# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 26 17:13:15 2022
#   Inital geometry file: a 155 line input string
#   Ligand name: 5-(3-{3-chloro-5-[(3-fluorophenyl)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: Fc1cccc(COc2cc(Cl)cc(c2)C3=CC(=CN(C3=O)c4cccnc4)C5=CNC(=O)NC5=O)c1
#
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
 YSM  YSM  5-(3-{3-chloro-5-[(3-fluorophenyl)methoxy]phenyl}-2-oxo-2H-[1,3'-bipyridin]-5-yl)pyrimidine-2,4(1H,3H)-dione  ligand  55  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_YSM
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
 YSM  C1   C   CR6   0   0.540  -20.5918  -4.2223  -27.1815
 YSM  F1   F   F     0  -0.314  -17.2845  -7.0776  -35.1693
 YSM  N1   N   NR6   0  -0.620  -20.3510  -4.3697  -25.8156
 YSM  C2   C   CR6   0   0.176  -18.9968  -4.5606  -25.4082
 YSM  C3   C   CR16  0  -0.053  -18.2124  -3.4631  -25.0897
 YSM  N3   N   NR16  0  -0.719  -24.5278  -3.4066  -22.0292
 YSM  O3   O   O     0  -0.462  -26.5969  -4.0520  -21.3401
 YSM  C4   C   CR16  0  -0.054  -16.4397  -4.7954  -24.5847
 YSM  O4   O   O2    0  -0.466  -21.7418  -5.2865  -32.2605
 YSM  C5   C   CR16  0  -0.330  -17.1480  -5.9509  -24.8808
 YSM  C6   C   CR16  0  -0.137  -18.4609  -5.8322  -25.3059
 YSM  C7   C   CR16  0   0.030  -21.3125  -4.3408  -24.8588
 YSM  C8   C   CR6   0  -0.012  -22.6217  -4.1460  -25.1719
 YSM  C9   C   CR6   0  -0.242  -23.6627  -4.1245  -24.1379
 YSM  C10  C   CR6   0   0.560  -23.4633  -3.3604  -22.9138
 YSM  C11  C   CR16  0   0.065  -24.8355  -4.7742  -24.2935
 YSM  C12  C   CR6   0   0.681  -25.7221  -4.0658  -22.1776
 YSM  C13  C   CR16  0  -0.200  -22.9339  -3.9849  -26.5458
 YSM  C14  C   CR6   0  -0.171  -21.9865  -4.0304  -27.5244
 YSM  C15  C   CR6   0   0.121  -22.3400  -3.8331  -28.9433
 YSM  C16  C   CR16  0  -0.298  -23.1714  -2.7786  -29.3044
 YSM  C17  C   CR6   0  -0.005  -23.5024  -2.6170  -30.6420
 YSM  C18  C   CR16  0  -0.320  -23.0254  -3.4604  -31.6239
 YSM  C20  C   CH2   0  -0.269  -20.8346  -6.3390  -31.9625
 YSM  C21  C   CR6   0   0.115  -20.3435  -6.8939  -33.2660
 YSM  C22  C   CR16  0  -0.293  -21.2113  -7.5624  -34.1263
 YSM  C23  C   CR16  0  -0.225  -20.7486  -8.0565  -35.3362
 YSM  C24  C   CR16  0  -0.416  -19.4179  -7.8989  -35.7052
 YSM  C26  C   CR16  0  -0.462  -19.0117  -6.7301  -33.6261
 YSM  C19  C   CR6   0   0.410  -22.1868  -4.5142  -31.2531
 YSM  C25  C   CR6   0   0.545  -18.5748  -7.2385  -34.8351
 YSM  C27  C   CR16  0  -0.414  -21.8549  -4.7066  -29.9177
 YSM  N2   N   N     0  -0.398  -16.9563  -3.5760  -24.6842
 YSM  N4   N   NR16  0  -0.674  -25.8245  -4.7409  -23.3652
 YSM  O1   O   O     0  -0.463  -19.6583  -4.2450  -27.9694
 YSM  O2   O   O     0  -0.436  -22.4688  -2.7170  -22.6410
 YSM  CL1  CL  CL    0  -0.125  -24.5314  -1.2978  -31.0964
 YSM  H1   H   HCR6  0   0.280  -18.6243  -2.4618  -25.1647
 YSM  H6   H   HNR6  0   0.427  -24.4175  -2.8898  -21.1650
 YSM  H2   H   HCR6  0   0.274  -15.4103  -4.8587  -24.2512
 YSM  H3   H   HCR6  0   0.282  -16.6803  -6.9202  -24.7798
 YSM  H4   H   HCR6  0   0.288  -19.0562  -6.7034  -25.5480
 YSM  H5   H   HCR6  0   0.315  -20.9657  -4.4963  -23.8482
 YSM  H7   H   HCR6  0   0.322  -25.0545  -5.3693  -25.1697
 YSM  H9   H   HCR6  0   0.278  -23.9685  -3.8221  -26.8267
 YSM  H10  H   HCR6  0   0.275  -23.5353  -2.0825  -28.5609
 YSM  H11  H   HCR6  0   0.285  -23.2813  -3.3113  -32.6647
 YSM  H13  H   HCH2  0   0.248  -21.3379  -7.1142  -31.3747
 YSM  H12  H   HCH2  0   0.253  -19.9902  -5.9683  -31.3733
 YSM  H14  H   HCR6  0   0.260  -22.2491  -7.7011  -33.8498
 YSM  H15  H   HCR6  0   0.269  -21.4255  -8.5746  -36.0023
 YSM  H16  H   HCR6  0   0.281  -19.0477  -8.2847  -36.6461
 YSM  H17  H   HCR6  0   0.278  -18.3198  -6.2120  -32.9732
 YSM  H18  H   HCR6  0   0.283  -21.2252  -5.5306  -29.6173
 YSM  H8   H   HNR6  0   0.439  -26.6795  -5.2510  -23.5357

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
 YSM  F1   C25  single    1.342  0.020  1.342
 YSM  C25  C24  aromatic  1.380  0.020  1.380
 YSM  C25  C26  aromatic  1.382  0.020  1.382
 YSM  C24  C23  aromatic  1.390  0.020  1.390
 YSM  C26  C21  aromatic  1.389  0.020  1.389
 YSM  C23  C22  aromatic  1.386  0.020  1.386
 YSM  C21  C22  aromatic  1.393  0.020  1.393
 YSM  C21  C20  single    1.499  0.020  1.499
 YSM  C20  O4   single    1.421  0.020  1.421
 YSM  O4   C19  single    1.345  0.020  1.345
 YSM  C18  C19  aromatic  1.397  0.020  1.397
 YSM  C18  C17  aromatic  1.379  0.020  1.379
 YSM  CL1  C17  single    1.734  0.020  1.734
 YSM  C19  C27  aromatic  1.389  0.020  1.389
 YSM  C17  C16  aromatic  1.387  0.020  1.387
 YSM  C27  C15  aromatic  1.396  0.020  1.396
 YSM  C16  C15  aromatic  1.390  0.020  1.390
 YSM  C15  C14  single    1.476  0.020  1.476
 YSM  O1   C1   double    1.222  0.020  1.222
 YSM  C14  C1   single    1.449  0.020  1.449
 YSM  C14  C13  double    1.363  0.020  1.363
 YSM  C1   N1   single    1.395  0.020  1.395
 YSM  C13  C8   single    1.418  0.020  1.418
 YSM  N1   C2   single    1.427  0.020  1.427
 YSM  N1   C7   single    1.357  0.020  1.357
 YSM  C2   C3   aromatic  1.386  0.020  1.386
 YSM  C2   C6   aromatic  1.384  0.020  1.384
 YSM  C3   N2   aromatic  1.325  0.020  1.325
 YSM  C8   C7   double    1.360  0.020  1.360
 YSM  C8   C9   single    1.467  0.020  1.467
 YSM  C6   C5   aromatic  1.385  0.020  1.385
 YSM  N2   C4   aromatic  1.328  0.020  1.328
 YSM  C11  C9   double    1.350  0.020  1.350
 YSM  C11  N4   single    1.357  0.020  1.357
 YSM  C5   C4   aromatic  1.387  0.020  1.387
 YSM  C9   C10  single    1.457  0.020  1.457
 YSM  N4   C12  single    1.370  0.020  1.370
 YSM  C10  O2   double    1.216  0.020  1.216
 YSM  C10  N3   single    1.385  0.020  1.385
 YSM  C12  N3   single    1.372  0.020  1.372
 YSM  C12  O3   double    1.211  0.020  1.211
 YSM  C3   H1   single    0.930  0.020  1.080
 YSM  N3   H6   single    0.860  0.020  1.020
 YSM  C4   H2   single    0.930  0.020  1.080
 YSM  C5   H3   single    0.930  0.020  1.080
 YSM  C6   H4   single    0.930  0.020  1.080
 YSM  C7   H5   single    0.930  0.020  1.080
 YSM  C11  H7   single    0.930  0.020  1.080
 YSM  C13  H9   single    0.930  0.020  1.080
 YSM  C16  H10  single    0.930  0.020  1.080
 YSM  C18  H11  single    0.930  0.020  1.080
 YSM  C20  H13  single    0.970  0.020  1.090
 YSM  C20  H12  single    0.970  0.020  1.090
 YSM  C22  H14  single    0.930  0.020  1.080
 YSM  C23  H15  single    0.930  0.020  1.080
 YSM  C24  H16  single    0.930  0.020  1.080
 YSM  C26  H17  single    0.930  0.020  1.080
 YSM  C27  H18  single    0.930  0.020  1.080
 YSM  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
 YSM  O1   C1   C14  125.82  3.000
 YSM  C14  C1   N1   114.32  3.000
 YSM  O1   C1   N1   119.85  3.000
 YSM  C7   N1   C2   118.30  3.000
 YSM  C7   N1   C1   124.47  3.000
 YSM  C2   N1   C1   117.23  3.000
 YSM  C6   C2   C3   119.44  3.000
 YSM  C6   C2   N1   120.77  3.000
 YSM  C3   C2   N1   119.78  3.000
 YSM  H1   C3   N2   117.36  3.000
 YSM  H1   C3   C2   119.99  3.000
 YSM  N2   C3   C2   122.65  3.000
 YSM  H6   N3   C12  115.60  3.000
 YSM  H6   N3   C10  116.38  3.000
 YSM  C12  N3   C10  128.02  3.000
 YSM  H2   C4   N2   116.49  3.000
 YSM  H2   C4   C5   120.13  3.000
 YSM  N2   C4   C5   123.38  3.000
 YSM  C19  O4   C20  118.64  3.000
 YSM  H3   C5   C6   121.04  3.000
 YSM  H3   C5   C4   120.40  3.000
 YSM  C6   C5   C4   118.56  3.000
 YSM  H4   C6   C5   121.39  3.000
 YSM  H4   C6   C2   120.67  3.000
 YSM  C5   C6   C2   117.94  3.000
 YSM  H5   C7   C8   123.05  3.000
 YSM  H5   C7   N1   115.43  3.000
 YSM  C8   C7   N1   121.52  3.000
 YSM  C13  C8   C9   121.66  3.000
 YSM  C9   C8   C7   121.52  3.000
 YSM  C13  C8   C7   116.82  3.000
 YSM  C11  C9   C10  117.93  3.000
 YSM  C10  C9   C8   120.18  3.000
 YSM  C11  C9   C8   121.88  3.000
 YSM  O2   C10  C9   125.33  3.000
 YSM  O2   C10  N3   120.21  3.000
 YSM  C9   C10  N3   114.46  3.000
 YSM  H7   C11  N4   114.85  3.000
 YSM  H7   C11  C9   122.29  3.000
 YSM  N4   C11  C9   122.86  3.000
 YSM  N4   C12  O3   123.44  3.000
 YSM  O3   C12  N3   123.25  3.000
 YSM  N4   C12  N3   113.31  3.000
 YSM  H9   C13  C14  118.83  3.000
 YSM  H9   C13  C8   118.56  3.000
 YSM  C14  C13  C8   122.61  3.000
 YSM  C15  C14  C13  121.30  3.000
 YSM  C13  C14  C1   120.24  3.000
 YSM  C15  C14  C1   118.41  3.000
 YSM  C27  C15  C16  120.07  3.000
 YSM  C16  C15  C14  119.63  3.000
 YSM  C27  C15  C14  120.29  3.000
 YSM  H10  C16  C17  120.50  3.000
 YSM  H10  C16  C15  120.71  3.000
 YSM  C17  C16  C15  118.77  3.000
 YSM  CL1  C17  C18  118.94  3.000
 YSM  CL1  C17  C16  118.88  3.000
 YSM  C18  C17  C16  122.18  3.000
 YSM  H11  C18  C19  120.08  3.000
 YSM  H11  C18  C17  121.24  3.000
 YSM  C19  C18  C17  118.68  3.000
 YSM  H12  C20  H13  107.78  3.000
 YSM  H12  C20  C21  109.92  3.000
 YSM  H13  C20  C21  110.80  3.000
 YSM  H12  C20  O4   110.77  3.000
 YSM  H13  C20  O4   110.08  3.000
 YSM  C21  C20  O4   107.51  3.000
 YSM  C26  C21  C22  119.59  3.000
 YSM  C22  C21  C20  120.70  3.000
 YSM  C26  C21  C20  119.71  3.000
 YSM  H14  C22  C23  119.80  3.000
 YSM  H14  C22  C21  120.06  3.000
 YSM  C23  C22  C21  120.14  3.000
 YSM  H15  C23  C24  119.33  3.000
 YSM  H15  C23  C22  119.95  3.000
 YSM  C24  C23  C22  120.72  3.000
 YSM  H16  C24  C25  120.66  3.000
 YSM  H16  C24  C23  121.19  3.000
 YSM  C25  C24  C23  118.15  3.000
 YSM  H17  C26  C25  120.08  3.000
 YSM  H17  C26  C21  120.83  3.000
 YSM  C25  C26  C21  119.10  3.000
 YSM  C27  C19  C18  120.19  3.000
 YSM  C27  C19  O4   124.15  3.000
 YSM  C18  C19  O4   115.66  3.000
 YSM  C26  C25  C24  122.30  3.000
 YSM  C26  C25  F1   118.52  3.000
 YSM  C24  C25  F1   119.18  3.000
 YSM  H18  C27  C19  120.82  3.000
 YSM  H18  C27  C15  119.09  3.000
 YSM  C19  C27  C15  120.09  3.000
 YSM  C4   N2   C3   118.04  3.000
 YSM  H8   N4   C12  117.29  3.000
 YSM  H8   N4   C11  119.28  3.000
 YSM  C12  N4   C11  123.42  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
 YSM  CONST_01  C4   N2   C3   C2      0.00   0.0  0
 YSM  CONST_02  C4   C5   C6   C2      0.00   0.0  0
 YSM  CONST_03  C5   C6   C2   C3      0.00   0.0  0
 YSM  CONST_04  C5   C4   N2   C3      0.00   0.0  0
 YSM  CONST_05  N2   C3   C2   C6      0.00   0.0  0
 YSM  CONST_06  N2   C4   C5   C6      0.00   0.0  0
 YSM  CONST_07  C18  C19  C27  C15     0.00   0.0  0
 YSM  CONST_08  C18  C17  C16  C15     0.00   0.0  0
 YSM  CONST_09  C19  C18  C17  C16     0.00   0.0  0
 YSM  CONST_10  C19  C27  C15  C16     0.00   0.0  0
 YSM  CONST_11  C27  C19  C18  C17     0.00   0.0  0
 YSM  CONST_12  C27  C15  C16  C17     0.00   0.0  0
 YSM  CONST_13  C24  C25  C26  C21     0.00   0.0  0
 YSM  CONST_14  C24  C23  C22  C21     0.00   0.0  0
 YSM  CONST_15  C25  C24  C23  C22     0.00   0.0  0
 YSM  CONST_16  C25  C26  C21  C22     0.00   0.0  0
 YSM  CONST_17  C26  C25  C24  C23     0.00   0.0  0
 YSM  CONST_18  C26  C21  C22  C23     0.00   0.0  0
 YSM  CONST_19  N2   C3   C2   N1    180.00   0.0  0
 YSM  CONST_20  C5   C6   C2   N1    180.00   0.0  0
 YSM  CONST_21  C19  C27  C15  C14   180.00   0.0  0
 YSM  CONST_22  C17  C16  C15  C14   180.00   0.0  0
 YSM  CONST_23  C14  C1   N1   C2    180.00   0.0  0
 YSM  CONST_24  C11  N4   C12  N3      0.00   0.0  0
 YSM  CONST_25  C14  C1   N1   C7      0.00   0.0  0
 YSM  CONST_26  C12  N3   C10  C9      0.00   0.0  0
 YSM  CONST_27  N4   C12  N3   C10     0.00   0.0  0
 YSM  CONST_28  C23  C24  C25  F1    180.00   0.0  0
 YSM  CONST_29  C21  C26  C25  F1    180.00   0.0  0
 YSM  CONST_30  C17  C18  C19  O4    180.00   0.0  0
 YSM  CONST_31  C15  C27  C19  O4    180.00   0.0  0
 YSM  CONST_32  CL1  C17  C16  C15   180.00   0.0  0
 YSM  CONST_33  C25  C26  C21  C20   180.00   0.0  0
 YSM  CONST_34  C23  C22  C21  C20   180.00   0.0  0
 YSM  CONST_35  CL1  C17  C18  C19   180.00   0.0  0
 YSM  CONST_36  O1   C1   N1   C2      0.00   0.0  0
 YSM  CONST_37  C11  N4   C12  O3    180.00   0.0  0
 YSM  CONST_38  C10  N3   C12  O3    180.00   0.0  0
 YSM  CONST_39  O1   C1   N1   C7    180.00   0.0  0
 YSM  CONST_40  O2   C10  N3   C12   180.00   0.0  0
 YSM  CONST_41  H1   C3   C2   N1      0.00   0.0  0
 YSM  CONST_42  H4   C6   C2   N1      0.00   0.0  0
 YSM  CONST_43  H3   C5   C6   C2    180.00   0.0  0
 YSM  CONST_44  H2   C4   N2   C3    180.00   0.0  0
 YSM  CONST_45  H18  C27  C15  C14     0.00   0.0  0
 YSM  CONST_46  H10  C16  C15  C14     0.00   0.0  0
 YSM  CONST_47  H11  C18  C17  C16   180.00   0.0  0
 YSM  CONST_48  H15  C23  C22  C21   180.00   0.0  0
 YSM  CONST_49  H16  C24  C23  C22   180.00   0.0  0
 YSM  CONST_50  H17  C26  C21  C22   180.00   0.0  0
 YSM  CONST_51  H14  C22  C23  C24   180.00   0.0  0
 YSM  CONST_52  H8   N4   C12  N3    180.00   0.0  0
 YSM  CONST_53  H6   N3   C10  C9    180.00   0.0  0
 YSM  Var_01    C27  C15  C14  C1     49.59  30.0  3
 YSM  Var_02    C3   C2   N1   C1     90.87  30.0  2
 YSM  Var_03    C11  C9   C8   C7   -135.68  30.0  2
 YSM  Var_04    C26  C21  C20  O4    112.81  30.0  2
 YSM  Var_05    C27  C19  O4   C20    -2.47  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
 YSM  plan-1  N1   0.020
 YSM  plan-1  C2   0.020
 YSM  plan-1  C3   0.020
 YSM  plan-1  C4   0.020
 YSM  plan-1  C5   0.020
 YSM  plan-1  C6   0.020
 YSM  plan-1  N2   0.020
 YSM  plan-1  H1   0.020
 YSM  plan-1  H2   0.020
 YSM  plan-1  H3   0.020
 YSM  plan-1  H4   0.020
 YSM  plan-2  N3   0.020
 YSM  plan-2  O3   0.020
 YSM  plan-2  C8   0.020
 YSM  plan-2  C9   0.020
 YSM  plan-2  C10  0.020
 YSM  plan-2  C11  0.020
 YSM  plan-2  C12  0.020
 YSM  plan-2  N4   0.020
 YSM  plan-2  O2   0.020
 YSM  plan-2  H6   0.020
 YSM  plan-2  H7   0.020
 YSM  plan-2  H8   0.020
 YSM  plan-3  C1   0.020
 YSM  plan-3  N1   0.020
 YSM  plan-3  C2   0.020
 YSM  plan-3  C7   0.020
 YSM  plan-3  C8   0.020
 YSM  plan-3  C9   0.020
 YSM  plan-3  C13  0.020
 YSM  plan-3  C14  0.020
 YSM  plan-3  C15  0.020
 YSM  plan-3  O1   0.020
 YSM  plan-3  H5   0.020
 YSM  plan-3  H9   0.020
 YSM  plan-4  O4   0.020
 YSM  plan-4  C14  0.020
 YSM  plan-4  C15  0.020
 YSM  plan-4  C16  0.020
 YSM  plan-4  C17  0.020
 YSM  plan-4  C18  0.020
 YSM  plan-4  C19  0.020
 YSM  plan-4  C27  0.020
 YSM  plan-4  CL1  0.020
 YSM  plan-4  H10  0.020
 YSM  plan-4  H11  0.020
 YSM  plan-4  H18  0.020
 YSM  plan-5  F1   0.020
 YSM  plan-5  C20  0.020
 YSM  plan-5  C21  0.020
 YSM  plan-5  C22  0.020
 YSM  plan-5  C23  0.020
 YSM  plan-5  C24  0.020
 YSM  plan-5  C26  0.020
 YSM  plan-5  C25  0.020
 YSM  plan-5  H14  0.020
 YSM  plan-5  H15  0.020
 YSM  plan-5  H16  0.020
 YSM  plan-5  H17  0.020

