# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 15:57:53 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: 2-{[2-(4-chlorophenyl)-2-oxoethyl]sulfanyl}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccccc1SCC(=O)c2ccc(Cl)cc2
#
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
 8YJ  8YJ  '2-{[2-(4-chlorophenyl)-2-oxoethyl]sulfanyl}benzoic acid'  ligand  30  20  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8YJ
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
 8YJ  CAA  C   CR6    0  -0.114   3.4705  -0.5129   0.7324
 8YJ  CAB  C   CR16   0  -0.279   4.5740  -1.3588   0.6644
 8YJ  CAC  C   CR16   0  -0.260   4.6295  -2.4272  -0.2148
 8YJ  CAD  C   CR16   0  -0.245   3.5498  -2.6592  -1.0522
 8YJ  CAE  C   CR16   0  -0.255   2.4389  -1.8307  -1.0084
 8YJ  CAF  C   CR6    0  -0.126   2.3810  -0.7504  -0.1244
 8YJ  CAH  C   CH2    0  -0.764  -0.0600  -0.3710  -1.4130
 8YJ  CAI  C   C      0   0.402  -1.2599   0.5383  -1.5537
 8YJ  CAJ  C   CR6    0  -0.012  -2.3415   0.4561  -0.5376
 8YJ  CAK  C   CR16   0  -0.263  -3.4393   1.3113  -0.6495
 8YJ  CAL  C   CR16   0  -0.199  -4.4703   1.2682   0.2703
 8YJ  CAM  C   CR6    0  -0.039  -4.4007   0.3586   1.3170
 8YJ  CAN  C   CR16   0  -0.192  -3.3230  -0.5023   1.4527
 8YJ  CAO  C   CR16   0  -0.283  -2.2973  -0.4478   0.5232
 8YJ  CAP  C   C      0   0.424   3.4845   0.6286   1.7305
 8YJ  OAQ  O   OC    -1  -0.581   4.5105   0.7874   2.4134
 8YJ  OAR  O   O      0  -0.580   2.4436   1.3170   1.7771
 8YJ  OAS  O   O      0  -0.375  -1.3282   1.3249  -2.4732
 8YJ  SAG  S   S2     0   0.091   0.9679   0.3210  -0.0634
 8YJ  CLA  CL  CL     0  -0.108  -5.6828   0.2994   2.4731
 8YJ  H1   H   HCR6   0   0.249   5.4056  -1.1606   1.3274
 8YJ  H2   H   HCR6   0   0.251   5.5004  -3.0685  -0.2463
 8YJ  H3   H   HCR6   0   0.258   3.5615  -3.4878  -1.7485
 8YJ  H4   H   HCR6   0   0.268   1.6235  -2.0510  -1.6806
 8YJ  H5   H   HCH2   0   0.292  -0.3721  -1.3936  -1.1916
 8YJ  H6   H   HCH2   0   0.309   0.4834  -0.3629  -2.3576
 8YJ  H7   H   HCR6   0   0.277  -3.4924   2.0210  -1.4637
 8YJ  H8   H   HCR6   0   0.288  -5.3174   1.9334   0.1748
 8YJ  H9   H   HCR6   0   0.290  -3.2798  -1.2063   2.2719
 8YJ  H10  H   HCR6   0   0.275  -1.4619  -1.1225   0.6481

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
 8YJ  CLA  CAM  single    1.727  0.020  1.727
 8YJ  CAM  CAL  aromatic  1.389  0.020  1.389
 8YJ  CAM  CAN  aromatic  1.386  0.020  1.386
 8YJ  CAL  CAK  aromatic  1.382  0.020  1.382
 8YJ  CAN  CAO  aromatic  1.385  0.020  1.385
 8YJ  CAK  CAJ  aromatic  1.396  0.020  1.396
 8YJ  CAO  CAJ  aromatic  1.394  0.020  1.394
 8YJ  CAJ  CAI  single    1.486  0.020  1.486
 8YJ  CAI  OAS  double    1.212  0.020  1.212
 8YJ  CAI  CAH  single    1.512  0.020  1.512
 8YJ  SAG  CAF  single    1.774  0.020  1.774
 8YJ  SAG  CAH  single    1.832  0.020  1.832
 8YJ  CAE  CAD  aromatic  1.387  0.020  1.387
 8YJ  CAE  CAF  aromatic  1.397  0.020  1.397
 8YJ  CAD  CAC  aromatic  1.386  0.020  1.386
 8YJ  CAF  CAA  aromatic  1.406  0.020  1.406
 8YJ  CAC  CAB  aromatic  1.385  0.020  1.385
 8YJ  CAA  CAB  aromatic  1.392  0.020  1.392
 8YJ  CAA  CAP  single    1.516  0.020  1.516
 8YJ  OAR  CAP  deloc     1.249  0.020  1.249
 8YJ  CAP  OAQ  deloc     1.243  0.020  1.243
 8YJ  CAB  H1   single    0.930  0.020  1.080
 8YJ  CAC  H2   single    0.930  0.020  1.080
 8YJ  CAD  H3   single    0.930  0.020  1.080
 8YJ  CAE  H4   single    0.930  0.020  1.080
 8YJ  CAH  H5   single    0.970  0.020  1.090
 8YJ  CAH  H6   single    0.970  0.020  1.090
 8YJ  CAK  H7   single    0.930  0.020  1.080
 8YJ  CAL  H8   single    0.930  0.020  1.080
 8YJ  CAN  H9   single    0.930  0.020  1.080
 8YJ  CAO  H10  single    0.930  0.020  1.080

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
 8YJ  CAP  CAA  CAF  122.37  3.000
 8YJ  CAP  CAA  CAB  118.83  3.000
 8YJ  CAF  CAA  CAB  118.80  3.000
 8YJ  H1   CAB  CAC  119.98  3.000
 8YJ  H1   CAB  CAA  117.91  3.000
 8YJ  CAC  CAB  CAA  122.11  3.000
 8YJ  H2   CAC  CAD  120.68  3.000
 8YJ  H2   CAC  CAB  120.53  3.000
 8YJ  CAD  CAC  CAB  118.79  3.000
 8YJ  H3   CAD  CAE  119.11  3.000
 8YJ  H3   CAD  CAC  120.56  3.000
 8YJ  CAE  CAD  CAC  120.34  3.000
 8YJ  H4   CAE  CAF  121.37  3.000
 8YJ  H4   CAE  CAD  117.62  3.000
 8YJ  CAF  CAE  CAD  121.01  3.000
 8YJ  SAG  CAF  CAE  121.45  3.000
 8YJ  CAE  CAF  CAA  118.95  3.000
 8YJ  SAG  CAF  CAA  119.60  3.000
 8YJ  H6   CAH  H5   108.98  3.000
 8YJ  H6   CAH  SAG  110.85  3.000
 8YJ  H5   CAH  SAG  111.40  3.000
 8YJ  H6   CAH  CAI  108.09  3.000
 8YJ  H5   CAH  CAI  110.81  3.000
 8YJ  SAG  CAH  CAI  106.65  3.000
 8YJ  OAS  CAI  CAJ  120.90  3.000
 8YJ  OAS  CAI  CAH  120.38  3.000
 8YJ  CAJ  CAI  CAH  118.72  3.000
 8YJ  CAO  CAJ  CAK  118.88  3.000
 8YJ  CAO  CAJ  CAI  122.20  3.000
 8YJ  CAK  CAJ  CAI  118.92  3.000
 8YJ  H7   CAK  CAL  119.01  3.000
 8YJ  H7   CAK  CAJ  120.06  3.000
 8YJ  CAL  CAK  CAJ  120.93  3.000
 8YJ  H8   CAL  CAM  120.58  3.000
 8YJ  H8   CAL  CAK  120.42  3.000
 8YJ  CAM  CAL  CAK  118.99  3.000
 8YJ  CLA  CAM  CAN  119.37  3.000
 8YJ  CAN  CAM  CAL  121.31  3.000
 8YJ  CLA  CAM  CAL  119.33  3.000
 8YJ  H9   CAN  CAO  120.30  3.000
 8YJ  H9   CAN  CAM  120.65  3.000
 8YJ  CAO  CAN  CAM  119.06  3.000
 8YJ  H10  CAO  CAN  118.05  3.000
 8YJ  H10  CAO  CAJ  121.12  3.000
 8YJ  CAN  CAO  CAJ  120.83  3.000
 8YJ  OAR  CAP  OAQ  126.67  3.000
 8YJ  OAQ  CAP  CAA  117.75  3.000
 8YJ  OAR  CAP  CAA  115.58  3.000
 8YJ  CAH  SAG  CAF  101.15  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
 8YJ  CONST_01  CAD  CAE  CAF  CAA     0.00   0.0  0
 8YJ  CONST_02  CAD  CAC  CAB  CAA     0.00   0.0  0
 8YJ  CONST_03  CAE  CAD  CAC  CAB     0.00   0.0  0
 8YJ  CONST_04  CAE  CAF  CAA  CAB     0.00   0.0  0
 8YJ  CONST_05  CAF  CAE  CAD  CAC     0.00   0.0  0
 8YJ  CONST_06  CAF  CAA  CAB  CAC     0.00   0.0  0
 8YJ  CONST_07  CAM  CAL  CAK  CAJ     0.00   0.0  0
 8YJ  CONST_08  CAM  CAN  CAO  CAJ     0.00   0.0  0
 8YJ  CONST_09  CAN  CAM  CAL  CAK     0.00   0.0  0
 8YJ  CONST_10  CAN  CAO  CAJ  CAK     0.00   0.0  0
 8YJ  CONST_11  CAO  CAN  CAM  CAL     0.00   0.0  0
 8YJ  CONST_12  CAO  CAJ  CAK  CAL     0.00   0.0  0
 8YJ  CONST_13  SAG  CAF  CAA  CAB   180.00   0.0  0
 8YJ  CONST_14  CAP  CAA  CAB  CAC   180.00   0.0  0
 8YJ  CONST_15  SAG  CAF  CAE  CAD   180.00   0.0  0
 8YJ  CONST_16  CAP  CAA  CAF  CAE   180.00   0.0  0
 8YJ  CONST_17  CAL  CAK  CAJ  CAI   180.00   0.0  0
 8YJ  CONST_18  CAN  CAO  CAJ  CAI   180.00   0.0  0
 8YJ  CONST_19  CLA  CAM  CAL  CAK   180.00   0.0  0
 8YJ  CONST_20  CLA  CAM  CAN  CAO   180.00   0.0  0
 8YJ  CONST_21  H4   CAE  CAF  CAA   180.00   0.0  0
 8YJ  CONST_22  H2   CAC  CAB  CAA   180.00   0.0  0
 8YJ  CONST_23  H3   CAD  CAC  CAB   180.00   0.0  0
 8YJ  CONST_24  H1   CAB  CAC  CAD   180.00   0.0  0
 8YJ  CONST_25  H8   CAL  CAK  CAJ   180.00   0.0  0
 8YJ  CONST_26  H9   CAN  CAO  CAJ   180.00   0.0  0
 8YJ  CONST_27  H10  CAO  CAJ  CAK   180.00   0.0  0
 8YJ  CONST_28  H7   CAK  CAL  CAM   180.00   0.0  0
 8YJ  Var_01    OAR  CAP  CAA  CAB  -177.29  30.0  2
 8YJ  Var_02    CAK  CAJ  CAI  CAH   178.81  30.0  2
 8YJ  Var_03    CAI  CAH  SAG  CAF  -175.04  30.0  3
 8YJ  Var_04    SAG  CAH  CAI  CAJ   -75.37  30.0  3

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
 8YJ  plan-1  CAA  0.020
 8YJ  plan-1  CAB  0.020
 8YJ  plan-1  CAC  0.020
 8YJ  plan-1  CAD  0.020
 8YJ  plan-1  CAE  0.020
 8YJ  plan-1  CAF  0.020
 8YJ  plan-1  CAP  0.020
 8YJ  plan-1  SAG  0.020
 8YJ  plan-1  H1   0.020
 8YJ  plan-1  H2   0.020
 8YJ  plan-1  H3   0.020
 8YJ  plan-1  H4   0.020
 8YJ  plan-2  CAI  0.020
 8YJ  plan-2  CAJ  0.020
 8YJ  plan-2  CAK  0.020
 8YJ  plan-2  CAL  0.020
 8YJ  plan-2  CAM  0.020
 8YJ  plan-2  CAN  0.020
 8YJ  plan-2  CAO  0.020
 8YJ  plan-2  CLA  0.020
 8YJ  plan-2  H7   0.020
 8YJ  plan-2  H8   0.020
 8YJ  plan-2  H9   0.020
 8YJ  plan-2  H10  0.020
 8YJ  plan-3  CAH  0.020
 8YJ  plan-3  CAI  0.020
 8YJ  plan-3  CAJ  0.020
 8YJ  plan-3  OAS  0.020
 8YJ  plan-4  CAA  0.020
 8YJ  plan-4  CAP  0.020
 8YJ  plan-4  OAQ  0.020
 8YJ  plan-4  OAR  0.020

