# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 16:55:17 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: [2-(1H-indol-3-yl)-1H-imidazol-4-yl](8-methoxy-1,4-benzodioxin-6-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(cc2OC=COc12)C(=O)c3c[nH]c(n3)c4c[nH]c5ccccc45
#
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
 G9K  G9K  '[2-(1H-indol-3-yl)-1H-imidazol-4-yl](8-methoxy-1,4-benzodioxin-6-yl)methanone'  ligand  43  28  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G9K
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
 G9K  C1   C  CH3   0  -0.441   6.0776   1.2895   0.6423
 G9K  C10  C  CR5   0   0.022  -0.3073   2.3833  -0.1134
 G9K  C11  C  CR15  0  -0.040  -1.0607   3.5284  -0.2333
 G9K  C12  C  CR5   0   0.434  -2.3598   1.7614  -0.0585
 G9K  C13  C  CR5   0  -0.063  -3.5625   0.9681   0.0074
 G9K  C14  C  CR15  0  -0.055  -4.8568   1.4133  -0.1105
 G9K  C15  C  CR56  0   0.360  -5.0076  -0.7893   0.1787
 G9K  C16  C  CR56  0   0.034  -3.6377  -0.4542   0.1959
 G9K  C17  C  CR16  0  -0.380  -2.6938  -1.4714   0.3791
 G9K  C18  C  CR16  0  -0.261  -3.1371  -2.7704   0.5326
 G9K  C19  C  CR16  0  -0.280  -4.5063  -3.0816   0.5087
 G9K  C2   C  CR6   0   0.308   4.1158   0.0769   0.1127
 G9K  C20  C  CR16  0  -0.299  -5.4596  -2.0981   0.3332
 G9K  C21  C  CR16  0  -0.439   3.3074   1.2027   0.1465
 G9K  C3   C  CR66  0   0.254   3.5510  -1.1620  -0.2065
 G9K  C4   C  CR66  0   0.394   2.1943  -1.2503  -0.4822
 G9K  C5   C  CR16  0  -0.056   2.4626  -3.5204  -0.7993
 G9K  C6   C  CR16  0  -0.057   3.7536  -3.4278  -0.5329
 G9K  C7   C  CR16  0  -0.457   1.3861  -0.1299  -0.4438
 G9K  C8   C  CR6   0  -0.010   1.9404   1.1068  -0.1245
 G9K  C9   C  C     0   0.296   1.1576   2.3754  -0.0968
 G9K  N1   N  NR15  0  -0.637  -2.3460   3.1180  -0.1999
 G9K  N2   N  NR15  0  -0.682  -5.7123   0.3674  -0.0077
 G9K  N3   N  N     0  -0.490  -1.1376   1.2990  -0.0026
 G9K  O1   O  O2    0  -0.463   5.4339   0.0603   0.3609
 G9K  O2   O  O     0  -0.476   1.6127  -2.4458  -0.8008
 G9K  O3   O  O     0  -0.463   4.3766  -2.2415  -0.2322
 G9K  O4   O  O     0  -0.417   1.7468   3.4452  -0.0593
 G9K  H1   H  HCH3  0   0.234   5.9649   2.0033  -0.1771
 G9K  H2   H  HCH3  0   0.233   5.7021   1.7447   1.5622
 G9K  H3   H  HCH3  0   0.265   7.1322   1.0604   0.7691
 G9K  H4   H  HCR5  0   0.304  -0.7916   4.5647  -0.3427
 G9K  H5   H  HCR5  0   0.294  -5.2367   2.4109  -0.2665
 G9K  H6   H  HCR6  0   0.251  -1.6376  -1.2418   0.4041
 G9K  H7   H  HCR6  0   0.249  -2.4175  -3.5662   0.6750
 G9K  H8   H  HCR6  0   0.253  -4.8195  -4.1101   0.6323
 G9K  H9   H  HCR6  0   0.264  -6.5162  -2.3327   0.3173
 G9K  H10  H  HCR6  0   0.291   3.7268   2.1688   0.3883
 G9K  H11  H  HCR6  0   0.294   1.9792  -4.4551  -1.0369
 G9K  H12  H  HCR6  0   0.294   4.4184  -4.2771  -0.5312
 G9K  H13  H  HCR6  0   0.292   0.3334  -0.2323  -0.6591
 G9K  H14  H  HNR5  0   0.428  -3.1463   3.7278  -0.2687
 G9K  H15  H  HNR5  0   0.418  -6.7148   0.4417  -0.0625

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
 G9K  N2   C14  aromatic  1.355  0.020  1.355
 G9K  N2   C15  aromatic  1.367  0.020  1.367
 G9K  C20  C15  aromatic  1.393  0.020  1.393
 G9K  C20  C19  aromatic  1.381  0.020  1.381
 G9K  C14  C13  aromatic  1.374  0.020  1.374
 G9K  C15  C16  aromatic  1.410  0.020  1.410
 G9K  C19  C18  aromatic  1.404  0.020  1.404
 G9K  C13  C16  aromatic  1.437  0.020  1.437
 G9K  C13  C12  single    1.442  0.020  1.442
 G9K  C16  C17  aromatic  1.400  0.020  1.400
 G9K  C18  C17  aromatic  1.381  0.020  1.381
 G9K  N1   C12  aromatic  1.364  0.020  1.364
 G9K  N1   C11  aromatic  1.350  0.020  1.350
 G9K  C12  N3   aromatic  1.308  0.020  1.308
 G9K  C11  C10  aromatic  1.376  0.020  1.376
 G9K  N3   C10  aromatic  1.370  0.020  1.370
 G9K  C10  C9   single    1.465  0.020  1.465
 G9K  C1   O1   single    1.416  0.020  1.416
 G9K  C9   O4   double    1.222  0.020  1.222
 G9K  C9   C8   single    1.491  0.020  1.491
 G9K  C21  C8   aromatic  1.397  0.020  1.397
 G9K  C21  C2   aromatic  1.386  0.020  1.386
 G9K  O1   C2   single    1.341  0.020  1.341
 G9K  C8   C7   aromatic  1.392  0.020  1.392
 G9K  C2   C3   aromatic  1.398  0.020  1.398
 G9K  C7   C4   aromatic  1.382  0.020  1.382
 G9K  C3   C4   aromatic  1.387  0.020  1.387
 G9K  C3   O3   single    1.359  0.020  1.359
 G9K  C4   O2   single    1.367  0.020  1.367
 G9K  O3   C6   single    1.373  0.020  1.373
 G9K  O2   C5   single    1.370  0.020  1.370
 G9K  C6   C5   double    1.321  0.020  1.321
 G9K  C1   H1   single    0.970  0.020  1.090
 G9K  C1   H2   single    0.970  0.020  1.090
 G9K  C1   H3   single    0.970  0.020  1.090
 G9K  C11  H4   single    0.930  0.020  1.080
 G9K  C14  H5   single    0.930  0.020  1.080
 G9K  C17  H6   single    0.930  0.020  1.080
 G9K  C18  H7   single    0.930  0.020  1.080
 G9K  C19  H8   single    0.930  0.020  1.080
 G9K  C20  H9   single    0.930  0.020  1.080
 G9K  C21  H10  single    0.930  0.020  1.080
 G9K  C5   H11  single    0.930  0.020  1.080
 G9K  C6   H12  single    0.930  0.020  1.080
 G9K  C7   H13  single    0.930  0.020  1.080
 G9K  N1   H14  single    0.860  0.020  1.020
 G9K  N2   H15  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
 G9K  H3   C1   H2   108.85  3.000
 G9K  H3   C1   H1   108.99  3.000
 G9K  H2   C1   H1   108.89  3.000
 G9K  H3   C1   O1   106.34  3.000
 G9K  H2   C1   O1   111.88  3.000
 G9K  H1   C1   O1   111.79  3.000
 G9K  N3   C10  C9   126.92  3.000
 G9K  C9   C10  C11  123.57  3.000
 G9K  N3   C10  C11  109.50  3.000
 G9K  H4   C11  N1   122.24  3.000
 G9K  H4   C11  C10  132.32  3.000
 G9K  N1   C11  C10  105.44  3.000
 G9K  N3   C12  N1   110.28  3.000
 G9K  N3   C12  C13  125.65  3.000
 G9K  N1   C12  C13  124.07  3.000
 G9K  C16  C13  C14  106.43  3.000
 G9K  C16  C13  C12  126.45  3.000
 G9K  C14  C13  C12  127.12  3.000
 G9K  H5   C14  N2   120.16  3.000
 G9K  H5   C14  C13  130.08  3.000
 G9K  N2   C14  C13  109.76  3.000
 G9K  N2   C15  C20  129.99  3.000
 G9K  C20  C15  C16  122.48  3.000
 G9K  N2   C15  C16  107.54  3.000
 G9K  C17  C16  C15  118.94  3.000
 G9K  C17  C16  C13  134.53  3.000
 G9K  C15  C16  C13  106.53  3.000
 G9K  H6   C17  C18  120.72  3.000
 G9K  H6   C17  C16  120.49  3.000
 G9K  C18  C17  C16  118.79  3.000
 G9K  H7   C18  C19  119.18  3.000
 G9K  H7   C18  C17  119.52  3.000
 G9K  C19  C18  C17  121.30  3.000
 G9K  H8   C19  C20  119.45  3.000
 G9K  H8   C19  C18  119.39  3.000
 G9K  C20  C19  C18  121.16  3.000
 G9K  O1   C2   C3   115.35  3.000
 G9K  C3   C2   C21  119.30  3.000
 G9K  O1   C2   C21  125.35  3.000
 G9K  H9   C20  C19  121.42  3.000
 G9K  H9   C20  C15  121.24  3.000
 G9K  C19  C20  C15  117.33  3.000
 G9K  H10  C21  C8   118.99  3.000
 G9K  H10  C21  C2   120.34  3.000
 G9K  C8   C21  C2   120.67  3.000
 G9K  O3   C3   C4   122.66  3.000
 G9K  O3   C3   C2   117.55  3.000
 G9K  C4   C3   C2   119.79  3.000
 G9K  O2   C4   C7   117.82  3.000
 G9K  O2   C4   C3   121.20  3.000
 G9K  C7   C4   C3   120.99  3.000
 G9K  H11  C5   O2   113.66  3.000
 G9K  H11  C5   C6   122.88  3.000
 G9K  O2   C5   C6   123.46  3.000
 G9K  H12  C6   O3   113.59  3.000
 G9K  H12  C6   C5   123.19  3.000
 G9K  O3   C6   C5   123.22  3.000
 G9K  H13  C7   C8   121.22  3.000
 G9K  H13  C7   C4   119.20  3.000
 G9K  C8   C7   C4   119.58  3.000
 G9K  C9   C8   C7   123.44  3.000
 G9K  C7   C8   C21  119.67  3.000
 G9K  C9   C8   C21  116.86  3.000
 G9K  O4   C9   C8   119.50  3.000
 G9K  C8   C9   C10  121.96  3.000
 G9K  O4   C9   C10  118.54  3.000
 G9K  H14  N1   C12  126.90  3.000
 G9K  H14  N1   C11  124.76  3.000
 G9K  C12  N1   C11  108.33  3.000
 G9K  H15  N2   C15  125.67  3.000
 G9K  H15  N2   C14  124.58  3.000
 G9K  C15  N2   C14  109.75  3.000
 G9K  C12  N3   C10  106.44  3.000
 G9K  C2   O1   C1   118.22  3.000
 G9K  C5   O2   C4   114.94  3.000
 G9K  C6   O3   C3   114.50  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
 G9K  CONST_01  C12  N1   C11  C10     0.00   0.0  0
 G9K  CONST_02  C13  C12  N3   C10   180.00   0.0  0
 G9K  CONST_03  N1   C12  N3   C10     0.00   0.0  0
 G9K  CONST_04  C13  C12  N1   C11   180.00   0.0  0
 G9K  CONST_05  N3   C12  N1   C11     0.00   0.0  0
 G9K  CONST_06  C12  N3   C10  C11     0.00   0.0  0
 G9K  CONST_07  N2   C14  C13  C12   180.00   0.0  0
 G9K  CONST_08  C15  C16  C13  C12   180.00   0.0  0
 G9K  CONST_09  C17  C16  C13  C12     0.00   0.0  0
 G9K  CONST_10  C15  N2   C14  C13     0.00   0.0  0
 G9K  CONST_11  N2   C15  C16  C13     0.00   0.0  0
 G9K  CONST_12  C20  C15  C16  C13   180.00   0.0  0
 G9K  CONST_13  C18  C17  C16  C13   180.00   0.0  0
 G9K  CONST_14  C20  C15  N2   C14   180.00   0.0  0
 G9K  CONST_15  C16  C15  N2   C14     0.00   0.0  0
 G9K  CONST_16  C15  C16  C13  C14     0.00   0.0  0
 G9K  CONST_17  C17  C16  C13  C14   180.00   0.0  0
 G9K  CONST_18  N1   C12  C13  C14     0.00   0.0  0
 G9K  CONST_19  N3   C12  C13  C14   180.00   0.0  0
 G9K  CONST_20  C18  C19  C20  C15     0.00   0.0  0
 G9K  CONST_21  C18  C17  C16  C15     0.00   0.0  0
 G9K  CONST_22  C19  C20  C15  C16     0.00   0.0  0
 G9K  CONST_23  N2   C14  C13  C16     0.00   0.0  0
 G9K  CONST_24  N1   C12  C13  C16   180.00   0.0  0
 G9K  CONST_25  N3   C12  C13  C16     0.00   0.0  0
 G9K  CONST_26  C19  C18  C17  C16     0.00   0.0  0
 G9K  CONST_27  N2   C15  C16  C17   180.00   0.0  0
 G9K  CONST_28  C20  C15  C16  C17     0.00   0.0  0
 G9K  CONST_29  C20  C19  C18  C17     0.00   0.0  0
 G9K  CONST_30  N2   C15  C20  C19   180.00   0.0  0
 G9K  CONST_31  C7   C8   C21  C2      0.00   0.0  0
 G9K  CONST_32  C7   C4   C3   C2      0.00   0.0  0
 G9K  CONST_33  C4   C7   C8   C21     0.00   0.0  0
 G9K  CONST_34  C4   C3   C2   C21     0.00   0.0  0
 G9K  CONST_35  C8   C21  C2   C3      0.00   0.0  0
 G9K  CONST_36  C8   C7   C4   C3      0.00   0.0  0
 G9K  CONST_37  N3   C10  C11  N1      0.00   0.0  0
 G9K  CONST_38  C9   C10  N3   C12   180.00   0.0  0
 G9K  CONST_39  C9   C8   C21  C2    180.00   0.0  0
 G9K  CONST_40  C9   C8   C7   C4    180.00   0.0  0
 G9K  CONST_41  O1   C2   C3   C4    180.00   0.0  0
 G9K  CONST_42  O1   C2   C21  C8    180.00   0.0  0
 G9K  CONST_43  N1   C11  C10  C9    180.00   0.0  0
 G9K  CONST_44  O3   C3   C2   O1      0.00   0.0  0
 G9K  CONST_45  H14  N1   C11  C10   180.00   0.0  0
 G9K  CONST_46  H5   C14  C13  C12     0.00   0.0  0
 G9K  CONST_47  H4   C11  N1   C12   180.00   0.0  0
 G9K  CONST_48  H15  N2   C14  C13   180.00   0.0  0
 G9K  CONST_49  H6   C17  C16  C13     0.00   0.0  0
 G9K  CONST_50  H8   C19  C20  C15   180.00   0.0  0
 G9K  CONST_51  H9   C20  C15  C16   180.00   0.0  0
 G9K  CONST_52  H7   C18  C17  C16   180.00   0.0  0
 G9K  CONST_53  H13  C7   C8   C21   180.00   0.0  0
 G9K  CONST_54  H10  C21  C2   C3    180.00   0.0  0
 G9K  Var_01    C5   C6   O3   C3      1.10  30.0  1
 G9K  Var_02    C6   C5   O2   C4     -0.98  30.0  1
 G9K  Var_03    C7   C4   O2   C5   -178.94  30.0  1
 G9K  Var_04    O3   C6   C5   O2     -0.13  30.0  1
 G9K  Var_05    C21  C8   C9   C10  -168.31  30.0  2
 G9K  Var_06    C8   C9   C10  C11  -172.77  30.0  2
 G9K  Var_07    C21  C2   O1   C1     -2.06  30.0  2
 G9K  Var_08    H1   C1   O1   C2    -58.80  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
 G9K  plan-1  C10  0.020
 G9K  plan-1  C11  0.020
 G9K  plan-1  C12  0.020
 G9K  plan-1  C13  0.020
 G9K  plan-1  C9   0.020
 G9K  plan-1  N1   0.020
 G9K  plan-1  N3   0.020
 G9K  plan-1  H4   0.020
 G9K  plan-1  H14  0.020
 G9K  plan-2  C12  0.020
 G9K  plan-2  C13  0.020
 G9K  plan-2  C14  0.020
 G9K  plan-2  C15  0.020
 G9K  plan-2  C16  0.020
 G9K  plan-2  C17  0.020
 G9K  plan-2  C18  0.020
 G9K  plan-2  C19  0.020
 G9K  plan-2  C20  0.020
 G9K  plan-2  N2   0.020
 G9K  plan-2  H5   0.020
 G9K  plan-2  H6   0.020
 G9K  plan-2  H7   0.020
 G9K  plan-2  H8   0.020
 G9K  plan-2  H9   0.020
 G9K  plan-2  H15  0.020
 G9K  plan-3  C2   0.020
 G9K  plan-3  C21  0.020
 G9K  plan-3  C3   0.020
 G9K  plan-3  C4   0.020
 G9K  plan-3  C7   0.020
 G9K  plan-3  C8   0.020
 G9K  plan-3  C9   0.020
 G9K  plan-3  O1   0.020
 G9K  plan-3  O2   0.020
 G9K  plan-3  O3   0.020
 G9K  plan-3  H10  0.020
 G9K  plan-3  H13  0.020
 G9K  plan-4  C10  0.020
 G9K  plan-4  C8   0.020
 G9K  plan-4  C9   0.020
 G9K  plan-4  O4   0.020

