# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:54:05 2022
#   Inital geometry file: a 59 line input string
#   Ligand name: 2-amino-6-(methylamino)-5-nitrosopyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC1=C(N=O)C(=O)NC(=N1)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
 7VJ  7VJ  2-amino-6-(methylamino)-5-nitrosopyrimidin-4(3H)-one  ligand  19  12  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7VJ
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
 7VJ  N3  N  N     0  -0.057  -1.6116  -1.5010  -0.0035
 7VJ  O2  O  O     0  -0.420  -2.8269  -1.3385  -0.0065
 7VJ  C2  C  CR6   0  -0.117  -0.7826  -0.4344  -0.0071
 7VJ  C1  C  CR6   0   0.543   0.6211  -0.7429   0.0034
 7VJ  N2  N  NH1   0  -0.618   1.0215  -2.0033   0.0036
 7VJ  C5  C  CH3   0  -0.515   2.4060  -2.4124   0.0131
 7VJ  N1  N  N     0  -0.529   1.5685   0.1957   0.0153
 7VJ  C4  C  CR6   0   0.725   1.1904   1.4575   0.0160
 7VJ  N5  N  NH2   0  -0.806   2.1149   2.4041   0.0388
 7VJ  N4  N  NR16  0  -0.724  -0.1071   1.8399  -0.0071
 7VJ  C3  C  CR6   0   0.533  -1.1838   0.9506  -0.0190
 7VJ  O1  O  O     0  -0.448  -2.3141   1.3972  -0.0385
 7VJ  H1  H  HNH1  0   0.406   0.3000  -2.7066  -0.0051
 7VJ  H2  H  HCH3  0   0.257   2.4339  -3.4982   0.0031
 7VJ  H3  H  HCH3  0   0.245   2.9399  -2.0414  -0.8615
 7VJ  H4  H  HCH3  0   0.245   2.9237  -2.0594   0.9050
 7VJ  H5  H  HNH2  0   0.425   3.0859   2.1413   0.0522
 7VJ  H6  H  HNH2  0   0.428   1.8893   3.3842   0.0417
 7VJ  H7  H  HNR6  0   0.427  -0.3383   2.8256  -0.0026

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
 7VJ  O1  C3  double  1.215  0.020  1.215
 7VJ  N3  O2  double  1.226  0.020  1.226
 7VJ  N3  C2  single  1.351  0.020  1.351
 7VJ  C3  C2  single  1.442  0.020  1.442
 7VJ  C3  N4  single  1.397  0.020  1.397
 7VJ  C2  C1  double  1.437  0.020  1.437
 7VJ  N4  C4  single  1.353  0.020  1.353
 7VJ  C1  N1  single  1.334  0.020  1.334
 7VJ  C1  N2  single  1.322  0.020  1.322
 7VJ  C4  N5  single  1.323  0.020  1.323
 7VJ  C4  N1  double  1.317  0.020  1.317
 7VJ  N2  C5  single  1.444  0.020  1.444
 7VJ  N2  H1  single  0.860  0.020  1.020
 7VJ  C5  H2  single  0.970  0.020  1.090
 7VJ  C5  H3  single  0.970  0.020  1.090
 7VJ  C5  H4  single  0.970  0.020  1.090
 7VJ  N5  H5  single  0.860  0.020  1.020
 7VJ  N5  H6  single  0.860  0.020  1.020
 7VJ  N4  H7  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
 7VJ  C2  N3  O2  120.24  3.000
 7VJ  C3  C2  C1  118.55  3.000
 7VJ  C1  C2  N3  115.46  3.000
 7VJ  C3  C2  N3  125.99  3.000
 7VJ  N1  C1  N2  117.10  3.000
 7VJ  N2  C1  C2  120.02  3.000
 7VJ  N1  C1  C2  122.87  3.000
 7VJ  H1  N2  C5  119.27  3.000
 7VJ  H1  N2  C1  116.64  3.000
 7VJ  C5  N2  C1  124.09  3.000
 7VJ  H4  C5  H3  108.29  3.000
 7VJ  H4  C5  H2  108.61  3.000
 7VJ  H3  C5  H2  108.69  3.000
 7VJ  H4  C5  N2  111.66  3.000
 7VJ  H3  C5  N2  111.59  3.000
 7VJ  H2  C5  N2  107.93  3.000
 7VJ  C4  N1  C1  118.05  3.000
 7VJ  N4  C4  N5  117.91  3.000
 7VJ  N5  C4  N1  118.99  3.000
 7VJ  N4  C4  N1  123.09  3.000
 7VJ  H6  N5  H5  118.10  3.000
 7VJ  H6  N5  C4  122.71  3.000
 7VJ  H5  N5  C4  119.19  3.000
 7VJ  H7  N4  C3  116.36  3.000
 7VJ  H7  N4  C4  119.61  3.000
 7VJ  C3  N4  C4  124.03  3.000
 7VJ  O1  C3  N4  118.89  3.000
 7VJ  N4  C3  C2  113.39  3.000
 7VJ  O1  C3  C2  127.72  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
 7VJ  CONST_01  C4  N4  C3  C2     0.00   0.0  0
 7VJ  CONST_02  C4  N1  C1  C2     0.00   0.0  0
 7VJ  CONST_03  N4  C4  N1  C1     0.00   0.0  0
 7VJ  CONST_04  C3  N4  C4  N1     0.00   0.0  0
 7VJ  CONST_05  N5  C4  N1  C1   180.00   0.0  0
 7VJ  CONST_06  C4  N1  C1  N2   180.00   0.0  0
 7VJ  CONST_07  O1  C3  N4  C4   180.00   0.0  0
 7VJ  CONST_08  C3  N4  C4  N5   180.00   0.0  0
 7VJ  CONST_09  H7  N4  C3  C2   180.00   0.0  0
 7VJ  CONST_10  C5  N2  C1  C2   180.00   0.0  0
 7VJ  CONST_11  N1  C1  N2  C5     0.00   0.0  0
 7VJ  CONST_12  H1  N2  C1  C2     0.00   0.0  0
 7VJ  CONST_13  H5  N5  C4  N1     0.00   0.0  0
 7VJ  CONST_14  H6  N5  C4  N1   180.00   0.0  0
 7VJ  Var_01    C3  C2  N3  O2    -0.22  30.0  3
 7VJ  Var_02    H2  C5  N2  C1  -179.57  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
 7VJ  plan-1  N3  0.020
 7VJ  plan-1  C2  0.020
 7VJ  plan-1  C1  0.020
 7VJ  plan-1  N2  0.020
 7VJ  plan-1  C5  0.020
 7VJ  plan-1  N1  0.020
 7VJ  plan-1  C4  0.020
 7VJ  plan-1  N5  0.020
 7VJ  plan-1  N4  0.020
 7VJ  plan-1  C3  0.020
 7VJ  plan-1  O1  0.020
 7VJ  plan-1  H1  0.020
 7VJ  plan-1  H5  0.020
 7VJ  plan-1  H6  0.020
 7VJ  plan-1  H7  0.020
 7VJ  plan-2  N3  0.020
 7VJ  plan-2  O2  0.020
 7VJ  plan-2  C2  0.020

