# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 01:56:39 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: N-(naphthalen-2-yl)-2-[2-(pyridin-2-yl)-1H-benzimidazol-1-yl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Cn1c2ccccc2nc1c3ccccn3)Nc4ccc5ccccc5c4
#
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
 C91  C91  N-(naphthalen-2-yl)-2-[2-(pyridin-2-yl)-1H-benzimidazol-1-yl]acetamide  ligand  47  29  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C91
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
 C91  O    O  O     0  -0.457   0.0946  -0.7775   0.8326
 C91  C13  C  C     0   0.551   0.0070  -0.5564  -0.3574
 C91  N4   N  NH1   0  -0.741  -1.1155  -0.1320  -0.9800
 C91  C4   C  CR6   0   0.360  -2.3496   0.1179  -0.3591
 C91  C2   C  CR16  0  -0.287  -2.4146   0.8118   0.8735
 C91  C5   C  CR16  0  -0.311  -3.6268   1.0821   1.4419
 C91  C18  C  CR66  0   0.104  -4.8356   0.6913   0.8199
 C91  C25  C  CR16  0  -0.307  -6.1003   0.9638   1.3903
 C91  C26  C  CR16  0  -0.261  -7.2489   0.5760   0.7552
 C91  C27  C  CR16  0  -0.256  -7.1828  -0.1011  -0.4810
 C91  C28  C  CR16  0  -0.316  -5.9726  -0.3766  -1.0572
 C91  C16  C  CR66  0   0.132  -4.7683   0.0124  -0.4234
 C91  C12  C  CR16  0  -0.397  -3.5048  -0.2689  -0.9884
 C91  C17  C  CH2   0  -0.453   1.1645  -0.8036  -1.3120
 C91  N1   N  NR5   0  -0.557   2.4184  -0.8675  -0.6122
 C91  C6   C  CR5   0   0.483   3.0961   0.1282   0.0393
 C91  C37  C  CR6   0   0.180   2.6589   1.5259   0.1155
 C91  C38  C  CR16  0  -0.308   3.4891   2.4754   0.7102
 C91  C39  C  CR16  0  -0.149   3.0464   3.7842   0.7792
 C91  C40  C  CR16  0  -0.324   1.8003   4.1040   0.2583
 C91  C41  C  CR16  0  -0.057   1.0498   3.0883  -0.3140
 C91  N42  N  N     0  -0.442   1.4675   1.8333  -0.3850
 C91  N3   N  N     0  -0.483   4.1972  -0.2951   0.6021
 C91  C11  C  CR56  0   0.153   4.2607  -1.6330   0.3323
 C91  C10  C  CR56  0   0.345   3.1433  -2.0175  -0.4238
 C91  C1   C  CR16  0  -0.315   2.9454  -3.3300  -0.8414
 C91  C3   C  CR16  0  -0.271   3.9091  -4.2516  -0.4739
 C91  C14  C  CR16  0  -0.272   5.0335  -3.8818   0.2823
 C91  C9   C  CR16  0  -0.336   5.2241  -2.5769   0.6932
 C91  H1   H  HNH1  0   0.415  -1.1014  -0.0794  -1.9876
 C91  H2   H  HCR6  0   0.270  -1.5086   1.1499   1.3542
 C91  H3   H  HCR6  0   0.259  -3.6686   1.6200   2.3813
 C91  H4   H  HCR6  0   0.256  -6.1479   1.4867   2.3382
 C91  H5   H  HCR6  0   0.259  -8.2131   0.7866   1.1986
 C91  H6   H  HCR6  0   0.259  -8.0981  -0.4008  -0.9745
 C91  H7   H  HCR6  0   0.255  -5.9242  -0.8987  -2.0054
 C91  H8   H  HCR6  0   0.266  -3.4558  -0.7998  -1.9327
 C91  H9   H  HCH2  0   0.311   1.0035  -1.7655  -1.8029
 C91  H10  H  HCH2  0   0.305   1.1952  -0.0505  -2.0971
 C91  H11  H  HCR6  0   0.276   4.4526   2.1879   1.1057
 C91  H12  H  HCR6  0   0.279   3.6662   4.5457   1.2333
 C91  H13  H  HCR6  0   0.277   1.4176   5.1145   0.2926
 C91  H14  H  HCR6  0   0.267   0.0711   3.2937  -0.7317
 C91  H15  H  HCR6  0   0.269   2.0842  -3.6332  -1.4226
 C91  H16  H  HCR6  0   0.259   3.7933  -5.2837  -0.7771
 C91  H17  H  HCR6  0   0.255   5.7613  -4.6379   0.5462
 C91  H18  H  HCR6  0   0.257   6.0904  -2.2901   1.2754

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
 C91  C26  C27  aromatic  1.411  0.020  1.411
 C91  C26  C25  aromatic  1.369  0.020  1.369
 C91  C27  C28  aromatic  1.368  0.020  1.368
 C91  C25  C18  aromatic  1.414  0.020  1.414
 C91  C28  C16  aromatic  1.415  0.020  1.415
 C91  C18  C16  aromatic  1.418  0.020  1.418
 C91  C18  C5   aromatic  1.414  0.020  1.414
 C91  C16  C12  aromatic  1.412  0.020  1.412
 C91  C5   C2   aromatic  1.366  0.020  1.366
 C91  C12  C4   aromatic  1.371  0.020  1.371
 C91  C2   C4   aromatic  1.416  0.020  1.416
 C91  C4   N4   single    1.404  0.020  1.404
 C91  O    C13  double    1.213  0.020  1.213
 C91  N4   C13  single    1.352  0.020  1.352
 C91  C13  C17  single    1.521  0.020  1.521
 C91  C40  C39  aromatic  1.388  0.020  1.388
 C91  C40  C41  aromatic  1.387  0.020  1.387
 C91  C39  C38  aromatic  1.383  0.020  1.383
 C91  C41  N42  aromatic  1.325  0.020  1.325
 C91  C38  C37  aromatic  1.394  0.020  1.394
 C91  N42  C37  aromatic  1.328  0.020  1.328
 C91  C37  C6   single    1.466  0.020  1.466
 C91  C17  N1   single    1.437  0.020  1.437
 C91  C6   N1   aromatic  1.369  0.020  1.369
 C91  C6   N3   aromatic  1.307  0.020  1.307
 C91  N1   C10  aromatic  1.372  0.020  1.372
 C91  N3   C11  aromatic  1.366  0.020  1.366
 C91  C10  C11  aromatic  1.403  0.020  1.403
 C91  C10  C1   aromatic  1.391  0.020  1.391
 C91  C11  C9   aromatic  1.396  0.020  1.396
 C91  C1   C3   aromatic  1.383  0.020  1.383
 C91  C9   C14  aromatic  1.381  0.020  1.381
 C91  C3   C14  aromatic  1.405  0.020  1.405
 C91  N4   H1   single    0.860  0.020  1.020
 C91  C2   H2   single    0.930  0.020  1.080
 C91  C5   H3   single    0.930  0.020  1.080
 C91  C25  H4   single    0.930  0.020  1.080
 C91  C26  H5   single    0.930  0.020  1.080
 C91  C27  H6   single    0.930  0.020  1.080
 C91  C28  H7   single    0.930  0.020  1.080
 C91  C12  H8   single    0.930  0.020  1.080
 C91  C17  H9   single    0.970  0.020  1.090
 C91  C17  H10  single    0.970  0.020  1.090
 C91  C38  H11  single    0.930  0.020  1.080
 C91  C39  H12  single    0.930  0.020  1.080
 C91  C40  H13  single    0.930  0.020  1.080
 C91  C41  H14  single    0.930  0.020  1.080
 C91  C1   H15  single    0.930  0.020  1.080
 C91  C3   H16  single    0.930  0.020  1.080
 C91  C14  H17  single    0.930  0.020  1.080
 C91  C9   H18  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
 C91  C17  C13  N4   113.20  3.000
 C91  C17  C13  O    122.08  3.000
 C91  N4   C13  O    124.66  3.000
 C91  H1   N4   C4   116.40  3.000
 C91  H1   N4   C13  117.69  3.000
 C91  C4   N4   C13  125.59  3.000
 C91  C12  C4   C2   119.94  3.000
 C91  C2   C4   N4   120.84  3.000
 C91  C12  C4   N4   119.17  3.000
 C91  H2   C2   C5   119.83  3.000
 C91  H2   C2   C4   120.16  3.000
 C91  C5   C2   C4   120.00  3.000
 C91  H3   C5   C18  119.04  3.000
 C91  H3   C5   C2   119.56  3.000
 C91  C18  C5   C2   121.39  3.000
 C91  C16  C18  C25  119.24  3.000
 C91  C16  C18  C5   118.50  3.000
 C91  C25  C18  C5   122.26  3.000
 C91  H4   C25  C26  120.38  3.000
 C91  H4   C25  C18  119.03  3.000
 C91  C26  C25  C18  120.59  3.000
 C91  H5   C26  C27  119.62  3.000
 C91  H5   C26  C25  120.17  3.000
 C91  C27  C26  C25  120.22  3.000
 C91  H6   C27  C28  120.02  3.000
 C91  H6   C27  C26  119.52  3.000
 C91  C28  C27  C26  120.46  3.000
 C91  H7   C28  C16  119.10  3.000
 C91  H7   C28  C27  120.33  3.000
 C91  C16  C28  C27  120.57  3.000
 C91  C12  C16  C28  121.82  3.000
 C91  C12  C16  C18  119.24  3.000
 C91  C28  C16  C18  118.93  3.000
 C91  H8   C12  C16  119.10  3.000
 C91  H8   C12  C4   119.98  3.000
 C91  C16  C12  C4   120.92  3.000
 C91  H10  C17  H9   106.83  3.000
 C91  H10  C17  N1   110.93  3.000
 C91  H9   C17  N1   107.96  3.000
 C91  H10  C17  C13  111.22  3.000
 C91  H9   C17  C13  108.26  3.000
 C91  N1   C17  C13  111.44  3.000
 C91  C10  N1   C6   106.42  3.000
 C91  C10  N1   C17  124.39  3.000
 C91  C6   N1   C17  129.13  3.000
 C91  N3   C6   C37  122.51  3.000
 C91  N3   C6   N1   112.72  3.000
 C91  C37  C6   N1   124.77  3.000
 C91  N42  C37  C38  122.49  3.000
 C91  N42  C37  C6   117.93  3.000
 C91  C38  C37  C6   119.58  3.000
 C91  H11  C38  C39  121.25  3.000
 C91  H11  C38  C37  120.39  3.000
 C91  C39  C38  C37  118.35  3.000
 C91  H12  C39  C40  120.65  3.000
 C91  H12  C39  C38  120.23  3.000
 C91  C40  C39  C38  119.12  3.000
 C91  H13  C40  C41  120.42  3.000
 C91  H13  C40  C39  121.42  3.000
 C91  C41  C40  C39  118.16  3.000
 C91  H14  C41  N42  116.34  3.000
 C91  H14  C41  C40  120.59  3.000
 C91  N42  C41  C40  123.06  3.000
 C91  C41  N42  C37  118.81  3.000
 C91  C11  N3   C6   105.74  3.000
 C91  C9   C11  C10  120.24  3.000
 C91  C9   C11  N3   130.02  3.000
 C91  C10  C11  N3   109.74  3.000
 C91  C1   C10  C11  122.24  3.000
 C91  C1   C10  N1   132.38  3.000
 C91  C11  C10  N1   105.37  3.000
 C91  H15  C1   C3   120.70  3.000
 C91  H15  C1   C10  122.58  3.000
 C91  C3   C1   C10  116.72  3.000
 C91  H16  C3   C14  119.19  3.000
 C91  H16  C3   C1   119.12  3.000
 C91  C14  C3   C1   121.70  3.000
 C91  H17  C14  C9   119.65  3.000
 C91  H17  C14  C3   119.06  3.000
 C91  C9   C14  C3   121.29  3.000
 C91  H18  C9   C14  121.39  3.000
 C91  H18  C9   C11  120.80  3.000
 C91  C14  C9   C11  117.81  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
 C91  CONST_01  C28  C16  C12  C4   180.00   0.0  0
 C91  CONST_02  C18  C16  C12  C4     0.00   0.0  0
 C91  CONST_03  C18  C5   C2   C4     0.00   0.0  0
 C91  CONST_04  C25  C18  C5   C2   180.00   0.0  0
 C91  CONST_05  C16  C18  C5   C2     0.00   0.0  0
 C91  CONST_06  C16  C12  C4   C2     0.00   0.0  0
 C91  CONST_07  C26  C25  C18  C5   180.00   0.0  0
 C91  CONST_08  C28  C16  C18  C5   180.00   0.0  0
 C91  CONST_09  C12  C16  C18  C5     0.00   0.0  0
 C91  CONST_10  C12  C4   C2   C5     0.00   0.0  0
 C91  CONST_11  C27  C26  C25  C18    0.00   0.0  0
 C91  CONST_12  C27  C28  C16  C18    0.00   0.0  0
 C91  CONST_13  C28  C27  C26  C25    0.00   0.0  0
 C91  CONST_14  C28  C16  C18  C25    0.00   0.0  0
 C91  CONST_15  C12  C16  C18  C25  180.00   0.0  0
 C91  CONST_16  C16  C28  C27  C26    0.00   0.0  0
 C91  CONST_17  C16  C18  C25  C26    0.00   0.0  0
 C91  CONST_18  C12  C16  C28  C27  180.00   0.0  0
 C91  CONST_19  C38  C37  C6   N1   180.00   0.0  0
 C91  CONST_20  N42  C37  C6   N1     0.00   0.0  0
 C91  CONST_21  C11  N3   C6   N1     0.00   0.0  0
 C91  CONST_22  N3   C11  C10  N1     0.00   0.0  0
 C91  CONST_23  C9   C11  C10  N1   180.00   0.0  0
 C91  CONST_24  C3   C1   C10  N1   180.00   0.0  0
 C91  CONST_25  C39  C38  C37  C6   180.00   0.0  0
 C91  CONST_26  C41  N42  C37  C6   180.00   0.0  0
 C91  CONST_27  C11  C10  N1   C6     0.00   0.0  0
 C91  CONST_28  C1   C10  N1   C6   180.00   0.0  0
 C91  CONST_29  C10  C11  N3   C6     0.00   0.0  0
 C91  CONST_30  C9   C11  N3   C6   180.00   0.0  0
 C91  CONST_31  C40  C39  C38  C37    0.00   0.0  0
 C91  CONST_32  C40  C41  N42  C37    0.00   0.0  0
 C91  CONST_33  C10  N1   C6   C37  180.00   0.0  0
 C91  CONST_34  C11  N3   C6   C37  180.00   0.0  0
 C91  CONST_35  C41  C40  C39  C38    0.00   0.0  0
 C91  CONST_36  C41  N42  C37  C38    0.00   0.0  0
 C91  CONST_37  N3   C6   C37  C38    0.00   0.0  0
 C91  CONST_38  N42  C41  C40  C39    0.00   0.0  0
 C91  CONST_39  N42  C37  C38  C39    0.00   0.0  0
 C91  CONST_40  N3   C6   C37  N42  180.00   0.0  0
 C91  CONST_41  C10  N1   C6   N3     0.00   0.0  0
 C91  CONST_42  C1   C10  C11  N3   180.00   0.0  0
 C91  CONST_43  C14  C9   C11  N3   180.00   0.0  0
 C91  CONST_44  C3   C1   C10  C11    0.00   0.0  0
 C91  CONST_45  C3   C14  C9   C11    0.00   0.0  0
 C91  CONST_46  C14  C9   C11  C10    0.00   0.0  0
 C91  CONST_47  C14  C3   C1   C10    0.00   0.0  0
 C91  CONST_48  C9   C11  C10  C1     0.00   0.0  0
 C91  CONST_49  C9   C14  C3   C1     0.00   0.0  0
 C91  CONST_50  C16  C12  C4   N4   180.00   0.0  0
 C91  CONST_51  C5   C2   C4   N4   180.00   0.0  0
 C91  CONST_52  C37  C6   N1   C17    0.00   0.0  0
 C91  CONST_53  N3   C6   N1   C17  180.00   0.0  0
 C91  CONST_54  C11  C10  N1   C17  180.00   0.0  0
 C91  CONST_55  C1   C10  N1   C17    0.00   0.0  0
 C91  CONST_56  H3   C5   C2   C4   180.00   0.0  0
 C91  CONST_57  H8   C12  C4   C2   180.00   0.0  0
 C91  CONST_58  H4   C25  C18  C5     0.00   0.0  0
 C91  CONST_59  H5   C26  C25  C18  180.00   0.0  0
 C91  CONST_60  H7   C28  C16  C18  180.00   0.0  0
 C91  CONST_61  H2   C2   C5   C18  180.00   0.0  0
 C91  CONST_62  H6   C27  C26  C25  180.00   0.0  0
 C91  CONST_63  H15  C1   C10  N1     0.00   0.0  0
 C91  CONST_64  H11  C38  C37  C6     0.00   0.0  0
 C91  CONST_65  H12  C39  C38  C37  180.00   0.0  0
 C91  CONST_66  H14  C41  N42  C37  180.00   0.0  0
 C91  CONST_67  H13  C40  C39  C38  180.00   0.0  0
 C91  CONST_68  H18  C9   C11  N3     0.00   0.0  0
 C91  CONST_69  H17  C14  C9   C11  180.00   0.0  0
 C91  CONST_70  H16  C3   C1   C10  180.00   0.0  0
 C91  CONST_74  C4   N4   C13  O      0.00   0.0  0
 C91  CONST_75  C17  C13  N4   C4   180.00   0.0  0
 C91  Var_01    C6   N1   C17  C13  -67.96  30.0  2
 C91  Var_02    N1   C17  C13  O    -19.67  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
 C91  plan-1  C6   0.020
 C91  plan-1  C37  0.020
 C91  plan-1  C38  0.020
 C91  plan-1  C39  0.020
 C91  plan-1  C40  0.020
 C91  plan-1  C41  0.020
 C91  plan-1  N42  0.020
 C91  plan-1  H11  0.020
 C91  plan-1  H12  0.020
 C91  plan-1  H13  0.020
 C91  plan-1  H14  0.020
 C91  plan-2  C17  0.020
 C91  plan-2  N1   0.020
 C91  plan-2  C6   0.020
 C91  plan-2  C37  0.020
 C91  plan-2  N3   0.020
 C91  plan-2  C11  0.020
 C91  plan-2  C10  0.020
 C91  plan-2  C1   0.020
 C91  plan-2  C3   0.020
 C91  plan-2  C14  0.020
 C91  plan-2  C9   0.020
 C91  plan-2  H15  0.020
 C91  plan-2  H16  0.020
 C91  plan-2  H17  0.020
 C91  plan-2  H18  0.020
 C91  plan-3  N4   0.020
 C91  plan-3  C4   0.020
 C91  plan-3  C2   0.020
 C91  plan-3  C5   0.020
 C91  plan-3  C18  0.020
 C91  plan-3  C25  0.020
 C91  plan-3  C26  0.020
 C91  plan-3  C27  0.020
 C91  plan-3  C28  0.020
 C91  plan-3  C16  0.020
 C91  plan-3  C12  0.020
 C91  plan-3  H2   0.020
 C91  plan-3  H3   0.020
 C91  plan-3  H4   0.020
 C91  plan-3  H5   0.020
 C91  plan-3  H6   0.020
 C91  plan-3  H7   0.020
 C91  plan-3  H8   0.020
 C91  plan-4  O    0.020
 C91  plan-4  C13  0.020
 C91  plan-4  N4   0.020
 C91  plan-4  C4   0.020
 C91  plan-4  C17  0.020
 C91  plan-4  H1   0.020

