# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 19:36:55 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 5-methyl-5-(4-phenoxyphenyl)pyrimidine-2,4,6(1H,3H,5H)-trione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C(=O)NC(=O)NC1=O)c2ccc(Oc3ccccc3)cc2
#
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
 HQQ  HQQ  5-methyl-5-(4-phenoxyphenyl)pyrimidine-2,4,6(1H,3H,5H)-trione  ligand  37  23  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HQQ
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
 HQQ  N1   N  NR16  0  -0.706  -1.2887   0.1682   3.8939
 HQQ  C2   C  CR6   0   0.700  -0.9379  -1.0272   4.4755
 HQQ  O2   O  O     0  -0.437  -1.5690  -1.5123   5.3816
 HQQ  N3   N  NR16  0  -0.705   0.1686  -1.6425   3.9405
 HQQ  C4   C  CR6   0   0.627   0.9562  -1.1850   2.9188
 HQQ  O4   O  O     0  -0.399   1.8461  -1.8594   2.4634
 HQQ  C5   C  CR6   0  -0.532   0.7007   0.2403   2.4514
 HQQ  C6   C  CR6   0   0.627  -0.6514   0.8030   2.8619
 HQQ  O6   O  O     0  -0.399  -1.1121   1.7965   2.3565
 HQQ  C7   C  CH3   0  -0.663   1.7421   1.1075   3.1934
 HQQ  C8   C  CR6   0   0.219   0.8252   0.2901   0.9423
 HQQ  C9   C  CR16  0  -0.328   1.8206   1.0016   0.2893
 HQQ  C10  C  CR16  0  -0.316   1.9020   1.0097  -1.0963
 HQQ  C11  C  CR6   0   0.344   0.9837   0.2920  -1.8473
 HQQ  C12  C  CR16  0  -0.320  -0.0206  -0.4321  -1.2114
 HQQ  C13  C  CR16  0  -0.258  -0.0886  -0.4237   0.1703
 HQQ  O11  O  O2    0  -0.509   1.1511   0.2961  -3.1988
 HQQ  C14  C  CR6   0   0.323   0.0645   0.1408  -4.0200
 HQQ  C15  C  CR16  0  -0.307  -1.0431   0.9730  -3.9122
 HQQ  C16  C  CR16  0  -0.249  -2.0964   0.8168  -4.8013
 HQQ  C17  C  CR16  0  -0.262  -2.0445  -0.1543  -5.7940
 HQQ  C18  C  CR16  0  -0.251  -0.9281  -0.9729  -5.8947
 HQQ  C19  C  CR16  0  -0.324   0.1289  -0.8338  -5.0044
 HQQ  HN1  H  HNR6  0   0.438  -2.1406   0.5922   4.2433
 HQQ  HN3  H  HNR6  0   0.438   0.3896  -2.5546   4.3230
 HQQ  H71  H  HCH3  0   0.275   1.6074   1.0375   4.2728
 HQQ  H72  H  HCH3  0   0.275   2.7523   0.7775   2.9590
 HQQ  H73  H  HCH3  0   0.275   1.6393   2.1523   2.9059
 HQQ  H9   H  HCR6  0   0.266   2.5544   1.5689   0.8445
 HQQ  H10  H  HCR6  0   0.273   2.6849   1.5693  -1.5919
 HQQ  H12  H  HCR6  0   0.284  -0.7439  -1.0038  -1.7779
 HQQ  H13  H  HCR6  0   0.264  -0.8760  -0.9988   0.6457
 HQQ  H15  H  HCR6  0   0.279  -1.0846   1.7402  -3.1491
 HQQ  H16  H  HCR6  0   0.264  -2.9597   1.4640  -4.7197
 HQQ  H17  H  HCR6  0   0.260  -2.8685  -0.2698  -6.4853
 HQQ  H18  H  HCR6  0   0.264  -0.8777  -1.7313  -6.6647
 HQQ  H19  H  HCR6  0   0.270   1.0000  -1.4728  -5.0753

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
 HQQ  N1   C2   single    1.375  0.020  1.375
 HQQ  N1   C6   single    1.369  0.020  1.369
 HQQ  N1   HN1  single    0.860  0.020  1.020
 HQQ  C2   O2   double    1.206  0.020  1.206
 HQQ  C2   N3   single    1.375  0.020  1.375
 HQQ  N3   C4   single    1.369  0.020  1.369
 HQQ  N3   HN3  single    0.860  0.020  1.020
 HQQ  C4   O4   double    1.206  0.020  1.206
 HQQ  C4   C5   single    1.522  0.020  1.522
 HQQ  C5   C6   single    1.521  0.020  1.521
 HQQ  C5   C7   single    1.545  0.020  1.545
 HQQ  C5   C8   single    1.515  0.020  1.515
 HQQ  C6   O6   double    1.206  0.020  1.206
 HQQ  C7   H71  single    0.970  0.020  1.090
 HQQ  C7   H72  single    0.970  0.020  1.090
 HQQ  C7   H73  single    0.970  0.020  1.090
 HQQ  C8   C9   aromatic  1.387  0.020  1.387
 HQQ  C8   C13  aromatic  1.393  0.020  1.393
 HQQ  C9   C10  aromatic  1.388  0.020  1.388
 HQQ  C9   H9   single    0.930  0.020  1.080
 HQQ  C10  C11  aromatic  1.387  0.020  1.387
 HQQ  C10  H10  single    0.930  0.020  1.080
 HQQ  C11  C12  aromatic  1.392  0.020  1.392
 HQQ  C11  O11  single    1.362  0.020  1.362
 HQQ  C12  C13  aromatic  1.383  0.020  1.383
 HQQ  C12  H12  single    0.930  0.020  1.080
 HQQ  C13  H13  single    0.930  0.020  1.080
 HQQ  O11  C14  single    1.371  0.020  1.371
 HQQ  C14  C15  aromatic  1.390  0.020  1.390
 HQQ  C14  C19  aromatic  1.387  0.020  1.387
 HQQ  C15  C16  aromatic  1.387  0.020  1.387
 HQQ  C15  H15  single    0.930  0.020  1.080
 HQQ  C16  C17  aromatic  1.390  0.020  1.390
 HQQ  C16  H16  single    0.930  0.020  1.080
 HQQ  C17  C18  aromatic  1.388  0.020  1.388
 HQQ  C17  H17  single    0.930  0.020  1.080
 HQQ  C18  C19  aromatic  1.389  0.020  1.389
 HQQ  C18  H18  single    0.930  0.020  1.080
 HQQ  C19  H19  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
 HQQ  HN1  N1   C6   117.20  3.000
 HQQ  HN1  N1   C2   115.61  3.000
 HQQ  C6   N1   C2   127.11  3.000
 HQQ  N3   C2   O2   122.25  3.000
 HQQ  N3   C2   N1   115.47  3.000
 HQQ  O2   C2   N1   122.28  3.000
 HQQ  HN3  N3   C4   117.20  3.000
 HQQ  HN3  N3   C2   115.57  3.000
 HQQ  C4   N3   C2   127.16  3.000
 HQQ  C5   C4   O4   122.12  3.000
 HQQ  C5   C4   N3   116.48  3.000
 HQQ  O4   C4   N3   121.31  3.000
 HQQ  C8   C5   C7   113.86  3.000
 HQQ  C8   C5   C6   109.25  3.000
 HQQ  C7   C5   C6   105.18  3.000
 HQQ  C8   C5   C4   108.85  3.000
 HQQ  C7   C5   C4   105.37  3.000
 HQQ  C6   C5   C4   114.39  3.000
 HQQ  O6   C6   C5   122.09  3.000
 HQQ  O6   C6   N1   121.33  3.000
 HQQ  C5   C6   N1   116.47  3.000
 HQQ  H73  C7   H72  108.77  3.000
 HQQ  H73  C7   H71  108.15  3.000
 HQQ  H72  C7   H71  107.97  3.000
 HQQ  H73  C7   C5   110.38  3.000
 HQQ  H72  C7   C5   110.61  3.000
 HQQ  H71  C7   C5   110.87  3.000
 HQQ  C13  C8   C9   118.22  3.000
 HQQ  C13  C8   C5   118.77  3.000
 HQQ  C9   C8   C5   123.01  3.000
 HQQ  H9   C9   C10  118.02  3.000
 HQQ  H9   C9   C8   120.97  3.000
 HQQ  C10  C9   C8   121.00  3.000
 HQQ  H10  C10  C11  119.90  3.000
 HQQ  H10  C10  C9   120.17  3.000
 HQQ  C11  C10  C9   119.92  3.000
 HQQ  O11  C11  C12  122.93  3.000
 HQQ  O11  C11  C10  117.04  3.000
 HQQ  C12  C11  C10  119.98  3.000
 HQQ  H12  C12  C13  119.55  3.000
 HQQ  H12  C12  C11  121.19  3.000
 HQQ  C13  C12  C11  119.25  3.000
 HQQ  H13  C13  C12  118.05  3.000
 HQQ  H13  C13  C8   120.33  3.000
 HQQ  C12  C13  C8   121.62  3.000
 HQQ  C14  O11  C11  119.78  3.000
 HQQ  C19  C14  C15  120.87  3.000
 HQQ  C19  C14  O11  117.90  3.000
 HQQ  C15  C14  O11  121.16  3.000
 HQQ  H15  C15  C16  120.16  3.000
 HQQ  H15  C15  C14  120.63  3.000
 HQQ  C16  C15  C14  119.21  3.000
 HQQ  H16  C16  C17  120.11  3.000
 HQQ  H16  C16  C15  119.34  3.000
 HQQ  C17  C16  C15  120.54  3.000
 HQQ  H17  C17  C18  120.22  3.000
 HQQ  H17  C17  C16  120.18  3.000
 HQQ  C18  C17  C16  119.60  3.000
 HQQ  H18  C18  C19  119.40  3.000
 HQQ  H18  C18  C17  120.17  3.000
 HQQ  C19  C18  C17  120.43  3.000
 HQQ  H19  C19  C18  120.75  3.000
 HQQ  H19  C19  C14  119.92  3.000
 HQQ  C18  C19  C14  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
 HQQ  CONST_01  C11  C10  C9   C8     0.00   0.0  0
 HQQ  CONST_02  C11  C12  C13  C8     0.00   0.0  0
 HQQ  CONST_03  C12  C13  C8   C9     0.00   0.0  0
 HQQ  CONST_04  C12  C11  C10  C9     0.00   0.0  0
 HQQ  CONST_05  C13  C8   C9   C10    0.00   0.0  0
 HQQ  CONST_06  C13  C12  C11  C10    0.00   0.0  0
 HQQ  CONST_07  C17  C16  C15  C14    0.00   0.0  0
 HQQ  CONST_08  C17  C18  C19  C14    0.00   0.0  0
 HQQ  CONST_09  C18  C19  C14  C15    0.00   0.0  0
 HQQ  CONST_10  C18  C17  C16  C15    0.00   0.0  0
 HQQ  CONST_11  C19  C14  C15  C16    0.00   0.0  0
 HQQ  CONST_12  C19  C18  C17  C16    0.00   0.0  0
 HQQ  CONST_13  C10  C9   C8   C5   180.00   0.0  0
 HQQ  CONST_14  C12  C13  C8   C5   180.00   0.0  0
 HQQ  CONST_15  C4   N3   C2   N1     0.00   0.0  0
 HQQ  CONST_16  C5   C4   N3   C2     0.00   0.0  0
 HQQ  CONST_17  C6   N1   C2   N3     0.00   0.0  0
 HQQ  CONST_18  O11  C11  C10  C9   180.00   0.0  0
 HQQ  CONST_19  O11  C11  C12  C13  180.00   0.0  0
 HQQ  CONST_20  C16  C15  C14  O11  180.00   0.0  0
 HQQ  CONST_21  C18  C19  C14  O11  180.00   0.0  0
 HQQ  CONST_22  O4   C4   N3   C2   180.00   0.0  0
 HQQ  CONST_23  C6   N1   C2   O2   180.00   0.0  0
 HQQ  CONST_24  C4   N3   C2   O2   180.00   0.0  0
 HQQ  CONST_25  H9   C9   C8   C5     0.00   0.0  0
 HQQ  CONST_26  H13  C13  C8   C5     0.00   0.0  0
 HQQ  CONST_27  H10  C10  C9   C8   180.00   0.0  0
 HQQ  CONST_28  H12  C12  C13  C8   180.00   0.0  0
 HQQ  CONST_29  H16  C16  C15  C14  180.00   0.0  0
 HQQ  CONST_30  H18  C18  C19  C14  180.00   0.0  0
 HQQ  CONST_31  H19  C19  C14  C15  180.00   0.0  0
 HQQ  CONST_32  H17  C17  C16  C15  180.00   0.0  0
 HQQ  CONST_33  H15  C15  C16  C17  180.00   0.0  0
 HQQ  CONST_34  HN3  N3   C2   N1   180.00   0.0  0
 HQQ  CONST_35  HN1  N1   C2   N3   180.00   0.0  0
 HQQ  Var_01    C15  C14  O11  C11   54.60  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 HQQ  chir_01  C5  C6  C4  C8  negativ

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
 HQQ  plan-1  C5   0.020
 HQQ  plan-1  C8   0.020
 HQQ  plan-1  C9   0.020
 HQQ  plan-1  C10  0.020
 HQQ  plan-1  C11  0.020
 HQQ  plan-1  C12  0.020
 HQQ  plan-1  C13  0.020
 HQQ  plan-1  O11  0.020
 HQQ  plan-1  H9   0.020
 HQQ  plan-1  H10  0.020
 HQQ  plan-1  H12  0.020
 HQQ  plan-1  H13  0.020
 HQQ  plan-2  O11  0.020
 HQQ  plan-2  C14  0.020
 HQQ  plan-2  C15  0.020
 HQQ  plan-2  C16  0.020
 HQQ  plan-2  C17  0.020
 HQQ  plan-2  C18  0.020
 HQQ  plan-2  C19  0.020
 HQQ  plan-2  H15  0.020
 HQQ  plan-2  H16  0.020
 HQQ  plan-2  H17  0.020
 HQQ  plan-2  H18  0.020
 HQQ  plan-2  H19  0.020
 HQQ  plan-3  N1   0.020
 HQQ  plan-3  C2   0.020
 HQQ  plan-3  O2   0.020
 HQQ  plan-3  N3   0.020
 HQQ  plan-3  C4   0.020
 HQQ  plan-3  O4   0.020
 HQQ  plan-3  C5   0.020
 HQQ  plan-3  C6   0.020
 HQQ  plan-3  O6   0.020
 HQQ  plan-3  HN1  0.020
 HQQ  plan-3  HN3  0.020

