# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 08:46:17 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: 2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C1=CC(=O)NC(=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
 ORO  ORO  '2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  14  11  .  2020-10-20  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ORO
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
 ORO  N1   N  NR16   0  -0.703   1.0964  -0.0046   0.0446
 ORO  C2   C  CR6    0   0.663   1.2792   0.0161  -1.3073
 ORO  O2   O  OC     0  -0.484   2.3735   0.0138  -1.8362
 ORO  N3   N  NR16   0  -0.715   0.1060   0.0400  -2.0188
 ORO  C4   C  CR6    0   0.579  -1.1866   0.0435  -1.5113
 ORO  O4   O  OC     0  -0.475  -2.1408   0.0651  -2.2706
 ORO  C5   C  CR16   0  -0.517  -1.2558   0.0196  -0.0711
 ORO  C6   C  CR6    0   0.249  -0.1198  -0.0034   0.6534
 ORO  C7   C  C      0   0.425  -0.0796  -0.0297   2.1876
 ORO  O71  O  O      0  -0.556  -1.1758  -0.0330   2.7582
 ORO  O72  O  OC    -1  -0.582   1.0634  -0.0445   2.6747
 ORO  HN1  H  HNR6   0   0.417   1.9078  -0.0229   0.6504
 ORO  HN3  H  HNR6   0   0.422   0.2007   0.0554  -3.0263
 ORO  H5   H  HCR6   0   0.277  -2.2203   0.0205   0.4124

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
 ORO  N1  C2   aromatic  1.364  0.020  1.364
 ORO  N1  C6   aromatic  1.360  0.020  1.360
 ORO  N1  HN1  single    0.860  0.020  1.020
 ORO  C2  O2   double    1.215  0.020  1.215
 ORO  C2  N3   aromatic  1.372  0.020  1.372
 ORO  N3  C4   aromatic  1.389  0.020  1.389
 ORO  N3  HN3  single    0.860  0.020  1.020
 ORO  C4  O4   double    1.220  0.020  1.220
 ORO  C4  C5   aromatic  1.442  0.020  1.442
 ORO  C5  C6   aromatic  1.348  0.020  1.348
 ORO  C5  H5   single    0.930  0.020  1.080
 ORO  C6  C7   single    1.535  0.020  1.535
 ORO  C7  O71  deloc     1.236  0.020  1.236
 ORO  C7  O72  deloc     1.243  0.020  1.243

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
 ORO  HN1  N1  C6   116.65  3.000
 ORO  HN1  N1  C2   119.05  3.000
 ORO  C6   N1  C2   124.29  3.000
 ORO  N3   C2  O2   122.97  3.000
 ORO  N3   C2  N1   113.54  3.000
 ORO  O2   C2  N1   123.49  3.000
 ORO  HN3  N3  C4   116.80  3.000
 ORO  HN3  N3  C2   115.88  3.000
 ORO  C4   N3  C2   127.33  3.000
 ORO  C5   C4  O4   125.77  3.000
 ORO  C5   C4  N3   114.18  3.000
 ORO  O4   C4  N3   120.05  3.000
 ORO  H5   C5  C6   120.84  3.000
 ORO  H5   C5  C4   119.37  3.000
 ORO  C6   C5  C4   119.79  3.000
 ORO  C7   C6  C5   124.04  3.000
 ORO  C7   C6  N1   115.09  3.000
 ORO  C5   C6  N1   120.87  3.000
 ORO  O72  C7  O71  129.41  3.000
 ORO  O72  C7  C6   114.59  3.000
 ORO  O71  C7  C6   116.00  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
 ORO  CONST_01  C4   N3  C2  N1     0.00   0.0  0
 ORO  CONST_02  C4   C5  C6  N1     0.00   0.0  0
 ORO  CONST_03  C5   C6  N1  C2     0.00   0.0  0
 ORO  CONST_04  C5   C4  N3  C2     0.00   0.0  0
 ORO  CONST_05  C6   N1  C2  N3     0.00   0.0  0
 ORO  CONST_06  C6   C5  C4  N3     0.00   0.0  0
 ORO  CONST_07  C7   C6  N1  C2   180.00   0.0  0
 ORO  CONST_08  O4   C4  N3  C2   180.00   0.0  0
 ORO  CONST_09  C6   N1  C2  O2   180.00   0.0  0
 ORO  CONST_10  C4   N3  C2  O2   180.00   0.0  0
 ORO  CONST_11  C7   C6  C5  C4   180.00   0.0  0
 ORO  CONST_12  C6   C5  C4  O4   180.00   0.0  0
 ORO  CONST_13  HN3  N3  C2  N1   180.00   0.0  0
 ORO  CONST_14  H5   C5  C6  N1   180.00   0.0  0
 ORO  CONST_15  HN1  N1  C2  N3   180.00   0.0  0
 ORO  Var_01    O71  C7  C6  N1  -179.79  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
 ORO  plan-1  N1   0.020
 ORO  plan-1  C2   0.020
 ORO  plan-1  O2   0.020
 ORO  plan-1  N3   0.020
 ORO  plan-1  C4   0.020
 ORO  plan-1  O4   0.020
 ORO  plan-1  C5   0.020
 ORO  plan-1  C6   0.020
 ORO  plan-1  C7   0.020
 ORO  plan-1  HN1  0.020
 ORO  plan-1  HN3  0.020
 ORO  plan-1  H5   0.020
 ORO  plan-2  C6   0.020
 ORO  plan-2  C7   0.020
 ORO  plan-2  O71  0.020
 ORO  plan-2  O72  0.020

