# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 22:49:23 2020
#   Inital geometry file: a 42 line input string
#   Ligand name: (4-chloropyridin-2-yl)methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCc1cc(Cl)ccn1
#
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
 HM3  HM3  (4-chloropyridin-2-yl)methanol  ligand  15  9  .  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_HM3
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
 HM3  C1   C   CH2   0  -0.180   2.7020   0.3201  -0.0005
 HM3  N1   N   N     0  -0.426   1.2510  -1.5834  -0.0032
 HM3  C2   C   CR6   0   0.193   1.3134  -0.2545  -0.0085
 HM3  C3   C   CR16  0  -0.310   0.1810   0.5508  -0.0305
 HM3  C4   C   CR6   0   0.079  -1.0530  -0.0774  -0.0476
 HM3  C5   C   CR16  0  -0.302  -1.1377  -1.4579  -0.0449
 HM3  C6   C   CR16  0  -0.071   0.0589  -2.1590  -0.0229
 HM3  O1   O   OH1   0  -0.663   2.6490   1.7165   0.1005
 HM3  H3   H   HCR6  0   0.291   0.2565   1.6279  -0.0355
 HM3  CL1  CL  CL    0  -0.102  -2.4935   0.8726  -0.0755
 HM3  H4   H   HCR6  0   0.291  -2.0855  -1.9767  -0.0594
 HM3  H5   H   HCR6  0   0.274   0.0409  -3.2429  -0.0203
 HM3  H6   H   HOH1  0   0.467   3.5393   2.0601  -0.0138
 HM3  HOM  H   HCH2  0   0.227   3.2522  -0.1362   0.8327
 HM3  H61  H   HCH2  0   0.232   3.2048  -0.0075  -0.9200

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
 HM3  C1  C2   single    1.503  0.020  1.503
 HM3  C1  O1   single    1.401  0.020  1.401
 HM3  N1  C2   aromatic  1.330  0.020  1.330
 HM3  N1  C6   aromatic  1.324  0.020  1.324
 HM3  C2  C3   aromatic  1.390  0.020  1.390
 HM3  C3  C4   aromatic  1.385  0.020  1.385
 HM3  C3  H3   single    0.930  0.020  1.080
 HM3  C4  C5   aromatic  1.383  0.020  1.383
 HM3  C4  CL1  single    1.726  0.020  1.726
 HM3  C5  C6   aromatic  1.387  0.020  1.387
 HM3  C5  H4   single    0.930  0.020  1.080
 HM3  C6  H5   single    0.930  0.020  1.080
 HM3  O1  H6   single    0.850  0.020  0.980
 HM3  C1  HOM  single    0.970  0.020  1.090
 HM3  C1  H61  single    0.970  0.020  1.090

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
 HM3  H61  C1  HOM  106.38  3.000
 HM3  H61  C1  O1   112.02  3.000
 HM3  HOM  C1  O1   112.24  3.000
 HM3  H61  C1  C2   107.74  3.000
 HM3  HOM  C1  C2   107.96  3.000
 HM3  O1   C1  C2   110.27  3.000
 HM3  C6   N1  C2   118.45  3.000
 HM3  C3   C2  N1   122.73  3.000
 HM3  C3   C2  C1   122.11  3.000
 HM3  N1   C2  C1   115.16  3.000
 HM3  H3   C3  C4   120.98  3.000
 HM3  H3   C3  C2   121.41  3.000
 HM3  C4   C3  C2   117.61  3.000
 HM3  CL1  C4  C5   119.89  3.000
 HM3  CL1  C4  C3   119.62  3.000
 HM3  C5   C4  C3   120.49  3.000
 HM3  H4   C5  C6   120.95  3.000
 HM3  H4   C5  C4   122.20  3.000
 HM3  C6   C5  C4   116.85  3.000
 HM3  H5   C6  C5   119.41  3.000
 HM3  H5   C6  N1   116.72  3.000
 HM3  C5   C6  N1   123.87  3.000
 HM3  H6   O1  C1   108.22  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
 HM3  CONST_01  C4   C3  C2  N1     0.00   0.0  0
 HM3  CONST_02  C4   C5  C6  N1     0.00   0.0  0
 HM3  CONST_03  C5   C6  N1  C2     0.00   0.0  0
 HM3  CONST_04  C5   C4  C3  C2     0.00   0.0  0
 HM3  CONST_05  C6   N1  C2  C3     0.00   0.0  0
 HM3  CONST_06  C6   C5  C4  C3     0.00   0.0  0
 HM3  CONST_07  C6   N1  C2  C1   180.00   0.0  0
 HM3  CONST_08  C4   C3  C2  C1   180.00   0.0  0
 HM3  CONST_09  CL1  C4  C3  C2   180.00   0.0  0
 HM3  CONST_10  CL1  C4  C5  C6   180.00   0.0  0
 HM3  CONST_11  H3   C3  C2  N1   180.00   0.0  0
 HM3  CONST_12  H4   C5  C6  N1   180.00   0.0  0
 HM3  CONST_13  H5   C6  N1  C2   180.00   0.0  0
 HM3  Var_01    O1   C1  C2  N1  -175.31  30.0  1

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
 HM3  plan-1  C1   0.020
 HM3  plan-1  N1   0.020
 HM3  plan-1  C2   0.020
 HM3  plan-1  C3   0.020
 HM3  plan-1  C4   0.020
 HM3  plan-1  C5   0.020
 HM3  plan-1  C6   0.020
 HM3  plan-1  H3   0.020
 HM3  plan-1  CL1  0.020
 HM3  plan-1  H4   0.020
 HM3  plan-1  H5   0.020

