# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 23 05:35:02 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  15  11  .  2022-07-22  2022-07-26
;
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  -0.658   1.5785  -1.2603  -0.0311
 1RT  C2   C  CR6    0   0.543   2.2290  -0.0288  -0.0101
 1RT  O2   O  O      0  -0.529   3.4551  -0.0049  -0.0161
 1RT  N3   N  N      0  -0.540   1.4577   1.0729   0.0158
 1RT  C4   C  CR6    0   0.488   0.1346   0.9806   0.0213
 1RT  N4   N  NH2    0  -0.813  -0.5676   2.1066   0.0476
 1RT  C5   C  CR6    0  -0.363  -0.5654  -0.2830   0.0009
 1RT  C6   C  CR16   0   0.086   0.2404  -1.3729  -0.0255
 1RT  C21  C  C      0   0.452  -2.0672  -0.4544   0.0065
 1RT  O22  O  O      0  -0.583  -2.4968  -1.6198  -0.0099
 1RT  O23  O  OC    -1  -0.601  -2.7632   0.5888   0.0274
 1RT  H1   H  HNH2   0   0.410  -1.5790   2.0178   0.0496
 1RT  H2   H  HNH2   0   0.388  -0.1017   2.9974   0.0590
 1RT  H4   H  HCR6   0   0.304  -0.1575  -2.3774  -0.0428
 1RT  H6   H  HNR6   0   0.417   2.1483  -2.0929  -0.0526

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  deloc   1.242  0.020  1.242
 1RT  O23  C21  deloc   1.254  0.020  1.254
 1RT  N4   C4   single  1.327  0.020  1.327
 1RT  C21  C5   single  1.512  0.020  1.512
 1RT  C4   C5   single  1.445  0.020  1.445
 1RT  C4   N3   double  1.326  0.020  1.326
 1RT  C5   C6   double  1.356  0.020  1.356
 1RT  N3   C2   single  1.345  0.020  1.345
 1RT  C6   N1   single  1.343  0.020  1.343
 1RT  C2   N1   single  1.393  0.020  1.393
 1RT  C2   O2   double  1.226  0.020  1.226
 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  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   119.57  3.000
 1RT  H6   N1   C2   117.78  3.000
 1RT  C6   N1   C2   122.64  3.000
 1RT  N3   C2   O2   123.88  3.000
 1RT  O2   C2   N1   118.95  3.000
 1RT  N3   C2   N1   117.17  3.000
 1RT  C4   N3   C2   121.01  3.000
 1RT  C5   C4   N4   119.08  3.000
 1RT  C5   C4   N3   122.96  3.000
 1RT  N4   C4   N3   117.96  3.000
 1RT  H2   N4   H1   122.62  3.000
 1RT  H2   N4   C4   120.45  3.000
 1RT  H1   N4   C4   116.93  3.000
 1RT  C21  C5   C6   119.96  3.000
 1RT  C6   C5   C4   114.55  3.000
 1RT  C21  C5   C4   125.49  3.000
 1RT  H4   C6   C5   121.92  3.000
 1RT  H4   C6   N1   116.41  3.000
 1RT  C5   C6   N1   121.66  3.000
 1RT  O23  C21  O22  126.06  3.000
 1RT  O23  C21  C5   117.20  3.000
 1RT  O22  C21  C5   116.74  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  Var_01    O22  C21  C5  C4  -179.80  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

