# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 02:47:49 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: [(4-chlorophenyl)sulfanyl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CSc1ccc(Cl)cc1
#
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
 JNG  JNG  '[(4-chlorophenyl)sulfanyl]acetic acid'  ligand  18  12  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_JNG
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
 JNG  O01   O   O      0  -0.591   4.2392  -0.8580  -0.0214
 JNG  C02   C   C      0   0.448   3.8935   0.3345   0.0316
 JNG  O03   O   OC    -1  -0.604   4.6162   1.3426   0.0950
 JNG  C04   C   CH2    0  -0.722   2.3764   0.6173   0.0175
 JNG  S05   S   S2     0   0.041   1.4895  -0.9537  -0.0611
 JNG  C06   C   CR6    0  -0.088  -0.2026  -0.4708  -0.0236
 JNG  C07   C   CR16   0  -0.279  -1.1507  -1.4985   0.0121
 JNG  C08   C   CR16   0  -0.198  -2.5052  -1.2192   0.0400
 JNG  C09   C   CR6    0  -0.061  -2.9294   0.1021   0.0341
 JNG  CL10  CL  CL     0  -0.138  -4.6272   0.4568   0.0743
 JNG  C11   C   CR16   0  -0.191  -2.0110   1.1361  -0.0009
 JNG  C12   C   CR16   0  -0.273  -0.6526   0.8483  -0.0307
 JNG  H042  H   HCH2   0   0.278   2.0907   1.1671   0.9172
 JNG  H041  H   HCH2   0   0.277   2.1263   1.2436  -0.8418
 JNG  H071  H   HCR6   0   0.269  -0.8305  -2.5336   0.0207
 JNG  H081  H   HCR6   0   0.280  -3.2227  -2.0279   0.0690
 JNG  H111  H   HCR6   0   0.279  -2.3403   2.1667  -0.0051
 JNG  H121  H   HCR6   0   0.273   0.0442   1.6734  -0.0603

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
 JNG  C04  S05   single    1.806  0.020  1.806
 JNG  C04  C02   single    1.543  0.020  1.543
 JNG  S05  C06   single    1.760  0.020  1.760
 JNG  C12  C06   aromatic  1.394  0.020  1.394
 JNG  C12  C11   aromatic  1.389  0.020  1.389
 JNG  C06  C07   aromatic  1.399  0.020  1.399
 JNG  C02  O01   deloc     1.243  0.020  1.243
 JNG  C02  O03   deloc     1.242  0.020  1.242
 JNG  C11  C09   aromatic  1.383  0.020  1.383
 JNG  C07  C08   aromatic  1.383  0.020  1.383
 JNG  C09  C08   aromatic  1.388  0.020  1.388
 JNG  C09  CL10  single    1.735  0.020  1.735
 JNG  C04  H042  single    0.970  0.020  1.090
 JNG  C04  H041  single    0.970  0.020  1.090
 JNG  C07  H071  single    0.930  0.020  1.080
 JNG  C08  H081  single    0.930  0.020  1.080
 JNG  C11  H111  single    0.930  0.020  1.080
 JNG  C12  H121  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
 JNG  C04   C02  O03   115.07  3.000
 JNG  O03   C02  O01   128.25  3.000
 JNG  C04   C02  O01   116.67  3.000
 JNG  H041  C04  H042  107.42  3.000
 JNG  H041  C04  S05   110.62  3.000
 JNG  H042  C04  S05   110.20  3.000
 JNG  H041  C04  C02   109.71  3.000
 JNG  H042  C04  C02   109.98  3.000
 JNG  S05   C04  C02   108.89  3.000
 JNG  C06   S05  C04   103.45  3.000
 JNG  C12   C06  C07   118.47  3.000
 JNG  C07   C06  S05   116.78  3.000
 JNG  C12   C06  S05   124.75  3.000
 JNG  H071  C07  C08   118.83  3.000
 JNG  H071  C07  C06   120.12  3.000
 JNG  C08   C07  C06   121.06  3.000
 JNG  H081  C08  C09   120.62  3.000
 JNG  H081  C08  C07   119.95  3.000
 JNG  C09   C08  C07   119.44  3.000
 JNG  C11   C09  CL10  119.83  3.000
 JNG  CL10  C09  C08   119.58  3.000
 JNG  C11   C09  C08   120.59  3.000
 JNG  H111  C11  C12   119.67  3.000
 JNG  H111  C11  C09   120.66  3.000
 JNG  C12   C11  C09   119.67  3.000
 JNG  H121  C12  C11   118.24  3.000
 JNG  H121  C12  C06   120.98  3.000
 JNG  C11   C12  C06   120.78  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
 JNG  CONST_01  C09   C11  C12  C06     0.00   0.0  0
 JNG  CONST_02  C09   C08  C07  C06     0.00   0.0  0
 JNG  CONST_03  C11   C12  C06  C07     0.00   0.0  0
 JNG  CONST_04  C11   C09  C08  C07     0.00   0.0  0
 JNG  CONST_05  C12   C06  C07  C08     0.00   0.0  0
 JNG  CONST_06  C12   C11  C09  C08     0.00   0.0  0
 JNG  CONST_07  C11   C12  C06  S05   180.00   0.0  0
 JNG  CONST_08  C08   C07  C06  S05   180.00   0.0  0
 JNG  CONST_09  CL10  C09  C08  C07   180.00   0.0  0
 JNG  CONST_10  C12   C11  C09  CL10  180.00   0.0  0
 JNG  CONST_11  H111  C11  C12  C06   180.00   0.0  0
 JNG  CONST_12  H081  C08  C07  C06   180.00   0.0  0
 JNG  CONST_13  H121  C12  C06  C07   180.00   0.0  0
 JNG  CONST_14  H071  C07  C08  C09   180.00   0.0  0
 JNG  Var_01    C12   C06  S05  C04     4.06  30.0  2
 JNG  Var_02    H042  C04  S05  C06    57.73  30.0  1
 JNG  Var_03    S05   C04  C02  O01     0.55  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
 JNG  plan-1  S05   0.020
 JNG  plan-1  C06   0.020
 JNG  plan-1  C07   0.020
 JNG  plan-1  C08   0.020
 JNG  plan-1  C09   0.020
 JNG  plan-1  CL10  0.020
 JNG  plan-1  C11   0.020
 JNG  plan-1  C12   0.020
 JNG  plan-1  H071  0.020
 JNG  plan-1  H081  0.020
 JNG  plan-1  H111  0.020
 JNG  plan-1  H121  0.020
 JNG  plan-2  O01   0.020
 JNG  plan-2  C02   0.020
 JNG  plan-2  O03   0.020
 JNG  plan-2  C04   0.020

