# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 26 14:52:57 2022
#   Inital geometry file: a 141 line input string
#   Ligand name: 5-{3-[3-chloro-5-(3,3,3-trifluoropropoxy)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: FC(F)(F)CCOc1cc(Cl)cc(c1)C2=CC(=CN(C2=O)c3cccnc3)C4=CNC(=O)NC4=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
 YU4  YU4  5-{3-[3-chloro-5-(3,3,3-trifluoropropoxy)phenyl]-2-oxo-2H-[1,3'-bipyridin]-5-yl}pyrimidine-2,4(1H,3H)-dione  ligand  51  35  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_YU4
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
 YU4  C7   C   CR16  0   0.026   9.4406   -7.2355  20.4667
 YU4  C4   C   CR16  0  -0.329   9.1064  -10.5105  17.5094
 YU4  C5   C   CR16  0  -0.055   7.9501  -10.1709  16.8235
 YU4  C6   C   CR16  0  -0.052   7.3010   -8.7123  18.4438
 YU4  C1   C   CR6   0   0.540   7.9810   -8.8527  21.5645
 YU4  C2   C   CR6   0   0.178   8.4272   -8.9932  19.2028
 YU4  C10  C   CR6   0   0.560  10.4870   -4.3528  20.6158
 YU4  C14  C   CR6   0  -0.163   8.2146   -8.1174  22.7902
 YU4  C15  C   CR6   0   0.116   7.5474   -8.5499  24.0337
 YU4  C16  C   CR16  0  -0.400   7.5451   -9.8921  24.4158
 YU4  C11  C   CR16  0   0.060  11.3778   -5.1481  22.7026
 YU4  C18  C   CH2   0  -0.250   7.2047  -12.6239  25.2265
 YU4  C23  C   CR16  0  -0.300   6.9549   -7.5932  24.8537
 YU4  C19  C   CH2   0  -0.678   6.0893  -12.8973  24.2269
 YU4  C20  C   CT    0   0.993   4.7619  -13.2383  24.8533
 YU4  C21  C   CR16  0  -0.321   6.3750   -9.3179  26.4490
 YU4  C12  C   CR6   0   0.681  12.1503   -3.0260  21.8893
 YU4  C13  C   CR16  0  -0.209   9.0172   -7.0155  22.7821
 YU4  C17  C   CR6   0   0.413   6.9619  -10.2728  25.6182
 YU4  C22  C   CR6   0  -0.007   6.3869   -7.9969  26.0516
 YU4  C3   C   CR16  0  -0.139   9.3509   -9.9093  18.7336
 YU4  C8   C   CR6   0  -0.007   9.6665   -6.5408  21.6147
 YU4  C9   C   CR6   0  -0.233  10.5416   -5.3631  21.6640
 YU4  F1   F   F     0  -0.310   3.8802  -13.6648  23.9353
 YU4  F2   F   F     0  -0.312   4.8679  -14.2152  25.7677
 YU4  F3   F   F     0  -0.307   4.1896  -12.1954  25.4721
 YU4  N1   N   NR6   0  -0.622   8.6296   -8.3242  20.4468
 YU4  N2   N   N     0  -0.398   7.0644   -9.2903  17.2764
 YU4  N3   N   NR16  0  -0.719  11.3104   -3.2596  20.8294
 YU4  N4   N   NR16  0  -0.674  12.1458   -4.0356  22.8151
 YU4  O1   O   O     0  -0.463   7.2772   -9.8444  21.4434
 YU4  O3   O   O     0  -0.462  12.8286   -2.0282  21.9936
 YU4  O4   O   O2    0  -0.479   6.9413  -11.5351  26.0905
 YU4  CL1  CL  CL    0  -0.124   5.6501   -6.8080  27.0752
 YU4  H5   H   HCR6  0   0.315   9.8904   -6.9746  19.5208
 YU4  H2   H   HCR6  0   0.282   9.7974  -11.2308  17.0944
 YU4  H3   H   HCR6  0   0.274   7.7308  -10.6278  15.8653
 YU4  H4   H   HCR6  0   0.279   6.5722   -7.9912  18.7998
 YU4  H10  H   HCR6  0   0.280   8.0230  -10.6180  23.7750
 YU4  H7   H   HCR6  0   0.323  11.4876   -5.8573  23.5117
 YU4  H12  H   HCH2  0   0.279   7.3479  -13.4804  25.8838
 YU4  H11  H   HCH2  0   0.263   8.1422  -12.4927  24.6807
 YU4  H16  H   HCR6  0   0.277   6.9242   -6.5535  24.5570
 YU4  H13  H   HCH2  0   0.293   5.9475  -12.0582  23.5409
 YU4  H14  H   HCH2  0   0.299   6.4022  -13.7470  23.6157
 YU4  H15  H   HCR6  0   0.286   5.9202   -9.6192  27.3834
 YU4  H9   H   HCR6  0   0.279   9.1677   -6.4773  23.7111
 YU4  H1   H   HCR6  0   0.288  10.2374  -10.1448  19.3088
 YU4  H6   H   HNR6  0   0.427  11.2870   -2.5354  20.1213
 YU4  H8   H   HNR6  0   0.439  12.7521   -3.9322  23.6165
 YU4  O2   O   O     0  -0.437   9.7922   -4.4093  19.6201

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
 YU4  C5   N2   aromatic  1.329  0.020  1.329
 YU4  C5   C4   aromatic  1.387  0.020  1.387
 YU4  N2   C6   aromatic  1.324  0.020  1.324
 YU4  C4   C3   aromatic  1.386  0.020  1.386
 YU4  C6   C2   aromatic  1.387  0.020  1.387
 YU4  C3   C2   aromatic  1.383  0.020  1.383
 YU4  C2   N1   single    1.427  0.020  1.427
 YU4  O2   C10  double    1.216  0.020  1.216
 YU4  N1   C7   single    1.358  0.020  1.358
 YU4  N1   C1   single    1.396  0.020  1.396
 YU4  C7   C8   double    1.361  0.020  1.361
 YU4  C10  N3   single    1.385  0.020  1.385
 YU4  C10  C9   single    1.457  0.020  1.457
 YU4  N3   C12  single    1.372  0.020  1.372
 YU4  O1   C1   double    1.222  0.020  1.222
 YU4  C1   C14  single    1.448  0.020  1.448
 YU4  C9   C8   single    1.468  0.020  1.468
 YU4  C9   C11  double    1.351  0.020  1.351
 YU4  C8   C13  single    1.418  0.020  1.418
 YU4  C12  O3   double    1.211  0.020  1.211
 YU4  C12  N4   single    1.370  0.020  1.370
 YU4  C11  N4   single    1.357  0.020  1.357
 YU4  C14  C13  double    1.363  0.020  1.363
 YU4  C14  C15  single    1.476  0.020  1.476
 YU4  C15  C16  aromatic  1.396  0.020  1.396
 YU4  C15  C23  aromatic  1.392  0.020  1.392
 YU4  C16  C17  aromatic  1.390  0.020  1.390
 YU4  C19  C18  single    1.522  0.020  1.522
 YU4  C19  C20  single    1.507  0.020  1.507
 YU4  C23  C22  aromatic  1.386  0.020  1.386
 YU4  C18  O4   single    1.415  0.020  1.415
 YU4  C17  O4   single    1.348  0.020  1.348
 YU4  C17  C21  aromatic  1.395  0.020  1.395
 YU4  C20  F1   single    1.342  0.020  1.342
 YU4  C20  F2   single    1.342  0.020  1.342
 YU4  C20  F3   single    1.341  0.020  1.341
 YU4  C22  C21  aromatic  1.380  0.020  1.380
 YU4  C22  CL1  single    1.733  0.020  1.733
 YU4  C7   H5   single    0.930  0.020  1.080
 YU4  C4   H2   single    0.930  0.020  1.080
 YU4  C5   H3   single    0.930  0.020  1.080
 YU4  C6   H4   single    0.930  0.020  1.080
 YU4  C16  H10  single    0.930  0.020  1.080
 YU4  C11  H7   single    0.930  0.020  1.080
 YU4  C18  H12  single    0.970  0.020  1.090
 YU4  C18  H11  single    0.970  0.020  1.090
 YU4  C23  H16  single    0.930  0.020  1.080
 YU4  C19  H13  single    0.970  0.020  1.090
 YU4  C19  H14  single    0.970  0.020  1.090
 YU4  C21  H15  single    0.930  0.020  1.080
 YU4  C13  H9   single    0.930  0.020  1.080
 YU4  C3   H1   single    0.930  0.020  1.080
 YU4  N3   H6   single    0.860  0.020  1.020
 YU4  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
 YU4  H5   C7   N1   115.46  3.000
 YU4  H5   C7   C8   123.15  3.000
 YU4  N1   C7   C8   121.40  3.000
 YU4  H2   C4   C3   121.04  3.000
 YU4  H2   C4   C5   120.41  3.000
 YU4  C3   C4   C5   118.55  3.000
 YU4  H3   C5   N2   116.48  3.000
 YU4  H3   C5   C4   120.18  3.000
 YU4  N2   C5   C4   123.34  3.000
 YU4  H4   C6   N2   117.34  3.000
 YU4  H4   C6   C2   120.03  3.000
 YU4  N2   C6   C2   122.63  3.000
 YU4  O1   C1   N1   119.70  3.000
 YU4  O1   C1   C14  126.07  3.000
 YU4  N1   C1   C14  114.23  3.000
 YU4  N1   C2   C3   120.77  3.000
 YU4  N1   C2   C6   119.82  3.000
 YU4  C3   C2   C6   119.40  3.000
 YU4  O2   C10  N3   120.18  3.000
 YU4  N3   C10  C9   114.46  3.000
 YU4  O2   C10  C9   125.35  3.000
 YU4  C13  C14  C15  120.53  3.000
 YU4  C15  C14  C1   119.43  3.000
 YU4  C13  C14  C1   120.02  3.000
 YU4  C23  C15  C16  119.93  3.000
 YU4  C23  C15  C14  119.16  3.000
 YU4  C16  C15  C14  120.88  3.000
 YU4  H10  C16  C17  121.00  3.000
 YU4  H10  C16  C15  118.91  3.000
 YU4  C17  C16  C15  120.07  3.000
 YU4  H7   C11  N4   114.73  3.000
 YU4  H7   C11  C9   122.26  3.000
 YU4  N4   C11  C9   123.02  3.000
 YU4  H11  C18  H12  106.45  3.000
 YU4  H11  C18  O4   111.86  3.000
 YU4  H12  C18  O4   105.14  3.000
 YU4  H11  C18  C19  108.80  3.000
 YU4  H12  C18  C19  110.57  3.000
 YU4  O4   C18  C19  113.75  3.000
 YU4  H16  C23  C22  120.36  3.000
 YU4  H16  C23  C15  120.73  3.000
 YU4  C22  C23  C15  118.90  3.000
 YU4  H14  C19  H13  106.45  3.000
 YU4  H14  C19  C20  107.99  3.000
 YU4  H13  C19  C20  108.69  3.000
 YU4  H14  C19  C18  107.28  3.000
 YU4  H13  C19  C18  111.67  3.000
 YU4  C20  C19  C18  114.40  3.000
 YU4  F3   C20  F2   106.58  3.000
 YU4  F3   C20  F1   106.40  3.000
 YU4  F2   C20  F1   106.65  3.000
 YU4  F3   C20  C19  113.06  3.000
 YU4  F2   C20  C19  112.23  3.000
 YU4  F1   C20  C19  111.49  3.000
 YU4  H15  C21  C22  121.27  3.000
 YU4  H15  C21  C17  120.03  3.000
 YU4  C22  C21  C17  118.70  3.000
 YU4  O3   C12  N4   123.43  3.000
 YU4  N4   C12  N3   113.23  3.000
 YU4  O3   C12  N3   123.34  3.000
 YU4  H9   C13  C8   118.42  3.000
 YU4  H9   C13  C14  118.55  3.000
 YU4  C8   C13  C14  123.03  3.000
 YU4  O4   C17  C21  115.20  3.000
 YU4  C21  C17  C16  120.29  3.000
 YU4  O4   C17  C16  124.49  3.000
 YU4  CL1  C22  C21  118.88  3.000
 YU4  CL1  C22  C23  119.01  3.000
 YU4  C21  C22  C23  122.10  3.000
 YU4  H1   C3   C2   120.72  3.000
 YU4  H1   C3   C4   121.29  3.000
 YU4  C2   C3   C4   117.99  3.000
 YU4  C9   C8   C13  120.93  3.000
 YU4  C13  C8   C7   116.60  3.000
 YU4  C9   C8   C7   122.47  3.000
 YU4  C8   C9   C11  121.51  3.000
 YU4  C11  C9   C10  117.78  3.000
 YU4  C8   C9   C10  120.65  3.000
 YU4  C2   N1   C1   117.03  3.000
 YU4  C1   N1   C7   124.70  3.000
 YU4  C2   N1   C7   118.26  3.000
 YU4  C6   N2   C5   118.09  3.000
 YU4  H6   N3   C12  115.61  3.000
 YU4  H6   N3   C10  116.27  3.000
 YU4  C12  N3   C10  128.11  3.000
 YU4  H8   N4   C12  117.31  3.000
 YU4  H8   N4   C11  119.31  3.000
 YU4  C12  N4   C11  123.38  3.000
 YU4  C17  O4   C18  120.26  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
 YU4  CONST_01  C6   N2   C5   C4      0.00   0.0  0
 YU4  CONST_02  C6   C2   C3   C4      0.00   0.0  0
 YU4  CONST_03  C2   C6   N2   C5      0.00   0.0  0
 YU4  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 YU4  CONST_05  C21  C17  C16  C15     0.00   0.0  0
 YU4  CONST_06  C21  C22  C23  C15     0.00   0.0  0
 YU4  CONST_07  C22  C23  C15  C16     0.00   0.0  0
 YU4  CONST_08  C22  C21  C17  C16     0.00   0.0  0
 YU4  CONST_09  C17  C16  C15  C23     0.00   0.0  0
 YU4  CONST_10  C17  C21  C22  C23     0.00   0.0  0
 YU4  CONST_11  N2   C5   C4   C3      0.00   0.0  0
 YU4  CONST_12  N2   C6   C2   C3      0.00   0.0  0
 YU4  CONST_13  N1   C2   C3   C4    180.00   0.0  0
 YU4  CONST_14  C17  C16  C15  C14   180.00   0.0  0
 YU4  CONST_15  C22  C23  C15  C14   180.00   0.0  0
 YU4  CONST_16  N2   C6   C2   N1    180.00   0.0  0
 YU4  CONST_17  C14  C1   N1   C7      0.00   0.0  0
 YU4  CONST_18  C14  C1   N1   C2    180.00   0.0  0
 YU4  CONST_19  N4   C12  N3   C10     0.00   0.0  0
 YU4  CONST_20  N3   C12  N4   C11     0.00   0.0  0
 YU4  CONST_21  C9   C10  N3   C12     0.00   0.0  0
 YU4  CONST_22  O4   C17  C16  C15   180.00   0.0  0
 YU4  CONST_23  CL1  C22  C23  C15   180.00   0.0  0
 YU4  CONST_24  CL1  C22  C21  C17   180.00   0.0  0
 YU4  CONST_25  O4   C17  C21  C22   180.00   0.0  0
 YU4  CONST_26  O1   C1   N1   C7    180.00   0.0  0
 YU4  CONST_27  O1   C1   N1   C2      0.00   0.0  0
 YU4  CONST_28  O3   C12  N3   C10   180.00   0.0  0
 YU4  CONST_29  O3   C12  N4   C11   180.00   0.0  0
 YU4  CONST_30  O2   C10  N3   C12   180.00   0.0  0
 YU4  CONST_31  H4   C6   N2   C5    180.00   0.0  0
 YU4  CONST_32  H1   C3   C4   C5    180.00   0.0  0
 YU4  CONST_33  H3   C5   N2   C6    180.00   0.0  0
 YU4  CONST_34  H2   C4   C3   C2    180.00   0.0  0
 YU4  CONST_35  H10  C16  C15  C14     0.00   0.0  0
 YU4  CONST_36  H16  C23  C15  C14     0.00   0.0  0
 YU4  CONST_37  H15  C21  C17  C16   180.00   0.0  0
 YU4  CONST_38  H6   N3   C10  C9    180.00   0.0  0
 YU4  CONST_39  H8   N4   C12  N3    180.00   0.0  0
 YU4  Var_01    C6   C2   N1   C7    -97.16  30.0  2
 YU4  Var_02    C10  C9   C8   C7     42.76  30.0  2
 YU4  Var_03    C16  C15  C14  C1     47.08  30.0  2
 YU4  Var_04    C21  C17  O4   C18   164.80  30.0  2
 YU4  Var_05    H12  C18  O4   C17   167.60  30.0  2
 YU4  Var_06    F1   C20  C19  C18  -170.55  30.0  3
 YU4  Var_07    O4   C18  C19  C20   -60.54  30.0  3

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
 YU4  plan-1  C4   0.020
 YU4  plan-1  C5   0.020
 YU4  plan-1  C6   0.020
 YU4  plan-1  C2   0.020
 YU4  plan-1  C3   0.020
 YU4  plan-1  N1   0.020
 YU4  plan-1  N2   0.020
 YU4  plan-1  H2   0.020
 YU4  plan-1  H3   0.020
 YU4  plan-1  H4   0.020
 YU4  plan-1  H1   0.020
 YU4  plan-2  C10  0.020
 YU4  plan-2  C11  0.020
 YU4  plan-2  C12  0.020
 YU4  plan-2  C8   0.020
 YU4  plan-2  C9   0.020
 YU4  plan-2  N3   0.020
 YU4  plan-2  N4   0.020
 YU4  plan-2  O3   0.020
 YU4  plan-2  H7   0.020
 YU4  plan-2  H6   0.020
 YU4  plan-2  H8   0.020
 YU4  plan-2  O2   0.020
 YU4  plan-3  C14  0.020
 YU4  plan-3  C15  0.020
 YU4  plan-3  C16  0.020
 YU4  plan-3  C23  0.020
 YU4  plan-3  C21  0.020
 YU4  plan-3  C17  0.020
 YU4  plan-3  C22  0.020
 YU4  plan-3  O4   0.020
 YU4  plan-3  CL1  0.020
 YU4  plan-3  H10  0.020
 YU4  plan-3  H16  0.020
 YU4  plan-3  H15  0.020
 YU4  plan-4  C7   0.020
 YU4  plan-4  C1   0.020
 YU4  plan-4  C2   0.020
 YU4  plan-4  C14  0.020
 YU4  plan-4  C15  0.020
 YU4  plan-4  C13  0.020
 YU4  plan-4  C8   0.020
 YU4  plan-4  C9   0.020
 YU4  plan-4  N1   0.020
 YU4  plan-4  O1   0.020
 YU4  plan-4  H5   0.020
 YU4  plan-4  H9   0.020

