# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 06:14:28 2020
#   Inital geometry file: a 41 line input string
#   Ligand name: 3-aminopyridinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc[nH+]c1
#
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
 3AP  3AP  '3-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 GRAND
;

data_comp_3AP
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
 3AP  N1    N  NR16  1  -0.531  -1.1229  -1.0815   0.0331
 3AP  C2    C  CR16  0  -0.004   0.2061  -1.1729  -0.0054
 3AP  C3    C  CR6   0   0.263   0.9841  -0.0167  -0.0541
 3AP  C4    C  CR16  0  -0.173   0.2945   1.2081  -0.0522
 3AP  C5    C  CR16  0  -0.332  -1.0838   1.2427  -0.0103
 3AP  C6    C  CR16  0   0.038  -1.8017   0.0640   0.0322
 3AP  N3    N  NH2   0  -0.850   2.3327  -0.0836  -0.1401
 3AP  HN1   H  HNR6  0   0.467  -1.6470  -1.9480   0.0704
 3AP  H2    H  HCR6  0   0.345   0.6230  -2.1686   0.0018
 3AP  H4    H  HCR6  0   0.312   0.8549   2.1338  -0.0854
 3AP  H5    H  HCR6  0   0.312  -1.6104   2.1852  -0.0084
 3AP  H6    H  HCR6  0   0.341  -2.8769   0.0026   0.0677
 3AP  HN31  H  HNH2  0   0.407   2.8613   0.7428   0.0843
 3AP  HN32  H  HNH2  0   0.405   2.7904  -0.9464   0.1028

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
 3AP  N1  C2    aromatic  1.333  0.020  1.333
 3AP  N1  C6    aromatic  1.332  0.020  1.332
 3AP  N1  HN1   single    0.860  0.020  1.020
 3AP  C2  C3    aromatic  1.394  0.020  1.394
 3AP  C2  H2    single    0.930  0.020  1.080
 3AP  C3  C4    aromatic  1.406  0.020  1.406
 3AP  C3  N3    single    1.353  0.020  1.353
 3AP  C4  C5    aromatic  1.379  0.020  1.379
 3AP  C4  H4    single    0.930  0.020  1.080
 3AP  C5  C6    aromatic  1.381  0.020  1.381
 3AP  C5  H5    single    0.930  0.020  1.080
 3AP  C6  H6    single    0.930  0.020  1.080
 3AP  N3  HN31  single    0.890  0.020  1.040
 3AP  N3  HN32  single    0.890  0.020  1.040

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
 3AP  HN1   N1  C6    118.17  3.000
 3AP  HN1   N1  C2    117.26  3.000
 3AP  C6    N1  C2    124.57  3.000
 3AP  H2    C2  C3    123.33  3.000
 3AP  H2    C2  N1    116.63  3.000
 3AP  C3    C2  N1    120.03  3.000
 3AP  N3    C3  C4    122.15  3.000
 3AP  N3    C3  C2    121.16  3.000
 3AP  C4    C3  C2    116.66  3.000
 3AP  H4    C4  C5    119.79  3.000
 3AP  H4    C4  C3    119.41  3.000
 3AP  C5    C4  C3    120.81  3.000
 3AP  H5    C5  C6    119.44  3.000
 3AP  H5    C5  C4    120.62  3.000
 3AP  C6    C5  C4    119.94  3.000
 3AP  H6    C6  C5    124.64  3.000
 3AP  H6    C6  N1    117.36  3.000
 3AP  C5    C6  N1    117.99  3.000
 3AP  HN32  N3  HN31  114.30  3.000
 3AP  HN32  N3  C3    118.70  3.000
 3AP  HN31  N3  C3    117.96  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
 3AP  CONST_01  C4   C3  C2  N1    0.00  0.0  0
 3AP  CONST_02  C4   C5  C6  N1    0.00  0.0  0
 3AP  CONST_03  C5   C6  N1  C2    0.00  0.0  0
 3AP  CONST_04  C5   C4  C3  C2    0.00  0.0  0
 3AP  CONST_05  C6   N1  C2  C3    0.00  0.0  0
 3AP  CONST_06  C6   C5  C4  C3    0.00  0.0  0
 3AP  CONST_07  N3   C3  C2  N1  180.00  0.0  0
 3AP  CONST_08  N3   C3  C4  C5  180.00  0.0  0
 3AP  CONST_09  H5   C5  C6  N1  180.00  0.0  0
 3AP  CONST_10  H6   C6  N1  C2  180.00  0.0  0
 3AP  CONST_11  H4   C4  C3  C2  180.00  0.0  0
 3AP  CONST_12  HN1  N1  C2  C3  180.00  0.0  0
 3AP  CONST_13  H2   C2  C3  C4  180.00  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
 3AP  plan-1  N1    0.020
 3AP  plan-1  C2    0.020
 3AP  plan-1  C3    0.020
 3AP  plan-1  C4    0.020
 3AP  plan-1  C5    0.020
 3AP  plan-1  C6    0.020
 3AP  plan-1  N3    0.020
 3AP  plan-1  HN1   0.020
 3AP  plan-1  H2    0.020
 3AP  plan-1  H4    0.020
 3AP  plan-1  H5    0.020
 3AP  plan-1  H6    0.020
 3AP  plan-2  C3    0.020
 3AP  plan-2  N3    0.020
 3AP  plan-2  HN31  0.020
 3AP  plan-2  HN32  0.020

