# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 11:35:34 2021
#   Inital geometry file: a 71 line input string
#   Ligand name: 2-[(3-fluorophenyl)methyl]-1lambda~6~,2-thiazolidine-1,1-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cccc(CN2CCC[S]2(=O)=O)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
 WHM  WHM  2-[(3-fluorophenyl)methyl]-1lambda~6~,2-thiazolidine-1,1-dione  ligand  27  15  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WHM
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
 WHM  C4   C  CR6   0   0.125  -11.5770   2.3831  -23.0164
 WHM  C5   C  CH2   0  -0.355  -10.5490   3.1877  -23.7717
 WHM  C6   C  CH2   0  -0.222  -11.4738   2.9804  -26.1099
 WHM  C7   C  CH2   0  -0.513  -10.8318   2.8329  -27.4962
 WHM  C8   C  CH2   0  -0.614   -9.6572   1.8794  -27.3360
 WHM  N    N  N     0  -0.617  -10.4215   2.7299  -25.1342
 WHM  C    C  CR6   0   0.541  -13.4428   2.2702  -21.5297
 WHM  C1   C  CR16  0  -0.421  -13.4536   0.8913  -21.5746
 WHM  C2   C  CR16  0  -0.227  -12.5000   0.2566  -22.3622
 WHM  C3   C  CR16  0  -0.286  -11.5681   0.9920  -23.0779
 WHM  C9   C  CR16  0  -0.467  -12.5276   3.0287  -22.2366
 WHM  F    F  F     0  -0.317  -14.3587   2.9047  -20.7791
 WHM  S    S  S     0   1.383   -8.9451   2.4177  -25.7887
 WHM  H3   H  HCH2  0   0.270  -10.8079   4.2508  -23.7463
 WHM  H4   H  HCH2  0   0.283   -9.5828   3.0926  -23.2689
 WHM  H5   H  HCH2  0   0.253  -12.2752   2.2521  -25.9688
 WHM  H6   H  HCH2  0   0.257  -11.8920   3.9803  -25.9764
 WHM  H7   H  HCH2  0   0.291  -11.5466   2.4485  -28.2205
 WHM  H8   H  HCH2  0   0.272  -10.4778   3.7986  -27.8561
 WHM  H9   H  HCH2  0   0.309   -9.9718   0.8425  -27.2166
 WHM  H10  H  HCH2  0   0.322   -8.9064   1.9507  -28.1204
 WHM  H    H  HCR6  0   0.280  -14.1872   0.3259  -21.0154
 WHM  H1   H  HCR6  0   0.268  -12.4892  -0.8241  -22.4136
 WHM  H2   H  HCR6  0   0.253  -10.8309   0.4853  -23.6883
 WHM  H11  H  HCR6  0   0.276  -12.5604   4.1102  -22.1819
 WHM  O    O  OS    0  -0.676   -8.1556   3.6290  -26.0012
 WHM  O1   O  OS    0  -0.668   -8.2926   1.3574  -25.0285

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
 WHM  F   C    single    1.343  0.020  1.343
 WHM  C   C1   aromatic  1.380  0.020  1.380
 WHM  C1  C2   aromatic  1.390  0.020  1.390
 WHM  C2  C3   aromatic  1.386  0.020  1.386
 WHM  C3  C4   aromatic  1.393  0.020  1.393
 WHM  C4  C5   single    1.508  0.020  1.508
 WHM  C5  N    single    1.443  0.020  1.443
 WHM  N   C6   single    1.457  0.020  1.457
 WHM  C6  C7   single    1.535  0.020  1.535
 WHM  C7  C8   single    1.521  0.020  1.521
 WHM  C8  S    single    1.786  0.020  1.786
 WHM  N   S    single    1.645  0.020  1.645
 WHM  O   S    double    1.461  0.020  1.461
 WHM  S   O1   double    1.459  0.020  1.459
 WHM  C9  C4   aromatic  1.389  0.020  1.389
 WHM  C   C9   aromatic  1.383  0.020  1.383
 WHM  C5  H3   single    0.970  0.020  1.090
 WHM  C5  H4   single    0.970  0.020  1.090
 WHM  C6  H5   single    0.970  0.020  1.090
 WHM  C6  H6   single    0.970  0.020  1.090
 WHM  C7  H7   single    0.970  0.020  1.090
 WHM  C7  H8   single    0.970  0.020  1.090
 WHM  C8  H9   single    0.970  0.020  1.090
 WHM  C8  H10  single    0.970  0.020  1.090
 WHM  C1  H    single    0.930  0.020  1.080
 WHM  C2  H1   single    0.930  0.020  1.080
 WHM  C3  H2   single    0.930  0.020  1.080
 WHM  C9  H11  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
 WHM  C9   C4  C3  119.58  3.000
 WHM  C9   C4  C5  119.99  3.000
 WHM  C3   C4  C5  120.43  3.000
 WHM  H4   C5  H3  106.44  3.000
 WHM  H4   C5  N   109.18  3.000
 WHM  H3   C5  N   110.54  3.000
 WHM  H4   C5  C4  109.01  3.000
 WHM  H3   C5  C4  110.20  3.000
 WHM  N    C5  C4  111.33  3.000
 WHM  H6   C6  H5  108.29  3.000
 WHM  H6   C6  N   110.62  3.000
 WHM  H5   C6  N   109.20  3.000
 WHM  H6   C6  C7  111.01  3.000
 WHM  H5   C6  C7  111.07  3.000
 WHM  N    C6  C7  106.64  3.000
 WHM  H8   C7  H7  107.85  3.000
 WHM  H8   C7  C8  109.84  3.000
 WHM  H7   C7  C8  110.86  3.000
 WHM  H8   C7  C6  110.43  3.000
 WHM  H7   C7  C6  111.13  3.000
 WHM  C8   C7  C6  106.74  3.000
 WHM  H10  C8  H9  109.89  3.000
 WHM  H10  C8  S   109.24  3.000
 WHM  H9   C8  S   107.87  3.000
 WHM  H10  C8  C7  114.57  3.000
 WHM  H9   C8  C7  112.64  3.000
 WHM  S    C8  C7  102.13  3.000
 WHM  S    N   C6  114.49  3.000
 WHM  S    N   C5  121.01  3.000
 WHM  C6   N   C5  120.94  3.000
 WHM  F    C   C9  118.54  3.000
 WHM  C9   C   C1  122.46  3.000
 WHM  F    C   C1  119.01  3.000
 WHM  H    C1  C2  121.29  3.000
 WHM  H    C1  C   120.71  3.000
 WHM  C2   C1  C   118.00  3.000
 WHM  H1   C2  C3  119.91  3.000
 WHM  H1   C2  C1  119.33  3.000
 WHM  C3   C2  C1  120.76  3.000
 WHM  H2   C3  C2  120.03  3.000
 WHM  H2   C3  C4  119.78  3.000
 WHM  C2   C3  C4  120.19  3.000
 WHM  H11  C9  C   120.11  3.000
 WHM  H11  C9  C4  120.87  3.000
 WHM  C    C9  C4  119.02  3.000
 WHM  O1   S   O   115.89  3.000
 WHM  O1   S   N   109.40  3.000
 WHM  O    S   N   112.67  3.000
 WHM  O1   S   C8  114.25  3.000
 WHM  O    S   C8  109.83  3.000
 WHM  N    S   C8   92.52  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
 WHM  CONST_01  C1   C2  C3  C4    0.00   0.0  0
 WHM  CONST_02  C1   C   C9  C4    0.00   0.0  0
 WHM  CONST_03  C3   C2  C1  C     0.00   0.0  0
 WHM  CONST_04  C3   C4  C9  C     0.00   0.0  0
 WHM  CONST_05  C9   C   C1  C2    0.00   0.0  0
 WHM  CONST_06  C9   C4  C3  C2    0.00   0.0  0
 WHM  CONST_07  F    C   C9  C4  180.00   0.0  0
 WHM  CONST_08  C2   C3  C4  C5  180.00   0.0  0
 WHM  CONST_09  C    C9  C4  C5  180.00   0.0  0
 WHM  CONST_10  F    C   C1  C2  180.00   0.0  0
 WHM  CONST_11  H1   C2  C3  C4  180.00   0.0  0
 WHM  CONST_12  H11  C9  C   C1  180.00   0.0  0
 WHM  CONST_13  H2   C3  C2  C1  180.00   0.0  0
 WHM  CONST_14  H    C1  C2  C3  180.00   0.0  0
 WHM  Var_01    C8   S   N   C6  -23.37  30.0  1
 WHM  Var_02    S    C8  C7  C6  -41.14  30.0  1
 WHM  Var_03    S    N   C6  C7    1.26  30.0  1
 WHM  Var_04    N    S   C8  C7   37.07  30.0  1
 WHM  Var_05    N    C6  C7  C8   26.87  30.0  1
 WHM  Var_06    C6   N   C5  C4   71.59  30.0  3
 WHM  Var_07    C3   C4  C5  N    47.42  30.0  2

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
 WHM  plan-1  C4   0.020
 WHM  plan-1  C5   0.020
 WHM  plan-1  C    0.020
 WHM  plan-1  C1   0.020
 WHM  plan-1  C2   0.020
 WHM  plan-1  C3   0.020
 WHM  plan-1  C9   0.020
 WHM  plan-1  F    0.020
 WHM  plan-1  H    0.020
 WHM  plan-1  H1   0.020
 WHM  plan-1  H2   0.020
 WHM  plan-1  H11  0.020
 WHM  plan-2  C5   0.020
 WHM  plan-2  C6   0.020
 WHM  plan-2  N    0.020
 WHM  plan-2  S    0.020

