# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 21:09:58 2020
#   Inital geometry file: a 158 line input string
#   Ligand name: 3-[2-[(3~{Z},6~{R})-6-[(5-chloranyl-2-methoxy-phenyl)methyl]-3-(dimethylhydrazinylidene)-7-oxidanylidene-1,4-diazepan-1-yl]ethanoylamino]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(Cl)cc1C[C@@H]2CNC(/CN(CC(=O)Nc3cccc(c3)C(O)=O)C2=O)=N\N(C)C
#
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
 8R3  8R3  '3-[2-[(3~{Z},6~{R})-6-[(5-chloranyl-2-methoxy-phenyl)methyl]-3-(dimethylhydrazinylidene)-7-oxidanylidene-1,4-diazepan-1-yl]ethanoylamino]benzoic acid'  ligand  63  35  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8R3
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
 8R3  C1   C   C     0   0.567  -0.3769  -0.2030  -1.2407
 8R3  O2   O   O     0  -0.474   0.3556   0.5057  -1.9124
 8R3  O32  O   OH1   0  -0.592   9.3767   1.0717  -0.0591
 8R3  O33  O   O     0  -0.436   8.4644  -0.1988  -1.6466
 8R3  C26  C   CR6   0  -0.069   7.0836   0.6185   0.1113
 8R3  C25  C   CR16  0  -0.369   5.9572  -0.0264  -0.3821
 8R3  C27  C   CR16  0  -0.280   6.9922   1.3970   1.2631
 8R3  C28  C   CR16  0  -0.232   5.7674   1.5101   1.8985
 8R3  C29  C   CR16  0  -0.304   4.6360   0.8690   1.4149
 8R3  C21  C   CR6   0   0.410   4.7262   0.0893   0.2599
 8R3  N20  N   NH1   0  -0.753   3.6540  -0.6036  -0.3080
 8R3  C19  C   C     0   0.558   2.3501  -0.6175   0.0599
 8R3  O30  O   O     0  -0.455   1.8764   0.0293   0.9725
 8R3  C17  C   CH2   0  -0.472   1.5027  -1.5801  -0.7628
 8R3  N16  N   NT    0  -0.444   0.0974  -1.3093  -0.6157
 8R3  C15  C   CH2   0  -0.411  -0.5921  -1.9078   0.5157
 8R3  C13  C   C     0   0.477  -1.8166  -2.7169   0.1953
 8R3  N14  N   N     0  -0.367  -1.9031  -3.8352   0.8318
 8R3  N62  N   NT    0  -0.343  -3.1393  -4.5006   0.6044
 8R3  C68  C   CH3   0  -0.510  -4.0319  -4.2298   1.7183
 8R3  C63  C   CH3   0  -0.496  -2.8767  -5.9191   0.4836
 8R3  N12  N   NH1   0  -0.628  -2.7832  -2.2120  -0.5927
 8R3  C11  C   CH2   0  -0.265  -2.6849  -1.1530  -1.5685
 8R3  C3   C   CH1   0  -0.419  -1.8704   0.0722  -1.1646
 8R3  C4   C   CH2   0  -0.516  -2.3286   0.7533   0.1442
 8R3  C5   C   CR6   0   0.031  -3.5483   1.6084  -0.0780
 8R3  C10  C   CR16  0  -0.247  -3.3865   2.9055  -0.5431
 8R3  C6   C   CR6   0   0.355  -4.8488   1.1282   0.1420
 8R3  O23  O   O2    0  -0.460  -4.9529  -0.1317   0.5977
 8R3  C24  C   CH3   0  -0.438  -6.2362  -0.6973   0.7636
 8R3  C7   C   CR16  0  -0.381  -5.9448   1.9499  -0.1133
 8R3  C8   C   CR16  0  -0.212  -5.7650   3.2439  -0.5818
 8R3  C9   C   CR6   0  -0.054  -4.4837   3.7148  -0.7936
 8R3  CL2  CL  CL    0  -0.142  -4.2400   5.3332  -1.3732
 8R3  H1   H   HOH1  0   0.489  10.1835   0.9338  -0.5775
 8R3  H2   H   HCR6  0   0.280   6.0385  -0.6308  -1.2774
 8R3  H3   H   HCR6  0   0.269   7.8532   1.9117   1.6642
 8R3  H4   H   HCR6  0   0.270   5.6835   2.1115   2.7938
 8R3  H5   H   HCR6  0   0.290   3.7004   0.9813   1.9370
 8R3  H6   H   HNH1  0   0.422   3.8924  -1.1618  -1.1148
 8R3  H7   H   HCH2  0   0.296   1.7890  -1.5457  -1.8148
 8R3  H8   H   HCH2  0   0.315   1.7047  -2.5969  -0.4198
 8R3  H9   H   HCH2  0   0.297   0.0975  -2.5836   1.0142
 8R3  H10  H   HCH2  0   0.286  -0.8442  -1.1485   1.2594
 8R3  H12  H   HCH3  0   0.233  -4.2237  -3.1587   1.7921
 8R3  H13  H   HCH3  0   0.230  -4.9861  -4.7296   1.5466
 8R3  H14  H   HCH3  0   0.202  -3.6303  -4.5737   2.6812
 8R3  H15  H   HCH3  0   0.193  -2.3946  -6.3433   1.3754
 8R3  H16  H   HCH3  0   0.227  -3.8173  -6.4463   0.3212
 8R3  H17  H   HCH3  0   0.232  -2.2321  -6.1073  -0.3746
 8R3  H18  H   HCH2  0   0.250  -2.2859  -1.5282  -2.5181
 8R3  H19  H   HCH2  0   0.261  -3.7031  -0.8259  -1.7778
 8R3  H20  H   HCH1  0   0.298  -2.0300   0.7950  -1.9680
 8R3  H21  H   HCH2  0   0.269  -2.5214   0.0166   0.9216
 8R3  H22  H   HCH2  0   0.275  -1.5234   1.3922   0.5142
 8R3  H23  H   HCR6  0   0.272  -2.3854   3.2825  -0.7139
 8R3  H24  H   HCH3  0   0.256  -6.0801  -1.7215   1.0924
 8R3  H25  H   HCH3  0   0.231  -6.8225  -0.1718   1.5220
 8R3  H26  H   HCH3  0   0.231  -6.8009  -0.7124  -0.1722
 8R3  H27  H   HCR6  0   0.289  -6.9553   1.6019   0.0491
 8R3  H28  H   HCR6  0   0.280  -6.6264   3.8689  -0.7743
 8R3  H30  H   HNH1  0   0.392  -3.5404  -2.8675  -0.7355
 8R3  C31  C   C     0   0.540   8.3592   0.4452  -0.6304

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
 8R3  C8   C7   aromatic  1.388  0.020  1.388
 8R3  C8   C9   aromatic  1.381  0.020  1.381
 8R3  C7   C6   aromatic  1.393  0.020  1.393
 8R3  C24  O23  single    1.412  0.020  1.412
 8R3  CL2  C9   single    1.736  0.020  1.736
 8R3  C9   C10  aromatic  1.386  0.020  1.386
 8R3  C6   O23  single    1.344  0.020  1.344
 8R3  C6   C5   aromatic  1.404  0.020  1.404
 8R3  C10  C5   aromatic  1.387  0.020  1.387
 8R3  C5   C4   single    1.506  0.020  1.506
 8R3  C4   C3   single    1.545  0.020  1.545
 8R3  C63  N62  single    1.448  0.020  1.448
 8R3  C3   C11  single    1.526  0.020  1.526
 8R3  C3   C1   single    1.521  0.020  1.521
 8R3  C11  N12  single    1.443  0.020  1.443
 8R3  N12  C13  single    1.345  0.020  1.345
 8R3  N62  N14  single    1.422  0.020  1.422
 8R3  N62  C68  single    1.453  0.020  1.453
 8R3  C13  N14  double    1.290  0.020  1.290
 8R3  C13  C15  single    1.502  0.020  1.502
 8R3  C15  N16  single    1.454  0.020  1.454
 8R3  C1   N16  single    1.356  0.020  1.356
 8R3  C1   O2   double    1.221  0.020  1.221
 8R3  O33  C31  double    1.208  0.020  1.208
 8R3  N16  C17  single    1.439  0.020  1.439
 8R3  O30  C19  double    1.215  0.020  1.215
 8R3  C31  O32  single    1.324  0.020  1.324
 8R3  C31  C26  single    1.486  0.020  1.486
 8R3  C19  C17  single    1.524  0.020  1.524
 8R3  C19  N20  single    1.355  0.020  1.355
 8R3  C25  C26  aromatic  1.388  0.020  1.388
 8R3  C25  C21  aromatic  1.393  0.020  1.393
 8R3  C26  C27  aromatic  1.393  0.020  1.393
 8R3  N20  C21  single    1.397  0.020  1.397
 8R3  C21  C29  aromatic  1.396  0.020  1.396
 8R3  C27  C28  aromatic  1.384  0.020  1.384
 8R3  C29  C28  aromatic  1.387  0.020  1.387
 8R3  O32  H1   single    0.850  0.020  0.980
 8R3  C25  H2   single    0.930  0.020  1.080
 8R3  C27  H3   single    0.930  0.020  1.080
 8R3  C28  H4   single    0.930  0.020  1.080
 8R3  C29  H5   single    0.930  0.020  1.080
 8R3  N20  H6   single    0.860  0.020  1.020
 8R3  C17  H7   single    0.970  0.020  1.090
 8R3  C17  H8   single    0.970  0.020  1.090
 8R3  C15  H9   single    0.970  0.020  1.090
 8R3  C15  H10  single    0.970  0.020  1.090
 8R3  C68  H12  single    0.970  0.020  1.090
 8R3  C68  H13  single    0.970  0.020  1.090
 8R3  C68  H14  single    0.970  0.020  1.090
 8R3  C63  H15  single    0.970  0.020  1.090
 8R3  C63  H16  single    0.970  0.020  1.090
 8R3  C63  H17  single    0.970  0.020  1.090
 8R3  C11  H18  single    0.970  0.020  1.090
 8R3  C11  H19  single    0.970  0.020  1.090
 8R3  C3   H20  single    0.970  0.020  1.090
 8R3  C4   H21  single    0.970  0.020  1.090
 8R3  C4   H22  single    0.970  0.020  1.090
 8R3  C10  H23  single    0.930  0.020  1.080
 8R3  C24  H24  single    0.970  0.020  1.090
 8R3  C24  H25  single    0.970  0.020  1.090
 8R3  C24  H26  single    0.970  0.020  1.090
 8R3  C7   H27  single    0.930  0.020  1.080
 8R3  C8   H28  single    0.930  0.020  1.080
 8R3  N12  H30  single    0.890  0.020  1.040

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
 8R3  C3   C1   N16  117.91  3.000
 8R3  N16  C1   O2   121.15  3.000
 8R3  C3   C1   O2   120.79  3.000
 8R3  H1   O32  C31  109.98  3.000
 8R3  C27  C26  C25  120.00  3.000
 8R3  C27  C26  C31  122.29  3.000
 8R3  C25  C26  C31  117.71  3.000
 8R3  H2   C25  C21  119.57  3.000
 8R3  H2   C25  C26  119.47  3.000
 8R3  C21  C25  C26  120.96  3.000
 8R3  H3   C27  C28  119.72  3.000
 8R3  H3   C27  C26  121.39  3.000
 8R3  C28  C27  C26  118.89  3.000
 8R3  H4   C28  C29  118.82  3.000
 8R3  H4   C28  C27  119.60  3.000
 8R3  C29  C28  C27  121.58  3.000
 8R3  H5   C29  C21  121.01  3.000
 8R3  H5   C29  C28  119.41  3.000
 8R3  C21  C29  C28  119.58  3.000
 8R3  N20  C21  C29  124.30  3.000
 8R3  C29  C21  C25  118.98  3.000
 8R3  N20  C21  C25  116.72  3.000
 8R3  H6   N20  C19  116.01  3.000
 8R3  H6   N20  C21  114.70  3.000
 8R3  C19  N20  C21  129.29  3.000
 8R3  C17  C19  O30  121.68  3.000
 8R3  C17  C19  N20  113.27  3.000
 8R3  O30  C19  N20  125.02  3.000
 8R3  H8   C17  H7   106.48  3.000
 8R3  H8   C17  N16  108.90  3.000
 8R3  H7   C17  N16  110.43  3.000
 8R3  H8   C17  C19  108.41  3.000
 8R3  H7   C17  C19  110.78  3.000
 8R3  N16  C17  C19  111.67  3.000
 8R3  C15  N16  C17  117.74  3.000
 8R3  C17  N16  C1   116.61  3.000
 8R3  C15  N16  C1   121.91  3.000
 8R3  H10  C15  H9   105.46  3.000
 8R3  H10  C15  C13  109.36  3.000
 8R3  H9   C15  C13  106.27  3.000
 8R3  H10  C15  N16  110.68  3.000
 8R3  H9   C15  N16  108.18  3.000
 8R3  C13  C15  N16  116.25  3.000
 8R3  N12  C13  N14  124.50  3.000
 8R3  N14  C13  C15  114.60  3.000
 8R3  N12  C13  C15  120.56  3.000
 8R3  N62  N14  C13  112.64  3.000
 8R3  C63  N62  C68  110.98  3.000
 8R3  C68  N62  N14  108.91  3.000
 8R3  C63  N62  N14  108.31  3.000
 8R3  H14  C68  H13  108.32  3.000
 8R3  H14  C68  H12  108.21  3.000
 8R3  H13  C68  H12  107.87  3.000
 8R3  H14  C68  N62  112.89  3.000
 8R3  H13  C68  N62  109.35  3.000
 8R3  H12  C68  N62  110.05  3.000
 8R3  H17  C63  H16  108.02  3.000
 8R3  H17  C63  H15  108.24  3.000
 8R3  H16  C63  H15  108.22  3.000
 8R3  H17  C63  N62  110.01  3.000
 8R3  H16  C63  N62  109.25  3.000
 8R3  H15  C63  N62  112.96  3.000
 8R3  H30  N12  C11  115.53  3.000
 8R3  H30  N12  C13  112.16  3.000
 8R3  C11  N12  C13  128.49  3.000
 8R3  H19  C11  H18  106.04  3.000
 8R3  H19  C11  C3   107.98  3.000
 8R3  H18  C11  C3   108.05  3.000
 8R3  H19  C11  N12  106.64  3.000
 8R3  H18  C11  N12  111.06  3.000
 8R3  C3   C11  N12  116.53  3.000
 8R3  H20  C3   C4   106.74  3.000
 8R3  H20  C3   C11  104.99  3.000
 8R3  C4   C3   C11  114.83  3.000
 8R3  H20  C3   C1   103.09  3.000
 8R3  C11  C3   C1   111.46  3.000
 8R3  C4   C3   C1   114.43  3.000
 8R3  H22  C4   H21  106.53  3.000
 8R3  H22  C4   C5   108.35  3.000
 8R3  H21  C4   C5   110.26  3.000
 8R3  H22  C4   C3   109.04  3.000
 8R3  H21  C4   C3   111.05  3.000
 8R3  C5   C4   C3   111.44  3.000
 8R3  C6   C5   C10  118.71  3.000
 8R3  C10  C5   C4   119.07  3.000
 8R3  C6   C5   C4   122.21  3.000
 8R3  H23  C10  C9   119.99  3.000
 8R3  H23  C10  C5   119.07  3.000
 8R3  C9   C10  C5   120.94  3.000
 8R3  C7   C6   O23  123.64  3.000
 8R3  O23  C6   C5   116.47  3.000
 8R3  C7   C6   C5   119.89  3.000
 8R3  C24  O23  C6   119.06  3.000
 8R3  H26  C24  H25  108.88  3.000
 8R3  H26  C24  H24  108.67  3.000
 8R3  H25  C24  H24  108.67  3.000
 8R3  H26  C24  O23  111.99  3.000
 8R3  H25  C24  O23  112.10  3.000
 8R3  H24  C24  O23  106.40  3.000
 8R3  H27  C7   C8   118.16  3.000
 8R3  H27  C7   C6   121.19  3.000
 8R3  C8   C7   C6   120.64  3.000
 8R3  H28  C8   C9   120.96  3.000
 8R3  H28  C8   C7   119.72  3.000
 8R3  C9   C8   C7   119.32  3.000
 8R3  CL2  C9   C8   119.94  3.000
 8R3  CL2  C9   C10  119.57  3.000
 8R3  C8   C9   C10  120.49  3.000
 8R3  C26  C31  O33  123.85  3.000
 8R3  C26  C31  O32  112.90  3.000
 8R3  O33  C31  O32  123.25  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
 8R3  CONST_01  C29  C21  C25  C26     0.00   0.0  0
 8R3  CONST_02  C29  C28  C27  C26     0.00   0.0  0
 8R3  CONST_03  C28  C27  C26  C25     0.00   0.0  0
 8R3  CONST_04  C28  C29  C21  C25     0.00   0.0  0
 8R3  CONST_05  C21  C25  C26  C27     0.00   0.0  0
 8R3  CONST_06  C21  C29  C28  C27     0.00   0.0  0
 8R3  CONST_07  C8   C7   C6   C5      0.00   0.0  0
 8R3  CONST_08  C8   C9   C10  C5      0.00   0.0  0
 8R3  CONST_09  C7   C8   C9   C10     0.00   0.0  0
 8R3  CONST_10  C7   C6   C5   C10     0.00   0.0  0
 8R3  CONST_11  C9   C8   C7   C6      0.00   0.0  0
 8R3  CONST_12  C9   C10  C5   C6      0.00   0.0  0
 8R3  CONST_13  C21  C25  C26  C31   180.00   0.0  0
 8R3  CONST_14  C28  C27  C26  C31   180.00   0.0  0
 8R3  CONST_15  N20  C21  C25  C26   180.00   0.0  0
 8R3  CONST_16  N20  C21  C29  C28   180.00   0.0  0
 8R3  CONST_17  C7   C6   C5   C4    180.00   0.0  0
 8R3  CONST_18  C9   C10  C5   C4    180.00   0.0  0
 8R3  CONST_19  CL2  C9   C10  C5    180.00   0.0  0
 8R3  CONST_20  O23  C6   C5   C10   180.00   0.0  0
 8R3  CONST_21  C8   C7   C6   O23   180.00   0.0  0
 8R3  CONST_22  CL2  C9   C8   C7    180.00   0.0  0
 8R3  CONST_23  H4   C28  C27  C26   180.00   0.0  0
 8R3  CONST_24  H3   C27  C26  C25   180.00   0.0  0
 8R3  CONST_25  H5   C29  C21  C25   180.00   0.0  0
 8R3  CONST_26  H2   C25  C26  C27   180.00   0.0  0
 8R3  CONST_27  H27  C7   C6   C5    180.00   0.0  0
 8R3  CONST_28  H28  C8   C9   C10   180.00   0.0  0
 8R3  CONST_29  H23  C10  C5   C6    180.00   0.0  0
 8R3  CONST_30  C19  N20  C21  C25   180.00   0.0  0
 8R3  CONST_31  C19  N20  C21  C29     0.00   0.0  0
 8R3  CONST_32  H6   N20  C21  C25     0.00   0.0  0
 8R3  CONST_33  O30  C19  N20  C21     0.00   0.0  0
 8R3  CONST_34  C17  C19  N20  C21   180.00   0.0  0
 8R3  CONST_35  H1   O32  C31  C26   180.00   0.0  0
 8R3  Var_01    C6   C5   C4   C3     94.51  30.0  2
 8R3  Var_02    C25  C26  C31  O32  -178.37  30.0  2
 8R3  Var_03    C7   C6   O23  C24     3.64  30.0  1
 8R3  Var_04    N16  C17  C19  N20  -163.84  30.0  3
 8R3  Var_05    C63  N62  N14  C13   140.43  30.0  2
 8R3  Var_06    H24  C24  O23  C6    177.46  30.0  3
 8R3  Var_07    H15  C63  N62  N14    58.78  30.0  3
 8R3  Var_08    H12  C68  N62  N14    61.16  30.0  3

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
 8R3  chir_01  C3  C4  C11  C1  positiv

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
 8R3  plan-1  C26  0.020
 8R3  plan-1  C25  0.020
 8R3  plan-1  C27  0.020
 8R3  plan-1  C28  0.020
 8R3  plan-1  C29  0.020
 8R3  plan-1  C21  0.020
 8R3  plan-1  N20  0.020
 8R3  plan-1  H2   0.020
 8R3  plan-1  H3   0.020
 8R3  plan-1  H4   0.020
 8R3  plan-1  H5   0.020
 8R3  plan-1  C31  0.020
 8R3  plan-2  O32  0.020
 8R3  plan-2  O33  0.020
 8R3  plan-2  C26  0.020
 8R3  plan-2  H1   0.020
 8R3  plan-2  C31  0.020
 8R3  plan-3  C4   0.020
 8R3  plan-3  C5   0.020
 8R3  plan-3  C10  0.020
 8R3  plan-3  C6   0.020
 8R3  plan-3  O23  0.020
 8R3  plan-3  C7   0.020
 8R3  plan-3  C8   0.020
 8R3  plan-3  C9   0.020
 8R3  plan-3  CL2  0.020
 8R3  plan-3  H23  0.020
 8R3  plan-3  H27  0.020
 8R3  plan-3  H28  0.020
 8R3  plan-4  C1   0.020
 8R3  plan-4  O2   0.020
 8R3  plan-4  C17  0.020
 8R3  plan-4  N16  0.020
 8R3  plan-4  C15  0.020
 8R3  plan-4  C3   0.020
 8R3  plan-5  C21  0.020
 8R3  plan-5  N20  0.020
 8R3  plan-5  C19  0.020
 8R3  plan-5  O30  0.020
 8R3  plan-5  C17  0.020
 8R3  plan-5  H6   0.020
 8R3  plan-6  C15  0.020
 8R3  plan-6  C13  0.020
 8R3  plan-6  N14  0.020
 8R3  plan-6  N62  0.020
 8R3  plan-6  N12  0.020
 8R3  plan-6  C11  0.020
 8R3  plan-6  H30  0.020

