# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 01:54:35 2020
#   Inital geometry file: a 39 line input string
#   Ligand name: 2,3-dichlorophenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cccc(Cl)c1Cl
#
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
 5JF  5JF  '2,3-dichlorophenol       '  ligand  13  9  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_5JF
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
 5JF  CL1  CL  CL    0  -0.042   0.3547  -2.0166   0.0002
 5JF  CAI  C   CR6   0  -0.095  -0.1783  -0.3842  -0.0045
 5JF  CAH  C   CR6   0  -0.027   0.7325   0.6671   0.0008
 5JF  CL2  CL  CL    0  -0.129   2.4249   0.3445   0.0105
 5JF  CAF  C   CR16  0  -0.259   0.2926   1.9817  -0.0127
 5JF  CAD  C   CR16  0  -0.231  -1.0683   2.2421  -0.0223
 5JF  CAE  C   CR16  0  -0.378  -1.9842   1.2022  -0.0110
 5JF  CAG  C   CR6   0   0.488  -1.5491  -0.1165  -0.0016
 5JF  OAA  O   OH1   0  -0.656  -2.4167  -1.1525   0.0550
 5JF  H1   H   HCR6  0   0.288   1.0142   2.7864  -0.0127
 5JF  H2   H   HCR6  0   0.297  -1.4146   3.2665  -0.0285
 5JF  H3   H   HCR6  0   0.260  -3.0471   1.4074  -0.0032
 5JF  H4   H   HOH1  0   0.482  -2.9900  -1.1559  -0.7208

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
 5JF  CAD  CAF  aromatic  1.386  0.020  1.386
 5JF  CAD  CAE  aromatic  1.386  0.020  1.386
 5JF  CAF  CAH  aromatic  1.386  0.020  1.386
 5JF  CAE  CAG  aromatic  1.389  0.020  1.389
 5JF  CAH  CL2  single    1.723  0.020  1.723
 5JF  CAH  CAI  aromatic  1.391  0.020  1.391
 5JF  CAG  CAI  aromatic  1.397  0.020  1.397
 5JF  CAG  OAA  single    1.353  0.020  1.353
 5JF  CAI  CL1  single    1.717  0.020  1.717
 5JF  CAF  H1   single    0.930  0.020  1.080
 5JF  CAD  H2   single    0.930  0.020  1.080
 5JF  CAE  H3   single    0.930  0.020  1.080
 5JF  OAA  H4   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
 5JF  CAG  CAI  CAH  119.85  3.000
 5JF  CAG  CAI  CL1  119.13  3.000
 5JF  CAH  CAI  CL1  121.01  3.000
 5JF  CAF  CAH  CL2  119.30  3.000
 5JF  CL2  CAH  CAI  120.11  3.000
 5JF  CAF  CAH  CAI  120.59  3.000
 5JF  H1   CAF  CAD  121.05  3.000
 5JF  H1   CAF  CAH  119.61  3.000
 5JF  CAD  CAF  CAH  119.34  3.000
 5JF  H2   CAD  CAE  119.95  3.000
 5JF  H2   CAD  CAF  119.51  3.000
 5JF  CAE  CAD  CAF  120.53  3.000
 5JF  H3   CAE  CAG  119.19  3.000
 5JF  H3   CAE  CAD  120.45  3.000
 5JF  CAG  CAE  CAD  120.37  3.000
 5JF  OAA  CAG  CAE  121.78  3.000
 5JF  OAA  CAG  CAI  118.87  3.000
 5JF  CAE  CAG  CAI  119.31  3.000
 5JF  H4   OAA  CAG  110.51  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
 5JF  CONST_01  CAD  CAF  CAH  CAI    0.00  0.0  0
 5JF  CONST_02  CAD  CAE  CAG  CAI    0.00  0.0  0
 5JF  CONST_03  CAE  CAD  CAF  CAH    0.00  0.0  0
 5JF  CONST_04  CAE  CAG  CAI  CAH    0.00  0.0  0
 5JF  CONST_05  CAG  CAE  CAD  CAF    0.00  0.0  0
 5JF  CONST_06  CAG  CAI  CAH  CAF    0.00  0.0  0
 5JF  CONST_07  CAF  CAH  CAI  CL1  180.00  0.0  0
 5JF  CONST_08  CAE  CAG  CAI  CL1  180.00  0.0  0
 5JF  CONST_09  OAA  CAG  CAI  CAH  180.00  0.0  0
 5JF  CONST_10  CAD  CAF  CAH  CL2  180.00  0.0  0
 5JF  CONST_11  CAG  CAI  CAH  CL2  180.00  0.0  0
 5JF  CONST_12  OAA  CAG  CAE  CAD  180.00  0.0  0
 5JF  CONST_13  H1   CAF  CAH  CAI  180.00  0.0  0
 5JF  CONST_14  H3   CAE  CAG  CAI  180.00  0.0  0
 5JF  CONST_15  H2   CAD  CAF  CAH  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
 5JF  plan-1  CL1  0.020
 5JF  plan-1  CAI  0.020
 5JF  plan-1  CAH  0.020
 5JF  plan-1  CL2  0.020
 5JF  plan-1  CAF  0.020
 5JF  plan-1  CAD  0.020
 5JF  plan-1  CAE  0.020
 5JF  plan-1  CAG  0.020
 5JF  plan-1  OAA  0.020
 5JF  plan-1  H1   0.020
 5JF  plan-1  H2   0.020
 5JF  plan-1  H3   0.020

