# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 23:20:04 2022
#   Inital geometry file: a 161 line input string
#   Ligand name: 5-{3-[3-chloro-5-(2-phenylethoxy)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: Clc1cc(OCCc2ccccc2)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
 YTM  YTM  5-{3-[3-chloro-5-(2-phenylethoxy)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_YTM
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
 YTM  C1   C   CR6   0   0.541  -13.9466  -27.2668   1.1969
 YTM  C2   C   CR6   0  -0.177  -14.7116  -27.7855   0.0831
 YTM  C3   C   CR6   0   0.102  -16.0963  -27.3079  -0.1074
 YTM  C4   C   CR16  0  -0.293  -17.1358  -28.2377  -0.1701
 YTM  C5   C   CR6   0  -0.005  -18.4220  -27.7802  -0.3842
 YTM  C6   C   CR16  0  -0.351  -18.7165  -26.4351  -0.5472
 YTM  O1   O   O     0  -0.462  -14.3359  -26.4375   2.0050
 YTM  C7   C   CR6   0   0.418  -17.6698  -25.5169  -0.4905
 YTM  C8   C   CH2   0  -0.188  -19.1196  -23.6774  -0.9261
 YTM  C9   C   CH2   0  -0.544  -18.9918  -22.1794  -1.1340
 YTM  O3   O   O     0  -0.437  -11.2955  -31.5775   0.1420
 YTM  O4   O   O     0  -0.463  -10.8823  -32.9392  -4.1594
 YTM  C10  C   CR6   0   0.129  -18.1352  -21.8258  -2.3182
 YTM  C11  C   CR16  0  -0.303  -18.6742  -21.8252  -3.6034
 YTM  C12  C   CR16  0  -0.238  -17.8856  -21.5264  -4.7062
 YTM  C13  C   CR16  0  -0.270  -16.5407  -21.2223  -4.5386
 YTM  C14  C   CR16  0  -0.240  -15.9930  -21.2195  -3.2624
 YTM  C15  C   CR16  0  -0.303  -16.7857  -21.5210  -2.1623
 YTM  C16  C   CR16  0  -0.382  -16.3662  -25.9562  -0.2607
 YTM  C17  C   CR16  0  -0.192  -14.1773  -28.7260  -0.7431
 YTM  C18  C   CR6   0  -0.014  -12.8573  -29.2215  -0.5841
 YTM  C19  C   CR6   0  -0.239  -12.2946  -30.2024  -1.5194
 YTM  C20  C   CR6   0   0.560  -11.5446  -31.3494  -1.0257
 YTM  C21  C   CR16  0   0.064  -12.4859  -30.0996  -2.8521
 YTM  C22  C   CR6   0   0.681  -11.3028  -32.1241  -3.3683
 YTM  C23  C   CR16  0   0.028  -12.1430  -28.7329   0.4649
 YTM  C24  C   CR6   0   0.181  -11.8650  -27.3692   2.4089
 YTM  C25  C   CR16  0  -0.141  -10.8736  -26.4232   2.2208
 YTM  C26  C   CR16  0  -0.329  -10.1135  -26.0506   3.3184
 YTM  C27  C   CR16  0  -0.055  -10.3886  -26.6360   4.5446
 YTM  C28  C   CR16  0  -0.053  -12.0647  -27.9032   3.6737
 YTM  N1   N   NR16  0  -0.719  -11.1087  -32.2180  -2.0129
 YTM  N2   N   NR16  0  -0.673  -12.0191  -31.0163  -3.7367
 YTM  N3   N   NR6   0  -0.621  -12.6680  -27.8147   1.3173
 YTM  N4   N   N     0  -0.398  -11.3423  -27.5442   4.7232
 YTM  CL1  CL  CL    0  -0.125  -19.7243  -28.9233  -0.4414
 YTM  H1   H   HCR6  0   0.274  -16.9397  -29.2929  -0.0364
 YTM  H2   H   HCR6  0   0.300  -19.7393  -26.1275  -0.7123
 YTM  H4   H   HCH2  0   0.232  -19.5359  -24.1476  -1.8241
 YTM  H3   H   HCH2  0   0.240  -19.8017  -23.8810  -0.0937
 YTM  H6   H   HCH2  0   0.258  -18.6008  -21.7181  -0.2242
 YTM  H5   H   HCH2  0   0.262  -20.0033  -21.7900  -1.2712
 YTM  H7   H   HCR6  0   0.247  -19.7248  -22.0553  -3.7414
 YTM  H8   H   HCR6  0   0.251  -18.3229  -21.5260  -5.6966
 YTM  H9   H   HCR6  0   0.252  -15.9251  -20.9845  -5.3965
 YTM  H10  H   HCR6  0   0.251  -14.9463  -20.9811  -3.1221
 YTM  H11  H   HCR6  0   0.245  -16.3523  -21.5115  -1.1694
 YTM  H12  H   HCR6  0   0.261  -15.5661  -25.2282  -0.2262
 YTM  H13  H   HCR6  0   0.277  -14.7820  -29.1092  -1.5576
 YTM  H15  H   HCR6  0   0.322  -13.0205  -29.2711  -3.2961
 YTM  H17  H   HCR6  0   0.314  -11.1280  -29.0346   0.6769
 YTM  H18  H   HCR6  0   0.288  -10.7002  -25.9914   1.2432
 YTM  H19  H   HCR6  0   0.282   -9.3244  -25.3175   3.2260
 YTM  H20  H   HCR6  0   0.273   -9.8122  -26.3614   5.4206
 YTM  H21  H   HCR6  0   0.279  -12.8354  -28.6505   3.8323
 YTM  H14  H   HNR6  0   0.427  -10.5842  -33.0265  -1.7004
 YTM  H16  H   HNR6  0   0.439  -12.1912  -30.8849  -4.7232
 YTM  O2   O   O2    0  -0.465  -17.8288  -24.1938  -0.6482

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
 YTM  C13  C14  aromatic  1.389  0.020  1.389
 YTM  C13  C12  aromatic  1.389  0.020  1.389
 YTM  C14  C15  aromatic  1.389  0.020  1.389
 YTM  N2   C21  single    1.357  0.020  1.357
 YTM  N2   C22  single    1.370  0.020  1.370
 YTM  C12  C11  aromatic  1.388  0.020  1.388
 YTM  O4   C22  double    1.211  0.020  1.211
 YTM  C15  C10  aromatic  1.392  0.020  1.392
 YTM  C21  C19  double    1.350  0.020  1.350
 YTM  C22  N1   single    1.372  0.020  1.372
 YTM  O2   C7   single    1.342  0.020  1.342
 YTM  O2   C8   single    1.418  0.020  1.418
 YTM  C11  C10  aromatic  1.394  0.020  1.394
 YTM  C6   C7   aromatic  1.394  0.020  1.394
 YTM  C6   C5   aromatic  1.387  0.020  1.387
 YTM  C7   C16  aromatic  1.395  0.020  1.395
 YTM  CL1  C5   single    1.734  0.020  1.734
 YTM  C10  C9   single    1.504  0.020  1.504
 YTM  C5   C4   aromatic  1.382  0.020  1.382
 YTM  C8   C9   single    1.518  0.020  1.518
 YTM  C16  C3   aromatic  1.387  0.020  1.387
 YTM  C4   C3   aromatic  1.396  0.020  1.396
 YTM  C19  C18  single    1.468  0.020  1.468
 YTM  C19  C20  single    1.457  0.020  1.457
 YTM  C3   C2   single    1.477  0.020  1.477
 YTM  N1   C20  single    1.385  0.020  1.385
 YTM  C17  C18  single    1.419  0.020  1.419
 YTM  C17  C2   double    1.361  0.020  1.361
 YTM  C18  C23  double    1.360  0.020  1.360
 YTM  C2   C1   single    1.447  0.020  1.447
 YTM  C20  O3   double    1.216  0.020  1.216
 YTM  C23  N3   single    1.358  0.020  1.358
 YTM  C1   N3   single    1.396  0.020  1.396
 YTM  C1   O1   double    1.222  0.020  1.222
 YTM  N3   C24  single    1.427  0.020  1.427
 YTM  C25  C24  aromatic  1.383  0.020  1.383
 YTM  C25  C26  aromatic  1.386  0.020  1.386
 YTM  C24  C28  aromatic  1.387  0.020  1.387
 YTM  C26  C27  aromatic  1.386  0.020  1.386
 YTM  C28  N4   aromatic  1.324  0.020  1.324
 YTM  C27  N4   aromatic  1.329  0.020  1.329
 YTM  C4   H1   single    0.930  0.020  1.080
 YTM  C6   H2   single    0.930  0.020  1.080
 YTM  C8   H4   single    0.970  0.020  1.090
 YTM  C8   H3   single    0.970  0.020  1.090
 YTM  C9   H6   single    0.970  0.020  1.090
 YTM  C9   H5   single    0.970  0.020  1.090
 YTM  C11  H7   single    0.930  0.020  1.080
 YTM  C12  H8   single    0.930  0.020  1.080
 YTM  C13  H9   single    0.930  0.020  1.080
 YTM  C14  H10  single    0.930  0.020  1.080
 YTM  C15  H11  single    0.930  0.020  1.080
 YTM  C16  H12  single    0.930  0.020  1.080
 YTM  C17  H13  single    0.930  0.020  1.080
 YTM  C21  H15  single    0.930  0.020  1.080
 YTM  C23  H17  single    0.930  0.020  1.080
 YTM  C25  H18  single    0.930  0.020  1.080
 YTM  C26  H19  single    0.930  0.020  1.080
 YTM  C27  H20  single    0.930  0.020  1.080
 YTM  C28  H21  single    0.930  0.020  1.080
 YTM  N1   H14  single    0.860  0.020  1.020
 YTM  N2   H16  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
 YTM  N3   C1   O1   120.08  3.000
 YTM  O1   C1   C2   125.72  3.000
 YTM  N3   C1   C2   114.19  3.000
 YTM  C17  C2   C3   120.87  3.000
 YTM  C17  C2   C1   120.48  3.000
 YTM  C3   C2   C1   118.62  3.000
 YTM  C16  C3   C4   119.95  3.000
 YTM  C4   C3   C2   119.24  3.000
 YTM  C16  C3   C2   120.79  3.000
 YTM  H1   C4   C5   120.73  3.000
 YTM  H1   C4   C3   120.61  3.000
 YTM  C5   C4   C3   118.66  3.000
 YTM  CL1  C5   C6   118.44  3.000
 YTM  CL1  C5   C4   119.08  3.000
 YTM  C6   C5   C4   122.48  3.000
 YTM  H2   C6   C7   121.97  3.000
 YTM  H2   C6   C5   119.68  3.000
 YTM  C7   C6   C5   118.35  3.000
 YTM  C16  C7   O2   116.15  3.000
 YTM  C16  C7   C6   120.08  3.000
 YTM  O2   C7   C6   123.77  3.000
 YTM  H3   C8   H4   107.85  3.000
 YTM  H3   C8   C9   109.88  3.000
 YTM  H4   C8   C9   110.07  3.000
 YTM  H3   C8   O2   110.51  3.000
 YTM  H4   C8   O2   110.50  3.000
 YTM  C9   C8   O2   108.04  3.000
 YTM  H5   C9   H6   106.59  3.000
 YTM  H5   C9   C10  110.17  3.000
 YTM  H6   C9   C10  110.65  3.000
 YTM  H5   C9   C8   106.92  3.000
 YTM  H6   C9   C8   109.44  3.000
 YTM  C10  C9   C8   112.83  3.000
 YTM  C15  C10  C11  118.56  3.000
 YTM  C11  C10  C9   120.40  3.000
 YTM  C15  C10  C9   121.03  3.000
 YTM  H7   C11  C12  119.66  3.000
 YTM  H7   C11  C10  119.47  3.000
 YTM  C12  C11  C10  120.86  3.000
 YTM  H8   C12  C13  120.10  3.000
 YTM  H8   C12  C11  119.82  3.000
 YTM  C13  C12  C11  120.08  3.000
 YTM  H9   C13  C14  120.24  3.000
 YTM  H9   C13  C12  120.20  3.000
 YTM  C14  C13  C12  119.55  3.000
 YTM  H10  C14  C15  119.80  3.000
 YTM  H10  C14  C13  120.05  3.000
 YTM  C15  C14  C13  120.15  3.000
 YTM  H11  C15  C14  119.71  3.000
 YTM  H11  C15  C10  119.49  3.000
 YTM  C14  C15  C10  120.80  3.000
 YTM  H12  C16  C7   118.97  3.000
 YTM  H12  C16  C3   120.54  3.000
 YTM  C7   C16  C3   120.47  3.000
 YTM  H13  C17  C18  118.66  3.000
 YTM  H13  C17  C2   118.76  3.000
 YTM  C18  C17  C2   122.58  3.000
 YTM  C23  C18  C19  122.03  3.000
 YTM  C23  C18  C17  116.73  3.000
 YTM  C19  C18  C17  121.24  3.000
 YTM  C21  C19  C20  117.87  3.000
 YTM  C20  C19  C18  120.51  3.000
 YTM  C21  C19  C18  121.59  3.000
 YTM  N1   C20  C19  114.47  3.000
 YTM  N1   C20  O3   120.16  3.000
 YTM  C19  C20  O3   125.37  3.000
 YTM  H15  C21  N2   114.84  3.000
 YTM  H15  C21  C19  122.25  3.000
 YTM  N2   C21  C19  122.91  3.000
 YTM  N2   C22  N1   113.26  3.000
 YTM  N1   C22  O4   123.36  3.000
 YTM  N2   C22  O4   123.38  3.000
 YTM  H17  C23  N3   115.40  3.000
 YTM  H17  C23  C18  123.01  3.000
 YTM  N3   C23  C18  121.59  3.000
 YTM  N3   C24  C28  119.76  3.000
 YTM  C28  C24  C25  119.37  3.000
 YTM  N3   C24  C25  120.87  3.000
 YTM  H18  C25  C26  121.33  3.000
 YTM  H18  C25  C24  120.69  3.000
 YTM  C26  C25  C24  117.98  3.000
 YTM  H19  C26  C27  120.45  3.000
 YTM  H19  C26  C25  120.99  3.000
 YTM  C27  C26  C25  118.56  3.000
 YTM  H20  C27  N4   116.49  3.000
 YTM  H20  C27  C26  120.16  3.000
 YTM  N4   C27  C26  123.35  3.000
 YTM  H21  C28  N4   117.28  3.000
 YTM  H21  C28  C24  120.04  3.000
 YTM  N4   C28  C24  122.68  3.000
 YTM  H14  N1   C22  115.62  3.000
 YTM  H14  N1   C20  116.32  3.000
 YTM  C22  N1   C20  128.05  3.000
 YTM  H16  N2   C22  117.20  3.000
 YTM  H16  N2   C21  119.36  3.000
 YTM  C22  N2   C21  123.44  3.000
 YTM  C24  N3   C23  118.27  3.000
 YTM  C24  N3   C1   117.32  3.000
 YTM  C23  N3   C1   124.41  3.000
 YTM  C28  N4   C27  118.06  3.000
 YTM  C8   O2   C7   119.34  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
 YTM  CONST_01  C6   C7   C16  C3      0.00   0.0  0
 YTM  CONST_02  C6   C5   C4   C3      0.00   0.0  0
 YTM  CONST_03  C7   C6   C5   C4      0.00   0.0  0
 YTM  CONST_04  C7   C16  C3   C4      0.00   0.0  0
 YTM  CONST_05  C16  C7   C6   C5      0.00   0.0  0
 YTM  CONST_06  C16  C3   C4   C5      0.00   0.0  0
 YTM  CONST_07  C13  C14  C15  C10     0.00   0.0  0
 YTM  CONST_08  C13  C12  C11  C10     0.00   0.0  0
 YTM  CONST_09  C14  C13  C12  C11     0.00   0.0  0
 YTM  CONST_10  C14  C15  C10  C11     0.00   0.0  0
 YTM  CONST_11  C15  C14  C13  C12     0.00   0.0  0
 YTM  CONST_12  C15  C10  C11  C12     0.00   0.0  0
 YTM  CONST_13  C27  C26  C25  C24     0.00   0.0  0
 YTM  CONST_14  C27  N4   C28  C24     0.00   0.0  0
 YTM  CONST_15  N4   C28  C24  C25     0.00   0.0  0
 YTM  CONST_16  N4   C27  C26  C25     0.00   0.0  0
 YTM  CONST_17  C28  C24  C25  C26     0.00   0.0  0
 YTM  CONST_18  C28  N4   C27  C26     0.00   0.0  0
 YTM  CONST_19  C7   C16  C3   C2    180.00   0.0  0
 YTM  CONST_20  C5   C4   C3   C2    180.00   0.0  0
 YTM  CONST_21  N3   C24  C25  C26   180.00   0.0  0
 YTM  CONST_22  N4   C28  C24  N3    180.00   0.0  0
 YTM  CONST_23  C23  N3   C1   C2      0.00   0.0  0
 YTM  CONST_24  C24  N3   C1   C2    180.00   0.0  0
 YTM  CONST_25  C22  N1   C20  C19     0.00   0.0  0
 YTM  CONST_26  N2   C22  N1   C20     0.00   0.0  0
 YTM  CONST_27  N1   C22  N2   C21     0.00   0.0  0
 YTM  CONST_28  O2   C7   C16  C3    180.00   0.0  0
 YTM  CONST_29  CL1  C5   C4   C3    180.00   0.0  0
 YTM  CONST_30  O2   C7   C6   C5    180.00   0.0  0
 YTM  CONST_31  CL1  C5   C6   C7    180.00   0.0  0
 YTM  CONST_32  C14  C15  C10  C9    180.00   0.0  0
 YTM  CONST_33  C12  C11  C10  C9    180.00   0.0  0
 YTM  CONST_34  C23  N3   C1   O1    180.00   0.0  0
 YTM  CONST_35  C24  N3   C1   O1      0.00   0.0  0
 YTM  CONST_36  C22  N1   C20  O3    180.00   0.0  0
 YTM  CONST_37  C21  N2   C22  O4    180.00   0.0  0
 YTM  CONST_38  C20  N1   C22  O4    180.00   0.0  0
 YTM  CONST_39  H12  C16  C3   C2      0.00   0.0  0
 YTM  CONST_40  H1   C4   C3   C2      0.00   0.0  0
 YTM  CONST_41  H2   C6   C5   C4    180.00   0.0  0
 YTM  CONST_42  H10  C14  C15  C10   180.00   0.0  0
 YTM  CONST_43  H8   C12  C11  C10   180.00   0.0  0
 YTM  CONST_44  H9   C13  C12  C11   180.00   0.0  0
 YTM  CONST_45  H11  C15  C10  C11   180.00   0.0  0
 YTM  CONST_46  H7   C11  C12  C13   180.00   0.0  0
 YTM  CONST_47  H19  C26  C25  C24   180.00   0.0  0
 YTM  CONST_48  H21  C28  C24  C25   180.00   0.0  0
 YTM  CONST_49  H20  C27  C26  C25   180.00   0.0  0
 YTM  CONST_50  H18  C25  C26  C27   180.00   0.0  0
 YTM  CONST_51  H14  N1   C20  C19   180.00   0.0  0
 YTM  CONST_52  H16  N2   C22  N1    180.00   0.0  0
 YTM  Var_01    C16  C3   C2   C1     57.39  30.0  3
 YTM  Var_02    C25  C24  N3   C1   -100.64  30.0  2
 YTM  Var_03    C21  C19  C18  C17    42.06  30.0  3
 YTM  Var_04    C16  C7   O2   C8    178.08  30.0  2
 YTM  Var_05    C15  C10  C9   C8    -95.99  30.0  2
 YTM  Var_06    C10  C9   C8   O2     62.93  30.0  3
 YTM  Var_07    C9   C8   O2   C7   -176.75  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
 YTM  plan-1  C2   0.020
 YTM  plan-1  C3   0.020
 YTM  plan-1  C4   0.020
 YTM  plan-1  C5   0.020
 YTM  plan-1  C6   0.020
 YTM  plan-1  C7   0.020
 YTM  plan-1  C16  0.020
 YTM  plan-1  CL1  0.020
 YTM  plan-1  H1   0.020
 YTM  plan-1  H2   0.020
 YTM  plan-1  H12  0.020
 YTM  plan-1  O2   0.020
 YTM  plan-2  C9   0.020
 YTM  plan-2  C10  0.020
 YTM  plan-2  C11  0.020
 YTM  plan-2  C12  0.020
 YTM  plan-2  C13  0.020
 YTM  plan-2  C14  0.020
 YTM  plan-2  C15  0.020
 YTM  plan-2  H7   0.020
 YTM  plan-2  H8   0.020
 YTM  plan-2  H9   0.020
 YTM  plan-2  H10  0.020
 YTM  plan-2  H11  0.020
 YTM  plan-3  C1   0.020
 YTM  plan-3  C2   0.020
 YTM  plan-3  C3   0.020
 YTM  plan-3  O1   0.020
 YTM  plan-3  C17  0.020
 YTM  plan-3  C18  0.020
 YTM  plan-3  C19  0.020
 YTM  plan-3  C23  0.020
 YTM  plan-3  C24  0.020
 YTM  plan-3  N3   0.020
 YTM  plan-3  H13  0.020
 YTM  plan-3  H17  0.020
 YTM  plan-4  C24  0.020
 YTM  plan-4  C25  0.020
 YTM  plan-4  C26  0.020
 YTM  plan-4  C27  0.020
 YTM  plan-4  C28  0.020
 YTM  plan-4  N3   0.020
 YTM  plan-4  N4   0.020
 YTM  plan-4  H18  0.020
 YTM  plan-4  H19  0.020
 YTM  plan-4  H20  0.020
 YTM  plan-4  H21  0.020
 YTM  plan-5  O3   0.020
 YTM  plan-5  O4   0.020
 YTM  plan-5  C18  0.020
 YTM  plan-5  C19  0.020
 YTM  plan-5  C20  0.020
 YTM  plan-5  C21  0.020
 YTM  plan-5  C22  0.020
 YTM  plan-5  N1   0.020
 YTM  plan-5  N2   0.020
 YTM  plan-5  H15  0.020
 YTM  plan-5  H14  0.020
 YTM  plan-5  H16  0.020

