# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 10:45:50 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: 2,6-diamino-5-nitropyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=C(C(=O)N1)[N+]([O-])=O)N
#
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
 B57  B57  2,6-diamino-5-nitropyrimidin-4(3H)-one  ligand  17  12  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_B57
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
 B57  O7    O  O      0  -0.420   0.2657  -2.4403  -0.0995
 B57  C1    C  CR6    0   0.545  -0.1459  -1.3033  -0.0573
 B57  C6    C  CR6    0  -0.061   0.5748  -0.0570  -0.0068
 B57  N8    N  N      1   0.361   1.9945  -0.0905   0.0461
 B57  O10   O  O     -1  -0.441   2.6018   0.9743   0.0132
 B57  O9    O  O      0  -0.349   2.5564  -1.1527   0.1264
 B57  N2    N  NR16   0  -0.720  -1.5409  -1.1234  -0.0711
 B57  C3    C  CR6    0   0.717  -2.1514   0.0751  -0.0409
 B57  N11   N  NH2    0  -0.812  -3.4926   0.1035  -0.0674
 B57  N4    N  N      0  -0.507  -1.4960   1.1981  -0.0153
 B57  C5    C  CR6    0   0.515  -0.1469   1.1639  -0.0091
 B57  N12   N  NH2    0  -0.792   0.4153   2.3637   0.0035
 B57  HN2   H  HNR6   0   0.385  -2.0722  -1.9807  -0.1154
 B57  HN11  H  HNH2   0   0.379  -4.0453  -0.7128   0.1201
 B57  HN1A  H  HNH2   0   0.397  -3.9356   0.9960   0.0592
 B57  HN12  H  HNH2   0   0.422   1.4177   2.4535   0.0122
 B57  HN1B  H  HNH2   0   0.381  -0.1881   3.1666   0.0177

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
 B57  O7   C1    double  1.210  0.020  1.210
 B57  C1   C6    single  1.441  0.020  1.441
 B57  C1   N2    single  1.407  0.020  1.407
 B57  C6   N8    single  1.421  0.020  1.421
 B57  C6   C5    double  1.418  0.020  1.418
 B57  N8   O10   single  1.226  0.020  1.226
 B57  N8   O9    double  1.204  0.020  1.204
 B57  N2   C3    single  1.345  0.020  1.345
 B57  N2   HN2   single  0.860  0.020  1.020
 B57  C3   N11   single  1.342  0.020  1.342
 B57  C3   N4    double  1.301  0.020  1.301
 B57  N11  HN11  single  0.890  0.020  1.040
 B57  N11  HN1A  single  0.890  0.020  1.040
 B57  N4   C5    single  1.350  0.020  1.350
 B57  C5   N12   single  1.325  0.020  1.325
 B57  N12  HN12  single  0.860  0.020  1.020
 B57  N12  HN1B  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
 B57  N2    C1   C6    112.70  3.000
 B57  N2    C1   O7    117.21  3.000
 B57  C6    C1   O7    130.09  3.000
 B57  C5    C6   N8    121.92  3.000
 B57  C5    C6   C1    119.35  3.000
 B57  N8    C6   C1    118.73  3.000
 B57  O9    N8   O10   122.45  3.000
 B57  O9    N8   C6    119.30  3.000
 B57  O10   N8   C6    118.25  3.000
 B57  HN2   N2   C3    121.24  3.000
 B57  HN2   N2   C1    114.44  3.000
 B57  C3    N2   C1    124.31  3.000
 B57  N4    C3   N11   119.07  3.000
 B57  N4    C3   N2    122.75  3.000
 B57  N11   C3   N2    118.16  3.000
 B57  HN1A  N11  HN11  117.16  3.000
 B57  HN1A  N11  C3    117.20  3.000
 B57  HN11  N11  C3    121.98  3.000
 B57  C5    N4   C3    118.82  3.000
 B57  N12   C5   N4    113.65  3.000
 B57  N12   C5   C6    124.31  3.000
 B57  N4    C5   C6    122.04  3.000
 B57  HN1B  N12  HN12  121.79  3.000
 B57  HN1B  N12  C5    117.98  3.000
 B57  HN12  N12  C5    120.23  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
 B57  CONST_01  N4    C3   N2  C1     0.00   0.0  0
 B57  CONST_02  C3    N2   C1  C6     0.00   0.0  0
 B57  CONST_03  C3    N4   C5  C6     0.00   0.0  0
 B57  CONST_04  C5    N4   C3  N2     0.00   0.0  0
 B57  CONST_05  C3    N2   C1  O7   180.00   0.0  0
 B57  CONST_06  N11   C3   N2  C1   180.00   0.0  0
 B57  CONST_07  N12   C5   N4  C3   180.00   0.0  0
 B57  CONST_08  C5    N4   C3  N11  180.00   0.0  0
 B57  CONST_09  HN2   N2   C1  C6   180.00   0.0  0
 B57  CONST_10  HN12  N12  C5  C6     0.00   0.0  0
 B57  CONST_11  HN1B  N12  C5  C6   180.00   0.0  0
 B57  CONST_13  HN1A  N11  C3  N2   180.00   0.0  0
 B57  Var_01    O10   N8   C6  C1   175.99  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
 B57  plan-1  O7    0.020
 B57  plan-1  C1    0.020
 B57  plan-1  C6    0.020
 B57  plan-1  N8    0.020
 B57  plan-1  N2    0.020
 B57  plan-1  C3    0.020
 B57  plan-1  N11   0.020
 B57  plan-1  N4    0.020
 B57  plan-1  C5    0.020
 B57  plan-1  N12   0.020
 B57  plan-1  HN2   0.020
 B57  plan-1  HN11  0.020
 B57  plan-1  HN1A  0.020
 B57  plan-1  HN12  0.020
 B57  plan-1  HN1B  0.020
 B57  plan-2  C6    0.020
 B57  plan-2  N8    0.020
 B57  plan-2  O10   0.020
 B57  plan-2  O9    0.020

