# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 11:53:09 2020
#   Inital geometry file: a 37 line input string
#   Ligand name: pyridine 1-oxide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][n+]1ccccc1
#
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
 9PO  9PO  'pyridine 1-oxide         '  ligand  12  7  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9PO
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
 9PO  C4  C  CR16   0  -0.351  -1.1648   1.1925   0.0328
 9PO  C5  C  CR16   0  -0.153  -1.8733   0.0011   0.0516
 9PO  C1  C  CR16   0  -0.012   0.2290  -1.1501  -0.0055
 9PO  N2  N  NR6    1  -0.015   0.9089   0.0215  -0.0232
 9PO  O8  O  O     -1  -0.592   2.1801   0.0307  -0.0569
 9PO  C3  C  CR16   0  -0.013   0.2120   1.1827  -0.0041
 9PO  C6  C  CR16   0  -0.351  -1.1473  -1.1799   0.0320
 9PO  H4  H  HCR6   0   0.291  -1.6690   2.1484   0.0472
 9PO  H5  H  HCR6   0   0.282  -2.9530  -0.0071   0.0808
 9PO  H3  H  HCR6   0   0.311   0.8102   2.0812  -0.0210
 9PO  H6  H  HCR6   0   0.291  -1.6380  -2.1429   0.0452
 9PO  H1  H  HCR6   0   0.311   0.8407  -2.0393  -0.0228

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
 9PO  C4  C5  aromatic  1.386  0.020  1.386
 9PO  C4  C3  aromatic  1.377  0.020  1.377
 9PO  C5  C6  aromatic  1.386  0.020  1.386
 9PO  C6  C1  aromatic  1.377  0.020  1.377
 9PO  N2  O8  single    1.272  0.020  1.272
 9PO  N2  C3  aromatic  1.354  0.020  1.354
 9PO  N2  C1  aromatic  1.355  0.020  1.355
 9PO  C4  H4  single    0.930  0.020  1.080
 9PO  C5  H5  single    0.930  0.020  1.080
 9PO  C3  H3  single    0.930  0.020  1.080
 9PO  C6  H6  single    0.930  0.020  1.080
 9PO  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
 9PO  H4  C4  C3  118.22  3.000
 9PO  H4  C4  C5  121.44  3.000
 9PO  C3  C4  C5  120.34  3.000
 9PO  H5  C5  C6  121.16  3.000
 9PO  H5  C5  C4  121.18  3.000
 9PO  C6  C5  C4  117.66  3.000
 9PO  H1  C1  C6  123.29  3.000
 9PO  H1  C1  N2  115.33  3.000
 9PO  C6  C1  N2  121.38  3.000
 9PO  C3  N2  O8  120.56  3.000
 9PO  C3  N2  C1  118.88  3.000
 9PO  O8  N2  C1  120.55  3.000
 9PO  H3  C3  N2  115.35  3.000
 9PO  H3  C3  C4  123.26  3.000
 9PO  N2  C3  C4  121.39  3.000
 9PO  H6  C6  C1  118.25  3.000
 9PO  H6  C6  C5  121.40  3.000
 9PO  C1  C6  C5  120.35  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
 9PO  CONST_01  C1  C6  C5  C4    0.00  0.0  0
 9PO  CONST_02  C1  N2  C3  C4    0.00  0.0  0
 9PO  CONST_03  N2  C3  C4  C5    0.00  0.0  0
 9PO  CONST_04  N2  C1  C6  C5    0.00  0.0  0
 9PO  CONST_05  C6  C5  C4  C3    0.00  0.0  0
 9PO  CONST_06  C6  C1  N2  C3    0.00  0.0  0
 9PO  CONST_07  O8  N2  C3  C4  180.00  0.0  0
 9PO  CONST_08  C6  C1  N2  O8  180.00  0.0  0
 9PO  CONST_09  H6  C6  C5  C4  180.00  0.0  0
 9PO  CONST_10  H3  C3  C4  C5  180.00  0.0  0
 9PO  CONST_11  H1  C1  C6  C5  180.00  0.0  0
 9PO  CONST_12  H5  C5  C6  C1  180.00  0.0  0
 9PO  CONST_13  H4  C4  C3  N2  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
 9PO  plan-1  C4  0.020
 9PO  plan-1  C5  0.020
 9PO  plan-1  C1  0.020
 9PO  plan-1  N2  0.020
 9PO  plan-1  O8  0.020
 9PO  plan-1  C3  0.020
 9PO  plan-1  C6  0.020
 9PO  plan-1  H4  0.020
 9PO  plan-1  H5  0.020
 9PO  plan-1  H3  0.020
 9PO  plan-1  H6  0.020
 9PO  plan-1  H1  0.020

