# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 03:41:39 2021
#   Inital geometry file: a 80 line input string
#   Ligand name: 5-ethyl-5-phenylpyrimidine-2,4,6(1H,3H,5H)-trione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC1(C(=O)NC(=O)NC1=O)c2ccccc2
#
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
 UQA  UQA  5-ethyl-5-phenylpyrimidine-2,4,6(1H,3H,5H)-trione  ligand  29  17  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_UQA
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
 UQA  C01  C  CH3   0  -0.688  109.3098  96.7177  104.6066
 UQA  C02  C  CH2   0  -0.437  109.0572  95.2756  104.1887
 UQA  C03  C  CR6   0  -0.486  109.6609  94.2242  105.1476
 UQA  C04  C  CR6   0   0.616  108.9764  94.4106  106.4938
 UQA  C07  C  CR6   0   0.700  111.1057  95.0713  107.5290
 UQA  C10  C  CR6   0   0.616  111.1668  94.4404  105.1539
 UQA  C12  C  CR6   0   0.217  109.4164  92.7820  104.7151
 UQA  C13  C  CR16  0  -0.336  108.7302  92.4523  103.5546
 UQA  C14  C  CR16  0  -0.236  108.5377  91.1197  103.2071
 UQA  C15  C  CR16  0  -0.262  109.0280  90.1051  104.0143
 UQA  C16  C  CR16  0  -0.244  109.7154  90.4280  105.1779
 UQA  C17  C  CR16  0  -0.271  109.9074  91.7560  105.5222
 UQA  N06  N  NR16  0  -0.706  109.7537  94.8227  107.5414
 UQA  N09  N  NR16  0  -0.705  111.7358  94.8573  106.3257
 UQA  O05  O  O     0  -0.399  107.7931  94.2186  106.6324
 UQA  O08  O  O     0  -0.433  111.7004  95.4449  108.5088
 UQA  O11  O  O     0  -0.400  111.8335  94.2679  104.1627
 UQA  H1   H  HCH3  0   0.260  108.8460  97.3900  103.8862
 UQA  H2   H  HCH3  0   0.238  108.8842  96.9542  105.5828
 UQA  H3   H  HCH3  0   0.237  110.3719  96.9654  104.6342
 UQA  H4   H  HCH2  0   0.269  107.9838  95.0946  104.1188
 UQA  H5   H  HCH2  0   0.268  109.4716  95.1077  103.1941
 UQA  H6   H  HCR6  0   0.263  108.3358  93.2216  102.9055
 UQA  H7   H  HCR6  0   0.262  108.0011  90.8790  102.2988
 UQA  H8   H  HCR6  0   0.262  108.8771  89.0694  103.7398
 UQA  H9   H  HCR6  0   0.263  110.1025  89.6465  105.8184
 UQA  H10  H  HCR6  0   0.256  110.4482  91.9852  106.4345
 UQA  H11  H  HNR6  0   0.437  109.2913  94.9659  108.4319
 UQA  H12  H  HNR6  0   0.437  112.7367  95.0172  106.3219

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
 UQA  C14  C13  aromatic  1.391  0.020  1.391
 UQA  C14  C15  aromatic  1.386  0.020  1.386
 UQA  C13  C12  aromatic  1.388  0.020  1.388
 UQA  C15  C16  aromatic  1.389  0.020  1.389
 UQA  C02  C01  single    1.523  0.020  1.523
 UQA  C02  C03  single    1.546  0.020  1.546
 UQA  O11  C10  double    1.207  0.020  1.207
 UQA  C12  C03  single    1.525  0.020  1.525
 UQA  C12  C17  aromatic  1.395  0.020  1.395
 UQA  C16  C17  aromatic  1.385  0.020  1.385
 UQA  C03  C10  single    1.521  0.020  1.521
 UQA  C03  C04  single    1.522  0.020  1.522
 UQA  C10  N09  single    1.368  0.020  1.368
 UQA  C04  O05  double    1.207  0.020  1.207
 UQA  C04  N06  single    1.368  0.020  1.368
 UQA  N09  C07  single    1.375  0.020  1.375
 UQA  N06  C07  single    1.375  0.020  1.375
 UQA  C07  O08  double    1.206  0.020  1.206
 UQA  C01  H1   single    0.970  0.020  1.090
 UQA  C01  H2   single    0.970  0.020  1.090
 UQA  C01  H3   single    0.970  0.020  1.090
 UQA  C02  H4   single    0.970  0.020  1.090
 UQA  C02  H5   single    0.970  0.020  1.090
 UQA  C13  H6   single    0.930  0.020  1.080
 UQA  C14  H7   single    0.930  0.020  1.080
 UQA  C15  H8   single    0.930  0.020  1.080
 UQA  C16  H9   single    0.930  0.020  1.080
 UQA  C17  H10  single    0.930  0.020  1.080
 UQA  N06  H11  single    0.860  0.020  1.020
 UQA  N09  H12  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
 UQA  H3   C01  H2   107.94  3.000
 UQA  H3   C01  H1   106.93  3.000
 UQA  H2   C01  H1   106.98  3.000
 UQA  H3   C01  C02  112.55  3.000
 UQA  H2   C01  C02  112.72  3.000
 UQA  H1   C01  C02  109.42  3.000
 UQA  H5   C02  H4   106.85  3.000
 UQA  H5   C02  C03  108.22  3.000
 UQA  H4   C02  C03  108.13  3.000
 UQA  H5   C02  C01  109.47  3.000
 UQA  H4   C02  C01  109.75  3.000
 UQA  C03  C02  C01  114.15  3.000
 UQA  C12  C03  C10  107.11  3.000
 UQA  C10  C03  C04  115.10  3.000
 UQA  C12  C03  C04  107.13  3.000
 UQA  C04  C03  C02  106.85  3.000
 UQA  C10  C03  C02  107.00  3.000
 UQA  C12  C03  C02  113.86  3.000
 UQA  O05  C04  N06  121.14  3.000
 UQA  N06  C04  C03  117.31  3.000
 UQA  O05  C04  C03  121.55  3.000
 UQA  O08  C07  N09  122.24  3.000
 UQA  O08  C07  N06  122.27  3.000
 UQA  N09  C07  N06  115.50  3.000
 UQA  O11  C10  N09  121.15  3.000
 UQA  N09  C10  C03  117.30  3.000
 UQA  O11  C10  C03  121.54  3.000
 UQA  C17  C12  C13  118.89  3.000
 UQA  C17  C12  C03  118.36  3.000
 UQA  C13  C12  C03  122.75  3.000
 UQA  H6   C13  C14  118.78  3.000
 UQA  H6   C13  C12  120.88  3.000
 UQA  C14  C13  C12  120.34  3.000
 UQA  H7   C14  C15  120.09  3.000
 UQA  H7   C14  C13  119.44  3.000
 UQA  C15  C14  C13  120.46  3.000
 UQA  H8   C15  C16  120.26  3.000
 UQA  H8   C15  C14  120.23  3.000
 UQA  C16  C15  C14  119.51  3.000
 UQA  H9   C16  C17  119.71  3.000
 UQA  H9   C16  C15  120.32  3.000
 UQA  C17  C16  C15  119.97  3.000
 UQA  H10  C17  C16  118.73  3.000
 UQA  H10  C17  C12  120.44  3.000
 UQA  C16  C17  C12  120.84  3.000
 UQA  H11  N06  C07  115.53  3.000
 UQA  H11  N06  C04  117.14  3.000
 UQA  C07  N06  C04  127.33  3.000
 UQA  H12  N09  C10  117.11  3.000
 UQA  H12  N09  C07  115.55  3.000
 UQA  C10  N09  C07  127.34  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
 UQA  CONST_01  C15  C14  C13  C12     0.00   0.0  0
 UQA  CONST_02  C15  C16  C17  C12     0.00   0.0  0
 UQA  CONST_03  C16  C15  C14  C13     0.00   0.0  0
 UQA  CONST_04  C16  C17  C12  C13     0.00   0.0  0
 UQA  CONST_05  C17  C12  C13  C14     0.00   0.0  0
 UQA  CONST_06  C17  C16  C15  C14     0.00   0.0  0
 UQA  CONST_07  C14  C13  C12  C03   180.00   0.0  0
 UQA  CONST_08  C16  C17  C12  C03   180.00   0.0  0
 UQA  CONST_09  C07  N06  C04  C03     0.00   0.0  0
 UQA  CONST_10  N09  C07  N06  C04     0.00   0.0  0
 UQA  CONST_11  N06  C07  N09  C10     0.00   0.0  0
 UQA  CONST_12  O08  C07  N06  C04   180.00   0.0  0
 UQA  CONST_13  O05  C04  N06  C07   180.00   0.0  0
 UQA  CONST_14  O08  C07  N09  C10   180.00   0.0  0
 UQA  CONST_15  H6   C13  C12  C03     0.00   0.0  0
 UQA  CONST_16  H10  C17  C12  C03     0.00   0.0  0
 UQA  CONST_17  H7   C14  C13  C12   180.00   0.0  0
 UQA  CONST_18  H9   C16  C17  C12   180.00   0.0  0
 UQA  CONST_19  H8   C15  C14  C13   180.00   0.0  0
 UQA  CONST_20  H11  N06  C04  C03   180.00   0.0  0
 UQA  CONST_21  H12  N09  C07  N06   180.00   0.0  0
 UQA  Var_01    H1   C01  C02  C03  -179.48  30.0  3

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
 UQA  chir_01  C03  C12  C10  C04  positiv

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
 UQA  plan-1  C03  0.020
 UQA  plan-1  C12  0.020
 UQA  plan-1  C13  0.020
 UQA  plan-1  C14  0.020
 UQA  plan-1  C15  0.020
 UQA  plan-1  C16  0.020
 UQA  plan-1  C17  0.020
 UQA  plan-1  H6   0.020
 UQA  plan-1  H7   0.020
 UQA  plan-1  H8   0.020
 UQA  plan-1  H9   0.020
 UQA  plan-1  H10  0.020
 UQA  plan-2  C03  0.020
 UQA  plan-2  C04  0.020
 UQA  plan-2  C07  0.020
 UQA  plan-2  C10  0.020
 UQA  plan-2  N06  0.020
 UQA  plan-2  N09  0.020
 UQA  plan-2  O05  0.020
 UQA  plan-2  O08  0.020
 UQA  plan-2  O11  0.020
 UQA  plan-2  H11  0.020
 UQA  plan-2  H12  0.020

