# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 20:57:19 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 5-(4-cyano-2-methyl-1H-benzimidazol-1-yl)-N-cyclopropylthiophene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc2c(cccc2n1c3sc(cc3)C(=O)NC4CC4)C#N
#
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
 JBW  JBW  5-(4-cyano-2-methyl-1H-benzimidazol-1-yl)-N-cyclopropylthiophene-2-carboxamide  ligand  37  23  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_JBW
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
 JBW  O     O  O     0  -0.467   4.6830  -1.2471  -0.7374
 JBW  C13   C  C     0   0.554   3.8388  -0.4242  -0.4237
 JBW  N3    N  NH1   0  -0.667   4.1342   0.8123   0.0187
 JBW  C14   C  CH1   0  -0.081   5.4828   1.2602   0.1464
 JBW  C16   C  CH2   0  -0.511   5.8046   2.1504   1.3023
 JBW  C15   C  CH2   0  -0.483   6.3091   0.7407   1.2785
 JBW  C12   C  CR5   0  -0.306   2.3986  -0.7636  -0.5146
 JBW  C11   C  CR15  0  -0.181   1.8878  -1.7956  -1.2493
 JBW  C10   C  CR15  0  -0.162   0.4790  -1.8822  -1.1782
 JBW  S     S  S2    0   0.279   1.1587   0.0936   0.3161
 JBW  C9    C  CR5   0   0.013  -0.0505  -0.9227  -0.3698
 JBW  N2    N  NR5   0  -0.631  -1.3921  -0.7350  -0.0421
 JBW  C1    C  CR5   0   0.446  -2.1728  -1.5684   0.7257
 JBW  C     C  CH3   0  -0.759  -1.6516  -2.8344   1.2893
 JBW  C3    C  CR56  0   0.350  -2.1782   0.3424  -0.3964
 JBW  C4    C  CR16  0  -0.275  -1.9316   1.4756  -1.1524
 JBW  C5    C  CR16  0  -0.274  -2.9860   2.3650  -1.3087
 JBW  C6    C  CR16  0  -0.265  -4.2348   2.1282  -0.7353
 JBW  C7    C  CR6   0  -0.071  -4.4660   0.9811   0.0199
 JBW  C2    C  CR56  0   0.177  -3.4181   0.0727   0.1922
 JBW  N     N  N     0  -0.454  -3.3834  -1.1105   0.8755
 JBW  C8    C  CSP   0   0.043  -5.7376   0.7258   0.6054
 JBW  N1    N  NS    0  -0.248  -6.7685   0.5190   1.0774
 JBW  H3    H  HNH1  0   0.406   3.4098   1.5122   0.0657
 JBW  H14   H  HCH1  0   0.273   5.9942   1.4586  -0.7905
 JBW  H161  H  HCH2  0   0.261   6.5036   2.9581   1.1322
 JBW  H162  H  HCH2  0   0.260   5.0038   2.3856   1.9925
 JBW  H151  H  HCH2  0   0.258   5.8450   0.0304   1.9503
 JBW  H152  H  HCH2  0   0.258   7.3605   0.5665   1.0924
 JBW  H11   H  HCR5  0   0.284   2.5028  -2.4581  -1.8401
 JBW  H10   H  HCR5  0   0.296  -0.1190  -2.6168  -1.6975
 JBW  HC1   H  HCH3  0   0.270  -0.6808  -2.6909   1.7635
 JBW  HC2   H  HCH3  0   0.281  -2.3512  -3.2163   2.0278
 JBW  HC3   H  HCH3  0   0.277  -1.5303  -3.5894   0.5111
 JBW  H4    H  HCR6  0   0.289  -0.9679   1.6676  -1.6055
 JBW  H5    H  HCR6  0   0.277  -2.8385   3.2631  -1.8920
 JBW  H6    H  HCR6  0   0.283  -5.0343   2.8414  -0.8811

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
 JBW  O    C13   double    1.220  0.020  1.220
 JBW  C13  N3    single    1.346  0.020  1.346
 JBW  C13  C12   single    1.482  0.020  1.482
 JBW  N3   C14   single    1.427  0.020  1.427
 JBW  C14  C16   single    1.494  0.020  1.494
 JBW  C14  C15   single    1.495  0.020  1.495
 JBW  C16  C15   single    1.497  0.020  1.497
 JBW  C12  C11   aromatic  1.366  0.020  1.366
 JBW  C12  S     aromatic  1.721  0.020  1.721
 JBW  C11  C10   aromatic  1.413  0.020  1.413
 JBW  C10  C9    aromatic  1.362  0.020  1.362
 JBW  S    C9    aromatic  1.722  0.020  1.722
 JBW  C9   N2    single    1.394  0.020  1.394
 JBW  N2   C1    aromatic  1.376  0.020  1.376
 JBW  N2   C3    aromatic  1.380  0.020  1.380
 JBW  C1   C     single    1.481  0.020  1.481
 JBW  C1   N     aromatic  1.303  0.020  1.303
 JBW  C3   C4    aromatic  1.384  0.020  1.384
 JBW  C3   C2    aromatic  1.399  0.020  1.399
 JBW  C4   C5    aromatic  1.388  0.020  1.388
 JBW  C5   C6    aromatic  1.394  0.020  1.394
 JBW  C6   C7    aromatic  1.393  0.020  1.393
 JBW  C7   C2    aromatic  1.397  0.020  1.397
 JBW  C7   C8    single    1.423  0.020  1.423
 JBW  C2   N     aromatic  1.367  0.020  1.367
 JBW  C8   N1    triple    1.153  0.020  1.153
 JBW  N3   H3    single    0.860  0.020  1.020
 JBW  C14  H14   single    0.970  0.020  1.090
 JBW  C16  H161  single    0.970  0.020  1.090
 JBW  C16  H162  single    0.970  0.020  1.090
 JBW  C15  H151  single    0.970  0.020  1.090
 JBW  C15  H152  single    0.970  0.020  1.090
 JBW  C11  H11   single    0.930  0.020  1.080
 JBW  C10  H10   single    0.930  0.020  1.080
 JBW  C    HC1   single    0.970  0.020  1.090
 JBW  C    HC2   single    0.970  0.020  1.090
 JBW  C    HC3   single    0.970  0.020  1.090
 JBW  C4   H4    single    0.930  0.020  1.080
 JBW  C5   H5    single    0.930  0.020  1.080
 JBW  C6   H6    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
 JBW  C12   C13  N3    116.34  3.000
 JBW  C12   C13  O     120.14  3.000
 JBW  N3    C13  O     123.52  3.000
 JBW  H3    N3   C14   117.19  3.000
 JBW  H3    N3   C13   119.69  3.000
 JBW  C14   N3   C13   121.69  3.000
 JBW  H14   C14  C15   117.17  3.000
 JBW  H14   C14  C16   117.21  3.000
 JBW  C15   C14  C16    60.13  3.000
 JBW  H14   C14  N3    115.18  3.000
 JBW  C15   C14  N3    118.76  3.000
 JBW  C16   C14  N3    117.38  3.000
 JBW  H162  C16  H161  114.57  3.000
 JBW  H162  C16  C15   117.63  3.000
 JBW  H161  C16  C15   118.87  3.000
 JBW  H162  C16  C14   117.60  3.000
 JBW  H161  C16  C14   117.55  3.000
 JBW  C15   C16  C14    59.96  3.000
 JBW  H152  C15  H151  114.69  3.000
 JBW  H152  C15  C16   118.80  3.000
 JBW  H151  C15  C16   117.62  3.000
 JBW  H152  C15  C14   117.58  3.000
 JBW  H151  C15  C14   117.46  3.000
 JBW  C16   C15  C14    59.91  3.000
 JBW  S     C12  C11   111.50  3.000
 JBW  S     C12  C13   123.80  3.000
 JBW  C11   C12  C13   124.70  3.000
 JBW  H11   C11  C10   123.89  3.000
 JBW  H11   C11  C12   123.01  3.000
 JBW  C10   C11  C12   113.08  3.000
 JBW  H10   C10  C9    123.32  3.000
 JBW  H10   C10  C11   124.70  3.000
 JBW  C9    C10  C11   111.98  3.000
 JBW  C9    S    C12    91.13  3.000
 JBW  N2    C9   S     120.19  3.000
 JBW  N2    C9   C10   127.49  3.000
 JBW  S     C9   C10   112.29  3.000
 JBW  C3    N2   C1    107.04  3.000
 JBW  C3    N2   C9    126.38  3.000
 JBW  C1    N2   C9    126.56  3.000
 JBW  N     C1   C     125.72  3.000
 JBW  N     C1   N2    112.23  3.000
 JBW  C     C1   N2    122.05  3.000
 JBW  HC3   C    HC2   108.25  3.000
 JBW  HC3   C    HC1   107.60  3.000
 JBW  HC2   C    HC1   108.91  3.000
 JBW  HC3   C    C1    111.06  3.000
 JBW  HC2   C    C1    109.42  3.000
 JBW  HC1   C    C1    111.51  3.000
 JBW  C2    C3   C4    123.06  3.000
 JBW  C2    C3   N2    104.26  3.000
 JBW  C4    C3   N2    132.68  3.000
 JBW  H4    C4   C5    121.03  3.000
 JBW  H4    C4   C3    122.18  3.000
 JBW  C5    C4   C3    116.79  3.000
 JBW  H5    C5   C6    119.02  3.000
 JBW  H5    C5   C4    119.30  3.000
 JBW  C6    C5   C4    121.68  3.000
 JBW  H6    C6   C7    119.58  3.000
 JBW  H6    C6   C5    119.65  3.000
 JBW  C7    C6   C5    120.76  3.000
 JBW  C8    C7   C2    120.18  3.000
 JBW  C8    C7   C6    121.28  3.000
 JBW  C2    C7   C6    118.54  3.000
 JBW  N     C2   C7    130.05  3.000
 JBW  N     C2   C3    110.78  3.000
 JBW  C7    C2   C3    119.17  3.000
 JBW  C2    N    C1    105.69  3.000
 JBW  N1    C8   C7    180.00  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
 JBW  CONST_01  C9    C10  C11  C12     0.00   0.0  0
 JBW  CONST_02  C10   C9   S    C12     0.00   0.0  0
 JBW  CONST_03  N2    C9   S    C12   180.00   0.0  0
 JBW  CONST_04  C9    S    C12  C11     0.00   0.0  0
 JBW  CONST_05  S     C9   C10  C11     0.00   0.0  0
 JBW  CONST_06  N2    C9   C10  C11   180.00   0.0  0
 JBW  CONST_07  S     C12  C11  C10     0.00   0.0  0
 JBW  CONST_12  N     C1   N2   C9    180.00   0.0  0
 JBW  CONST_13  C4    C3   N2   C9      0.00   0.0  0
 JBW  CONST_14  C2    C3   N2   C9    180.00   0.0  0
 JBW  CONST_15  C2    N    C1   N2      0.00   0.0  0
 JBW  CONST_16  C5    C4   C3   N2    180.00   0.0  0
 JBW  CONST_17  C7    C2   C3   N2    180.00   0.0  0
 JBW  CONST_18  N     C2   C3   N2      0.00   0.0  0
 JBW  CONST_19  C4    C3   N2   C1    180.00   0.0  0
 JBW  CONST_20  C2    C3   N2   C1      0.00   0.0  0
 JBW  CONST_21  C3    C2   N    C1      0.00   0.0  0
 JBW  CONST_22  C7    C2   N    C1    180.00   0.0  0
 JBW  CONST_23  N     C1   N2   C3      0.00   0.0  0
 JBW  CONST_24  C6    C5   C4   C3      0.00   0.0  0
 JBW  CONST_25  C6    C7   C2   C3      0.00   0.0  0
 JBW  CONST_26  C7    C2   C3   C4      0.00   0.0  0
 JBW  CONST_27  N     C2   C3   C4    180.00   0.0  0
 JBW  CONST_28  C7    C6   C5   C4      0.00   0.0  0
 JBW  CONST_29  C2    C3   C4   C5      0.00   0.0  0
 JBW  CONST_30  C2    C7   C6   C5      0.00   0.0  0
 JBW  CONST_31  N     C2   C7   C6    180.00   0.0  0
 JBW  CONST_32  C10   C11  C12  C13   180.00   0.0  0
 JBW  CONST_33  C9    S    C12  C13   180.00   0.0  0
 JBW  CONST_34  C     C1   N2   C9      0.00   0.0  0
 JBW  CONST_35  C3    N2   C1   C     180.00   0.0  0
 JBW  CONST_36  C2    N    C1   C     180.00   0.0  0
 JBW  CONST_37  C8    C7   C2   C3    180.00   0.0  0
 JBW  CONST_38  C8    C7   C6   C5    180.00   0.0  0
 JBW  CONST_39  C8    C7   C2   N       0.00   0.0  0
 JBW  CONST_40  H10   C10  C11  C12   180.00   0.0  0
 JBW  CONST_41  H11   C11  C12  S     180.00   0.0  0
 JBW  CONST_42  H4    C4   C3   N2      0.00   0.0  0
 JBW  CONST_43  H5    C5   C4   C3    180.00   0.0  0
 JBW  CONST_44  H6    C6   C5   C4    180.00   0.0  0
 JBW  CONST_45  C12   C13  N3   C14   180.00   0.0  0
 JBW  CONST_46  C14   N3   C13  O       0.00   0.0  0
 JBW  CONST_47  H3    N3   C13  C12     0.00   0.0  0
 JBW  Var_01    C15   C16  C14  N3    109.12  30.0  1
 JBW  Var_02    H151  C15  C16  C14  -107.36  30.0  1
 JBW  Var_03    C11   C12  C13  O     -18.32  30.0  2
 JBW  Var_04    C16   C14  N3   C13  -143.49  30.0  3
 JBW  Var_05    HC1   C    C1   N2     47.10  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
 JBW  chir_01  C14  N3  C16  C15  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
 JBW  plan-1  C13  0.020
 JBW  plan-1  C12  0.020
 JBW  plan-1  C11  0.020
 JBW  plan-1  C10  0.020
 JBW  plan-1  S    0.020
 JBW  plan-1  C9   0.020
 JBW  plan-1  N2   0.020
 JBW  plan-1  H11  0.020
 JBW  plan-1  H10  0.020
 JBW  plan-2  C9   0.020
 JBW  plan-2  N2   0.020
 JBW  plan-2  C1   0.020
 JBW  plan-2  C    0.020
 JBW  plan-2  C3   0.020
 JBW  plan-2  C4   0.020
 JBW  plan-2  C5   0.020
 JBW  plan-2  C6   0.020
 JBW  plan-2  C7   0.020
 JBW  plan-2  C2   0.020
 JBW  plan-2  N    0.020
 JBW  plan-2  C8   0.020
 JBW  plan-2  N1   0.020
 JBW  plan-2  H4   0.020
 JBW  plan-2  H5   0.020
 JBW  plan-2  H6   0.020
 JBW  plan-3  O    0.020
 JBW  plan-3  C13  0.020
 JBW  plan-3  N3   0.020
 JBW  plan-3  C14  0.020
 JBW  plan-3  C12  0.020
 JBW  plan-3  H3   0.020

