# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 26 04:13:15 2022
#   Inital geometry file: a 155 line input string
#   Ligand name: 5-(3-{3-chloro-5-[(2-chlorophenyl)methoxy]-4-fluorophenyl}-2-oxo-2H-[1,3'-bipyridin]-5-yl)pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1c(Cl)cc(cc1OCc2ccccc2Cl)C3=CC(=CN(C3=O)c4cccnc4)C5=CNC(=O)NC5=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
 YSJ  YSJ  5-(3-{3-chloro-5-[(2-chlorophenyl)methoxy]-4-fluorophenyl}-2-oxo-2H-[1,3'-bipyridin]-5-yl)pyrimidine-2,4(1H,3H)-dione  ligand  55  38  .  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_YSJ
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
 YSJ  C10  C   CR6   0   0.682  -25.5262  -4.5013  -23.1529
 YSJ  C11  C   CR16  0   0.030  -21.1451  -4.8344  -25.8830
 YSJ  C12  C   CR6   0   0.179  -18.8427  -5.1045  -26.4699
 YSJ  C14  C   CR16  0  -0.055  -16.2673  -5.4083  -25.7276
 YSJ  C15  C   CR16  0  -0.329  -17.0756  -6.5332  -25.7847
 YSJ  C16  C   CR16  0  -0.140  -18.3980  -6.3795  -26.1702
 YSJ  C18  C   CR16  0  -0.392  -21.8035  -5.1610  -30.9393
 YSJ  C19  C   CR6   0   0.269  -22.1675  -4.9639  -32.2624
 YSJ  C20  C   CH2   0  -0.279  -20.6563  -6.5619  -33.1518
 YSJ  C22  C   CR6   0  -0.099  -19.6789  -5.8776  -35.3744
 YSJ  C23  C   CR16  0  -0.197  -19.2287  -6.1625  -36.6528
 YSJ  C24  C   CR16  0  -0.270  -19.2654  -7.4723  -37.1108
 YSJ  C26  C   CR16  0  -0.314  -20.1959  -8.1776  -35.0156
 YSJ  C27  C   CR6   0   0.531  -22.9592  -3.8618  -32.5850
 YSJ  C1   C   CR6   0  -0.222  -23.3876  -2.9911  -31.6069
 YSJ  C13  C   CR16  0  -0.052  -17.9617  -4.0371  -26.3778
 YSJ  C17  C   CR6   0   0.542  -20.4583  -4.7261  -28.2167
 YSJ  C2   C   CR16  0  -0.288  -23.0182  -3.1856  -30.2833
 YSJ  C21  C   CR6   0   0.193  -20.1688  -6.8744  -34.5321
 YSJ  C25  C   CR16  0  -0.228  -19.7470  -8.4827  -36.2926
 YSJ  C3   C   CR6   0   0.099  -22.2226  -4.2734  -29.9462
 YSJ  C4   C   CR6   0  -0.172  -21.8520  -4.4953  -28.5359
 YSJ  C5   C   CR16  0  -0.198  -22.7842  -4.4396  -27.5440
 YSJ  C6   C   CR6   0  -0.014  -22.4552  -4.6169  -26.1761
 YSJ  C7   C   CR6   0  -0.243  -23.4839  -4.5852  -25.1298
 YSJ  C8   C   CR6   0   0.560  -23.2656  -3.8225  -23.9083
 YSJ  C9   C   CR16  0   0.066  -24.6643  -5.2236  -25.2742
 YSJ  N1   N   NR16  0  -0.720  -24.3235  -3.8552  -23.0150
 YSJ  N2   N   NR16  0  -0.674  -25.6444  -5.1800  -24.3369
 YSJ  N3   N   NR6   0  -0.621  -20.1977  -4.8769  -26.8542
 YSJ  N4   N   N     0  -0.398  -16.6969  -4.1843  -26.0160
 YSJ  O1   O   O     0  -0.436  -22.2614  -3.1904  -23.6447
 YSJ  O2   O   O     0  -0.462  -26.3953  -4.4748  -22.3098
 YSJ  O4   O   O2    0  -0.465  -21.8250  -5.7608  -33.2845
 YSJ  CL1  CL  CL    0  -0.088  -24.3539  -1.6388  -32.0584
 YSJ  H6   H   HCR6  0   0.315  -20.7863  -4.9956  -24.8774
 YSJ  H8   H   HCR6  0   0.274  -15.2278  -5.4986  -25.4342
 YSJ  H9   H   HCR6  0   0.282  -16.6774  -7.5068  -25.5355
 YSJ  H10  H   HCR6  0   0.289  -19.0676  -7.2277  -26.2359
 YSJ  H11  H   HCR6  0   0.292  -21.2070  -6.0206  -30.6679
 YSJ  H13  H   HCH2  0   0.262  -20.8841  -7.4856  -32.6130
 YSJ  H12  H   HCH2  0   0.255  -19.8893  -6.0252  -32.5839
 YSJ  H14  H   HCR6  0   0.281  -18.8516  -5.3708  -37.2860
 YSJ  H15  H   HCR6  0   0.270  -18.9144  -7.6963  -38.1094
 YSJ  H17  H   HCR6  0   0.266  -20.5757  -8.9646  -34.3755
 YSJ  H7   H   HCR6  0   0.279  -18.3019  -3.0317  -26.6036
 YSJ  H1   H   HCR6  0   0.284  -23.3368  -2.4784  -29.5295
 YSJ  H16  H   HCR6  0   0.264  -19.7776  -9.5044  -36.6462
 YSJ  H2   H   HCR6  0   0.278  -23.8196  -4.2549  -27.8082
 YSJ  H4   H   HCR6  0   0.322  -24.8969  -5.8169  -26.1480
 YSJ  H3   H   HNR6  0   0.427  -24.2005  -3.3379  -22.1526
 YSJ  H5   H   HNR6  0   0.439  -26.5075  -5.6783  -24.5009
 YSJ  O3   O   O     0  -0.463  -19.5422  -4.7812  -29.0232
 YSJ  F1   F   F     0  -0.287  -23.2910  -3.6559  -33.8587
 YSJ  CL2  CL  CL    0  -0.123  -19.6093  -4.2363  -34.8188

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
 YSJ  C24  C23  aromatic  1.388  0.020  1.388
 YSJ  C24  C25  aromatic  1.386  0.020  1.386
 YSJ  C23  C22  aromatic  1.385  0.020  1.385
 YSJ  C25  C26  aromatic  1.388  0.020  1.388
 YSJ  C22  CL2  single    1.734  0.020  1.734
 YSJ  C22  C21  aromatic  1.394  0.020  1.394
 YSJ  C26  C21  aromatic  1.390  0.020  1.390
 YSJ  C21  C20  single    1.497  0.020  1.497
 YSJ  F1   C27  single    1.332  0.020  1.332
 YSJ  O4   C20  single    1.423  0.020  1.423
 YSJ  O4   C19  single    1.341  0.020  1.341
 YSJ  C27  C19  aromatic  1.395  0.020  1.395
 YSJ  C27  C1   aromatic  1.378  0.020  1.378
 YSJ  C19  C18  aromatic  1.386  0.020  1.386
 YSJ  CL1  C1   single    1.722  0.020  1.722
 YSJ  C1   C2   aromatic  1.388  0.020  1.388
 YSJ  C18  C3   aromatic  1.396  0.020  1.396
 YSJ  C2   C3   aromatic  1.389  0.020  1.389
 YSJ  C3   C4   single    1.475  0.020  1.475
 YSJ  O3   C17  double    1.222  0.020  1.222
 YSJ  C4   C17  single    1.448  0.020  1.448
 YSJ  C4   C5   double    1.362  0.020  1.362
 YSJ  C17  N3   single    1.395  0.020  1.395
 YSJ  C5   C6   single    1.418  0.020  1.418
 YSJ  N3   C12  single    1.427  0.020  1.427
 YSJ  N3   C11  single    1.357  0.020  1.357
 YSJ  C12  C13  aromatic  1.387  0.020  1.387
 YSJ  C12  C16  aromatic  1.383  0.020  1.383
 YSJ  C13  N4   aromatic  1.324  0.020  1.324
 YSJ  C6   C11  double    1.360  0.020  1.360
 YSJ  C6   C7   single    1.468  0.020  1.468
 YSJ  C16  C15  aromatic  1.386  0.020  1.386
 YSJ  N4   C14  aromatic  1.329  0.020  1.329
 YSJ  C15  C14  aromatic  1.386  0.020  1.386
 YSJ  C9   C7   double    1.350  0.020  1.350
 YSJ  C9   N2   single    1.357  0.020  1.357
 YSJ  C7   C8   single    1.456  0.020  1.456
 YSJ  N2   C10  single    1.370  0.020  1.370
 YSJ  C8   O1   double    1.216  0.020  1.216
 YSJ  C8   N1   single    1.385  0.020  1.385
 YSJ  C10  N1   single    1.372  0.020  1.372
 YSJ  C10  O2   double    1.211  0.020  1.211
 YSJ  C11  H6   single    0.930  0.020  1.080
 YSJ  C14  H8   single    0.930  0.020  1.080
 YSJ  C15  H9   single    0.930  0.020  1.080
 YSJ  C16  H10  single    0.930  0.020  1.080
 YSJ  C18  H11  single    0.930  0.020  1.080
 YSJ  C20  H13  single    0.970  0.020  1.090
 YSJ  C20  H12  single    0.970  0.020  1.090
 YSJ  C23  H14  single    0.930  0.020  1.080
 YSJ  C24  H15  single    0.930  0.020  1.080
 YSJ  C26  H17  single    0.930  0.020  1.080
 YSJ  C13  H7   single    0.930  0.020  1.080
 YSJ  C2   H1   single    0.930  0.020  1.080
 YSJ  C25  H16  single    0.930  0.020  1.080
 YSJ  C5   H2   single    0.930  0.020  1.080
 YSJ  C9   H4   single    0.930  0.020  1.080
 YSJ  N1   H3   single    0.860  0.020  1.020
 YSJ  N2   H5   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
 YSJ  O2   C10  N2   123.41  3.000
 YSJ  O2   C10  N1   123.28  3.000
 YSJ  N2   C10  N1   113.31  3.000
 YSJ  H6   C11  N3   115.45  3.000
 YSJ  H6   C11  C6   123.00  3.000
 YSJ  N3   C11  C6   121.54  3.000
 YSJ  N3   C12  C13  119.89  3.000
 YSJ  C13  C12  C16  119.39  3.000
 YSJ  N3   C12  C16  120.72  3.000
 YSJ  H8   C14  N4   116.46  3.000
 YSJ  H8   C14  C15  120.17  3.000
 YSJ  N4   C14  C15  123.36  3.000
 YSJ  H9   C15  C16  121.02  3.000
 YSJ  H9   C15  C14  120.44  3.000
 YSJ  C16  C15  C14  118.54  3.000
 YSJ  H10  C16  C15  121.34  3.000
 YSJ  H10  C16  C12  120.67  3.000
 YSJ  C15  C16  C12  117.98  3.000
 YSJ  H11  C18  C3   119.50  3.000
 YSJ  H11  C18  C19  119.84  3.000
 YSJ  C3   C18  C19  120.64  3.000
 YSJ  O4   C19  C27  116.00  3.000
 YSJ  C27  C19  C18  118.82  3.000
 YSJ  O4   C19  C18  125.18  3.000
 YSJ  H12  C20  H13  107.72  3.000
 YSJ  H12  C20  O4   110.35  3.000
 YSJ  H13  C20  O4   110.52  3.000
 YSJ  H12  C20  C21  110.64  3.000
 YSJ  H13  C20  C21  110.23  3.000
 YSJ  O4   C20  C21  107.40  3.000
 YSJ  CL2  C22  C21  119.82  3.000
 YSJ  C21  C22  C23  121.66  3.000
 YSJ  CL2  C22  C23  118.51  3.000
 YSJ  H14  C23  C24  120.44  3.000
 YSJ  H14  C23  C22  120.21  3.000
 YSJ  C24  C23  C22  119.35  3.000
 YSJ  H15  C24  C25  120.43  3.000
 YSJ  H15  C24  C23  119.43  3.000
 YSJ  C25  C24  C23  120.14  3.000
 YSJ  H17  C26  C25  119.83  3.000
 YSJ  H17  C26  C21  118.84  3.000
 YSJ  C25  C26  C21  121.32  3.000
 YSJ  F1   C27  C1   120.24  3.000
 YSJ  C1   C27  C19  120.77  3.000
 YSJ  F1   C27  C19  118.99  3.000
 YSJ  CL1  C1   C2   120.62  3.000
 YSJ  C2   C1   C27  120.38  3.000
 YSJ  CL1  C1   C27  118.98  3.000
 YSJ  H7   C13  N4   117.35  3.000
 YSJ  H7   C13  C12  120.01  3.000
 YSJ  N4   C13  C12  122.64  3.000
 YSJ  O3   C17  N3   119.98  3.000
 YSJ  N3   C17  C4   114.34  3.000
 YSJ  O3   C17  C4   125.68  3.000
 YSJ  H1   C2   C3   120.76  3.000
 YSJ  H1   C2   C1   119.65  3.000
 YSJ  C3   C2   C1   119.58  3.000
 YSJ  C26  C21  C22  117.84  3.000
 YSJ  C26  C21  C20  120.67  3.000
 YSJ  C22  C21  C20  121.49  3.000
 YSJ  H16  C25  C26  119.96  3.000
 YSJ  H16  C25  C24  120.35  3.000
 YSJ  C26  C25  C24  119.69  3.000
 YSJ  C4   C3   C2   119.58  3.000
 YSJ  C4   C3   C18  120.60  3.000
 YSJ  C2   C3   C18  119.80  3.000
 YSJ  C5   C4   C3   121.20  3.000
 YSJ  C5   C4   C17  120.30  3.000
 YSJ  C3   C4   C17  118.46  3.000
 YSJ  H2   C5   C6   118.55  3.000
 YSJ  H2   C5   C4   118.88  3.000
 YSJ  C6   C5   C4   122.57  3.000
 YSJ  C7   C6   C5   121.49  3.000
 YSJ  C7   C6   C11  121.67  3.000
 YSJ  C5   C6   C11  116.84  3.000
 YSJ  C9   C7   C8   117.94  3.000
 YSJ  C8   C7   C6   120.27  3.000
 YSJ  C9   C7   C6   121.77  3.000
 YSJ  O1   C8   N1   120.23  3.000
 YSJ  N1   C8   C7   114.46  3.000
 YSJ  O1   C8   C7   125.31  3.000
 YSJ  H4   C9   N2   114.86  3.000
 YSJ  H4   C9   C7   122.27  3.000
 YSJ  N2   C9   C7   122.86  3.000
 YSJ  H3   N1   C8   116.37  3.000
 YSJ  H3   N1   C10  115.62  3.000
 YSJ  C8   N1   C10  128.01  3.000
 YSJ  H5   N2   C9   119.30  3.000
 YSJ  H5   N2   C10  117.29  3.000
 YSJ  C9   N2   C10  123.41  3.000
 YSJ  C17  N3   C12  117.23  3.000
 YSJ  C12  N3   C11  118.37  3.000
 YSJ  C17  N3   C11  124.40  3.000
 YSJ  C13  N4   C14  118.08  3.000
 YSJ  C20  O4   C19  118.25  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
 YSJ  CONST_01  C14  N4   C13  C12     0.00   0.0  0
 YSJ  CONST_02  C14  C15  C16  C12     0.00   0.0  0
 YSJ  CONST_03  C13  C12  C16  C15     0.00   0.0  0
 YSJ  CONST_04  C13  N4   C14  C15     0.00   0.0  0
 YSJ  CONST_05  N4   C13  C12  C16     0.00   0.0  0
 YSJ  CONST_06  N4   C14  C15  C16     0.00   0.0  0
 YSJ  CONST_07  C1   C27  C19  C18     0.00   0.0  0
 YSJ  CONST_08  C1   C2   C3   C18     0.00   0.0  0
 YSJ  CONST_09  C2   C1   C27  C19     0.00   0.0  0
 YSJ  CONST_10  C2   C3   C18  C19     0.00   0.0  0
 YSJ  CONST_11  C25  C24  C23  C22     0.00   0.0  0
 YSJ  CONST_12  C25  C26  C21  C22     0.00   0.0  0
 YSJ  CONST_13  C26  C25  C24  C23     0.00   0.0  0
 YSJ  CONST_14  C26  C21  C22  C23     0.00   0.0  0
 YSJ  CONST_15  C21  C22  C23  C24     0.00   0.0  0
 YSJ  CONST_16  C21  C26  C25  C24     0.00   0.0  0
 YSJ  CONST_17  C3   C18  C19  C27     0.00   0.0  0
 YSJ  CONST_18  C3   C2   C1   C27     0.00   0.0  0
 YSJ  CONST_19  N3   C12  C16  C15   180.00   0.0  0
 YSJ  CONST_20  C4   C3   C18  C19   180.00   0.0  0
 YSJ  CONST_21  C4   C3   C2   C1    180.00   0.0  0
 YSJ  CONST_22  N4   C13  C12  N3    180.00   0.0  0
 YSJ  CONST_23  C4   C17  N3   C11     0.00   0.0  0
 YSJ  CONST_24  C4   C17  N3   C12   180.00   0.0  0
 YSJ  CONST_25  N2   C10  N1   C8      0.00   0.0  0
 YSJ  CONST_26  N1   C10  N2   C9      0.00   0.0  0
 YSJ  CONST_27  F1   C27  C19  C18   180.00   0.0  0
 YSJ  CONST_28  CL1  C1   C27  C19   180.00   0.0  0
 YSJ  CONST_29  C23  C22  C21  C20   180.00   0.0  0
 YSJ  CONST_30  C25  C26  C21  C20   180.00   0.0  0
 YSJ  CONST_31  CL2  C22  C23  C24   180.00   0.0  0
 YSJ  CONST_32  CL2  C22  C21  C26   180.00   0.0  0
 YSJ  CONST_33  O4   C19  C27  C1    180.00   0.0  0
 YSJ  CONST_34  F1   C27  C1   C2    180.00   0.0  0
 YSJ  CONST_35  O4   C19  C18  C3    180.00   0.0  0
 YSJ  CONST_36  CL1  C1   C2   C3    180.00   0.0  0
 YSJ  CONST_37  O3   C17  N3   C11   180.00   0.0  0
 YSJ  CONST_38  O3   C17  N3   C12     0.00   0.0  0
 YSJ  CONST_39  O2   C10  N1   C8    180.00   0.0  0
 YSJ  CONST_40  O2   C10  N2   C9    180.00   0.0  0
 YSJ  CONST_41  H9   C15  C16  C12   180.00   0.0  0
 YSJ  CONST_42  H7   C13  N4   C14   180.00   0.0  0
 YSJ  CONST_43  H10  C16  C15  C14   180.00   0.0  0
 YSJ  CONST_44  H8   C14  C15  C16   180.00   0.0  0
 YSJ  CONST_45  H1   C2   C3   C18   180.00   0.0  0
 YSJ  CONST_46  H15  C24  C23  C22   180.00   0.0  0
 YSJ  CONST_47  H17  C26  C21  C22   180.00   0.0  0
 YSJ  CONST_48  H16  C25  C24  C23   180.00   0.0  0
 YSJ  CONST_49  H11  C18  C19  C27   180.00   0.0  0
 YSJ  CONST_50  H14  C23  C22  C21   180.00   0.0  0
 YSJ  CONST_51  H5   N2   C10  N1    180.00   0.0  0
 YSJ  CONST_52  H3   N1   C10  N2    180.00   0.0  0
 YSJ  Var_01    C13  C12  N3   C11  -100.19  30.0  2
 YSJ  Var_02    C9   C7   C6   C11  -135.20  30.0  2
 YSJ  Var_03    C17  C4   C3   C18    51.03  30.0  2
 YSJ  Var_04    C21  C20  O4   C19  -156.16  30.0  3
 YSJ  Var_05    C27  C19  O4   C20   156.31  30.0  2
 YSJ  Var_06    O4   C20  C21  C22    66.34  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
 YSJ  plan-1  C12  0.020
 YSJ  plan-1  C14  0.020
 YSJ  plan-1  C15  0.020
 YSJ  plan-1  C16  0.020
 YSJ  plan-1  C13  0.020
 YSJ  plan-1  N3   0.020
 YSJ  plan-1  N4   0.020
 YSJ  plan-1  H8   0.020
 YSJ  plan-1  H9   0.020
 YSJ  plan-1  H10  0.020
 YSJ  plan-1  H7   0.020
 YSJ  plan-2  C20  0.020
 YSJ  plan-2  C22  0.020
 YSJ  plan-2  C23  0.020
 YSJ  plan-2  C24  0.020
 YSJ  plan-2  C26  0.020
 YSJ  plan-2  C21  0.020
 YSJ  plan-2  C25  0.020
 YSJ  plan-2  H14  0.020
 YSJ  plan-2  H15  0.020
 YSJ  plan-2  H17  0.020
 YSJ  plan-2  H16  0.020
 YSJ  plan-2  CL2  0.020
 YSJ  plan-3  C18  0.020
 YSJ  plan-3  C19  0.020
 YSJ  plan-3  C27  0.020
 YSJ  plan-3  C1   0.020
 YSJ  plan-3  C2   0.020
 YSJ  plan-3  C3   0.020
 YSJ  plan-3  C4   0.020
 YSJ  plan-3  O4   0.020
 YSJ  plan-3  CL1  0.020
 YSJ  plan-3  H11  0.020
 YSJ  plan-3  H1   0.020
 YSJ  plan-3  F1   0.020
 YSJ  plan-4  C11  0.020
 YSJ  plan-4  C12  0.020
 YSJ  plan-4  C17  0.020
 YSJ  plan-4  C3   0.020
 YSJ  plan-4  C4   0.020
 YSJ  plan-4  C5   0.020
 YSJ  plan-4  C6   0.020
 YSJ  plan-4  C7   0.020
 YSJ  plan-4  N3   0.020
 YSJ  plan-4  H6   0.020
 YSJ  plan-4  H2   0.020
 YSJ  plan-4  O3   0.020
 YSJ  plan-5  C10  0.020
 YSJ  plan-5  C6   0.020
 YSJ  plan-5  C7   0.020
 YSJ  plan-5  C8   0.020
 YSJ  plan-5  C9   0.020
 YSJ  plan-5  N1   0.020
 YSJ  plan-5  N2   0.020
 YSJ  plan-5  O1   0.020
 YSJ  plan-5  O2   0.020
 YSJ  plan-5  H4   0.020
 YSJ  plan-5  H3   0.020
 YSJ  plan-5  H5   0.020

