# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 22:22:56 2020
#   Inital geometry file: a 42 line input string
#   Ligand name: pyridin-3-ylmethanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCc1cccnc1
#
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
 PYF  PYF  'pyridin-3-ylmethanol     '  ligand  15  8  .  2021-08-20  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PYF
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
 PYF  N1   N  N     0  -0.401   1.1633   0.1234  -1.6459
 PYF  C2   C  CR16  0  -0.104   1.1695   0.3085  -0.3303
 PYF  C3   C  CR6   0  -0.014   0.0344   0.2587   0.4693
 PYF  C4   C  CR16  0  -0.168  -1.1762  -0.0204  -0.1575
 PYF  C5   C  CR16  0  -0.320  -1.1957  -0.2207  -1.5273
 PYF  C6   C  CR16  0  -0.070  -0.0001  -0.1353  -2.2281
 PYF  C7   C  CH2   0  -0.215   0.1135   0.5043   1.9471
 PYF  O7   O  OH1   0  -0.666  -0.5488  -0.5426   2.6196
 PYF  H2   H  HCR6  0   0.258   2.1364   0.5092   0.1219
 PYF  H4   H  HCR6  0   0.269  -2.0934  -0.0769   0.4155
 PYF  H5   H  HCR6  0   0.271  -2.1178  -0.4382  -2.0487
 PYF  H6   H  HCR6  0   0.263   0.0157  -0.2842  -3.3021
 PYF  H71  H  HCH2  0   0.223  -0.3472   1.4743   2.1715
 PYF  H72  H  HCH2  0   0.214   1.1668   0.5832   2.2446
 PYF  HO7  H  HOH1  0   0.459  -0.6689  -0.2779   3.5363

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
 PYF  N1  C2   aromatic  1.329  0.020  1.329
 PYF  N1  C6   aromatic  1.326  0.020  1.326
 PYF  C2  C3   aromatic  1.389  0.020  1.389
 PYF  C2  H2   single    0.930  0.020  1.080
 PYF  C3  C4   aromatic  1.392  0.020  1.392
 PYF  C3  C7   single    1.500  0.020  1.500
 PYF  C4  C5   aromatic  1.384  0.020  1.384
 PYF  C4  H4   single    0.930  0.020  1.080
 PYF  C5  C6   aromatic  1.388  0.020  1.388
 PYF  C5  H5   single    0.930  0.020  1.080
 PYF  C6  H6   single    0.930  0.020  1.080
 PYF  C7  O7   single    1.410  0.020  1.410
 PYF  C7  H71  single    0.970  0.020  1.090
 PYF  C7  H72  single    0.970  0.020  1.090
 PYF  O7  HO7  single    0.850  0.020  0.980

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
 PYF  C6   N1  C2   117.77  3.000
 PYF  H2   C2  C3   119.63  3.000
 PYF  H2   C2  N1   116.24  3.000
 PYF  C3   C2  N1   124.13  3.000
 PYF  C7   C3  C4   121.50  3.000
 PYF  C7   C3  C2   121.20  3.000
 PYF  C4   C3  C2   117.30  3.000
 PYF  H4   C4  C5   120.27  3.000
 PYF  H4   C4  C3   120.59  3.000
 PYF  C5   C4  C3   119.14  3.000
 PYF  H5   C5  C6   120.22  3.000
 PYF  H5   C5  C4   121.20  3.000
 PYF  C6   C5  C4   118.58  3.000
 PYF  H6   C6  C5   120.27  3.000
 PYF  H6   C6  N1   116.66  3.000
 PYF  C5   C6  N1   123.07  3.000
 PYF  H72  C7  H71  106.50  3.000
 PYF  H72  C7  O7   112.03  3.000
 PYF  H71  C7  O7   111.21  3.000
 PYF  H72  C7  C3   109.24  3.000
 PYF  H71  C7  C3   108.91  3.000
 PYF  O7   C7  C3   108.88  3.000
 PYF  HO7  O7  C7   108.00  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
 PYF  CONST_01  C4  C3  C2  N1     0.00   0.0  0
 PYF  CONST_02  C4  C5  C6  N1     0.00   0.0  0
 PYF  CONST_03  C5  C6  N1  C2     0.00   0.0  0
 PYF  CONST_04  C5  C4  C3  C2     0.00   0.0  0
 PYF  CONST_05  C6  N1  C2  C3     0.00   0.0  0
 PYF  CONST_06  C6  C5  C4  C3     0.00   0.0  0
 PYF  CONST_07  C7  C3  C2  N1   180.00   0.0  0
 PYF  CONST_08  C7  C3  C4  C5   180.00   0.0  0
 PYF  CONST_09  H5  C5  C6  N1   180.00   0.0  0
 PYF  CONST_10  H6  C6  N1  C2   180.00   0.0  0
 PYF  CONST_11  H4  C4  C3  C2   180.00   0.0  0
 PYF  CONST_12  H2  C2  C3  C4   180.00   0.0  0
 PYF  Var_01    O7  C7  C3  C2  -129.74  30.0  2

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
 PYF  plan-1  N1  0.020
 PYF  plan-1  C2  0.020
 PYF  plan-1  C3  0.020
 PYF  plan-1  C4  0.020
 PYF  plan-1  C5  0.020
 PYF  plan-1  C6  0.020
 PYF  plan-1  C7  0.020
 PYF  plan-1  H2  0.020
 PYF  plan-1  H4  0.020
 PYF  plan-1  H5  0.020
 PYF  plan-1  H6  0.020

