# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 20:14:16 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 4-(4-hydroxy-3-methylphenyl)-6-phenylpyrimidin-2(5H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(ccc1O)C2=NC(=O)N=C(C2)c3ccccc3
#
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
 55E  55E  4-(4-hydroxy-3-methylphenyl)-6-phenylpyrimidin-2(5H)-one  ligand  35  21  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_55E
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
 55E  O3    O  O     0  -0.419   0.8001  -3.6393  -0.1840
 55E  C2    C  C     0   0.492   0.7581  -2.4305  -0.1152
 55E  N4    N  N     0  -0.467  -0.4785  -1.7994  -0.0674
 55E  C5    C  C     0   0.291  -0.5425  -0.5180  -0.0439
 55E  C6    C  CR6   0   0.041  -1.8543   0.1262  -0.0009
 55E  C21   C  CR16  0  -0.308  -3.0170  -0.6529   0.0261
 55E  C19   C  CR6   0   0.020  -4.2810  -0.0967   0.0672
 55E  C20   C  CH3   0  -0.775  -5.5115  -0.9543   0.0969
 55E  C17   C  CR6   0   0.330  -4.3859   1.3044   0.0789
 55E  O18   O  OH1   0  -0.608  -5.5672   1.9342   0.1171
 55E  C16   C  CR16  0  -0.318  -3.2421   2.0996   0.0508
 55E  C15   C  CR16  0  -0.315  -1.9923   1.5161   0.0116
 55E  C7    C  CH2   0  -0.640   0.6767   0.3440  -0.0598
 55E  C8    C  C     0   0.291   1.9432  -0.4438  -0.0577
 55E  N1    N  N     0  -0.457   1.9613  -1.7220  -0.0811
 55E  C9    C  CR6   0   0.051   3.2252   0.2815  -0.0291
 55E  C14   C  CR16  0  -0.311   3.2695   1.6769  -0.0239
 55E  C13   C  CR16  0  -0.235   4.4862   2.3418  -0.0008
 55E  C12   C  CR16  0  -0.246   5.6726   1.6226   0.0191
 55E  C11   C  CR16  0  -0.237   5.6393   0.2322   0.0149
 55E  C10   C  CR16  0  -0.257   4.4269  -0.4331  -0.0098
 55E  H21   H  HCR6  0   0.260  -2.9222  -1.7312   0.0157
 55E  H20   H  HCH3  0   0.258  -6.1129  -0.7809   0.9927
 55E  H20A  H  HCH3  0   0.258  -6.1557  -0.7800  -0.7684
 55E  H20B  H  HCH3  0   0.272  -5.2457  -2.0092   0.0896
 55E  HO18  H  HOH1  0   0.488  -6.3033   1.3117   0.1329
 55E  H16   H  HCR6  0   0.274  -3.3418   3.1774   0.0598
 55E  H15   H  HCR6  0   0.268  -1.1295   2.1681  -0.0091
 55E  H7    H  HCH2  0   0.336   0.6539   0.9940  -0.9401
 55E  H7A   H  HCH2  0   0.332   0.6635   1.0151   0.8036
 55E  H14   H  HCR6  0   0.268   2.3625   2.2661  -0.0404
 55E  H13   H  HCR6  0   0.268   4.5053   3.4232   0.0017
 55E  H12   H  HCR6  0   0.269   6.6213   2.1429   0.0379
 55E  H11   H  HCR6  0   0.266   6.5615  -0.3332   0.0310
 55E  H10   H  HCR6  0   0.264   4.4027  -1.5140  -0.0143

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
 55E  O3   C2    double    1.211  0.020  1.211
 55E  N4   C2    single    1.389  0.020  1.389
 55E  C2   N1    single    1.397  0.020  1.397
 55E  N4   C5    double    1.283  0.020  1.283
 55E  C6   C5    single    1.462  0.020  1.462
 55E  C5   C7    single    1.493  0.020  1.493
 55E  C15  C6    aromatic  1.397  0.020  1.397
 55E  C6   C21   aromatic  1.400  0.020  1.400
 55E  C19  C21   aromatic  1.382  0.020  1.382
 55E  C21  H21   single    0.930  0.020  1.080
 55E  C17  C19   aromatic  1.405  0.020  1.405
 55E  C19  C20   single    1.500  0.020  1.500
 55E  C20  H20   single    0.970  0.020  1.090
 55E  C20  H20A  single    0.970  0.020  1.090
 55E  C20  H20B  single    0.970  0.020  1.090
 55E  C16  C17   aromatic  1.393  0.020  1.393
 55E  O18  C17   single    1.339  0.020  1.339
 55E  O18  HO18  single    0.850  0.020  0.980
 55E  C16  C15   aromatic  1.380  0.020  1.380
 55E  C16  H16   single    0.930  0.020  1.080
 55E  C15  H15   single    0.930  0.020  1.080
 55E  C7   C8    single    1.492  0.020  1.492
 55E  C7   H7    single    0.970  0.020  1.090
 55E  C7   H7A   single    0.970  0.020  1.090
 55E  N1   C8    double    1.279  0.020  1.279
 55E  C8   C9    single    1.473  0.020  1.473
 55E  C9   C10   aromatic  1.398  0.020  1.398
 55E  C9   C14   aromatic  1.396  0.020  1.396
 55E  C14  C13   aromatic  1.387  0.020  1.387
 55E  C14  H14   single    0.930  0.020  1.080
 55E  C13  C12   aromatic  1.388  0.020  1.388
 55E  C13  H13   single    0.930  0.020  1.080
 55E  C11  C12   aromatic  1.391  0.020  1.391
 55E  C12  H12   single    0.930  0.020  1.080
 55E  C10  C11   aromatic  1.383  0.020  1.383
 55E  C11  H11   single    0.930  0.020  1.080
 55E  C10  H10   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
 55E  N1    C2   N4    122.38  3.000
 55E  N1    C2   O3    118.53  3.000
 55E  N4    C2   O3    119.08  3.000
 55E  C5    N4   C2    119.92  3.000
 55E  C7    C5   C6    118.59  3.000
 55E  C7    C5   N4    122.38  3.000
 55E  C6    C5   N4    119.04  3.000
 55E  C15   C6   C21   118.13  3.000
 55E  C21   C6   C5    120.04  3.000
 55E  C15   C6   C5    121.83  3.000
 55E  H21   C21  C19   118.78  3.000
 55E  H21   C21  C6    118.78  3.000
 55E  C19   C21  C6    122.44  3.000
 55E  C17   C19  C20   120.57  3.000
 55E  C20   C19  C21   121.39  3.000
 55E  C17   C19  C21   118.03  3.000
 55E  H20B  C20  H20A  107.06  3.000
 55E  H20B  C20  H20   107.09  3.000
 55E  H20A  C20  H20   107.42  3.000
 55E  H20B  C20  C19   110.72  3.000
 55E  H20A  C20  C19   112.13  3.000
 55E  H20   C20  C19   112.14  3.000
 55E  C16   C17  O18   117.15  3.000
 55E  O18   C17  C19   122.34  3.000
 55E  C16   C17  C19   120.51  3.000
 55E  HO18  O18  C17   111.74  3.000
 55E  H16   C16  C15   120.31  3.000
 55E  H16   C16  C17   119.51  3.000
 55E  C15   C16  C17   120.18  3.000
 55E  H15   C15  C16   117.91  3.000
 55E  H15   C15  C6    121.39  3.000
 55E  C16   C15  C6    120.70  3.000
 55E  H7A   C7   H7    105.68  3.000
 55E  H7A   C7   C8    109.47  3.000
 55E  H7    C7   C8    109.42  3.000
 55E  H7A   C7   C5    109.64  3.000
 55E  H7    C7   C5    109.53  3.000
 55E  C8    C7   C5    112.85  3.000
 55E  C9    C8   N1    118.71  3.000
 55E  C9    C8   C7    118.61  3.000
 55E  N1    C8   C7    122.68  3.000
 55E  C8    N1   C2    119.70  3.000
 55E  C10   C9   C14   118.91  3.000
 55E  C14   C9   C8    121.32  3.000
 55E  C10   C9   C8    119.77  3.000
 55E  H14   C14  C13   118.34  3.000
 55E  H14   C14  C9    121.18  3.000
 55E  C13   C14  C9    120.48  3.000
 55E  H13   C13  C12   120.21  3.000
 55E  H13   C13  C14   119.67  3.000
 55E  C12   C13  C14   120.13  3.000
 55E  H12   C12  C11   120.11  3.000
 55E  H12   C12  C13   120.04  3.000
 55E  C11   C12  C13   119.84  3.000
 55E  H11   C11  C10   119.74  3.000
 55E  H11   C11  C12   120.13  3.000
 55E  C10   C11  C12   120.13  3.000
 55E  H10   C10  C11   120.04  3.000
 55E  H10   C10  C9    119.45  3.000
 55E  C11   C10  C9    120.51  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
 55E  CONST_01  C17  C16  C15  C6      0.00   0.0  0
 55E  CONST_02  C17  C19  C21  C6      0.00   0.0  0
 55E  CONST_03  C16  C15  C6   C21     0.00   0.0  0
 55E  CONST_04  C16  C17  C19  C21     0.00   0.0  0
 55E  CONST_05  C15  C6   C21  C19     0.00   0.0  0
 55E  CONST_06  C15  C16  C17  C19     0.00   0.0  0
 55E  CONST_07  C12  C11  C10  C9      0.00   0.0  0
 55E  CONST_08  C12  C13  C14  C9      0.00   0.0  0
 55E  CONST_09  C11  C10  C9   C14     0.00   0.0  0
 55E  CONST_10  C11  C12  C13  C14     0.00   0.0  0
 55E  CONST_11  C10  C9   C14  C13     0.00   0.0  0
 55E  CONST_12  C10  C11  C12  C13     0.00   0.0  0
 55E  CONST_13  C16  C15  C6   C5    180.00   0.0  0
 55E  CONST_14  C19  C21  C6   C5    180.00   0.0  0
 55E  CONST_15  C11  C10  C9   C8    180.00   0.0  0
 55E  CONST_16  C13  C14  C9   C8    180.00   0.0  0
 55E  CONST_17  C8   N1   C2   N4      0.00   0.0  0
 55E  CONST_18  N1   C2   N4   C5      0.00   0.0  0
 55E  CONST_19  C20  C19  C21  C6    180.00   0.0  0
 55E  CONST_20  O18  C17  C19  C21   180.00   0.0  0
 55E  CONST_21  C16  C17  C19  C20   180.00   0.0  0
 55E  CONST_22  C15  C16  C17  O18   180.00   0.0  0
 55E  CONST_23  C5   N4   C2   O3    180.00   0.0  0
 55E  CONST_24  C8   N1   C2   O3    180.00   0.0  0
 55E  CONST_25  H15  C15  C6   C5      0.00   0.0  0
 55E  CONST_26  H21  C21  C6   C5      0.00   0.0  0
 55E  CONST_27  H16  C16  C15  C6    180.00   0.0  0
 55E  CONST_28  H10  C10  C9   C8      0.00   0.0  0
 55E  CONST_29  H14  C14  C9   C8      0.00   0.0  0
 55E  CONST_30  H11  C11  C10  C9    180.00   0.0  0
 55E  CONST_31  H13  C13  C14  C9    180.00   0.0  0
 55E  CONST_32  H12  C12  C13  C14   180.00   0.0  0
 55E  Var_01    C6   C5   N4   C2    179.67  30.0  1
 55E  Var_02    C7   C8   N1   C2      0.24  30.0  1
 55E  Var_03    C15  C6   C5   N4   -179.30  30.0  2
 55E  Var_04    C8   C7   C5   N4     -1.97  30.0  1
 55E  Var_05    N1   C8   C7   C5      1.99  30.0  1
 55E  Var_06    C10  C9   C8   C7    179.21  30.0  2
 55E  Var_07    H20  C20  C19  C21   120.01  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
 55E  plan-1  C5   0.020
 55E  plan-1  C6   0.020
 55E  plan-1  C21  0.020
 55E  plan-1  C19  0.020
 55E  plan-1  C20  0.020
 55E  plan-1  C17  0.020
 55E  plan-1  O18  0.020
 55E  plan-1  C16  0.020
 55E  plan-1  C15  0.020
 55E  plan-1  H21  0.020
 55E  plan-1  H16  0.020
 55E  plan-1  H15  0.020
 55E  plan-2  C8   0.020
 55E  plan-2  C9   0.020
 55E  plan-2  C14  0.020
 55E  plan-2  C13  0.020
 55E  plan-2  C12  0.020
 55E  plan-2  C11  0.020
 55E  plan-2  C10  0.020
 55E  plan-2  H14  0.020
 55E  plan-2  H13  0.020
 55E  plan-2  H12  0.020
 55E  plan-2  H11  0.020
 55E  plan-2  H10  0.020
 55E  plan-3  O3   0.020
 55E  plan-3  C2   0.020
 55E  plan-3  N4   0.020
 55E  plan-3  C5   0.020
 55E  plan-3  C8   0.020
 55E  plan-3  N1   0.020

