  0.020
 3GK  plan-2  C10  0.020
 3GK  plan-2  C11  0.020
 3GK  plan-2  C3   0.020
 3GK  plan-2  H2   0.020
 3GK  plan-2  H3   0.020
 3GK  plan-2  H10  0.020
 3GK  plan-2  H11  0.020
 3GK  plan-3  C13  0.020
 3GK  plan-3  C17  0.020
 3GK  plan-3  C18  0.020
 3GK  plan-3  C22  0.020
 3GK  plan-3  C19  0.020
 3GK  plan-3  N23  0.020
 3GK  plan-3  N21  0.020
 3GK  plan-3  C16  0.020
 3GK  plan-3  C20  0.020
 3GK  plan-3  C15  0.020
 3GK  plan-3  H4   0.020
 3GK  plan-3  H5   0.020
 3GK  plan-3  H6   0.020
 3GK  plan-3  H8   0.020
 3GK  plan-3  C24  0.020
 3GK  plan-4  C8   0.020
 3GK  plan-4  C13  0.020
 3GK  plan-4  C15  0.020
 3GK  plan-4  O14  0.020
 3GK  plan-4  N12  0.020
 3GK  plan-4  H9   0.020

