# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 04:51:49 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: 4-amino-2-oxo-1,2-dihydropyrimidine-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)NC=C1C(O)=O
#
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
 1RT  1RT  '4-amino-2-oxo-1,2-dihydropyrimidine-5-carboxylic acid'  ligand  16  11  .  2022-07-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_1RT
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
 1RT  N1   N  NR16  0  -0.651   1.5348  -1.2552  -0.0484
 1RT  C2   C  CR6   0   0.564   2.2070  -0.0243  -0.0335
 1RT  O2   O  O     0  -0.500   3.4268  -0.0228  -0.0430
 1RT  N3   N  N     0  -0.533   1.4463   1.0823  -0.0094
 1RT  C4   C  CR6   0   0.522   0.1246   1.0281  -0.0003
 1RT  N4   N  NH2   0  -0.804  -0.5104   2.1938   0.0230
 1RT  C5   C  CR6   0  -0.319  -0.5834  -0.2349  -0.0145
 1RT  C6   C  CR16  0   0.137   0.2114  -1.3463  -0.0391
 1RT  C21  C  C     0   0.561  -2.0320  -0.4693  -0.0061
 1RT  O22  O  O     0  -0.448  -2.5339  -1.5695  -0.0213
 1RT  O23  O  OH1   0  -0.615  -2.7548   0.6453   0.0206
 1RT  H1   H  HNH2  0   0.423  -1.5119   2.2669   0.0276
 1RT  H2   H  HNH2  0   0.406   0.0352   3.0395   0.0288
 1RT  H4   H  HCR6  0   0.329  -0.2020  -2.3449  -0.0520
 1RT  H5   H  HOH1  0   0.495  -3.7002   0.4322   0.0244
 1RT  H6   H  HNR6  0   0.433   2.0915  -2.0983  -0.0692

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
 1RT  O22  C21  double  1.209  0.020  1.209
 1RT  O23  C21  single  1.329  0.020  1.329
 1RT  N4   C4   single  1.328  0.020  1.328
 1RT  C21  C5   single  1.467  0.020  1.467
 1RT  C4   C5   single  1.448  0.020  1.448
 1RT  C4   N3   double  1.323  0.020  1.323
 1RT  C5   C6   double  1.367  0.020  1.367
 1RT  N3   C2   single  1.343  0.020  1.343
 1RT  C6   N1   single  1.327  0.020  1.327
 1RT  C2   N1   single  1.403  0.020  1.403
 1RT  C2   O2   double  1.220  0.020  1.220
 1RT  N4   H1   single  0.860  0.020  1.020
 1RT  N4   H2   single  0.860  0.020  1.020
 1RT  C6   H4   single  0.930  0.020  1.080
 1RT  O23  H5   single  0.850  0.020  0.980
 1RT  N1   H6   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
 1RT  H6   N1   C6   119.50  3.000
 1RT  H6   N1   C2   117.93  3.000
 1RT  C6   N1   C2   122.57  3.000
 1RT  N3   C2   O2   124.43  3.000
 1RT  O2   C2   N1   118.70  3.000
 1RT  N3   C2   N1   116.87  3.000
 1RT  C4   N3   C2   122.15  3.000
 1RT  C5   C4   N4   122.15  3.000
 1RT  C5   C4   N3   121.61  3.000
 1RT  N4   C4   N3   116.23  3.000
 1RT  H2   N4   H1   118.65  3.000
 1RT  H2   N4   C4   118.60  3.000
 1RT  H1   N4   C4   122.75  3.000
 1RT  C21  C5   C6   116.38  3.000
 1RT  C6   C5   C4   115.17  3.000
 1RT  C21  C5   C4   128.46  3.000
 1RT  H4   C6   C5   121.95  3.000
 1RT  H4   C6   N1   116.42  3.000
 1RT  C5   C6   N1   121.63  3.000
 1RT  O23  C21  O22  122.52  3.000
 1RT  O23  C21  C5   113.77  3.000
 1RT  O22  C21  C5   123.71  3.000
 1RT  H5   O23  C21  110.27  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
 1RT  CONST_01  C4   N3   C2   N1    0.00   0.0  0
 1RT  CONST_02  C5   C4   N3   C2    0.00   0.0  0
 1RT  CONST_03  C6   N1   C2   N3    0.00   0.0  0
 1RT  CONST_04  N4   C4   N3   C2  180.00   0.0  0
 1RT  CONST_05  C4   N3   C2   O2  180.00   0.0  0
 1RT  CONST_06  C6   N1   C2   O2  180.00   0.0  0
 1RT  CONST_07  H6   N1   C2   N3  180.00   0.0  0
 1RT  CONST_08  H1   N4   C4   N3  180.00   0.0  0
 1RT  CONST_09  H2   N4   C4   N3    0.00   0.0  0
 1RT  CONST_10  H5   O23  C21  C5  180.00   0.0  0
 1RT  Var_01    O22  C21  C5   C4  179.89  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
 1RT  plan-1  N1   0.020
 1RT  plan-1  C2   0.020
 1RT  plan-1  O2   0.020
 1RT  plan-1  N3   0.020
 1RT  plan-1  C4   0.020
 1RT  plan-1  N4   0.020
 1RT  plan-1  C5   0.020
 1RT  plan-1  C6   0.020
 1RT  plan-1  C21  0.020
 1RT  plan-1  H1   0.020
 1RT  plan-1  H2   0.020
 1RT  plan-1  H4   0.020
 1RT  plan-1  H6   0.020
 1RT  plan-2  C5   0.020
 1RT  plan-2  C21  0.020
 1RT  plan-2  O22  0.020
 1RT  plan-2  O23  0.020
 1RT  plan-2  H5   0.020

