# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 14:36:36 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: [(methylsulfanyl)methyl]benzene
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCc1ccccc1
#
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
 PTF  PTF  '[(methylsulfanyl)methyl]benzene'  ligand  19  9  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PTF
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
 PTF  C1   C  CH3   0  -0.769   0.0555  -0.1829   3.6789
 PTF  S2   S  S2    0  -0.030   0.0979   0.5930   2.0482
 PTF  C3   C  CH2   0  -0.617  -0.0725  -0.8831   0.9950
 PTF  C4   C  CR6   0   0.110  -0.0416  -0.4513  -0.4400
 PTF  C5   C  CR16  0  -0.292  -1.2226  -0.2754  -1.1553
 PTF  C6   C  CR16  0  -0.242  -1.1929   0.1487  -2.4776
 PTF  C7   C  CR16  0  -0.267   0.0214   0.4099  -3.0980
 PTF  C8   C  CR16  0  -0.242   1.2052   0.2428  -2.3896
 PTF  C9   C  CR16  0  -0.284   1.1726  -0.1831  -1.0694
 PTF  H11  H  HCH3  0   0.275   0.1517   0.6068   4.4219
 PTF  H12  H  HCH3  0   0.262  -0.8873  -0.7031   3.8425
 PTF  H13  H  HCH3  0   0.262   0.8811  -0.8824   3.8042
 PTF  H31  H  HCH2  0   0.280   0.7448  -1.5721   1.2159
 PTF  H32  H  HCH2  0   0.280  -1.0124  -1.3833   1.2326
 PTF  H5   H  HCR6  0   0.253  -2.1735  -0.4784  -0.6771
 PTF  H6   H  HCR6  0   0.256  -2.1196   0.2751  -3.0224
 PTF  H7   H  HCR6  0   0.256   0.0461   0.7399  -4.1285
 PTF  H8   H  HCR6  0   0.256   2.1556   0.4436  -2.8669
 PTF  H9   H  HCR6  0   0.253   2.0992  -0.3132  -0.5227

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
 PTF  C1  S2   single    1.806  0.020  1.806
 PTF  C1  H11  single    0.970  0.020  1.090
 PTF  C1  H12  single    0.970  0.020  1.090
 PTF  C1  H13  single    0.970  0.020  1.090
 PTF  S2  C3   single    1.821  0.020  1.821
 PTF  C3  C4   single    1.499  0.020  1.499
 PTF  C3  H31  single    0.970  0.020  1.090
 PTF  C3  H32  single    0.970  0.020  1.090
 PTF  C4  C5   aromatic  1.392  0.020  1.392
 PTF  C4  C9   aromatic  1.394  0.020  1.394
 PTF  C5  C6   aromatic  1.389  0.020  1.389
 PTF  C5  H5   single    0.930  0.020  1.080
 PTF  C6  C7   aromatic  1.388  0.020  1.388
 PTF  C6  H6   single    0.930  0.020  1.080
 PTF  C7  C8   aromatic  1.390  0.020  1.390
 PTF  C7  H7   single    0.930  0.020  1.080
 PTF  C8  C9   aromatic  1.388  0.020  1.388
 PTF  C8  H8   single    0.930  0.020  1.080
 PTF  C9  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
 PTF  H13  C1  H12  109.39  3.000
 PTF  H13  C1  H11  108.69  3.000
 PTF  H12  C1  H11  108.69  3.000
 PTF  H13  C1  S2   111.22  3.000
 PTF  H12  C1  S2   111.17  3.000
 PTF  H11  C1  S2   107.61  3.000
 PTF  C3   S2  C1    99.89  3.000
 PTF  H32  C3  H31  108.16  3.000
 PTF  H32  C3  C4   111.00  3.000
 PTF  H31  C3  C4   111.11  3.000
 PTF  H32  C3  S2   109.04  3.000
 PTF  H31  C3  S2   108.93  3.000
 PTF  C4   C3  S2   108.55  3.000
 PTF  C9   C4  C5   118.87  3.000
 PTF  C9   C4  C3   120.38  3.000
 PTF  C5   C4  C3   120.72  3.000
 PTF  H5   C5  C6   119.74  3.000
 PTF  H5   C5  C4   119.61  3.000
 PTF  C6   C5  C4   120.64  3.000
 PTF  H6   C6  C7   120.13  3.000
 PTF  H6   C6  C5   119.77  3.000
 PTF  C7   C6  C5   120.10  3.000
 PTF  H7   C7  C8   120.17  3.000
 PTF  H7   C7  C6   120.19  3.000
 PTF  C8   C7  C6   119.64  3.000
 PTF  H8   C8  C9   119.81  3.000
 PTF  H8   C8  C7   120.06  3.000
 PTF  C9   C8  C7   120.13  3.000
 PTF  H9   C9  C8   119.78  3.000
 PTF  H9   C9  C4   119.61  3.000
 PTF  C8   C9  C4   120.61  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
 PTF  CONST_01  C7   C6  C5  C4     0.00   0.0  0
 PTF  CONST_02  C7   C8  C9  C4     0.00   0.0  0
 PTF  CONST_03  C8   C9  C4  C5     0.00   0.0  0
 PTF  CONST_04  C8   C7  C6  C5     0.00   0.0  0
 PTF  CONST_05  C9   C4  C5  C6     0.00   0.0  0
 PTF  CONST_06  C9   C8  C7  C6     0.00   0.0  0
 PTF  CONST_07  C6   C5  C4  C3   180.00   0.0  0
 PTF  CONST_08  C8   C9  C4  C3   180.00   0.0  0
 PTF  CONST_09  H6   C6  C5  C4   180.00   0.0  0
 PTF  CONST_10  H8   C8  C9  C4   180.00   0.0  0
 PTF  CONST_11  H9   C9  C4  C5   180.00   0.0  0
 PTF  CONST_12  H7   C7  C6  C5   180.00   0.0  0
 PTF  CONST_13  H5   C5  C6  C7   180.00   0.0  0
 PTF  Var_01    C5   C4  C3  S2   -97.87  30.0  2
 PTF  Var_02    C4   C3  S2  C1  -179.25  30.0  3
 PTF  Var_03    H11  C1  S2  C3   179.94  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
 PTF  plan-1  C3  0.020
 PTF  plan-1  C4  0.020
 PTF  plan-1  C5  0.020
 PTF  plan-1  C6  0.020
 PTF  plan-1  C7  0.020
 PTF  plan-1  C8  0.020
 PTF  plan-1  C9  0.020
 PTF  plan-1  H5  0.020
 PTF  plan-1  H6  0.020
 PTF  plan-1  H7  0.020
 PTF  plan-1  H8  0.020
 PTF  plan-1  H9  0.020

