# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 23:16:44 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: N-[4-methyl-3-(1-methyl-2-oxo-2,3-dihydro-1H-benzimidazol-5-yl)phenyl]-3-(trifluoromethyl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)Nc2cc(ccc12)c3cc(NC(=O)c4cccc(c4)C(F)(F)F)ccc3C
#
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
 K7S  K7S  N-[4-methyl-3-(1-methyl-2-oxo-2,3-dihydro-1H-benzimidazol-5-yl)phenyl]-3-(trifluoromethyl)benzamide  ligand  49  31  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_K7S
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
 K7S  C1   C  CR6   0   0.015  -3.0897   0.5965   0.3339
 K7S  C2   C  CR16  0  -0.314  -2.9640  -0.5542   1.1154
 K7S  C3   C  CR16  0  -0.307  -3.9090  -1.5763   1.0808
 K7S  C12  C  CR6   0   0.054  -2.0331   1.6351   0.3846
 K7S  C13  C  CR16  0  -0.337  -0.7250   1.2409   0.1065
 K7S  C14  C  CR6   0   0.376   0.3213   2.1571   0.1356
 K7S  C15  C  CR16  0  -0.334   0.0424   3.4858   0.4409
 K7S  C16  C  CR16  0  -0.283  -1.2564   3.8729   0.7193
 K7S  C17  C  CR6   0   0.050  -2.3164   2.9699   0.7064
 K7S  C19  C  CH3   0  -0.742  -3.6984   3.4454   1.0542
 K7S  C20  C  C     0   0.529   2.2569   0.6286   0.0451
 K7S  C21  C  CR6   0  -0.029   3.6788   0.5553  -0.4123
 K7S  C22  C  CR16  0  -0.282   4.1574   1.2783  -1.5034
 K7S  C23  C  CR16  0  -0.224   5.4751   1.1387  -1.9067
 K7S  C24  C  CR16  0  -0.281   6.3313   0.2867  -1.2247
 K7S  C25  C  CR6   0  -0.173   5.8549  -0.4368  -0.1394
 K7S  C26  C  CR16  0  -0.293   4.5301  -0.3140   0.2578
 K7S  C28  C  CT    0   1.056   6.7404  -1.3718   0.6249
 K7S  C4   C  CR56  0   0.325  -4.9872  -1.4178   0.2330
 K7S  C5   C  CR56  0   0.343  -5.1223  -0.2698  -0.5546
 K7S  C6   C  CR16  0  -0.338  -4.1883   0.7437  -0.5197
 K7S  N7   N  NR5   0  -0.574  -6.0661  -2.2291  -0.0402
 K7S  C8   C  CR5   0   0.631  -6.8807  -1.6297  -0.9754
 K7S  N9   N  NR15  0  -0.750  -6.2820  -0.4325  -1.2775
 K7S  O10  O  O     0  -0.499  -7.9162  -2.0740  -1.4372
 K7S  N18  N  NH1   0  -0.762   1.6461   1.8174  -0.1772
 K7S  O27  O  O     0  -0.455   1.7198  -0.3245   0.5807
 K7S  F29  F  F     0  -0.313   6.7962  -1.0449   1.9238
 K7S  F30  F  F     0  -0.313   6.2905  -2.6332   0.5697
 K7S  F31  F  F     0  -0.300   7.9948  -1.3827   0.1691
 K7S  H1   H  HCR6  0   0.253  -2.1122  -0.6516   1.7764
 K7S  H2   H  HCR6  0   0.274  -3.7947  -2.4566   1.6995
 K7S  H3   H  HCH3  0   0.268  -7.1936  -3.9566   0.1106
 K7S  H4   H  HCH3  0   0.255  -5.4664  -4.1790   0.4064
 K7S  H5   H  HCH3  0   0.255  -6.4866  -3.4102   1.6359
 K7S  H6   H  HCR6  0   0.266  -0.5444   0.2104  -0.1597
 K7S  H7   H  HCR6  0   0.269   0.8402   4.2182   0.4687
 K7S  H8   H  HCR6  0   0.253  -1.4489   4.9093   0.9694
 K7S  H9   H  HCH3  0   0.246  -4.2980   3.6463   0.1644
 K7S  H10  H  HCH3  0   0.245  -4.2447   2.7135   1.6490
 K7S  H11  H  HCH3  0   0.250  -3.6515   4.3740   1.6227
 K7S  H12  H  HCR6  0   0.277   3.5057   1.9364  -2.0636
 K7S  H13  H  HCR6  0   0.279   5.8382   1.6918  -2.7618
 K7S  H14  H  HCR6  0   0.281   7.3580   0.1970  -1.5509
 K7S  H15  H  HCR6  0   0.281   4.1493  -0.8835   1.0964
 K7S  H16  H  HCR6  0   0.265  -4.2924   1.6173  -1.1499
 K7S  H17  H  HNR5  0   0.419  -6.6688   0.2234  -1.9371
 K7S  H18  H  HNH1  0   0.421   2.2338   2.5916  -0.4478
 K7S  C11  C  CH3   0  -0.533  -6.3131  -3.5119   0.5647

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
 K7S  C19  C17  single    1.502  0.020  1.502
 K7S  C11  N7   single    1.440  0.020  1.440
 K7S  O10  C8   double    1.218  0.020  1.218
 K7S  C17  C16  aromatic  1.393  0.020  1.393
 K7S  C17  C12  aromatic  1.402  0.020  1.402
 K7S  N7   C8   single    1.377  0.020  1.377
 K7S  N7   C4   single    1.377  0.020  1.377
 K7S  C8   N9   single    1.372  0.020  1.372
 K7S  C3   C4   aromatic  1.381  0.020  1.381
 K7S  C3   C2   aromatic  1.392  0.020  1.392
 K7S  C4   C5   aromatic  1.399  0.020  1.399
 K7S  C16  C15  aromatic  1.384  0.020  1.384
 K7S  N9   C5   single    1.376  0.020  1.376
 K7S  C2   C1   aromatic  1.397  0.020  1.397
 K7S  C5   C6   aromatic  1.379  0.020  1.379
 K7S  C1   C6   aromatic  1.399  0.020  1.399
 K7S  C1   C12  single    1.482  0.020  1.482
 K7S  C12  C13  aromatic  1.394  0.020  1.394
 K7S  C15  C14  aromatic  1.392  0.020  1.392
 K7S  C13  C14  aromatic  1.391  0.020  1.391
 K7S  C14  N18  single    1.403  0.020  1.403
 K7S  N18  C20  single    1.355  0.020  1.355
 K7S  C20  O27  double    1.218  0.020  1.218
 K7S  C20  C21  single    1.495  0.020  1.495
 K7S  C21  C22  aromatic  1.394  0.020  1.394
 K7S  C21  C26  aromatic  1.389  0.020  1.389
 K7S  C22  C23  aromatic  1.385  0.020  1.385
 K7S  C26  C25  aromatic  1.388  0.020  1.388
 K7S  C23  C24  aromatic  1.387  0.020  1.387
 K7S  C25  C24  aromatic  1.389  0.020  1.389
 K7S  C25  C28  single    1.498  0.020  1.498
 K7S  F29  C28  single    1.341  0.020  1.341
 K7S  C28  F31  single    1.335  0.020  1.335
 K7S  C28  F30  single    1.340  0.020  1.340
 K7S  C2   H1   single    0.930  0.020  1.080
 K7S  C3   H2   single    0.930  0.020  1.080
 K7S  C11  H3   single    0.970  0.020  1.090
 K7S  C11  H4   single    0.970  0.020  1.090
 K7S  C11  H5   single    0.970  0.020  1.090
 K7S  C13  H6   single    0.930  0.020  1.080
 K7S  C15  H7   single    0.930  0.020  1.080
 K7S  C16  H8   single    0.930  0.020  1.080
 K7S  C19  H9   single    0.970  0.020  1.090
 K7S  C19  H10  single    0.970  0.020  1.090
 K7S  C19  H11  single    0.970  0.020  1.090
 K7S  C22  H12  single    0.930  0.020  1.080
 K7S  C23  H13  single    0.930  0.020  1.080
 K7S  C24  H14  single    0.930  0.020  1.080
 K7S  C26  H15  single    0.930  0.020  1.080
 K7S  C6   H16  single    0.930  0.020  1.080
 K7S  N9   H17  single    0.860  0.020  1.020
 K7S  N18  H18  single    0.860  0.020  1.020

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
 K7S  C6   C1   C12  120.46  3.000
 K7S  C12  C1   C2   119.60  3.000
 K7S  C6   C1   C2   119.92  3.000
 K7S  H1   C2   C3   118.89  3.000
 K7S  H1   C2   C1   119.11  3.000
 K7S  C3   C2   C1   121.99  3.000
 K7S  H2   C3   C4   121.80  3.000
 K7S  H2   C3   C2   120.75  3.000
 K7S  C4   C3   C2   117.44  3.000
 K7S  C17  C12  C13  120.31  3.000
 K7S  C13  C12  C1   117.63  3.000
 K7S  C17  C12  C1   122.06  3.000
 K7S  H6   C13  C14  120.53  3.000
 K7S  H6   C13  C12  118.43  3.000
 K7S  C14  C13  C12  121.01  3.000
 K7S  N18  C14  C15  117.99  3.000
 K7S  N18  C14  C13  123.10  3.000
 K7S  C15  C14  C13  118.87  3.000
 K7S  H7   C15  C16  119.80  3.000
 K7S  H7   C15  C14  120.24  3.000
 K7S  C16  C15  C14  119.96  3.000
 K7S  H8   C16  C17  119.16  3.000
 K7S  H8   C16  C15  118.74  3.000
 K7S  C17  C16  C15  122.09  3.000
 K7S  C19  C17  C16  119.53  3.000
 K7S  C16  C17  C12  117.76  3.000
 K7S  C19  C17  C12  122.71  3.000
 K7S  H11  C19  H10  108.01  3.000
 K7S  H11  C19  H9   106.98  3.000
 K7S  H10  C19  H9   107.05  3.000
 K7S  H11  C19  C17  110.54  3.000
 K7S  H10  C19  C17  112.02  3.000
 K7S  H9   C19  C17  112.01  3.000
 K7S  O27  C20  N18  124.05  3.000
 K7S  O27  C20  C21  121.02  3.000
 K7S  N18  C20  C21  114.93  3.000
 K7S  C26  C21  C22  119.46  3.000
 K7S  C26  C21  C20  117.77  3.000
 K7S  C22  C21  C20  122.72  3.000
 K7S  H12  C22  C23  118.90  3.000
 K7S  H12  C22  C21  120.92  3.000
 K7S  C23  C22  C21  120.16  3.000
 K7S  H13  C23  C24  119.72  3.000
 K7S  H13  C23  C22  119.88  3.000
 K7S  C24  C23  C22  120.39  3.000
 K7S  H14  C24  C25  121.23  3.000
 K7S  H14  C24  C23  119.26  3.000
 K7S  C25  C24  C23  119.51  3.000
 K7S  C28  C25  C26  118.26  3.000
 K7S  C28  C25  C24  121.42  3.000
 K7S  C26  C25  C24  120.32  3.000
 K7S  H15  C26  C25  120.70  3.000
 K7S  H15  C26  C21  119.16  3.000
 K7S  C25  C26  C21  120.14  3.000
 K7S  F31  C28  F30  107.08  3.000
 K7S  F30  C28  F29  106.46  3.000
 K7S  F31  C28  F29  107.09  3.000
 K7S  F30  C28  C25  111.60  3.000
 K7S  F31  C28  C25  112.74  3.000
 K7S  F29  C28  C25  111.52  3.000
 K7S  N7   C4   C5   107.22  3.000
 K7S  C5   C4   C3   121.03  3.000
 K7S  N7   C4   C3   131.75  3.000
 K7S  N9   C5   C6   132.15  3.000
 K7S  C6   C5   C4   121.58  3.000
 K7S  N9   C5   C4   106.27  3.000
 K7S  H16  C6   C5   120.90  3.000
 K7S  H16  C6   C1   121.05  3.000
 K7S  C5   C6   C1   118.04  3.000
 K7S  C8   N7   C4   109.98  3.000
 K7S  C4   N7   C11  125.16  3.000
 K7S  C8   N7   C11  124.86  3.000
 K7S  O10  C8   N9   127.29  3.000
 K7S  N9   C8   N7   105.73  3.000
 K7S  O10  C8   N7   126.98  3.000
 K7S  H17  N9   C8   123.00  3.000
 K7S  H17  N9   C5   126.19  3.000
 K7S  C8   N9   C5   110.81  3.000
 K7S  H18  N18  C20  117.04  3.000
 K7S  H18  N18  C14  115.09  3.000
 K7S  C20  N18  C14  126.98  3.000
 K7S  H5   C11  H4   108.88  3.000
 K7S  H5   C11  H3   108.67  3.000
 K7S  H4   C11  H3   108.58  3.000
 K7S  H5   C11  N7   110.93  3.000
 K7S  H4   C11  N7   110.56  3.000
 K7S  H3   C11  N7   109.17  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
 K7S  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 K7S  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 K7S  CONST_03  C16  C17  C12  C1    180.00   0.0  0
 K7S  CONST_04  C14  C13  C12  C1    180.00   0.0  0
 K7S  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 K7S  CONST_06  C5   C6   C1   C2      0.00   0.0  0
 K7S  CONST_09  C6   C5   C4   C3      0.00   0.0  0
 K7S  CONST_10  C6   C1   C2   C3      0.00   0.0  0
 K7S  CONST_11  C12  C1   C2   C3    180.00   0.0  0
 K7S  CONST_12  C15  C16  C17  C12     0.00   0.0  0
 K7S  CONST_13  C5   C6   C1   C12   180.00   0.0  0
 K7S  CONST_14  C15  C14  C13  C12     0.00   0.0  0
 K7S  CONST_15  C16  C17  C12  C13     0.00   0.0  0
 K7S  CONST_17  C16  C15  C14  C13     0.00   0.0  0
 K7S  CONST_18  C17  C16  C15  C14     0.00   0.0  0
 K7S  CONST_19  C17  C12  C13  C14     0.00   0.0  0
 K7S  CONST_21  C24  C23  C22  C21     0.00   0.0  0
 K7S  CONST_22  C24  C25  C26  C21     0.00   0.0  0
 K7S  CONST_23  C25  C26  C21  C22     0.00   0.0  0
 K7S  CONST_24  C25  C24  C23  C22     0.00   0.0  0
 K7S  CONST_25  C26  C21  C22  C23     0.00   0.0  0
 K7S  CONST_26  C26  C25  C24  C23     0.00   0.0  0
 K7S  CONST_27  N9   C8   N7   C4      0.00   0.0  0
 K7S  CONST_28  C8   N9   C5   C4      0.00   0.0  0
 K7S  CONST_29  C8   N7   C4   C5      0.00   0.0  0
 K7S  CONST_30  N7   C8   N9   C5      0.00   0.0  0
 K7S  CONST_31  N9   C5   C4   N7      0.00   0.0  0
 K7S  CONST_32  C19  C17  C12  C1      0.00   0.0  0
 K7S  CONST_33  N18  C14  C13  C12   180.00   0.0  0
 K7S  CONST_34  C19  C17  C12  C13   180.00   0.0  0
 K7S  CONST_35  C19  C17  C16  C15   180.00   0.0  0
 K7S  CONST_36  N18  C14  C15  C16   180.00   0.0  0
 K7S  CONST_37  C23  C22  C21  C20   180.00   0.0  0
 K7S  CONST_38  C25  C26  C21  C20   180.00   0.0  0
 K7S  CONST_39  C28  C25  C26  C21   180.00   0.0  0
 K7S  CONST_40  C28  C25  C24  C23   180.00   0.0  0
 K7S  CONST_41  N9   C8   N7   C11   180.00   0.0  0
 K7S  CONST_42  C5   C4   N7   C11   180.00   0.0  0
 K7S  CONST_43  O10  C8   N7   C4    180.00   0.0  0
 K7S  CONST_44  O10  C8   N9   C5    180.00   0.0  0
 K7S  CONST_45  H2   C3   C2   C1    180.00   0.0  0
 K7S  CONST_46  H6   C13  C12  C1      0.00   0.0  0
 K7S  CONST_47  H16  C6   C1   C2    180.00   0.0  0
 K7S  CONST_48  H8   C16  C17  C12   180.00   0.0  0
 K7S  CONST_49  H1   C2   C1   C12     0.00   0.0  0
 K7S  CONST_50  H7   C15  C14  C13   180.00   0.0  0
 K7S  CONST_51  H13  C23  C22  C21   180.00   0.0  0
 K7S  CONST_52  H15  C26  C21  C22   180.00   0.0  0
 K7S  CONST_53  H14  C24  C23  C22   180.00   0.0  0
 K7S  CONST_54  H12  C22  C23  C24   180.00   0.0  0
 K7S  CONST_55  H17  N9   C5   C4    180.00   0.0  0
 K7S  CONST_56  C21  C20  N18  C14   180.00   0.0  0
 K7S  CONST_59  O10  C8   N7   C11     0.00   0.0  0
 K7S  CONST_61  O27  C20  N18  C14     0.00   0.0  0
 K7S  Var_01    N18  C20  C21  C22   -30.61  30.0  2
 K7S  Var_02    F29  C28  C25  C24   122.35  30.0  2
 K7S  Var_03    H9   C19  C17  C12   -82.39  30.0  2
 K7S  Var_04    H3   C11  N7   C4   -175.96  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
 K7S  plan-1  C1   0.020
 K7S  plan-1  C12  0.020
 K7S  plan-1  C13  0.020
 K7S  plan-1  C14  0.020
 K7S  plan-1  C15  0.020
 K7S  plan-1  C16  0.020
 K7S  plan-1  C17  0.020
 K7S  plan-1  C19  0.020
 K7S  plan-1  N18  0.020
 K7S  plan-1  H6   0.020
 K7S  plan-1  H7   0.020
 K7S  plan-1  H8   0.020
 K7S  plan-2  C20  0.020
 K7S  plan-2  C21  0.020
 K7S  plan-2  C22  0.020
 K7S  plan-2  C23  0.020
 K7S  plan-2  C24  0.020
 K7S  plan-2  C25  0.020
 K7S  plan-2  C26  0.020
 K7S  plan-2  C28  0.020
 K7S  plan-2  H12  0.020
 K7S  plan-2  H13  0.020
 K7S  plan-2  H14  0.020
 K7S  plan-2  H15  0.020
 K7S  plan-3  C1   0.020
 K7S  plan-3  C2   0.020
 K7S  plan-3  C3   0.020
 K7S  plan-3  C12  0.020
 K7S  plan-3  C4   0.020
 K7S  plan-3  C5   0.020
 K7S  plan-3  C6   0.020
 K7S  plan-3  N7   0.020
 K7S  plan-3  C8   0.020
 K7S  plan-3  N9   0.020
 K7S  plan-3  O10  0.020
 K7S  plan-3  H1   0.020
 K7S  plan-3  H2   0.020
 K7S  plan-3  H16  0.020
 K7S  plan-3  H17  0.020
 K7S  plan-3  C11  0.020
 K7S  plan-4  C14  0.020
 K7S  plan-4  C20  0.020
 K7S  plan-4  C21  0.020
 K7S  plan-4  N18  0.020
 K7S  plan-4  O27  0.020
 K7S  plan-4  H18  0.020

