# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 04:56:50 2021
#   Inital geometry file: a 65 line input string
#   Ligand name: 1,3-bis[(methylsulfanyl)methyl]benzene
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCc1cccc(CSC)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
 V7S  V7S  1,3-bis[(methylsulfanyl)methyl]benzene  ligand  26  12  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_V7S
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
 V7S  C1   C  CH3   0  -0.770  14.8470  -13.0609  -35.2343
 V7S  S2   S  S2    0  -0.028  15.5654  -11.5100  -34.6490
 V7S  C3   C  CH2   0  -0.619  16.1704  -10.8342  -36.2281
 V7S  C4   C  CR6   0   0.123  16.8325   -9.5173  -35.9581
 V7S  C5   C  CR16  0  -0.321  18.1850   -9.4603  -35.6460
 V7S  C6   C  CR6   0   0.161  18.8136   -8.2476  -35.3735
 V7S  C7   C  CH2   0  -0.657  20.2745   -8.2044  -35.0398
 V7S  S8   S  S2    0  -0.026  20.6520   -8.8518  -33.3820
 V7S  C9   C  CH3   0  -0.769  19.7399   -7.6769  -32.3599
 V7S  C10  C  CR16  0  -0.311  18.0596   -7.0793  -35.4016
 V7S  C11  C  CR16  0  -0.229  16.7035   -7.1244  -35.7019
 V7S  C12  C  CR16  0  -0.302  16.0912   -8.3368  -35.9763
 V7S  H1   H  HCH3  0   0.275  14.4541  -13.5918  -34.3690
 V7S  H2   H  HCH3  0   0.262  14.0312  -12.8777  -35.9321
 V7S  H3   H  HCH3  0   0.262  15.6005  -13.6847  -35.7136
 V7S  H4   H  HCH2  0   0.280  15.3283  -10.7162  -36.9123
 V7S  H5   H  HCH2  0   0.280  16.8710  -11.5436  -36.6718
 V7S  H6   H  HCR6  0   0.247  18.7644  -10.3772  -35.6189
 V7S  H7   H  HCH2  0   0.295  20.8515   -8.8301  -35.7227
 V7S  H8   H  HCH2  0   0.285  20.6613   -7.1875  -35.1205
 V7S  H9   H  HCH3  0   0.277  19.9501   -7.9199  -31.3199
 V7S  H10  H  HCH3  0   0.261  20.0634   -6.6544  -32.5511
 V7S  H11  H  HCH3  0   0.263  18.6662   -7.7527  -32.5249
 V7S  H12  H  HCR6  0   0.253  18.5343   -6.1278  -35.1933
 V7S  H13  H  HCR6  0   0.255  16.1250   -6.2099  -35.7253
 V7S  H14  H  HCR6  0   0.252  15.0344   -8.3694  -36.2126

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
 V7S  C3   C4   single    1.499  0.020  1.499
 V7S  C3   S2   single    1.821  0.020  1.821
 V7S  C4   C12  aromatic  1.394  0.020  1.394
 V7S  C4   C5   aromatic  1.389  0.020  1.389
 V7S  C12  C11  aromatic  1.386  0.020  1.386
 V7S  C5   C6   aromatic  1.393  0.020  1.393
 V7S  C11  C10  aromatic  1.390  0.020  1.390
 V7S  C1   S2   single    1.807  0.020  1.807
 V7S  C6   C10  aromatic  1.391  0.020  1.391
 V7S  C6   C7   single    1.499  0.020  1.499
 V7S  C7   S8   single    1.819  0.020  1.819
 V7S  S8   C9   single    1.805  0.020  1.805
 V7S  C1   H1   single    0.970  0.020  1.090
 V7S  C1   H2   single    0.970  0.020  1.090
 V7S  C1   H3   single    0.970  0.020  1.090
 V7S  C3   H4   single    0.970  0.020  1.090
 V7S  C3   H5   single    0.970  0.020  1.090
 V7S  C5   H6   single    0.930  0.020  1.080
 V7S  C7   H7   single    0.970  0.020  1.090
 V7S  C7   H8   single    0.970  0.020  1.090
 V7S  C9   H9   single    0.970  0.020  1.090
 V7S  C9   H10  single    0.970  0.020  1.090
 V7S  C9   H11  single    0.970  0.020  1.090
 V7S  C10  H12  single    0.930  0.020  1.080
 V7S  C11  H13  single    0.930  0.020  1.080
 V7S  C12  H14  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
 V7S  H3   C1   H2   109.42  3.000
 V7S  H3   C1   H1   108.67  3.000
 V7S  H2   C1   H1   108.72  3.000
 V7S  H3   C1   S2   111.05  3.000
 V7S  H2   C1   S2   111.17  3.000
 V7S  H1   C1   S2   107.74  3.000
 V7S  C3   S2   C1    99.77  3.000
 V7S  H5   C3   H4   108.11  3.000
 V7S  H5   C3   C4   111.15  3.000
 V7S  H4   C3   C4   111.03  3.000
 V7S  H5   C3   S2   108.94  3.000
 V7S  H4   C3   S2   109.12  3.000
 V7S  C4   C3   S2   108.46  3.000
 V7S  C12  C4   C5   119.07  3.000
 V7S  C5   C4   C3   120.45  3.000
 V7S  C12  C4   C3   120.46  3.000
 V7S  H6   C5   C6   119.33  3.000
 V7S  H6   C5   C4   119.40  3.000
 V7S  C6   C5   C4   121.27  3.000
 V7S  C10  C6   C7   120.57  3.000
 V7S  C7   C6   C5   120.56  3.000
 V7S  C10  C6   C5   118.87  3.000
 V7S  H8   C7   H7   107.50  3.000
 V7S  H8   C7   S8   108.99  3.000
 V7S  H7   C7   S8   104.86  3.000
 V7S  H8   C7   C6   110.85  3.000
 V7S  H7   C7   C6   111.07  3.000
 V7S  S8   C7   C6   113.25  3.000
 V7S  C9   S8   C7   100.34  3.000
 V7S  H11  C9   H10  109.37  3.000
 V7S  H11  C9   H9   108.64  3.000
 V7S  H10  C9   H9   108.65  3.000
 V7S  H11  C9   S8   111.54  3.000
 V7S  H10  C9   S8   111.20  3.000
 V7S  H9   C9   S8   107.35  3.000
 V7S  H12  C10  C11  119.84  3.000
 V7S  H12  C10  C6   119.76  3.000
 V7S  C11  C10  C6   120.41  3.000
 V7S  H13  C11  C12  119.92  3.000
 V7S  H13  C11  C10  119.92  3.000
 V7S  C12  C11  C10  120.16  3.000
 V7S  H14  C12  C11  120.04  3.000
 V7S  H14  C12  C4   119.74  3.000
 V7S  C11  C12  C4   120.22  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
 V7S  CONST_01  C10  C11  C12  C4      0.00   0.0  0
 V7S  CONST_02  C10  C6   C5   C4      0.00   0.0  0
 V7S  CONST_03  C11  C12  C4   C5      0.00   0.0  0
 V7S  CONST_04  C11  C10  C6   C5      0.00   0.0  0
 V7S  CONST_05  C12  C4   C5   C6      0.00   0.0  0
 V7S  CONST_06  C12  C11  C10  C6      0.00   0.0  0
 V7S  CONST_07  C11  C12  C4   C3    180.00   0.0  0
 V7S  CONST_08  C6   C5   C4   C3    180.00   0.0  0
 V7S  CONST_09  C7   C6   C5   C4    180.00   0.0  0
 V7S  CONST_10  C11  C10  C6   C7    180.00   0.0  0
 V7S  CONST_11  H13  C11  C12  C4    180.00   0.0  0
 V7S  CONST_12  H14  C12  C4   C5    180.00   0.0  0
 V7S  CONST_13  H12  C10  C6   C5    180.00   0.0  0
 V7S  CONST_14  H6   C5   C6   C10   180.00   0.0  0
 V7S  Var_01    C12  C4   C3   S2    -89.19  30.0  2
 V7S  Var_02    S8   C7   C6   C5    -72.45  30.0  2
 V7S  Var_03    C4   C3   S2   C1   -179.43  30.0  1
 V7S  Var_04    H1   C1   S2   C3    178.90  30.0  3
 V7S  Var_05    H9   C9   S8   C7   -175.90  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
 V7S  plan-1  C3   0.020
 V7S  plan-1  C4   0.020
 V7S  plan-1  C5   0.020
 V7S  plan-1  C6   0.020
 V7S  plan-1  C7   0.020
 V7S  plan-1  C10  0.020
 V7S  plan-1  C11  0.020
 V7S  plan-1  C12  0.020
 V7S  plan-1  H6   0.020
 V7S  plan-1  H12  0.020
 V7S  plan-1  H13  0.020
 V7S  plan-1  H14  0.020

