# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 15:13:39 2020
#   Inital geometry file: a 39 line input string
#   Ligand name: (4R,5R)-1,2-dithiane-4,5-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1CSSC[C@@H]1O
#
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
 DTD  DTD  (4R,5R)-1,2-dithiane-4,5-diol  ligand  16  8  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_DTD
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
 DTD  S1   S  S2    0  -0.042   0.9302   0.3692  -1.6944
 DTD  C1   C  CH2   0  -0.616   1.4908  -0.3446  -0.1271
 DTD  C2   C  CH1   0   0.066   0.7371   0.2093   1.0846
 DTD  O2   O  OH1   0  -0.661   1.3023  -0.3186   2.2605
 DTD  C3   C  CH1   0   0.065  -0.7449  -0.1671   1.1032
 DTD  O3   O  OH1   0  -0.661  -1.2852   0.3804   2.2820
 DTD  C4   C  CH2   0  -0.615  -1.5246   0.3677  -0.1007
 DTD  S4   S  S2    0  -0.042  -0.9952  -0.3652  -1.6698
 DTD  H11  H  HCH2  0   0.299   2.5489  -0.0796  -0.0491
 DTD  H12  H  HCH2  0   0.284   1.4174  -1.4325  -0.1770
 DTD  H21  H  HCH1  0   0.216   0.8130   1.3070   1.0613
 DTD  HO2  H  HOH1  0   0.455   2.2111  -0.0078   2.3259
 DTD  H31  H  HCH1  0   0.216  -0.8212  -1.2649   1.1001
 DTD  HO3  H  HOH1  0   0.455  -2.1876   0.0600   2.3794
 DTD  H41  H  HCH2  0   0.284  -1.4557   1.4551  -0.1658
 DTD  H42  H  HCH2  0   0.298  -2.5799   0.1001   0.0024

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
 DTD  S1  C1   single  1.811  0.020  1.811
 DTD  S1  S4   single  2.061  0.020  2.061
 DTD  C1  C2   single  1.531  0.020  1.531
 DTD  C1  H11  single  0.970  0.020  1.090
 DTD  C1  H12  single  0.970  0.020  1.090
 DTD  C2  O2   single  1.407  0.020  1.407
 DTD  C2  C3   single  1.529  0.020  1.529
 DTD  C2  H21  single  0.970  0.020  1.090
 DTD  O2  HO2  single  0.850  0.020  0.980
 DTD  C3  O3   single  1.408  0.020  1.408
 DTD  C3  C4   single  1.531  0.020  1.531
 DTD  C3  H31  single  0.970  0.020  1.090
 DTD  O3  HO3  single  0.850  0.020  0.980
 DTD  C4  S4   single  1.811  0.020  1.811
 DTD  C4  H41  single  0.970  0.020  1.090
 DTD  C4  H42  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
 DTD  S4   S1  C1    97.96  3.000
 DTD  H12  C1  H11  108.05  3.000
 DTD  H12  C1  C2   111.33  3.000
 DTD  H11  C1  C2   109.40  3.000
 DTD  H12  C1  S1   109.42  3.000
 DTD  H11  C1  S1   105.41  3.000
 DTD  C2   C1  S1   112.96  3.000
 DTD  H21  C2  C3   108.22  3.000
 DTD  H21  C2  O2   111.35  3.000
 DTD  C3   C2  O2   106.66  3.000
 DTD  H21  C2  C1   108.07  3.000
 DTD  C3   C2  C1   113.44  3.000
 DTD  O2   C2  C1   109.14  3.000
 DTD  HO2  O2  C2   108.35  3.000
 DTD  H31  C3  C4   108.12  3.000
 DTD  H31  C3  O3   111.33  3.000
 DTD  C4   C3  O3   109.10  3.000
 DTD  H31  C3  C2   108.22  3.000
 DTD  C4   C3  C2   113.46  3.000
 DTD  O3   C3  C2   106.65  3.000
 DTD  HO3  O3  C3   108.37  3.000
 DTD  H42  C4  H41  108.08  3.000
 DTD  H42  C4  S4   105.35  3.000
 DTD  H41  C4  S4   109.46  3.000
 DTD  H42  C4  C3   109.38  3.000
 DTD  H41  C4  C3   111.27  3.000
 DTD  S4   C4  C3   113.02  3.000
 DTD  C4   S4  S1    98.01  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
 DTD  Var_01  C3   C4  S4  S1  -64.21  30.0  1
 DTD  Var_02  H11  C1  S1  S4  176.22  30.0  1

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
 DTD  chir_01  C2  C1  O2  C3  positiv
 DTD  chir_02  C3  O3  C2  C4  positiv

