# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 16:52:41 2021
#   Inital geometry file: a 137 line input string
#   Ligand name: (5,7-dihydro-6H-pyrrolo[3,4-b]pyridin-6-yl){2,4-dihydroxy-6-[(1-methyl-3-phenyl-1H-pyrazol-5-yl)amino]phenyl}methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1nc(cc1Nc2cc(O)cc(O)c2C(=O)N3Cc4cccnc4C3)c5ccccc5
#
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
 W8Y  W8Y  (5,7-dihydro-6H-pyrrolo[3,4-b]pyridin-6-yl){2,4-dihydroxy-6-[(1-methyl-3-phenyl-1H-pyrazol-5-yl)amino]phenyl}methanone  ligand  53  32  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_W8Y
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
 W8Y  C13  C  CR6   0   0.391  -2.4637  10.9624  11.3936
 W8Y  C15  C  CR6   0  -0.268  -1.6615   9.8227  11.3932
 W8Y  C20  C  CR56  0  -0.001  -2.1188   7.6881   7.2645
 W8Y  C22  C  CH2   0  -0.281  -1.5981   9.6145   8.5531
 W8Y  C24  C  CR16  0  -0.085  -1.3133   8.8663   4.9701
 W8Y  C04  C  CR5   0   0.295   3.5789   8.4484  13.5816
 W8Y  C06  C  CR5   0   0.578   1.6549   8.7091  12.5466
 W8Y  O17  O  O     0  -0.494  -2.4493   7.5790  11.4006
 W8Y  C27  C  CR6   0   0.065   4.6550   8.0880  14.5085
 W8Y  C09  C  CR16  0  -0.495   0.0068  11.0373  12.6582
 W8Y  C31  C  CR16  0  -0.235   5.3857   7.1225  16.6032
 W8Y  C16  C  C     0   0.528  -2.1170   8.5587  10.7406
 W8Y  O14  O  OH1   0  -0.625  -3.6546  10.8583  10.7786
 W8Y  C26  C  CR16  0  -0.185  -2.2217   6.9549   6.0974
 W8Y  C08  C  CR6   0   0.372  -0.4298   9.8598  12.0560
 W8Y  C29  C  CR16  0  -0.237   7.0045   8.0177  15.0764
 W8Y  N23  N  N     0  -0.419  -1.2148   9.5761   6.0918
 W8Y  C05  C  CR15  0  -0.570   2.2082   8.1390  13.6702
 W8Y  C10  C  CR6   0   0.403  -0.7994  12.1698  12.6148
 W8Y  C12  C  CR16  0  -0.504  -2.0413  12.1429  11.9895
 W8Y  C19  C  CH2   0  -0.291  -2.4709   7.3298   8.6696
 W8Y  C21  C  CR56  0   0.170  -1.6148   8.9772   7.1982
 W8Y  C25  C  CR16  0  -0.322  -1.8061   7.5681   4.9220
 W8Y  C28  C  CR16  0  -0.296   5.9893   8.3599  14.1973
 W8Y  C30  C  CR16  0  -0.269   6.7086   7.3971  16.2842
 W8Y  C32  C  CR16  0  -0.332   4.3689   7.4659  15.7243
 W8Y  N02  N  NR5   0  -0.284   2.6663   9.2955  11.8664
 W8Y  N03  N  N     0  -0.318   3.8284   9.1620  12.4928
 W8Y  N07  N  NH1   0  -0.807   0.3593   8.7146  12.0601
 W8Y  N18  N  NR5   0  -0.478  -2.0952   8.5379   9.4024
 W8Y  O11  O  OH1   0  -0.630  -0.4245  13.3264  13.1863
 W8Y  H1   H  HCH2  0   0.270  -0.5940   9.9318   8.8462
 W8Y  H2   H  HCH2  0   0.275  -2.2465  10.4937   8.5765
 W8Y  H3   H  HCR6  0   0.265  -0.9874   9.3555   4.0594
 W8Y  H4   H  HCR6  0   0.285   0.9531  11.0671  13.1858
 W8Y  H5   H  HCR6  0   0.257   5.1410   6.6401  17.5407
 W8Y  H6   H  HCH3  0   0.276   3.5460  10.0303  10.1519
 W8Y  H7   H  HCH3  0   0.258   1.8512   9.5520   9.9724
 W8Y  H8   H  HCH3  0   0.258   2.2569  11.0622  10.8035
 W8Y  H9   H  HOH1  0   0.481  -4.1120  11.7072  10.7716
 W8Y  H10  H  HCR6  0   0.274  -2.6115   5.9449   6.0922
 W8Y  H11  H  HCR6  0   0.257   8.0324   8.2332  14.8148
 W8Y  H12  H  HCR5  0   0.272   1.6845   7.5867  14.4328
 W8Y  H13  H  HCR6  0   0.277  -2.6667  13.0278  11.9795
 W8Y  H14  H  HCH2  0   0.269  -3.5348   7.1065   8.7894
 W8Y  H15  H  HCH2  0   0.269  -1.9126   6.4614   9.0291
 W8Y  H16  H  HCR6  0   0.274  -1.8638   7.0497   3.9751
 W8Y  H17  H  HCR6  0   0.250   6.2338   8.8395  13.2586
 W8Y  H18  H  HCR6  0   0.256   7.5026   7.1296  16.9693
 W8Y  H19  H  HCR6  0   0.248   3.3434   7.2507  15.9967
 W8Y  H20  H  HNH1  0   0.404  -0.1322   7.8377  12.1432
 W8Y  H21  H  HOH1  0   0.478   0.4456  13.2355  13.5915
 W8Y  C01  C  CH3   0  -0.529   2.5716  10.0326  10.6307

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
 W8Y  C25  C24  aromatic  1.389  0.020  1.389
 W8Y  C25  C26  aromatic  1.389  0.020  1.389
 W8Y  C24  N23  aromatic  1.331  0.020  1.331
 W8Y  C26  C20  aromatic  1.382  0.020  1.382
 W8Y  N23  C21  aromatic  1.320  0.020  1.320
 W8Y  C20  C21  aromatic  1.386  0.020  1.386
 W8Y  C20  C19  single    1.492  0.020  1.492
 W8Y  C21  C22  single    1.497  0.020  1.497
 W8Y  C19  N18  single    1.462  0.020  1.462
 W8Y  C22  N18  single    1.459  0.020  1.459
 W8Y  N18  C16  single    1.338  0.020  1.338
 W8Y  C01  N02  single    1.442  0.020  1.442
 W8Y  C16  O17  double    1.227  0.020  1.227
 W8Y  C16  C15  single    1.494  0.020  1.494
 W8Y  O14  C13  single    1.344  0.020  1.344
 W8Y  N02  N03  aromatic  1.327  0.020  1.327
 W8Y  N02  C06  aromatic  1.353  0.020  1.353
 W8Y  C15  C13  aromatic  1.394  0.020  1.394
 W8Y  C15  C08  aromatic  1.399  0.020  1.399
 W8Y  C13  C12  aromatic  1.388  0.020  1.388
 W8Y  N07  C08  single    1.391  0.020  1.391
 W8Y  N07  C06  single    1.384  0.020  1.384
 W8Y  C08  C09  aromatic  1.393  0.020  1.393
 W8Y  N03  C04  aromatic  1.325  0.020  1.325
 W8Y  C06  C05  aromatic  1.376  0.020  1.376
 W8Y  C12  C10  aromatic  1.391  0.020  1.391
 W8Y  C09  C10  aromatic  1.391  0.020  1.391
 W8Y  C10  O11  single    1.343  0.020  1.343
 W8Y  C04  C05  aromatic  1.408  0.020  1.408
 W8Y  C04  C27  single    1.465  0.020  1.465
 W8Y  C28  C27  aromatic  1.397  0.020  1.397
 W8Y  C28  C29  aromatic  1.386  0.020  1.386
 W8Y  C27  C32  aromatic  1.395  0.020  1.395
 W8Y  C29  C30  aromatic  1.390  0.020  1.390
 W8Y  C32  C31  aromatic  1.387  0.020  1.387
 W8Y  C30  C31  aromatic  1.388  0.020  1.388
 W8Y  C22  H1   single    0.970  0.020  1.090
 W8Y  C22  H2   single    0.970  0.020  1.090
 W8Y  C24  H3   single    0.930  0.020  1.080
 W8Y  C09  H4   single    0.930  0.020  1.080
 W8Y  C31  H5   single    0.930  0.020  1.080
 W8Y  C01  H6   single    0.970  0.020  1.090
 W8Y  C01  H7   single    0.970  0.020  1.090
 W8Y  C01  H8   single    0.970  0.020  1.090
 W8Y  O14  H9   single    0.850  0.020  0.980
 W8Y  C26  H10  single    0.930  0.020  1.080
 W8Y  C29  H11  single    0.930  0.020  1.080
 W8Y  C05  H12  single    0.930  0.020  1.080
 W8Y  C12  H13  single    0.930  0.020  1.080
 W8Y  C19  H14  single    0.970  0.020  1.090
 W8Y  C19  H15  single    0.970  0.020  1.090
 W8Y  C25  H16  single    0.930  0.020  1.080
 W8Y  C28  H17  single    0.930  0.020  1.080
 W8Y  C30  H18  single    0.930  0.020  1.080
 W8Y  C32  H19  single    0.930  0.020  1.080
 W8Y  N07  H20  single    0.890  0.020  1.040
 W8Y  O11  H21  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
 W8Y  C12  C13  O14  122.12  3.000
 W8Y  C12  C13  C15  121.36  3.000
 W8Y  O14  C13  C15  116.52  3.000
 W8Y  C08  C15  C16  119.86  3.000
 W8Y  C08  C15  C13  119.00  3.000
 W8Y  C16  C15  C13  121.10  3.000
 W8Y  C21  C20  C19  110.75  3.000
 W8Y  C19  C20  C26  130.55  3.000
 W8Y  C21  C20  C26  118.70  3.000
 W8Y  H2   C22  H1   107.80  3.000
 W8Y  H2   C22  N18  112.28  3.000
 W8Y  H1   C22  N18  111.79  3.000
 W8Y  H2   C22  C21  110.81  3.000
 W8Y  H1   C22  C21  112.11  3.000
 W8Y  N18  C22  C21  102.07  3.000
 W8Y  H3   C24  C25  119.95  3.000
 W8Y  H3   C24  N23  116.43  3.000
 W8Y  C25  C24  N23  123.62  3.000
 W8Y  N03  C04  C05  110.69  3.000
 W8Y  C05  C04  C27  128.39  3.000
 W8Y  N03  C04  C27  120.92  3.000
 W8Y  N07  C06  N02  121.43  3.000
 W8Y  N07  C06  C05  131.69  3.000
 W8Y  N02  C06  C05  106.83  3.000
 W8Y  C32  C27  C28  118.47  3.000
 W8Y  C32  C27  C04  120.68  3.000
 W8Y  C28  C27  C04  120.85  3.000
 W8Y  H4   C09  C10  119.93  3.000
 W8Y  H4   C09  C08  120.49  3.000
 W8Y  C10  C09  C08  119.55  3.000
 W8Y  H5   C31  C32  119.57  3.000
 W8Y  H5   C31  C30  120.18  3.000
 W8Y  C32  C31  C30  120.26  3.000
 W8Y  N18  C16  O17  121.99  3.000
 W8Y  O17  C16  C15  121.55  3.000
 W8Y  N18  C16  C15  116.42  3.000
 W8Y  H9   O14  C13  110.82  3.000
 W8Y  H10  C26  C25  121.02  3.000
 W8Y  H10  C26  C20  121.73  3.000
 W8Y  C25  C26  C20  117.25  3.000
 W8Y  N07  C08  C09  121.13  3.000
 W8Y  C09  C08  C15  120.21  3.000
 W8Y  N07  C08  C15  118.62  3.000
 W8Y  H11  C29  C30  120.07  3.000
 W8Y  H11  C29  C28  119.56  3.000
 W8Y  C30  C29  C28  120.37  3.000
 W8Y  C21  N23  C24  116.23  3.000
 W8Y  H12  C05  C06  126.50  3.000
 W8Y  H12  C05  C04  129.08  3.000
 W8Y  C06  C05  C04  104.42  3.000
 W8Y  O11  C10  C12  117.20  3.000
 W8Y  O11  C10  C09  121.73  3.000
 W8Y  C12  C10  C09  121.06  3.000
 W8Y  H13  C12  C10  120.25  3.000
 W8Y  H13  C12  C13  120.99  3.000
 W8Y  C10  C12  C13  118.76  3.000
 W8Y  H15  C19  H14  107.37  3.000
 W8Y  H15  C19  N18  111.12  3.000
 W8Y  H14  C19  N18  111.33  3.000
 W8Y  H15  C19  C20  112.33  3.000
 W8Y  H14  C19  C20  112.44  3.000
 W8Y  N18  C19  C20  102.29  3.000
 W8Y  N23  C21  C22  124.19  3.000
 W8Y  C22  C21  C20  110.90  3.000
 W8Y  N23  C21  C20  124.91  3.000
 W8Y  H16  C25  C26  120.89  3.000
 W8Y  H16  C25  C24  119.82  3.000
 W8Y  C26  C25  C24  119.29  3.000
 W8Y  H17  C28  C29  119.61  3.000
 W8Y  H17  C28  C27  119.70  3.000
 W8Y  C29  C28  C27  120.69  3.000
 W8Y  H18  C30  C29  120.29  3.000
 W8Y  H18  C30  C31  120.31  3.000
 W8Y  C29  C30  C31  119.40  3.000
 W8Y  H19  C32  C31  119.06  3.000
 W8Y  H19  C32  C27  120.13  3.000
 W8Y  C31  C32  C27  120.81  3.000
 W8Y  N03  N02  C01  120.90  3.000
 W8Y  N03  N02  C06  111.95  3.000
 W8Y  C01  N02  C06  127.12  3.000
 W8Y  N02  N03  C04  106.08  3.000
 W8Y  H20  N07  C08  116.08  3.000
 W8Y  H20  N07  C06  115.07  3.000
 W8Y  C08  N07  C06  122.38  3.000
 W8Y  C19  N18  C16  120.64  3.000
 W8Y  C16  N18  C22  125.19  3.000
 W8Y  C19  N18  C22  113.93  3.000
 W8Y  H21  O11  C10  110.45  3.000
 W8Y  H8   C01  H7   108.79  3.000
 W8Y  H8   C01  H6   109.32  3.000
 W8Y  H7   C01  H6   109.06  3.000
 W8Y  H8   C01  N02  111.46  3.000
 W8Y  H7   C01  N02  109.65  3.000
 W8Y  H6   C01  N02  108.53  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
 W8Y  CONST_01  C09  C08  C15  C13     0.00   0.0  0
 W8Y  CONST_02  C09  C10  C12  C13     0.00   0.0  0
 W8Y  CONST_03  C10  C12  C13  C15     0.00   0.0  0
 W8Y  CONST_04  C10  C09  C08  C15     0.00   0.0  0
 W8Y  CONST_05  C24  C25  C26  C20     0.00   0.0  0
 W8Y  CONST_06  C24  N23  C21  C20     0.00   0.0  0
 W8Y  CONST_07  C06  N02  N03  C04     0.00   0.0  0
 W8Y  CONST_08  N02  C06  C05  C04     0.00   0.0  0
 W8Y  CONST_09  C29  C28  C27  C04   180.00   0.0  0
 W8Y  CONST_10  C31  C32  C27  C04   180.00   0.0  0
 W8Y  CONST_11  N03  C04  C05  C06     0.00   0.0  0
 W8Y  CONST_12  C27  C04  C05  C06   180.00   0.0  0
 W8Y  CONST_13  N02  N03  C04  C27   180.00   0.0  0
 W8Y  CONST_14  C30  C29  C28  C27     0.00   0.0  0
 W8Y  CONST_15  C30  C31  C32  C27     0.00   0.0  0
 W8Y  CONST_16  C28  C27  C32  C31     0.00   0.0  0
 W8Y  CONST_17  C28  C29  C30  C31     0.00   0.0  0
 W8Y  CONST_18  N23  C24  C25  C26     0.00   0.0  0
 W8Y  CONST_19  N23  C21  C20  C26     0.00   0.0  0
 W8Y  CONST_20  C12  C13  C15  C08     0.00   0.0  0
 W8Y  CONST_21  C12  C10  C09  C08     0.00   0.0  0
 W8Y  CONST_22  C32  C27  C28  C29     0.00   0.0  0
 W8Y  CONST_23  C32  C31  C30  C29     0.00   0.0  0
 W8Y  CONST_24  N03  N02  C06  C05     0.00   0.0  0
 W8Y  CONST_25  N02  N03  C04  C05     0.00   0.0  0
 W8Y  CONST_26  C28  C27  C04  C05   180.00   0.0  0
 W8Y  CONST_27  C32  C27  C04  C05     0.00   0.0  0
 W8Y  CONST_28  C25  C24  N23  C21     0.00   0.0  0
 W8Y  CONST_29  C25  C26  C20  C21     0.00   0.0  0
 W8Y  CONST_30  N03  C04  C27  C28     0.00   0.0  0
 W8Y  CONST_31  N03  C04  C27  C32   180.00   0.0  0
 W8Y  CONST_32  N07  C08  C15  C13   180.00   0.0  0
 W8Y  CONST_33  O11  C10  C12  C13   180.00   0.0  0
 W8Y  CONST_34  C01  N02  N03  C04   180.00   0.0  0
 W8Y  CONST_35  N07  C06  C05  C04   180.00   0.0  0
 W8Y  CONST_36  C16  C15  C08  C09   180.00   0.0  0
 W8Y  CONST_37  C05  C06  N02  C01   180.00   0.0  0
 W8Y  CONST_38  C12  C13  C15  C16   180.00   0.0  0
 W8Y  CONST_39  C08  C15  C13  O14   180.00   0.0  0
 W8Y  CONST_40  C10  C12  C13  O14   180.00   0.0  0
 W8Y  CONST_41  O11  C10  C09  C08   180.00   0.0  0
 W8Y  CONST_42  N07  C08  C09  C10   180.00   0.0  0
 W8Y  CONST_43  N07  C06  N02  N03   180.00   0.0  0
 W8Y  CONST_44  C19  N18  C16  C15   180.00   0.0  0
 W8Y  CONST_45  C22  N18  C16  C15     0.00   0.0  0
 W8Y  CONST_46  H13  C12  C13  C15   180.00   0.0  0
 W8Y  CONST_47  H4   C09  C08  C15   180.00   0.0  0
 W8Y  CONST_48  H16  C25  C26  C20   180.00   0.0  0
 W8Y  CONST_49  H10  C26  C25  C24   180.00   0.0  0
 W8Y  CONST_50  H17  C28  C27  C04     0.00   0.0  0
 W8Y  CONST_51  H19  C32  C27  C04     0.00   0.0  0
 W8Y  CONST_52  H12  C05  C04  C27     0.00   0.0  0
 W8Y  CONST_53  H11  C29  C28  C27   180.00   0.0  0
 W8Y  CONST_54  H5   C31  C32  C27   180.00   0.0  0
 W8Y  CONST_55  H3   C24  C25  C26   180.00   0.0  0
 W8Y  CONST_56  H18  C30  C29  C28   180.00   0.0  0
 W8Y  CONST_57  O17  C16  N18  C22   180.00   0.0  0
 W8Y  CONST_58  C19  N18  C16  O17     0.00   0.0  0
 W8Y  Var_01    N18  C22  C21  C20     2.11  30.0  1
 W8Y  Var_02    C22  N18  C19  C20     2.39  30.0  1
 W8Y  Var_03    N18  C19  C20  C26   179.10  30.0  1
 W8Y  Var_04    C21  C22  N18  C19    -2.80  30.0  1
 W8Y  Var_05    N18  C16  C15  C13    74.31  30.0  2
 W8Y  Var_06    C06  N07  C08  C15   171.93  30.0  2
 W8Y  Var_07    N02  C06  N07  C08   -72.77  30.0  2
 W8Y  Var_08    H6   C01  N02  C06  -157.83  30.0  2

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
 W8Y  plan-1  C04  0.020
 W8Y  plan-1  C06  0.020
 W8Y  plan-1  C27  0.020
 W8Y  plan-1  C05  0.020
 W8Y  plan-1  N02  0.020
 W8Y  plan-1  N03  0.020
 W8Y  plan-1  N07  0.020
 W8Y  plan-1  H12  0.020
 W8Y  plan-1  C01  0.020
 W8Y  plan-2  C13  0.020
 W8Y  plan-2  C15  0.020
 W8Y  plan-2  C09  0.020
 W8Y  plan-2  C16  0.020
 W8Y  plan-2  O14  0.020
 W8Y  plan-2  C08  0.020
 W8Y  plan-2  C10  0.020
 W8Y  plan-2  C12  0.020
 W8Y  plan-2  N07  0.020
 W8Y  plan-2  O11  0.020
 W8Y  plan-2  H4   0.020
 W8Y  plan-2  H13  0.020
 W8Y  plan-3  C20  0.020
 W8Y  plan-3  C22  0.020
 W8Y  plan-3  C24  0.020
 W8Y  plan-3  C26  0.020
 W8Y  plan-3  N23  0.020
 W8Y  plan-3  C19  0.020
 W8Y  plan-3  C21  0.020
 W8Y  plan-3  C25  0.020
 W8Y  plan-3  H3   0.020
 W8Y  plan-3  H10  0.020
 W8Y  plan-3  H16  0.020
 W8Y  plan-4  C04  0.020
 W8Y  plan-4  C27  0.020
 W8Y  plan-4  C31  0.020
 W8Y  plan-4  C29  0.020
 W8Y  plan-4  C28  0.020
 W8Y  plan-4  C30  0.020
 W8Y  plan-4  C32  0.020
 W8Y  plan-4  H5   0.020
 W8Y  plan-4  H11  0.020
 W8Y  plan-4  H17  0.020
 W8Y  plan-4  H18  0.020
 W8Y  plan-4  H19  0.020
 W8Y  plan-5  C15  0.020
 W8Y  plan-5  C22  0.020
 W8Y  plan-5  O17  0.020
 W8Y  plan-5  C16  0.020
 W8Y  plan-5  C19  0.020
 W8Y  plan-5  N18  0.020

