# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 04:40:00 2022
#   Inital geometry file: a 155 line input string
#   Ligand name: 5-(3-{3-chloro-5-[(2-chlorophenyl)methoxy]phenyl}-2-oxo[2H-[1,3'-bipyridine]]-5-yl)pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cc(OCc2ccccc2Cl)cc(c1)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
 XF7  XF7  5-(3-{3-chloro-5-[(2-chlorophenyl)methoxy]phenyl}-2-oxo[2H-[1,3'-bipyridine]]-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_XF7
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
 XF7  C1    C   CR6   0   0.540  -20.3426  -4.5218  -27.9790
 XF7  C2    C   CR16  0  -0.202  -22.6889  -4.2701  -27.3639
 XF7  C3    C   CR6   0  -0.168  -21.7291  -4.2902  -28.3322
 XF7  C4    C   CR6   0   0.122  -22.0683  -4.0318  -29.7452
 XF7  C5    C   CR16  0  -0.300  -22.9242  -2.9810  -30.0610
 XF7  C6    C   CR6   0   0.182  -18.7805  -4.9717  -26.1954
 XF7  C7    C   CR6   0  -0.006  -23.2608  -2.7668  -31.3892
 XF7  C8    C   CR16  0  -0.322  -22.7630  -3.5515  -32.4088
 XF7  C9    C   CR6   0   0.411  -21.9018  -4.6014  -32.0849
 XF7  C10   C   CH2   0  -0.276  -20.4080  -6.2628  -32.9000
 XF7  C11   C   CR6   0   0.189  -19.9184  -6.7225  -34.2378
 XF7  C12   C   CR16  0  -0.413  -21.5604  -4.8449  -30.7600
 XF7  C13   C   CR16  0  -0.052  -17.8639  -3.9322  -26.1272
 XF7  C14   C   CR16  0  -0.056  -16.2346  -5.3321  -25.3769
 XF7  C15   C   CR16  0  -0.328  -17.0807  -6.4294  -25.4057
 XF7  C16   C   CR16  0  -0.143  -18.3874  -6.2466  -25.8307
 XF7  C17   C   CR16  0   0.029  -21.0952  -4.7076  -25.6705
 XF7  C18   C   CR6   0  -0.013  -22.3970  -4.4841  -25.9936
 XF7  C24   C   CR6   0  -0.244  -23.4490  -4.4790  -24.9701
 XF7  C26   C   CR6   0   0.560  -23.2593  -3.7374  -23.7308
 XF7  C25   C   CR16  0   0.066  -24.6222  -5.1214  -25.1500
 XF7  C30   C   CR6   0   0.682  -25.5260  -4.4522  -23.0287
 XF7  C32   C   CR16  0  -0.315  -20.1703  -8.0197  -34.6710
 XF7  C33   C   CR16  0  -0.228  -19.7256  -8.4680  -35.9063
 XF7  C34   C   CR16  0  -0.270  -19.0188  -7.6094  -36.7343
 XF7  C35   C   CR16  0  -0.196  -18.7541  -6.3095  -36.3268
 XF7  C36   C   CR6   0  -0.100  -19.2041  -5.8810  -35.0885
 XF7  N19   N   NR6   0  -0.621  -20.1204  -4.7180  -26.6145
 XF7  N20   N   N     0  -0.399  -16.6141  -4.1079  -25.7289
 XF7  N28   N   NR16  0  -0.719  -24.3320  -3.7981  -22.8569
 XF7  N29   N   NR16  0  -0.673  -25.6199  -5.1028  -24.2305
 XF7  O21   O   O     0  -0.463  -19.4017  -4.5442  -28.7576
 XF7  O22   O   O2    0  -0.465  -21.4564  -5.3308  -33.1236
 XF7  O27   O   O     0  -0.436  -22.2664  -3.1003  -23.4380
 XF7  O31   O   O     0  -0.462  -26.4077  -4.4534  -22.1984
 XF7  CL23  CL  CL    0  -0.125  -24.3197  -1.4521  -31.7840
 XF7  CL24  CL  CL    0  -0.125  -18.8452  -4.2574  -34.5963
 XF7  H1    H   HCR6  0   0.278  -23.7184  -4.0857  -27.6500
 XF7  H2    H   HCR6  0   0.276  -23.3054  -2.3276  -29.2879
 XF7  H3    H   HCR6  0   0.285  -23.0220  -3.3615  -33.4421
 XF7  H4    H   HCH2  0   0.258  -20.7694  -7.1192  -32.3225
 XF7  H5    H   HCH2  0   0.249  -19.5962  -5.7972  -32.3311
 XF7  H6    H   HCR6  0   0.283  -20.9137  -5.6695  -30.5000
 XF7  H7    H   HCR6  0   0.279  -18.1621  -2.9255  -26.4010
 XF7  H8    H   HCR6  0   0.273  -15.2062  -5.4448  -25.0536
 XF7  H9    H   HCR6  0   0.282  -16.7238  -7.4048  -25.1060
 XF7  H10   H   HCR6  0   0.290  -19.0843  -7.0740  -25.8768
 XF7  H11   H   HCR6  0   0.315  -20.7651  -4.8971  -24.6600
 XF7  H13   H   HCR6  0   0.322  -24.8343  -5.6976  -26.0403
 XF7  H14   H   HCR6  0   0.266  -20.7243  -8.6875  -34.0228
 XF7  H15   H   HCR6  0   0.265  -19.9322  -9.4825  -36.2195
 XF7  H16   H   HCR6  0   0.270  -18.6668  -7.9452  -37.7007
 XF7  H17   H   HCR6  0   0.281  -18.2001  -5.6362  -36.9668
 XF7  H18   H   HNR6  0   0.427  -24.2291  -3.2982  -21.9820
 XF7  H12   H   HNR6  0   0.439  -26.4747  -5.6071  -24.4186

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
 XF7  C34   C35   aromatic  1.388  0.020  1.388
 XF7  C34   C33   aromatic  1.386  0.020  1.386
 XF7  C35   C36   aromatic  1.385  0.020  1.385
 XF7  C33   C32   aromatic  1.387  0.020  1.387
 XF7  C36   CL24  single    1.734  0.020  1.734
 XF7  C36   C11   aromatic  1.394  0.020  1.394
 XF7  C32   C11   aromatic  1.391  0.020  1.391
 XF7  C11   C10   single    1.497  0.020  1.497
 XF7  O22   C10   single    1.421  0.020  1.421
 XF7  O22   C9    single    1.345  0.020  1.345
 XF7  C8    C9    aromatic  1.396  0.020  1.396
 XF7  C8    C7    aromatic  1.380  0.020  1.380
 XF7  C9    C12   aromatic  1.390  0.020  1.390
 XF7  CL23  C7    single    1.734  0.020  1.734
 XF7  C7    C5    aromatic  1.387  0.020  1.387
 XF7  C12   C4    aromatic  1.396  0.020  1.396
 XF7  C5    C4    aromatic  1.392  0.020  1.392
 XF7  C4    C3    single    1.476  0.020  1.476
 XF7  O21   C1    double    1.222  0.020  1.222
 XF7  C3    C1    single    1.449  0.020  1.449
 XF7  C3    C2    double    1.363  0.020  1.363
 XF7  C1    N19   single    1.396  0.020  1.396
 XF7  C2    C18   single    1.417  0.020  1.417
 XF7  N19   C6    single    1.427  0.020  1.427
 XF7  N19   C17   single    1.357  0.020  1.357
 XF7  C6    C13   aromatic  1.388  0.020  1.388
 XF7  C6    C16   aromatic  1.383  0.020  1.383
 XF7  C13   N20   aromatic  1.323  0.020  1.323
 XF7  C18   C17   double    1.360  0.020  1.360
 XF7  C18   C24   single    1.468  0.020  1.468
 XF7  C16   C15   aromatic  1.386  0.020  1.386
 XF7  N20   C14   aromatic  1.329  0.020  1.329
 XF7  C15   C14   aromatic  1.386  0.020  1.386
 XF7  C25   C24   double    1.350  0.020  1.350
 XF7  C25   N29   single    1.357  0.020  1.357
 XF7  C24   C26   single    1.457  0.020  1.457
 XF7  N29   C30   single    1.370  0.020  1.370
 XF7  C26   O27   double    1.216  0.020  1.216
 XF7  C26   N28   single    1.385  0.020  1.385
 XF7  C30   N28   single    1.372  0.020  1.372
 XF7  C30   O31   double    1.211  0.020  1.211
 XF7  C2    H1    single    0.930  0.020  1.080
 XF7  C5    H2    single    0.930  0.020  1.080
 XF7  C8    H3    single    0.930  0.020  1.080
 XF7  C10   H4    single    0.970  0.020  1.090
 XF7  C10   H5    single    0.970  0.020  1.090
 XF7  C12   H6    single    0.930  0.020  1.080
 XF7  C13   H7    single    0.930  0.020  1.080
 XF7  C14   H8    single    0.930  0.020  1.080
 XF7  C15   H9    single    0.930  0.020  1.080
 XF7  C16   H10   single    0.930  0.020  1.080
 XF7  C17   H11   single    0.930  0.020  1.080
 XF7  C25   H13   single    0.930  0.020  1.080
 XF7  C32   H14   single    0.930  0.020  1.080
 XF7  C33   H15   single    0.930  0.020  1.080
 XF7  C34   H16   single    0.930  0.020  1.080
 XF7  C35   H17   single    0.930  0.020  1.080
 XF7  N28   H18   single    0.860  0.020  1.020
 XF7  N29   H12   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
 XF7  O21   C1   N19  119.85  3.000
 XF7  N19   C1   C3   114.38  3.000
 XF7  O21   C1   C3   125.76  3.000
 XF7  H1    C2   C18  118.45  3.000
 XF7  H1    C2   C3   118.91  3.000
 XF7  C18   C2   C3   122.64  3.000
 XF7  C4    C3   C2   121.03  3.000
 XF7  C2    C3   C1   120.17  3.000
 XF7  C4    C3   C1   118.76  3.000
 XF7  C12   C4   C5   119.91  3.000
 XF7  C5    C4   C3   119.39  3.000
 XF7  C12   C4   C3   120.69  3.000
 XF7  H2    C5   C7   120.38  3.000
 XF7  H2    C5   C4   120.71  3.000
 XF7  C7    C5   C4   118.89  3.000
 XF7  N19   C6   C16  120.55  3.000
 XF7  C16   C6   C13  119.33  3.000
 XF7  N19   C6   C13  120.11  3.000
 XF7  CL23  C7   C8   118.91  3.000
 XF7  CL23  C7   C5   118.91  3.000
 XF7  C8    C7   C5   122.17  3.000
 XF7  H3    C8   C9   120.09  3.000
 XF7  H3    C8   C7   121.30  3.000
 XF7  C9    C8   C7   118.61  3.000
 XF7  O22   C9   C12  124.05  3.000
 XF7  C12   C9   C8   120.30  3.000
 XF7  O22   C9   C8   115.65  3.000
 XF7  H5    C10  H4   107.66  3.000
 XF7  H5    C10  O22  110.48  3.000
 XF7  H4    C10  O22  110.66  3.000
 XF7  H5    C10  C11  110.63  3.000
 XF7  H4    C10  C11  109.84  3.000
 XF7  O22   C10  C11  107.59  3.000
 XF7  C36   C11  C32  117.77  3.000
 XF7  C32   C11  C10  120.37  3.000
 XF7  C36   C11  C10  121.86  3.000
 XF7  H6    C12  C9   120.69  3.000
 XF7  H6    C12  C4   119.19  3.000
 XF7  C9    C12  C4   120.11  3.000
 XF7  H7    C13  N20  117.30  3.000
 XF7  H7    C13  C6   120.08  3.000
 XF7  N20   C13  C6   122.62  3.000
 XF7  H8    C14  N20  116.47  3.000
 XF7  H8    C14  C15  120.20  3.000
 XF7  N20   C14  C15  123.33  3.000
 XF7  H9    C15  C16  121.01  3.000
 XF7  H9    C15  C14  120.47  3.000
 XF7  C16   C15  C14  118.52  3.000
 XF7  H10   C16  C15  121.27  3.000
 XF7  H10   C16  C6   120.67  3.000
 XF7  C15   C16  C6   118.06  3.000
 XF7  H11   C17  N19  115.47  3.000
 XF7  H11   C17  C18  122.95  3.000
 XF7  N19   C17  C18  121.58  3.000
 XF7  C24   C18  C17  121.40  3.000
 XF7  C24   C18  C2   121.74  3.000
 XF7  C17   C18  C2   116.86  3.000
 XF7  C25   C24  C26  117.97  3.000
 XF7  C26   C24  C18  120.12  3.000
 XF7  C25   C24  C18  121.90  3.000
 XF7  O27   C26  N28  120.24  3.000
 XF7  N28   C26  C24  114.44  3.000
 XF7  O27   C26  C24  125.32  3.000
 XF7  H13   C25  N29  114.89  3.000
 XF7  H13   C25  C24  122.27  3.000
 XF7  N29   C25  C24  122.84  3.000
 XF7  O31   C30  N29  123.45  3.000
 XF7  O31   C30  N28  123.23  3.000
 XF7  N29   C30  N28  113.32  3.000
 XF7  H14   C32  C33  119.84  3.000
 XF7  H14   C32  C11  118.78  3.000
 XF7  C33   C32  C11  121.38  3.000
 XF7  H15   C33  C34  120.35  3.000
 XF7  H15   C33  C32  119.98  3.000
 XF7  C34   C33  C32  119.67  3.000
 XF7  H16   C34  C35  119.41  3.000
 XF7  H16   C34  C33  120.47  3.000
 XF7  C35   C34  C33  120.13  3.000
 XF7  H17   C35  C36  120.18  3.000
 XF7  H17   C35  C34  120.46  3.000
 XF7  C36   C35  C34  119.36  3.000
 XF7  CL24  C36  C35  118.43  3.000
 XF7  CL24  C36  C11  119.88  3.000
 XF7  C35   C36  C11  121.69  3.000
 XF7  C17   N19  C6   118.15  3.000
 XF7  C17   N19  C1   124.36  3.000
 XF7  C6    N19  C1   117.48  3.000
 XF7  C14   N20  C13  118.14  3.000
 XF7  H18   N28  C30  115.58  3.000
 XF7  H18   N28  C26  116.40  3.000
 XF7  C30   N28  C26  128.01  3.000
 XF7  H12   N29  C30  117.29  3.000
 XF7  H12   N29  C25  119.29  3.000
 XF7  C30   N29  C25  123.41  3.000
 XF7  C10   O22  C9   118.59  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
 XF7  CONST_01  C8    C9   C12  C4      0.00   0.0  0
 XF7  CONST_02  C8    C7   C5   C4      0.00   0.0  0
 XF7  CONST_03  C9    C8   C7   C5      0.00   0.0  0
 XF7  CONST_04  C9    C12  C4   C5      0.00   0.0  0
 XF7  CONST_05  C14   N20  C13  C6      0.00   0.0  0
 XF7  CONST_06  C14   C15  C16  C6      0.00   0.0  0
 XF7  CONST_07  C12   C9   C8   C7      0.00   0.0  0
 XF7  CONST_08  C12   C4   C5   C7      0.00   0.0  0
 XF7  CONST_09  C34   C35  C36  C11     0.00   0.0  0
 XF7  CONST_10  C34   C33  C32  C11     0.00   0.0  0
 XF7  CONST_11  C15   C16  C6   C13     0.00   0.0  0
 XF7  CONST_12  C15   C14  N20  C13     0.00   0.0  0
 XF7  CONST_13  N20   C13  C6   C16     0.00   0.0  0
 XF7  CONST_14  N20   C14  C15  C16     0.00   0.0  0
 XF7  CONST_15  C35   C34  C33  C32     0.00   0.0  0
 XF7  CONST_16  C35   C36  C11  C32     0.00   0.0  0
 XF7  CONST_17  C36   C35  C34  C33     0.00   0.0  0
 XF7  CONST_18  C36   C11  C32  C33     0.00   0.0  0
 XF7  CONST_19  C9    C12  C4   C3    180.00   0.0  0
 XF7  CONST_20  C7    C5   C4   C3    180.00   0.0  0
 XF7  CONST_21  N19   C6   C16  C15   180.00   0.0  0
 XF7  CONST_22  N20   C13  C6   N19   180.00   0.0  0
 XF7  CONST_23  C6    N19  C1   C3    180.00   0.0  0
 XF7  CONST_24  C17   N19  C1   C3      0.00   0.0  0
 XF7  CONST_25  C30   N28  C26  C24     0.00   0.0  0
 XF7  CONST_26  N29   C30  N28  C26     0.00   0.0  0
 XF7  CONST_27  N28   C30  N29  C25     0.00   0.0  0
 XF7  CONST_28  O22   C9   C12  C4    180.00   0.0  0
 XF7  CONST_29  CL23  C7   C5   C4    180.00   0.0  0
 XF7  CONST_30  O22   C9   C8   C7    180.00   0.0  0
 XF7  CONST_31  CL23  C7   C8   C9    180.00   0.0  0
 XF7  CONST_32  C35   C36  C11  C10   180.00   0.0  0
 XF7  CONST_33  C33   C32  C11  C10   180.00   0.0  0
 XF7  CONST_34  CL24  C36  C11  C32   180.00   0.0  0
 XF7  CONST_35  CL24  C36  C35  C34   180.00   0.0  0
 XF7  CONST_36  O21   C1   N19  C6      0.00   0.0  0
 XF7  CONST_37  O21   C1   N19  C17   180.00   0.0  0
 XF7  CONST_38  O31   C30  N28  C26   180.00   0.0  0
 XF7  CONST_39  O31   C30  N29  C25   180.00   0.0  0
 XF7  CONST_40  O27   C26  N28  C30   180.00   0.0  0
 XF7  CONST_41  H6    C12  C4   C3      0.00   0.0  0
 XF7  CONST_42  H2    C5   C4   C3      0.00   0.0  0
 XF7  CONST_43  H3    C8   C7   C5    180.00   0.0  0
 XF7  CONST_44  H9    C15  C16  C6    180.00   0.0  0
 XF7  CONST_45  H17   C35  C36  C11   180.00   0.0  0
 XF7  CONST_46  H15   C33  C32  C11   180.00   0.0  0
 XF7  CONST_47  H10   C16  C6   C13   180.00   0.0  0
 XF7  CONST_48  H8    C14  N20  C13   180.00   0.0  0
 XF7  CONST_49  H7    C13  N20  C14   180.00   0.0  0
 XF7  CONST_50  H16   C34  C33  C32   180.00   0.0  0
 XF7  CONST_51  H14   C32  C33  C34   180.00   0.0  0
 XF7  CONST_52  H18   N28  C26  C24   180.00   0.0  0
 XF7  CONST_53  H12   N29  C30  N28   180.00   0.0  0
 XF7  Var_01    C12   C4   C3   C1     47.48  30.0  2
 XF7  Var_02    C13   C6   N19  C1     76.15  30.0  2
 XF7  Var_03    C25   C24  C18  C2     44.61  30.0  2
 XF7  Var_04    C11   C10  O22  C9   -168.55  30.0  3
 XF7  Var_05    C12   C9   O22  C10   -10.94  30.0  2
 XF7  Var_06    O22   C10  C11  C32  -109.64  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
 XF7  plan-1  C1    0.020
 XF7  plan-1  C2    0.020
 XF7  plan-1  C3    0.020
 XF7  plan-1  C4    0.020
 XF7  plan-1  C6    0.020
 XF7  plan-1  C17   0.020
 XF7  plan-1  C18   0.020
 XF7  plan-1  C24   0.020
 XF7  plan-1  N19   0.020
 XF7  plan-1  O21   0.020
 XF7  plan-1  H1    0.020
 XF7  plan-1  H11   0.020
 XF7  plan-2  C6    0.020
 XF7  plan-2  C13   0.020
 XF7  plan-2  C14   0.020
 XF7  plan-2  C15   0.020
 XF7  plan-2  C16   0.020
 XF7  plan-2  N19   0.020
 XF7  plan-2  N20   0.020
 XF7  plan-2  H7    0.020
 XF7  plan-2  H8    0.020
 XF7  plan-2  H9    0.020
 XF7  plan-2  H10   0.020
 XF7  plan-3  C3    0.020
 XF7  plan-3  C4    0.020
 XF7  plan-3  C5    0.020
 XF7  plan-3  C7    0.020
 XF7  plan-3  C8    0.020
 XF7  plan-3  C9    0.020
 XF7  plan-3  C12   0.020
 XF7  plan-3  O22   0.020
 XF7  plan-3  CL23  0.020
 XF7  plan-3  H2    0.020
 XF7  plan-3  H3    0.020
 XF7  plan-3  H6    0.020
 XF7  plan-4  C18   0.020
 XF7  plan-4  C24   0.020
 XF7  plan-4  C26   0.020
 XF7  plan-4  C25   0.020
 XF7  plan-4  C30   0.020
 XF7  plan-4  N28   0.020
 XF7  plan-4  N29   0.020
 XF7  plan-4  O27   0.020
 XF7  plan-4  O31   0.020
 XF7  plan-4  H13   0.020
 XF7  plan-4  H18   0.020
 XF7  plan-4  H12   0.020
 XF7  plan-5  C10   0.020
 XF7  plan-5  C11   0.020
 XF7  plan-5  C32   0.020
 XF7  plan-5  C33   0.020
 XF7  plan-5  C34   0.020
 XF7  plan-5  C35   0.020
 XF7  plan-5  C36   0.020
 XF7  plan-5  CL24  0.020
 XF7  plan-5  H14   0.020
 XF7  plan-5  H15   0.020
 XF7  plan-5  H16   0.020
 XF7  plan-5  H17   0.020

