# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 26 00:56:32 2022
#   Inital geometry file: a 146 line input string
#   Ligand name: 2-{3-[3-chloro-5-(2-methoxyethoxy)phenyl]-2-oxo-2H-[1,3'-bipyridin]-5-yl}benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCOc1cc(Cl)cc(c1)C2=CC(=CN(C2=O)c3cccnc3)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
 YTJ  YTJ  2-{3-[3-chloro-5-(2-methoxyethoxy)phenyl]-2-oxo-2H-[1,3'-bipyridin]-5-yl}benzonitrile  ligand  53  33  .  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_YTJ
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
 YTJ  C24  C   CH2   0  -0.197   6.6005  -5.4775  25.6844
 YTJ  C23  C   CH2   0  -0.218   6.9879  -4.1318  25.1070
 YTJ  C22  C   CR6   0   0.418   6.4934  -1.8242  25.4561
 YTJ  C25  C   CH3   0  -0.392   4.2468  -5.3135  26.0005
 YTJ  C26  C   CR16  0  -0.414   7.2422  -1.4202  24.3563
 YTJ  C21  C   CR16  0  -0.322   5.8095  -0.8805  26.2265
 YTJ  C10  C   CR6   0  -0.016  10.3864   4.2850  21.1553
 YTJ  C1   C   CR6   0   0.547   7.9595  -0.2919  21.5880
 YTJ  C12  C   CR16  0  -0.230  11.2095   5.4021  21.3031
 YTJ  C13  C   CR16  0  -0.254  12.1513   5.4326  22.3151
 YTJ  C14  C   CR16  0  -0.218  12.2670   4.3508  23.1784
 YTJ  C15  C   CR16  0  -0.304  11.4543   3.2383  23.0250
 YTJ  C16  C   CR16  0  -0.183   8.9186   1.4763  22.9674
 YTJ  C17  C   CR6   0  -0.168   8.1047   0.3895  22.8608
 YTJ  C18  C   CR6   0   0.116   7.3037  -0.0685  24.0129
 YTJ  C19  C   CR16  0  -0.299   6.6206   0.8758  24.7728
 YTJ  C2   C   CR6   0   0.186   8.5796  -0.3290  19.2540
 YTJ  C20  C   CR6   0  -0.005   5.8912   0.4497  25.8723
 YTJ  C3   C   CR16  0  -0.058   7.9033   0.3655  18.2627
 YTJ  C4   C   CR16  0  -0.054   8.2764  -1.2920  16.7527
 YTJ  C5   C   CR16  0  -0.332   8.9662  -2.0609  17.6804
 YTJ  C6   C   CR16  0  -0.139   9.1241  -1.5689  18.9645
 YTJ  C7   C   CR16  0   0.023   9.5199   1.3414  20.6792
 YTJ  C8   C   CR6   0  -0.092   9.6446   1.9926  21.8646
 YTJ  C9   C   CR6   0   0.143  10.5061   3.1774  22.0085
 YTJ  N1   N   NR6   0  -0.623   8.7163   0.2566  20.5467
 YTJ  N2   N   N     0  -0.396   7.7571  -0.1032  17.0315
 YTJ  N3   N   NS    0  -0.239   8.5686   4.3662  19.3252
 YTJ  O2   O   O2    0  -0.474   6.3668  -3.0995  25.8573
 YTJ  O3   O   O2    0  -0.477   5.3215  -5.9331  25.3344
 YTJ  CL1  CL  CL    0  -0.125   5.0384   1.6252  26.8189
 YTJ  H15  H   HCH2  0   0.244   7.3060  -6.2090  25.2838
 YTJ  H16  H   HCH2  0   0.211   6.7375  -5.4619  26.7750
 YTJ  H13  H   HCH2  0   0.237   8.0780  -4.0290  25.1565
 YTJ  H14  H   HCH2  0   0.235   6.6935  -4.0798  24.0528
 YTJ  H19  H   HCH3  0   0.227   3.3668  -5.9396  25.8537
 YTJ  H17  H   HCH3  0   0.201   4.4270  -5.2271  27.0782
 YTJ  H18  H   HCH3  0   0.209   4.0212  -4.3160  25.6139
 YTJ  H20  H   HCR6  0   0.281   7.7931  -2.1386  23.7680
 YTJ  H12  H   HCR6  0   0.285   5.2275  -1.1992  27.0813
 YTJ  H6   H   HCR6  0   0.284  11.0970   6.2437  20.6329
 YTJ  H7   H   HCR6  0   0.276  12.7878   6.2986  22.4335
 YTJ  H8   H   HCR6  0   0.276  13.0007   4.3694  23.9733
 YTJ  H9   H   HCR6  0   0.272  11.5681   2.3961  23.6957
 YTJ  H10  H   HCR6  0   0.283   9.0120   1.9749  23.9255
 YTJ  H11  H   HCR6  0   0.277   6.6412   1.9227  24.5022
 YTJ  H1   H   HCR6  0   0.281   7.4703   1.3373  18.4799
 YTJ  H2   H   HCR6  0   0.274   8.1401  -1.6544  15.7402
 YTJ  H3   H   HCR6  0   0.282   9.3734  -3.0217  17.3985
 YTJ  H4   H   HCR6  0   0.289   9.6639  -2.1283  19.7172
 YTJ  H5   H   HCR6  0   0.327  10.0682   1.6290  19.7923
 YTJ  O1   O   O     0  -0.456   7.2420  -1.2545  21.3720
 YTJ  C11  C   CSP   0  -0.003   9.3809   4.3137  20.1411

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
 YTJ  C4   C5   aromatic  1.388  0.020  1.388
 YTJ  C4   N2   aromatic  1.327  0.020  1.327
 YTJ  C5   C6   aromatic  1.384  0.020  1.384
 YTJ  N2   C3   aromatic  1.325  0.020  1.325
 YTJ  C6   C2   aromatic  1.385  0.020  1.385
 YTJ  C3   C2   aromatic  1.386  0.020  1.386
 YTJ  N3   C11  triple    1.153  0.020  1.153
 YTJ  C2   N1   single    1.426  0.020  1.426
 YTJ  C11  C10  single    1.428  0.020  1.428
 YTJ  N1   C7   single    1.356  0.020  1.356
 YTJ  N1   C1   single    1.399  0.020  1.399
 YTJ  C7   C8   double    1.358  0.020  1.358
 YTJ  C10  C12  aromatic  1.395  0.020  1.395
 YTJ  C10  C9   aromatic  1.403  0.020  1.403
 YTJ  C12  C13  aromatic  1.383  0.020  1.383
 YTJ  O1   C1   double    1.220  0.020  1.220
 YTJ  C1   C17  single    1.451  0.020  1.451
 YTJ  C8   C9   single    1.472  0.020  1.472
 YTJ  C8   C16  single    1.418  0.020  1.418
 YTJ  C9   C15  aromatic  1.391  0.020  1.391
 YTJ  C13  C14  aromatic  1.389  0.020  1.389
 YTJ  C17  C16  double    1.362  0.020  1.362
 YTJ  C17  C18  single    1.476  0.020  1.476
 YTJ  C15  C14  aromatic  1.386  0.020  1.386
 YTJ  C18  C26  aromatic  1.396  0.020  1.396
 YTJ  C18  C19  aromatic  1.391  0.020  1.391
 YTJ  C26  C22  aromatic  1.390  0.020  1.390
 YTJ  C19  C20  aromatic  1.387  0.020  1.387
 YTJ  C23  C24  single    1.515  0.020  1.515
 YTJ  C23  O2   single    1.419  0.020  1.419
 YTJ  O3   C24  single    1.402  0.020  1.402
 YTJ  O3   C25  single    1.408  0.020  1.408
 YTJ  C22  O2   single    1.343  0.020  1.343
 YTJ  C22  C21  aromatic  1.397  0.020  1.397
 YTJ  C20  C21  aromatic  1.379  0.020  1.379
 YTJ  C20  CL1  single    1.734  0.020  1.734
 YTJ  C24  H15  single    0.970  0.020  1.090
 YTJ  C24  H16  single    0.970  0.020  1.090
 YTJ  C23  H13  single    0.970  0.020  1.090
 YTJ  C23  H14  single    0.970  0.020  1.090
 YTJ  C25  H19  single    0.970  0.020  1.090
 YTJ  C25  H17  single    0.970  0.020  1.090
 YTJ  C25  H18  single    0.970  0.020  1.090
 YTJ  C26  H20  single    0.930  0.020  1.080
 YTJ  C21  H12  single    0.930  0.020  1.080
 YTJ  C12  H6   single    0.930  0.020  1.080
 YTJ  C13  H7   single    0.930  0.020  1.080
 YTJ  C14  H8   single    0.930  0.020  1.080
 YTJ  C15  H9   single    0.930  0.020  1.080
 YTJ  C16  H10  single    0.930  0.020  1.080
 YTJ  C19  H11  single    0.930  0.020  1.080
 YTJ  C3   H1   single    0.930  0.020  1.080
 YTJ  C4   H2   single    0.930  0.020  1.080
 YTJ  C5   H3   single    0.930  0.020  1.080
 YTJ  C6   H4   single    0.930  0.020  1.080
 YTJ  C7   H5   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
 YTJ  H16  C24  H15  107.03  3.000
 YTJ  H16  C24  O3   111.47  3.000
 YTJ  H15  C24  O3   106.26  3.000
 YTJ  H16  C24  C23  109.50  3.000
 YTJ  H15  C24  C23  106.85  3.000
 YTJ  O3   C24  C23  115.26  3.000
 YTJ  H14  C23  H13  107.83  3.000
 YTJ  H14  C23  O2   110.89  3.000
 YTJ  H13  C23  O2   110.07  3.000
 YTJ  H14  C23  C24  109.89  3.000
 YTJ  H13  C23  C24  108.69  3.000
 YTJ  O2   C23  C24  109.43  3.000
 YTJ  O2   C22  C21  115.50  3.000
 YTJ  C21  C22  C26  120.23  3.000
 YTJ  O2   C22  C26  124.27  3.000
 YTJ  H18  C25  H17  108.04  3.000
 YTJ  H18  C25  H19  108.05  3.000
 YTJ  H17  C25  H19  108.09  3.000
 YTJ  H18  C25  O3   113.06  3.000
 YTJ  H17  C25  O3   111.98  3.000
 YTJ  H19  C25  O3   107.44  3.000
 YTJ  H20  C26  C18  119.19  3.000
 YTJ  H20  C26  C22  120.82  3.000
 YTJ  C18  C26  C22  119.98  3.000
 YTJ  H12  C21  C20  121.25  3.000
 YTJ  H12  C21  C22  120.00  3.000
 YTJ  C20  C21  C22  118.75  3.000
 YTJ  C9   C10  C12  121.15  3.000
 YTJ  C9   C10  C11  120.50  3.000
 YTJ  C12  C10  C11  118.32  3.000
 YTJ  O1   C1   N1   119.71  3.000
 YTJ  O1   C1   C17  125.78  3.000
 YTJ  N1   C1   C17  114.50  3.000
 YTJ  H6   C12  C13  120.47  3.000
 YTJ  H6   C12  C10  119.73  3.000
 YTJ  C13  C12  C10  119.79  3.000
 YTJ  H7   C13  C14  120.45  3.000
 YTJ  H7   C13  C12  119.91  3.000
 YTJ  C14  C13  C12  119.64  3.000
 YTJ  H8   C14  C15  119.52  3.000
 YTJ  H8   C14  C13  119.99  3.000
 YTJ  C15  C14  C13  120.49  3.000
 YTJ  H9   C15  C9   119.35  3.000
 YTJ  H9   C15  C14  119.61  3.000
 YTJ  C9   C15  C14  121.03  3.000
 YTJ  H10  C16  C8   118.42  3.000
 YTJ  H10  C16  C17  119.19  3.000
 YTJ  C8   C16  C17  122.39  3.000
 YTJ  C18  C17  C16  120.72  3.000
 YTJ  C18  C17  C1   118.99  3.000
 YTJ  C16  C17  C1   120.21  3.000
 YTJ  C19  C18  C17  118.83  3.000
 YTJ  C19  C18  C26  120.08  3.000
 YTJ  C17  C18  C26  121.09  3.000
 YTJ  H11  C19  C20  120.39  3.000
 YTJ  H11  C19  C18  120.73  3.000
 YTJ  C20  C19  C18  118.87  3.000
 YTJ  N1   C2   C6   121.31  3.000
 YTJ  N1   C2   C3   119.29  3.000
 YTJ  C6   C2   C3   119.39  3.000
 YTJ  CL1  C20  C19  118.91  3.000
 YTJ  CL1  C20  C21  119.00  3.000
 YTJ  C19  C20  C21  122.09  3.000
 YTJ  H1   C3   N2   117.27  3.000
 YTJ  H1   C3   C2   119.99  3.000
 YTJ  N2   C3   C2   122.74  3.000
 YTJ  H2   C4   N2   116.52  3.000
 YTJ  H2   C4   C5   120.10  3.000
 YTJ  N2   C4   C5   123.38  3.000
 YTJ  H3   C5   C6   120.99  3.000
 YTJ  H3   C5   C4   120.34  3.000
 YTJ  C6   C5   C4   118.67  3.000
 YTJ  H4   C6   C5   121.24  3.000
 YTJ  H4   C6   C2   120.90  3.000
 YTJ  C5   C6   C2   117.86  3.000
 YTJ  H5   C7   N1   115.65  3.000
 YTJ  H5   C7   C8   122.80  3.000
 YTJ  N1   C7   C8   121.54  3.000
 YTJ  C9   C8   C7   121.66  3.000
 YTJ  C9   C8   C16  121.12  3.000
 YTJ  C7   C8   C16  117.21  3.000
 YTJ  C8   C9   C15  120.36  3.000
 YTJ  C15  C9   C10  117.89  3.000
 YTJ  C8   C9   C10  121.74  3.000
 YTJ  C7   N1   C2   118.29  3.000
 YTJ  C7   N1   C1   124.14  3.000
 YTJ  C2   N1   C1   117.51  3.000
 YTJ  C4   N2   C3   117.96  3.000
 YTJ  C22  O2   C23  119.44  3.000
 YTJ  C25  O3   C24  115.79  3.000
 YTJ  N3   C11  C10  180.00  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
 YTJ  CONST_01  C19  C18  C26  C22     0.00   0.0  0
 YTJ  CONST_02  C19  C20  C21  C22     0.00   0.0  0
 YTJ  CONST_03  C20  C19  C18  C26     0.00   0.0  0
 YTJ  CONST_04  C20  C21  C22  C26     0.00   0.0  0
 YTJ  CONST_05  C18  C26  C22  C21     0.00   0.0  0
 YTJ  CONST_06  C18  C19  C20  C21     0.00   0.0  0
 YTJ  CONST_07  C14  C13  C12  C10     0.00   0.0  0
 YTJ  CONST_08  C14  C15  C9   C10     0.00   0.0  0
 YTJ  CONST_09  C15  C9   C10  C12     0.00   0.0  0
 YTJ  CONST_10  C15  C14  C13  C12     0.00   0.0  0
 YTJ  CONST_11  C9   C10  C12  C13     0.00   0.0  0
 YTJ  CONST_12  C9   C15  C14  C13     0.00   0.0  0
 YTJ  CONST_13  C4   C5   C6   C2      0.00   0.0  0
 YTJ  CONST_14  C4   N2   C3   C2      0.00   0.0  0
 YTJ  CONST_15  C5   C4   N2   C3      0.00   0.0  0
 YTJ  CONST_16  C5   C6   C2   C3      0.00   0.0  0
 YTJ  CONST_17  N2   C4   C5   C6      0.00   0.0  0
 YTJ  CONST_18  N2   C3   C2   C6      0.00   0.0  0
 YTJ  CONST_19  C17  C18  C26  C22   180.00   0.0  0
 YTJ  CONST_20  C8   C9   C10  C12   180.00   0.0  0
 YTJ  CONST_21  C8   C9   C15  C14   180.00   0.0  0
 YTJ  CONST_22  C20  C19  C18  C17   180.00   0.0  0
 YTJ  CONST_23  N1   C2   C6   C5    180.00   0.0  0
 YTJ  CONST_24  N2   C3   C2   N1    180.00   0.0  0
 YTJ  CONST_25  C2   N1   C1   C17   180.00   0.0  0
 YTJ  CONST_26  C7   N1   C1   C17     0.00   0.0  0
 YTJ  CONST_27  CL1  C20  C21  C22   180.00   0.0  0
 YTJ  CONST_28  C13  C12  C10  C11   180.00   0.0  0
 YTJ  CONST_29  C8   C9   C10  C11     0.00   0.0  0
 YTJ  CONST_30  C15  C9   C10  C11   180.00   0.0  0
 YTJ  CONST_31  O2   C22  C26  C18   180.00   0.0  0
 YTJ  CONST_32  CL1  C20  C19  C18   180.00   0.0  0
 YTJ  CONST_33  O2   C22  C21  C20   180.00   0.0  0
 YTJ  CONST_34  O1   C1   N1   C2      0.00   0.0  0
 YTJ  CONST_35  O1   C1   N1   C7    180.00   0.0  0
 YTJ  CONST_36  H11  C19  C18  C26   180.00   0.0  0
 YTJ  CONST_37  H12  C21  C22  C26   180.00   0.0  0
 YTJ  CONST_38  H20  C26  C22  C21   180.00   0.0  0
 YTJ  CONST_39  H7   C13  C12  C10   180.00   0.0  0
 YTJ  CONST_40  H9   C15  C9   C10   180.00   0.0  0
 YTJ  CONST_41  H8   C14  C13  C12   180.00   0.0  0
 YTJ  CONST_42  H6   C12  C13  C14   180.00   0.0  0
 YTJ  CONST_43  H3   C5   C6   C2    180.00   0.0  0
 YTJ  CONST_44  H2   C4   N2   C3    180.00   0.0  0
 YTJ  CONST_45  H4   C6   C2   C3    180.00   0.0  0
 YTJ  CONST_46  H1   C3   N2   C4    180.00   0.0  0
 YTJ  Var_01    C1   C17  C18  C26    48.78  30.0  2
 YTJ  Var_02    C7   C8   C9   C10    52.95  30.0  3
 YTJ  Var_03    C6   C2   N1   C1    -72.91  30.0  3
 YTJ  Var_04    C26  C22  O2   C23    -2.22  30.0  2
 YTJ  Var_05    H13  C23  O2   C22    65.59  30.0  1
 YTJ  Var_06    O3   C24  C23  O2     78.30  30.0  3
 YTJ  Var_07    H19  C25  O3   C24  -164.16  30.0  3
 YTJ  Var_08    H15  C24  O3   C25   166.16  30.0  3

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
 YTJ  plan-1  C10  0.020
 YTJ  plan-1  C12  0.020
 YTJ  plan-1  C13  0.020
 YTJ  plan-1  C14  0.020
 YTJ  plan-1  C15  0.020
 YTJ  plan-1  C8   0.020
 YTJ  plan-1  C9   0.020
 YTJ  plan-1  N3   0.020
 YTJ  plan-1  H6   0.020
 YTJ  plan-1  H7   0.020
 YTJ  plan-1  H8   0.020
 YTJ  plan-1  H9   0.020
 YTJ  plan-1  C11  0.020
 YTJ  plan-2  C22  0.020
 YTJ  plan-2  C26  0.020
 YTJ  plan-2  C21  0.020
 YTJ  plan-2  C17  0.020
 YTJ  plan-2  C18  0.020
 YTJ  plan-2  C19  0.020
 YTJ  plan-2  C20  0.020
 YTJ  plan-2  O2   0.020
 YTJ  plan-2  CL1  0.020
 YTJ  plan-2  H20  0.020
 YTJ  plan-2  H12  0.020
 YTJ  plan-2  H11  0.020
 YTJ  plan-3  C2   0.020
 YTJ  plan-3  C3   0.020
 YTJ  plan-3  C4   0.020
 YTJ  plan-3  C5   0.020
 YTJ  plan-3  C6   0.020
 YTJ  plan-3  N1   0.020
 YTJ  plan-3  N2   0.020
 YTJ  plan-3  H1   0.020
 YTJ  plan-3  H2   0.020
 YTJ  plan-3  H3   0.020
 YTJ  plan-3  H4   0.020
 YTJ  plan-4  C1   0.020
 YTJ  plan-4  C16  0.020
 YTJ  plan-4  C17  0.020
 YTJ  plan-4  C18  0.020
 YTJ  plan-4  C2   0.020
 YTJ  plan-4  C7   0.020
 YTJ  plan-4  C8   0.020
 YTJ  plan-4  C9   0.020
 YTJ  plan-4  N1   0.020
 YTJ  plan-4  H10  0.020
 YTJ  plan-4  H5   0.020
 YTJ  plan-4  O1   0.020

