# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 12:59:24 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: 1-{[2-(difluoromethoxy)phenyl]methyl}-2-methyl-6-[6-(piperazin-1-yl)pyridin-3-yl]-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc2ccc(cc2n1Cc3ccccc3OC(F)F)c4ccc(nc4)N5CCNCC5
#
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
 A7G  A7G  1-{[2-(difluoromethoxy)phenyl]methyl}-2-methyl-6-[6-(piperazin-1-yl)pyridin-3-yl]-1H-benzimidazole  ligand  58  33  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A7G
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
 A7G  F2   F  F     0  -0.331   4.8006  -0.9701  -2.5427
 A7G  C16  C  CH1   0   0.671   4.4740  -0.0699  -1.5826
 A7G  F1   F  F     0  -0.324   3.2251   0.3460  -1.8771
 A7G  O    O  O2    0  -0.508   4.5294  -0.6230  -0.3452
 A7G  C15  C  CR6   0   0.329   3.5300  -1.4806   0.0738
 A7G  C14  C  CR16  0  -0.308   3.3069  -2.6975  -0.5524
 A7G  C13  C  CR16  0  -0.260   2.3356  -3.5542  -0.0526
 A7G  C12  C  CR16  0  -0.244   1.6044  -3.2012   1.0705
 A7G  C11  C  CR16  0  -0.310   1.8508  -1.9862   1.6924
 A7G  C10  C  CR6   0   0.037   2.8090  -1.1050   1.2043
 A7G  C9   C  CH2   0  -0.397   3.0591   0.1990   1.9207
 A7G  N2   N  NR5   0  -0.541   2.8301   1.3628   1.0926
 A7G  C2   C  CR5   0   0.422   3.7354   2.3232   0.7328
 A7G  C1   C  CH3   0  -0.777   5.1370   2.3355   1.2235
 A7G  C8   C  CR56  0   0.385   1.6388   1.6951   0.4974
 A7G  C3   C  CR56  0   0.117   1.9058   2.8717  -0.2157
 A7G  N1   N  N     0  -0.482   3.2194   3.2344  -0.0471
 A7G  C7   C  CR16  0  -0.370   0.3804   1.1145   0.5412
 A7G  C6   C  CR6   0   0.076  -0.6402   1.7280  -0.1812
 A7G  C5   C  CR16  0  -0.337  -0.3709   2.9026  -0.9125
 A7G  C4   C  CR16  0  -0.318   0.8826   3.4846  -0.9344
 A7G  C17  C  CR6   0  -0.028  -1.9945   1.1523  -0.1800
 A7G  C21  C  CR16  0  -0.102  -2.2133  -0.2198  -0.1521
 A7G  N3   N  N     0  -0.471  -3.4038  -0.7960  -0.1402
 A7G  C20  C  CR6   0   0.538  -4.5058  -0.0438  -0.1646
 A7G  C19  C  CR16  0  -0.401  -4.4003   1.3631  -0.1815
 A7G  C18  C  CR16  0  -0.196  -3.1506   1.9387  -0.1940
 A7G  N4   N  NT    0  -0.508  -5.7077  -0.6984  -0.1967
 A7G  C25  C  CH2   0  -0.288  -5.7789  -2.0941   0.2098
 A7G  C24  C  CH2   0  -0.305  -6.9458  -2.7902  -0.4627
 A7G  N5   N  NH1   0  -0.599  -8.1731  -2.0754  -0.1742
 A7G  C23  C  CH2   0  -0.295  -8.0962  -0.7343  -0.7147
 A7G  C22  C  CH2   0  -0.292  -6.9568   0.0267  -0.0590
 A7G  H1   H  HCH1  0   0.223   5.1709   0.7650  -1.6250
 A7G  H2   H  HCR6  0   0.280   3.8931  -2.9979  -1.4092
 A7G  H3   H  HCR6  0   0.269   2.1613  -4.5030  -0.5422
 A7G  H4   H  HCR6  0   0.264   0.8514  -3.8683   1.4675
 A7G  H5   H  HCR6  0   0.269   1.2878  -1.7109   2.5763
 A7G  H6   H  HCH2  0   0.291   2.4058   0.2504   2.7941
 A7G  H7   H  HCH2  0   0.300   4.0811   0.2433   2.2966
 A7G  H8   H  HCH3  0   0.261   5.6633   1.4079   1.0004
 A7G  H9   H  HCH3  0   0.275   5.6728   3.1555   0.7526
 A7G  H10  H  HCH3  0   0.270   5.1767   2.4800   2.3046
 A7G  H11  H  HCR6  0   0.259   0.1830   0.2313   1.1337
 A7G  H12  H  HCR6  0   0.247  -1.1672   3.3569  -1.4890
 A7G  H13  H  HCR6  0   0.252   1.0635   4.3890  -1.5010
 A7G  H14  H  HCR6  0   0.240  -1.3677  -0.9021  -0.1548
 A7G  H15  H  HCR6  0   0.269  -5.2674   2.0052  -0.1652
 A7G  H16  H  HCR6  0   0.259  -3.0743   3.0192  -0.1885
 A7G  H17  H  HCH2  0   0.261  -4.8520  -2.5924  -0.0574
 A7G  H18  H  HCH2  0   0.217  -5.8929  -2.1644   1.3001
 A7G  H19  H  HCH2  0   0.196  -6.7421  -2.8630  -1.5432
 A7G  H20  H  HCH2  0   0.239  -7.0158  -3.8083  -0.0755
 A7G  H21  H  HNH1  0   0.357  -8.9589  -2.5642  -0.5824
 A7G  H23  H  HCH2  0   0.197  -7.9393  -0.7250  -1.8051
 A7G  H24  H  HCH2  0   0.241  -9.0277  -0.2025  -0.5133
 A7G  H25  H  HCH2  0   0.224  -7.1895   0.2058   0.9993
 A7G  H26  H  HCH2  0   0.254  -6.8838   0.9960  -0.5472

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
 A7G  C1   C2   single    1.485  0.020  1.485
 A7G  N1   C2   aromatic  1.306  0.020  1.306
 A7G  N1   C3   aromatic  1.373  0.020  1.373
 A7G  C2   N2   aromatic  1.368  0.020  1.368
 A7G  C3   C4   aromatic  1.393  0.020  1.393
 A7G  C3   C8   aromatic  1.401  0.020  1.401
 A7G  N2   C9   single    1.447  0.020  1.447
 A7G  N2   C8   aromatic  1.373  0.020  1.373
 A7G  C4   C5   aromatic  1.382  0.020  1.382
 A7G  C9   C10  single    1.509  0.020  1.509
 A7G  C8   C7   aromatic  1.387  0.020  1.387
 A7G  C11  C10  aromatic  1.390  0.020  1.390
 A7G  C11  C12  aromatic  1.387  0.020  1.387
 A7G  C5   C6   aromatic  1.410  0.020  1.410
 A7G  C10  C15  aromatic  1.392  0.020  1.392
 A7G  C7   C6   aromatic  1.393  0.020  1.393
 A7G  C6   C17  single    1.472  0.020  1.472
 A7G  C12  C13  aromatic  1.386  0.020  1.386
 A7G  C15  O    single    1.382  0.020  1.382
 A7G  C15  C14  aromatic  1.387  0.020  1.387
 A7G  F1   C16  single    1.349  0.020  1.349
 A7G  O    C16  single    1.357  0.020  1.357
 A7G  C16  F2   single    1.356  0.020  1.356
 A7G  C13  C14  aromatic  1.388  0.020  1.388
 A7G  C17  C18  aromatic  1.398  0.020  1.398
 A7G  C17  C21  aromatic  1.390  0.020  1.390
 A7G  C18  C19  aromatic  1.376  0.020  1.376
 A7G  C21  N3   aromatic  1.323  0.020  1.323
 A7G  C19  C20  aromatic  1.411  0.020  1.411
 A7G  N3   C20  aromatic  1.334  0.020  1.334
 A7G  C20  N4   single    1.369  0.020  1.369
 A7G  N4   C25  single    1.455  0.020  1.455
 A7G  N4   C22  single    1.451  0.020  1.451
 A7G  C25  C24  single    1.516  0.020  1.516
 A7G  C22  C23  single    1.519  0.020  1.519
 A7G  C24  N5   single    1.449  0.020  1.449
 A7G  C23  N5   single    1.448  0.020  1.448
 A7G  C16  H1   single    0.970  0.020  1.090
 A7G  C14  H2   single    0.930  0.020  1.080
 A7G  C13  H3   single    0.930  0.020  1.080
 A7G  C12  H4   single    0.930  0.020  1.080
 A7G  C11  H5   single    0.930  0.020  1.080
 A7G  C9   H6   single    0.970  0.020  1.090
 A7G  C9   H7   single    0.970  0.020  1.090
 A7G  C1   H8   single    0.970  0.020  1.090
 A7G  C1   H9   single    0.970  0.020  1.090
 A7G  C1   H10  single    0.970  0.020  1.090
 A7G  C7   H11  single    0.930  0.020  1.080
 A7G  C5   H12  single    0.930  0.020  1.080
 A7G  C4   H13  single    0.930  0.020  1.080
 A7G  C21  H14  single    0.930  0.020  1.080
 A7G  C19  H15  single    0.930  0.020  1.080
 A7G  C18  H16  single    0.930  0.020  1.080
 A7G  C25  H17  single    0.970  0.020  1.090
 A7G  C25  H18  single    0.970  0.020  1.090
 A7G  C24  H19  single    0.970  0.020  1.090
 A7G  C24  H20  single    0.970  0.020  1.090
 A7G  N5   H21  single    0.890  0.020  1.040
 A7G  C23  H23  single    0.970  0.020  1.090
 A7G  C23  H24  single    0.970  0.020  1.090
 A7G  C22  H25  single    0.970  0.020  1.090
 A7G  C22  H26  single    0.970  0.020  1.090

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
 A7G  H1   C16  O    108.79  3.000
 A7G  H1   C16  F1   110.36  3.000
 A7G  O    C16  F1   111.27  3.000
 A7G  H1   C16  F2   109.11  3.000
 A7G  O    C16  F2   111.43  3.000
 A7G  F1   C16  F2   105.85  3.000
 A7G  C15  O    C16  120.00  3.000
 A7G  C10  C15  C14  121.34  3.000
 A7G  C14  C15  O    121.60  3.000
 A7G  C10  C15  O    116.95  3.000
 A7G  H2   C14  C13  119.57  3.000
 A7G  H2   C14  C15  120.98  3.000
 A7G  C13  C14  C15  119.44  3.000
 A7G  H3   C13  C12  120.34  3.000
 A7G  H3   C13  C14  119.41  3.000
 A7G  C12  C13  C14  120.25  3.000
 A7G  H4   C12  C11  119.96  3.000
 A7G  H4   C12  C13  120.51  3.000
 A7G  C11  C12  C13  119.52  3.000
 A7G  H5   C11  C10  118.92  3.000
 A7G  H5   C11  C12  119.74  3.000
 A7G  C10  C11  C12  121.34  3.000
 A7G  C9   C10  C11  119.69  3.000
 A7G  C11  C10  C15  118.10  3.000
 A7G  C9   C10  C15  122.20  3.000
 A7G  H7   C9   H6   106.45  3.000
 A7G  H7   C9   N2   108.25  3.000
 A7G  H6   C9   N2   108.99  3.000
 A7G  H7   C9   C10  110.76  3.000
 A7G  H6   C9   C10  108.74  3.000
 A7G  N2   C9   C10  113.41  3.000
 A7G  C8   N2   C2   106.88  3.000
 A7G  C8   N2   C9   125.48  3.000
 A7G  C2   N2   C9   127.63  3.000
 A7G  N1   C2   C1   124.38  3.000
 A7G  N1   C2   N2   112.67  3.000
 A7G  C1   C2   N2   122.92  3.000
 A7G  H10  C1   H9   108.14  3.000
 A7G  H10  C1   H8   107.34  3.000
 A7G  H9   C1   H8   108.39  3.000
 A7G  H10  C1   C2   111.27  3.000
 A7G  H9   C1   C2   109.17  3.000
 A7G  H8   C1   C2   112.41  3.000
 A7G  C7   C8   C3   122.72  3.000
 A7G  C7   C8   N2   132.27  3.000
 A7G  C3   C8   N2   104.98  3.000
 A7G  C4   C3   N1   130.54  3.000
 A7G  C4   C3   C8   119.48  3.000
 A7G  N1   C3   C8   109.97  3.000
 A7G  C3   N1   C2   105.49  3.000
 A7G  H11  C7   C6   120.67  3.000
 A7G  H11  C7   C8   121.65  3.000
 A7G  C6   C7   C8   117.66  3.000
 A7G  C17  C6   C5   120.14  3.000
 A7G  C17  C6   C7   120.11  3.000
 A7G  C5   C6   C7   119.75  3.000
 A7G  H12  C5   C4   118.80  3.000
 A7G  H12  C5   C6   119.03  3.000
 A7G  C4   C5   C6   122.16  3.000
 A7G  H13  C4   C5   120.77  3.000
 A7G  H13  C4   C3   121.01  3.000
 A7G  C5   C4   C3   118.22  3.000
 A7G  C18  C17  C21  115.17  3.000
 A7G  C21  C17  C6   122.09  3.000
 A7G  C18  C17  C6   122.74  3.000
 A7G  H14  C21  N3   115.27  3.000
 A7G  H14  C21  C17  119.83  3.000
 A7G  N3   C21  C17  124.90  3.000
 A7G  C20  N3   C21  119.83  3.000
 A7G  N4   C20  C19  122.83  3.000
 A7G  N4   C20  N3   117.12  3.000
 A7G  C19  C20  N3   120.04  3.000
 A7G  H15  C19  C18  118.75  3.000
 A7G  H15  C19  C20  122.22  3.000
 A7G  C18  C19  C20  119.02  3.000
 A7G  H16  C18  C19  118.76  3.000
 A7G  H16  C18  C17  120.18  3.000
 A7G  C19  C18  C17  121.04  3.000
 A7G  C22  N4   C25  114.24  3.000
 A7G  C22  N4   C20  120.98  3.000
 A7G  C25  N4   C20  119.67  3.000
 A7G  H18  C25  H17  107.67  3.000
 A7G  H18  C25  C24  109.32  3.000
 A7G  H17  C25  C24  109.70  3.000
 A7G  H18  C25  N4   110.10  3.000
 A7G  H17  C25  N4   109.25  3.000
 A7G  C24  C25  N4   110.74  3.000
 A7G  H20  C24  H19  107.35  3.000
 A7G  H20  C24  N5   109.58  3.000
 A7G  H19  C24  N5   112.60  3.000
 A7G  H20  C24  C25  108.68  3.000
 A7G  H19  C24  C25  108.84  3.000
 A7G  N5   C24  C25  109.70  3.000
 A7G  H21  N5   C23  109.76  3.000
 A7G  H21  N5   C24  109.83  3.000
 A7G  C23  N5   C24  109.72  3.000
 A7G  H24  C23  H23  107.47  3.000
 A7G  H24  C23  C22  108.45  3.000
 A7G  H23  C23  C22  108.43  3.000
 A7G  H24  C23  N5   109.70  3.000
 A7G  H23  C23  N5   112.64  3.000
 A7G  C22  C23  N5   110.04  3.000
 A7G  H26  C22  H25  107.54  3.000
 A7G  H26  C22  C23  107.64  3.000
 A7G  H25  C22  C23  109.80  3.000
 A7G  H26  C22  N4   110.18  3.000
 A7G  H25  C22  N4   110.81  3.000
 A7G  C23  C22  N4   110.77  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
 A7G  CONST_01  C12  C11  C10  C15     0.00   0.0  0
 A7G  CONST_02  C12  C13  C14  C15     0.00   0.0  0
 A7G  CONST_03  C11  C10  C15  C14     0.00   0.0  0
 A7G  CONST_04  C11  C12  C13  C14     0.00   0.0  0
 A7G  CONST_05  C10  C11  C12  C13     0.00   0.0  0
 A7G  CONST_06  C10  C15  C14  C13     0.00   0.0  0
 A7G  CONST_07  C3   N1   C2   N2      0.00   0.0  0
 A7G  CONST_08  N1   C3   C8   N2      0.00   0.0  0
 A7G  CONST_09  C4   C3   C8   N2    180.00   0.0  0
 A7G  CONST_10  C6   C7   C8   N2    180.00   0.0  0
 A7G  CONST_11  C4   C3   N1   C2    180.00   0.0  0
 A7G  CONST_12  C8   C3   N1   C2      0.00   0.0  0
 A7G  CONST_13  C3   C8   N2   C2      0.00   0.0  0
 A7G  CONST_14  C7   C8   N2   C2    180.00   0.0  0
 A7G  CONST_15  C5   C4   C3   C8      0.00   0.0  0
 A7G  CONST_16  N1   C2   N2   C8      0.00   0.0  0
 A7G  CONST_17  C5   C6   C7   C8      0.00   0.0  0
 A7G  CONST_18  C17  C6   C7   C8    180.00   0.0  0
 A7G  CONST_19  C6   C5   C4   C3      0.00   0.0  0
 A7G  CONST_20  C6   C7   C8   C3      0.00   0.0  0
 A7G  CONST_21  C5   C4   C3   N1    180.00   0.0  0
 A7G  CONST_22  C7   C8   C3   N1    180.00   0.0  0
 A7G  CONST_23  C4   C3   C8   C7      0.00   0.0  0
 A7G  CONST_24  C4   C5   C6   C7      0.00   0.0  0
 A7G  CONST_27  C19  C18  C17  C6    180.00   0.0  0
 A7G  CONST_28  N3   C21  C17  C6    180.00   0.0  0
 A7G  CONST_31  C17  C6   C5   C4    180.00   0.0  0
 A7G  CONST_32  C20  C19  C18  C17     0.00   0.0  0
 A7G  CONST_33  C20  N3   C21  C17     0.00   0.0  0
 A7G  CONST_34  C19  C18  C17  C21     0.00   0.0  0
 A7G  CONST_35  C19  C20  N3   C21     0.00   0.0  0
 A7G  CONST_36  C18  C17  C21  N3      0.00   0.0  0
 A7G  CONST_37  C18  C19  C20  N3      0.00   0.0  0
 A7G  CONST_38  N4   C20  N3   C21   180.00   0.0  0
 A7G  CONST_39  N4   C20  C19  C18   180.00   0.0  0
 A7G  CONST_40  C11  C10  C15  O     180.00   0.0  0
 A7G  CONST_41  C13  C14  C15  O     180.00   0.0  0
 A7G  CONST_42  C9   C10  C15  C14   180.00   0.0  0
 A7G  CONST_43  C9   C10  C11  C12   180.00   0.0  0
 A7G  CONST_44  N1   C2   N2   C9    180.00   0.0  0
 A7G  CONST_45  C3   C8   N2   C9    180.00   0.0  0
 A7G  CONST_46  C7   C8   N2   C9      0.00   0.0  0
 A7G  CONST_47  C3   N1   C2   C1    180.00   0.0  0
 A7G  CONST_48  C8   N2   C2   C1    180.00   0.0  0
 A7G  CONST_49  H5   C11  C10  C15   180.00   0.0  0
 A7G  CONST_50  H3   C13  C14  C15   180.00   0.0  0
 A7G  CONST_51  H4   C12  C13  C14   180.00   0.0  0
 A7G  CONST_52  H2   C14  C13  C12   180.00   0.0  0
 A7G  CONST_53  H11  C7   C8   N2      0.00   0.0  0
 A7G  CONST_54  H13  C4   C3   C8    180.00   0.0  0
 A7G  CONST_55  H12  C5   C4   C3    180.00   0.0  0
 A7G  CONST_56  H16  C18  C17  C6      0.00   0.0  0
 A7G  CONST_57  H14  C21  C17  C6      0.00   0.0  0
 A7G  CONST_58  H15  C19  C18  C17   180.00   0.0  0
 A7G  Var_01    C25  N4   C20  N3     19.07  30.0  2
 A7G  Var_02    C24  C25  N4   C20  -154.01  30.0  1
 A7G  Var_03    C23  C22  N4   C20   154.86  30.0  1
 A7G  Var_04    N5   C24  C25  N4    -55.77  30.0  1
 A7G  Var_05    N5   C23  C22  N4     55.05  30.0  1
 A7G  Var_06    C23  N5   C24  C25    62.13  30.0  1
 A7G  Var_07    C22  C23  N5   C24   -61.80  30.0  1
 A7G  Var_08    N2   C9   C10  C15    60.92  30.0  1
 A7G  Var_09    C2   N2   C9   C10  -118.70  30.0  1
 A7G  Var_10    C10  C15  O    C16  -119.73  30.0  2
 A7G  Var_11    H8   C1   C2   N2     56.23  30.0  2
 A7G  Var_12    H1   C16  O    C15   164.46  30.0  3

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
 A7G  plan-1  O    0.020
 A7G  plan-1  C15  0.020
 A7G  plan-1  C14  0.020
 A7G  plan-1  C13  0.020
 A7G  plan-1  C12  0.020
 A7G  plan-1  C11  0.020
 A7G  plan-1  C10  0.020
 A7G  plan-1  C9   0.020
 A7G  plan-1  H2   0.020
 A7G  plan-1  H3   0.020
 A7G  plan-1  H4   0.020
 A7G  plan-1  H5   0.020
 A7G  plan-2  C6   0.020
 A7G  plan-2  C17  0.020
 A7G  plan-2  C21  0.020
 A7G  plan-2  N3   0.020
 A7G  plan-2  C20  0.020
 A7G  plan-2  C19  0.020
 A7G  plan-2  C18  0.020
 A7G  plan-2  N4   0.020
 A7G  plan-2  H14  0.020
 A7G  plan-2  H15  0.020
 A7G  plan-2  H16  0.020
 A7G  plan-3  C9   0.020
 A7G  plan-3  N2   0.020
 A7G  plan-3  C2   0.020
 A7G  plan-3  C1   0.020
 A7G  plan-3  C8   0.020
 A7G  plan-3  C3   0.020
 A7G  plan-3  N1   0.020
 A7G  plan-3  C7   0.020
 A7G  plan-3  C6   0.020
 A7G  plan-3  C5   0.020
 A7G  plan-3  C4   0.020
 A7G  plan-3  C17  0.020
 A7G  plan-3  H11  0.020
 A7G  plan-3  H12  0.020
 A7G  plan-3  H13  0.020

