# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 05:06:39 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: 2-amino-6-(methylamino)-5-nitropyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC1=C(C(=O)NC(=N1)N)[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
 680  680  2-amino-6-(methylamino)-5-nitropyrimidin-4(3H)-one  ligand  20  13  .  2022-07-23  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_680
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
 680  O3    O  O     -1  -0.476   2.6097   0.8651  -0.0255
 680  N3    N  N      1   0.355   2.0510  -0.2342  -0.0010
 680  O2    O  O      0  -0.419   2.7047  -1.2583   0.0186
 680  C2    C  CR6    0  -0.061   0.6526  -0.2886   0.0021
 680  C1    C  CR6    0   0.543  -0.1621   0.8959  -0.0311
 680  N2    N  NH1    0  -0.626   0.3339   2.1216  -0.0586
 680  C5    C  CH3    0  -0.514  -0.4832   3.3121  -0.0890
 680  N1    N  N      0  -0.531  -1.4989   0.8252  -0.0361
 680  C4    C  CR6    0   0.722  -2.0825  -0.3487  -0.0028
 680  N5    N  NH2    0  -0.808  -3.4053  -0.4192  -0.0144
 680  N4    N  NR16   0  -0.720  -1.3842  -1.5019   0.0390
 680  C3    C  CR6    0   0.531   0.0066  -1.5802   0.0443
 680  O1    O  O      0  -0.449   0.5109  -2.6856   0.0841
 680  HN2   H  HNH1   0   0.426   1.3384   2.2064  -0.0572
 680  H51   H  HCH3   0   0.246  -1.1072   3.3504  -0.9813
 680  H52   H  HCH3   0   0.246  -1.1313   3.3778   0.7842
 680  H53   H  HCH3   0   0.256   0.1831   4.1695  -0.0934
 680  HN51  H  HNH2   0   0.427  -3.9027  -1.2921   0.0351
 680  HN52  H  HNH2   0   0.424  -3.9416   0.4316  -0.0263
 680  HN4   H  HNR6   0   0.429  -1.8721  -2.3874   0.0727

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
 680  O3  N3    single  1.233  0.020  1.233
 680  N3  O2    double  1.215  0.020  1.215
 680  N3  C2    single  1.399  0.020  1.399
 680  C2  C1    double  1.438  0.020  1.438
 680  C2  C3    single  1.445  0.020  1.445
 680  C1  N2    single  1.323  0.020  1.323
 680  C1  N1    single  1.339  0.020  1.339
 680  N2  C5    single  1.444  0.020  1.444
 680  N2  HN2   single  0.860  0.020  1.020
 680  C5  H51   single  0.970  0.020  1.090
 680  C5  H52   single  0.970  0.020  1.090
 680  C5  H53   single  0.970  0.020  1.090
 680  N1  C4    double  1.311  0.020  1.311
 680  C4  N5    single  1.325  0.020  1.325
 680  C4  N4    single  1.349  0.020  1.349
 680  N5  HN51  single  0.860  0.020  1.020
 680  N5  HN52  single  0.860  0.020  1.020
 680  N4  C3    single  1.393  0.020  1.393
 680  N4  HN4   single  0.860  0.020  1.020
 680  C3  O1    double  1.216  0.020  1.216

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
 680  C2    N3  O2    120.31  3.000
 680  C2    N3  O3    119.17  3.000
 680  O2    N3  O3    120.52  3.000
 680  C3    C2  C1    118.93  3.000
 680  C3    C2  N3    118.79  3.000
 680  C1    C2  N3    122.28  3.000
 680  N1    C1  N2    115.05  3.000
 680  N1    C1  C2    121.49  3.000
 680  N2    C1  C2    123.46  3.000
 680  HN2   N2  C5    119.64  3.000
 680  HN2   N2  C1    116.84  3.000
 680  C5    N2  C1    123.52  3.000
 680  H53   C5  H52   108.71  3.000
 680  H53   C5  H51   108.69  3.000
 680  H52   C5  H51   108.28  3.000
 680  H53   C5  N2    107.68  3.000
 680  H52   C5  N2    111.67  3.000
 680  H51   C5  N2    111.73  3.000
 680  C4    N1  C1    119.45  3.000
 680  N4    C4  N5    118.15  3.000
 680  N4    C4  N1    122.39  3.000
 680  N5    C4  N1    119.46  3.000
 680  HN52  N5  HN51  118.10  3.000
 680  HN52  N5  C4    119.18  3.000
 680  HN51  N5  C4    122.65  3.000
 680  HN4   N4  C3    115.61  3.000
 680  HN4   N4  C4    119.98  3.000
 680  C3    N4  C4    124.41  3.000
 680  O1    C3  N4    117.74  3.000
 680  O1    C3  C2    128.93  3.000
 680  N4    C3  C2    113.33  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
 680  CONST_01  C4    N1  C1  C2    0.00   0.0  0
 680  CONST_02  C4    N4  C3  C2    0.00   0.0  0
 680  CONST_03  N4    C4  N1  C1    0.00   0.0  0
 680  CONST_04  C3    N4  C4  N1    0.00   0.0  0
 680  CONST_05  N5    C4  N1  C1  180.00   0.0  0
 680  CONST_06  C4    N1  C1  N2  180.00   0.0  0
 680  CONST_07  O1    C3  N4  C4  180.00   0.0  0
 680  CONST_08  C3    N4  C4  N5  180.00   0.0  0
 680  CONST_09  HN4   N4  C3  C2  180.00   0.0  0
 680  CONST_10  C5    N2  C1  C2  180.00   0.0  0
 680  CONST_11  N1    C1  N2  C5    0.00   0.0  0
 680  CONST_12  HN2   N2  C1  C2    0.00   0.0  0
 680  CONST_13  HN51  N5  C4  N1  180.00   0.0  0
 680  CONST_14  HN52  N5  C4  N1    0.00   0.0  0
 680  Var_01    C1    C2  N3  O3    0.41  30.0  2
 680  Var_02    H51   C5  N2  C1  -61.48  30.0  3

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
 680  plan-1  N3    0.020
 680  plan-1  C2    0.020
 680  plan-1  C1    0.020
 680  plan-1  N2    0.020
 680  plan-1  C5    0.020
 680  plan-1  N1    0.020
 680  plan-1  C4    0.020
 680  plan-1  N5    0.020
 680  plan-1  N4    0.020
 680  plan-1  C3    0.020
 680  plan-1  O1    0.020
 680  plan-1  HN2   0.020
 680  plan-1  HN51  0.020
 680  plan-1  HN52  0.020
 680  plan-1  HN4   0.020
 680  plan-2  O3    0.020
 680  plan-2  N3    0.020
 680  plan-2  O2    0.020
 680  plan-2  C2    0.020

