# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 10:21:04 2020
#   Inital geometry file: a 41 line input string
#   Ligand name: 2-aminopyridinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cccc[nH+]1
#
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
 2AP  2AP  '2-aminopyridinium        '  ligand  14  7  .  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_2AP
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
 2AP  N1    N  NR16  1  -0.646   0.2698  -1.0914   0.0134
 2AP  C2    C  CR6   0   0.680   0.9444   0.0742  -0.0055
 2AP  C3    C  CR16  0  -0.383   0.1844   1.2628  -0.0179
 2AP  C4    C  CR16  0  -0.104  -1.1795   1.1901  -0.0130
 2AP  C5    C  CR16  0  -0.369  -1.8410  -0.0528   0.0065
 2AP  C6    C  CR16  0   0.066  -1.0807  -1.1774   0.0200
 2AP  N     N  NH2   0  -0.819   2.2682   0.0625  -0.0064
 2AP  HN1   H  HNR6  0   0.454   0.7942  -1.9576   0.0157
 2AP  H3    H  HCR6  0   0.312   0.7010   2.2117  -0.0323
 2AP  H4    H  HCR6  0   0.304  -1.7582   2.1036  -0.0248
 2AP  H5    H  HCR6  0   0.299  -2.9172  -0.1233   0.0107
 2AP  H6    H  HCR6  0   0.338  -1.4811  -2.1789   0.0380
 2AP  HN1A  H  HNH2  0   0.437   2.7799   0.9269  -0.0579
 2AP  HN2   H  HNH2  0   0.431   2.8025  -0.7908  -0.0283

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
 2AP  N1  C2    aromatic  1.347  0.020  1.347
 2AP  N1  C6    aromatic  1.353  0.020  1.353
 2AP  N1  HN1   single    0.860  0.020  1.020
 2AP  C2  C3    aromatic  1.411  0.020  1.411
 2AP  C2  N     single    1.324  0.020  1.324
 2AP  C3  C4    aromatic  1.366  0.020  1.366
 2AP  C3  H3    single    0.930  0.020  1.080
 2AP  C4  C5    aromatic  1.408  0.020  1.408
 2AP  C4  H4    single    0.930  0.020  1.080
 2AP  C5  C6    aromatic  1.358  0.020  1.358
 2AP  C5  H5    single    0.930  0.020  1.080
 2AP  C6  H6    single    0.930  0.020  1.080
 2AP  N   HN1A  single    0.860  0.020  1.020
 2AP  N   HN2   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
 2AP  HN1   N1  C6    117.55  3.000
 2AP  HN1   N1  C2    118.75  3.000
 2AP  C6    N1  C2    123.70  3.000
 2AP  N     C2  C3    123.10  3.000
 2AP  N     C2  N1    119.55  3.000
 2AP  C3    C2  N1    117.35  3.000
 2AP  H3    C3  C4    121.62  3.000
 2AP  H3    C3  C2    118.84  3.000
 2AP  C4    C3  C2    119.54  3.000
 2AP  H4    C4  C5    119.63  3.000
 2AP  H4    C4  C3    119.30  3.000
 2AP  C5    C4  C3    121.07  3.000
 2AP  H5    C5  C6    120.31  3.000
 2AP  H5    C5  C4    121.76  3.000
 2AP  C6    C5  C4    117.92  3.000
 2AP  H6    C6  C5    124.15  3.000
 2AP  H6    C6  N1    115.44  3.000
 2AP  C5    C6  N1    120.42  3.000
 2AP  HN2   N   HN1A  117.20  3.000
 2AP  HN2   N   C2    122.55  3.000
 2AP  HN1A  N   C2    120.08  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
 2AP  CONST_01  C4    C3  C2  N1    0.00  0.0  0
 2AP  CONST_02  C4    C5  C6  N1    0.00  0.0  0
 2AP  CONST_03  C5    C6  N1  C2    0.00  0.0  0
 2AP  CONST_04  C5    C4  C3  C2    0.00  0.0  0
 2AP  CONST_05  C6    N1  C2  C3    0.00  0.0  0
 2AP  CONST_06  C6    C5  C4  C3    0.00  0.0  0
 2AP  CONST_07  N     C2  C3  C4  180.00  0.0  0
 2AP  CONST_08  N     C2  N1  C6  180.00  0.0  0
 2AP  CONST_09  H3    C3  C2  N1  180.00  0.0  0
 2AP  CONST_10  H5    C5  C6  N1  180.00  0.0  0
 2AP  CONST_11  H6    C6  N1  C2  180.00  0.0  0
 2AP  CONST_12  H4    C4  C3  C2  180.00  0.0  0
 2AP  CONST_13  HN1   N1  C2  C3  180.00  0.0  0
 2AP  CONST_14  HN1A  N   C2  N1  180.00  0.0  0
 2AP  CONST_15  HN2   N   C2  N1    0.00  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
 2AP  plan-1  N1    0.020
 2AP  plan-1  C2    0.020
 2AP  plan-1  C3    0.020
 2AP  plan-1  C4    0.020
 2AP  plan-1  C5    0.020
 2AP  plan-1  C6    0.020
 2AP  plan-1  N     0.020
 2AP  plan-1  HN1   0.020
 2AP  plan-1  H3    0.020
 2AP  plan-1  H4    0.020
 2AP  plan-1  H5    0.020
 2AP  plan-1  H6    0.020
 2AP  plan-2  C2    0.020
 2AP  plan-2  N     0.020
 2AP  plan-2  HN1A  0.020
 2AP  plan-2  HN2   0.020

