# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 11:27:41 2020
#   Inital geometry file: a 48 line input string
#   Ligand name: 5-nitropyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)C1=CNC(=O)NC1=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
 5NU  5NU  5-nitropyrimidine-2,4(1H,3H)-dione  ligand  14  11  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5NU
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
 5NU  O4   O  O      0  -0.413  -0.4242  -2.1866  -0.0142
 5NU  C4   C  CR6    0   0.579   0.0792  -1.0894   0.0093
 5NU  N3   N  NR16   0  -0.724   1.4639  -0.9628   0.0138
 5NU  C2   C  CR6    0   0.710   2.2250   0.1719   0.0295
 5NU  O2   O  O      0  -0.440   3.4307   0.1794   0.0302
 5NU  N1   N  NR16   0  -0.655   1.4740   1.3351   0.0440
 5NU  C6   C  CR16   0   0.103   0.1417   1.3504   0.0448
 5NU  C5   C  CR6    0   0.003  -0.5918   0.2060   0.0315
 5NU  N51  N  N      1   0.348  -2.0184   0.3193   0.0389
 5NU  O53  O  O      0  -0.404  -2.4981   1.4341   0.0162
 5NU  O52  O  O     -1  -0.372  -2.6760  -0.6918   0.0701
 5NU  H1   H  HNR6   0   0.441   1.9810  -1.8343  -0.0009
 5NU  H2   H  HCR6   0   0.364  -0.3159   2.3288   0.0585
 5NU  H4   H  HNR6   0   0.459   1.9783   2.2120   0.0535

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
 5NU  O52  N51  single  1.207  0.020  1.207
 5NU  O53  N51  double  1.214  0.020  1.214
 5NU  N51  C5   single  1.431  0.020  1.431
 5NU  O4   C4   double  1.207  0.020  1.207
 5NU  C5   C4   single  1.459  0.020  1.459
 5NU  C5   C6   double  1.359  0.020  1.359
 5NU  C4   N3   single  1.391  0.020  1.391
 5NU  C6   N1   single  1.332  0.020  1.332
 5NU  N3   C2   single  1.366  0.020  1.366
 5NU  N1   C2   single  1.385  0.020  1.385
 5NU  C2   O2   double  1.206  0.020  1.206
 5NU  N3   H1   single  0.860  0.020  1.020
 5NU  C6   H2   single  0.930  0.020  1.080
 5NU  N1   H4   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
 5NU  C5   C4   N3   112.15  3.000
 5NU  N3   C4   O4   119.87  3.000
 5NU  C5   C4   O4   127.98  3.000
 5NU  H1   N3   C2   115.47  3.000
 5NU  H1   N3   C4   115.45  3.000
 5NU  C2   N3   C4   129.07  3.000
 5NU  N1   C2   O2   122.49  3.000
 5NU  O2   C2   N3   124.21  3.000
 5NU  N1   C2   N3   113.30  3.000
 5NU  H4   N1   C6   119.25  3.000
 5NU  H4   N1   C2   117.25  3.000
 5NU  C6   N1   C2   123.51  3.000
 5NU  H2   C6   C5   122.28  3.000
 5NU  H2   C6   N1   115.72  3.000
 5NU  C5   C6   N1   122.00  3.000
 5NU  N51  C5   C6   118.11  3.000
 5NU  C6   C5   C4   119.96  3.000
 5NU  N51  C5   C4   121.92  3.000
 5NU  O52  N51  O53  123.69  3.000
 5NU  O53  N51  C5   117.81  3.000
 5NU  O52  N51  C5   118.50  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
 5NU  CONST_01  N1   C2   N3  C4    0.00   0.0  0
 5NU  CONST_02  C6   N1   C2  N3    0.00   0.0  0
 5NU  CONST_03  C5   C4   N3  C2    0.00   0.0  0
 5NU  CONST_04  C2   N3   C4  O4  180.00   0.0  0
 5NU  CONST_05  O2   C2   N3  C4  180.00   0.0  0
 5NU  CONST_06  C6   N1   C2  O2  180.00   0.0  0
 5NU  CONST_07  H4   N1   C2  N3  180.00   0.0  0
 5NU  CONST_08  H1   N3   C2  N1  180.00   0.0  0
 5NU  Var_01    O52  N51  C5  C4    2.36  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
 5NU  plan-1  O4   0.020
 5NU  plan-1  C4   0.020
 5NU  plan-1  N3   0.020
 5NU  plan-1  C2   0.020
 5NU  plan-1  O2   0.020
 5NU  plan-1  N1   0.020
 5NU  plan-1  C6   0.020
 5NU  plan-1  C5   0.020
 5NU  plan-1  N51  0.020
 5NU  plan-1  H1   0.020
 5NU  plan-1  H2   0.020
 5NU  plan-1  H4   0.020
 5NU  plan-2  C5   0.020
 5NU  plan-2  N51  0.020
 5NU  plan-2  O53  0.020
 5NU  plan-2  O52  0.020

