# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 08:37:41 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 2-(biphenyl-3-yl)-5-hydroxy-3-methylpyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)C(=CN=C1c2cccc(c2)c3ccccc3)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
 43J  43J  2-(biphenyl-3-yl)-5-hydroxy-3-methylpyrimidin-4(3H)-one  ligand  35  21  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_43J
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
 43J  C12  C  CR16  0  -0.272   0.2413   2.1758  -0.5727
 43J  C13  C  CR6   0   0.085  -3.3371  -0.0787   0.0722
 43J  C18  C  CR16  0  -0.309  -4.5065   0.2028  -0.6362
 43J  C14  C  CR16  0  -0.310  -3.3578  -1.1158   1.0066
 43J  C15  C  CR16  0  -0.240  -4.5140  -1.8504   1.2253
 43J  C16  C  CR16  0  -0.265  -5.6714  -1.5612   0.5145
 43J  C11  C  CR16  0  -0.227  -0.9952   2.7995  -0.6236
 43J  C9   C  CR6   0   0.109  -2.1048   0.7015  -0.1598
 43J  C1   C  CR6   0   0.179   4.0141  -1.1359  -0.5657
 43J  C6   C  CR6   0   0.003   0.3109   0.8079  -0.3199
 43J  C4   C  CR6   0   0.453   1.6061   0.0911  -0.3447
 43J  N    N  N     0  -0.419   1.7199  -0.9058  -1.1569
 43J  C    C  CR16  0  -0.196   2.9172  -1.5384  -1.2503
 43J  C2   C  CR6   0   0.526   3.9073  -0.0262   0.3579
 43J  N3   N  NR6   0  -0.529   2.6320   0.5155   0.4549
 43J  O    O  O     0  -0.480   4.8355   0.3980   1.0266
 43J  C7   C  CH3   0  -0.547   2.4478   1.5186   1.5016
 43J  C8   C  CR16  0  -0.332  -0.8573   0.0802  -0.1279
 43J  C10  C  CR16  0  -0.310  -2.1573   2.0726  -0.4140
 43J  C17  C  CR16  0  -0.240  -5.6628  -0.5316  -0.4176
 43J  H1   H  HCR6  0   0.271   1.1422   2.7511  -0.7447
 43J  H2   H  HCR6  0   0.256  -4.5099   0.9885  -1.3814
 43J  H3   H  HCR6  0   0.256  -2.4690  -1.3407   1.5837
 43J  H4   H  HCR6  0   0.259  -4.5114  -2.6462   1.9585
 43J  H5   H  HCR6  0   0.259  -6.5733  -2.1347   0.6846
 43J  H6   H  HCR6  0   0.266  -1.0540   3.8614  -0.8219
 43J  H7   H  HCR6  0   0.283   2.9620  -2.3833  -1.9297
 43J  H8   H  HOH1  0   0.479   5.2352  -2.4305  -1.2422
 43J  H9   H  HCH3  0   0.276   2.9825   1.2048   2.3932
 43J  H10  H  HCH3  0   0.267   2.8264   2.4892   1.1874
 43J  H11  H  HCH3  0   0.276   1.3959   1.6076   1.7452
 43J  H12  H  HCR6  0   0.260  -0.7902  -0.9874   0.0392
 43J  H13  H  HCR6  0   0.261  -3.1117   2.5835  -0.4341
 43J  H14  H  HCR6  0   0.259  -6.5569  -0.3035  -0.9836
 43J  O5   O  OH1   0  -0.608   5.2364  -1.6810  -0.6350

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
 43J  O5   C1   single    1.340  0.020  1.340
 43J  O    C2   double    1.220  0.020  1.220
 43J  C1   C2   single    1.448  0.020  1.448
 43J  C1   C    double    1.354  0.020  1.354
 43J  C2   N3   single    1.389  0.020  1.389
 43J  C    N    single    1.357  0.020  1.357
 43J  N3   C7   single    1.461  0.020  1.461
 43J  N3   C4   single    1.368  0.020  1.368
 43J  N    C4   double    1.291  0.020  1.291
 43J  C4   C6   single    1.481  0.020  1.481
 43J  C6   C12  aromatic  1.393  0.020  1.393
 43J  C6   C8   aromatic  1.390  0.020  1.390
 43J  C12  C11  aromatic  1.386  0.020  1.386
 43J  C8   C9   aromatic  1.394  0.020  1.394
 43J  C11  C10  aromatic  1.387  0.020  1.387
 43J  C9   C10  aromatic  1.395  0.020  1.395
 43J  C9   C13  single    1.477  0.020  1.477
 43J  C13  C18  aromatic  1.396  0.020  1.396
 43J  C13  C14  aromatic  1.396  0.020  1.396
 43J  C18  C17  aromatic  1.387  0.020  1.387
 43J  C14  C15  aromatic  1.387  0.020  1.387
 43J  C17  C16  aromatic  1.389  0.020  1.389
 43J  C15  C16  aromatic  1.389  0.020  1.389
 43J  C12  H1   single    0.930  0.020  1.080
 43J  C18  H2   single    0.930  0.020  1.080
 43J  C14  H3   single    0.930  0.020  1.080
 43J  C15  H4   single    0.930  0.020  1.080
 43J  C16  H5   single    0.930  0.020  1.080
 43J  C11  H6   single    0.930  0.020  1.080
 43J  C    H7   single    0.930  0.020  1.080
 43J  O5   H8   single    0.850  0.020  0.980
 43J  C7   H9   single    0.970  0.020  1.090
 43J  C7   H10  single    0.970  0.020  1.090
 43J  C7   H11  single    0.970  0.020  1.090
 43J  C8   H12  single    0.930  0.020  1.080
 43J  C10  H13  single    0.930  0.020  1.080
 43J  C17  H14  single    0.930  0.020  1.080

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
 43J  H1   C12  C6   120.60  3.000
 43J  H1   C12  C11  119.83  3.000
 43J  C6   C12  C11  119.56  3.000
 43J  C9   C13  C14  120.66  3.000
 43J  C14  C13  C18  118.50  3.000
 43J  C9   C13  C18  120.84  3.000
 43J  H2   C18  C17  119.33  3.000
 43J  H2   C18  C13  119.89  3.000
 43J  C17  C18  C13  120.76  3.000
 43J  H3   C14  C15  119.33  3.000
 43J  H3   C14  C13  119.91  3.000
 43J  C15  C14  C13  120.75  3.000
 43J  H4   C15  C16  120.14  3.000
 43J  H4   C15  C14  119.62  3.000
 43J  C16  C15  C14  120.24  3.000
 43J  H5   C16  C17  120.24  3.000
 43J  H5   C16  C15  120.24  3.000
 43J  C17  C16  C15  119.52  3.000
 43J  H6   C11  C10  119.78  3.000
 43J  H6   C11  C12  119.80  3.000
 43J  C10  C11  C12  120.42  3.000
 43J  C10  C9   C8   118.41  3.000
 43J  C10  C9   C13  121.08  3.000
 43J  C8   C9   C13  120.50  3.000
 43J  O5   C1   C2   114.34  3.000
 43J  C2   C1   C    119.38  3.000
 43J  O5   C1   C    126.28  3.000
 43J  C8   C6   C4   118.96  3.000
 43J  C8   C6   C12  119.82  3.000
 43J  C4   C6   C12  121.08  3.000
 43J  N3   C4   N    122.76  3.000
 43J  N    C4   C6   117.49  3.000
 43J  N3   C4   C6   119.73  3.000
 43J  C    N    C4   118.75  3.000
 43J  H7   C    N    116.26  3.000
 43J  H7   C    C1   120.96  3.000
 43J  N    C    C1   122.76  3.000
 43J  O    C2   N3   121.65  3.000
 43J  N3   C2   C1   114.28  3.000
 43J  O    C2   C1   124.06  3.000
 43J  C7   N3   C2   115.68  3.000
 43J  C7   N3   C4   122.47  3.000
 43J  C2   N3   C4   121.79  3.000
 43J  H11  C7   H10  109.24  3.000
 43J  H11  C7   H9   108.49  3.000
 43J  H10  C7   H9   108.88  3.000
 43J  H11  C7   N3   109.86  3.000
 43J  H10  C7   N3   111.20  3.000
 43J  H9   C7   N3   109.12  3.000
 43J  H12  C8   C6   119.05  3.000
 43J  H12  C8   C9   119.90  3.000
 43J  C6   C8   C9   121.05  3.000
 43J  H13  C10  C9   120.01  3.000
 43J  H13  C10  C11  119.25  3.000
 43J  C9   C10  C11  120.73  3.000
 43J  H14  C17  C16  120.13  3.000
 43J  H14  C17  C18  119.64  3.000
 43J  C16  C17  C18  120.23  3.000
 43J  H8   O5   C1   110.34  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
 43J  CONST_01  C9   C8   C6   C12    0.00   0.0  0
 43J  CONST_02  C9   C10  C11  C12    0.00   0.0  0
 43J  CONST_03  C6   C8   C9   C13  180.00   0.0  0
 43J  CONST_04  C11  C10  C9   C13  180.00   0.0  0
 43J  CONST_05  C16  C17  C18  C13    0.00   0.0  0
 43J  CONST_06  C16  C15  C14  C13    0.00   0.0  0
 43J  CONST_09  C15  C14  C13  C18    0.00   0.0  0
 43J  CONST_10  C15  C16  C17  C18    0.00   0.0  0
 43J  CONST_13  C17  C18  C13  C14    0.00   0.0  0
 43J  CONST_14  C17  C16  C15  C14    0.00   0.0  0
 43J  CONST_15  C9   C13  C14  C15  180.00   0.0  0
 43J  CONST_16  C8   C6   C12  C11    0.00   0.0  0
 43J  CONST_17  C8   C9   C10  C11    0.00   0.0  0
 43J  CONST_18  C17  C18  C13  C9   180.00   0.0  0
 43J  CONST_19  C10  C11  C12  C6     0.00   0.0  0
 43J  CONST_20  C10  C9   C8   C6     0.00   0.0  0
 43J  CONST_21  C4   C6   C12  C11  180.00   0.0  0
 43J  CONST_22  C4   C6   C8   C9   180.00   0.0  0
 43J  CONST_23  C4   N3   C2   C1     0.00   0.0  0
 43J  CONST_24  C2   N3   C4   C6   180.00   0.0  0
 43J  CONST_25  C    N    C4   C6   180.00   0.0  0
 43J  CONST_26  C2   N3   C4   N      0.00   0.0  0
 43J  CONST_27  N3   C4   N    C      0.00   0.0  0
 43J  CONST_28  C7   N3   C2   C1   180.00   0.0  0
 43J  CONST_29  C7   N3   C4   C6     0.00   0.0  0
 43J  CONST_30  O    C2   N3   C4   180.00   0.0  0
 43J  CONST_31  C7   N3   C4   N    180.00   0.0  0
 43J  CONST_32  H12  C8   C6   C12  180.00   0.0  0
 43J  CONST_33  H13  C10  C11  C12  180.00   0.0  0
 43J  CONST_34  H14  C17  C18  C13  180.00   0.0  0
 43J  CONST_35  H4   C15  C14  C13  180.00   0.0  0
 43J  CONST_36  H3   C14  C13  C18  180.00   0.0  0
 43J  CONST_37  H5   C16  C17  C18  180.00   0.0  0
 43J  CONST_38  H2   C18  C13  C14  180.00   0.0  0
 43J  CONST_39  H6   C11  C10  C9   180.00   0.0  0
 43J  CONST_40  H1   C12  C6   C4     0.00   0.0  0
 43J  CONST_41  C7   N3   C2   O      0.00   0.0  0
 43J  Var_01    N3   C4   C6   C12   55.88  30.0  2
 43J  Var_02    H9   C7   N3   C4   137.05  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
 43J  plan-1  C13  0.020
 43J  plan-1  C18  0.020
 43J  plan-1  C14  0.020
 43J  plan-1  C15  0.020
 43J  plan-1  C16  0.020
 43J  plan-1  C9   0.020
 43J  plan-1  C17  0.020
 43J  plan-1  H2   0.020
 43J  plan-1  H3   0.020
 43J  plan-1  H4   0.020
 43J  plan-1  H5   0.020
 43J  plan-1  H14  0.020
 43J  plan-2  C1   0.020
 43J  plan-2  C6   0.020
 43J  plan-2  C4   0.020
 43J  plan-2  N    0.020
 43J  plan-2  C    0.020
 43J  plan-2  C2   0.020
 43J  plan-2  N3   0.020
 43J  plan-2  O    0.020
 43J  plan-2  C7   0.020
 43J  plan-2  H7   0.020
 43J  plan-2  O5   0.020
 43J  plan-3  C12  0.020
 43J  plan-3  C13  0.020
 43J  plan-3  C11  0.020
 43J  plan-3  C9   0.020
 43J  plan-3  C6   0.020
 43J  plan-3  C4   0.020
 43J  plan-3  C8   0.020
 43J  plan-3  C10  0.020
 43J  plan-3  H1   0.020
 43J  plan-3  H6   0.020
 43J  plan-3  H12  0.020
 43J  plan-3  H13  0.020

