# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 05:35:38 2022
#   Inital geometry file: a 63 line input string
#   Ligand name: 1-chloranyl-3-methylsulfinyl-6,7-dihydro-5~{H}-2-benzothiophen-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S@](=O)c1sc(Cl)c2CCCC(=O)c12
#
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
 HFX  HFX  "1-chloranyl-3-methylsulfinyl-6,7-dihydro-5H-2-benzothiophen-4-one"
  ligand  23  14  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HFX
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
 HFX  C4   C   CR5   0  -0.376   9.7677  -42.9627  -48.8012
 HFX  C5   C   CH2   0  -0.498  10.8383  -45.0312  -49.8582
 HFX  C6   C   CH2   0  -0.470  12.2433  -45.6168  -49.7587
 HFX  C7   C   CH2   0  -0.570  13.2724  -44.6986  -50.4105
 HFX  C8   C   C     0   0.375  13.2934  -43.3166  -49.8115
 HFX  C1   C   CR5   0  -0.478  11.8043  -41.5944  -48.7157
 HFX  C2   C   CR5   0   0.095  12.0037  -42.8312  -49.2810
 HFX  C3   C   CR5   0   0.297  10.8280  -43.6357  -49.3243
 HFX  C9   C   CH3   0  -0.833  12.1644  -39.1954  -47.4785
 HFX  O1   O   O     0  -0.386  14.2837  -42.6175  -49.7858
 HFX  O2   O   O     0  -0.748  13.3064  -39.6568  -49.8046
 HFX  S1   S   S2    0   0.364  10.1709  -41.3861  -48.2551
 HFX  S2   S   S3    0   0.790  13.0907  -40.3630  -48.4982
 HFX  CL1  CL  CL    0  -0.052   8.1748  -43.5451  -48.6380
 HFX  H1   H   HCH2  0   0.267  10.5118  -45.0243  -50.9030
 HFX  H2   H   HCH2  0   0.267  10.1245  -45.6501  -49.3127
 HFX  H3   H   HCH2  0   0.262  12.2700  -46.5935  -50.2415
 HFX  H4   H   HCH2  0   0.247  12.5018  -45.7757  -48.7087
 HFX  H5   H   HCH2  0   0.281  14.2772  -45.1199  -50.3675
 HFX  H6   H   HCH2  0   0.280  13.0277  -44.5758  -51.4733
 HFX  H7   H   HCH3  0   0.310  12.8451  -38.3648  -47.2984
 HFX  H8   H   HCH3  0   0.289  11.2893  -38.8248  -48.0117
 HFX  H9   H   HCH3  0   0.287  11.8916  -39.6431  -46.5249

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
 HFX  C7  C6   single    1.525  0.020  1.525
 HFX  C7  C8   single    1.506  0.020  1.506
 HFX  C6  C5   single    1.525  0.020  1.525
 HFX  C5  C3   single    1.494  0.020  1.494
 HFX  C8  O1   double    1.212  0.020  1.212
 HFX  C8  C2   single    1.477  0.020  1.477
 HFX  C3  C2   aromatic  1.425  0.020  1.425
 HFX  C3  C4   aromatic  1.360  0.020  1.360
 HFX  C2  C1   aromatic  1.374  0.020  1.374
 HFX  O2  S2   double    1.501  0.020  1.501
 HFX  C4  CL1  single    1.704  0.020  1.704
 HFX  C4  S1   aromatic  1.717  0.020  1.717
 HFX  C1  S1   aromatic  1.710  0.020  1.710
 HFX  C1  S2   single    1.794  0.020  1.794
 HFX  S2  C9   single    1.806  0.020  1.806
 HFX  C5  H1   single    0.970  0.020  1.090
 HFX  C5  H2   single    0.970  0.020  1.090
 HFX  C6  H3   single    0.970  0.020  1.090
 HFX  C6  H4   single    0.970  0.020  1.090
 HFX  C7  H5   single    0.970  0.020  1.090
 HFX  C7  H6   single    0.970  0.020  1.090
 HFX  C9  H7   single    0.970  0.020  1.090
 HFX  C9  H8   single    0.970  0.020  1.090
 HFX  C9  H9   single    0.970  0.020  1.090

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
 HFX  CL1  C4  S1  120.20  3.000
 HFX  S1   C4  C3  113.18  3.000
 HFX  CL1  C4  C3  126.61  3.000
 HFX  H2   C5  H1  106.60  3.000
 HFX  H2   C5  C3  110.28  3.000
 HFX  H1   C5  C3  109.46  3.000
 HFX  H2   C5  C6  110.62  3.000
 HFX  H1   C5  C6  109.84  3.000
 HFX  C3   C5  C6  109.97  3.000
 HFX  H4   C6  H3  106.84  3.000
 HFX  H4   C6  C7  109.78  3.000
 HFX  H3   C6  C7  109.48  3.000
 HFX  H4   C6  C5  109.65  3.000
 HFX  H3   C6  C5  109.74  3.000
 HFX  C7   C6  C5  111.25  3.000
 HFX  H6   C7  H5  106.67  3.000
 HFX  H6   C7  C8  106.59  3.000
 HFX  H5   C7  C8  109.02  3.000
 HFX  H6   C7  C6  109.32  3.000
 HFX  H5   C7  C6  111.85  3.000
 HFX  C8   C7  C6  113.06  3.000
 HFX  O1   C8  C2  121.08  3.000
 HFX  C2   C8  C7  115.61  3.000
 HFX  O1   C8  C7  123.28  3.000
 HFX  S2   C1  S1  124.66  3.000
 HFX  S2   C1  C2  124.30  3.000
 HFX  S1   C1  C2  111.04  3.000
 HFX  C3   C2  C1  113.62  3.000
 HFX  C1   C2  C8  124.77  3.000
 HFX  C3   C2  C8  121.60  3.000
 HFX  C2   C3  C5  122.16  3.000
 HFX  C2   C3  C4  110.61  3.000
 HFX  C5   C3  C4  127.21  3.000
 HFX  H9   C9  H8  111.56  3.000
 HFX  H9   C9  H7  109.00  3.000
 HFX  H8   C9  H7  108.88  3.000
 HFX  H9   C9  S2  110.94  3.000
 HFX  H8   C9  S2  110.82  3.000
 HFX  H7   C9  S2  105.42  3.000
 HFX  C1   S1  C4   91.54  3.000
 HFX  O2   S2  C9  105.13  3.000
 HFX  C9   S2  C1   98.31  3.000
 HFX  O2   S2  C1  108.70  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
 HFX  CONST_01  C1   C2  C3  C4     0.00   0.0  0
 HFX  CONST_02  C2   C1  S1  C4     0.00   0.0  0
 HFX  CONST_03  C3   C4  S1  C1     0.00   0.0  0
 HFX  CONST_04  S1   C4  C3  C2     0.00   0.0  0
 HFX  CONST_05  S1   C1  C2  C3     0.00   0.0  0
 HFX  CONST_06  S2   C1  S1  C4   180.00   0.0  0
 HFX  CONST_07  CL1  C4  C3  C5     0.00   0.0  0
 HFX  CONST_08  S2   C1  C2  C8     0.00   0.0  0
 HFX  CONST_09  CL1  C4  S1  C1   180.00   0.0  0
 HFX  CONST_10  CL1  C4  C3  C2   180.00   0.0  0
 HFX  CONST_11  S2   C1  C2  C3   180.00   0.0  0
 HFX  Var_01    C6   C5  C3  C4  -154.59  30.0  1
 HFX  Var_02    C8   C7  C6  C5    57.93  30.0  1
 HFX  Var_03    C2   C8  C7  C6   -30.60  30.0  1
 HFX  Var_04    C2   C3  C5  C6    23.99  30.0  1
 HFX  Var_05    C3   C5  C6  C7   -52.88  30.0  1
 HFX  Var_06    C3   C2  C8  C7     0.77  30.0  1
 HFX  Var_07    C1   C2  C8  C7  -178.88  30.0  1
 HFX  Var_08    O1   C8  C7  C6   151.20  30.0  1
 HFX  Var_09    O1   C8  C2  C1    -0.64  30.0  1
 HFX  Var_10    O1   C8  C2  C3   179.02  30.0  1
 HFX  Var_11    H1   C5  C3  C4    84.65  30.0  1
 HFX  Var_12    H2   C5  C3  C4   -32.33  30.0  1
 HFX  Var_13    H5   C7  C6  C5  -178.54  30.0  1
 HFX  Var_14    H6   C7  C6  C5   -60.63  30.0  1
 HFX  Var_15    H1   C5  C6  C7    67.65  30.0  1
 HFX  Var_16    H2   C5  C6  C7  -174.95  30.0  1
 HFX  Var_17    H3   C6  C7  C8   179.39  30.0  1
 HFX  Var_18    H4   C6  C7  C8   -63.63  30.0  1
 HFX  Var_19    H5   C7  C8  C2  -155.67  30.0  1
 HFX  Var_20    H6   C7  C8  C2    89.54  30.0  1
 HFX  Var_21    H1   C5  C3  C2   -96.77  30.0  1
 HFX  Var_22    H2   C5  C3  C2   146.25  30.0  1
 HFX  Var_23    H3   C6  C5  C3  -174.19  30.0  1
 HFX  Var_24    H4   C6  C5  C3    68.75  30.0  1
 HFX  Var_25    O2   S2  C1  C2    79.99  30.0  2
 HFX  Var_26    C9   S2  C1  C2  -170.87  30.0  2
 HFX  Var_27    S1   C1  S2  C9     9.37  30.0  2
 HFX  Var_28    S1   C1  S2  O2   -99.77  30.0  2
 HFX  Var_29    H5   C7  C8  O1    26.12  30.0  1
 HFX  Var_30    H6   C7  C8  O1   -88.67  30.0  1
 HFX  Var_31    H7   C9  S2  C1  -178.31  30.0  3
 HFX  Var_32    H8   C9  S2  C1   -60.66  30.0  3
 HFX  Var_33    H9   C9  S2  C1    63.84  30.0  3
 HFX  Var_34    H7   C9  S2  O2   -66.28  30.0  3
 HFX  Var_35    H8   C9  S2  O2    51.36  30.0  3
 HFX  Var_36    H9   C9  S2  O2   175.87  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
 HFX  plan-1  C7   0.020
 HFX  plan-1  C8   0.020
 HFX  plan-1  C2   0.020
 HFX  plan-1  O1   0.020
 HFX  plan-2  C4   0.020
 HFX  plan-2  C5   0.020
 HFX  plan-2  C8   0.020
 HFX  plan-2  C1   0.020
 HFX  plan-2  C2   0.020
 HFX  plan-2  C3   0.020
 HFX  plan-2  S1   0.020
 HFX  plan-2  S2   0.020
 HFX  plan-2  CL1  0.020
 HFX  plan-3  C1   0.020
 HFX  plan-3  C9   0.020
 HFX  plan-3  O2   0.020
 HFX  plan-3  S2   0.020

