# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 19:23:35 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: (3S)-3-(2-benzyl-3-chloro-7-oxo-2,4,5,7-tetrahydro-6H-pyrazolo[3,4-c]pyridin-6-yl)-5-methyl-4-oxo-2,3,4,5-tetrahydro-1,5-benzoxazepine-8-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)[C@H](COc2cc(ccc12)C#N)N3CCc4c(Cl)n(Cc5ccccc5)nc4C3=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
 EJP  EJP  (3S)-3-(2-benzyl-3-chloro-7-oxo-2,4,5,7-tetrahydro-6H-pyrazolo[3,4-c]pyridin-6-yl)-5-methyl-4-oxo-2,3,4,5-tetrahydro-1,5-benzoxazepine-8-carbonitrile  ligand  53  33  .  2021-08-08  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_EJP
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
 EJP  N1   N   NS    0  -0.249  -8.9007   1.9936  -0.1889
 EJP  N3   N   NR5   0  -0.290   3.7447   0.7916  -0.8885
 EJP  C4   C   CR16  0  -0.240   6.2301  -2.5614   0.2770
 EJP  C5   C   CR16  0  -0.244  -6.5998  -0.1463   1.3258
 EJP  C6   C   CR16  0  -0.298   7.0724   0.0701   0.0416
 EJP  C7   C   CR16  0  -0.282   5.4857  -1.6584  -0.4668
 EJP  C8   C   CR16  0  -0.293  -5.4647  -0.9155   1.4953
 EJP  C10  C   CR6   0   0.002  -6.7905   0.5473   0.1323
 EJP  C13  C   CR6   0   0.284  -4.5120  -1.0074   0.4832
 EJP  C15  C   CR56  0   0.162   1.6802   0.4657  -0.7201
 EJP  C17  C   CR6   0   0.568   0.3256  -0.0585  -0.9593
 EJP  C20  C   C     0  -0.306  -0.3529   1.7533   0.5831
 EJP  C21  C   CH2   0  -0.151  -2.6254   0.2274  -1.6048
 EJP  C22  C   CH1   0  -0.309  -1.9898   0.0467  -0.2147
 EJP  C24  C   CH2   0  -0.404   5.0942   0.6443  -1.4009
 EJP  C1   C   CSP   0   0.059  -7.9576   1.3470  -0.0472
 EJP  C2   C   CR16  0  -0.262   7.4014  -2.1513   0.9035
 EJP  C3   C   CR16  0  -0.242   7.8230  -0.8353   0.7819
 EJP  C9   C   CR16  0  -0.327  -5.8485   0.4643  -0.8910
 EJP  C11  C   CR56  0  -0.058   2.0095   1.2781   0.3682
 EJP  C12  C   CR6   0   0.108   5.9025  -0.3347  -0.5894
 EJP  C14  C   CR6   0   0.340  -4.7260  -0.3231  -0.7188
 EJP  C16  C   CR5   0   0.267   3.3579   1.4589   0.2257
 EJP  C18  C   C     0   0.592  -2.1064  -1.3674   0.3637
 EJP  C19  C   C     0  -0.517   0.9721   1.7151   1.3325
 EJP  N2   N   N     0  -0.279   2.7303   0.1719  -1.4681
 EJP  N4   N   NT    0  -0.551  -3.3725  -1.8092   0.6366
 EJP  N5   N   NR6   0  -0.515  -0.6255   0.5212  -0.1738
 EJP  O1   O   O     0  -0.476   0.1069  -0.9467  -1.7643
 EJP  O2   O   O     0  -0.439  -1.1362  -2.0336   0.6496
 EJP  O3   O   O2    0  -0.484  -3.8451  -0.4832  -1.7338
 EJP  CL1  CL  CL    0  -0.073   4.4456   2.3460   1.1794
 EJP  H1   H   HCR6  0   0.259   5.8986  -3.5880   0.3655
 EJP  H2   H   HCR6  0   0.289  -7.3298  -0.0784   2.1199
 EJP  H3   H   HCR6  0   0.257   7.4023   1.0984  -0.0448
 EJP  H4   H   HCR6  0   0.256   4.5758  -1.9881  -0.9544
 EJP  H5   H   HCR6  0   0.296  -5.3178  -1.4418   2.4288
 EJP  H6   H   H     0   0.274  -1.1639   1.8940   1.2937
 EJP  H7   H   H     0   0.260  -0.3634   2.6113  -0.0954
 EJP  H8   H   HCH2  0   0.248  -2.7813   1.2980  -1.7744
 EJP  H9   H   HCH2  0   0.268  -1.9802  -0.1596  -2.3855
 EJP  H10  H   HCH1  0   0.315  -2.5459   0.6868   0.4765
 EJP  H11  H   HCH2  0   0.305   4.9895   0.3116  -2.4324
 EJP  H12  H   HCH2  0   0.293   5.5738   1.6229  -1.4210
 EJP  H13  H   HCR6  0   0.259   7.9815  -2.8564   1.4847
 EJP  H14  H   HCR6  0   0.259   8.7335  -0.5088   1.2672
 EJP  H15  H   HCR6  0   0.295  -5.9993   0.9851  -1.8276
 EJP  H16  H   H     0   0.271   1.1768   2.7057   1.7396
 EJP  H17  H   H     0   0.269   0.9158   1.0213   2.1759
 EJP  H18  H   HCH3  0   0.271  -2.8694  -3.8313   0.8467
 EJP  H19  H   HCH3  0   0.254  -3.2435  -3.0216   2.3740
 EJP  H20  H   HCH3  0   0.261  -4.5378  -3.4287   1.2338
 EJP  C23  C   CH3   0  -0.551  -3.5092  -3.0906   1.3189

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
 EJP  C4   C2   aromatic  1.390  0.020  1.390
 EJP  C4   C7   aromatic  1.387  0.020  1.387
 EJP  C2   C3   aromatic  1.387  0.020  1.387
 EJP  C7   C12  aromatic  1.393  0.020  1.393
 EJP  C3   C6   aromatic  1.390  0.020  1.390
 EJP  C12  C6   aromatic  1.389  0.020  1.389
 EJP  C12  C24  single    1.507  0.020  1.507
 EJP  C24  N3   single    1.451  0.020  1.451
 EJP  N2   N3   aromatic  1.322  0.020  1.322
 EJP  N2   C15  aromatic  1.322  0.020  1.322
 EJP  N3   C16  aromatic  1.355  0.020  1.355
 EJP  O1   C17  double    1.218  0.020  1.218
 EJP  C15  C17  single    1.472  0.020  1.472
 EJP  C15  C11  aromatic  1.397  0.020  1.397
 EJP  C16  CL1  single    1.697  0.020  1.697
 EJP  C16  C11  aromatic  1.368  0.020  1.368
 EJP  C17  N5   single    1.363  0.020  1.363
 EJP  N1   C1   triple    1.152  0.020  1.152
 EJP  C11  C19  single    1.482  0.020  1.482
 EJP  C1   C10  single    1.426  0.020  1.426
 EJP  N5   C20  single    1.471  0.020  1.471
 EJP  N5   C22  single    1.445  0.020  1.445
 EJP  C21  C22  single    1.539  0.020  1.539
 EJP  C21  O3   single    1.418  0.020  1.418
 EJP  C20  C19  single    1.523  0.020  1.523
 EJP  C9   C10  aromatic  1.393  0.020  1.393
 EJP  C9   C14  aromatic  1.382  0.020  1.382
 EJP  C10  C5   aromatic  1.393  0.020  1.393
 EJP  C22  C18  single    1.532  0.020  1.532
 EJP  O3   C14  single    1.353  0.020  1.353
 EJP  C5   C8   aromatic  1.382  0.020  1.382
 EJP  C14  C13  aromatic  1.400  0.020  1.400
 EJP  C8   C13  aromatic  1.393  0.020  1.393
 EJP  C13  N4   single    1.402  0.020  1.402
 EJP  C18  N4   single    1.368  0.020  1.368
 EJP  C18  O2   double    1.211  0.020  1.211
 EJP  N4   C23  single    1.458  0.020  1.458
 EJP  C4   H1   single    0.930  0.020  1.080
 EJP  C5   H2   single    0.930  0.020  1.080
 EJP  C6   H3   single    0.930  0.020  1.080
 EJP  C7   H4   single    0.930  0.020  1.080
 EJP  C8   H5   single    0.930  0.020  1.080
 EJP  C20  H6   single    0.970  0.020  1.090
 EJP  C20  H7   single    0.970  0.020  1.090
 EJP  C21  H8   single    0.970  0.020  1.090
 EJP  C21  H9   single    0.970  0.020  1.090
 EJP  C22  H10  single    0.970  0.020  1.090
 EJP  C24  H11  single    0.970  0.020  1.090
 EJP  C24  H12  single    0.970  0.020  1.090
 EJP  C2   H13  single    0.930  0.020  1.080
 EJP  C3   H14  single    0.930  0.020  1.080
 EJP  C9   H15  single    0.930  0.020  1.080
 EJP  C19  H16  single    0.970  0.020  1.090
 EJP  C19  H17  single    0.970  0.020  1.090
 EJP  C23  H18  single    0.970  0.020  1.090
 EJP  C23  H19  single    0.970  0.020  1.090
 EJP  C23  H20  single    0.970  0.020  1.090

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
 EJP  N2   N3   C16  111.85  3.000
 EJP  C16  N3   C24  127.29  3.000
 EJP  N2   N3   C24  120.73  3.000
 EJP  H1   C4   C2   120.07  3.000
 EJP  H1   C4   C7   119.81  3.000
 EJP  C2   C4   C7   120.13  3.000
 EJP  H2   C5   C10  120.37  3.000
 EJP  H2   C5   C8   119.99  3.000
 EJP  C10  C5   C8   119.64  3.000
 EJP  H3   C6   C12  119.78  3.000
 EJP  H3   C6   C3   119.76  3.000
 EJP  C12  C6   C3   120.46  3.000
 EJP  H4   C7   C12  120.04  3.000
 EJP  H4   C7   C4   119.60  3.000
 EJP  C12  C7   C4   120.36  3.000
 EJP  H5   C8   C13  120.14  3.000
 EJP  H5   C8   C5   119.23  3.000
 EJP  C13  C8   C5   120.63  3.000
 EJP  C9   C10  C1   119.61  3.000
 EJP  C9   C10  C5   120.46  3.000
 EJP  C1   C10  C5   119.93  3.000
 EJP  N4   C13  C14  119.87  3.000
 EJP  N4   C13  C8   120.94  3.000
 EJP  C14  C13  C8   119.15  3.000
 EJP  N2   C15  C11  112.49  3.000
 EJP  C11  C15  C17  123.40  3.000
 EJP  N2   C15  C17  124.04  3.000
 EJP  O1   C17  N5   124.44  3.000
 EJP  N5   C17  C15  113.39  3.000
 EJP  O1   C17  C15  122.14  3.000
 EJP  H7   C20  H6   107.25  3.000
 EJP  H7   C20  N5   109.63  3.000
 EJP  H6   C20  N5   107.84  3.000
 EJP  H7   C20  C19  109.47  3.000
 EJP  H6   C20  C19  109.30  3.000
 EJP  N5   C20  C19  113.16  3.000
 EJP  H9   C21  H8   108.79  3.000
 EJP  H9   C21  O3   105.52  3.000
 EJP  H8   C21  O3   110.70  3.000
 EJP  H9   C21  C22  111.27  3.000
 EJP  H8   C21  C22  108.27  3.000
 EJP  O3   C21  C22  112.25  3.000
 EJP  H10  C22  N5   105.66  3.000
 EJP  H10  C22  C18  105.24  3.000
 EJP  N5   C22  C18  111.36  3.000
 EJP  H10  C22  C21  106.98  3.000
 EJP  C18  C22  C21  114.70  3.000
 EJP  N5   C22  C21  112.14  3.000
 EJP  H12  C24  H11  107.40  3.000
 EJP  H12  C24  C12  110.93  3.000
 EJP  H11  C24  C12  111.30  3.000
 EJP  H12  C24  N3   108.94  3.000
 EJP  H11  C24  N3   106.03  3.000
 EJP  C12  C24  N3   112.00  3.000
 EJP  C10  C1   N1   180.00  3.000
 EJP  H13  C2   C3   120.14  3.000
 EJP  H13  C2   C4   120.09  3.000
 EJP  C3   C2   C4   119.76  3.000
 EJP  H14  C3   C2   120.17  3.000
 EJP  H14  C3   C6   119.79  3.000
 EJP  C2   C3   C6   120.04  3.000
 EJP  H15  C9   C14  119.68  3.000
 EJP  H15  C9   C10  120.85  3.000
 EJP  C14  C9   C10  119.44  3.000
 EJP  C19  C11  C16  135.95  3.000
 EJP  C19  C11  C15  120.87  3.000
 EJP  C16  C11  C15  103.18  3.000
 EJP  C24  C12  C7   120.28  3.000
 EJP  C24  C12  C6   120.46  3.000
 EJP  C7   C12  C6   119.26  3.000
 EJP  O3   C14  C9   120.17  3.000
 EJP  O3   C14  C13  119.12  3.000
 EJP  C9   C14  C13  120.66  3.000
 EJP  CL1  C16  C11  129.97  3.000
 EJP  C11  C16  N3   107.57  3.000
 EJP  CL1  C16  N3   122.45  3.000
 EJP  O2   C18  N4   121.10  3.000
 EJP  O2   C18  C22  122.40  3.000
 EJP  N4   C18  C22  116.33  3.000
 EJP  H17  C19  H16  107.35  3.000
 EJP  H17  C19  C11  110.53  3.000
 EJP  H16  C19  C11  112.29  3.000
 EJP  H17  C19  C20  110.53  3.000
 EJP  H16  C19  C20  108.93  3.000
 EJP  C11  C19  C20  107.23  3.000
 EJP  C15  N2   N3   104.90  3.000
 EJP  C23  N4   C18  117.63  3.000
 EJP  C23  N4   C13  118.53  3.000
 EJP  C18  N4   C13  123.07  3.000
 EJP  C22  N5   C20  117.67  3.000
 EJP  C22  N5   C17  120.19  3.000
 EJP  C20  N5   C17  121.56  3.000
 EJP  C14  O3   C21  115.63  3.000
 EJP  H20  C23  H19  109.05  3.000
 EJP  H20  C23  H18  108.15  3.000
 EJP  H19  C23  H18  108.67  3.000
 EJP  H20  C23  N4   109.01  3.000
 EJP  H19  C23  N4   111.98  3.000
 EJP  H18  C23  N4   109.90  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
 EJP  CONST_01  C11  C15  N2   N3      0.00   0.0  0
 EJP  CONST_02  C15  C11  C16  N3      0.00   0.0  0
 EJP  CONST_03  C6   C3   C2   C4      0.00   0.0  0
 EJP  CONST_04  C6   C12  C7   C4      0.00   0.0  0
 EJP  CONST_05  C14  C9   C10  C5      0.00   0.0  0
 EJP  CONST_06  C3   C2   C4   C7      0.00   0.0  0
 EJP  CONST_07  C3   C6   C12  C7      0.00   0.0  0
 EJP  CONST_08  C9   C10  C5   C8      0.00   0.0  0
 EJP  CONST_09  C13  C8   C5   C10     0.00   0.0  0
 EJP  CONST_10  C16  N3   N2   C15     0.00   0.0  0
 EJP  CONST_11  C12  C7   C4   C2      0.00   0.0  0
 EJP  CONST_12  C12  C6   C3   C2      0.00   0.0  0
 EJP  CONST_13  N2   N3   C16  C11     0.00   0.0  0
 EJP  CONST_14  N2   C15  C11  C16     0.00   0.0  0
 EJP  CONST_15  C20  N5   C17  C15     0.00   0.0  0
 EJP  CONST_16  C22  N5   C17  C15   180.00   0.0  0
 EJP  CONST_17  C24  C12  C7   C4    180.00   0.0  0
 EJP  CONST_18  C1   C10  C5   C8    180.00   0.0  0
 EJP  CONST_19  C24  N3   N2   C15   180.00   0.0  0
 EJP  CONST_20  CL1  C16  C11  C15   180.00   0.0  0
 EJP  CONST_21  C3   C6   C12  C24   180.00   0.0  0
 EJP  CONST_22  C11  C16  N3   C24   180.00   0.0  0
 EJP  CONST_23  C14  C9   C10  C1    180.00   0.0  0
 EJP  CONST_24  CL1  C16  C11  C19     0.00   0.0  0
 EJP  CONST_25  CL1  C16  N3   N2    180.00   0.0  0
 EJP  CONST_26  O1   C17  N5   C20   180.00   0.0  0
 EJP  CONST_27  O1   C17  N5   C22     0.00   0.0  0
 EJP  CONST_28  H14  C3   C2   C4    180.00   0.0  0
 EJP  CONST_29  H15  C9   C10  C5    180.00   0.0  0
 EJP  CONST_30  H13  C2   C3   C6    180.00   0.0  0
 EJP  CONST_31  H4   C7   C12  C6    180.00   0.0  0
 EJP  CONST_32  H3   C6   C12  C7    180.00   0.0  0
 EJP  CONST_33  H5   C8   C5   C10   180.00   0.0  0
 EJP  CONST_34  H2   C5   C8   C13   180.00   0.0  0
 EJP  CONST_35  H1   C4   C2   C3    180.00   0.0  0
 EJP  Var_01    C20  C19  C11  C15   -27.72  30.0  1
 EJP  Var_02    C19  C20  N5   C17   -46.43  30.0  1
 EJP  Var_03    N5   C17  C15  C11    11.76  30.0  1
 EJP  Var_04    N5   C20  C19  C11    49.67  30.0  1
 EJP  Var_05    C7   C12  C24  N3     59.88  30.0  1
 EJP  Var_06    N2   N3   C24  C12  -100.97  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
 EJP  chir_01  C22  N5  C21  C18  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
 EJP  plan-1  C4   0.020
 EJP  plan-1  C6   0.020
 EJP  plan-1  C7   0.020
 EJP  plan-1  C24  0.020
 EJP  plan-1  C2   0.020
 EJP  plan-1  C3   0.020
 EJP  plan-1  C12  0.020
 EJP  plan-1  H1   0.020
 EJP  plan-1  H3   0.020
 EJP  plan-1  H4   0.020
 EJP  plan-1  H13  0.020
 EJP  plan-1  H14  0.020
 EJP  plan-2  N3   0.020
 EJP  plan-2  C15  0.020
 EJP  plan-2  C17  0.020
 EJP  plan-2  C24  0.020
 EJP  plan-2  C11  0.020
 EJP  plan-2  C16  0.020
 EJP  plan-2  C19  0.020
 EJP  plan-2  N2   0.020
 EJP  plan-2  CL1  0.020
 EJP  plan-3  N1   0.020
 EJP  plan-3  C5   0.020
 EJP  plan-3  C8   0.020
 EJP  plan-3  C10  0.020
 EJP  plan-3  C13  0.020
 EJP  plan-3  C1   0.020
 EJP  plan-3  C9   0.020
 EJP  plan-3  C14  0.020
 EJP  plan-3  N4   0.020
 EJP  plan-3  O3   0.020
 EJP  plan-3  H2   0.020
 EJP  plan-3  H5   0.020
 EJP  plan-3  H15  0.020
 EJP  plan-4  C13  0.020
 EJP  plan-4  C22  0.020
 EJP  plan-4  C18  0.020
 EJP  plan-4  N4   0.020
 EJP  plan-4  O2   0.020
 EJP  plan-4  C23  0.020
 EJP  plan-5  C15  0.020
 EJP  plan-5  C17  0.020
 EJP  plan-5  C20  0.020
 EJP  plan-5  C22  0.020
 EJP  plan-5  N5   0.020
 EJP  plan-5  O1   0.020

