# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 09:31:14 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 4-[6-(1H-imidazol-1-ylmethyl)-7-methoxy-2,4-dihydroindeno[1,2-c]pyrazol-3-yl]benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc2c(Cc3c([nH]nc23)c4ccc(cc4)C#N)cc1Cn5ccnc5
#
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
 HK5  HK5  4-[6-(1H-imidazol-1-ylmethyl)-7-methoxy-2,4-dihydroindeno[1,2-c]pyrazol-3-yl]benzonitrile  ligand  45  28  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HK5
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
 HK5  N5   N  NS    0  -0.249   8.7588   2.0207  -0.1564
 HK5  C22  C  CSP   0   0.056   7.7294   1.5070  -0.0890
 HK5  C19  C  CR6   0  -0.010   6.4525   0.8780  -0.0055
 HK5  C18  C  CR16  0  -0.224   6.3663  -0.5057   0.1418
 HK5  C17  C  CR16  0  -0.288   5.1272  -1.1111   0.2204
 HK5  C20  C  CR16  0  -0.214   5.2914   1.6487  -0.0715
 HK5  C21  C  CR16  0  -0.335   4.0582   1.0344   0.0126
 HK5  C16  C  CR6   0   0.080   3.9559  -0.3515   0.1619
 HK5  C15  C  CR5   0   0.379   2.6373  -0.9612   0.2390
 HK5  N4   N  NR15  0  -0.529   2.4204  -2.2389   0.6595
 HK5  N3   N  N     0  -0.263   1.1452  -2.6138   0.6412
 HK5  C14  C  CR55  0   0.159   0.5196  -1.5452   0.1879
 HK5  C4   C  CR56  0   0.139  -0.8434  -1.1631  -0.1390
 HK5  C3   C  CR16  0  -0.456  -2.0423  -1.8550  -0.0545
 HK5  C13  C  CR55  0  -0.112   1.3865  -0.4786  -0.0772
 HK5  C12  C  CH2   0  -0.564   0.6338   0.6969  -0.6097
 HK5  C5   C  CR56  0   0.018  -0.7827   0.1521  -0.6147
 HK5  C6   C  CR16  0  -0.358  -1.9503   0.7761  -1.0124
 HK5  C7   C  CR6   0   0.040  -3.1685   0.1104  -0.9385
 HK5  C2   C  CR6   0   0.380  -3.2098  -1.2095  -0.4558
 HK5  O    O  O2    0  -0.472  -4.4260  -1.7822  -0.4157
 HK5  C1   C  CH3   0  -0.438  -4.5432  -3.1065   0.0652
 HK5  C8   C  CH2   0  -0.423  -4.4309   0.8189  -1.3510
 HK5  N1   N  NR5   0  -0.385  -5.1324   1.4106  -0.2223
 HK5  C11  C  CR15  0   0.101  -4.8713   2.6202   0.3179
 HK5  N2   N  N     0  -0.455  -5.6142   2.8602   1.3670
 HK5  C10  C  CR15  0  -0.223  -6.3925   1.7473   1.5184
 HK5  C9   C  CR15  0  -0.097  -6.1071   0.8349   0.5434
 HK5  H15  H  HCR6  0   0.288   7.2638  -1.1067   0.1892
 HK5  H14  H  HCR6  0   0.263   5.0892  -2.1881   0.3124
 HK5  H16  H  HCR6  0   0.287   5.3554   2.7221  -0.1833
 HK5  H17  H  HCR6  0   0.277   3.1681   1.6470  -0.0266
 HK5  H1   H  HNR5  0   0.425   3.1083  -2.8875   1.0095
 HK5  H5   H  HCR6  0   0.279  -2.0542  -2.8704   0.3178
 HK5  H13  H  HCH2  0   0.278   0.7171   1.5824   0.0270
 HK5  H12  H  HCH2  0   0.280   0.9619   0.9947  -1.6095
 HK5  H6   H  HCR6  0   0.254  -1.9276   1.7923  -1.3908
 HK5  H4   H  HCH3  0   0.231  -3.9811  -3.8143  -0.5488
 HK5  H2   H  HCH3  0   0.231  -4.2090  -3.1946   1.1019
 HK5  H3   H  HCH3  0   0.263  -5.5991  -3.3587   0.0149
 HK5  H8   H  HCH2  0   0.291  -4.1898   1.6227  -2.0466
 HK5  H7   H  HCH2  0   0.289  -5.1211   0.1530  -1.8656
 HK5  H11  H  HCR5  0   0.275  -4.1341   3.2885  -0.1027
 HK5  H10  H  HCR5  0   0.249  -7.1175   1.6598   2.3129
 HK5  H9   H  HCR5  0   0.284  -6.5049  -0.1422   0.3306

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
 HK5  C10  C9   aromatic  1.365  0.020  1.365
 HK5  C10  N2   aromatic  1.366  0.020  1.366
 HK5  C1   O    single    1.414  0.020  1.414
 HK5  C9   N1   aromatic  1.367  0.020  1.367
 HK5  N2   C11  aromatic  1.308  0.020  1.308
 HK5  O    C2   single    1.345  0.020  1.345
 HK5  C3   C2   aromatic  1.393  0.020  1.393
 HK5  C3   C4   aromatic  1.387  0.020  1.387
 HK5  N1   C11  aromatic  1.350  0.020  1.350
 HK5  N1   C8   single    1.455  0.020  1.455
 HK5  C2   C7   aromatic  1.406  0.020  1.406
 HK5  N3   C14  aromatic  1.319  0.020  1.319
 HK5  N3   N4   aromatic  1.329  0.020  1.329
 HK5  C4   C14  aromatic  1.453  0.020  1.453
 HK5  C4   C5   aromatic  1.400  0.020  1.400
 HK5  C14  C13  aromatic  1.400  0.020  1.400
 HK5  N4   C15  aromatic  1.363  0.020  1.363
 HK5  C7   C8   single    1.505  0.020  1.505
 HK5  C7   C6   aromatic  1.390  0.020  1.390
 HK5  C5   C6   aromatic  1.382  0.020  1.382
 HK5  C5   C12  single    1.518  0.020  1.518
 HK5  C13  C15  aromatic  1.377  0.020  1.377
 HK5  C13  C12  single    1.494  0.020  1.494
 HK5  C15  C16  single    1.455  0.020  1.455
 HK5  C17  C16  aromatic  1.397  0.020  1.397
 HK5  C17  C18  aromatic  1.381  0.020  1.381
 HK5  C16  C21  aromatic  1.398  0.020  1.398
 HK5  C18  C19  aromatic  1.394  0.020  1.394
 HK5  C21  C20  aromatic  1.380  0.020  1.380
 HK5  C19  C20  aromatic  1.395  0.020  1.395
 HK5  C19  C22  single    1.426  0.020  1.426
 HK5  C22  N5   triple    1.152  0.020  1.152
 HK5  C18  H15  single    0.930  0.020  1.080
 HK5  C17  H14  single    0.930  0.020  1.080
 HK5  C20  H16  single    0.930  0.020  1.080
 HK5  C21  H17  single    0.930  0.020  1.080
 HK5  N4   H1   single    0.860  0.020  1.020
 HK5  C3   H5   single    0.930  0.020  1.080
 HK5  C12  H13  single    0.970  0.020  1.090
 HK5  C12  H12  single    0.970  0.020  1.090
 HK5  C6   H6   single    0.930  0.020  1.080
 HK5  C1   H4   single    0.970  0.020  1.090
 HK5  C1   H2   single    0.970  0.020  1.090
 HK5  C1   H3   single    0.970  0.020  1.090
 HK5  C8   H8   single    0.970  0.020  1.090
 HK5  C8   H7   single    0.970  0.020  1.090
 HK5  C11  H11  single    0.930  0.020  1.080
 HK5  C10  H10  single    0.930  0.020  1.080
 HK5  C9   H9   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
 HK5  C19  C22  N5   180.00  3.000
 HK5  C20  C19  C18  120.12  3.000
 HK5  C20  C19  C22  119.92  3.000
 HK5  C18  C19  C22  119.96  3.000
 HK5  H15  C18  C17  119.90  3.000
 HK5  H15  C18  C19  120.33  3.000
 HK5  C17  C18  C19  119.76  3.000
 HK5  H14  C17  C16  121.02  3.000
 HK5  H14  C17  C18  118.22  3.000
 HK5  C16  C17  C18  120.75  3.000
 HK5  H16  C20  C21  120.07  3.000
 HK5  H16  C20  C19  120.27  3.000
 HK5  C21  C20  C19  119.66  3.000
 HK5  H17  C21  C16  120.36  3.000
 HK5  H17  C21  C20  118.76  3.000
 HK5  C16  C21  C20  120.88  3.000
 HK5  C15  C16  C21  119.18  3.000
 HK5  C21  C16  C17  118.82  3.000
 HK5  C15  C16  C17  121.99  3.000
 HK5  C13  C15  N4   104.76  3.000
 HK5  C13  C15  C16  131.61  3.000
 HK5  N4   C15  C16  123.62  3.000
 HK5  H1   N4   N3   118.55  3.000
 HK5  H1   N4   C15  127.00  3.000
 HK5  N3   N4   C15  114.39  3.000
 HK5  C14  N3   N4   103.38  3.000
 HK5  C13  C14  C4   109.76  3.000
 HK5  C13  C14  N3   112.88  3.000
 HK5  C4   C14  N3   137.36  3.000
 HK5  C5   C4   C3   121.79  3.000
 HK5  C5   C4   C14  106.43  3.000
 HK5  C3   C4   C14  131.77  3.000
 HK5  H5   C3   C2   121.67  3.000
 HK5  H5   C3   C4   119.92  3.000
 HK5  C2   C3   C4   118.41  3.000
 HK5  C12  C13  C14  110.80  3.000
 HK5  C12  C13  C15  144.58  3.000
 HK5  C14  C13  C15  104.59  3.000
 HK5  H12  C12  H13  106.79  3.000
 HK5  H12  C12  C5   112.01  3.000
 HK5  H13  C12  C5   111.32  3.000
 HK5  H12  C12  C13  112.89  3.000
 HK5  H13  C12  C13  113.03  3.000
 HK5  C5   C12  C13  100.89  3.000
 HK5  C6   C5   C12  128.85  3.000
 HK5  C12  C5   C4   112.12  3.000
 HK5  C6   C5   C4   119.03  3.000
 HK5  H6   C6   C7   119.05  3.000
 HK5  H6   C6   C5   120.37  3.000
 HK5  C7   C6   C5   120.58  3.000
 HK5  C8   C7   C2   120.75  3.000
 HK5  C8   C7   C6   119.67  3.000
 HK5  C2   C7   C6   119.57  3.000
 HK5  O    C2   C7   115.89  3.000
 HK5  C7   C2   C3   120.61  3.000
 HK5  O    C2   C3   123.50  3.000
 HK5  C1   O    C2   118.95  3.000
 HK5  H3   C1   H2   108.81  3.000
 HK5  H3   C1   H4   108.88  3.000
 HK5  H2   C1   H4   108.88  3.000
 HK5  H3   C1   O    106.39  3.000
 HK5  H2   C1   O    111.89  3.000
 HK5  H4   C1   O    111.90  3.000
 HK5  H7   C8   H8   106.84  3.000
 HK5  H7   C8   N1   108.05  3.000
 HK5  H8   C8   N1   107.57  3.000
 HK5  H7   C8   C7   111.92  3.000
 HK5  H8   C8   C7   109.66  3.000
 HK5  N1   C8   C7   112.54  3.000
 HK5  C9   N1   C11  106.92  3.000
 HK5  C11  N1   C8   125.56  3.000
 HK5  C9   N1   C8   127.40  3.000
 HK5  H11  C11  N2   125.91  3.000
 HK5  H11  C11  N1   122.03  3.000
 HK5  N2   C11  N1   112.06  3.000
 HK5  C10  N2   C11  105.25  3.000
 HK5  H10  C10  C9   127.74  3.000
 HK5  H10  C10  N2   122.02  3.000
 HK5  C9   C10  N2   110.24  3.000
 HK5  H9   C9   C10  132.11  3.000
 HK5  H9   C9   N1   122.36  3.000
 HK5  C10  C9   N1   105.53  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
 HK5  CONST_01  C16  C17  C18  C19    0.00   0.0  0
 HK5  CONST_02  C16  C21  C20  C19    0.00   0.0  0
 HK5  CONST_03  C15  C16  C17  C18  180.00   0.0  0
 HK5  CONST_04  C21  C16  C17  C18    0.00   0.0  0
 HK5  CONST_05  C21  C20  C19  C18    0.00   0.0  0
 HK5  CONST_06  N4   C15  C16  C17    0.00   0.0  0
 HK5  CONST_08  C20  C21  C16  C17    0.00   0.0  0
 HK5  CONST_09  C20  C19  C18  C17    0.00   0.0  0
 HK5  CONST_10  C15  C16  C21  C20  180.00   0.0  0
 HK5  CONST_11  N4   C15  C16  C21  180.00   0.0  0
 HK5  CONST_13  N3   N4   C15  C16  180.00   0.0  0
 HK5  CONST_14  C14  C13  C15  C16  180.00   0.0  0
 HK5  CONST_15  C14  N3   N4   C15    0.00   0.0  0
 HK5  CONST_16  N3   C14  C13  C15    0.00   0.0  0
 HK5  CONST_17  C4   C14  C13  C15  180.00   0.0  0
 HK5  CONST_18  C4   C14  N3   N4   180.00   0.0  0
 HK5  CONST_19  C13  C14  N3   N4     0.00   0.0  0
 HK5  CONST_20  C14  C13  C15  N4     0.00   0.0  0
 HK5  CONST_21  C3   C4   C14  N3     0.00   0.0  0
 HK5  CONST_22  C5   C4   C14  N3   180.00   0.0  0
 HK5  CONST_23  C13  C15  N4   N3     0.00   0.0  0
 HK5  CONST_24  C2   C3   C4   C14  180.00   0.0  0
 HK5  CONST_25  C6   C5   C4   C14  180.00   0.0  0
 HK5  CONST_26  C7   C2   C3   C4     0.00   0.0  0
 HK5  CONST_27  C7   C6   C5   C4     0.00   0.0  0
 HK5  CONST_28  C6   C7   C2   C3     0.00   0.0  0
 HK5  CONST_29  C13  C14  C4   C3   180.00   0.0  0
 HK5  CONST_30  C6   C5   C4   C3     0.00   0.0  0
 HK5  CONST_31  C5   C4   C14  C13    0.00   0.0  0
 HK5  CONST_32  C2   C3   C4   C5     0.00   0.0  0
 HK5  CONST_33  C2   C7   C6   C5     0.00   0.0  0
 HK5  CONST_34  N2   C10  C9   N1     0.00   0.0  0
 HK5  CONST_35  C10  N2   C11  N1     0.00   0.0  0
 HK5  CONST_36  C9   C10  N2   C11    0.00   0.0  0
 HK5  CONST_37  C10  C9   N1   C11    0.00   0.0  0
 HK5  CONST_38  C9   N1   C11  N2     0.00   0.0  0
 HK5  CONST_39  C12  C13  C15  C16    0.00   0.0  0
 HK5  CONST_40  C17  C18  C19  C22  180.00   0.0  0
 HK5  CONST_41  C21  C20  C19  C22  180.00   0.0  0
 HK5  CONST_42  O    C2   C3   C4   180.00   0.0  0
 HK5  CONST_43  C8   C7   C2   C3   180.00   0.0  0
 HK5  CONST_44  C8   C7   C6   C5   180.00   0.0  0
 HK5  CONST_45  O    C2   C7   C6   180.00   0.0  0
 HK5  CONST_46  C10  C9   N1   C8   180.00   0.0  0
 HK5  CONST_47  N2   C11  N1   C8   180.00   0.0  0
 HK5  CONST_48  H14  C17  C18  C19  180.00   0.0  0
 HK5  CONST_49  H17  C21  C20  C19  180.00   0.0  0
 HK5  CONST_50  H16  C20  C19  C18  180.00   0.0  0
 HK5  CONST_51  H15  C18  C19  C20  180.00   0.0  0
 HK5  CONST_52  H1   N4   C15  C16    0.00   0.0  0
 HK5  CONST_53  H5   C3   C4   C14    0.00   0.0  0
 HK5  CONST_54  H6   C6   C5   C4   180.00   0.0  0
 HK5  CONST_55  H10  C10  C9   N1   180.00   0.0  0
 HK5  CONST_56  H9   C9   N1   C11  180.00   0.0  0
 HK5  CONST_57  H11  C11  N2   C10  180.00   0.0  0
 HK5  Var_01    N1   C8   C7   C6   -95.68  30.0  2
 HK5  Var_02    C9   N1   C8   C7   -91.06  30.0  2
 HK5  Var_03    H13  C12  C13  C15  -63.50  30.0  1
 HK5  Var_04    H4   C1   O    C2   -61.57  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
 HK5  plan-1  C8   0.020
 HK5  plan-1  N1   0.020
 HK5  plan-1  C11  0.020
 HK5  plan-1  N2   0.020
 HK5  plan-1  C10  0.020
 HK5  plan-1  C9   0.020
 HK5  plan-1  H11  0.020
 HK5  plan-1  H10  0.020
 HK5  plan-1  H9   0.020
 HK5  plan-2  N5   0.020
 HK5  plan-2  C22  0.020
 HK5  plan-2  C19  0.020
 HK5  plan-2  C18  0.020
 HK5  plan-2  C17  0.020
 HK5  plan-2  C20  0.020
 HK5  plan-2  C21  0.020
 HK5  plan-2  C16  0.020
 HK5  plan-2  C15  0.020
 HK5  plan-2  H15  0.020
 HK5  plan-2  H14  0.020
 HK5  plan-2  H16  0.020
 HK5  plan-2  H17  0.020
 HK5  plan-3  C16  0.020
 HK5  plan-3  C15  0.020
 HK5  plan-3  N4   0.020
 HK5  plan-3  N3   0.020
 HK5  plan-3  C14  0.020
 HK5  plan-3  C4   0.020
 HK5  plan-3  C3   0.020
 HK5  plan-3  C13  0.020
 HK5  plan-3  C12  0.020
 HK5  plan-3  C5   0.020
 HK5  plan-3  C6   0.020
 HK5  plan-3  C7   0.020
 HK5  plan-3  C2   0.020
 HK5  plan-3  O    0.020
 HK5  plan-3  C8   0.020
 HK5  plan-3  H1   0.020
 HK5  plan-3  H5   0.020
 HK5  plan-3  H6   0.020

