# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 02:46:32 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 4-[3-(1H-benzimidazol-2-yl)-1H-indazol-6-yl]-3-ethylphenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1cc(O)ccc1c2ccc3c([nH]nc3c4[nH]c5ccccc5n4)c2
#
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
 7GZ  7GZ  4-[3-(1H-benzimidazol-2-yl)-1H-indazol-6-yl]-3-ethylphenol  ligand  45  27  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7GZ
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
 7GZ  C4   C  CR16  0  -0.377   5.7656   0.7069   0.4274
 7GZ  C7   C  CR16  0  -0.272   3.9715   0.1745  -1.5814
 7GZ  C6   C  CR16  0  -0.388   5.3116   0.3062  -1.8948
 7GZ  C9   C  CR6   0   0.028   2.0427   0.1229  -0.0477
 7GZ  C13  C  CR56  0   0.449   0.1683  -0.9326   0.9600
 7GZ  C20  C  CR56  0   0.337  -5.4931  -0.1038  -0.0315
 7GZ  C21  C  CR16  0  -0.313  -6.8740  -0.2497   0.0316
 7GZ  C8   C  CR6   0  -0.001   3.4978   0.2882  -0.2727
 7GZ  C18  C  CR5   0   0.444  -3.3071  -0.1818   0.1513
 7GZ  C1   C  CH3   0  -0.662   4.4250  -0.4298   3.0753
 7GZ  C3   C  CR6   0   0.115   4.4177   0.5683   0.7494
 7GZ  C5   C  CR6   0   0.360   6.2235   0.5728  -0.8772
 7GZ  C10  C  CR16  0  -0.303   1.1429   0.9124  -0.8099
 7GZ  C11  C  CR16  0  -0.322  -0.2209   0.7856  -0.7000
 7GZ  C12  C  CR56  0  -0.101  -0.7251  -0.1580   0.2036
 7GZ  C14  C  CR16  0  -0.349   1.5550  -0.8127   0.8437
 7GZ  N15  N  NR15  0  -0.544  -0.5997  -1.7493   1.7232
 7GZ  N16  N  N     0  -0.250  -1.8954  -1.5641   1.5197
 7GZ  C17  C  CR5   0   0.150  -2.0086  -0.6174   0.6135
 7GZ  N19  N  NR15  0  -0.709  -4.4623  -0.7300   0.6126
 7GZ  C22  C  CR16  0  -0.278  -7.6234   0.5731  -0.7918
 7GZ  C23  C  CR16  0  -0.270  -7.0180   1.5076  -1.6464
 7GZ  C24  C  CR16  0  -0.344  -5.6432   1.6476  -1.7029
 7GZ  C25  C  CR56  0   0.151  -4.8692   0.8275  -0.8816
 7GZ  N26  N  N     0  -0.488  -3.5059   0.7527  -0.7412
 7GZ  O27  O  OH1   0  -0.632   7.5445   0.7178  -1.1023
 7GZ  H1   H  HCR6  0   0.255   6.4777   0.9371   1.2130
 7GZ  H2   H  HCR6  0   0.256   3.2704  -0.0367  -2.3798
 7GZ  H3   H  HCR6  0   0.270   5.6414   0.2005  -2.9221
 7GZ  H4   H  HCR6  0   0.266  -7.3443  -0.9700   0.6881
 7GZ  H5   H  HCH3  0   0.229   3.9610  -1.3584   2.7404
 7GZ  H6   H  HCH3  0   0.229   5.5046  -0.5839   3.0676
 7GZ  H7   H  HCH3  0   0.235   4.1207  -0.2589   4.1083
 7GZ  H8   H  HCH2  0   0.246   2.9563   0.9339   2.2841
 7GZ  H9   H  HCH2  0   0.251   4.5221   1.6515   2.5730
 7GZ  H10  H  HCR6  0   0.255   1.5542   1.6419  -1.4960
 7GZ  H11  H  HCR6  0   0.257  -0.8881   1.3969  -1.2912
 7GZ  H12  H  HCR6  0   0.274   2.2184  -1.4488   1.4140
 7GZ  H13  H  HNR5  0   0.424  -0.2942  -2.4402   2.3898
 7GZ  H14  H  HNR5  0   0.420  -4.5315  -1.4662   1.2977
 7GZ  H15  H  HCR6  0   0.256  -8.7025   0.4929  -0.7771
 7GZ  H16  H  HCR6  0   0.253  -7.6442   2.1286  -2.2734
 7GZ  H17  H  HCR6  0   0.254  -5.1775   2.3689  -2.3625
 7GZ  H19  H  HOH1  0   0.474   7.7373   0.6196  -2.0414
 7GZ  C2   C  CH2   0  -0.536   4.0276   0.7536   2.1939

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
 7GZ  C24  C23  aromatic  1.383  0.020  1.383
 7GZ  C24  C25  aromatic  1.395  0.020  1.395
 7GZ  C23  C22  aromatic  1.404  0.020  1.404
 7GZ  N26  C25  aromatic  1.373  0.020  1.373
 7GZ  N26  C18  aromatic  1.307  0.020  1.307
 7GZ  C25  C20  aromatic  1.407  0.020  1.407
 7GZ  N16  N15  aromatic  1.325  0.020  1.325
 7GZ  N16  C17  aromatic  1.315  0.020  1.315
 7GZ  C22  C21  aromatic  1.384  0.020  1.384
 7GZ  C18  C17  single    1.445  0.020  1.445
 7GZ  C18  N19  aromatic  1.359  0.020  1.359
 7GZ  N15  C13  aromatic  1.356  0.020  1.356
 7GZ  C20  C21  aromatic  1.390  0.020  1.390
 7GZ  C20  N19  aromatic  1.367  0.020  1.367
 7GZ  C17  C12  aromatic  1.424  0.020  1.424
 7GZ  C13  C12  aromatic  1.404  0.020  1.404
 7GZ  C13  C14  aromatic  1.397  0.020  1.397
 7GZ  C12  C11  aromatic  1.400  0.020  1.400
 7GZ  C1   C2   single    1.528  0.020  1.528
 7GZ  C14  C9   aromatic  1.381  0.020  1.381
 7GZ  C11  C10  aromatic  1.374  0.020  1.374
 7GZ  C2   C3   single    1.508  0.020  1.508
 7GZ  C9   C10  aromatic  1.419  0.020  1.419
 7GZ  C9   C8   single    1.482  0.020  1.482
 7GZ  C3   C8   aromatic  1.403  0.020  1.403
 7GZ  C3   C4   aromatic  1.393  0.020  1.393
 7GZ  C8   C7   aromatic  1.396  0.020  1.396
 7GZ  C4   C5   aromatic  1.389  0.020  1.389
 7GZ  C7   C6   aromatic  1.382  0.020  1.382
 7GZ  C5   C6   aromatic  1.392  0.020  1.392
 7GZ  C5   O27  single    1.348  0.020  1.348
 7GZ  C4   H1   single    0.930  0.020  1.080
 7GZ  C7   H2   single    0.930  0.020  1.080
 7GZ  C6   H3   single    0.930  0.020  1.080
 7GZ  C21  H4   single    0.930  0.020  1.080
 7GZ  C1   H5   single    0.970  0.020  1.090
 7GZ  C1   H6   single    0.970  0.020  1.090
 7GZ  C1   H7   single    0.970  0.020  1.090
 7GZ  C2   H8   single    0.970  0.020  1.090
 7GZ  C2   H9   single    0.970  0.020  1.090
 7GZ  C10  H10  single    0.930  0.020  1.080
 7GZ  C11  H11  single    0.930  0.020  1.080
 7GZ  C14  H12  single    0.930  0.020  1.080
 7GZ  N15  H13  single    0.860  0.020  1.020
 7GZ  N19  H14  single    0.860  0.020  1.020
 7GZ  C22  H15  single    0.930  0.020  1.080
 7GZ  C23  H16  single    0.930  0.020  1.080
 7GZ  C24  H17  single    0.930  0.020  1.080
 7GZ  O27  H19  single    0.850  0.020  0.980

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
 7GZ  H1   C4   C5   118.95  3.000
 7GZ  H1   C4   C3   119.28  3.000
 7GZ  C5   C4   C3   121.77  3.000
 7GZ  H2   C7   C8   119.14  3.000
 7GZ  H2   C7   C6   118.61  3.000
 7GZ  C8   C7   C6   122.24  3.000
 7GZ  H3   C6   C5   120.80  3.000
 7GZ  H3   C6   C7   120.02  3.000
 7GZ  C5   C6   C7   119.18  3.000
 7GZ  C14  C9   C10  119.97  3.000
 7GZ  C10  C9   C8   118.63  3.000
 7GZ  C14  C9   C8   121.35  3.000
 7GZ  N15  C13  C14  131.35  3.000
 7GZ  C14  C13  C12  122.66  3.000
 7GZ  N15  C13  C12  105.97  3.000
 7GZ  C25  C20  N19  104.69  3.000
 7GZ  N19  C20  C21  132.80  3.000
 7GZ  C25  C20  C21  122.51  3.000
 7GZ  H4   C21  C22  121.41  3.000
 7GZ  H4   C21  C20  121.95  3.000
 7GZ  C22  C21  C20  116.63  3.000
 7GZ  C3   C8   C9   123.74  3.000
 7GZ  C3   C8   C7   118.45  3.000
 7GZ  C9   C8   C7   117.80  3.000
 7GZ  N26  C18  N19  113.00  3.000
 7GZ  N19  C18  C17  122.23  3.000
 7GZ  N26  C18  C17  124.77  3.000
 7GZ  H7   C1   H6   107.77  3.000
 7GZ  H7   C1   H5   107.79  3.000
 7GZ  H6   C1   H5   107.37  3.000
 7GZ  H7   C1   C2   110.64  3.000
 7GZ  H6   C1   C2   111.27  3.000
 7GZ  H5   C1   C2   111.81  3.000
 7GZ  C2   C3   C8   123.56  3.000
 7GZ  C8   C3   C4   119.07  3.000
 7GZ  C2   C3   C4   117.36  3.000
 7GZ  O27  C5   C6   122.72  3.000
 7GZ  O27  C5   C4   118.00  3.000
 7GZ  C6   C5   C4   119.27  3.000
 7GZ  H10  C10  C11  119.34  3.000
 7GZ  H10  C10  C9   118.32  3.000
 7GZ  C11  C10  C9   122.35  3.000
 7GZ  H11  C11  C12  120.78  3.000
 7GZ  H11  C11  C10  121.11  3.000
 7GZ  C12  C11  C10  118.11  3.000
 7GZ  C17  C12  C11  136.71  3.000
 7GZ  C11  C12  C13  119.37  3.000
 7GZ  C17  C12  C13  103.92  3.000
 7GZ  H12  C14  C13  120.97  3.000
 7GZ  H12  C14  C9   121.47  3.000
 7GZ  C13  C14  C9   117.54  3.000
 7GZ  H13  N15  N16  119.61  3.000
 7GZ  H13  N15  C13  127.85  3.000
 7GZ  N16  N15  C13  112.54  3.000
 7GZ  C17  N16  N15  106.90  3.000
 7GZ  N16  C17  C12  110.67  3.000
 7GZ  C12  C17  C18  128.36  3.000
 7GZ  N16  C17  C18  120.96  3.000
 7GZ  H14  N19  C18  125.70  3.000
 7GZ  H14  N19  C20  127.07  3.000
 7GZ  C18  N19  C20  107.22  3.000
 7GZ  H15  C22  C23  119.19  3.000
 7GZ  H15  C22  C21  119.18  3.000
 7GZ  C23  C22  C21  121.63  3.000
 7GZ  H16  C23  C24  119.57  3.000
 7GZ  H16  C23  C22  119.03  3.000
 7GZ  C24  C23  C22  121.40  3.000
 7GZ  H17  C24  C25  120.77  3.000
 7GZ  H17  C24  C23  121.33  3.000
 7GZ  C25  C24  C23  117.90  3.000
 7GZ  N26  C25  C24  130.04  3.000
 7GZ  N26  C25  C20  110.03  3.000
 7GZ  C24  C25  C20  119.93  3.000
 7GZ  C25  N26  C18  105.06  3.000
 7GZ  H19  O27  C5   110.35  3.000
 7GZ  H9   C2   H8   106.26  3.000
 7GZ  H9   C2   C3   108.44  3.000
 7GZ  H8   C2   C3   110.72  3.000
 7GZ  H9   C2   C1   108.57  3.000
 7GZ  H8   C2   C1   109.63  3.000
 7GZ  C3   C2   C1   112.96  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
 7GZ  CONST_01  C9   C8   C3   C4   180.00   0.0  0
 7GZ  CONST_02  C7   C8   C3   C4     0.00   0.0  0
 7GZ  CONST_03  C7   C6   C5   C4     0.00   0.0  0
 7GZ  CONST_06  C9   C8   C7   C6   180.00   0.0  0
 7GZ  CONST_07  C3   C8   C7   C6     0.00   0.0  0
 7GZ  CONST_08  C3   C4   C5   C6     0.00   0.0  0
 7GZ  CONST_09  N15  C13  C14  C9   180.00   0.0  0
 7GZ  CONST_10  C12  C13  C14  C9     0.00   0.0  0
 7GZ  CONST_11  C12  C11  C10  C9     0.00   0.0  0
 7GZ  CONST_12  C17  N16  N15  C13    0.00   0.0  0
 7GZ  CONST_13  N16  C17  C12  C13    0.00   0.0  0
 7GZ  CONST_14  C18  C17  C12  C13  180.00   0.0  0
 7GZ  CONST_15  C10  C11  C12  C13    0.00   0.0  0
 7GZ  CONST_16  C10  C9   C14  C13    0.00   0.0  0
 7GZ  CONST_17  C8   C9   C14  C13  180.00   0.0  0
 7GZ  CONST_18  C23  C24  C25  C20    0.00   0.0  0
 7GZ  CONST_19  C18  N26  C25  C20    0.00   0.0  0
 7GZ  CONST_20  C23  C22  C21  C20    0.00   0.0  0
 7GZ  CONST_21  N26  C18  N19  C20    0.00   0.0  0
 7GZ  CONST_22  C17  C18  N19  C20  180.00   0.0  0
 7GZ  CONST_23  C24  C23  C22  C21    0.00   0.0  0
 7GZ  CONST_24  C24  C25  C20  C21    0.00   0.0  0
 7GZ  CONST_25  N26  C25  C20  C21  180.00   0.0  0
 7GZ  CONST_26  C18  N19  C20  C21  180.00   0.0  0
 7GZ  CONST_27  C11  C10  C9   C8   180.00   0.0  0
 7GZ  CONST_28  C5   C4   C3   C8     0.00   0.0  0
 7GZ  CONST_29  C5   C6   C7   C8     0.00   0.0  0
 7GZ  CONST_30  C24  C25  N26  C18  180.00   0.0  0
 7GZ  CONST_31  N15  N16  C17  C18  180.00   0.0  0
 7GZ  CONST_32  C11  C12  C17  C18    0.00   0.0  0
 7GZ  CONST_33  C25  C20  N19  C18    0.00   0.0  0
 7GZ  CONST_36  C17  C12  C11  C10  180.00   0.0  0
 7GZ  CONST_37  N16  C17  C12  C11  180.00   0.0  0
 7GZ  CONST_38  N15  C13  C12  C11  180.00   0.0  0
 7GZ  CONST_39  C14  C13  C12  C11    0.00   0.0  0
 7GZ  CONST_40  C14  C9   C10  C11    0.00   0.0  0
 7GZ  CONST_41  N15  N16  C17  C12    0.00   0.0  0
 7GZ  CONST_42  N26  C18  C17  C12    0.00   0.0  0
 7GZ  CONST_43  N19  C18  C17  C12  180.00   0.0  0
 7GZ  CONST_44  N16  N15  C13  C12    0.00   0.0  0
 7GZ  CONST_45  N16  N15  C13  C14  180.00   0.0  0
 7GZ  CONST_46  C17  C12  C13  C14  180.00   0.0  0
 7GZ  CONST_47  C17  C12  C13  N15    0.00   0.0  0
 7GZ  CONST_48  N26  C18  C17  N16  180.00   0.0  0
 7GZ  CONST_49  N19  C18  C17  N16    0.00   0.0  0
 7GZ  CONST_50  C25  N26  C18  C17  180.00   0.0  0
 7GZ  CONST_51  C25  N26  C18  N19    0.00   0.0  0
 7GZ  CONST_52  C24  C25  C20  N19  180.00   0.0  0
 7GZ  CONST_53  N26  C25  C20  N19    0.00   0.0  0
 7GZ  CONST_54  C22  C21  C20  N19  180.00   0.0  0
 7GZ  CONST_55  C25  C24  C23  C22    0.00   0.0  0
 7GZ  CONST_56  C25  C20  C21  C22    0.00   0.0  0
 7GZ  CONST_57  N26  C25  C24  C23  180.00   0.0  0
 7GZ  CONST_58  C2   C3   C8   C7   180.00   0.0  0
 7GZ  CONST_59  O27  C5   C6   C7   180.00   0.0  0
 7GZ  CONST_60  C2   C3   C8   C9     0.00   0.0  0
 7GZ  CONST_61  C5   C4   C3   C2   180.00   0.0  0
 7GZ  CONST_62  O27  C5   C4   C3   180.00   0.0  0
 7GZ  CONST_63  H3   C6   C5   C4   180.00   0.0  0
 7GZ  CONST_64  H1   C4   C5   C6   180.00   0.0  0
 7GZ  CONST_65  H11  C11  C10  C9   180.00   0.0  0
 7GZ  CONST_66  H2   C7   C8   C9     0.00   0.0  0
 7GZ  CONST_67  H17  C24  C25  C20  180.00   0.0  0
 7GZ  CONST_68  H15  C22  C21  C20  180.00   0.0  0
 7GZ  CONST_69  H16  C23  C22  C21  180.00   0.0  0
 7GZ  CONST_70  H14  N19  C20  C21    0.00   0.0  0
 7GZ  CONST_71  H12  C14  C9   C8     0.00   0.0  0
 7GZ  CONST_72  H10  C10  C9   C8     0.00   0.0  0
 7GZ  CONST_73  H13  N15  C13  C12  180.00   0.0  0
 7GZ  CONST_74  H4   C21  C20  N19    0.00   0.0  0
 7GZ  Var_01    C1   C2   C3   C4   -74.34  30.0  1
 7GZ  Var_02    H5   C1   C2   C3   -59.51  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
 7GZ  plan-1  C4   0.020
 7GZ  plan-1  C7   0.020
 7GZ  plan-1  C6   0.020
 7GZ  plan-1  C9   0.020
 7GZ  plan-1  C8   0.020
 7GZ  plan-1  C3   0.020
 7GZ  plan-1  C5   0.020
 7GZ  plan-1  O27  0.020
 7GZ  plan-1  H1   0.020
 7GZ  plan-1  H2   0.020
 7GZ  plan-1  H3   0.020
 7GZ  plan-1  C2   0.020
 7GZ  plan-2  C9   0.020
 7GZ  plan-2  C13  0.020
 7GZ  plan-2  C8   0.020
 7GZ  plan-2  C18  0.020
 7GZ  plan-2  C10  0.020
 7GZ  plan-2  C11  0.020
 7GZ  plan-2  C12  0.020
 7GZ  plan-2  C14  0.020
 7GZ  plan-2  N15  0.020
 7GZ  plan-2  N16  0.020
 7GZ  plan-2  C17  0.020
 7GZ  plan-2  H10  0.020
 7GZ  plan-2  H11  0.020
 7GZ  plan-2  H12  0.020
 7GZ  plan-2  H13  0.020
 7GZ  plan-3  C20  0.020
 7GZ  plan-3  C21  0.020
 7GZ  plan-3  C18  0.020
 7GZ  plan-3  C17  0.020
 7GZ  plan-3  N19  0.020
 7GZ  plan-3  C22  0.020
 7GZ  plan-3  C23  0.020
 7GZ  plan-3  C24  0.020
 7GZ  plan-3  C25  0.020
 7GZ  plan-3  N26  0.020
 7GZ  plan-3  H4   0.020
 7GZ  plan-3  H14  0.020
 7GZ  plan-3  H15  0.020
 7GZ  plan-3  H16  0.020
 7GZ  plan-3  H17  0.020

