# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 05:34:34 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 4-({1-[(4-methyl-1-benzothiophen-3-yl)methyl]-1H-benzimidazol-2-yl}sulfanyl)butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc2scc(Cn3c(SCCCC(O)=O)nc4ccccc34)c12
#
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
 KPK  KPK  '4-({1-[(4-methyl-1-benzothiophen-3-yl)methyl]-1H-benzimidazol-2-yl}sulfanyl)butanoic acid'  ligand  47  27  .  2021-08-12  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_KPK
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
 KPK  O27  O  O     0  -0.443   6.2326  -3.0190  -0.3848
 KPK  C24  C  C     0   0.553   6.5497  -1.9254   0.0111
 KPK  O26  O  OH1   0  -0.596   7.7965  -1.6033   0.3393
 KPK  C20  C  CH2   0  -0.575   5.6103  -0.7663   0.1988
 KPK  C16  C  CH2   0  -0.436   4.1787  -1.0844  -0.2019
 KPK  C12  C  CH2   0  -0.546   3.3015   0.1415   0.0039
 KPK  S8   S  S2    0   0.048   1.5991  -0.2850  -0.4672
 KPK  C3   C  CR5   0   0.312   0.8269   1.2601  -0.2667
 KPK  N7   N  N     0  -0.466   1.3831   2.3451   0.1893
 KPK  C5   C  CR56  0   0.149   0.3801   3.2889   0.1777
 KPK  C10  C  CR16  0  -0.335   0.4038   4.6287   0.5575
 KPK  C15  C  CR16  0  -0.270  -0.7714   5.3539   0.4480
 KPK  C11  C  CR16  0  -0.278  -1.9516   4.7663  -0.0267
 KPK  C6   C  CR16  0  -0.307  -1.9934   3.4349  -0.4108
 KPK  C2   C  CR56  0   0.333  -0.8091   2.7208  -0.3021
 KPK  N1   N  NR5   0  -0.554  -0.4895   1.4144  -0.5959
 KPK  C4   C  CH2   0  -0.386  -1.3928   0.4087  -1.0949
 KPK  C9   C  CR5   0   0.125  -2.1060  -0.3336   0.0022
 KPK  C14  C  CR15  0  -0.532  -1.8907  -0.0792   1.3132
 KPK  S19  S  S2    0   0.223  -2.8272  -1.0582   2.3763
 KPK  C17  C  CR56  0  -0.227  -3.5634  -1.8672   1.0354
 KPK  C21  C  CR16  0  -0.293  -4.5143  -2.8795   1.1351
 KPK  C25  C  CR16  0  -0.256  -5.0000  -3.4188  -0.0353
 KPK  C22  C  CR16  0  -0.315  -4.5414  -2.9552  -1.2722
 KPK  C18  C  CR6   0   0.043  -3.5958  -1.9502  -1.3879
 KPK  C13  C  CR56  0   0.209  -3.0862  -1.3822  -0.1984
 KPK  C23  C  CH3   0  -0.765  -3.1613  -1.5169  -2.7592
 KPK  H1   H  HOH1  0   0.480   8.3831  -2.3631   0.2078
 KPK  H2   H  HCH2  0   0.286   5.6572  -0.4574   1.2477
 KPK  H3   H  HCH2  0   0.285   5.9927   0.0827  -0.3757
 KPK  H4   H  HCH2  0   0.253   4.1434  -1.3922  -1.2487
 KPK  H5   H  HCH2  0   0.253   3.8017  -1.9192   0.3924
 KPK  H6   H  HCH2  0   0.284   3.3056   0.4616   1.0454
 KPK  H7   H  HCH2  0   0.285   3.6362   0.9752  -0.6128
 KPK  H8   H  HCR6  0   0.256   1.3135   5.0841   0.9269
 KPK  H9   H  HCR6  0   0.254  -0.7827   6.3968   0.7367
 KPK  H10  H  HCR6  0   0.257  -2.8506   5.3648  -0.0924
 KPK  H11  H  HCR6  0   0.270  -2.9088   2.9828  -0.7697
 KPK  H12  H  HCH2  0   0.291  -2.1052   0.9072  -1.7526
 KPK  H13  H  HCH2  0   0.288  -0.8283  -0.2777  -1.7283
 KPK  H14  H  HCR5  0   0.297  -1.2190   0.6521   1.7376
 KPK  H15  H  HCR6  0   0.268  -4.8567  -3.2287   2.1004
 KPK  H16  H  HCR6  0   0.261  -5.7402  -4.2070  -0.0013
 KPK  H17  H  HCR6  0   0.253  -4.9412  -3.3971  -2.1766
 KPK  H18  H  HCH3  0   0.250  -3.3905  -0.4685  -2.9511
 KPK  H19  H  HCH3  0   0.249  -2.0917  -1.6586  -2.9158
 KPK  H20  H  HCH3  0   0.267  -3.6759  -2.1013  -3.5203

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
 KPK  C16  C20  single    1.520  0.020  1.520
 KPK  C16  C12  single    1.521  0.020  1.521
 KPK  C20  C24  single    1.504  0.020  1.504
 KPK  C12  S8   single    1.817  0.020  1.817
 KPK  C24  O27  double    1.206  0.020  1.206
 KPK  C24  O26  single    1.329  0.020  1.329
 KPK  N7   C3   aromatic  1.302  0.020  1.302
 KPK  N7   C5   aromatic  1.377  0.020  1.377
 KPK  S8   C3   single    1.739  0.020  1.739
 KPK  C10  C5   aromatic  1.393  0.020  1.393
 KPK  C10  C15  aromatic  1.385  0.020  1.385
 KPK  C3   N1   aromatic  1.366  0.020  1.366
 KPK  C5   C2   aromatic  1.403  0.020  1.403
 KPK  C15  C11  aromatic  1.401  0.020  1.401
 KPK  N1   C2   aromatic  1.377  0.020  1.377
 KPK  N1   C4   single    1.441  0.020  1.441
 KPK  C2   C6   aromatic  1.387  0.020  1.387
 KPK  C11  C6   aromatic  1.386  0.020  1.386
 KPK  C4   C9   single    1.504  0.020  1.504
 KPK  C14  C9   aromatic  1.353  0.020  1.353
 KPK  C14  S19  aromatic  1.722  0.020  1.722
 KPK  C9   C13  aromatic  1.449  0.020  1.449
 KPK  S19  C17  aromatic  1.730  0.020  1.730
 KPK  C13  C18  aromatic  1.413  0.020  1.413
 KPK  C13  C17  aromatic  1.409  0.020  1.409
 KPK  C23  C18  single    1.502  0.020  1.502
 KPK  C18  C22  aromatic  1.385  0.020  1.385
 KPK  C17  C21  aromatic  1.392  0.020  1.392
 KPK  C22  C25  aromatic  1.398  0.020  1.398
 KPK  C21  C25  aromatic  1.377  0.020  1.377
 KPK  O26  H1   single    0.850  0.020  0.980
 KPK  C20  H2   single    0.970  0.020  1.090
 KPK  C20  H3   single    0.970  0.020  1.090
 KPK  C16  H4   single    0.970  0.020  1.090
 KPK  C16  H5   single    0.970  0.020  1.090
 KPK  C12  H6   single    0.970  0.020  1.090
 KPK  C12  H7   single    0.970  0.020  1.090
 KPK  C10  H8   single    0.930  0.020  1.080
 KPK  C15  H9   single    0.930  0.020  1.080
 KPK  C11  H10  single    0.930  0.020  1.080
 KPK  C6   H11  single    0.930  0.020  1.080
 KPK  C4   H12  single    0.970  0.020  1.090
 KPK  C4   H13  single    0.970  0.020  1.090
 KPK  C14  H14  single    0.930  0.020  1.080
 KPK  C21  H15  single    0.930  0.020  1.080
 KPK  C25  H16  single    0.930  0.020  1.080
 KPK  C22  H17  single    0.930  0.020  1.080
 KPK  C23  H18  single    0.970  0.020  1.090
 KPK  C23  H19  single    0.970  0.020  1.090
 KPK  C23  H20  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
 KPK  C20  C24  O26  111.62  3.000
 KPK  O26  C24  O27  123.22  3.000
 KPK  C20  C24  O27  125.16  3.000
 KPK  H1   O26  C24  110.15  3.000
 KPK  H3   C20  H2   105.62  3.000
 KPK  H3   C20  C16  110.68  3.000
 KPK  H2   C20  C16  110.61  3.000
 KPK  H3   C20  C24  108.31  3.000
 KPK  H2   C20  C24  108.08  3.000
 KPK  C16  C20  C24  113.21  3.000
 KPK  H5   C16  H4   107.17  3.000
 KPK  H5   C16  C12  110.08  3.000
 KPK  H4   C16  C12  109.77  3.000
 KPK  H5   C16  C20  109.98  3.000
 KPK  H4   C16  C20  110.01  3.000
 KPK  C12  C16  C20  109.79  3.000
 KPK  H7   C12  H6   108.37  3.000
 KPK  H7   C12  S8   108.70  3.000
 KPK  H6   C12  S8   108.68  3.000
 KPK  H7   C12  C16  111.28  3.000
 KPK  H6   C12  C16  111.34  3.000
 KPK  S8   C12  C16  108.42  3.000
 KPK  C3   S8   C12  100.23  3.000
 KPK  N1   C3   N7   113.71  3.000
 KPK  N1   C3   S8   120.04  3.000
 KPK  N7   C3   S8   126.25  3.000
 KPK  C5   N7   C3   104.90  3.000
 KPK  C2   C5   C10  119.82  3.000
 KPK  C2   C5   N7   110.05  3.000
 KPK  C10  C5   N7   130.13  3.000
 KPK  H8   C10  C15  121.32  3.000
 KPK  H8   C10  C5   120.80  3.000
 KPK  C15  C10  C5   117.88  3.000
 KPK  H9   C15  C11  119.06  3.000
 KPK  H9   C15  C10  119.49  3.000
 KPK  C11  C15  C10  121.45  3.000
 KPK  H10  C11  C6   119.30  3.000
 KPK  H10  C11  C15  119.24  3.000
 KPK  C6   C11  C15  121.46  3.000
 KPK  H11  C6   C2   122.21  3.000
 KPK  H11  C6   C11  121.24  3.000
 KPK  C2   C6   C11  116.55  3.000
 KPK  N1   C2   C6   132.07  3.000
 KPK  C6   C2   C5   122.83  3.000
 KPK  N1   C2   C5   105.10  3.000
 KPK  C4   N1   C2   126.21  3.000
 KPK  C4   N1   C3   127.51  3.000
 KPK  C2   N1   C3   106.23  3.000
 KPK  H13  C4   H12  105.99  3.000
 KPK  H13  C4   C9   110.99  3.000
 KPK  H12  C4   C9   110.84  3.000
 KPK  H13  C4   N1   108.41  3.000
 KPK  H12  C4   N1   107.42  3.000
 KPK  C9   C4   N1   112.89  3.000
 KPK  C13  C9   C14  112.20  3.000
 KPK  C13  C9   C4   125.22  3.000
 KPK  C14  C9   C4   122.58  3.000
 KPK  H14  C14  S19  118.73  3.000
 KPK  H14  C14  C9   127.39  3.000
 KPK  S19  C14  C9   113.88  3.000
 KPK  C17  S19  C14   91.08  3.000
 KPK  C13  C17  C21  122.97  3.000
 KPK  C21  C17  S19  125.10  3.000
 KPK  C13  C17  S19  111.93  3.000
 KPK  H15  C21  C25  121.34  3.000
 KPK  H15  C21  C17  120.97  3.000
 KPK  C25  C21  C17  117.69  3.000
 KPK  H16  C25  C22  119.59  3.000
 KPK  H16  C25  C21  120.00  3.000
 KPK  C22  C25  C21  120.41  3.000
 KPK  H17  C22  C18  118.58  3.000
 KPK  H17  C22  C25  118.83  3.000
 KPK  C18  C22  C25  122.59  3.000
 KPK  C23  C18  C13  123.23  3.000
 KPK  C23  C18  C22  118.89  3.000
 KPK  C13  C18  C22  117.88  3.000
 KPK  C18  C13  C17  118.46  3.000
 KPK  C17  C13  C9   110.91  3.000
 KPK  C18  C13  C9   130.63  3.000
 KPK  H20  C23  H19  107.07  3.000
 KPK  H20  C23  H18  107.08  3.000
 KPK  H19  C23  H18  107.82  3.000
 KPK  H20  C23  C18  110.27  3.000
 KPK  H19  C23  C18  112.17  3.000
 KPK  H18  C23  C18  112.16  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
 KPK  CONST_01  C10  C5   N7   C3    180.00   0.0  0
 KPK  CONST_02  C2   C5   N7   C3      0.00   0.0  0
 KPK  CONST_03  C5   C2   N1   C3      0.00   0.0  0
 KPK  CONST_04  C6   C2   N1   C3    180.00   0.0  0
 KPK  CONST_05  C2   N1   C3   N7      0.00   0.0  0
 KPK  CONST_06  C15  C10  C5   N7    180.00   0.0  0
 KPK  CONST_07  N1   C2   C5   N7      0.00   0.0  0
 KPK  CONST_08  C6   C2   C5   N7    180.00   0.0  0
 KPK  CONST_09  N1   C3   N7   C5      0.00   0.0  0
 KPK  CONST_10  C11  C15  C10  C5      0.00   0.0  0
 KPK  CONST_11  C11  C6   C2   C5      0.00   0.0  0
 KPK  CONST_12  N1   C2   C5   C10   180.00   0.0  0
 KPK  CONST_13  C6   C2   C5   C10     0.00   0.0  0
 KPK  CONST_14  C6   C11  C15  C10     0.00   0.0  0
 KPK  CONST_15  C2   C5   C10  C15     0.00   0.0  0
 KPK  CONST_16  C2   C6   C11  C15     0.00   0.0  0
 KPK  CONST_17  N1   C2   C6   C11   180.00   0.0  0
 KPK  CONST_18  C17  S19  C14  C9      0.00   0.0  0
 KPK  CONST_19  C22  C18  C13  C9    180.00   0.0  0
 KPK  CONST_20  S19  C17  C13  C9      0.00   0.0  0
 KPK  CONST_21  C21  C17  C13  C9    180.00   0.0  0
 KPK  CONST_22  C18  C13  C9   C14   180.00   0.0  0
 KPK  CONST_23  C17  C13  C9   C14     0.00   0.0  0
 KPK  CONST_24  C13  C17  S19  C14     0.00   0.0  0
 KPK  CONST_25  C21  C17  S19  C14   180.00   0.0  0
 KPK  CONST_26  C13  C9   C14  S19     0.00   0.0  0
 KPK  CONST_27  C18  C13  C17  S19   180.00   0.0  0
 KPK  CONST_28  C25  C21  C17  S19   180.00   0.0  0
 KPK  CONST_29  C22  C18  C13  C17     0.00   0.0  0
 KPK  CONST_30  C22  C25  C21  C17     0.00   0.0  0
 KPK  CONST_31  C18  C13  C17  C21     0.00   0.0  0
 KPK  CONST_32  C18  C22  C25  C21     0.00   0.0  0
 KPK  CONST_33  C13  C18  C22  C25     0.00   0.0  0
 KPK  CONST_34  C13  C17  C21  C25     0.00   0.0  0
 KPK  CONST_35  C5   N7   C3   S8    180.00   0.0  0
 KPK  CONST_36  C2   N1   C3   S8    180.00   0.0  0
 KPK  CONST_37  C4   N1   C3   N7    180.00   0.0  0
 KPK  CONST_38  C4   N1   C2   C5    180.00   0.0  0
 KPK  CONST_39  C4   N1   C2   C6      0.00   0.0  0
 KPK  CONST_40  S19  C14  C9   C4    180.00   0.0  0
 KPK  CONST_41  C18  C13  C9   C4      0.00   0.0  0
 KPK  CONST_42  C17  C13  C9   C4    180.00   0.0  0
 KPK  CONST_43  C23  C18  C13  C9      0.00   0.0  0
 KPK  CONST_44  C23  C18  C13  C17   180.00   0.0  0
 KPK  CONST_45  C23  C18  C22  C25   180.00   0.0  0
 KPK  CONST_46  H8   C10  C5   N7      0.00   0.0  0
 KPK  CONST_47  H9   C15  C10  C5    180.00   0.0  0
 KPK  CONST_48  H11  C6   C2   C5    180.00   0.0  0
 KPK  CONST_49  H10  C11  C15  C10   180.00   0.0  0
 KPK  CONST_50  H15  C21  C17  S19     0.00   0.0  0
 KPK  CONST_51  H14  C14  S19  C17   180.00   0.0  0
 KPK  CONST_52  H16  C25  C21  C17   180.00   0.0  0
 KPK  CONST_53  H17  C22  C25  C21   180.00   0.0  0
 KPK  CONST_54  H1   O26  C24  O27     0.00   0.0  0
 KPK  Var_01    C9   C4   N1   C3     89.11  30.0  2
 KPK  Var_02    C14  C9   C4   N1     -0.91  30.0  2
 KPK  Var_03    N7   C3   S8   C12    -3.99  30.0  2
 KPK  Var_04    H18  C23  C18  C22   118.49  30.0  2
 KPK  Var_05    H6   C12  S8   C3     62.78  30.0  2
 KPK  Var_06    C16  C20  C24  O27    -1.62  30.0  3
 KPK  Var_07    C12  C16  C20  C24  -179.37  30.0  1
 KPK  Var_08    S8   C12  C16  C20  -179.35  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
 KPK  plan-1  S8   0.020
 KPK  plan-1  C3   0.020
 KPK  plan-1  N7   0.020
 KPK  plan-1  C5   0.020
 KPK  plan-1  C10  0.020
 KPK  plan-1  C15  0.020
 KPK  plan-1  C11  0.020
 KPK  plan-1  C6   0.020
 KPK  plan-1  C2   0.020
 KPK  plan-1  N1   0.020
 KPK  plan-1  C4   0.020
 KPK  plan-1  H8   0.020
 KPK  plan-1  H9   0.020
 KPK  plan-1  H10  0.020
 KPK  plan-1  H11  0.020
 KPK  plan-2  C4   0.020
 KPK  plan-2  C9   0.020
 KPK  plan-2  C14  0.020
 KPK  plan-2  S19  0.020
 KPK  plan-2  C17  0.020
 KPK  plan-2  C21  0.020
 KPK  plan-2  C25  0.020
 KPK  plan-2  C22  0.020
 KPK  plan-2  C18  0.020
 KPK  plan-2  C13  0.020
 KPK  plan-2  C23  0.020
 KPK  plan-2  H14  0.020
 KPK  plan-2  H15  0.020
 KPK  plan-2  H16  0.020
 KPK  plan-2  H17  0.020
 KPK  plan-3  O27  0.020
 KPK  plan-3  C24  0.020
 KPK  plan-3  O26  0.020
 KPK  plan-3  C20  0.020
 KPK  plan-3  H1   0.020

