# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 17 20:39:25 2020
#   Inital geometry file: a 34 line input string
#   Ligand name: pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: c1ccncc1
#
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
 0PY  0PY  'pyridine                 '  ligand  11  6  .  2021-08-03  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_0PY
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
 0PY  C5  C  CR16  0  -0.067  -1.1446   0.6747   0.0140
 0PY  N1  N  N     0  -0.405  -0.0170   1.3774   0.0116
 0PY  C4  C  CR16  0  -0.325  -1.1809  -0.7123   0.0021
 0PY  C3  C  CR16  0  -0.156   0.0214  -1.4038  -0.0136
 0PY  C2  C  CR16  0  -0.325   1.2041  -0.6794  -0.0166
 0PY  C1  C  CR16  0  -0.067   1.1295   0.7062  -0.0033
 0PY  H5  H  HCR6  0   0.264  -2.0680   1.2436   0.0260
 0PY  H4  H  HCR6  0   0.271  -2.1289  -1.2328   0.0051
 0PY  H3  H  HCR6  0   0.276   0.0361  -2.4857  -0.0232
 0PY  H2  H  HCR6  0   0.271   2.1663  -1.1728  -0.0291
 0PY  H1  H  HCR6  0   0.264   2.0369   1.3003  -0.0046

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
 0PY  C4  C5  aromatic  1.388  0.020  1.388
 0PY  N1  C5  aromatic  1.329  0.020  1.329
 0PY  C5  H5  single    0.930  0.020  1.080
 0PY  C1  N1  aromatic  1.329  0.020  1.329
 0PY  C3  C4  aromatic  1.387  0.020  1.387
 0PY  C4  H4  single    0.930  0.020  1.080
 0PY  C2  C3  aromatic  1.387  0.020  1.387
 0PY  C3  H3  single    0.930  0.020  1.080
 0PY  C2  C1  aromatic  1.388  0.020  1.388
 0PY  C2  H2  single    0.930  0.020  1.080
 0PY  C1  H1  single    0.930  0.020  1.080

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
 0PY  H5  C5  C4  120.14  3.000
 0PY  H5  C5  N1  116.44  3.000
 0PY  C4  C5  N1  123.43  3.000
 0PY  C1  N1  C5  117.72  3.000
 0PY  H4  C4  C3  121.33  3.000
 0PY  H4  C4  C5  120.26  3.000
 0PY  C3  C4  C5  118.41  3.000
 0PY  H3  C3  C2  120.70  3.000
 0PY  H3  C3  C4  120.69  3.000
 0PY  C2  C3  C4  118.61  3.000
 0PY  H2  C2  C1  120.23  3.000
 0PY  H2  C2  C3  121.37  3.000
 0PY  C1  C2  C3  118.40  3.000
 0PY  H1  C1  C2  120.13  3.000
 0PY  H1  C1  N1  116.44  3.000
 0PY  C2  C1  N1  123.43  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
 0PY  CONST_01  C2  C3  C4  C5    0.00  0.0  0
 0PY  CONST_02  C2  C1  N1  C5    0.00  0.0  0
 0PY  CONST_03  C3  C4  C5  N1    0.00  0.0  0
 0PY  CONST_04  C3  C2  C1  N1    0.00  0.0  0
 0PY  CONST_05  C1  N1  C5  C4    0.00  0.0  0
 0PY  CONST_06  C1  C2  C3  C4    0.00  0.0  0
 0PY  CONST_07  H3  C3  C4  C5  180.00  0.0  0
 0PY  CONST_08  H1  C1  N1  C5  180.00  0.0  0
 0PY  CONST_09  H4  C4  C5  N1  180.00  0.0  0
 0PY  CONST_10  H2  C2  C1  N1  180.00  0.0  0
 0PY  CONST_11  H5  C5  C4  C3  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
 0PY  plan-1  C5  0.020
 0PY  plan-1  N1  0.020
 0PY  plan-1  C4  0.020
 0PY  plan-1  C3  0.020
 0PY  plan-1  C2  0.020
 0PY  plan-1  C1  0.020
 0PY  plan-1  H5  0.020
 0PY  plan-1  H4  0.020
 0PY  plan-1  H3  0.020
 0PY  plan-1  H2  0.020
 0PY  plan-1  H1  0.020

