# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 23:33:58 2022
#   Inital geometry file: a 155 line input string
#   Ligand name: 5-{3-[3-chloro-5-(3-hydroxy-3-methylbutoxy)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: CC(C)(O)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
 YTV  YTV  5-{3-[3-chloro-5-(3-hydroxy-3-methylbutoxy)phenyl]-2-oxo-2H-[1,3'-bipyridin]-5-yl}pyrimidine-2,4(1H,3H)-dione  ligand  58  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 PERFECT
;

data_comp_YTV
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
 YTV  C1   C   CR6   0   0.538   7.9321  -0.8675  21.6119
 YTV  C2   C   CR6   0  -0.162   8.1910  -0.1221  22.8266
 YTV  C3   C   CR6   0   0.122   7.5140  -0.5172  24.0775
 YTV  C4   C   CR16  0  -0.304   6.9592   0.4671  24.8906
 YTV  C5   C   CR6   0  -0.005   6.3786   0.0934  26.0931
 YTV  C6   C   CR16  0  -0.326   6.3202  -1.2218  26.5036
 YTV  O1   O   O     0  -0.463   7.1869  -1.8297  21.5055
 YTV  N3   N   NR6   0  -0.621   8.6112  -0.3905  20.4888
 YTV  C7   C   CR6   0   0.421   6.8713  -2.2064  25.6796
 YTV  C8   C   CH2   0  -0.209   7.2224  -4.5358  25.3177
 YTV  C9   C   CH2   0  -0.477   6.9777  -5.8513  26.0270
 YTV  O4   O   O     0  -0.437   9.8768   3.4767  19.5957
 YTV  O5   O   O     0  -0.462  12.9894   5.8086  21.9186
 YTV  C10  C   CT    0   0.215   5.5305  -6.3635  26.1517
 YTV  C11  C   CH3   0  -0.667   4.8861  -6.5349  24.7819
 YTV  C12  C   CH3   0  -0.665   4.6591  -5.4709  27.0317
 YTV  C13  C   CR16  0  -0.418   7.4653  -1.8556  24.4720
 YTV  C14  C   CR16  0  -0.209   9.0298   0.9522  22.8001
 YTV  C15  C   CR6   0  -0.009   9.6961   1.3841  21.6254
 YTV  C16  C   CR6   0  -0.234  10.6054   2.5362  21.6533
 YTV  C17  C   CR6   0   0.560  10.5764   3.5298  20.5883
 YTV  C18  C   CR16  0   0.060  11.4508   2.7449  22.6857
 YTV  C19  C   CR6   0   0.681  12.2821   4.8293  21.8336
 YTV  C20  C   CR16  0   0.026   9.4568   0.6717  20.4912
 YTV  C21  C   CR6   0   0.179   8.4079  -1.0931  19.2640
 YTV  C22  C   CR16  0  -0.139   9.3351  -2.0174  18.8184
 YTV  C23  C   CR16  0  -0.329   9.0870  -2.6614  17.6169
 YTV  C24  C   CR16  0  -0.056   7.9235  -2.3537  16.9286
 YTV  C25  C   CR16  0  -0.051   7.2748  -0.8453  18.5036
 YTV  N1   N   NR16  0  -0.719  11.4318   4.6020  20.7806
 YTV  N2   N   NR16  0  -0.674  12.2518   3.8359  22.7765
 YTV  N4   N   N     0  -0.399   7.0349  -1.4642  17.3584
 YTV  O3   O   OH1   0  -0.672   5.5868  -7.6713  26.7142
 YTV  CL1  CL  CL    0  -0.127   5.6903   1.3188  27.1088
 YTV  H1   H   HCR6  0   0.275   6.9653   1.5050  24.5862
 YTV  H2   H   HCR6  0   0.284   5.8562  -1.4979  27.4414
 YTV  H3   H   HCH2  0   0.238   8.2952  -4.4376  25.1203
 YTV  H4   H   HCH2  0   0.232   6.7096  -4.5055  24.3507
 YTV  H5   H   HCH2  0   0.244   7.5431  -6.6056  25.4720
 YTV  H6   H   HCH2  0   0.237   7.4312  -5.8006  27.0234
 YTV  H8   H   HCH3  0   0.235   3.9039  -7.0006  24.8777
 YTV  H9   H   HCH3  0   0.227   4.7425  -5.5742  24.2886
 YTV  H7   H   HCH3  0   0.230   5.4981  -7.1592  24.1282
 YTV  H12  H   HCH3  0   0.222   5.1220  -5.2996  28.0067
 YTV  H13  H   HCH3  0   0.228   4.4792  -4.4982  26.5772
 YTV  H11  H   HCH3  0   0.226   3.6901  -5.9456  27.1967
 YTV  H14  H   HCR6  0   0.281   7.9086  -2.6085  23.8383
 YTV  H15  H   HCR6  0   0.278   9.1981   1.5010  23.7197
 YTV  H17  H   HCR6  0   0.322  11.5428   2.0470  23.5067
 YTV  H19  H   HCR6  0   0.315   9.9216   0.8969  19.5434
 YTV  H20  H   HCR6  0   0.288  10.2261  -2.2287  19.3959
 YTV  H21  H   HCR6  0   0.281   9.7804  -3.3908  17.2223
 YTV  H22  H   HCR6  0   0.273   7.6999  -2.8450  15.9887
 YTV  H23  H   HCR6  0   0.279   6.5428  -0.1180  18.8392
 YTV  H16  H   HNR6  0   0.427  11.4267   5.3142  20.0600
 YTV  H18  H   HNR6  0   0.439  12.8622   3.9361  23.5751
 YTV  H10  H   HOH1  0   0.439   5.9360  -7.5977  27.6091
 YTV  O2   O   O2    0  -0.469   6.7858  -3.4636  26.1411

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
 YTV  C24  N4   aromatic  1.329  0.020  1.329
 YTV  C24  C23  aromatic  1.386  0.020  1.386
 YTV  N4   C25  aromatic  1.324  0.020  1.324
 YTV  C23  C22  aromatic  1.386  0.020  1.386
 YTV  C25  C21  aromatic  1.387  0.020  1.387
 YTV  C22  C21  aromatic  1.383  0.020  1.383
 YTV  C21  N3   single    1.427  0.020  1.427
 YTV  O4   C17  double    1.216  0.020  1.216
 YTV  N3   C20  single    1.358  0.020  1.358
 YTV  N3   C1   single    1.396  0.020  1.396
 YTV  C20  C15  double    1.361  0.020  1.361
 YTV  C17  N1   single    1.385  0.020  1.385
 YTV  C17  C16  single    1.457  0.020  1.457
 YTV  N1   C19  single    1.372  0.020  1.372
 YTV  O1   C1   double    1.222  0.020  1.222
 YTV  C1   C2   single    1.448  0.020  1.448
 YTV  C15  C16  single    1.468  0.020  1.468
 YTV  C15  C14  single    1.418  0.020  1.418
 YTV  C16  C18  double    1.351  0.020  1.351
 YTV  C19  O5   double    1.211  0.020  1.211
 YTV  C19  N2   single    1.370  0.020  1.370
 YTV  C2   C14  double    1.363  0.020  1.363
 YTV  C2   C3   single    1.476  0.020  1.476
 YTV  C18  N2   single    1.357  0.020  1.357
 YTV  C3   C13  aromatic  1.396  0.020  1.396
 YTV  C3   C4   aromatic  1.392  0.020  1.392
 YTV  C13  C7   aromatic  1.391  0.020  1.391
 YTV  C4   C5   aromatic  1.387  0.020  1.387
 YTV  C8   C9   single    1.514  0.020  1.514
 YTV  C8   O2   single    1.421  0.020  1.421
 YTV  C11  C10  single    1.523  0.020  1.523
 YTV  C7   O2   single    1.342  0.020  1.342
 YTV  C7   C6   aromatic  1.397  0.020  1.397
 YTV  C9   C10  single    1.540  0.020  1.540
 YTV  C5   C6   aromatic  1.379  0.020  1.379
 YTV  C5   CL1  single    1.734  0.020  1.734
 YTV  C10  O3   single    1.425  0.020  1.425
 YTV  C10  C12  single    1.527  0.020  1.527
 YTV  C4   H1   single    0.930  0.020  1.080
 YTV  C6   H2   single    0.930  0.020  1.080
 YTV  C8   H3   single    0.970  0.020  1.090
 YTV  C8   H4   single    0.970  0.020  1.090
 YTV  C9   H5   single    0.970  0.020  1.090
 YTV  C9   H6   single    0.970  0.020  1.090
 YTV  C11  H8   single    0.970  0.020  1.090
 YTV  C11  H9   single    0.970  0.020  1.090
 YTV  C11  H7   single    0.970  0.020  1.090
 YTV  C12  H12  single    0.970  0.020  1.090
 YTV  C12  H13  single    0.970  0.020  1.090
 YTV  C12  H11  single    0.970  0.020  1.090
 YTV  C13  H14  single    0.930  0.020  1.080
 YTV  C14  H15  single    0.930  0.020  1.080
 YTV  C18  H17  single    0.930  0.020  1.080
 YTV  C20  H19  single    0.930  0.020  1.080
 YTV  C22  H20  single    0.930  0.020  1.080
 YTV  C23  H21  single    0.930  0.020  1.080
 YTV  C24  H22  single    0.930  0.020  1.080
 YTV  C25  H23  single    0.930  0.020  1.080
 YTV  N1   H16  single    0.860  0.020  1.020
 YTV  N2   H18  single    0.860  0.020  1.020
 YTV  O3   H10  single    0.850  0.020  0.980

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
 YTV  N3   C1   O1   119.71  3.000
 YTV  O1   C1   C2   125.97  3.000
 YTV  N3   C1   C2   114.31  3.000
 YTV  C14  C2   C3   120.64  3.000
 YTV  C3   C2   C1   119.40  3.000
 YTV  C14  C2   C1   119.94  3.000
 YTV  C13  C3   C4   119.93  3.000
 YTV  C4   C3   C2   119.24  3.000
 YTV  C13  C3   C2   120.80  3.000
 YTV  H1   C4   C5   120.33  3.000
 YTV  H1   C4   C3   120.79  3.000
 YTV  C5   C4   C3   118.87  3.000
 YTV  CL1  C5   C6   118.86  3.000
 YTV  CL1  C5   C4   118.93  3.000
 YTV  C6   C5   C4   122.21  3.000
 YTV  H2   C6   C7   120.03  3.000
 YTV  H2   C6   C5   121.30  3.000
 YTV  C7   C6   C5   118.67  3.000
 YTV  C21  N3   C20  118.40  3.000
 YTV  C20  N3   C1   124.66  3.000
 YTV  C21  N3   C1   116.93  3.000
 YTV  C13  C7   O2   124.20  3.000
 YTV  O2   C7   C6   115.61  3.000
 YTV  C13  C7   C6   120.19  3.000
 YTV  H4   C8   H3   107.28  3.000
 YTV  H4   C8   C9   111.22  3.000
 YTV  H3   C8   C9   108.70  3.000
 YTV  H4   C8   O2   110.31  3.000
 YTV  H3   C8   O2   109.75  3.000
 YTV  C9   C8   O2   109.54  3.000
 YTV  H6   C9   H5   106.22  3.000
 YTV  H6   C9   C10  109.31  3.000
 YTV  H5   C9   C10  107.30  3.000
 YTV  H6   C9   C8   108.59  3.000
 YTV  H5   C9   C8   106.13  3.000
 YTV  C10  C9   C8   118.60  3.000
 YTV  O3   C10  C12  109.37  3.000
 YTV  C12  C10  C11  110.03  3.000
 YTV  O3   C10  C11  105.57  3.000
 YTV  C12  C10  C9   112.86  3.000
 YTV  O3   C10  C9   107.47  3.000
 YTV  C11  C10  C9   111.23  3.000
 YTV  H7   C11  H9   107.88  3.000
 YTV  H7   C11  H8   108.25  3.000
 YTV  H9   C11  H8   107.30  3.000
 YTV  H7   C11  C10  111.45  3.000
 YTV  H9   C11  C10  111.33  3.000
 YTV  H8   C11  C10  110.48  3.000
 YTV  H11  C12  H13  107.76  3.000
 YTV  H11  C12  H12  108.02  3.000
 YTV  H13  C12  H12  107.61  3.000
 YTV  H11  C12  C10  109.85  3.000
 YTV  H13  C12  C10  112.09  3.000
 YTV  H12  C12  C10  111.35  3.000
 YTV  H14  C13  C7   120.62  3.000
 YTV  H14  C13  C3   119.24  3.000
 YTV  C7   C13  C3   120.13  3.000
 YTV  H15  C14  C15  118.40  3.000
 YTV  H15  C14  C2   118.55  3.000
 YTV  C15  C14  C2   123.05  3.000
 YTV  C20  C15  C16  122.40  3.000
 YTV  C16  C15  C14  120.95  3.000
 YTV  C20  C15  C14  116.65  3.000
 YTV  C18  C16  C17  117.77  3.000
 YTV  C18  C16  C15  121.57  3.000
 YTV  C17  C16  C15  120.60  3.000
 YTV  N1   C17  C16  114.47  3.000
 YTV  C16  C17  O4   125.36  3.000
 YTV  N1   C17  O4   120.18  3.000
 YTV  H17  C18  N2   114.71  3.000
 YTV  H17  C18  C16  122.26  3.000
 YTV  N2   C18  C16  123.03  3.000
 YTV  N2   C19  N1   113.22  3.000
 YTV  N2   C19  O5   123.44  3.000
 YTV  N1   C19  O5   123.34  3.000
 YTV  H19  C20  C15  123.16  3.000
 YTV  H19  C20  N3   115.46  3.000
 YTV  C15  C20  N3   121.38  3.000
 YTV  C25  C21  C22  119.38  3.000
 YTV  C22  C21  N3   120.68  3.000
 YTV  C25  C21  N3   119.95  3.000
 YTV  H20  C22  C23  121.28  3.000
 YTV  H20  C22  C21  120.69  3.000
 YTV  C23  C22  C21  118.03  3.000
 YTV  H21  C23  C24  120.45  3.000
 YTV  H21  C23  C22  121.02  3.000
 YTV  C24  C23  C22  118.53  3.000
 YTV  H22  C24  N4   116.48  3.000
 YTV  H22  C24  C23  120.20  3.000
 YTV  N4   C24  C23  123.31  3.000
 YTV  H23  C25  N4   117.30  3.000
 YTV  H23  C25  C21  120.09  3.000
 YTV  N4   C25  C21  122.61  3.000
 YTV  H16  N1   C19  115.62  3.000
 YTV  H16  N1   C17  116.25  3.000
 YTV  C19  N1   C17  128.13  3.000
 YTV  H18  N2   C19  117.32  3.000
 YTV  H18  N2   C18  119.30  3.000
 YTV  C19  N2   C18  123.38  3.000
 YTV  C25  N4   C24  118.14  3.000
 YTV  H10  O3   C10  108.12  3.000
 YTV  C8   O2   C7   119.22  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
 YTV  CONST_01  C6   C7   C13  C3      0.00   0.0  0
 YTV  CONST_02  C6   C5   C4   C3      0.00   0.0  0
 YTV  CONST_03  C7   C13  C3   C4      0.00   0.0  0
 YTV  CONST_04  C7   C6   C5   C4      0.00   0.0  0
 YTV  CONST_05  C13  C3   C4   C5      0.00   0.0  0
 YTV  CONST_06  C13  C7   C6   C5      0.00   0.0  0
 YTV  CONST_07  C24  N4   C25  C21     0.00   0.0  0
 YTV  CONST_08  C24  C23  C22  C21     0.00   0.0  0
 YTV  CONST_09  N4   C24  C23  C22     0.00   0.0  0
 YTV  CONST_10  N4   C25  C21  C22     0.00   0.0  0
 YTV  CONST_11  C25  N4   C24  C23     0.00   0.0  0
 YTV  CONST_12  C25  C21  C22  C23     0.00   0.0  0
 YTV  CONST_13  C7   C13  C3   C2    180.00   0.0  0
 YTV  CONST_14  C5   C4   C3   C2    180.00   0.0  0
 YTV  CONST_15  N4   C25  C21  N3    180.00   0.0  0
 YTV  CONST_16  C23  C22  C21  N3    180.00   0.0  0
 YTV  CONST_17  C21  N3   C1   C2    180.00   0.0  0
 YTV  CONST_18  C20  N3   C1   C2      0.00   0.0  0
 YTV  CONST_19  C19  N1   C17  C16     0.00   0.0  0
 YTV  CONST_20  N2   C19  N1   C17     0.00   0.0  0
 YTV  CONST_21  N1   C19  N2   C18     0.00   0.0  0
 YTV  CONST_22  O2   C7   C13  C3    180.00   0.0  0
 YTV  CONST_23  CL1  C5   C4   C3    180.00   0.0  0
 YTV  CONST_24  O2   C7   C6   C5    180.00   0.0  0
 YTV  CONST_25  CL1  C5   C6   C7    180.00   0.0  0
 YTV  CONST_26  C21  N3   C1   O1      0.00   0.0  0
 YTV  CONST_27  C20  N3   C1   O1    180.00   0.0  0
 YTV  CONST_28  C19  N1   C17  O4    180.00   0.0  0
 YTV  CONST_29  C17  N1   C19  O5    180.00   0.0  0
 YTV  CONST_30  C18  N2   C19  O5    180.00   0.0  0
 YTV  CONST_31  H14  C13  C3   C2      0.00   0.0  0
 YTV  CONST_32  H1   C4   C3   C2      0.00   0.0  0
 YTV  CONST_33  H2   C6   C5   C4    180.00   0.0  0
 YTV  CONST_34  H23  C25  C21  N3      0.00   0.0  0
 YTV  CONST_35  H20  C22  C21  N3      0.00   0.0  0
 YTV  CONST_36  H21  C23  C22  C21   180.00   0.0  0
 YTV  CONST_37  H22  C24  C23  C22   180.00   0.0  0
 YTV  CONST_38  H16  N1   C17  C16   180.00   0.0  0
 YTV  CONST_39  H18  N2   C19  N1    180.00   0.0  0
 YTV  Var_01    C25  C21  N3   C1     80.96  30.0  3
 YTV  Var_02    C13  C3   C2   C1     46.63  30.0  2
 YTV  Var_03    C17  C16  C15  C14  -137.27  30.0  2
 YTV  Var_04    C13  C7   O2   C8     -5.43  30.0  2
 YTV  Var_05    C9   C8   O2   C7   -177.77  30.0  1
 YTV  Var_06    C10  C9   C8   O2     72.80  30.0  3
 YTV  Var_07    C11  C10  C9   C8     58.44  30.0  3
 YTV  Var_08    H8   C11  C10  C9    173.78  30.0  3
 YTV  Var_09    H12  C12  C10  C9    -52.76  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
 YTV  plan-1  C2   0.020
 YTV  plan-1  C3   0.020
 YTV  plan-1  C4   0.020
 YTV  plan-1  C5   0.020
 YTV  plan-1  C6   0.020
 YTV  plan-1  C7   0.020
 YTV  plan-1  C13  0.020
 YTV  plan-1  CL1  0.020
 YTV  plan-1  H1   0.020
 YTV  plan-1  H2   0.020
 YTV  plan-1  H14  0.020
 YTV  plan-1  O2   0.020
 YTV  plan-2  C1   0.020
 YTV  plan-2  C2   0.020
 YTV  plan-2  C3   0.020
 YTV  plan-2  O1   0.020
 YTV  plan-2  N3   0.020
 YTV  plan-2  C14  0.020
 YTV  plan-2  C15  0.020
 YTV  plan-2  C16  0.020
 YTV  plan-2  C20  0.020
 YTV  plan-2  C21  0.020
 YTV  plan-2  H15  0.020
 YTV  plan-2  H19  0.020
 YTV  plan-3  O4   0.020
 YTV  plan-3  O5   0.020
 YTV  plan-3  C15  0.020
 YTV  plan-3  C16  0.020
 YTV  plan-3  C17  0.020
 YTV  plan-3  C18  0.020
 YTV  plan-3  C19  0.020
 YTV  plan-3  N1   0.020
 YTV  plan-3  N2   0.020
 YTV  plan-3  H17  0.020
 YTV  plan-3  H16  0.020
 YTV  plan-3  H18  0.020
 YTV  plan-4  N3   0.020
 YTV  plan-4  C21  0.020
 YTV  plan-4  C22  0.020
 YTV  plan-4  C23  0.020
 YTV  plan-4  C24  0.020
 YTV  plan-4  C25  0.020
 YTV  plan-4  N4   0.020
 YTV  plan-4  H20  0.020
 YTV  plan-4  H21  0.020
 YTV  plan-4  H22  0.020
 YTV  plan-4  H23  0.020

