# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 10:23:48 2020
#   Inital geometry file: a 38 line input string
#   Ligand name: pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccccn1
#
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
 HVK  HVK  'pyridin-2-amine          '  ligand  13  7  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_HVK
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
 HVK  N1    N  N     0  -0.460   0.2821  -1.1609   0.0203
 HVK  C2    C  CR6   0   0.445   0.9045   0.0162   0.0335
 HVK  C3    C  CR16  0  -0.385   0.1983   1.2327   0.0095
 HVK  C4    C  CR16  0  -0.153  -1.1775   1.1935  -0.0275
 HVK  C5    C  CR16  0  -0.363  -1.8333  -0.0371  -0.0364
 HVK  C6    C  CR16  0  -0.065  -1.0476  -1.1731  -0.0119
 HVK  N     N  NH2   0  -0.832   2.2666  -0.0004   0.1156
 HVK  H3    H  HCR6  0   0.265   0.7319   2.1747   0.0183
 HVK  H4    H  HCR6  0   0.266  -1.7425   2.1168  -0.0505
 HVK  H5    H  HCR6  0   0.257  -2.9111  -0.1085  -0.0652
 HVK  H6    H  HCR6  0   0.254  -1.5101  -2.1549  -0.0204
 HVK  HN2   H  HNH2  0   0.381   2.7169  -0.8623  -0.1458
 HVK  HN1A  H  HNH2  0   0.389   2.7606   0.8250  -0.1800

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
 HVK  N1  C6    aromatic  1.330  0.020  1.330
 HVK  N1  C2    aromatic  1.332  0.020  1.332
 HVK  C6  C5    aromatic  1.381  0.020  1.381
 HVK  N   C2    single    1.365  0.020  1.365
 HVK  C2  C3    aromatic  1.407  0.020  1.407
 HVK  C5  C4    aromatic  1.394  0.020  1.394
 HVK  C4  C3    aromatic  1.377  0.020  1.377
 HVK  C3  H3    single    0.930  0.020  1.080
 HVK  C4  H4    single    0.930  0.020  1.080
 HVK  C5  H5    single    0.930  0.020  1.080
 HVK  C6  H6    single    0.930  0.020  1.080
 HVK  N   HN2   single    0.890  0.020  1.040
 HVK  N   HN1A  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
 HVK  C6    N1  C2   118.40  3.000
 HVK  N     C2  C3   120.84  3.000
 HVK  C3    C2  N1   121.98  3.000
 HVK  N     C2  N1   117.15  3.000
 HVK  H3    C3  C4   121.16  3.000
 HVK  H3    C3  C2   120.32  3.000
 HVK  C4    C3  C2   118.52  3.000
 HVK  H4    C4  C5   120.47  3.000
 HVK  H4    C4  C3   119.85  3.000
 HVK  C5    C4  C3   119.69  3.000
 HVK  H5    C5  C6   120.89  3.000
 HVK  H5    C5  C4   121.84  3.000
 HVK  C6    C5  C4   117.26  3.000
 HVK  H6    C6  C5   120.09  3.000
 HVK  H6    C6  N1   115.75  3.000
 HVK  C5    C6  N1   124.16  3.000
 HVK  HN1A  N   HN2  113.97  3.000
 HVK  HN1A  N   C2   117.54  3.000
 HVK  HN2   N   C2   116.18  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
 HVK  CONST_01  C4  C5  C6  N1    0.00  0.0  0
 HVK  CONST_02  C4  C3  C2  N1    0.00  0.0  0
 HVK  CONST_03  C5  C6  N1  C2    0.00  0.0  0
 HVK  CONST_04  C5  C4  C3  C2    0.00  0.0  0
 HVK  CONST_05  C6  N1  C2  C3    0.00  0.0  0
 HVK  CONST_06  C6  C5  C4  C3    0.00  0.0  0
 HVK  CONST_07  N   C2  C3  C4  180.00  0.0  0
 HVK  CONST_08  N   C2  N1  C6  180.00  0.0  0
 HVK  CONST_09  H5  C5  C6  N1  180.00  0.0  0
 HVK  CONST_10  H3  C3  C2  N1  180.00  0.0  0
 HVK  CONST_11  H6  C6  N1  C2  180.00  0.0  0
 HVK  CONST_12  H4  C4  C3  C2  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
 HVK  plan-1  N1    0.020
 HVK  plan-1  C2    0.020
 HVK  plan-1  C3    0.020
 HVK  plan-1  C4    0.020
 HVK  plan-1  C5    0.020
 HVK  plan-1  C6    0.020
 HVK  plan-1  N     0.020
 HVK  plan-1  H3    0.020
 HVK  plan-1  H4    0.020
 HVK  plan-1  H5    0.020
 HVK  plan-1  H6    0.020
 HVK  plan-2  C2    0.020
 HVK  plan-2  N     0.020
 HVK  plan-2  HN2   0.020
 HVK  plan-2  HN1A  0.020

