# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 00:14:52 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: 5-nitro-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=C(C(=O)NC(=O)N1)[N+]([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
 EJZ  EJZ  '5-nitro-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  17  14  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EJZ
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
 EJZ  O1   O  O      0  -0.380  -1.8986   1.7898   1.1460
 EJZ  C1   C  C      0   0.491  -1.4208   1.5168   0.0844
 EJZ  O4   O  OH1    0  -0.555  -1.7762   1.9476  -1.0990
 EJZ  C2   C  CR6    0   0.356  -0.1563   0.6889  -0.0094
 EJZ  C3   C  CR6    0   0.032  -0.1190  -0.6697   0.0108
 EJZ  N3   N  N      1   0.355  -1.3501  -1.3961   0.0458
 EJZ  O6   O  O      0  -0.398  -2.3651  -0.7823  -0.2195
 EJZ  O5   O  O     -1  -0.355  -1.3278  -2.5624   0.3419
 EJZ  N1   N  NR16   0  -0.707   0.9703   1.4103  -0.0372
 EJZ  C4   C  CR6    0   0.710   2.2445   0.8586  -0.0491
 EJZ  O2   O  O      0  -0.429   3.2353   1.5417  -0.0677
 EJZ  N2   N  NR16   0  -0.724   2.2457  -0.5058  -0.0405
 EJZ  C5   C  CR6    0   0.589   1.1632  -1.3713  -0.0244
 EJZ  O3   O  O      0  -0.406   1.3372  -2.5643  -0.0584
 EJZ  HN1  H  HNR6   0   0.463   0.9304   2.4226  -0.0360
 EJZ  HN2  H  HNR6   0   0.447   3.1594  -0.9450  -0.0655
 EJZ  H3   H  HOH1   0   0.509  -2.5526   2.5294  -1.0434

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
 EJZ  O1  C1   double  1.196  0.020  1.196
 EJZ  C1  O4   single  1.309  0.020  1.309
 EJZ  C1  C2   single  1.514  0.020  1.514
 EJZ  C2  C3   double  1.359  0.020  1.359
 EJZ  C2  N1   single  1.338  0.020  1.338
 EJZ  C3  N3   single  1.430  0.020  1.430
 EJZ  C3  C5   single  1.462  0.020  1.462
 EJZ  N3  O6   double  1.215  0.020  1.215
 EJZ  N3  O5   single  1.204  0.020  1.204
 EJZ  N1  C4   single  1.389  0.020  1.389
 EJZ  N1  HN1  single  0.860  0.020  1.020
 EJZ  C4  O2   double  1.204  0.020  1.204
 EJZ  C4  N2   single  1.364  0.020  1.364
 EJZ  N2  C5   single  1.386  0.020  1.386
 EJZ  N2  HN2  single  0.860  0.020  1.020
 EJZ  C5  O3   double  1.206  0.020  1.206
 EJZ  O4  H3   single  0.850  0.020  0.980

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
 EJZ  C2   C1  O4  110.53  3.000
 EJZ  C2   C1  O1  120.89  3.000
 EJZ  O4   C1  O1  128.26  3.000
 EJZ  H3   O4  C1  111.25  3.000
 EJZ  N1   C2  C3  121.07  3.000
 EJZ  N1   C2  C1  114.18  3.000
 EJZ  C3   C2  C1  124.64  3.000
 EJZ  C5   C3  N3  120.79  3.000
 EJZ  C5   C3  C2  120.22  3.000
 EJZ  N3   C3  C2  118.98  3.000
 EJZ  O5   N3  O6  123.95  3.000
 EJZ  O5   N3  C3  118.84  3.000
 EJZ  O6   N3  C3  117.20  3.000
 EJZ  HN1  N1  C4  115.67  3.000
 EJZ  HN1  N1  C2  120.37  3.000
 EJZ  C4   N1  C2  123.96  3.000
 EJZ  N2   C4  O2  124.53  3.000
 EJZ  N2   C4  N1  113.46  3.000
 EJZ  O2   C4  N1  122.01  3.000
 EJZ  HN2  N2  C5  115.69  3.000
 EJZ  HN2  N2  C4  115.71  3.000
 EJZ  C5   N2  C4  128.59  3.000
 EJZ  O3   C5  N2  120.31  3.000
 EJZ  O3   C5  C3  127.00  3.000
 EJZ  N2   C5  C3  112.68  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
 EJZ  CONST_01  N2   C4  N1  C2    0.00   0.0  0
 EJZ  CONST_02  C4   N2  C5  C3    0.00   0.0  0
 EJZ  CONST_03  C5   N2  C4  N1    0.00   0.0  0
 EJZ  CONST_04  O2   C4  N1  C2  180.00   0.0  0
 EJZ  CONST_05  O3   C5  N2  C4  180.00   0.0  0
 EJZ  CONST_06  C5   N2  C4  O2  180.00   0.0  0
 EJZ  CONST_07  HN2  N2  C5  C3  180.00   0.0  0
 EJZ  CONST_08  HN1  N1  C4  N2  180.00   0.0  0
 EJZ  CONST_09  H3   O4  C1  C2  180.00   0.0  0
 EJZ  Var_01    C3   C2  C1  O1   84.64  30.0  2
 EJZ  Var_02    O6   N3  C3  C2   14.76  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
 EJZ  plan-1  C1   0.020
 EJZ  plan-1  C2   0.020
 EJZ  plan-1  C3   0.020
 EJZ  plan-1  N3   0.020
 EJZ  plan-1  N1   0.020
 EJZ  plan-1  C4   0.020
 EJZ  plan-1  O2   0.020
 EJZ  plan-1  N2   0.020
 EJZ  plan-1  C5   0.020
 EJZ  plan-1  O3   0.020
 EJZ  plan-1  HN1  0.020
 EJZ  plan-1  HN2  0.020
 EJZ  plan-2  O1   0.020
 EJZ  plan-2  C1   0.020
 EJZ  plan-2  O4   0.020
 EJZ  plan-2  C2   0.020
 EJZ  plan-2  H3   0.020
 EJZ  plan-3  C3   0.020
 EJZ  plan-3  N3   0.020
 EJZ  plan-3  O6   0.020
 EJZ  plan-3  O5   0.020

