# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 18:11:47 2022
#   Inital geometry file: a 101 line input string
#   Ligand name: 4-[(2~{R})-2-oxidanyl-3-phenylselanyl-propyl]sulfanylbenzenesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[S](=O)(=O)c1ccc(SC[C@@H](O)C[Se]c2ccccc2)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
 VGT  VGT  "4-((2-hydroxy-3-(phenylselanyl)propyl)thio)benzenesulfonamide"
  ligand  39  22  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VGT
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
 VGT  C7   C   CR16  0  -0.262  -1.7022  11.2229  13.3195
 VGT  C8   C   CH2   0  -0.621  -2.2863   5.5674  13.2288
 VGT  C9   C   CR6   0  -0.085  -4.5026   4.1700  14.2185
 VGT  O1   O   OS    0  -0.662  -4.9375   0.7846  18.1394
 VGT  C1   C   CH2   0  -0.615  -2.3191   8.0773  12.6534
 VGT  C5   C   CR16  0  -0.263  -0.0482  12.8416  13.9942
 VGT  C6   C   CR16  0  -0.236  -1.1158  12.4741  13.1854
 VGT  C4   C   CR16  0  -0.237   0.4385  11.9444  14.9346
 VGT  C3   C   CR16  0  -0.271  -0.1259  10.6815  15.0578
 VGT  C2   C   CR6   0  -0.135  -1.1996  10.3158  14.2496
 VGT  O2   O   OS    0  -0.647  -7.2791   1.0604  17.2963
 VGT  N    N   NC2   0  -0.888  -5.5721  -0.4841  16.1050
 VGT  C12  C   CR6   0  -0.225  -5.3457   2.1468  15.9230
 VGT  C11  C   CR16  0  -0.220  -6.2882   2.9264  15.2653
 VGT  C10  C   CR16  0  -0.256  -5.8658   3.9318  14.4166
 VGT  C13  C   CR16  0  -0.200  -3.9892   2.3756  15.7425
 VGT  C14  C   CR16  0  -0.247  -3.5677   3.3833  14.8933
 VGT  S    S   S2    0   0.069  -4.0899   5.4473  13.0939
 VGT  C    C   CH1   0   0.050  -1.7722   6.6904  12.3294
 VGT  O    O   OH1   0  -0.650  -2.1138   6.4640  10.9826
 VGT  SE   SE  SE    0   0.100  -1.9848   8.5985  14.5169
 VGT  H1   H   HCR6  0   0.269  -2.5511  10.9670  12.6977
 VGT  H2   H   HCH2  0   0.301  -1.8287   4.6265  12.9145
 VGT  H3   H   HCH2  0   0.290  -2.0001   5.7378  14.2685
 VGT  H4   H   HCH2  0   0.295  -1.8213   8.8069  12.0128
 VGT  H5   H   HCH2  0   0.278  -3.3904   8.1338  12.4532
 VGT  H6   H   HCR6  0   0.259   0.4004  13.8210  13.8924
 VGT  H7   H   HCR6  0   0.260  -1.5068  13.1678  12.4522
 VGT  H8   H   HCR6  0   0.260   1.2722  12.2189  15.5680
 VGT  H9   H   HCR6  0   0.265   0.2828   9.9844  15.7792
 VGT  H10  H   HNC2  0   0.416  -5.5236  -1.3189  16.6826
 VGT  H11  H   HNC2  0   0.413  -6.2560  -0.6085  15.3650
 VGT  H12  H   HCR6  0   0.284  -7.3471   2.7611  15.4084
 VGT  H13  H   HCR6  0   0.278  -6.6043   4.5385  13.9074
 VGT  H14  H   HCR6  0   0.287  -3.2499   1.7754  16.2565
 VGT  H15  H   HCR6  0   0.279  -2.5063   3.5401  14.7693
 VGT  H16  H   HCH1  0   0.248  -0.6824   6.7097  12.4674
 VGT  H17  H   HOH1  0   0.457  -1.7211   5.6319  10.6969
 VGT  S1   S   S     0   1.359  -5.8629   0.8642  17.0192

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
 VGT  O    C    single    1.408  0.020  1.408
 VGT  C    C1   single    1.526  0.020  1.526
 VGT  C    C8   single    1.528  0.020  1.528
 VGT  C1   SE   single    1.964  0.020  1.964
 VGT  C8   S    single    1.813  0.020  1.813
 VGT  S    C9   single    1.751  0.020  1.751
 VGT  C6   C7   aromatic  1.388  0.020  1.388
 VGT  C6   C5   aromatic  1.389  0.020  1.389
 VGT  C7   C2   aromatic  1.393  0.020  1.393
 VGT  C5   C4   aromatic  1.388  0.020  1.388
 VGT  C2   SE   single    1.907  0.020  1.907
 VGT  C2   C3   aromatic  1.393  0.020  1.393
 VGT  C9   C10  aromatic  1.398  0.020  1.398
 VGT  C9   C14  aromatic  1.396  0.020  1.396
 VGT  C10  C11  aromatic  1.382  0.020  1.382
 VGT  C14  C13  aromatic  1.384  0.020  1.384
 VGT  C4   C3   aromatic  1.389  0.020  1.389
 VGT  C13  C12  aromatic  1.387  0.020  1.387
 VGT  C11  C12  aromatic  1.389  0.020  1.389
 VGT  C12  S1   single    1.765  0.020  1.765
 VGT  N    S1   single    1.655  0.020  1.655
 VGT  O2   S1   double    1.456  0.020  1.456
 VGT  S1   O1   double    1.455  0.020  1.455
 VGT  C7   H1   single    0.930  0.020  1.080
 VGT  C8   H2   single    0.970  0.020  1.090
 VGT  C8   H3   single    0.970  0.020  1.090
 VGT  C1   H4   single    0.970  0.020  1.090
 VGT  C1   H5   single    0.970  0.020  1.090
 VGT  C5   H6   single    0.930  0.020  1.080
 VGT  C6   H7   single    0.930  0.020  1.080
 VGT  C4   H8   single    0.930  0.020  1.080
 VGT  C3   H9   single    0.930  0.020  1.080
 VGT  N    H10  single    0.890  0.020  1.040
 VGT  N    H11  single    0.890  0.020  1.040
 VGT  C11  H12  single    0.930  0.020  1.080
 VGT  C10  H13  single    0.930  0.020  1.080
 VGT  C13  H14  single    0.930  0.020  1.080
 VGT  C14  H15  single    0.930  0.020  1.080
 VGT  C    H16  single    0.970  0.020  1.090
 VGT  O    H17  single    0.850  0.020  0.980

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
 VGT  H1   C7   C2   120.82  3.000
 VGT  H1   C7   C6   119.25  3.000
 VGT  C2   C7   C6   119.93  3.000
 VGT  H3   C8   H2   107.38  3.000
 VGT  H3   C8   C    110.96  3.000
 VGT  H2   C8   C    108.83  3.000
 VGT  H3   C8   S    110.00  3.000
 VGT  H2   C8   S    109.77  3.000
 VGT  C    C8   S    109.85  3.000
 VGT  S    C9   C14  124.31  3.000
 VGT  C14  C9   C10  119.25  3.000
 VGT  S    C9   C10  116.43  3.000
 VGT  H5   C1   H4   107.79  3.000
 VGT  H5   C1   SE   109.11  3.000
 VGT  H4   C1   SE   107.58  3.000
 VGT  H5   C1   C    111.10  3.000
 VGT  H4   C1   C    108.65  3.000
 VGT  SE   C1   C    112.45  3.000
 VGT  H6   C5   C4   120.23  3.000
 VGT  H6   C5   C6   120.22  3.000
 VGT  C4   C5   C6   119.55  3.000
 VGT  H7   C6   C5   120.17  3.000
 VGT  H7   C6   C7   119.37  3.000
 VGT  C5   C6   C7   120.45  3.000
 VGT  H8   C4   C3   119.45  3.000
 VGT  H8   C4   C5   120.18  3.000
 VGT  C3   C4   C5   120.36  3.000
 VGT  H9   C3   C2   120.56  3.000
 VGT  H9   C3   C4   119.40  3.000
 VGT  C2   C3   C4   120.04  3.000
 VGT  SE   C2   C3   118.20  3.000
 VGT  C3   C2   C7   119.64  3.000
 VGT  SE   C2   C7   122.10  3.000
 VGT  H11  N    H10  110.23  3.000
 VGT  H11  N    S1   112.59  3.000
 VGT  H10  N    S1   111.33  3.000
 VGT  C13  C12  C11  120.62  3.000
 VGT  C11  C12  S1   120.22  3.000
 VGT  C13  C12  S1   119.16  3.000
 VGT  H12  C11  C10  119.47  3.000
 VGT  H12  C11  C12  121.07  3.000
 VGT  C10  C11  C12  119.46  3.000
 VGT  H13  C10  C11  119.20  3.000
 VGT  H13  C10  C9   120.19  3.000
 VGT  C11  C10  C9   120.61  3.000
 VGT  H14  C13  C14  119.16  3.000
 VGT  H14  C13  C12  120.98  3.000
 VGT  C14  C13  C12  119.86  3.000
 VGT  H15  C14  C13  118.40  3.000
 VGT  H15  C14  C9   121.39  3.000
 VGT  C13  C14  C9   120.21  3.000
 VGT  C9   S    C8   103.59  3.000
 VGT  H16  C    O    111.33  3.000
 VGT  H16  C    C1   108.23  3.000
 VGT  O    C    C1   105.22  3.000
 VGT  H16  C    C8   105.82  3.000
 VGT  C1   C    C8   115.00  3.000
 VGT  O    C    C8   111.31  3.000
 VGT  H17  O    C    108.89  3.000
 VGT  C2   SE   C1   100.14  3.000
 VGT  C12  S1   N    101.39  3.000
 VGT  N    S1   O2   112.69  3.000
 VGT  C12  S1   O2   107.78  3.000
 VGT  O2   S1   O1   118.64  3.000
 VGT  N    S1   O1   105.60  3.000
 VGT  C12  S1   O1   109.36  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
 VGT  CONST_01  C4   C5   C6   C7      0.00   0.0  0
 VGT  CONST_02  C4   C3   C2   C7      0.00   0.0  0
 VGT  CONST_03  C12  C11  C10  C9      0.00   0.0  0
 VGT  CONST_04  C12  C13  C14  C9      0.00   0.0  0
 VGT  CONST_05  C2   C7   C6   C5      0.00   0.0  0
 VGT  CONST_06  C2   C3   C4   C5      0.00   0.0  0
 VGT  CONST_07  C3   C2   C7   C6      0.00   0.0  0
 VGT  CONST_08  C3   C4   C5   C6      0.00   0.0  0
 VGT  CONST_09  C14  C9   C10  C11     0.00   0.0  0
 VGT  CONST_10  C14  C13  C12  C11     0.00   0.0  0
 VGT  CONST_11  C13  C14  C9   C10     0.00   0.0  0
 VGT  CONST_12  C13  C12  C11  C10     0.00   0.0  0
 VGT  CONST_13  SE   C2   C7   C6    180.00   0.0  0
 VGT  CONST_14  SE   C2   C3   C4    180.00   0.0  0
 VGT  CONST_15  C14  C13  C12  S1    180.00   0.0  0
 VGT  CONST_16  C10  C11  C12  S1    180.00   0.0  0
 VGT  CONST_17  S    C9   C10  C11   180.00   0.0  0
 VGT  CONST_18  S    C9   C14  C13   180.00   0.0  0
 VGT  CONST_19  H6   C5   C6   C7    180.00   0.0  0
 VGT  CONST_20  H9   C3   C2   C7    180.00   0.0  0
 VGT  CONST_21  H12  C11  C10  C9    180.00   0.0  0
 VGT  CONST_22  H14  C13  C14  C9    180.00   0.0  0
 VGT  CONST_23  H1   C7   C6   C5    180.00   0.0  0
 VGT  CONST_24  H9   C3   C4   C5    180.00   0.0  0
 VGT  CONST_25  H8   C4   C5   C6    180.00   0.0  0
 VGT  CONST_26  H7   C6   C5   C4    180.00   0.0  0
 VGT  CONST_27  H1   C7   C2   C3    180.00   0.0  0
 VGT  CONST_28  H6   C5   C4   C3    180.00   0.0  0
 VGT  CONST_29  H7   C6   C7   C2    180.00   0.0  0
 VGT  CONST_30  H8   C4   C3   C2    180.00   0.0  0
 VGT  CONST_31  H15  C14  C13  C12   180.00   0.0  0
 VGT  CONST_32  H13  C10  C11  C12   180.00   0.0  0
 VGT  CONST_33  H14  C13  C12  C11   180.00   0.0  0
 VGT  CONST_34  H15  C14  C9   C10   180.00   0.0  0
 VGT  CONST_35  H12  C11  C12  C13   180.00   0.0  0
 VGT  CONST_36  H13  C10  C9   C14   180.00   0.0  0
 VGT  Var_01    C1   SE   C2   C7     42.41  30.0  2
 VGT  Var_02    C10  C9   S    C8    174.52  30.0  2
 VGT  Var_03    C14  C9   S    C8     -6.55  30.0  2
 VGT  Var_04    C13  C12  S1   O1     35.09  30.0  2
 VGT  Var_05    C11  C12  S1   O1   -144.05  30.0  2
 VGT  Var_06    C3   C2   SE   C1   -140.39  30.0  1
 VGT  Var_07    C13  C12  S1   O2    165.35  30.0  2
 VGT  Var_08    C11  C12  S1   O2    -13.80  30.0  2
 VGT  Var_09    C13  C12  S1   N     -76.11  30.0  2
 VGT  Var_10    C11  C12  S1   N     104.75  30.0  2
 VGT  Var_11    C    C8   S    C9   -178.00  30.0  1
 VGT  Var_12    C    C1   SE   C2    129.12  30.0  1
 VGT  Var_13    H2   C8   S    C9     62.37  30.0  1
 VGT  Var_14    H3   C8   S    C9    -55.58  30.0  1
 VGT  Var_15    H4   C1   SE   C2      9.53  30.0  1
 VGT  Var_16    H5   C1   SE   C2   -107.14  30.0  1
 VGT  Var_17    H10  N    S1   C12   161.15  30.0  3
 VGT  Var_18    H11  N    S1   C12   -74.48  30.0  3
 VGT  Var_19    H10  N    S1   O1     47.11  30.0  3
 VGT  Var_20    H11  N    S1   O1    171.47  30.0  3
 VGT  Var_21    H10  N    S1   O2    -83.90  30.0  3
 VGT  Var_22    H11  N    S1   O2     40.47  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 VGT  chir_01  C  O  C1  C8  negativ

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
 VGT  plan-1  C9   0.020
 VGT  plan-1  C12  0.020
 VGT  plan-1  C11  0.020
 VGT  plan-1  C10  0.020
 VGT  plan-1  C13  0.020
 VGT  plan-1  C14  0.020
 VGT  plan-1  S    0.020
 VGT  plan-1  H12  0.020
 VGT  plan-1  H13  0.020
 VGT  plan-1  H14  0.020
 VGT  plan-1  H15  0.020
 VGT  plan-1  S1   0.020
 VGT  plan-2  C7   0.020
 VGT  plan-2  C5   0.020
 VGT  plan-2  C6   0.020
 VGT  plan-2  C4   0.020
 VGT  plan-2  C3   0.020
 VGT  plan-2  C2   0.020
 VGT  plan-2  SE   0.020
 VGT  plan-2  H1   0.020
 VGT  plan-2  H6   0.020
 VGT  plan-2  H7   0.020
 VGT  plan-2  H8   0.020
 VGT  plan-2  H9   0.020

