# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 06:57:20 2021
#   Inital geometry file: a 144 line input string
#   Ligand name: 6-[(3~{S})-8-chloranyl-5-methyl-4-oxidanylidene-2,3-dihydro-1,5-benzoxazepin-3-yl]-7-oxidanylidene-2-(phenylmethyl)-4,5-dihydropyrazolo[3,4-c]pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)[C@H](COc2cc(Cl)ccc12)N3CCc4c(nn(Cc5ccccc5)c4C(N)=O)C3=O
#
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
 RXN  RXN  6-[(3~{S})-8-chloranyl-5-methyl-4-oxidanylidene-2,3-dihydro-1,5-benzoxazepin-3-yl]-7-oxidanylidene-2-(phenylmethyl)-4,5-dihydropyrazolo[3,4-c]pyridine-3-carboxamide  ligand  56  34  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RXN
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
 RXN  O1   O   O     0  -0.457  -38.5887  -24.7461   0.3954
 RXN  C1   C   CR6   0   0.267  -42.0786  -18.6901   7.0430
 RXN  O2   O   O     0  -0.478  -38.5148  -19.2025   3.9975
 RXN  C2   C   CR16  0  -0.303  -41.6135  -17.9401   8.1165
 RXN  C3   C   CR16  0  -0.219  -41.8177  -16.5709   8.1690
 RXN  C4   C   CR6   0  -0.041  -42.4859  -15.9480   7.1269
 RXN  C5   C   CR16  0  -0.293  -42.9505  -16.6690   6.0392
 RXN  C6   C   CR6   0   0.329  -42.7588  -18.0414   6.0104
 RXN  C7   C   CH2   0  -0.142  -42.3242  -19.2351   4.0383
 RXN  C8   C   CH1   0  -0.328  -41.0903  -19.8639   4.7031
 RXN  C9   C   CH2   0  -0.324  -40.9358  -21.6588   2.9487
 RXN  C10  C   CH2   0  -0.510  -40.0400  -22.8769   2.7763
 RXN  C11  C   CR5   0  -0.106  -38.7248  -22.3891   2.2869
 RXN  C12  C   CR5   0   0.134  -38.2890  -21.1025   2.6126
 RXN  C14  C   CR6   0   0.095  -35.8622  -21.9813  -0.8054
 RXN  C15  C   CR16  0  -0.288  -35.3703  -23.0095  -1.5996
 RXN  C16  C   CR16  0  -0.241  -35.6647  -23.0532  -2.9571
 RXN  C17  C   CR16  0  -0.262  -36.4604  -22.0701  -3.5268
 RXN  C18  C   CR16  0  -0.240  -36.9578  -21.0402  -2.7360
 RXN  N    N   NT    0  -0.542  -41.9149  -20.0870   7.0043
 RXN  C    C   CH3   0  -0.546  -42.1789  -20.8650   8.2082
 RXN  O    O   O2    0  -0.486  -43.2693  -18.7746   4.9892
 RXN  C19  C   CR16  0  -0.280  -36.6589  -20.9952  -1.3832
 RXN  C20  C   CR5   0   0.267  -37.6877  -22.9210   1.5582
 RXN  C21  C   C     0   0.468  -37.6123  -24.2773   0.9565
 RXN  C22  C   C     0   0.551  -39.0283  -20.1910   3.4975
 RXN  C23  C   C     0   0.581  -41.4401  -20.7385   5.9103
 RXN  N1   N   NT    0  -0.495  -40.3042  -20.5972   3.7433
 RXN  N2   N   N     0  -0.267  -37.0930  -20.8430   2.1110
 RXN  N3   N   NR5   0  -0.328  -36.7342  -21.9471   1.4877
 RXN  N4   N   NH2   0  -0.797  -36.4473  -24.9236   1.0995
 RXN  CL   CL  CL    0  -0.120  -42.7426  -14.2372   7.1783
 RXN  H1   H   HCR6  0   0.291  -41.0815  -18.4251   8.9244
 RXN  H2   H   HCR6  0   0.287  -41.4514  -16.0011   9.0114
 RXN  H3   H   HCR6  0   0.295  -43.4793  -16.1840   5.2294
 RXN  H4   H   HCH2  0   0.253  -41.9938  -18.4178   3.3887
 RXN  H5   H   HCH2  0   0.258  -42.8611  -19.9597   3.4281
 RXN  H6   H   HCH1  0   0.320  -40.4541  -19.0526   5.0643
 RXN  H7   H   HCH2  0   0.264  -41.2036  -21.2669   1.9630
 RXN  H8   H   HCH2  0   0.274  -41.8562  -21.9549   3.4421
 RXN  H9   H   HCH2  0   0.267  -40.5077  -23.5679   2.0768
 RXN  H10  H   HCH2  0   0.266  -39.9270  -23.3977   3.7304
 RXN  H11  H   HCH2  0   0.281  -34.8712  -22.7433   0.9431
 RXN  H12  H   HCH2  0   0.304  -35.0223  -20.9996   0.9166
 RXN  H13  H   HCR6  0   0.254  -34.7574  -23.7842  -1.1553
 RXN  H14  H   HCR6  0   0.258  -35.2738  -23.8578  -3.5661
 RXN  H15  H   HCR6  0   0.259  -36.6934  -22.1039  -4.5831
 RXN  H16  H   HCR6  0   0.259  -37.5751  -20.2682  -3.1767
 RXN  H17  H   HCH3  0   0.260  -42.7736  -20.2678   8.8930
 RXN  H18  H   HCH3  0   0.265  -42.7437  -21.7603   7.9589
 RXN  H19  H   HCH3  0   0.253  -41.2566  -21.1625   8.7076
 RXN  H20  H   HCR6  0   0.254  -37.0474  -20.1853  -0.7767
 RXN  H21  H   HNH2  0   0.413  -36.3537  -25.8625   0.7449
 RXN  H22  H   HNH2  0   0.416  -35.7389  -24.6125   1.7421
 RXN  O3   O   O     0  -0.455  -41.2584  -21.9407   5.9134
 RXN  C13  C   CH2   0  -0.393  -35.5343  -21.9263   0.6629

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
 RXN  C17  C16  aromatic  1.387  0.020  1.387
 RXN  C17  C18  aromatic  1.390  0.020  1.390
 RXN  C16  C15  aromatic  1.390  0.020  1.390
 RXN  C18  C19  aromatic  1.386  0.020  1.386
 RXN  C15  C14  aromatic  1.389  0.020  1.389
 RXN  C19  C14  aromatic  1.393  0.020  1.393
 RXN  C14  C13  single    1.505  0.020  1.505
 RXN  C13  N3   single    1.456  0.020  1.456
 RXN  O1   C21  double    1.220  0.020  1.220
 RXN  N3   C20  aromatic  1.365  0.020  1.365
 RXN  N3   N2   aromatic  1.318  0.020  1.318
 RXN  C21  C20  single    1.486  0.020  1.486
 RXN  C21  N4   single    1.340  0.020  1.340
 RXN  C20  C11  aromatic  1.375  0.020  1.375
 RXN  N2   C12  aromatic  1.323  0.020  1.323
 RXN  C11  C12  aromatic  1.397  0.020  1.397
 RXN  C11  C10  single    1.486  0.020  1.486
 RXN  C12  C22  single    1.470  0.020  1.470
 RXN  C10  C9   single    1.522  0.020  1.522
 RXN  C9   N1   single    1.469  0.020  1.469
 RXN  C22  O2   double    1.221  0.020  1.221
 RXN  C22  N1   single    1.361  0.020  1.361
 RXN  N1   C8   single    1.441  0.020  1.441
 RXN  C7   C8   single    1.536  0.020  1.536
 RXN  C7   O    single    1.418  0.020  1.418
 RXN  C8   C23  single    1.531  0.020  1.531
 RXN  O    C6   single    1.357  0.020  1.357
 RXN  O3   C23  double    1.216  0.020  1.216
 RXN  C23  N    single    1.359  0.020  1.359
 RXN  C5   C6   aromatic  1.386  0.020  1.386
 RXN  C5   C4   aromatic  1.385  0.020  1.385
 RXN  C6   C1   aromatic  1.396  0.020  1.396
 RXN  C4   CL   single    1.731  0.020  1.731
 RXN  C4   C3   aromatic  1.386  0.020  1.386
 RXN  C1   N    single    1.407  0.020  1.407
 RXN  C1   C2   aromatic  1.390  0.020  1.390
 RXN  N    C    single    1.458  0.020  1.458
 RXN  C3   C2   aromatic  1.385  0.020  1.385
 RXN  C2   H1   single    0.930  0.020  1.080
 RXN  C3   H2   single    0.930  0.020  1.080
 RXN  C5   H3   single    0.930  0.020  1.080
 RXN  C7   H4   single    0.970  0.020  1.090
 RXN  C7   H5   single    0.970  0.020  1.090
 RXN  C8   H6   single    0.970  0.020  1.090
 RXN  C9   H7   single    0.970  0.020  1.090
 RXN  C9   H8   single    0.970  0.020  1.090
 RXN  C10  H9   single    0.970  0.020  1.090
 RXN  C10  H10  single    0.970  0.020  1.090
 RXN  C13  H11  single    0.970  0.020  1.090
 RXN  C13  H12  single    0.970  0.020  1.090
 RXN  C15  H13  single    0.930  0.020  1.080
 RXN  C16  H14  single    0.930  0.020  1.080
 RXN  C17  H15  single    0.930  0.020  1.080
 RXN  C18  H16  single    0.930  0.020  1.080
 RXN  C    H17  single    0.970  0.020  1.090
 RXN  C    H18  single    0.970  0.020  1.090
 RXN  C    H19  single    0.970  0.020  1.090
 RXN  C19  H20  single    0.930  0.020  1.080
 RXN  N4   H21  single    0.860  0.020  1.020
 RXN  N4   H22  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
 RXN  N    C1   C6   119.84  3.000
 RXN  N    C1   C2   121.21  3.000
 RXN  C6   C1   C2   118.92  3.000
 RXN  H1   C2   C3   119.16  3.000
 RXN  H1   C2   C1   119.96  3.000
 RXN  C3   C2   C1   120.89  3.000
 RXN  H2   C3   C4   120.83  3.000
 RXN  H2   C3   C2   120.03  3.000
 RXN  C4   C3   C2   119.13  3.000
 RXN  CL   C4   C5   119.22  3.000
 RXN  CL   C4   C3   119.57  3.000
 RXN  C5   C4   C3   121.21  3.000
 RXN  H3   C5   C6   119.73  3.000
 RXN  H3   C5   C4   121.21  3.000
 RXN  C6   C5   C4   119.04  3.000
 RXN  O    C6   C5   119.91  3.000
 RXN  C5   C6   C1   120.80  3.000
 RXN  O    C6   C1   119.26  3.000
 RXN  H5   C7   H4   108.24  3.000
 RXN  H5   C7   O    105.27  3.000
 RXN  H4   C7   O    110.90  3.000
 RXN  H5   C7   C8   111.48  3.000
 RXN  H4   C7   C8   108.65  3.000
 RXN  O    C7   C8   112.22  3.000
 RXN  H6   C8   N1   106.28  3.000
 RXN  H6   C8   C23  107.25  3.000
 RXN  N1   C8   C23  111.04  3.000
 RXN  H6   C8   C7   107.88  3.000
 RXN  C23  C8   C7   113.05  3.000
 RXN  N1   C8   C7   110.99  3.000
 RXN  H8   C9   H7   107.44  3.000
 RXN  H8   C9   N1   108.42  3.000
 RXN  H7   C9   N1   109.49  3.000
 RXN  H8   C9   C10  109.41  3.000
 RXN  H7   C9   C10  109.19  3.000
 RXN  N1   C9   C10  112.75  3.000
 RXN  H10  C10  H9   107.63  3.000
 RXN  H10  C10  C11  110.64  3.000
 RXN  H9   C10  C11  112.15  3.000
 RXN  H10  C10  C9   110.08  3.000
 RXN  H9   C10  C9   109.14  3.000
 RXN  C11  C10  C9   107.20  3.000
 RXN  C20  C11  C12  104.16  3.000
 RXN  C12  C11  C10  120.12  3.000
 RXN  C20  C11  C10  135.68  3.000
 RXN  N2   C12  C22  124.16  3.000
 RXN  C22  C12  C11  123.69  3.000
 RXN  N2   C12  C11  111.98  3.000
 RXN  C19  C14  C15  119.29  3.000
 RXN  C19  C14  C13  120.21  3.000
 RXN  C15  C14  C13  120.50  3.000
 RXN  H13  C15  C16  119.88  3.000
 RXN  H13  C15  C14  119.68  3.000
 RXN  C16  C15  C14  120.44  3.000
 RXN  H14  C16  C17  120.20  3.000
 RXN  H14  C16  C15  119.77  3.000
 RXN  C17  C16  C15  120.03  3.000
 RXN  H15  C17  C18  120.08  3.000
 RXN  H15  C17  C16  120.15  3.000
 RXN  C18  C17  C16  119.77  3.000
 RXN  H16  C18  C19  119.82  3.000
 RXN  H16  C18  C17  120.05  3.000
 RXN  C19  C18  C17  120.13  3.000
 RXN  C23  N    C    118.19  3.000
 RXN  C    N    C1   119.09  3.000
 RXN  C23  N    C1   122.60  3.000
 RXN  H19  C    H18  108.65  3.000
 RXN  H19  C    H17  108.93  3.000
 RXN  H18  C    H17  108.24  3.000
 RXN  H19  C    N    111.76  3.000
 RXN  H18  C    N    110.13  3.000
 RXN  H17  C    N    109.06  3.000
 RXN  C7   O    C6   115.44  3.000
 RXN  H20  C19  C18  119.54  3.000
 RXN  H20  C19  C14  120.12  3.000
 RXN  C18  C19  C14  120.33  3.000
 RXN  N3   C20  C21  126.52  3.000
 RXN  C21  C20  C11  127.32  3.000
 RXN  N3   C20  C11  106.16  3.000
 RXN  N4   C21  C20  116.18  3.000
 RXN  N4   C21  O1   124.04  3.000
 RXN  C20  C21  O1   119.77  3.000
 RXN  N1   C22  C12  113.27  3.000
 RXN  N1   C22  O2   124.18  3.000
 RXN  C12  C22  O2   122.49  3.000
 RXN  N    C23  O3   121.62  3.000
 RXN  N    C23  C8   116.15  3.000
 RXN  O3   C23  C8   122.18  3.000
 RXN  C22  N1   C9   121.40  3.000
 RXN  C22  N1   C8   118.66  3.000
 RXN  C9   N1   C8   119.57  3.000
 RXN  N3   N2   C12  105.15  3.000
 RXN  N2   N3   C20  112.53  3.000
 RXN  N2   N3   C13  118.71  3.000
 RXN  C20  N3   C13  127.96  3.000
 RXN  H22  N4   H21  116.58  3.000
 RXN  H22  N4   C21  122.10  3.000
 RXN  H21  N4   C21  119.50  3.000
 RXN  H12  C13  H11  106.99  3.000
 RXN  H12  C13  N3   105.53  3.000
 RXN  H11  C13  N3   110.20  3.000
 RXN  H12  C13  C14  111.15  3.000
 RXN  H11  C13  C14  110.87  3.000
 RXN  N3   C13  C14  111.87  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
 RXN  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 RXN  CONST_02  C5   C4   C3   C2      0.00   0.0  0
 RXN  CONST_03  C6   C5   C4   C3      0.00   0.0  0
 RXN  CONST_04  N2   N3   C20  C11     0.00   0.0  0
 RXN  CONST_05  N3   N2   C12  C11     0.00   0.0  0
 RXN  CONST_06  C20  N3   N2   C12     0.00   0.0  0
 RXN  CONST_07  N3   C20  C11  C12     0.00   0.0  0
 RXN  CONST_08  C17  C16  C15  C14     0.00   0.0  0
 RXN  CONST_09  C17  C18  C19  C14     0.00   0.0  0
 RXN  CONST_10  C18  C17  C16  C15     0.00   0.0  0
 RXN  CONST_11  C18  C19  C14  C15     0.00   0.0  0
 RXN  CONST_12  C19  C18  C17  C16     0.00   0.0  0
 RXN  CONST_13  C19  C14  C15  C16     0.00   0.0  0
 RXN  CONST_14  N2   C12  C11  C20     0.00   0.0  0
 RXN  CONST_15  C12  C22  N1   C8    180.00   0.0  0
 RXN  CONST_16  C12  C22  N1   C9      0.00   0.0  0
 RXN  CONST_17  CL   C4   C3   C2    180.00   0.0  0
 RXN  CONST_18  CL   C4   C5   C6    180.00   0.0  0
 RXN  CONST_19  C21  C20  C11  C10     0.00   0.0  0
 RXN  CONST_20  C13  N3   C20  C11   180.00   0.0  0
 RXN  CONST_21  C13  N3   N2   C12   180.00   0.0  0
 RXN  CONST_22  C21  C20  C11  C12   180.00   0.0  0
 RXN  CONST_23  C16  C15  C14  C13   180.00   0.0  0
 RXN  CONST_24  C18  C19  C14  C13   180.00   0.0  0
 RXN  CONST_25  N2   N3   C20  C21   180.00   0.0  0
 RXN  CONST_26  C9   N1   C22  O2    180.00   0.0  0
 RXN  CONST_27  C8   N1   C22  O2      0.00   0.0  0
 RXN  CONST_28  H2   C3   C2   C1    180.00   0.0  0
 RXN  CONST_29  H3   C5   C4   C3    180.00   0.0  0
 RXN  CONST_30  H1   C2   C3   C4    180.00   0.0  0
 RXN  CONST_31  H14  C16  C15  C14   180.00   0.0  0
 RXN  CONST_32  H16  C18  C19  C14   180.00   0.0  0
 RXN  CONST_33  H15  C17  C16  C15   180.00   0.0  0
 RXN  CONST_34  H20  C19  C14  C15   180.00   0.0  0
 RXN  CONST_35  H13  C15  C16  C17   180.00   0.0  0
 RXN  CONST_36  H21  N4   C21  C20   180.00   0.0  0
 RXN  CONST_37  H22  N4   C21  C20     0.00   0.0  0
 RXN  Var_01    C10  C9   N1   C8   -139.85  30.0  1
 RXN  Var_02    C20  C11  C10  C9   -154.50  30.0  1
 RXN  Var_03    N1   C22  C12  C11   -13.20  30.0  1
 RXN  Var_04    N1   C9   C10  C11   -51.02  30.0  1
 RXN  Var_05    C20  N3   C13  C14    60.80  30.0  2
 RXN  Var_06    N3   C13  C14  C15  -121.34  30.0  2
 RXN  Var_07    N3   C20  C21  O1   -137.49  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 RXN  chir_01  C8  N1  C7  C23  negativ

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
 RXN  plan-1  C14  0.020
 RXN  plan-1  C15  0.020
 RXN  plan-1  C16  0.020
 RXN  plan-1  C17  0.020
 RXN  plan-1  C18  0.020
 RXN  plan-1  C19  0.020
 RXN  plan-1  H13  0.020
 RXN  plan-1  H14  0.020
 RXN  plan-1  H15  0.020
 RXN  plan-1  H16  0.020
 RXN  plan-1  H20  0.020
 RXN  plan-1  C13  0.020
 RXN  plan-2  C10  0.020
 RXN  plan-2  C11  0.020
 RXN  plan-2  C12  0.020
 RXN  plan-2  C20  0.020
 RXN  plan-2  C21  0.020
 RXN  plan-2  C22  0.020
 RXN  plan-2  N2   0.020
 RXN  plan-2  N3   0.020
 RXN  plan-2  C13  0.020
 RXN  plan-3  C1   0.020
 RXN  plan-3  C2   0.020
 RXN  plan-3  C3   0.020
 RXN  plan-3  C4   0.020
 RXN  plan-3  C5   0.020
 RXN  plan-3  C6   0.020
 RXN  plan-3  N    0.020
 RXN  plan-3  O    0.020
 RXN  plan-3  CL   0.020
 RXN  plan-3  H1   0.020
 RXN  plan-3  H2   0.020
 RXN  plan-3  H3   0.020
 RXN  plan-4  O1   0.020
 RXN  plan-4  C20  0.020
 RXN  plan-4  C21  0.020
 RXN  plan-4  N4   0.020
 RXN  plan-4  H21  0.020
 RXN  plan-4  H22  0.020
 RXN  plan-5  C1   0.020
 RXN  plan-5  C8   0.020
 RXN  plan-5  N    0.020
 RXN  plan-5  C    0.020
 RXN  plan-5  C23  0.020
 RXN  plan-5  O3   0.020
 RXN  plan-6  O2   0.020
 RXN  plan-6  C8   0.020
 RXN  plan-6  C9   0.020
 RXN  plan-6  C12  0.020
 RXN  plan-6  C22  0.020
 RXN  plan-6  N1   0.020

