# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 01:00:07 2020
#   Inital geometry file: a 39 line input string
#   Ligand name: 2,4-dichlorophenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(Cl)cc1Cl
#
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
 5JC  5JC  '2,4-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 PERFECT
;

data_comp_5JC
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
 5JC  CL1  CL  CL    0  -0.102  -2.3130  -1.2652   0.1880
 5JC  CAI  C   CR6   0  -0.165  -0.9370  -0.2172   0.0933
 5JC  CAF  C   CR16  0  -0.172   0.3315  -0.7653  -0.0035
 5JC  CAH  C   CR6   0  -0.067   1.4223   0.0825  -0.0756
 5JC  CL2  CL  CL    0  -0.125   3.0141  -0.5893  -0.1947
 5JC  CAE  C   CR16  0  -0.195   1.2527   1.4589  -0.0515
 5JC  CAD  C   CR16  0  -0.345  -0.0209   1.9891   0.0451
 5JC  CAG  C   CR6   0   0.426  -1.1403   1.1630   0.1191
 5JC  OAA  O   OH1   0  -0.608  -2.3462   1.7354   0.2114
 5JC  H1   H   HCR6  0   0.304   0.4574  -1.8389  -0.0207
 5JC  H2   H   HCR6  0   0.288   2.1059   2.1204  -0.1069
 5JC  H3   H   HCR6  0   0.288  -0.1584   3.0626   0.0637
 5JC  H4   H   HOH1  0   0.472  -3.0499   1.0748   0.2478

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
 5JC  CL1  CAI  single    1.732  0.020  1.732
 5JC  OAA  CAG  single    1.338  0.020  1.338
 5JC  CAI  CAG  aromatic  1.395  0.020  1.395
 5JC  CAI  CAF  aromatic  1.385  0.020  1.385
 5JC  CAG  CAD  aromatic  1.393  0.020  1.393
 5JC  CAF  CAH  aromatic  1.383  0.020  1.383
 5JC  CAD  CAE  aromatic  1.383  0.020  1.383
 5JC  CAH  CAE  aromatic  1.387  0.020  1.387
 5JC  CAH  CL2  single    1.732  0.020  1.732
 5JC  CAF  H1   single    0.930  0.020  1.080
 5JC  CAE  H2   single    0.930  0.020  1.080
 5JC  CAD  H3   single    0.930  0.020  1.080
 5JC  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
 5JC  CAG  CAI  CAF  121.75  3.000
 5JC  CAF  CAI  CL1  119.46  3.000
 5JC  CAG  CAI  CL1  118.80  3.000
 5JC  H1   CAF  CAH  121.06  3.000
 5JC  H1   CAF  CAI  120.05  3.000
 5JC  CAH  CAF  CAI  118.89  3.000
 5JC  CAE  CAH  CL2  119.90  3.000
 5JC  CL2  CAH  CAF  119.38  3.000
 5JC  CAE  CAH  CAF  120.72  3.000
 5JC  H2   CAE  CAD  119.73  3.000
 5JC  H2   CAE  CAH  120.66  3.000
 5JC  CAD  CAE  CAH  119.62  3.000
 5JC  H3   CAD  CAG  119.02  3.000
 5JC  H3   CAD  CAE  119.89  3.000
 5JC  CAG  CAD  CAE  121.09  3.000
 5JC  OAA  CAG  CAD  118.31  3.000
 5JC  CAD  CAG  CAI  117.93  3.000
 5JC  OAA  CAG  CAI  123.76  3.000
 5JC  H4   OAA  CAG  111.51  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
 5JC  CONST_01  CAE  CAD  CAG  CAI    0.00  0.0  0
 5JC  CONST_02  CAE  CAH  CAF  CAI    0.00  0.0  0
 5JC  CONST_03  CAD  CAG  CAI  CAF    0.00  0.0  0
 5JC  CONST_04  CAD  CAE  CAH  CAF    0.00  0.0  0
 5JC  CONST_05  CAG  CAI  CAF  CAH    0.00  0.0  0
 5JC  CONST_06  CAG  CAD  CAE  CAH    0.00  0.0  0
 5JC  CONST_07  CAD  CAG  CAI  CL1  180.00  0.0  0
 5JC  CONST_08  CAH  CAF  CAI  CL1  180.00  0.0  0
 5JC  CONST_09  CL2  CAH  CAF  CAI  180.00  0.0  0
 5JC  CONST_10  OAA  CAG  CAI  CAF  180.00  0.0  0
 5JC  CONST_11  CAD  CAE  CAH  CL2  180.00  0.0  0
 5JC  CONST_12  OAA  CAG  CAD  CAE  180.00  0.0  0
 5JC  CONST_13  H3   CAD  CAG  CAI  180.00  0.0  0
 5JC  CONST_14  H2   CAE  CAH  CAF  180.00  0.0  0
 5JC  CONST_15  H1   CAF  CAH  CAE  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
 5JC  plan-1  CL1  0.020
 5JC  plan-1  CAI  0.020
 5JC  plan-1  CAF  0.020
 5JC  plan-1  CAH  0.020
 5JC  plan-1  CL2  0.020
 5JC  plan-1  CAE  0.020
 5JC  plan-1  CAD  0.020
 5JC  plan-1  CAG  0.020
 5JC  plan-1  OAA  0.020
 5JC  plan-1  H1   0.020
 5JC  plan-1  H2   0.020
 5JC  plan-1  H3   0.020

