# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 23:06:56 2020
#   Inital geometry file: a 41 line input string
#   Ligand name: pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC=CC(=O)N1
#
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
 URA  URA  pyrimidine-2,4(1H,3H)-dione  ligand  12  8  .  2020-11-11  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_URA
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
 URA  N1   N  NR16  0  -0.669   1.0148  -0.0107  -1.1571
 URA  C2   C  CR6   0   0.685  -0.3553  -0.0091  -1.1798
 URA  O2   O  O     0  -0.476  -1.0021  -0.0017  -2.2059
 URA  N3   N  NR16  0  -0.716  -0.9266  -0.0166   0.0674
 URA  C4   C  CR6   0   0.569  -0.2823  -0.0222   1.2984
 URA  O4   O  O     0  -0.466  -0.9290  -0.0264   2.3297
 URA  C5   C  CR16  0  -0.497   1.1587  -0.0231   1.2049
 URA  C6   C  CR16  0   0.089   1.7389  -0.0178  -0.0075
 URA  HN1  H  HNR6  0   0.439   1.4923  -0.0092  -2.0463
 URA  HN3  H  HNR6  0   0.426  -1.9388  -0.0152   0.0847
 URA  H5   H  HCR6  0   0.292   1.7538  -0.0285   2.1043
 URA  H6   H  HCR6  0   0.325   2.8109  -0.0190  -0.1379

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
 URA  N1  C2   single  1.370  0.020  1.370
 URA  N1  C6   single  1.359  0.020  1.359
 URA  N1  HN1  single  0.860  0.020  1.020
 URA  C2  O2   double  1.213  0.020  1.213
 URA  C2  N3   single  1.372  0.020  1.372
 URA  N3  C4   single  1.389  0.020  1.389
 URA  N3  HN3  single  0.860  0.020  1.020
 URA  C4  O4   double  1.217  0.020  1.217
 URA  C4  C5   single  1.444  0.020  1.444
 URA  C5  C6   double  1.344  0.020  1.344
 URA  C5  H5   single  0.930  0.020  1.080
 URA  C6  H6   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
 URA  HN1  N1  C6  119.56  3.000
 URA  HN1  N1  C2  117.28  3.000
 URA  C6   N1  C2  123.16  3.000
 URA  N3   C2  O2  123.16  3.000
 URA  N3   C2  N1  113.66  3.000
 URA  O2   C2  N1  123.18  3.000
 URA  HN3  N3  C4  116.65  3.000
 URA  HN3  N3  C2  115.59  3.000
 URA  C4   N3  C2  127.76  3.000
 URA  C5   C4  O4  125.80  3.000
 URA  C5   C4  N3  113.92  3.000
 URA  O4   C4  N3  120.28  3.000
 URA  H5   C5  C6  120.94  3.000
 URA  H5   C5  C4  119.78  3.000
 URA  C6   C5  C4  119.29  3.000
 URA  H6   C6  C5  122.51  3.000
 URA  H6   C6  N1  115.27  3.000
 URA  C5   C6  N1  122.22  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
 URA  CONST_01  C4   N3  C2  N1    0.00  0.0  0
 URA  CONST_02  C5   C4  N3  C2    0.00  0.0  0
 URA  CONST_03  C6   N1  C2  N3    0.00  0.0  0
 URA  CONST_04  O4   C4  N3  C2  180.00  0.0  0
 URA  CONST_05  C6   N1  C2  O2  180.00  0.0  0
 URA  CONST_06  C4   N3  C2  O2  180.00  0.0  0
 URA  CONST_07  HN3  N3  C2  N1  180.00  0.0  0
 URA  CONST_08  HN1  N1  C2  N3  180.00  0.0  0

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
 URA  plan-1  N1   0.020
 URA  plan-1  C2   0.020
 URA  plan-1  O2   0.020
 URA  plan-1  N3   0.020
 URA  plan-1  C4   0.020
 URA  plan-1  O4   0.020
 URA  plan-1  C5   0.020
 URA  plan-1  C6   0.020
 URA  plan-1  HN1  0.020
 URA  plan-1  HN3  0.020
 URA  plan-1  H5   0.020
 URA  plan-1  H6   0.020

