# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 21:24:17 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: 5-amino-6-nitropyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=C(NC(=O)NC1=O)[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
 UNC  UNC  5-amino-6-nitropyrimidine-2,4(1H,3H)-dione  ligand  16  12  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UNC
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
 UNC  OD2   O  O      0  -0.415   2.3595  -1.7416   0.0482
 UNC  N4    N  N      1   0.351   2.0269  -0.5696   0.0302
 UNC  OD1   O  O     -1  -0.427   2.8238   0.3553   0.0112
 UNC  C4    C  CR6    0   0.479   0.6544  -0.2742   0.0319
 UNC  N3    N  NR16   0  -0.747  -0.1833  -1.3807   0.0569
 UNC  C2    C  CR6    0   0.671  -1.5294  -1.3157   0.0600
 UNC  O2    O  OC     0  -0.474  -2.2638  -2.2814   0.0808
 UNC  C5    C  CR6    0   0.202   0.1609   1.0029   0.0105
 UNC  N5    N  NH2    0  -0.801   0.8157   2.1531  -0.0137
 UNC  C6    C  CR6    0   0.565  -1.3267   1.1413   0.0154
 UNC  O6    O  OC     0  -0.422  -1.8548   2.2304  -0.0010
 UNC  N1    N  NR16   0  -0.715  -2.0282  -0.0229   0.0379
 UNC  HN3   H  HNR6   0   0.440   0.2425  -2.2978   0.0719
 UNC  HN51  H  HNH2   0   0.429   1.8192   2.1937  -0.0185
 UNC  HN52  H  HNH2   0   0.423   0.2890   3.0122  -0.0272
 UNC  HN1   H  HNR6   0   0.441  -3.0384   0.0576   0.0421

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
 UNC  OD2  N4    double    1.218  0.020  1.218
 UNC  N4   OD1   single    1.221  0.020  1.221
 UNC  N4   C4    single    1.404  0.020  1.404
 UNC  C4   N3    aromatic  1.388  0.020  1.388
 UNC  C4   C5    aromatic  1.369  0.020  1.369
 UNC  N3   C2    aromatic  1.348  0.020  1.348
 UNC  N3   HN3   single    0.860  0.020  1.020
 UNC  C2   O2    double    1.213  0.020  1.213
 UNC  C2   N1    aromatic  1.386  0.020  1.386
 UNC  C5   N5    single    1.324  0.020  1.324
 UNC  C5   C6    aromatic  1.494  0.020  1.494
 UNC  N5   HN51  single    0.860  0.020  1.020
 UNC  N5   HN52  single    0.860  0.020  1.020
 UNC  C6   O6    double    1.211  0.020  1.211
 UNC  C6   N1    aromatic  1.359  0.020  1.359
 UNC  N1   HN1   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
 UNC  C4    N4  OD1   118.60  3.000
 UNC  C4    N4  OD2   117.99  3.000
 UNC  OD1   N4  OD2   123.41  3.000
 UNC  C5    C4  N3    121.75  3.000
 UNC  C5    C4  N4    123.27  3.000
 UNC  N3    C4  N4    114.98  3.000
 UNC  HN3   N3  C2    117.66  3.000
 UNC  HN3   N3  C4    117.97  3.000
 UNC  C2    N3  C4    124.36  3.000
 UNC  N1    C2  O2    121.66  3.000
 UNC  N1    C2  N3    113.86  3.000
 UNC  O2    C2  N3    124.49  3.000
 UNC  C6    C5  N5    114.34  3.000
 UNC  C6    C5  C4    116.43  3.000
 UNC  N5    C5  C4    129.23  3.000
 UNC  HN52  N5  HN51  119.19  3.000
 UNC  HN52  N5  C5    118.85  3.000
 UNC  HN51  N5  C5    121.97  3.000
 UNC  N1    C6  O6    123.06  3.000
 UNC  N1    C6  C5    115.76  3.000
 UNC  O6    C6  C5    121.18  3.000
 UNC  HN1   N1  C6    116.52  3.000
 UNC  HN1   N1  C2    115.64  3.000
 UNC  C6    N1  C2    127.84  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
 UNC  CONST_01  N1    C2  N3  C4     0.00  0.0  0
 UNC  CONST_02  N1    C6  C5  C4     0.00  0.0  0
 UNC  CONST_03  C6    C5  C4  N3     0.00  0.0  0
 UNC  CONST_04  C6    N1  C2  N3     0.00  0.0  0
 UNC  CONST_05  C5    C4  N3  C2     0.00  0.0  0
 UNC  CONST_06  C5    C6  N1  C2     0.00  0.0  0
 UNC  CONST_07  C2    N3  C4  N4   180.00  0.0  0
 UNC  CONST_08  C6    C5  C4  N4   180.00  0.0  0
 UNC  CONST_09  O2    C2  N3  C4   180.00  0.0  0
 UNC  CONST_10  O6    C6  C5  C4   180.00  0.0  0
 UNC  CONST_11  N5    C5  C4  N3   180.00  0.0  0
 UNC  CONST_12  O6    C6  N1  C2   180.00  0.0  0
 UNC  CONST_13  C6    N1  C2  O2   180.00  0.0  0
 UNC  CONST_14  N1    C6  C5  N5   180.00  0.0  0
 UNC  CONST_15  HN1   N1  C2  N3   180.00  0.0  0
 UNC  CONST_16  HN3   N3  C4  C5   180.00  0.0  0
 UNC  CONST_17  N3    C4  N4  OD2    0.00  0.0  0
 UNC  CONST_18  C5    C4  N4  OD2  180.00  0.0  0
 UNC  CONST_19  N3    C4  N4  OD1  180.00  0.0  0
 UNC  CONST_20  C5    C4  N4  OD1    0.00  0.0  0
 UNC  CONST_21  HN51  N5  C5  C4     0.00  0.0  0
 UNC  CONST_22  HN52  N5  C5  C4   180.00  0.0  0

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
 UNC  plan-1  N4    0.020
 UNC  plan-1  C4    0.020
 UNC  plan-1  N3    0.020
 UNC  plan-1  C2    0.020
 UNC  plan-1  O2    0.020
 UNC  plan-1  C5    0.020
 UNC  plan-1  N5    0.020
 UNC  plan-1  C6    0.020
 UNC  plan-1  O6    0.020
 UNC  plan-1  N1    0.020
 UNC  plan-1  HN3   0.020
 UNC  plan-1  HN1   0.020
 UNC  plan-2  OD2   0.020
 UNC  plan-2  N4    0.020
 UNC  plan-2  OD1   0.020
 UNC  plan-2  C4    0.020
 UNC  plan-3  C5    0.020
 UNC  plan-3  N5    0.020
 UNC  plan-3  HN51  0.020
 UNC  plan-3  HN52  0.020

