# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 12:35:04 2020
#   Inital geometry file: a 33 line input string
#   Ligand name: propane-1,3-dithiol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: SCCCS
#
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
 PDT  PDT  'propane-1,3-dithiol      '  ligand  13  5  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PDT
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
 PDT  C2   C  CH2   0  -0.418  -0.1191  -0.0060   0.0195
 PDT  C1   C  CH2   0  -0.546   0.7376  -0.0196   1.2773
 PDT  S1   S  S2    0  -0.253  -0.3574  -0.0119   2.7357
 PDT  C3   C  CH2   0  -0.546   0.7579  -0.0118  -1.2246
 PDT  S2   S  S2    0  -0.254  -0.3131   0.0282  -2.7005
 PDT  H21  H  HCH2  0   0.248  -0.7765  -0.8790   0.0095
 PDT  H22  H  HCH2  0   0.247  -0.7586   0.8806   0.0175
 PDT  H11  H  HCH2  0   0.268   1.3863   0.8561   1.3060
 PDT  H12  H  HCH2  0   0.268   1.3644  -0.9112   1.3003
 PDT  HS1  H  HSH1  0   0.224   0.5938  -0.0403   3.6751
 PDT  H31  H  HCH2  0   0.268   1.4176   0.8559  -1.2316
 PDT  H32  H  HCH2  0   0.269   1.3738  -0.9109  -1.2497
 PDT  HS2  H  HSH1  0   0.224   0.6507  -0.0238  -3.6259

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
 PDT  C2  C1   single  1.522  0.020  1.522
 PDT  C2  C3   single  1.522  0.020  1.522
 PDT  C2  H21  single  0.970  0.020  1.090
 PDT  C2  H22  single  0.970  0.020  1.090
 PDT  C1  S1   single  1.824  0.020  1.824
 PDT  C1  H11  single  0.970  0.020  1.090
 PDT  C1  H12  single  0.970  0.020  1.090
 PDT  S1  HS1  single  1.200  0.020  1.300
 PDT  C3  S2   single  1.824  0.020  1.824
 PDT  C3  H31  single  0.970  0.020  1.090
 PDT  C3  H32  single  0.970  0.020  1.090
 PDT  S2  HS2  single  1.200  0.020  1.300

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
 PDT  H22  C2  H21  107.22  3.000
 PDT  H22  C2  C3   109.80  3.000
 PDT  H21  C2  C3   109.64  3.000
 PDT  H22  C2  C1   109.76  3.000
 PDT  H21  C2  C1   109.82  3.000
 PDT  C3   C2  C1   110.55  3.000
 PDT  H12  C1  H11  108.32  3.000
 PDT  H12  C1  S1   109.38  3.000
 PDT  H11  C1  S1   109.44  3.000
 PDT  H12  C1  C2   110.39  3.000
 PDT  H11  C1  C2   110.46  3.000
 PDT  S1   C1  C2   108.84  3.000
 PDT  HS1  S1  C1    97.74  3.000
 PDT  H32  C3  H31  108.33  3.000
 PDT  H32  C3  S2   109.34  3.000
 PDT  H31  C3  S2   109.43  3.000
 PDT  H32  C3  C2   110.34  3.000
 PDT  H31  C3  C2   110.54  3.000
 PDT  S2   C3  C2   108.84  3.000
 PDT  HS2  S2  C3    97.81  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
 PDT  Var_01  S2  C3  C2  C1  -179.23  30.0  3
 PDT  Var_02  C3  C2  C1  S1   180.00  30.0  1

