# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 12:40:45 2020
#   Inital geometry file: a 39 line input string
#   Ligand name: (4S,5S)-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
 D1D  D1D  (4S,5S)-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_D1D
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
 D1D  S1    S  S2    0  -0.043   0.9462  -0.3632  -1.6517
 D1D  C1    C  CH2   0  -0.615   1.5004   0.3427  -0.0786
 D1D  C2    C  CH1   0   0.065   0.7237  -0.1969   1.1251
 D1D  O2    O  OH1   0  -0.661   1.2828   0.3255   2.3063
 D1D  C3    C  CH1   0   0.065  -0.7525   0.2018   1.1260
 D1D  O3    O  OH1   0  -0.661  -1.3147  -0.3358   2.2993
 D1D  C4    C  CH2   0  -0.615  -1.5263  -0.3224  -0.0864
 D1D  S4    S  S2    0  -0.042  -0.9674   0.4016  -1.6496
 D1D  H1C1  H  HCH2  0   0.284   1.4454   1.4316  -0.1302
 D1D  H1C2  H  HCH2  0   0.298   2.5527   0.0595   0.0122
 D1D  H2    H  HCH1  0   0.216   0.7836  -1.2956   1.1053
 D1D  HA    H  HOH1  0   0.455   2.1833  -0.0051   2.3872
 D1D  H3    H  HCH1  0   0.216  -0.8120   1.3006   1.1207
 D1D  HB    H  HOH1  0   0.455  -2.2157  -0.0072   2.3819
 D1D  H4C1  H  HCH2  0   0.298  -2.5786  -0.0388   0.0046
 D1D  H4C2  H  HCH2  0   0.284  -1.4730  -1.4107  -0.1502

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
 D1D  S1  C1    single  1.811  0.020  1.811
 D1D  S1  S4    single  2.061  0.020  2.061
 D1D  C1  C2    single  1.531  0.020  1.531
 D1D  C1  H1C1  single  0.970  0.020  1.090
 D1D  C1  H1C2  single  0.970  0.020  1.090
 D1D  C2  O2    single  1.407  0.020  1.407
 D1D  C2  C3    single  1.529  0.020  1.529
 D1D  C2  H2    single  0.970  0.020  1.090
 D1D  O2  HA    single  0.850  0.020  0.980
 D1D  C3  O3    single  1.408  0.020  1.408
 D1D  C3  C4    single  1.531  0.020  1.531
 D1D  C3  H3    single  0.970  0.020  1.090
 D1D  O3  HB    single  0.850  0.020  0.980
 D1D  C4  S4    single  1.811  0.020  1.811
 D1D  C4  H4C1  single  0.970  0.020  1.090
 D1D  C4  H4C2  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
 D1D  S4    S1  C1     97.97  3.000
 D1D  H1C2  C1  H1C1  108.11  3.000
 D1D  H1C2  C1  C2    109.37  3.000
 D1D  H1C1  C1  C2    111.30  3.000
 D1D  H1C2  C1  S1    105.41  3.000
 D1D  H1C1  C1  S1    109.41  3.000
 D1D  C2    C1  S1    112.97  3.000
 D1D  H2    C2  C3    108.23  3.000
 D1D  H2    C2  O2    111.35  3.000
 D1D  C3    C2  O2    106.63  3.000
 D1D  H2    C2  C1    108.07  3.000
 D1D  C3    C2  C1    113.48  3.000
 D1D  O2    C2  C1    109.12  3.000
 D1D  HA    O2  C2    108.34  3.000
 D1D  H3    C3  C4    108.10  3.000
 D1D  H3    C3  O3    111.33  3.000
 D1D  C4    C3  O3    109.12  3.000
 D1D  H3    C3  C2    108.21  3.000
 D1D  C4    C3  C2    113.47  3.000
 D1D  O3    C3  C2    106.65  3.000
 D1D  HB    O3  C3    108.36  3.000
 D1D  H4C2  C4  H4C1  108.09  3.000
 D1D  H4C2  C4  S4    109.45  3.000
 D1D  H4C1  C4  S4    105.37  3.000
 D1D  H4C2  C4  C3    111.28  3.000
 D1D  H4C1  C4  C3    109.37  3.000
 D1D  S4    C4  C3    113.00  3.000
 D1D  C4    S4  S1     98.00  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
 D1D  Var_01  C3    C4  S4  S1   64.26  30.0  1
 D1D  Var_02  H1C1  C1  S1  S4  -60.28  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
 D1D  chir_01  C2  C1  O2  C3  negativ
 D1D  chir_02  C3  O3  C2  C4  negativ

