# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 01:22:55 2020
#   Inital geometry file: a 39 line input string
#   Ligand name: 3,4-dichlorophenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(Cl)c(Cl)c1
#
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
 5JD  5JD  '3,4-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 GRAND
;

data_comp_5JD
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
 5JD  CAF  C   CR16  0  -0.302   1.1449   1.0385   0.0455
 5JD  CAI  C   CR6   0   0.019  -0.1699   0.6148  -0.0401
 5JD  CL1  CL  CL    0  -0.097  -1.4196   1.7973  -0.1352
 5JD  CAH  C   CR6   0  -0.030  -0.4824  -0.7404  -0.0493
 5JD  CL2  CL  CL    0  -0.108  -2.1185  -1.2754  -0.1545
 5JD  CAE  C   CR16  0  -0.202   0.5446  -1.6681   0.0283
 5JD  CAD  C   CR16  0  -0.381   1.8633  -1.2581   0.1136
 5JD  CAG  C   CR6   0   0.367   2.1709   0.1004   0.1231
 5JD  OAA  O   OH1   0  -0.623   3.4277   0.5642   0.2036
 5JD  H1   H   HCR6  0   0.295   1.3755   2.0959   0.0522
 5JD  H2   H   HCR6  0   0.292   0.3138  -2.7247   0.0217
 5JD  H3   H   HCR6  0   0.289   2.6489  -2.0016   0.1718
 5JD  H4   H   HOH1  0   0.481   4.0569  -0.1649   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
 5JD  OAA  CAG  single    1.342  0.020  1.342
 5JD  CAG  CAF  aromatic  1.392  0.020  1.392
 5JD  CAG  CAD  aromatic  1.393  0.020  1.393
 5JD  CAF  CAI  aromatic  1.384  0.020  1.384
 5JD  CAD  CAE  aromatic  1.384  0.020  1.384
 5JD  CAI  CL1  single    1.723  0.020  1.723
 5JD  CAI  CAH  aromatic  1.391  0.020  1.391
 5JD  CAE  CAH  aromatic  1.386  0.020  1.386
 5JD  CAH  CL2  single    1.725  0.020  1.725
 5JD  CAF  H1   single    0.930  0.020  1.080
 5JD  CAE  H2   single    0.930  0.020  1.080
 5JD  CAD  H3   single    0.930  0.020  1.080
 5JD  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
 5JD  H1   CAF  CAG  120.06  3.000
 5JD  H1   CAF  CAI  120.12  3.000
 5JD  CAG  CAF  CAI  119.81  3.000
 5JD  CAH  CAI  CL1  120.36  3.000
 5JD  CAH  CAI  CAF  120.80  3.000
 5JD  CL1  CAI  CAF  118.84  3.000
 5JD  CAE  CAH  CL2  119.91  3.000
 5JD  CL2  CAH  CAI  121.05  3.000
 5JD  CAE  CAH  CAI  119.04  3.000
 5JD  H2   CAE  CAD  119.56  3.000
 5JD  H2   CAE  CAH  119.69  3.000
 5JD  CAD  CAE  CAH  120.75  3.000
 5JD  H3   CAD  CAG  120.59  3.000
 5JD  H3   CAD  CAE  119.41  3.000
 5JD  CAG  CAD  CAE  119.99  3.000
 5JD  OAA  CAG  CAD  122.97  3.000
 5JD  CAD  CAG  CAF  119.61  3.000
 5JD  OAA  CAG  CAF  117.42  3.000
 5JD  H4   OAA  CAG  110.64  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
 5JD  CONST_01  CAE  CAD  CAG  CAF    0.00  0.0  0
 5JD  CONST_02  CAE  CAH  CAI  CAF    0.00  0.0  0
 5JD  CONST_03  CAD  CAG  CAF  CAI    0.00  0.0  0
 5JD  CONST_04  CAD  CAE  CAH  CAI    0.00  0.0  0
 5JD  CONST_05  CAG  CAF  CAI  CAH    0.00  0.0  0
 5JD  CONST_06  CAG  CAD  CAE  CAH    0.00  0.0  0
 5JD  CONST_07  CL2  CAH  CAI  CAF  180.00  0.0  0
 5JD  CONST_08  OAA  CAG  CAF  CAI  180.00  0.0  0
 5JD  CONST_09  CAG  CAF  CAI  CL1  180.00  0.0  0
 5JD  CONST_10  CAE  CAH  CAI  CL1  180.00  0.0  0
 5JD  CONST_11  CAD  CAE  CAH  CL2  180.00  0.0  0
 5JD  CONST_12  OAA  CAG  CAD  CAE  180.00  0.0  0
 5JD  CONST_13  H3   CAD  CAG  CAF  180.00  0.0  0
 5JD  CONST_14  H2   CAE  CAH  CAI  180.00  0.0  0
 5JD  CONST_15  H1   CAF  CAI  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
 5JD  plan-1  CAF  0.020
 5JD  plan-1  CAI  0.020
 5JD  plan-1  CL1  0.020
 5JD  plan-1  CAH  0.020
 5JD  plan-1  CL2  0.020
 5JD  plan-1  CAE  0.020
 5JD  plan-1  CAD  0.020
 5JD  plan-1  CAG  0.020
 5JD  plan-1  OAA  0.020
 5JD  plan-1  H1   0.020
 5JD  plan-1  H2   0.020
 5JD  plan-1  H3   0.020

