# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 20:21:26 2020
#   Inital geometry file: a 41 line input string
#   Ligand name: 4-aminopyridinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cc[nH+]cc1
#
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
 4AP  4AP  '4-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_4AP
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
 4AP  N1    N  NR16  1  -0.598  -1.7556   0.0016  -0.0139
 4AP  C2    C  CR16  0   0.073  -1.0973  -1.1702  -0.0098
 4AP  C3    C  CR16  0  -0.416   0.2622  -1.2066   0.0023
 4AP  C4    C  CR6   0   0.506   0.9977   0.0039   0.0098
 4AP  C5    C  CR16  0  -0.417   0.2602   1.2133   0.0062
 4AP  C6    C  CR16  0   0.073  -1.0994   1.1745  -0.0060
 4AP  N4    N  NH2   0  -0.822   2.3217   0.0054   0.0200
 4AP  HN1   H  HNR6  0   0.453  -2.7654   0.0006  -0.0255
 4AP  H2    H  HCR6  0   0.340  -1.7033  -2.0630  -0.0166
 4AP  H3    H  HCR6  0   0.311   0.7684  -2.1614   0.0058
 4AP  H5    H  HCR6  0   0.311   0.7648   2.1689   0.0121
 4AP  H6    H  HCR6  0   0.340  -1.7069   2.0663  -0.0102
 4AP  HN41  H  HNH2  0   0.423   2.8456   0.8645   0.0225
 4AP  HN42  H  HNH2  0   0.423   2.8473  -0.8527   0.0182

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
 4AP  N1  C2    aromatic  1.344  0.020  1.344
 4AP  N1  C6    aromatic  1.344  0.020  1.344
 4AP  N1  HN1   single    0.860  0.020  1.020
 4AP  C2  C3    aromatic  1.360  0.020  1.360
 4AP  C2  H2    single    0.930  0.020  1.080
 4AP  C3  C4    aromatic  1.416  0.020  1.416
 4AP  C3  H3    single    0.930  0.020  1.080
 4AP  C4  C5    aromatic  1.417  0.020  1.417
 4AP  C4  N4    single    1.324  0.020  1.324
 4AP  C5  C6    aromatic  1.360  0.020  1.360
 4AP  C5  H5    single    0.930  0.020  1.080
 4AP  C6  H6    single    0.930  0.020  1.080
 4AP  N4  HN41  single    0.860  0.020  1.020
 4AP  N4  HN42  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
 4AP  HN1   N1  C6    119.29  3.000
 4AP  HN1   N1  C2    119.27  3.000
 4AP  C6    N1  C2    121.45  3.000
 4AP  H2    C2  C3    122.63  3.000
 4AP  H2    C2  N1    116.51  3.000
 4AP  C3    C2  N1    120.86  3.000
 4AP  H3    C3  C4    120.78  3.000
 4AP  H3    C3  C2    119.47  3.000
 4AP  C4    C3  C2    119.75  3.000
 4AP  N4    C4  C5    121.31  3.000
 4AP  N4    C4  C3    121.35  3.000
 4AP  C5    C4  C3    117.34  3.000
 4AP  H5    C5  C6    119.47  3.000
 4AP  H5    C5  C4    120.79  3.000
 4AP  C6    C5  C4    119.74  3.000
 4AP  H6    C6  C5    122.63  3.000
 4AP  H6    C6  N1    116.50  3.000
 4AP  C5    C6  N1    120.86  3.000
 4AP  HN42  N4  HN41  117.14  3.000
 4AP  HN42  N4  C4    121.43  3.000
 4AP  HN41  N4  C4    121.44  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
 4AP  CONST_01  C4    C3  C2  N1    0.00  0.0  0
 4AP  CONST_02  C4    C5  C6  N1    0.00  0.0  0
 4AP  CONST_03  C5    C6  N1  C2    0.00  0.0  0
 4AP  CONST_04  C5    C4  C3  C2    0.00  0.0  0
 4AP  CONST_05  C6    N1  C2  C3    0.00  0.0  0
 4AP  CONST_06  C6    C5  C4  C3    0.00  0.0  0
 4AP  CONST_07  N4    C4  C3  C2  180.00  0.0  0
 4AP  CONST_08  N4    C4  C5  C6  180.00  0.0  0
 4AP  CONST_09  H3    C3  C2  N1  180.00  0.0  0
 4AP  CONST_10  H5    C5  C6  N1  180.00  0.0  0
 4AP  CONST_11  H6    C6  N1  C2  180.00  0.0  0
 4AP  CONST_12  HN1   N1  C2  C3  180.00  0.0  0
 4AP  CONST_13  H2    C2  C3  C4  180.00  0.0  0
 4AP  CONST_14  HN41  N4  C4  C3  180.00  0.0  0
 4AP  CONST_15  HN42  N4  C4  C3    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
 4AP  plan-1  N1    0.020
 4AP  plan-1  C2    0.020
 4AP  plan-1  C3    0.020
 4AP  plan-1  C4    0.020
 4AP  plan-1  C5    0.020
 4AP  plan-1  C6    0.020
 4AP  plan-1  N4    0.020
 4AP  plan-1  HN1   0.020
 4AP  plan-1  H2    0.020
 4AP  plan-1  H3    0.020
 4AP  plan-1  H5    0.020
 4AP  plan-1  H6    0.020
 4AP  plan-2  C4    0.020
 4AP  plan-2  N4    0.020
 4AP  plan-2  HN41  0.020
 4AP  plan-2  HN42  0.020

