# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 02:28:08 2022
#   Inital geometry file: a 124 line input string
#   Ligand name: 2-[3-(3,5-dichlorophenyl)-2-oxo[2H-[1,3'-bipyridine]]-5-yl]benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cc(Cl)cc(c1)C2=CC(=CN(c3cccnc3)C2=O)c4ccccc4C#N
#
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
 XEY  XEY  2-[3-(3,5-dichlorophenyl)-2-oxo[2H-[1,3'-bipyridine]]-5-yl]benzonitrile  ligand  42  29  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XEY
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
 XEY  C1   C   CR6   0  -0.027   6.1239  -0.3393  25.8038
 XEY  C2   C   CR16  0  -0.256   6.8143   0.0771  24.6783
 XEY  C5   C   CR6   0  -0.168   8.2984  -0.3864  22.7542
 XEY  C6   C   CR16  0  -0.238   7.5249  -2.1924  24.3042
 XEY  C11  C   CR16  0  -0.179   9.0798   0.7260  22.8349
 XEY  C12  C   CR6   0   0.186   8.7954  -1.1854  19.1682
 XEY  C13  C   CR6   0   0.143  10.6329   2.4355  21.8383
 XEY  C14  C   CR16  0  -0.138   9.3648  -2.4247  18.9269
 XEY  C15  C   CR16  0  -0.332   9.2331  -2.9607  17.6579
 XEY  C16  C   CR16  0  -0.054   8.5442  -2.2340  16.6960
 XEY  C17  C   CR16  0  -0.059   8.1229  -0.5343  18.1456
 XEY  C10  C   CR6   0  -0.092   9.7904   1.2343  21.7192
 XEY  C18  C   CR6   0  -0.015  10.5059   3.5211  20.9583
 XEY  C19  C   CR16  0  -0.230  11.3154   4.6507  21.0849
 XEY  C20  C   CR16  0  -0.254  12.2501   4.7163  22.1018
 XEY  C21  C   CR16  0  -0.217  12.3723   3.6570  22.9915
 XEY  C22  C   CR16  0  -0.304  11.5733   2.5320  22.8593
 XEY  C23  C   CSP   0  -0.003   9.5063   3.5137  19.9382
 XEY  C3   C   CR16  0  -0.185   6.1119  -1.6651  26.2021
 XEY  C4   C   CR6   0   0.087   7.5274  -0.8511  23.9225
 XEY  C7   C   CR6   0  -0.029   6.8238  -2.5741  25.4342
 XEY  C8   C   CR6   0   0.551   8.1681  -1.1016  21.5000
 XEY  C9   C   CR16  0   0.026   9.6814   0.5507  20.5498
 XEY  N1   N   NR6   0  -0.624   8.9065  -0.5574  20.4435
 XEY  N2   N   N     0  -0.396   8.0022  -1.0456  16.9285
 XEY  N3   N   NS    0  -0.239   8.6924   3.5288  19.1223
 XEY  O1   O   O     0  -0.455   7.4773  -2.0895  21.3142
 XEY  CL1  CL  CL    0  -0.111   5.2407   0.8246  26.7293
 XEY  CL2  CL  CL    0  -0.111   6.8344  -4.2372  25.9123
 XEY  H1   H   HCR6  0   0.287   6.7872   1.1171  24.3812
 XEY  H2   H   HCR6  0   0.280   8.0811  -2.9275  23.7411
 XEY  H3   H   HCR6  0   0.286   9.1625   1.2478  23.7816
 XEY  H4   H   HCR6  0   0.289   9.9034  -2.9496  19.7048
 XEY  H5   H   HCR6  0   0.282   9.6600  -3.9230  17.4127
 XEY  H6   H   HCR6  0   0.274   8.4282  -2.6314  15.6942
 XEY  H7   H   HCR6  0   0.282   7.6716   0.4369  18.3247
 XEY  H8   H   HCR6  0   0.284  11.1974   5.4747  20.3940
 XEY  H9   H   HCR6  0   0.276  12.8759   5.5922  22.2031
 XEY  H10  H   HCR6  0   0.276  13.1004   3.7029  23.7904
 XEY  H11  H   HCR6  0   0.273  11.6932   1.7074  23.5504
 XEY  H12  H   HCR6  0   0.302   5.5657  -1.9814  27.0797
 XEY  H13  H   HCR6  0   0.328  10.2237   0.8293  19.6564

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
 XEY  C16  N2   aromatic  1.327  0.020  1.327
 XEY  C16  C15  aromatic  1.388  0.020  1.388
 XEY  N2   C17  aromatic  1.326  0.020  1.326
 XEY  C15  C14  aromatic  1.384  0.020  1.384
 XEY  C17  C12  aromatic  1.386  0.020  1.386
 XEY  C14  C12  aromatic  1.385  0.020  1.385
 XEY  N3   C23  triple    1.152  0.020  1.152
 XEY  C12  N1   single    1.426  0.020  1.426
 XEY  C23  C18  single    1.428  0.020  1.428
 XEY  N1   C9   single    1.356  0.020  1.356
 XEY  N1   C8   single    1.399  0.020  1.399
 XEY  C9   C10  double    1.359  0.020  1.359
 XEY  C18  C19  aromatic  1.395  0.020  1.395
 XEY  C18  C13  aromatic  1.403  0.020  1.403
 XEY  C19  C20  aromatic  1.383  0.020  1.383
 XEY  O1   C8   double    1.220  0.020  1.220
 XEY  C8   C5   single    1.450  0.020  1.450
 XEY  C10  C13  single    1.472  0.020  1.472
 XEY  C10  C11  single    1.417  0.020  1.417
 XEY  C13  C22  aromatic  1.391  0.020  1.391
 XEY  C20  C21  aromatic  1.389  0.020  1.389
 XEY  C5   C11  double    1.362  0.020  1.362
 XEY  C5   C4   single    1.475  0.020  1.475
 XEY  C22  C21  aromatic  1.386  0.020  1.386
 XEY  C4   C6   aromatic  1.395  0.020  1.395
 XEY  C4   C2   aromatic  1.393  0.020  1.393
 XEY  C6   C7   aromatic  1.383  0.020  1.383
 XEY  C2   C1   aromatic  1.384  0.020  1.384
 XEY  C7   CL2  single    1.730  0.020  1.730
 XEY  C7   C3   aromatic  1.387  0.020  1.387
 XEY  C1   C3   aromatic  1.384  0.020  1.384
 XEY  C1   CL1  single    1.730  0.020  1.730
 XEY  C2   H1   single    0.930  0.020  1.080
 XEY  C6   H2   single    0.930  0.020  1.080
 XEY  C11  H3   single    0.930  0.020  1.080
 XEY  C14  H4   single    0.930  0.020  1.080
 XEY  C15  H5   single    0.930  0.020  1.080
 XEY  C16  H6   single    0.930  0.020  1.080
 XEY  C17  H7   single    0.930  0.020  1.080
 XEY  C19  H8   single    0.930  0.020  1.080
 XEY  C20  H9   single    0.930  0.020  1.080
 XEY  C21  H10  single    0.930  0.020  1.080
 XEY  C22  H11  single    0.930  0.020  1.080
 XEY  C3   H12  single    0.930  0.020  1.080
 XEY  C9   H13  single    0.930  0.020  1.080

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
 XEY  CL1  C1   C3   119.08  3.000
 XEY  CL1  C1   C2   119.16  3.000
 XEY  C3   C1   C2   121.75  3.000
 XEY  H1   C2   C4   120.28  3.000
 XEY  H1   C2   C1   119.98  3.000
 XEY  C4   C2   C1   119.73  3.000
 XEY  C8   C5   C4   118.88  3.000
 XEY  C4   C5   C11  120.69  3.000
 XEY  C8   C5   C11  120.39  3.000
 XEY  H2   C6   C7   119.93  3.000
 XEY  H2   C6   C4   120.72  3.000
 XEY  C7   C6   C4   119.33  3.000
 XEY  H3   C11  C10  118.47  3.000
 XEY  H3   C11  C5   119.25  3.000
 XEY  C10  C11  C5   122.28  3.000
 XEY  N1   C12  C17  119.38  3.000
 XEY  N1   C12  C14  121.19  3.000
 XEY  C17  C12  C14  119.42  3.000
 XEY  C22  C13  C18  117.88  3.000
 XEY  C22  C13  C10  120.18  3.000
 XEY  C18  C13  C10  121.92  3.000
 XEY  H4   C14  C15  121.25  3.000
 XEY  H4   C14  C12  120.90  3.000
 XEY  C15  C14  C12  117.85  3.000
 XEY  H5   C15  C16  120.31  3.000
 XEY  H5   C15  C14  121.02  3.000
 XEY  C16  C15  C14  118.67  3.000
 XEY  H6   C16  N2   116.53  3.000
 XEY  H6   C16  C15  120.10  3.000
 XEY  N2   C16  C15  123.37  3.000
 XEY  H7   C17  N2   117.29  3.000
 XEY  H7   C17  C12  120.00  3.000
 XEY  N2   C17  C12  122.70  3.000
 XEY  C9   C10  C13  121.74  3.000
 XEY  C13  C10  C11  121.06  3.000
 XEY  C9   C10  C11  117.18  3.000
 XEY  C23  C18  C19  118.36  3.000
 XEY  C19  C18  C13  121.12  3.000
 XEY  C23  C18  C13  120.48  3.000
 XEY  H8   C19  C20  120.48  3.000
 XEY  H8   C19  C18  119.69  3.000
 XEY  C20  C19  C18  119.82  3.000
 XEY  H9   C20  C21  120.46  3.000
 XEY  H9   C20  C19  119.91  3.000
 XEY  C21  C20  C19  119.63  3.000
 XEY  H10  C21  C22  119.52  3.000
 XEY  H10  C21  C20  120.00  3.000
 XEY  C22  C21  C20  120.48  3.000
 XEY  H11  C22  C21  119.57  3.000
 XEY  H11  C22  C13  119.37  3.000
 XEY  C21  C22  C13  121.05  3.000
 XEY  N3   C23  C18  180.00  3.000
 XEY  H12  C3   C7   121.14  3.000
 XEY  H12  C3   C1   121.21  3.000
 XEY  C7   C3   C1   117.65  3.000
 XEY  C6   C4   C5   121.39  3.000
 XEY  C6   C4   C2   119.43  3.000
 XEY  C5   C4   C2   119.17  3.000
 XEY  CL2  C7   C3   118.70  3.000
 XEY  C3   C7   C6   122.11  3.000
 XEY  CL2  C7   C6   119.19  3.000
 XEY  O1   C8   N1   119.93  3.000
 XEY  O1   C8   C5   125.61  3.000
 XEY  N1   C8   C5   114.46  3.000
 XEY  H13  C9   N1   115.60  3.000
 XEY  H13  C9   C10  122.75  3.000
 XEY  N1   C9   C10  121.62  3.000
 XEY  C9   N1   C8   124.06  3.000
 XEY  C8   N1   C12  117.58  3.000
 XEY  C9   N1   C12  118.33  3.000
 XEY  C17  N2   C16  117.98  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
 XEY  CONST_01  C6   C4   C2   C1      0.00   0.0  0
 XEY  CONST_02  C6   C7   C3   C1      0.00   0.0  0
 XEY  CONST_03  C7   C6   C4   C2      0.00   0.0  0
 XEY  CONST_04  C7   C3   C1   C2      0.00   0.0  0
 XEY  CONST_05  C16  N2   C17  C12     0.00   0.0  0
 XEY  CONST_06  C16  C15  C14  C12     0.00   0.0  0
 XEY  CONST_07  C20  C19  C18  C13     0.00   0.0  0
 XEY  CONST_08  C20  C21  C22  C13     0.00   0.0  0
 XEY  CONST_09  N2   C16  C15  C14     0.00   0.0  0
 XEY  CONST_10  N2   C17  C12  C14     0.00   0.0  0
 XEY  CONST_11  C17  N2   C16  C15     0.00   0.0  0
 XEY  CONST_12  C17  C12  C14  C15     0.00   0.0  0
 XEY  CONST_13  C21  C20  C19  C18     0.00   0.0  0
 XEY  CONST_14  C21  C22  C13  C18     0.00   0.0  0
 XEY  CONST_15  C22  C13  C18  C19     0.00   0.0  0
 XEY  CONST_16  C22  C21  C20  C19     0.00   0.0  0
 XEY  CONST_17  C4   C6   C7   C3      0.00   0.0  0
 XEY  CONST_18  C4   C2   C1   C3      0.00   0.0  0
 XEY  CONST_19  C5   C4   C2   C1    180.00   0.0  0
 XEY  CONST_20  C7   C6   C4   C5    180.00   0.0  0
 XEY  CONST_21  N1   C12  C14  C15   180.00   0.0  0
 XEY  CONST_22  C19  C18  C13  C10   180.00   0.0  0
 XEY  CONST_23  C21  C22  C13  C10   180.00   0.0  0
 XEY  CONST_24  N2   C17  C12  N1    180.00   0.0  0
 XEY  CONST_25  C12  N1   C8   C5    180.00   0.0  0
 XEY  CONST_26  C9   N1   C8   C5      0.00   0.0  0
 XEY  CONST_27  CL2  C7   C3   C1    180.00   0.0  0
 XEY  CONST_28  C23  C18  C13  C10     0.00   0.0  0
 XEY  CONST_29  C23  C18  C19  C20   180.00   0.0  0
 XEY  CONST_30  C23  C18  C13  C22   180.00   0.0  0
 XEY  CONST_31  CL2  C7   C6   C4    180.00   0.0  0
 XEY  CONST_32  CL1  C1   C2   C4    180.00   0.0  0
 XEY  CONST_33  CL1  C1   C3   C7    180.00   0.0  0
 XEY  CONST_34  O1   C8   N1   C12     0.00   0.0  0
 XEY  CONST_35  O1   C8   N1   C9    180.00   0.0  0
 XEY  CONST_36  H2   C6   C4   C2    180.00   0.0  0
 XEY  CONST_37  H12  C3   C1   C2    180.00   0.0  0
 XEY  CONST_38  H1   C2   C4   C5      0.00   0.0  0
 XEY  CONST_39  H5   C15  C14  C12   180.00   0.0  0
 XEY  CONST_40  H8   C19  C18  C13   180.00   0.0  0
 XEY  CONST_41  H10  C21  C22  C13   180.00   0.0  0
 XEY  CONST_42  H6   C16  C15  C14   180.00   0.0  0
 XEY  CONST_43  H7   C17  C12  C14   180.00   0.0  0
 XEY  CONST_44  H4   C14  C15  C16   180.00   0.0  0
 XEY  CONST_45  H11  C22  C13  C10     0.00   0.0  0
 XEY  CONST_46  H9   C20  C19  C18   180.00   0.0  0
 XEY  Var_01    C8   C5   C4   C2   -132.50  30.0  2
 XEY  Var_02    C18  C13  C10  C11  -128.54  30.0  2
 XEY  Var_03    C9   N1   C12  C14   110.53  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
 XEY  plan-1  C12  0.020
 XEY  plan-1  C14  0.020
 XEY  plan-1  C15  0.020
 XEY  plan-1  C16  0.020
 XEY  plan-1  C17  0.020
 XEY  plan-1  N1   0.020
 XEY  plan-1  N2   0.020
 XEY  plan-1  H4   0.020
 XEY  plan-1  H5   0.020
 XEY  plan-1  H6   0.020
 XEY  plan-1  H7   0.020
 XEY  plan-2  C13  0.020
 XEY  plan-2  C10  0.020
 XEY  plan-2  C18  0.020
 XEY  plan-2  C19  0.020
 XEY  plan-2  C20  0.020
 XEY  plan-2  C21  0.020
 XEY  plan-2  C22  0.020
 XEY  plan-2  C23  0.020
 XEY  plan-2  N3   0.020
 XEY  plan-2  H8   0.020
 XEY  plan-2  H9   0.020
 XEY  plan-2  H10  0.020
 XEY  plan-2  H11  0.020
 XEY  plan-3  C1   0.020
 XEY  plan-3  C2   0.020
 XEY  plan-3  C5   0.020
 XEY  plan-3  C6   0.020
 XEY  plan-3  C3   0.020
 XEY  plan-3  C4   0.020
 XEY  plan-3  C7   0.020
 XEY  plan-3  CL1  0.020
 XEY  plan-3  CL2  0.020
 XEY  plan-3  H1   0.020
 XEY  plan-3  H2   0.020
 XEY  plan-3  H12  0.020
 XEY  plan-4  C5   0.020
 XEY  plan-4  C11  0.020
 XEY  plan-4  C12  0.020
 XEY  plan-4  C13  0.020
 XEY  plan-4  C10  0.020
 XEY  plan-4  C4   0.020
 XEY  plan-4  C8   0.020
 XEY  plan-4  C9   0.020
 XEY  plan-4  N1   0.020
 XEY  plan-4  O1   0.020
 XEY  plan-4  H3   0.020
 XEY  plan-4  H13  0.020

