# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 04:49:25 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: 4-methyl-3-nitropyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccnc(N)c1[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
 2ZV  2ZV  4-methyl-3-nitropyridin-2-amine  ligand  18  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_2ZV
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
 2ZV  C1   C  CH3    0  -0.710   0.2556   2.5901  -0.0054
 2ZV  C2   C  CR6    0   0.194  -0.4328   1.2576  -0.0144
 2ZV  C3   C  CR16   0  -0.403  -1.8185   1.2439   0.0086
 2ZV  C4   C  CR16   0  -0.031  -2.4837   0.0282   0.0138
 2ZV  N5   N  N      0  -0.458  -1.8860  -1.1435   0.0360
 2ZV  C6   C  CR6    0   0.471  -0.5470  -1.1932   0.0509
 2ZV  N7   N  NH2    0  -0.815  -0.0316  -2.4274   0.0688
 2ZV  C8   C  CR6    0   0.057   0.2133   0.0109  -0.0070
 2ZV  N9   N  N      1   0.343   1.6445  -0.0554  -0.0807
 2ZV  O10  O  O     -1  -0.413   2.2112  -1.0057   0.4270
 2ZV  O11  O  O      0  -0.381   2.2424   0.8279  -0.6523
 2ZV  H1   H  HCH3   0   0.269   0.6557   2.8349  -0.9881
 2ZV  H2   H  HCH3   0   0.253  -0.4644   3.3603   0.2630
 2ZV  H3   H  HCH3   0   0.257   1.0794   2.6346   0.7047
 2ZV  H4   H  HCR6   0   0.272  -2.3763   2.1691   0.0262
 2ZV  H5   H  HCR6   0   0.277  -3.5682   0.0091   0.0128
 2ZV  H6   H  HNH2   0   0.403  -0.6772  -3.1978   0.1038
 2ZV  H7   H  HNH2   0   0.416   0.9403  -2.6086   0.2339

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
 2ZV  C4  C3   aromatic  1.386  0.020  1.386
 2ZV  C4  N5   aromatic  1.316  0.020  1.316
 2ZV  C3  C2   aromatic  1.386  0.020  1.386
 2ZV  N5  C6   aromatic  1.340  0.020  1.340
 2ZV  C2  C1   single    1.500  0.020  1.500
 2ZV  C2  C8   aromatic  1.404  0.020  1.404
 2ZV  C6  C8   aromatic  1.425  0.020  1.425
 2ZV  C6  N7   single    1.338  0.020  1.338
 2ZV  C8  N9   single    1.435  0.020  1.435
 2ZV  N9  O10  single    1.217  0.020  1.217
 2ZV  N9  O11  double    1.210  0.020  1.210
 2ZV  C1  H1   single    0.970  0.020  1.090
 2ZV  C1  H2   single    0.970  0.020  1.090
 2ZV  C1  H3   single    0.970  0.020  1.090
 2ZV  C3  H4   single    0.930  0.020  1.080
 2ZV  C4  H5   single    0.930  0.020  1.080
 2ZV  N7  H6   single    0.860  0.020  1.020
 2ZV  N7  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
 2ZV  H3   C1  H2   108.12  3.000
 2ZV  H3   C1  H1   107.55  3.000
 2ZV  H2   C1  H1   107.86  3.000
 2ZV  H3   C1  C2   112.81  3.000
 2ZV  H2   C1  C2   109.06  3.000
 2ZV  H1   C1  C2   111.29  3.000
 2ZV  C8   C2  C3   116.82  3.000
 2ZV  C8   C2  C1   125.28  3.000
 2ZV  C3   C2  C1   117.88  3.000
 2ZV  H4   C3  C4   120.22  3.000
 2ZV  H4   C3  C2   120.53  3.000
 2ZV  C4   C3  C2   119.26  3.000
 2ZV  H5   C4  N5   116.01  3.000
 2ZV  H5   C4  C3   119.70  3.000
 2ZV  N5   C4  C3   124.28  3.000
 2ZV  C6   N5  C4   119.16  3.000
 2ZV  C8   C6  N7   125.07  3.000
 2ZV  N7   C6  N5   114.80  3.000
 2ZV  C8   C6  N5   120.08  3.000
 2ZV  H7   N7  H6   118.56  3.000
 2ZV  H7   N7  C6   122.87  3.000
 2ZV  H6   N7  C6   117.38  3.000
 2ZV  N9   C8  C6   119.68  3.000
 2ZV  N9   C8  C2   119.98  3.000
 2ZV  C6   C8  C2   120.32  3.000
 2ZV  O11  N9  O10  122.46  3.000
 2ZV  O11  N9  C8   118.91  3.000
 2ZV  O10  N9  C8   118.62  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
 2ZV  CONST_01  N5  C4  C3  C2     0.00   0.0  0
 2ZV  CONST_02  N5  C6  C8  C2     0.00   0.0  0
 2ZV  CONST_03  C6  N5  C4  C3     0.00   0.0  0
 2ZV  CONST_04  C6  C8  C2  C3     0.00   0.0  0
 2ZV  CONST_05  C8  C2  C3  C4     0.00   0.0  0
 2ZV  CONST_06  C8  C6  N5  C4     0.00   0.0  0
 2ZV  CONST_07  C4  C3  C2  C1   180.00   0.0  0
 2ZV  CONST_08  C6  C8  C2  C1   180.00   0.0  0
 2ZV  CONST_09  N7  C6  C8  C2   180.00   0.0  0
 2ZV  CONST_10  N9  C8  C2  C3   180.00   0.0  0
 2ZV  CONST_11  N7  C6  N5  C4   180.00   0.0  0
 2ZV  CONST_12  N9  C8  C6  N5   180.00   0.0  0
 2ZV  CONST_13  H5  C4  C3  C2   180.00   0.0  0
 2ZV  CONST_14  H4  C3  C4  N5   180.00   0.0  0
 2ZV  CONST_19  H6  N7  C6  N5     0.00   0.0  0
 2ZV  CONST_20  H7  N7  C6  N5   180.00   0.0  0
 2ZV  Var_01    H1  C1  C2  C3  -105.11  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
 2ZV  plan-1  C1   0.020
 2ZV  plan-1  C2   0.020
 2ZV  plan-1  C3   0.020
 2ZV  plan-1  C4   0.020
 2ZV  plan-1  N5   0.020
 2ZV  plan-1  C6   0.020
 2ZV  plan-1  N7   0.020
 2ZV  plan-1  C8   0.020
 2ZV  plan-1  N9   0.020
 2ZV  plan-1  H4   0.020
 2ZV  plan-1  H5   0.020
 2ZV  plan-2  C6   0.020
 2ZV  plan-2  N7   0.020
 2ZV  plan-2  H6   0.020
 2ZV  plan-2  H7   0.020
 2ZV  plan-3  C8   0.020
 2ZV  plan-3  N9   0.020
 2ZV  plan-3  O10  0.020
 2ZV  plan-3  O11  0.020

