# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 21:47:43 2020
#   Inital geometry file: a 42 line input string
#   Ligand name: pyridin-4-ylmethanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCc1ccncc1
#
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
 PY7  PY7  'pyridin-4-ylmethanol     '  ligand  15  8  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PY7
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
 PY7  N1   N  N     0  -0.406  -2.2503   0.0124  -0.2360
 PY7  C2   C  CR16  0  -0.061  -1.5737   1.1469  -0.1030
 PY7  C3   C  CR16  0  -0.358  -0.2165   1.1989   0.1787
 PY7  C4   C  CR6   0   0.175   0.4871   0.0117   0.3362
 PY7  C5   C  CR16  0  -0.355  -0.2206  -1.1757   0.1949
 PY7  C6   C  CR16  0  -0.061  -1.5771  -1.1230  -0.0873
 PY7  C7   C  CH2   0  -0.221   1.9676   0.0105   0.5894
 PY7  O8   O  OH1   0  -0.665   2.6096  -0.0511  -0.6667
 PY7  H2   H  HCR6  0   0.264  -2.1377   2.0648  -0.2282
 PY7  H3   H  HCR6  0   0.267   0.2775   2.1569   0.2812
 PY7  H5   H  HCR6  0   0.267   0.2700  -2.1341   0.3095
 PY7  H6   H  HCR6  0   0.264  -2.1437  -2.0411  -0.1979
 PY7  H71  H  HCH2  0   0.215   2.2288  -0.8472   1.2200
 PY7  H72  H  HCH2  0   0.215   2.2436   0.9159   1.1421
 PY7  HO8  H  HOH1  0   0.459   3.5591  -0.0652  -0.5105

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
 PY7  N1  C2   aromatic  1.328  0.020  1.328
 PY7  N1  C6   aromatic  1.328  0.020  1.328
 PY7  C2  C3   aromatic  1.387  0.020  1.387
 PY7  C2  H2   single    0.930  0.020  1.080
 PY7  C3  C4   aromatic  1.389  0.020  1.389
 PY7  C3  H3   single    0.930  0.020  1.080
 PY7  C4  C5   aromatic  1.390  0.020  1.390
 PY7  C4  C7   single    1.502  0.020  1.502
 PY7  C5  C6   aromatic  1.387  0.020  1.387
 PY7  C5  H5   single    0.930  0.020  1.080
 PY7  C6  H6   single    0.930  0.020  1.080
 PY7  C7  O8   single    1.412  0.020  1.412
 PY7  C7  H71  single    0.970  0.020  1.090
 PY7  C7  H72  single    0.970  0.020  1.090
 PY7  O8  HO8  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
 PY7  C6   N1  C2   117.44  3.000
 PY7  H2   C2  C3   120.03  3.000
 PY7  H2   C2  N1   116.53  3.000
 PY7  C3   C2  N1   123.44  3.000
 PY7  H3   C3  C4   120.96  3.000
 PY7  H3   C3  C2   119.93  3.000
 PY7  C4   C3  C2   119.12  3.000
 PY7  C7   C4  C5   121.23  3.000
 PY7  C7   C4  C3   121.27  3.000
 PY7  C5   C4  C3   117.44  3.000
 PY7  H5   C5  C6   119.90  3.000
 PY7  H5   C5  C4   120.99  3.000
 PY7  C6   C5  C4   119.11  3.000
 PY7  H6   C6  C5   119.98  3.000
 PY7  H6   C6  N1   116.58  3.000
 PY7  C5   C6  N1   123.44  3.000
 PY7  H72  C7  H71  107.23  3.000
 PY7  H72  C7  O8   111.72  3.000
 PY7  H71  C7  O8   111.67  3.000
 PY7  H72  C7  C4   109.43  3.000
 PY7  H71  C7  C4   109.42  3.000
 PY7  O8   C7  C4   107.35  3.000
 PY7  HO8  O8  C7   107.75  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
 PY7  CONST_01  C4  C3  C2  N1    0.00   0.0  0
 PY7  CONST_02  C4  C5  C6  N1    0.00   0.0  0
 PY7  CONST_03  C5  C6  N1  C2    0.00   0.0  0
 PY7  CONST_04  C5  C4  C3  C2    0.00   0.0  0
 PY7  CONST_05  C6  N1  C2  C3    0.00   0.0  0
 PY7  CONST_06  C6  C5  C4  C3    0.00   0.0  0
 PY7  CONST_07  C7  C4  C3  C2  180.00   0.0  0
 PY7  CONST_08  C7  C4  C5  C6  180.00   0.0  0
 PY7  CONST_09  H3  C3  C2  N1  180.00   0.0  0
 PY7  CONST_10  H5  C5  C6  N1  180.00   0.0  0
 PY7  CONST_11  H6  C6  N1  C2  180.00   0.0  0
 PY7  CONST_12  H2  C2  C3  C4  180.00   0.0  0
 PY7  Var_01    O8  C7  C4  C3  -90.84  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
 PY7  plan-1  N1  0.020
 PY7  plan-1  C2  0.020
 PY7  plan-1  C3  0.020
 PY7  plan-1  C4  0.020
 PY7  plan-1  C5  0.020
 PY7  plan-1  C6  0.020
 PY7  plan-1  C7  0.020
 PY7  plan-1  H2  0.020
 PY7  plan-1  H3  0.020
 PY7  plan-1  H5  0.020
 PY7  plan-1  H6  0.020

