# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 16:21:09 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: N-cyclopropyl-5-[2-methyl-5-(trifluoromethoxy)-1H-benzimidazol-1-yl]thiophene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc2cc(OC(F)(F)F)ccc2n1c3sc(cc3)C(=O)NC4CC4
#
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
 O8A  O8A  N-cyclopropyl-5-[2-methyl-5-(trifluoromethoxy)-1H-benzimidazol-1-yl]thiophene-2-carboxamide  ligand  40  26  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_O8A
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
 O8A  C1    C  CR56  0   0.151  -2.1886  -1.5664  -0.5743
 O8A  F1    F  F     0  -0.300  -5.3684   1.5699   1.2399
 O8A  N1    N  N     0  -0.465  -1.7355  -2.8512  -0.7635
 O8A  O1    O  O2    0  -0.526  -4.8300   0.9226  -0.8215
 O8A  S1    S  S2    0   0.268   2.2483  -0.3729  -0.5698
 O8A  C2    C  CR56  0   0.344  -1.1614  -0.7604  -0.0683
 O8A  F2    F  F     0  -0.300  -6.1277  -0.2971   0.5153
 O8A  N2    N  NR5   0  -0.631  -0.0791  -1.6070   0.0452
 O8A  O2    O  O     0  -0.470   5.7308  -0.0163   1.2288
 O8A  C3    C  CR16  0  -0.294  -1.3261   0.5870   0.2075
 O8A  F3    F  F     0  -0.278  -6.8289   1.5495  -0.3454
 O8A  N3    N  NH1   0  -0.671   5.0079   1.0104  -0.6454
 O8A  C4    C  CR16  0  -0.319  -2.5792   1.1236  -0.0345
 O8A  C5    C  CR6   0   0.308  -3.6064   0.3201  -0.5350
 O8A  C6    C  CR16  0  -0.385  -3.4458  -1.0222  -0.8160
 O8A  C7    C  CR5   0   0.436  -0.4893  -2.8467  -0.3958
 O8A  C8    C  CT    0   1.071  -5.7627   0.9298   0.1368
 O8A  C9    C  CH3   0  -0.757   0.4360  -4.0033  -0.4285
 O8A  C10   C  CR5   0   0.015   1.2015  -1.2612   0.4709
 O8A  C11   C  CR5   0  -0.307   3.5041  -0.4005   0.6070
 O8A  C12   C  CR15  0  -0.183   3.1202  -1.0809   1.7282
 O8A  C13   C  CR15  0  -0.157   1.7956  -1.5678   1.6573
 O8A  C14   C  C     0   0.562   4.8417   0.2143   0.4247
 O8A  C15   C  CH1   0  -0.078   6.2708   1.5973  -0.9549
 O8A  C16   C  CH2   0  -0.516   6.2741   2.9644  -1.5557
 O8A  C17   C  CH2   0  -0.481   6.7578   2.7622  -0.1527
 O8A  H3    H  HCR6  0   0.283  -0.5230   1.2018   0.5918
 O8A  HN3   H  HNH1  0   0.407   4.2499   1.1763  -1.2888
 O8A  H4    H  HCR6  0   0.282  -2.7594   2.1741   0.1486
 O8A  H6    H  HCR6  0   0.281  -4.2502  -1.6207  -1.2229
 O8A  H9    H  HCH3  0   0.267   1.3472  -3.7624  -0.9774
 O8A  H9A   H  HCH3  0   0.274   0.7308  -4.3043   0.5773
 O8A  H9B   H  HCH3  0   0.279  -0.0509  -4.8451  -0.9128
 O8A  H12   H  HCR5  0   0.283   3.7672  -1.2173   2.5821
 O8A  H13   H  HCR5  0   0.295   1.3007  -2.1203   2.4428
 O8A  H15   H  HCH1  0   0.273   7.0203   0.8994  -1.3147
 O8A  H16   H  HCH2  0   0.262   6.9983   3.1631  -2.3342
 O8A  H16A  H  HCH2  0   0.261   5.3197   3.4579  -1.6933
 O8A  H17   H  HCH2  0   0.258   6.1260   3.1153   0.6519
 O8A  H17A  H  HCH2  0   0.258   7.8195   2.8239   0.0466

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
 O8A  C1   N1    aromatic  1.375  0.020  1.375
 O8A  C1   C2    aromatic  1.400  0.020  1.400
 O8A  C1   C6    aromatic  1.391  0.020  1.391
 O8A  F1   C8    single    1.335  0.020  1.335
 O8A  N1   C7    aromatic  1.299  0.020  1.299
 O8A  O1   C5    single    1.394  0.020  1.394
 O8A  O1   C8    single    1.337  0.020  1.337
 O8A  S1   C10   aromatic  1.723  0.020  1.723
 O8A  S1   C11   aromatic  1.721  0.020  1.721
 O8A  C2   N2    aromatic  1.379  0.020  1.379
 O8A  C2   C3    aromatic  1.385  0.020  1.385
 O8A  F2   C8    single    1.335  0.020  1.335
 O8A  N2   C7    aromatic  1.378  0.020  1.378
 O8A  N2   C10   single    1.393  0.020  1.393
 O8A  O2   C14   double    1.221  0.020  1.221
 O8A  C3   C4    aromatic  1.384  0.020  1.384
 O8A  F3   C8    single    1.324  0.020  1.324
 O8A  N3   C14   single    1.344  0.020  1.344
 O8A  N3   C15   single    1.427  0.020  1.427
 O8A  C4   C5    aromatic  1.397  0.020  1.397
 O8A  C5   C6    aromatic  1.381  0.020  1.381
 O8A  C7   C9    single    1.482  0.020  1.482
 O8A  C10  C13   aromatic  1.362  0.020  1.362
 O8A  C11  C12   aromatic  1.367  0.020  1.367
 O8A  C11  C14   single    1.483  0.020  1.483
 O8A  C12  C13   aromatic  1.413  0.020  1.413
 O8A  C15  C16   single    1.493  0.020  1.493
 O8A  C15  C17   single    1.496  0.020  1.496
 O8A  C16  C17   single    1.498  0.020  1.498
 O8A  C3   H3    single    0.930  0.020  1.080
 O8A  N3   HN3   single    0.860  0.020  1.020
 O8A  C4   H4    single    0.930  0.020  1.080
 O8A  C6   H6    single    0.930  0.020  1.080
 O8A  C9   H9    single    0.970  0.020  1.090
 O8A  C9   H9A   single    0.970  0.020  1.090
 O8A  C9   H9B   single    0.970  0.020  1.090
 O8A  C12  H12   single    0.930  0.020  1.080
 O8A  C13  H13   single    0.930  0.020  1.080
 O8A  C15  H15   single    0.970  0.020  1.090
 O8A  C16  H16   single    0.970  0.020  1.090
 O8A  C16  H16A  single    0.970  0.020  1.090
 O8A  C17  H17   single    0.970  0.020  1.090
 O8A  C17  H17A  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
 O8A  C6    C1   C2   120.04  3.000
 O8A  C6    C1   N1   129.73  3.000
 O8A  C2    C1   N1   110.22  3.000
 O8A  C7    N1   C1   105.89  3.000
 O8A  C8    O1   C5   117.86  3.000
 O8A  C11   S1   C10   91.26  3.000
 O8A  C3    C2   N2   132.39  3.000
 O8A  C3    C2   C1   123.00  3.000
 O8A  N2    C2   C1   104.61  3.000
 O8A  C10   N2   C7   126.49  3.000
 O8A  C10   N2   C2   126.47  3.000
 O8A  C7    N2   C2   106.99  3.000
 O8A  H3    C3   C4   120.91  3.000
 O8A  H3    C3   C2   122.36  3.000
 O8A  C4    C3   C2   116.73  3.000
 O8A  HN3   N3   C15  117.36  3.000
 O8A  HN3   N3   C14  120.84  3.000
 O8A  C15   N3   C14  121.73  3.000
 O8A  H4    C4   C5   119.79  3.000
 O8A  H4    C4   C3   119.85  3.000
 O8A  C5    C4   C3   120.35  3.000
 O8A  C6    C5   C4   123.14  3.000
 O8A  C6    C5   O1   118.72  3.000
 O8A  C4    C5   O1   118.08  3.000
 O8A  H6    C6   C5   121.86  3.000
 O8A  H6    C6   C1   121.39  3.000
 O8A  C5    C6   C1   116.74  3.000
 O8A  C9    C7   N2   121.55  3.000
 O8A  C9    C7   N1   126.16  3.000
 O8A  N2    C7   N1   112.28  3.000
 O8A  F3    C8   F2   108.26  3.000
 O8A  F3    C8   O1   107.65  3.000
 O8A  F2    C8   O1   112.89  3.000
 O8A  F3    C8   F1   108.32  3.000
 O8A  F2    C8   F1   106.69  3.000
 O8A  O1    C8   F1   112.87  3.000
 O8A  H9B   C9   H9A  108.57  3.000
 O8A  H9B   C9   H9   108.74  3.000
 O8A  H9A   C9   H9   107.42  3.000
 O8A  H9B   C9   C7   109.56  3.000
 O8A  H9A   C9   C7   111.35  3.000
 O8A  H9    C9   C7   111.13  3.000
 O8A  C13   C10  N2   127.69  3.000
 O8A  C13   C10  S1   112.17  3.000
 O8A  N2    C10  S1   120.13  3.000
 O8A  C14   C11  C12  124.09  3.000
 O8A  C14   C11  S1   124.56  3.000
 O8A  C12   C11  S1   111.34  3.000
 O8A  H12   C12  C13  123.91  3.000
 O8A  H12   C12  C11  122.91  3.000
 O8A  C13   C12  C11  113.18  3.000
 O8A  H13   C13  C12  124.68  3.000
 O8A  H13   C13  C10  123.28  3.000
 O8A  C12   C13  C10  112.03  3.000
 O8A  C11   C14  N3   117.05  3.000
 O8A  C11   C14  O2   119.84  3.000
 O8A  N3    C14  O2   123.11  3.000
 O8A  H15   C15  C17  116.98  3.000
 O8A  H15   C15  C16  116.99  3.000
 O8A  C17   C15  C16   60.14  3.000
 O8A  H15   C15  N3   114.75  3.000
 O8A  C17   C15  N3   119.49  3.000
 O8A  C16   C15  N3   117.76  3.000
 O8A  H16A  C16  H16  114.50  3.000
 O8A  H16A  C16  C17  117.72  3.000
 O8A  H16   C16  C17  118.86  3.000
 O8A  H16A  C16  C15  117.80  3.000
 O8A  H16   C16  C15  117.33  3.000
 O8A  C17   C16  C15   60.02  3.000
 O8A  H17A  C17  H17  114.66  3.000
 O8A  H17A  C17  C16  118.80  3.000
 O8A  H17   C17  C16  117.63  3.000
 O8A  H17A  C17  C15  117.56  3.000
 O8A  H17   C17  C15  117.56  3.000
 O8A  C16   C17  C15   59.84  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
 O8A  CONST_01  N2   C7   N1   C1      0.00   0.0  0
 O8A  CONST_02  C7   N2   C2   C1      0.00   0.0  0
 O8A  CONST_03  C10  N2   C2   C1    180.00   0.0  0
 O8A  CONST_04  C4   C3   C2   C1      0.00   0.0  0
 O8A  CONST_05  C4   C5   C6   C1      0.00   0.0  0
 O8A  CONST_06  N2   C2   C1   N1      0.00   0.0  0
 O8A  CONST_07  C3   C2   C1   N1    180.00   0.0  0
 O8A  CONST_08  C5   C6   C1   N1    180.00   0.0  0
 O8A  CONST_09  C2   N2   C7   N1      0.00   0.0  0
 O8A  CONST_10  C10  N2   C7   N1    180.00   0.0  0
 O8A  CONST_13  C12  C13  C10  S1      0.00   0.0  0
 O8A  CONST_14  C13  C12  C11  S1      0.00   0.0  0
 O8A  CONST_15  C7   N1   C1   C2      0.00   0.0  0
 O8A  CONST_16  C5   C6   C1   C2      0.00   0.0  0
 O8A  CONST_18  C5   C4   C3   C2      0.00   0.0  0
 O8A  CONST_19  C6   C1   C2   N2    180.00   0.0  0
 O8A  CONST_20  C4   C3   C2   N2    180.00   0.0  0
 O8A  CONST_21  C11  S1   C10  N2    180.00   0.0  0
 O8A  CONST_22  C12  C13  C10  N2    180.00   0.0  0
 O8A  CONST_23  C6   C1   C2   C3      0.00   0.0  0
 O8A  CONST_24  C7   N2   C2   C3    180.00   0.0  0
 O8A  CONST_25  C10  N2   C2   C3      0.00   0.0  0
 O8A  CONST_26  C6   C5   C4   C3      0.00   0.0  0
 O8A  CONST_27  C7   N1   C1   C6    180.00   0.0  0
 O8A  CONST_29  C12  C11  S1   C10     0.00   0.0  0
 O8A  CONST_30  C11  C12  C13  C10     0.00   0.0  0
 O8A  CONST_31  C13  C10  S1   C11     0.00   0.0  0
 O8A  CONST_32  C9   C7   N1   C1    180.00   0.0  0
 O8A  CONST_33  O1   C5   C6   C1    180.00   0.0  0
 O8A  CONST_34  C3   C4   C5   O1    180.00   0.0  0
 O8A  CONST_35  C9   C7   N2   C2    180.00   0.0  0
 O8A  CONST_36  C10  N2   C7   C9      0.00   0.0  0
 O8A  CONST_37  C14  C11  S1   C10   180.00   0.0  0
 O8A  CONST_38  C14  C11  C12  C13   180.00   0.0  0
 O8A  CONST_39  H3   C3   C2   C1    180.00   0.0  0
 O8A  CONST_40  H6   C6   C1   N1      0.00   0.0  0
 O8A  CONST_41  H13  C13  C10  S1    180.00   0.0  0
 O8A  CONST_42  H12  C12  C11  S1    180.00   0.0  0
 O8A  CONST_43  H4   C4   C3   C2    180.00   0.0  0
 O8A  CONST_44  C15  N3   C14  C11   180.00   0.0  0
 O8A  CONST_45  C15  N3   C14  O2      0.00   0.0  0
 O8A  CONST_46  HN3  N3   C14  C11     0.00   0.0  0
 O8A  Var_01    C17  C16  C15  N3    109.83  30.0  1
 O8A  Var_02    H17  C17  C16  C15  -107.45  30.0  1
 O8A  Var_03    O2   C14  C11  S1   -169.55  30.0  2
 O8A  Var_04    C16  C15  N3   C14  -145.17  30.0  3
 O8A  Var_05    H9   C9   C7   N1    126.41  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 O8A  chir_01  C15  N3  C16  C17  both

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
 O8A  plan-1  S1   0.020
 O8A  plan-1  N2   0.020
 O8A  plan-1  C10  0.020
 O8A  plan-1  C11  0.020
 O8A  plan-1  C12  0.020
 O8A  plan-1  C13  0.020
 O8A  plan-1  C14  0.020
 O8A  plan-1  H12  0.020
 O8A  plan-1  H13  0.020
 O8A  plan-2  C1   0.020
 O8A  plan-2  N1   0.020
 O8A  plan-2  O1   0.020
 O8A  plan-2  C2   0.020
 O8A  plan-2  N2   0.020
 O8A  plan-2  C3   0.020
 O8A  plan-2  C4   0.020
 O8A  plan-2  C5   0.020
 O8A  plan-2  C6   0.020
 O8A  plan-2  C7   0.020
 O8A  plan-2  C9   0.020
 O8A  plan-2  C10  0.020
 O8A  plan-2  H3   0.020
 O8A  plan-2  H4   0.020
 O8A  plan-2  H6   0.020
 O8A  plan-3  O2   0.020
 O8A  plan-3  N3   0.020
 O8A  plan-3  C11  0.020
 O8A  plan-3  C14  0.020
 O8A  plan-3  C15  0.020
 O8A  plan-3  HN3  0.020

