# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 08:41:36 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: 3-[(4-chlorophenyl)sulfanyl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCSc1ccc(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
 4YZ  4YZ  '3-[(4-chlorophenyl)sulfanyl]propanoic acid'  ligand  22  13  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_4YZ
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
 4YZ  C10   C   CR6   0  -0.058  -3.2998   0.1804  -0.0015
 4YZ  C13   C   CR16  0  -0.273  -1.7336  -1.6287  -0.0170
 4YZ  O01   O   O     0  -0.439   4.2104   1.7933   0.0784
 4YZ  C02   C   C     0   0.561   4.4774   0.6191   0.0403
 4YZ  O03   O   OH1   0  -0.592   5.7176   0.1480   0.0485
 4YZ  C04   C   CH2   0  -0.575   3.4665  -0.4939  -0.0238
 4YZ  C05   C   CH2   0  -0.581   2.0399   0.0291  -0.0266
 4YZ  S06   S   S2    0   0.056   0.9452  -1.4108  -0.1285
 4YZ  C07   C   CR6   0  -0.089  -0.6715  -0.7232  -0.0714
 4YZ  C08   C   CR16  0  -0.265  -0.9486   0.6408  -0.0888
 4YZ  C09   C   CR16  0  -0.191  -2.2610   1.0927  -0.0521
 4YZ  CL11  CL  CL    0  -0.132  -4.9385   0.7437   0.0415
 4YZ  C12   C   CR16  0  -0.198  -3.0427  -1.1832   0.0161
 4YZ  H1    H   HCR6  0   0.275  -1.5433  -2.6948   0.0024
 4YZ  H2    H   HOH1  0   0.483   6.3515   0.8796   0.0909
 4YZ  H3    H   HCH2  0   0.297   3.6649  -1.0869  -0.9212
 4YZ  H4    H   HCH2  0   0.297   3.6336  -1.1634   0.8245
 4YZ  H5    H   HCH2  0   0.288   1.8295   0.5845   0.8875
 4YZ  H6    H   HCH2  0   0.287   1.8731   0.6858  -0.8804
 4YZ  H7    H   HCR6  0   0.278  -0.1577   1.3752  -0.1326
 4YZ  H8    H   HCR6  0   0.283  -2.4598   2.1559  -0.0656
 4YZ  H9    H   HCR6  0   0.284  -3.8535  -1.8975   0.0577

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
 4YZ  CL11  C10  single    1.733  0.020  1.733
 4YZ  C09   C10  aromatic  1.384  0.020  1.384
 4YZ  C09   C08  aromatic  1.388  0.020  1.388
 4YZ  C10   C12  aromatic  1.388  0.020  1.388
 4YZ  C08   C07  aromatic  1.392  0.020  1.392
 4YZ  C12   C13  aromatic  1.383  0.020  1.383
 4YZ  O01   C02  double    1.205  0.020  1.205
 4YZ  C07   C13  aromatic  1.397  0.020  1.397
 4YZ  C07   S06  single    1.758  0.020  1.758
 4YZ  C02   O03  single    1.327  0.020  1.327
 4YZ  C02   C04  single    1.505  0.020  1.505
 4YZ  C05   C04  single    1.520  0.020  1.520
 4YZ  C05   S06  single    1.812  0.020  1.812
 4YZ  C13   H1   single    0.930  0.020  1.080
 4YZ  O03   H2   single    0.850  0.020  0.980
 4YZ  C04   H3   single    0.970  0.020  1.090
 4YZ  C04   H4   single    0.970  0.020  1.090
 4YZ  C05   H5   single    0.970  0.020  1.090
 4YZ  C05   H6   single    0.970  0.020  1.090
 4YZ  C08   H7   single    0.930  0.020  1.080
 4YZ  C09   H8   single    0.930  0.020  1.080
 4YZ  C12   H9   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
 4YZ  C12   C10  CL11  119.62  3.000
 4YZ  C12   C10  C09   120.62  3.000
 4YZ  CL11  C10  C09   119.76  3.000
 4YZ  H1    C13  C12   118.87  3.000
 4YZ  H1    C13  C07   120.34  3.000
 4YZ  C12   C13  C07   120.78  3.000
 4YZ  C04   C02  O03   111.44  3.000
 4YZ  C04   C02  O01   124.98  3.000
 4YZ  O03   C02  O01   123.57  3.000
 4YZ  H2    O03  C02   110.10  3.000
 4YZ  H4    C04  H3    106.07  3.000
 4YZ  H4    C04  C05   110.84  3.000
 4YZ  H3    C04  C05   110.82  3.000
 4YZ  H4    C04  C02   108.49  3.000
 4YZ  H3    C04  C02   108.30  3.000
 4YZ  C05   C04  C02   112.09  3.000
 4YZ  H6    C05  H5    108.69  3.000
 4YZ  H6    C05  S06   110.02  3.000
 4YZ  H5    C05  S06   109.60  3.000
 4YZ  H6    C05  C04   110.64  3.000
 4YZ  H5    C05  C04   110.79  3.000
 4YZ  S06   C05  C04   107.09  3.000
 4YZ  C07   S06  C05   104.06  3.000
 4YZ  C08   C07  S06   124.47  3.000
 4YZ  S06   C07  C13   116.55  3.000
 4YZ  C08   C07  C13   118.97  3.000
 4YZ  H7    C08  C09   118.15  3.000
 4YZ  H7    C08  C07   121.40  3.000
 4YZ  C09   C08  C07   120.45  3.000
 4YZ  H8    C09  C08   119.56  3.000
 4YZ  H8    C09  C10   120.71  3.000
 4YZ  C08   C09  C10   119.73  3.000
 4YZ  H9    C12  C13   119.86  3.000
 4YZ  H9    C12  C10   120.71  3.000
 4YZ  C13   C12  C10   119.44  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
 4YZ  CONST_01  C07   C08  C09  C10    0.00   0.0  0
 4YZ  CONST_02  C07   C13  C12  C10    0.00   0.0  0
 4YZ  CONST_03  C09   C10  C12  C13    0.00   0.0  0
 4YZ  CONST_04  C09   C08  C07  C13    0.00   0.0  0
 4YZ  CONST_05  C12   C10  C09  C08    0.00   0.0  0
 4YZ  CONST_06  C12   C13  C07  C08    0.00   0.0  0
 4YZ  CONST_07  CL11  C10  C12  C13  180.00   0.0  0
 4YZ  CONST_08  C09   C08  C07  S06  180.00   0.0  0
 4YZ  CONST_09  C12   C13  C07  S06  180.00   0.0  0
 4YZ  CONST_10  CL11  C10  C09  C08  180.00   0.0  0
 4YZ  CONST_11  H7    C08  C09  C10  180.00   0.0  0
 4YZ  CONST_12  H1    C13  C12  C10  180.00   0.0  0
 4YZ  CONST_13  H8    C09  C08  C07  180.00   0.0  0
 4YZ  CONST_14  H9    C12  C13  C07  180.00   0.0  0
 4YZ  CONST_15  H2    O03  C02  O01    0.00   0.0  0
 4YZ  Var_01    C08   C07  S06  C05    5.94  30.0  2
 4YZ  Var_02    H5    C05  S06  C07   57.90  30.0  1
 4YZ  Var_03    C05   C04  C02  O01   -0.37  30.0  3
 4YZ  Var_04    S06   C05  C04  C02  179.25  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
 4YZ  plan-1  C10   0.020
 4YZ  plan-1  C13   0.020
 4YZ  plan-1  S06   0.020
 4YZ  plan-1  C07   0.020
 4YZ  plan-1  C08   0.020
 4YZ  plan-1  C09   0.020
 4YZ  plan-1  CL11  0.020
 4YZ  plan-1  C12   0.020
 4YZ  plan-1  H1    0.020
 4YZ  plan-1  H7    0.020
 4YZ  plan-1  H8    0.020
 4YZ  plan-1  H9    0.020
 4YZ  plan-2  O01   0.020
 4YZ  plan-2  C02   0.020
 4YZ  plan-2  O03   0.020
 4YZ  plan-2  C04   0.020
 4YZ  plan-2  H2    0.020

