# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 15:53:27 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 2-(1H-indol-6-yl)-4-(3,4,5-trimethoxyphenyl)-1H-imidazo[4,5-c]pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(cc(OC)c1OC)c2nccc3[nH]c(nc23)c4ccc5cc[nH]c5c4
#
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
 DJ9  DJ9  2-(1H-indol-6-yl)-4-(3,4,5-trimethoxyphenyl)-1H-imidazo[4,5-c]pyridine  ligand  50  30  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DJ9
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
 DJ9  C1   C  CH3   0  -0.410   4.7835   3.4857   0.8964
 DJ9  C10  C  CR56  0   0.434  -0.6782  -3.1117   0.1990
 DJ9  C11  C  CR5   0   0.517  -2.1287  -1.4658   0.0382
 DJ9  C12  C  CR6   0  -0.017  -3.4096  -0.7733  -0.0326
 DJ9  C13  C  CR16  0  -0.347  -3.4045   0.6131  -0.1238
 DJ9  C14  C  CR56  0   0.390  -4.6271   1.2641  -0.1871
 DJ9  C15  C  CR15  0  -0.018  -6.2631   2.7669  -0.3111
 DJ9  C16  C  CR15  0  -0.415  -6.8892   1.5534  -0.2428
 DJ9  C17  C  CR56  0   0.060  -5.8605   0.5702  -0.1623
 DJ9  C18  C  CR16  0  -0.325  -5.8412  -0.8265  -0.0712
 DJ9  C19  C  CR16  0  -0.316  -4.6311  -1.4807  -0.0084
 DJ9  C2   C  CR6   0   0.169   3.7807   1.6782  -0.1923
 DJ9  C20  C  CR56  0   0.093  -0.0286  -1.8695   0.0919
 DJ9  C21  C  CR16  0  -0.471   3.5746  -0.7046   0.1562
 DJ9  C22  C  CR6   0   0.364   4.3651   0.4336   0.0641
 DJ9  C23  C  CH3   0  -0.438   6.3620  -0.7868   0.4359
 DJ9  C3   C  CR6   0   0.381   2.3952   1.7687  -0.3344
 DJ9  C4   C  CH3   0  -0.443   0.5180   3.1594  -0.7298
 DJ9  C5   C  CR16  0  -0.548   1.6027   0.6288  -0.2413
 DJ9  C6   C  CR6   0   0.095   2.1901  -0.6114   0.0058
 DJ9  C7   C  CR6   0   0.155   1.3774  -1.8432   0.1059
 DJ9  C8   C  CR16  0  -0.100   1.3987  -4.1558   0.3218
 DJ9  C9   C  CR16  0  -0.383   0.0237  -4.3003   0.3166
 DJ9  N1   N  N     0  -0.452   2.0382  -2.9907   0.2216
 DJ9  N2   N  NR15  0  -0.741  -2.0062  -2.8189   0.1608
 DJ9  N3   N  NR15  0  -0.685  -4.9114   2.5951  -0.2781
 DJ9  N4   N  N     0  -0.508  -0.9628  -0.8733  -0.0051
 DJ9  O1   O  O2    0  -0.480   4.5570   2.7846  -0.3198
 DJ9  O2   O  O2    0  -0.467   1.9135   3.0033  -0.5687
 DJ9  O3   O  O2    0  -0.466   5.7036   0.4410   0.1976
 DJ9  H1   H  HCH3  0   0.238   5.4181   4.3384   0.6614
 DJ9  H2   H  HCH3  0   0.222   3.8513   3.8534   1.3319
 DJ9  H3   H  HCH3  0   0.222   5.2940   2.8619   1.6340
 DJ9  H4   H  HCR6  0   0.259  -2.4714   1.1609  -0.1425
 DJ9  H5   H  HCR5  0   0.287  -6.6855   3.7564  -0.3814
 DJ9  H6   H  HCR5  0   0.254  -7.9541   1.3865  -0.2485
 DJ9  H7   H  HCR6  0   0.255  -6.7633  -1.3930  -0.0504
 DJ9  H8   H  HCR6  0   0.238  -4.6410  -2.5610   0.0577
 DJ9  H9   H  HCR6  0   0.275   4.0116  -1.6733   0.3494
 DJ9  H10  H  HCH3  0   0.228   6.0434  -1.2477   1.3745
 DJ9  H11  H  HCH3  0   0.229   6.2028  -1.5006  -0.3762
 DJ9  H12  H  HCH3  0   0.261   7.4231  -0.5593   0.5005
 DJ9  H13  H  HCH3  0   0.264   0.3440   4.2185  -0.9024
 DJ9  H14  H  HCH3  0   0.229   0.1409   2.5970  -1.5880
 DJ9  H15  H  HCH3  0   0.227  -0.0335   2.8540   0.1637
 DJ9  H16  H  HCR6  0   0.305   0.5314   0.6938  -0.3523
 DJ9  H17  H  HCR6  0   0.260   2.0280  -5.0336   0.4128
 DJ9  H18  H  HCR6  0   0.278  -0.4504  -5.2679   0.4015
 DJ9  H19  H  HNR5  0   0.429  -2.7528  -3.4923   0.2199
 DJ9  H20  H  HNR5  0   0.413  -4.2343   3.3386  -0.3176

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
 DJ9  C15  N3   aromatic  1.363  0.020  1.363
 DJ9  C15  C16  aromatic  1.367  0.020  1.367
 DJ9  N3   C14  aromatic  1.364  0.020  1.364
 DJ9  C16  C17  aromatic  1.425  0.020  1.425
 DJ9  C14  C17  aromatic  1.415  0.020  1.415
 DJ9  C14  C13  aromatic  1.387  0.020  1.387
 DJ9  C17  C18  aromatic  1.400  0.020  1.400
 DJ9  C13  C12  aromatic  1.389  0.020  1.389
 DJ9  C18  C19  aromatic  1.377  0.020  1.377
 DJ9  C12  C19  aromatic  1.412  0.020  1.412
 DJ9  C12  C11  single    1.458  0.020  1.458
 DJ9  N2   C11  aromatic  1.364  0.020  1.364
 DJ9  N2   C10  aromatic  1.360  0.020  1.360
 DJ9  C11  N4   aromatic  1.309  0.020  1.309
 DJ9  C10  C9   aromatic  1.385  0.020  1.385
 DJ9  C10  C20  aromatic  1.406  0.020  1.406
 DJ9  C9   C8   aromatic  1.383  0.020  1.383
 DJ9  N4   C20  aromatic  1.369  0.020  1.369
 DJ9  C20  C7   aromatic  1.406  0.020  1.406
 DJ9  C8   N1   aromatic  1.333  0.020  1.333
 DJ9  C7   N1   aromatic  1.329  0.020  1.329
 DJ9  C7   C6   single    1.479  0.020  1.479
 DJ9  C23  O3   single    1.413  0.020  1.413
 DJ9  C21  C6   aromatic  1.396  0.020  1.396
 DJ9  C21  C22  aromatic  1.389  0.020  1.389
 DJ9  C6   C5   aromatic  1.394  0.020  1.394
 DJ9  O3   C22  single    1.345  0.020  1.345
 DJ9  C22  C2   aromatic  1.399  0.020  1.399
 DJ9  C5   C3   aromatic  1.391  0.020  1.391
 DJ9  C2   C3   aromatic  1.396  0.020  1.396
 DJ9  C2   O1   single    1.358  0.020  1.358
 DJ9  C3   O2   single    1.346  0.020  1.346
 DJ9  C1   O1   single    1.422  0.020  1.422
 DJ9  O2   C4   single    1.413  0.020  1.413
 DJ9  C1   H1   single    0.970  0.020  1.090
 DJ9  C1   H2   single    0.970  0.020  1.090
 DJ9  C1   H3   single    0.970  0.020  1.090
 DJ9  C13  H4   single    0.930  0.020  1.080
 DJ9  C15  H5   single    0.930  0.020  1.080
 DJ9  C16  H6   single    0.930  0.020  1.080
 DJ9  C18  H7   single    0.930  0.020  1.080
 DJ9  C19  H8   single    0.930  0.020  1.080
 DJ9  C21  H9   single    0.930  0.020  1.080
 DJ9  C23  H10  single    0.970  0.020  1.090
 DJ9  C23  H11  single    0.970  0.020  1.090
 DJ9  C23  H12  single    0.970  0.020  1.090
 DJ9  C4   H13  single    0.970  0.020  1.090
 DJ9  C4   H14  single    0.970  0.020  1.090
 DJ9  C4   H15  single    0.970  0.020  1.090
 DJ9  C5   H16  single    0.930  0.020  1.080
 DJ9  C8   H17  single    0.930  0.020  1.080
 DJ9  C9   H18  single    0.930  0.020  1.080
 DJ9  N2   H19  single    0.860  0.020  1.020
 DJ9  N3   H20  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
 DJ9  H3   C1   H2   108.77  3.000
 DJ9  H3   C1   H1   108.69  3.000
 DJ9  H2   C1   H1   108.65  3.000
 DJ9  H3   C1   O1   111.73  3.000
 DJ9  H2   C1   O1   111.77  3.000
 DJ9  H1   C1   O1   107.12  3.000
 DJ9  N2   C10  C9   132.97  3.000
 DJ9  C9   C10  C20  122.03  3.000
 DJ9  N2   C10  C20  104.99  3.000
 DJ9  N4   C11  N2   111.85  3.000
 DJ9  N4   C11  C12  124.48  3.000
 DJ9  N2   C11  C12  123.67  3.000
 DJ9  C19  C12  C13  120.28  3.000
 DJ9  C19  C12  C11  121.43  3.000
 DJ9  C13  C12  C11  118.29  3.000
 DJ9  H4   C13  C14  121.45  3.000
 DJ9  H4   C13  C12  120.62  3.000
 DJ9  C14  C13  C12  117.92  3.000
 DJ9  N3   C14  C17  107.33  3.000
 DJ9  C17  C14  C13  122.51  3.000
 DJ9  N3   C14  C13  130.16  3.000
 DJ9  H5   C15  N3   120.38  3.000
 DJ9  H5   C15  C16  129.68  3.000
 DJ9  N3   C15  C16  109.94  3.000
 DJ9  H6   C16  C17  127.34  3.000
 DJ9  H6   C16  C15  126.12  3.000
 DJ9  C17  C16  C15  106.54  3.000
 DJ9  C18  C17  C16  134.58  3.000
 DJ9  C18  C17  C14  118.58  3.000
 DJ9  C16  C17  C14  106.84  3.000
 DJ9  H7   C18  C19  119.94  3.000
 DJ9  H7   C18  C17  120.78  3.000
 DJ9  C19  C18  C17  119.28  3.000
 DJ9  H8   C19  C18  117.96  3.000
 DJ9  H8   C19  C12  120.60  3.000
 DJ9  C18  C19  C12  121.43  3.000
 DJ9  O1   C2   C3   120.35  3.000
 DJ9  O1   C2   C22  120.24  3.000
 DJ9  C3   C2   C22  119.41  3.000
 DJ9  N4   C20  C7   132.01  3.000
 DJ9  C7   C20  C10  118.54  3.000
 DJ9  N4   C20  C10  109.45  3.000
 DJ9  H9   C21  C6   118.72  3.000
 DJ9  H9   C21  C22  121.10  3.000
 DJ9  C6   C21  C22  120.18  3.000
 DJ9  O3   C22  C21  124.36  3.000
 DJ9  O3   C22  C2   115.40  3.000
 DJ9  C21  C22  C2   120.24  3.000
 DJ9  H12  C23  H11  108.85  3.000
 DJ9  H12  C23  H10  108.76  3.000
 DJ9  H11  C23  H10  108.67  3.000
 DJ9  H12  C23  O3   106.43  3.000
 DJ9  H11  C23  O3   111.98  3.000
 DJ9  H10  C23  O3   112.04  3.000
 DJ9  O2   C3   C5   124.01  3.000
 DJ9  O2   C3   C2   115.62  3.000
 DJ9  C5   C3   C2   120.36  3.000
 DJ9  H15  C4   H14  108.89  3.000
 DJ9  H15  C4   H13  108.73  3.000
 DJ9  H14  C4   H13  108.75  3.000
 DJ9  H15  C4   O2   111.96  3.000
 DJ9  H14  C4   O2   111.92  3.000
 DJ9  H13  C4   O2   106.48  3.000
 DJ9  H16  C5   C6   119.35  3.000
 DJ9  H16  C5   C3   120.61  3.000
 DJ9  C6   C5   C3   120.04  3.000
 DJ9  C7   C6   C5   121.42  3.000
 DJ9  C5   C6   C21  119.76  3.000
 DJ9  C7   C6   C21  118.82  3.000
 DJ9  N1   C7   C6   116.85  3.000
 DJ9  C6   C7   C20  124.35  3.000
 DJ9  N1   C7   C20  118.80  3.000
 DJ9  H17  C8   N1   115.83  3.000
 DJ9  H17  C8   C9   119.55  3.000
 DJ9  N1   C8   C9   124.62  3.000
 DJ9  H18  C9   C8   121.97  3.000
 DJ9  H18  C9   C10  123.53  3.000
 DJ9  C8   C9   C10  114.49  3.000
 DJ9  C8   N1   C7   121.51  3.000
 DJ9  H19  N2   C11  127.01  3.000
 DJ9  H19  N2   C10  125.31  3.000
 DJ9  C11  N2   C10  107.68  3.000
 DJ9  H20  N3   C15  124.97  3.000
 DJ9  H20  N3   C14  125.68  3.000
 DJ9  C15  N3   C14  109.35  3.000
 DJ9  C20  N4   C11  106.03  3.000
 DJ9  C2   O1   C1   114.37  3.000
 DJ9  C4   O2   C3   118.33  3.000
 DJ9  C23  O3   C22  118.39  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
 DJ9  CONST_01  C12  C11  N2   C10  180.00   0.0  0
 DJ9  CONST_02  N4   C11  N2   C10    0.00   0.0  0
 DJ9  CONST_03  N1   C8   C9   C10    0.00   0.0  0
 DJ9  CONST_04  C11  N4   C20  C10    0.00   0.0  0
 DJ9  CONST_05  N1   C7   C20  C10    0.00   0.0  0
 DJ9  CONST_06  C6   C7   C20  C10  180.00   0.0  0
 DJ9  CONST_07  C14  C13  C12  C11  180.00   0.0  0
 DJ9  CONST_08  C18  C19  C12  C11  180.00   0.0  0
 DJ9  CONST_09  C9   C10  N2   C11  180.00   0.0  0
 DJ9  CONST_10  C20  C10  N2   C11    0.00   0.0  0
 DJ9  CONST_11  C7   C20  N4   C11  180.00   0.0  0
 DJ9  CONST_12  N3   C14  C13  C12  180.00   0.0  0
 DJ9  CONST_13  C17  C14  C13  C12    0.00   0.0  0
 DJ9  CONST_14  C17  C18  C19  C12    0.00   0.0  0
 DJ9  CONST_15  C20  N4   C11  C12  180.00   0.0  0
 DJ9  CONST_16  C15  N3   C14  C13  180.00   0.0  0
 DJ9  CONST_17  C16  C17  C14  C13  180.00   0.0  0
 DJ9  CONST_18  C18  C17  C14  C13    0.00   0.0  0
 DJ9  CONST_19  C18  C19  C12  C13    0.00   0.0  0
 DJ9  CONST_20  N2   C11  C12  C13  180.00   0.0  0
 DJ9  CONST_21  N4   C11  C12  C13    0.00   0.0  0
 DJ9  CONST_22  C16  C15  N3   C14    0.00   0.0  0
 DJ9  CONST_23  C15  C16  C17  C14    0.00   0.0  0
 DJ9  CONST_24  C19  C18  C17  C14    0.00   0.0  0
 DJ9  CONST_25  C19  C12  C13  C14    0.00   0.0  0
 DJ9  CONST_26  C17  C14  N3   C15    0.00   0.0  0
 DJ9  CONST_27  C18  C17  C16  C15  180.00   0.0  0
 DJ9  CONST_28  N3   C14  C17  C16    0.00   0.0  0
 DJ9  CONST_29  C19  C18  C17  C16  180.00   0.0  0
 DJ9  CONST_30  N3   C15  C16  C17    0.00   0.0  0
 DJ9  CONST_31  N3   C14  C17  C18  180.00   0.0  0
 DJ9  CONST_32  N2   C11  C12  C19    0.00   0.0  0
 DJ9  CONST_33  N4   C11  C12  C19  180.00   0.0  0
 DJ9  CONST_34  C6   C21  C22  C2     0.00   0.0  0
 DJ9  CONST_35  C6   C5   C3   C2     0.00   0.0  0
 DJ9  CONST_36  C8   C9   C10  C20    0.00   0.0  0
 DJ9  CONST_37  N2   C11  N4   C20    0.00   0.0  0
 DJ9  CONST_38  C8   N1   C7   C20    0.00   0.0  0
 DJ9  CONST_39  C21  C6   C7   C20  180.00   0.0  0
 DJ9  CONST_40  C5   C6   C7   C20    0.00   0.0  0
 DJ9  CONST_41  N1   C7   C6   C21    0.00   0.0  0
 DJ9  CONST_42  C3   C5   C6   C21    0.00   0.0  0
 DJ9  CONST_43  C3   C2   C22  C21    0.00   0.0  0
 DJ9  CONST_44  C7   C6   C21  C22  180.00   0.0  0
 DJ9  CONST_45  C5   C6   C21  C22    0.00   0.0  0
 DJ9  CONST_46  C5   C3   C2   C22    0.00   0.0  0
 DJ9  CONST_47  C7   C6   C5   C3   180.00   0.0  0
 DJ9  CONST_48  N1   C7   C6   C5   180.00   0.0  0
 DJ9  CONST_49  N4   C20  C7   C6     0.00   0.0  0
 DJ9  CONST_50  C8   N1   C7   C6   180.00   0.0  0
 DJ9  CONST_51  N2   C10  C20  C7   180.00   0.0  0
 DJ9  CONST_52  C9   C10  C20  C7     0.00   0.0  0
 DJ9  CONST_53  C9   C8   N1   C7     0.00   0.0  0
 DJ9  CONST_54  N2   C10  C9   C8   180.00   0.0  0
 DJ9  CONST_55  N4   C20  C10  C9   180.00   0.0  0
 DJ9  CONST_56  N4   C20  C7   N1   180.00   0.0  0
 DJ9  CONST_57  N4   C20  C10  N2     0.00   0.0  0
 DJ9  CONST_58  O1   C2   C22  C21  180.00   0.0  0
 DJ9  CONST_59  O2   C3   C2   C22  180.00   0.0  0
 DJ9  CONST_60  O3   C22  C2   C3   180.00   0.0  0
 DJ9  CONST_61  O1   C2   C3   C5   180.00   0.0  0
 DJ9  CONST_62  O3   C22  C21  C6   180.00   0.0  0
 DJ9  CONST_63  O2   C3   C5   C6   180.00   0.0  0
 DJ9  CONST_64  H17  C8   C9   C10  180.00   0.0  0
 DJ9  CONST_65  H4   C13  C12  C11    0.00   0.0  0
 DJ9  CONST_66  H8   C19  C12  C11    0.00   0.0  0
 DJ9  CONST_67  H7   C18  C19  C12  180.00   0.0  0
 DJ9  CONST_68  H19  N2   C11  C12    0.00   0.0  0
 DJ9  CONST_69  H20  N3   C14  C13    0.00   0.0  0
 DJ9  CONST_70  H5   C15  N3   C14  180.00   0.0  0
 DJ9  CONST_71  H6   C16  C17  C14  180.00   0.0  0
 DJ9  CONST_72  H9   C21  C22  C2   180.00   0.0  0
 DJ9  CONST_73  H16  C5   C3   C2   180.00   0.0  0
 DJ9  CONST_74  H18  C9   C10  C20  180.00   0.0  0
 DJ9  Var_01    C22  C2   O1   C1   -90.56  30.0  2
 DJ9  Var_02    C5   C3   O2   C4     0.06  30.0  2
 DJ9  Var_03    H1   C1   O1   C2   179.62  30.0  3
 DJ9  Var_04    H10  C23  O3   C22  -61.79  30.0  3
 DJ9  Var_05    H13  C4   O2   C3   179.74  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
 DJ9  plan-1  C2   0.020
 DJ9  plan-1  C21  0.020
 DJ9  plan-1  C22  0.020
 DJ9  plan-1  C3   0.020
 DJ9  plan-1  C5   0.020
 DJ9  plan-1  C6   0.020
 DJ9  plan-1  C7   0.020
 DJ9  plan-1  O1   0.020
 DJ9  plan-1  O2   0.020
 DJ9  plan-1  O3   0.020
 DJ9  plan-1  H9   0.020
 DJ9  plan-1  H16  0.020
 DJ9  plan-2  C11  0.020
 DJ9  plan-2  C12  0.020
 DJ9  plan-2  C13  0.020
 DJ9  plan-2  C14  0.020
 DJ9  plan-2  C15  0.020
 DJ9  plan-2  C16  0.020
 DJ9  plan-2  C17  0.020
 DJ9  plan-2  C18  0.020
 DJ9  plan-2  C19  0.020
 DJ9  plan-2  N3   0.020
 DJ9  plan-2  H4   0.020
 DJ9  plan-2  H5   0.020
 DJ9  plan-2  H6   0.020
 DJ9  plan-2  H7   0.020
 DJ9  plan-2  H8   0.020
 DJ9  plan-2  H20  0.020
 DJ9  plan-3  C10  0.020
 DJ9  plan-3  C11  0.020
 DJ9  plan-3  C12  0.020
 DJ9  plan-3  C20  0.020
 DJ9  plan-3  C6   0.020
 DJ9  plan-3  C7   0.020
 DJ9  plan-3  C8   0.020
 DJ9  plan-3  C9   0.020
 DJ9  plan-3  N1   0.020
 DJ9  plan-3  N2   0.020
 DJ9  plan-3  N4   0.020
 DJ9  plan-3  H17  0.020
 DJ9  plan-3  H18  0.020
 DJ9  plan-3  H19  0.020

