# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 03:59:22 2022
#   Inital geometry file: a 155 line input string
#   Ligand name: 5-{3-[3-(benzyloxy)-5-chlorophenyl]-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(OCc2ccccc2)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
 XF4  XF4  5-{3-[3-(benzyloxy)-5-chlorophenyl]-2-oxo[2H-[1,3'-bipyridine]]-5-yl}pyrimidine-2,4(1H,3H)-dione  ligand  55  36  .  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_XF4
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
 XF4  C1    C   CR6   0   0.540  -13.8932  -26.7948   1.0626
 XF4  C2    C   CR16  0  -0.201  -14.1590  -28.7776  -0.3289
 XF4  C3    C   CR6   0  -0.166  -14.6636  -27.5986   0.1349
 XF4  C4    C   CR6   0   0.122  -16.0159  -27.1495  -0.2505
 XF4  C5    C   CR16  0  -0.302  -17.0606  -28.0692  -0.2456
 XF4  C6    C   CR6   0   0.180  -11.8628  -26.6141   2.3468
 XF4  C7    C   CR6   0  -0.004  -18.3238  -27.6513  -0.6366
 XF4  C8    C   CR16  0  -0.322  -18.5811  -26.3511  -1.0160
 XF4  C9    C   CR6   0   0.412  -17.5303  -25.4310  -1.0128
 XF4  C10   C   CH2   0  -0.273  -16.8856  -23.1480  -1.2645
 XF4  C11   C   CR6   0   0.102  -17.5912  -21.8476  -1.5033
 XF4  C12   C   CR16  0  -0.417  -16.2523  -25.8289  -0.6379
 XF4  C13   C   CR16  0  -0.052  -12.1338  -26.7054   3.7042
 XF4  C14   C   CR16  0  -0.055  -10.4054  -25.3158   4.2090
 XF4  C15   C   CR16  0  -0.329  -10.0585  -25.1658   2.8751
 XF4  C16   C   CR16  0  -0.141  -10.8087  -25.8292   1.9166
 XF4  C17   C   CR16  0   0.029  -12.1722  -28.5149   0.9294
 XF4  C18   C   CR6   0  -0.015  -12.8853  -29.2700   0.0515
 XF4  C24   C   CR6   0  -0.244  -12.3669  -30.5379  -0.4783
 XF4  C25   C   CR16  0   0.067  -12.4443  -30.8445  -1.7905
 XF4  C26   C   CR6   0   0.560  -11.7952  -31.5306   0.4215
 XF4  C30   C   CR6   0   0.682  -11.4693  -33.0238  -1.5304
 XF4  C32   C   CR16  0  -0.284  -18.4730  -21.3520  -0.5446
 XF4  C33   C   CR16  0  -0.240  -19.1513  -20.1626  -0.7608
 XF4  C34   C   CR16  0  -0.260  -18.9520  -19.4523  -1.9394
 XF4  C35   C   CR16  0  -0.239  -18.0731  -19.9374  -2.8969
 XF4  C36   C   CR16  0  -0.299  -17.3983  -21.1326  -2.6792
 XF4  N19   N   NR6   0  -0.621  -12.6588  -27.3444   1.4145
 XF4  N20   N   N     0  -0.398  -11.4205  -26.0687   4.6197
 XF4  N28   N   NR16  0  -0.719  -11.3929  -32.7022  -0.1984
 XF4  N29   N   NR16  0  -0.674  -12.0206  -32.0304  -2.2963
 XF4  O21   O   O     0  -0.463  -14.2401  -25.7280   1.5465
 XF4  O22   O   O2    0  -0.467  -17.8563  -24.1821  -1.3877
 XF4  O27   O   O     0  -0.436  -11.6634  -31.3974   1.6223
 XF4  O31   O   O     0  -0.462  -11.0845  -34.0794  -1.9823
 XF4  CL23  CL  CL    0  -0.126  -19.6273  -28.7939  -0.6253
 XF4  H1    H   HCR6  0   0.279  -14.7546  -29.3680  -1.0162
 XF4  H2    H   HCR6  0   0.276  -16.8980  -29.0891   0.0758
 XF4  H3    H   HCR6  0   0.284  -19.5752  -26.0364  -1.3050
 XF4  H4    H   HCH2  0   0.245  -16.4474  -23.1628  -0.2609
 XF4  H5    H   HCH2  0   0.248  -16.0757  -23.2916  -1.9870
 XF4  H6    H   HCR6  0   0.282  -15.4284  -25.1317  -0.6568
 XF4  H7    H   HCR6  0   0.279  -12.9556  -27.3220   4.0536
 XF4  H8    H   HCR6  0   0.274   -9.8372  -24.8080   4.9799
 XF4  H9    H   HCR6  0   0.282   -9.2215  -24.5423   2.5943
 XF4  H10   H   HCR6  0   0.289  -10.5801  -25.7404   0.8621
 XF4  H11   H   HCR6  0   0.315  -11.1900  -28.7923   1.2828
 XF4  H13   H   HCR6  0   0.323  -12.8479  -30.1557  -2.5201
 XF4  H14   H   HCR6  0   0.253  -18.6241  -21.8961   0.3804
 XF4  H15   H   HCR6  0   0.256  -19.8322  -19.7858  -0.0084
 XF4  H16   H   HCR6  0   0.257  -19.4794  -18.5221  -2.1073
 XF4  H17   H   HCR6  0   0.256  -17.9133  -19.3881  -3.8156
 XF4  H18   H   HCR6  0   0.255  -16.7151  -21.5105  -3.4306
 XF4  H19   H   HNR6  0   0.427  -10.9938  -33.4139   0.4023
 XF4  H12   H   HNR6  0   0.439  -12.0956  -32.2003  -3.2892

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
 XF4  C35   C36  aromatic  1.390  0.020  1.390
 XF4  C35   C34  aromatic  1.387  0.020  1.387
 XF4  C36   C11  aromatic  1.390  0.020  1.390
 XF4  N29   C25  single    1.357  0.020  1.357
 XF4  N29   C30  single    1.370  0.020  1.370
 XF4  C34   C33  aromatic  1.390  0.020  1.390
 XF4  O31   C30  double    1.211  0.020  1.211
 XF4  C25   C24  double    1.350  0.020  1.350
 XF4  C30   N28  single    1.372  0.020  1.372
 XF4  O22   C9   single    1.344  0.020  1.344
 XF4  O22   C10  single    1.424  0.020  1.424
 XF4  C11   C10  single    1.499  0.020  1.499
 XF4  C11   C32  aromatic  1.394  0.020  1.394
 XF4  C8    C9   aromatic  1.397  0.020  1.397
 XF4  C8    C7   aromatic  1.379  0.020  1.379
 XF4  CL23  C7   single    1.733  0.020  1.733
 XF4  C9    C12  aromatic  1.390  0.020  1.390
 XF4  C33   C32  aromatic  1.386  0.020  1.386
 XF4  C7    C5   aromatic  1.387  0.020  1.387
 XF4  C12   C4   aromatic  1.396  0.020  1.396
 XF4  C5    C4   aromatic  1.392  0.020  1.392
 XF4  C24   C18  single    1.469  0.020  1.469
 XF4  C24   C26  single    1.457  0.020  1.457
 XF4  C4    C3   single    1.476  0.020  1.476
 XF4  C2    C3   double    1.364  0.020  1.364
 XF4  C2    C18  single    1.418  0.020  1.418
 XF4  N28   C26  single    1.385  0.020  1.385
 XF4  C3    C1   single    1.449  0.020  1.449
 XF4  C18   C17  double    1.360  0.020  1.360
 XF4  C26   O27  double    1.215  0.020  1.215
 XF4  C1    N19  single    1.396  0.020  1.396
 XF4  C1    O21  double    1.222  0.020  1.222
 XF4  C17   N19  single    1.357  0.020  1.357
 XF4  N19   C6   single    1.427  0.020  1.427
 XF4  C16   C6   aromatic  1.383  0.020  1.383
 XF4  C16   C15  aromatic  1.386  0.020  1.386
 XF4  C6    C13  aromatic  1.387  0.020  1.387
 XF4  C15   C14  aromatic  1.386  0.020  1.386
 XF4  C13   N20  aromatic  1.324  0.020  1.324
 XF4  C14   N20  aromatic  1.329  0.020  1.329
 XF4  C2    H1   single    0.930  0.020  1.080
 XF4  C5    H2   single    0.930  0.020  1.080
 XF4  C8    H3   single    0.930  0.020  1.080
 XF4  C10   H4   single    0.970  0.020  1.090
 XF4  C10   H5   single    0.970  0.020  1.090
 XF4  C12   H6   single    0.930  0.020  1.080
 XF4  C13   H7   single    0.930  0.020  1.080
 XF4  C14   H8   single    0.930  0.020  1.080
 XF4  C15   H9   single    0.930  0.020  1.080
 XF4  C16   H10  single    0.930  0.020  1.080
 XF4  C17   H11  single    0.930  0.020  1.080
 XF4  C25   H13  single    0.930  0.020  1.080
 XF4  C32   H14  single    0.930  0.020  1.080
 XF4  C33   H15  single    0.930  0.020  1.080
 XF4  C34   H16  single    0.930  0.020  1.080
 XF4  C35   H17  single    0.930  0.020  1.080
 XF4  C36   H18  single    0.930  0.020  1.080
 XF4  N28   H19  single    0.860  0.020  1.020
 XF4  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
 XF4  O21   C1   N19  119.67  3.000
 XF4  O21   C1   C3   125.94  3.000
 XF4  N19   C1   C3   114.39  3.000
 XF4  H1    C2   C18  118.33  3.000
 XF4  H1    C2   C3   118.88  3.000
 XF4  C18   C2   C3   122.78  3.000
 XF4  C4    C3   C2   120.88  3.000
 XF4  C2    C3   C1   120.03  3.000
 XF4  C4    C3   C1   119.04  3.000
 XF4  C12   C4   C5   119.92  3.000
 XF4  C5    C4   C3   119.06  3.000
 XF4  C12   C4   C3   121.01  3.000
 XF4  H2    C5   C7   120.32  3.000
 XF4  H2    C5   C4   120.75  3.000
 XF4  C7    C5   C4   118.92  3.000
 XF4  N19   C6   C16  120.83  3.000
 XF4  C16   C6   C13  119.38  3.000
 XF4  N19   C6   C13  119.78  3.000
 XF4  CL23  C7   C8   118.89  3.000
 XF4  CL23  C7   C5   118.98  3.000
 XF4  C8    C7   C5   122.12  3.000
 XF4  H3    C8   C9   120.01  3.000
 XF4  H3    C8   C7   121.28  3.000
 XF4  C9    C8   C7   118.70  3.000
 XF4  O22   C9   C12  124.35  3.000
 XF4  C12   C9   C8   120.25  3.000
 XF4  O22   C9   C8   115.41  3.000
 XF4  H5    C10  H4   107.88  3.000
 XF4  H5    C10  O22  110.61  3.000
 XF4  H4    C10  O22  110.02  3.000
 XF4  H5    C10  C11  110.91  3.000
 XF4  H4    C10  C11  110.25  3.000
 XF4  O22   C10  C11  107.18  3.000
 XF4  C36   C11  C32  119.14  3.000
 XF4  C32   C11  C10  119.79  3.000
 XF4  C36   C11  C10  121.06  3.000
 XF4  H6    C12  C9   120.81  3.000
 XF4  H6    C12  C4   119.11  3.000
 XF4  C9    C12  C4   120.08  3.000
 XF4  H7    C13  N20  117.30  3.000
 XF4  H7    C13  C6   120.02  3.000
 XF4  N20   C13  C6   122.67  3.000
 XF4  H8    C14  N20  116.49  3.000
 XF4  H8    C14  C15  120.16  3.000
 XF4  N20   C14  C15  123.35  3.000
 XF4  H9    C15  C16  121.03  3.000
 XF4  H9    C15  C14  120.40  3.000
 XF4  C16   C15  C14  118.57  3.000
 XF4  H10   C16  C15  121.33  3.000
 XF4  H10   C16  C6   120.70  3.000
 XF4  C15   C16  C6   117.97  3.000
 XF4  H11   C17  N19  115.50  3.000
 XF4  H11   C17  C18  123.06  3.000
 XF4  N19   C17  C18  121.44  3.000
 XF4  C24   C18  C17  121.81  3.000
 XF4  C17   C18  C2   116.84  3.000
 XF4  C24   C18  C2   121.35  3.000
 XF4  C26   C24  C25  117.91  3.000
 XF4  C26   C24  C18  120.27  3.000
 XF4  C25   C24  C18  121.78  3.000
 XF4  H13   C25  N29  114.94  3.000
 XF4  H13   C25  C24  122.17  3.000
 XF4  N29   C25  C24  122.88  3.000
 XF4  O27   C26  N28  120.22  3.000
 XF4  O27   C26  C24  125.32  3.000
 XF4  N28   C26  C24  114.46  3.000
 XF4  O31   C30  N29  123.45  3.000
 XF4  O31   C30  N28  123.28  3.000
 XF4  N29   C30  N28  113.27  3.000
 XF4  H14   C32  C33  119.71  3.000
 XF4  H14   C32  C11  119.79  3.000
 XF4  C33   C32  C11  120.50  3.000
 XF4  H15   C33  C34  120.10  3.000
 XF4  H15   C33  C32  119.87  3.000
 XF4  C34   C33  C32  120.03  3.000
 XF4  H16   C34  C35  120.14  3.000
 XF4  H16   C34  C33  120.05  3.000
 XF4  C35   C34  C33  119.82  3.000
 XF4  H17   C35  C36  119.85  3.000
 XF4  H17   C35  C34  120.14  3.000
 XF4  C36   C35  C34  120.01  3.000
 XF4  H18   C36  C35  119.83  3.000
 XF4  H18   C36  C11  119.66  3.000
 XF4  C35   C36  C11  120.51  3.000
 XF4  C17   N19  C6   118.35  3.000
 XF4  C6    N19  C1   117.15  3.000
 XF4  C17   N19  C1   124.50  3.000
 XF4  C14   N20  C13  118.06  3.000
 XF4  H19   N28  C30  115.64  3.000
 XF4  H19   N28  C26  116.31  3.000
 XF4  C30   N28  C26  128.05  3.000
 XF4  H12   N29  C30  117.22  3.000
 XF4  H12   N29  C25  119.35  3.000
 XF4  C30   N29  C25  123.43  3.000
 XF4  C10   O22  C9   119.03  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
 XF4  CONST_01  C8    C9   C12  C4      0.00   0.0  0
 XF4  CONST_02  C8    C7   C5   C4      0.00   0.0  0
 XF4  CONST_03  C9    C8   C7   C5      0.00   0.0  0
 XF4  CONST_04  C9    C12  C4   C5      0.00   0.0  0
 XF4  CONST_05  C14   C15  C16  C6      0.00   0.0  0
 XF4  CONST_06  C14   N20  C13  C6      0.00   0.0  0
 XF4  CONST_07  C12   C9   C8   C7      0.00   0.0  0
 XF4  CONST_08  C12   C4   C5   C7      0.00   0.0  0
 XF4  CONST_09  C34   C35  C36  C11     0.00   0.0  0
 XF4  CONST_10  C34   C33  C32  C11     0.00   0.0  0
 XF4  CONST_11  C15   C16  C6   C13     0.00   0.0  0
 XF4  CONST_12  C15   C14  N20  C13     0.00   0.0  0
 XF4  CONST_13  N20   C13  C6   C16     0.00   0.0  0
 XF4  CONST_14  N20   C14  C15  C16     0.00   0.0  0
 XF4  CONST_15  C35   C36  C11  C32     0.00   0.0  0
 XF4  CONST_16  C35   C34  C33  C32     0.00   0.0  0
 XF4  CONST_17  C36   C35  C34  C33     0.00   0.0  0
 XF4  CONST_18  C36   C11  C32  C33     0.00   0.0  0
 XF4  CONST_19  C9    C12  C4   C3    180.00   0.0  0
 XF4  CONST_20  C7    C5   C4   C3    180.00   0.0  0
 XF4  CONST_21  N19   C6   C16  C15   180.00   0.0  0
 XF4  CONST_22  N20   C13  C6   N19   180.00   0.0  0
 XF4  CONST_23  C17   N19  C1   C3      0.00   0.0  0
 XF4  CONST_24  C6    N19  C1   C3    180.00   0.0  0
 XF4  CONST_25  C30   N28  C26  C24     0.00   0.0  0
 XF4  CONST_26  N28   C30  N29  C25     0.00   0.0  0
 XF4  CONST_27  N29   C30  N28  C26     0.00   0.0  0
 XF4  CONST_28  O22   C9   C12  C4    180.00   0.0  0
 XF4  CONST_29  CL23  C7   C5   C4    180.00   0.0  0
 XF4  CONST_30  O22   C9   C8   C7    180.00   0.0  0
 XF4  CONST_31  CL23  C7   C8   C9    180.00   0.0  0
 XF4  CONST_32  C35   C36  C11  C10   180.00   0.0  0
 XF4  CONST_33  C33   C32  C11  C10   180.00   0.0  0
 XF4  CONST_34  O21   C1   N19  C6      0.00   0.0  0
 XF4  CONST_35  O21   C1   N19  C17   180.00   0.0  0
 XF4  CONST_36  O31   C30  N29  C25   180.00   0.0  0
 XF4  CONST_37  O31   C30  N28  C26   180.00   0.0  0
 XF4  CONST_38  O27   C26  N28  C30   180.00   0.0  0
 XF4  CONST_39  H6    C12  C4   C3      0.00   0.0  0
 XF4  CONST_40  H2    C5   C4   C3      0.00   0.0  0
 XF4  CONST_41  H3    C8   C7   C5    180.00   0.0  0
 XF4  CONST_42  H9    C15  C16  C6    180.00   0.0  0
 XF4  CONST_43  H17   C35  C36  C11   180.00   0.0  0
 XF4  CONST_44  H15   C33  C32  C11   180.00   0.0  0
 XF4  CONST_45  H10   C16  C6   C13   180.00   0.0  0
 XF4  CONST_46  H8    C14  N20  C13   180.00   0.0  0
 XF4  CONST_47  H7    C13  N20  C14   180.00   0.0  0
 XF4  CONST_48  H18   C36  C11  C32   180.00   0.0  0
 XF4  CONST_49  H16   C34  C33  C32   180.00   0.0  0
 XF4  CONST_50  H14   C32  C33  C34   180.00   0.0  0
 XF4  CONST_51  H19   N28  C26  C24   180.00   0.0  0
 XF4  CONST_52  H12   N29  C30  N28   180.00   0.0  0
 XF4  Var_01    C12   C4   C3   C1     47.42  30.0  2
 XF4  Var_02    C16   C6   N19  C1   -100.42  30.0  2
 XF4  Var_03    C25   C24  C18  C2     45.66  30.0  2
 XF4  Var_04    C11   C10  O22  C9   -169.58  30.0  3
 XF4  Var_05    C12   C9   O22  C10    -7.19  30.0  2
 XF4  Var_06    O22   C10  C11  C32    71.70  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
 XF4  plan-1  C1    0.020
 XF4  plan-1  C2    0.020
 XF4  plan-1  C3    0.020
 XF4  plan-1  C4    0.020
 XF4  plan-1  C6    0.020
 XF4  plan-1  C17   0.020
 XF4  plan-1  C18   0.020
 XF4  plan-1  C24   0.020
 XF4  plan-1  N19   0.020
 XF4  plan-1  O21   0.020
 XF4  plan-1  H1    0.020
 XF4  plan-1  H11   0.020
 XF4  plan-2  C3    0.020
 XF4  plan-2  C4    0.020
 XF4  plan-2  C5    0.020
 XF4  plan-2  C7    0.020
 XF4  plan-2  C8    0.020
 XF4  plan-2  C9    0.020
 XF4  plan-2  C12   0.020
 XF4  plan-2  O22   0.020
 XF4  plan-2  CL23  0.020
 XF4  plan-2  H2    0.020
 XF4  plan-2  H3    0.020
 XF4  plan-2  H6    0.020
 XF4  plan-3  C6    0.020
 XF4  plan-3  C13   0.020
 XF4  plan-3  C14   0.020
 XF4  plan-3  C15   0.020
 XF4  plan-3  C16   0.020
 XF4  plan-3  N19   0.020
 XF4  plan-3  N20   0.020
 XF4  plan-3  H7    0.020
 XF4  plan-3  H8    0.020
 XF4  plan-3  H9    0.020
 XF4  plan-3  H10   0.020
 XF4  plan-4  C10   0.020
 XF4  plan-4  C11   0.020
 XF4  plan-4  C32   0.020
 XF4  plan-4  C33   0.020
 XF4  plan-4  C34   0.020
 XF4  plan-4  C35   0.020
 XF4  plan-4  C36   0.020
 XF4  plan-4  H14   0.020
 XF4  plan-4  H15   0.020
 XF4  plan-4  H16   0.020
 XF4  plan-4  H17   0.020
 XF4  plan-4  H18   0.020
 XF4  plan-5  C18   0.020
 XF4  plan-5  C24   0.020
 XF4  plan-5  C25   0.020
 XF4  plan-5  C26   0.020
 XF4  plan-5  C30   0.020
 XF4  plan-5  N28   0.020
 XF4  plan-5  N29   0.020
 XF4  plan-5  O27   0.020
 XF4  plan-5  O31   0.020
 XF4  plan-5  H13   0.020
 XF4  plan-5  H19   0.020
 XF4  plan-5  H12   0.020

