# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 26 00:12:25 2022
#   Inital geometry file: a 161 line input string
#   Ligand name: 5-(3-{3-chloro-5-[(2-methylphenyl)methoxy]phenyl}-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: Cc1ccccc1COc2cc(Cl)cc(c2)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
 YSP  YSP  5-(3-{3-chloro-5-[(2-methylphenyl)methoxy]phenyl}-2-oxo-2H-[1,3'-bipyridin]-5-yl)pyrimidine-2,4(1H,3H)-dione  ligand  58  37  .  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_YSP
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
 YSP  C7   C   CR16  0   0.028  -21.2255  -4.3172  -26.0342
 YSP  C6   C   CR16  0  -0.144  -18.4582  -5.7332  -26.2043
 YSP  C1   C   CR6   0   0.540  -20.4783  -4.0546  -28.3370
 YSP  C2   C   CR6   0   0.183  -18.9005  -4.4720  -26.5604
 YSP  C4   C   CR16  0  -0.056  -16.3400  -4.7405  -25.7520
 YSP  C5   C   CR16  0  -0.328  -17.1441  -5.8688  -25.7841
 YSP  C10  C   CR6   0   0.560  -23.4310  -3.4927  -24.0729
 YSP  C11  C   CR16  0   0.066  -24.7384  -4.8804  -25.5397
 YSP  C16  C   CR16  0  -0.412  -21.6877  -4.3910  -31.1216
 YSP  C17  C   CR6   0   0.414  -22.0220  -4.1299  -32.4452
 YSP  C22  C   CR16  0  -0.297  -18.8197  -5.9311  -36.6329
 YSP  C23  C   CR16  0  -0.246  -19.2069  -7.1793  -37.1032
 YSP  C20  C   CR6   0   0.081  -19.2379  -5.4608  -35.3914
 YSP  C24  C   CR16  0  -0.260  -20.0241  -7.9863  -36.3277
 YSP  C25  C   CR16  0  -0.294  -20.4504  -7.5292  -35.0881
 YSP  C26  C   CR16  0  -0.323  -22.8975  -3.0868  -32.7560
 YSP  C27  C   CR6   0  -0.006  -23.4176  -2.3299  -31.7269
 YSP  C28  C   CR16  0  -0.300  -23.0887  -2.5626  -30.3995
 YSP  C12  C   CR6   0   0.681  -25.6763  -4.3043  -23.4058
 YSP  C13  C   CR16  0  -0.201  -22.8340  -3.9118  -27.7219
 YSP  C14  C   CR6   0  -0.169  -21.8730  -3.8751  -28.6879
 YSP  C15  C   CR6   0   0.121  -22.2164  -3.6033  -30.0974
 YSP  C18  C   CH2   0  -0.298  -20.5591  -5.8218  -33.2736
 YSP  C19  C   CR6   0   0.076  -20.0682  -6.2800  -34.6130
 YSP  C3   C   CR16  0  -0.052  -18.0237  -3.3988  -26.4884
 YSP  C8   C   CR6   0  -0.013  -22.5352  -4.1418  -26.3551
 YSP  C9   C   CR6   0  -0.242  -23.5892  -4.2027  -25.3352
 YSP  N1   N   NR6   0  -0.620  -20.2496  -4.2675  -26.9762
 YSP  N2   N   N     0  -0.399  -16.7669  -3.5294  -26.0952
 YSP  N3   N   NR16  0  -0.719  -24.5059  -3.6155  -23.2081
 YSP  N4   N   NR16  0  -0.673  -25.7407  -4.9235  -24.6259
 YSP  O1   O   O     0  -0.463  -19.5371  -4.0213  -29.1149
 YSP  O3   O   O     0  -0.462  -26.5626  -4.3579  -22.5821
 YSP  O4   O   O2    0  -0.470  -21.5536  -4.8261  -33.4951
 YSP  CL1  CL  CL    0  -0.126  -24.4976  -1.0280  -32.1076
 YSP  H5   H   HCR6  0   0.315  -20.8884  -4.5133  -25.0274
 YSP  H4   H   HCR6  0   0.290  -19.1234  -6.5861  -26.2536
 YSP  H2   H   HCR6  0   0.273  -15.3068  -4.8161  -25.4332
 YSP  H3   H   HCR6  0   0.282  -16.7494  -6.8316  -25.4913
 YSP  H7   H   HCR6  0   0.322  -24.9265  -5.4370  -26.4477
 YSP  H10  H   HCR6  0   0.283  -21.0279  -5.2079  -30.8703
 YSP  H13  H   HCH3  0   0.251  -19.6336  -3.4039  -34.8772
 YSP  H14  H   HCH3  0   0.245  -18.3684  -4.1441  -33.9151
 YSP  H15  H   HCH3  0   0.252  -18.0467  -3.6850  -35.5826
 YSP  H16  H   HCR6  0   0.249  -18.1751  -5.3083  -37.2420
 YSP  H17  H   HCR6  0   0.254  -18.8647  -7.5189  -38.0724
 YSP  H18  H   HCR6  0   0.253  -20.3291  -8.9623  -36.6817
 YSP  H19  H   HCR6  0   0.252  -21.0904  -8.1548  -34.4768
 YSP  H20  H   HCR6  0   0.285  -23.1521  -2.8825  -33.7877
 YSP  H21  H   HCR6  0   0.275  -23.4872  -1.9309  -29.6172
 YSP  H9   H   HCR6  0   0.278  -23.8692  -3.7614  -28.0074
 YSP  H11  H   HCH2  0   0.256  -20.9827  -6.6619  -32.7141
 YSP  H12  H   HCH2  0   0.244  -19.7387  -5.4094  -32.6764
 YSP  H1   H   HCR6  0   0.279  -18.3604  -2.4024  -26.7552
 YSP  H6   H   HNR6  0   0.427  -24.4248  -3.1373  -22.3187
 YSP  H8   H   HNR6  0   0.439  -26.5768  -5.4504  -24.8344
 YSP  O2   O   O     0  -0.436  -22.4619  -2.8314  -23.7547
 YSP  C21  C   CH3   0  -0.743  -18.7992  -4.1052  -34.9172

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
 YSP  C23  C22  aromatic  1.389  0.020  1.389
 YSP  C23  C24  aromatic  1.386  0.020  1.386
 YSP  C22  C20  aromatic  1.392  0.020  1.392
 YSP  C24  C25  aromatic  1.388  0.020  1.388
 YSP  C20  C21  single    1.502  0.020  1.502
 YSP  C20  C19  aromatic  1.402  0.020  1.402
 YSP  C25  C19  aromatic  1.390  0.020  1.390
 YSP  C19  C18  single    1.498  0.020  1.498
 YSP  O4   C18  single    1.425  0.020  1.425
 YSP  O4   C17  single    1.344  0.020  1.344
 YSP  C26  C17  aromatic  1.397  0.020  1.397
 YSP  C26  C27  aromatic  1.379  0.020  1.379
 YSP  C17  C16  aromatic  1.390  0.020  1.390
 YSP  CL1  C27  single    1.734  0.020  1.734
 YSP  C27  C28  aromatic  1.387  0.020  1.387
 YSP  C16  C15  aromatic  1.396  0.020  1.396
 YSP  C28  C15  aromatic  1.391  0.020  1.391
 YSP  C15  C14  single    1.476  0.020  1.476
 YSP  O1   C1   double    1.222  0.020  1.222
 YSP  C14  C1   single    1.449  0.020  1.449
 YSP  C14  C13  double    1.363  0.020  1.363
 YSP  C1   N1   single    1.396  0.020  1.396
 YSP  C13  C8   single    1.418  0.020  1.418
 YSP  N1   C2   single    1.426  0.020  1.426
 YSP  N1   C7   single    1.357  0.020  1.357
 YSP  C3   C2   aromatic  1.388  0.020  1.388
 YSP  C3   N2   aromatic  1.323  0.020  1.323
 YSP  C2   C6   aromatic  1.383  0.020  1.383
 YSP  C8   C7   double    1.360  0.020  1.360
 YSP  C8   C9   single    1.468  0.020  1.468
 YSP  N2   C4   aromatic  1.329  0.020  1.329
 YSP  C6   C5   aromatic  1.386  0.020  1.386
 YSP  C4   C5   aromatic  1.386  0.020  1.386
 YSP  C11  C9   double    1.350  0.020  1.350
 YSP  C11  N4   single    1.357  0.020  1.357
 YSP  C9   C10  single    1.457  0.020  1.457
 YSP  N4   C12  single    1.370  0.020  1.370
 YSP  C10  O2   double    1.216  0.020  1.216
 YSP  C10  N3   single    1.385  0.020  1.385
 YSP  C12  N3   single    1.372  0.020  1.372
 YSP  C12  O3   double    1.211  0.020  1.211
 YSP  C7   H5   single    0.930  0.020  1.080
 YSP  C6   H4   single    0.930  0.020  1.080
 YSP  C4   H2   single    0.930  0.020  1.080
 YSP  C5   H3   single    0.930  0.020  1.080
 YSP  C11  H7   single    0.930  0.020  1.080
 YSP  C16  H10  single    0.930  0.020  1.080
 YSP  C21  H13  single    0.970  0.020  1.090
 YSP  C21  H14  single    0.970  0.020  1.090
 YSP  C21  H15  single    0.970  0.020  1.090
 YSP  C22  H16  single    0.930  0.020  1.080
 YSP  C23  H17  single    0.930  0.020  1.080
 YSP  C24  H18  single    0.930  0.020  1.080
 YSP  C25  H19  single    0.930  0.020  1.080
 YSP  C26  H20  single    0.930  0.020  1.080
 YSP  C28  H21  single    0.930  0.020  1.080
 YSP  C13  H9   single    0.930  0.020  1.080
 YSP  C18  H11  single    0.970  0.020  1.090
 YSP  C18  H12  single    0.970  0.020  1.090
 YSP  C3   H1   single    0.930  0.020  1.080
 YSP  N3   H6   single    0.860  0.020  1.020
 YSP  N4   H8   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
 YSP  H5   C7   N1   115.43  3.000
 YSP  H5   C7   C8   122.96  3.000
 YSP  N1   C7   C8   121.60  3.000
 YSP  H4   C6   C5   121.27  3.000
 YSP  H4   C6   C2   120.67  3.000
 YSP  C5   C6   C2   118.06  3.000
 YSP  O1   C1   N1   119.90  3.000
 YSP  N1   C1   C14  114.36  3.000
 YSP  O1   C1   C14  125.73  3.000
 YSP  N1   C2   C3   120.12  3.000
 YSP  C3   C2   C6   119.33  3.000
 YSP  N1   C2   C6   120.54  3.000
 YSP  H2   C4   N2   116.47  3.000
 YSP  H2   C4   C5   120.20  3.000
 YSP  N2   C4   C5   123.33  3.000
 YSP  H3   C5   C4   120.47  3.000
 YSP  H3   C5   C6   121.01  3.000
 YSP  C4   C5   C6   118.51  3.000
 YSP  O2   C10  N3   120.23  3.000
 YSP  N3   C10  C9   114.42  3.000
 YSP  O2   C10  C9   125.35  3.000
 YSP  H7   C11  N4   114.87  3.000
 YSP  H7   C11  C9   122.25  3.000
 YSP  N4   C11  C9   122.87  3.000
 YSP  H10  C16  C15  119.18  3.000
 YSP  H10  C16  C17  120.72  3.000
 YSP  C15  C16  C17  120.10  3.000
 YSP  O4   C17  C26  115.56  3.000
 YSP  C26  C17  C16  120.20  3.000
 YSP  O4   C17  C16  124.25  3.000
 YSP  H16  C22  C20  119.07  3.000
 YSP  H16  C22  C23  119.47  3.000
 YSP  C20  C22  C23  121.46  3.000
 YSP  H17  C23  C24  120.32  3.000
 YSP  H17  C23  C22  119.80  3.000
 YSP  C24  C23  C22  119.88  3.000
 YSP  C19  C20  C22  118.40  3.000
 YSP  C19  C20  C21  121.67  3.000
 YSP  C22  C20  C21  119.92  3.000
 YSP  H18  C24  C25  120.17  3.000
 YSP  H18  C24  C23  120.55  3.000
 YSP  C25  C24  C23  119.28  3.000
 YSP  H19  C25  C19  119.23  3.000
 YSP  H19  C25  C24  119.66  3.000
 YSP  C19  C25  C24  121.10  3.000
 YSP  H20  C26  C27  121.27  3.000
 YSP  H20  C26  C17  120.04  3.000
 YSP  C27  C26  C17  118.69  3.000
 YSP  CL1  C27  C28  118.93  3.000
 YSP  C28  C27  C26  122.18  3.000
 YSP  CL1  C27  C26  118.89  3.000
 YSP  H21  C28  C15  120.72  3.000
 YSP  H21  C28  C27  120.45  3.000
 YSP  C15  C28  C27  118.81  3.000
 YSP  O3   C12  N4   123.47  3.000
 YSP  O3   C12  N3   123.25  3.000
 YSP  N4   C12  N3   113.29  3.000
 YSP  H9   C13  C8   118.52  3.000
 YSP  H9   C13  C14  118.86  3.000
 YSP  C8   C13  C14  122.62  3.000
 YSP  C15  C14  C13  121.18  3.000
 YSP  C13  C14  C1   120.23  3.000
 YSP  C15  C14  C1   118.55  3.000
 YSP  C14  C15  C28  119.41  3.000
 YSP  C14  C15  C16  120.57  3.000
 YSP  C28  C15  C16  120.01  3.000
 YSP  H12  C18  H11  107.47  3.000
 YSP  H12  C18  O4   110.15  3.000
 YSP  H11  C18  O4   110.23  3.000
 YSP  H12  C18  C19  110.92  3.000
 YSP  H11  C18  C19  110.42  3.000
 YSP  O4   C18  C19  107.66  3.000
 YSP  C18  C19  C25  119.36  3.000
 YSP  C18  C19  C20  120.77  3.000
 YSP  C25  C19  C20  119.87  3.000
 YSP  H1   C3   N2   117.28  3.000
 YSP  H1   C3   C2   120.09  3.000
 YSP  N2   C3   C2   122.62  3.000
 YSP  C9   C8   C13  121.68  3.000
 YSP  C9   C8   C7   121.49  3.000
 YSP  C13  C8   C7   116.83  3.000
 YSP  C8   C9   C11  121.80  3.000
 YSP  C11  C9   C10  117.93  3.000
 YSP  C8   C9   C10  120.25  3.000
 YSP  C2   N1   C1   117.45  3.000
 YSP  C2   N1   C7   118.19  3.000
 YSP  C1   N1   C7   124.35  3.000
 YSP  C3   N2   C4   118.14  3.000
 YSP  H6   N3   C12  115.58  3.000
 YSP  H6   N3   C10  116.37  3.000
 YSP  C12  N3   C10  128.05  3.000
 YSP  H8   N4   C12  117.30  3.000
 YSP  H8   N4   C11  119.27  3.000
 YSP  C12  N4   C11  123.42  3.000
 YSP  C18  O4   C17  118.93  3.000
 YSP  H15  C21  H14  107.58  3.000
 YSP  H15  C21  H13  107.63  3.000
 YSP  H14  C21  H13  106.93  3.000
 YSP  H15  C21  C20  110.94  3.000
 YSP  H14  C21  C20  111.90  3.000
 YSP  H13  C21  C20  111.63  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
 YSP  CONST_01  N2   C3   C2   C6      0.00   0.0  0
 YSP  CONST_02  N2   C4   C5   C6      0.00   0.0  0
 YSP  CONST_03  C4   N2   C3   C2      0.00   0.0  0
 YSP  CONST_04  C4   C5   C6   C2      0.00   0.0  0
 YSP  CONST_05  C3   C2   C6   C5      0.00   0.0  0
 YSP  CONST_06  C3   N2   C4   C5      0.00   0.0  0
 YSP  CONST_07  C27  C26  C17  C16     0.00   0.0  0
 YSP  CONST_08  C27  C28  C15  C16     0.00   0.0  0
 YSP  CONST_09  C28  C27  C26  C17     0.00   0.0  0
 YSP  CONST_10  C28  C15  C16  C17     0.00   0.0  0
 YSP  CONST_11  C25  C24  C23  C22     0.00   0.0  0
 YSP  CONST_12  C25  C19  C20  C22     0.00   0.0  0
 YSP  CONST_13  C19  C20  C22  C23     0.00   0.0  0
 YSP  CONST_14  C19  C25  C24  C23     0.00   0.0  0
 YSP  CONST_15  C24  C23  C22  C20     0.00   0.0  0
 YSP  CONST_16  C24  C25  C19  C20     0.00   0.0  0
 YSP  CONST_17  C15  C16  C17  C26     0.00   0.0  0
 YSP  CONST_18  C15  C28  C27  C26     0.00   0.0  0
 YSP  CONST_19  N1   C2   C6   C5    180.00   0.0  0
 YSP  CONST_20  C14  C15  C16  C17   180.00   0.0  0
 YSP  CONST_21  C14  C15  C28  C27   180.00   0.0  0
 YSP  CONST_22  N2   C3   C2   N1    180.00   0.0  0
 YSP  CONST_23  C14  C1   N1   C7      0.00   0.0  0
 YSP  CONST_24  C14  C1   N1   C2    180.00   0.0  0
 YSP  CONST_25  N4   C12  N3   C10     0.00   0.0  0
 YSP  CONST_26  N3   C12  N4   C11     0.00   0.0  0
 YSP  CONST_27  C9   C10  N3   C12     0.00   0.0  0
 YSP  CONST_28  CL1  C27  C26  C17   180.00   0.0  0
 YSP  CONST_29  C23  C22  C20  C21   180.00   0.0  0
 YSP  CONST_30  C25  C19  C20  C21   180.00   0.0  0
 YSP  CONST_31  C18  C19  C20  C22   180.00   0.0  0
 YSP  CONST_32  C18  C19  C25  C24   180.00   0.0  0
 YSP  CONST_33  O4   C17  C26  C27   180.00   0.0  0
 YSP  CONST_34  O4   C17  C16  C15   180.00   0.0  0
 YSP  CONST_35  CL1  C27  C28  C15   180.00   0.0  0
 YSP  CONST_36  O1   C1   N1   C7    180.00   0.0  0
 YSP  CONST_37  O1   C1   N1   C2      0.00   0.0  0
 YSP  CONST_38  O3   C12  N3   C10   180.00   0.0  0
 YSP  CONST_39  O3   C12  N4   C11   180.00   0.0  0
 YSP  CONST_40  O2   C10  N3   C12   180.00   0.0  0
 YSP  CONST_41  H1   C3   C2   C6    180.00   0.0  0
 YSP  CONST_42  H2   C4   C5   C6    180.00   0.0  0
 YSP  CONST_43  H3   C5   C6   C2    180.00   0.0  0
 YSP  CONST_44  H4   C6   C5   C4    180.00   0.0  0
 YSP  CONST_45  H20  C26  C17  C16   180.00   0.0  0
 YSP  CONST_46  H21  C28  C15  C16   180.00   0.0  0
 YSP  CONST_47  H18  C24  C23  C22   180.00   0.0  0
 YSP  CONST_48  H19  C25  C24  C23   180.00   0.0  0
 YSP  CONST_49  H17  C23  C22  C20   180.00   0.0  0
 YSP  CONST_50  H16  C22  C23  C24   180.00   0.0  0
 YSP  CONST_51  H10  C16  C17  C26   180.00   0.0  0
 YSP  CONST_52  H6   N3   C10  C9    180.00   0.0  0
 YSP  CONST_53  H8   N4   C12  N3    180.00   0.0  0
 YSP  Var_01    C3   C2   N1   C7   -105.96  30.0  2
 YSP  Var_02    C11  C9   C8   C7   -135.38  30.0  2
 YSP  Var_03    C16  C15  C14  C1     48.64  30.0  3
 YSP  Var_04    C19  C18  O4   C17  -171.20  30.0  3
 YSP  Var_05    O4   C18  C19  C20    73.21  30.0  2
 YSP  Var_06    H13  C21  C20  C22   111.55  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
 YSP  plan-1  C10  0.020
 YSP  plan-1  C11  0.020
 YSP  plan-1  C12  0.020
 YSP  plan-1  C8   0.020
 YSP  plan-1  C9   0.020
 YSP  plan-1  N3   0.020
 YSP  plan-1  N4   0.020
 YSP  plan-1  O3   0.020
 YSP  plan-1  H7   0.020
 YSP  plan-1  H6   0.020
 YSP  plan-1  H8   0.020
 YSP  plan-1  O2   0.020
 YSP  plan-2  C22  0.020
 YSP  plan-2  C23  0.020
 YSP  plan-2  C20  0.020
 YSP  plan-2  C24  0.020
 YSP  plan-2  C25  0.020
 YSP  plan-2  C18  0.020
 YSP  plan-2  C19  0.020
 YSP  plan-2  H16  0.020
 YSP  plan-2  H17  0.020
 YSP  plan-2  H18  0.020
 YSP  plan-2  H19  0.020
 YSP  plan-2  C21  0.020
 YSP  plan-3  C16  0.020
 YSP  plan-3  C17  0.020
 YSP  plan-3  C26  0.020
 YSP  plan-3  C27  0.020
 YSP  plan-3  C28  0.020
 YSP  plan-3  C14  0.020
 YSP  plan-3  C15  0.020
 YSP  plan-3  O4   0.020
 YSP  plan-3  CL1  0.020
 YSP  plan-3  H10  0.020
 YSP  plan-3  H20  0.020
 YSP  plan-3  H21  0.020
 YSP  plan-4  C7   0.020
 YSP  plan-4  C1   0.020
 YSP  plan-4  C2   0.020
 YSP  plan-4  C13  0.020
 YSP  plan-4  C14  0.020
 YSP  plan-4  C15  0.020
 YSP  plan-4  C8   0.020
 YSP  plan-4  C9   0.020
 YSP  plan-4  N1   0.020
 YSP  plan-4  O1   0.020
 YSP  plan-4  H5   0.020
 YSP  plan-4  H9   0.020
 YSP  plan-5  C6   0.020
 YSP  plan-5  C2   0.020
 YSP  plan-5  C4   0.020
 YSP  plan-5  C5   0.020
 YSP  plan-5  C3   0.020
 YSP  plan-5  N1   0.020
 YSP  plan-5  N2   0.020
 YSP  plan-5  H4   0.020
 YSP  plan-5  H2   0.020
 YSP  plan-5  H3   0.020
 YSP  plan-5  H1   0.020

