# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 11:00:56 2020
#   Inital geometry file: a 47 line input string
#   Ligand name: (4S,5S)-4,5-bis(sulfanylmethyl)-1,3-dioxolan-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1O[C@H](CS)[C@@H](CS)O1
#
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
 DBC  DBC  (4S,5S)-4,5-bis(sulfanylmethyl)-1,3-dioxolan-2-ol  ligand  20  10  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DBC
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
 DBC  O4   O  OH1   0  -0.648   0.0656   2.9522  -0.5638
 DBC  C5   C  CR15  0   0.486   0.0512   1.9314   0.3491
 DBC  O3   O  O     0  -0.512  -1.0871   1.1511   0.1465
 DBC  O2   O  O     0  -0.508   1.1528   1.0950   0.1414
 DBC  C2   C  CR15  0   0.038   0.7342  -0.2486   0.2441
 DBC  C1   C  CH2   0  -0.586   1.6023  -1.1320  -0.6190
 DBC  S1   S  S2    0  -0.236   3.3405  -0.9675  -0.0923
 DBC  C3   C  CR15  0   0.040  -0.7235  -0.1693  -0.2105
 DBC  C4   C  CH2   0  -0.586  -1.6238  -1.1685   0.4777
 DBC  S4   S  S2    0  -0.238  -3.3545  -0.8686  -0.0120
 DBC  HO4  H  HOH1  0   0.473   0.4130   3.7519  -0.1547
 DBC  H5   H  HCR5  0   0.206   0.0478   2.3203   1.3767
 DBC  H2   H  HCR5  0   0.243   0.7909  -0.5907   1.2876
 DBC  H11  H  HCH2  0   0.287   1.2900  -2.1684  -0.4914
 DBC  H12  H  HCH2  0   0.277   1.4983  -0.8651  -1.6710
 DBC  HS1  H  HSH1  0   0.228   3.7791  -2.1252  -0.5960
 DBC  H3   H  HCR5  0   0.245  -0.7965  -0.3008  -1.2986
 DBC  H41  H  HCH2  0   0.285  -1.3364  -2.1731   0.1673
 DBC  H42  H  HCH2  0   0.276  -1.5203  -1.0967   1.5610
 DBC  HS4  H  HSH1  0   0.228  -3.8369  -2.0624   0.3473

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
 DBC  O4  C5   single  1.370  0.020  1.370
 DBC  O4  HO4  single  0.850  0.020  0.980
 DBC  C5  O3   single  1.395  0.020  1.395
 DBC  C5  O2   single  1.399  0.020  1.399
 DBC  C5  H5   single  0.970  0.020  1.090
 DBC  O3  C3   single  1.415  0.020  1.415
 DBC  O2  C2   single  1.411  0.020  1.411
 DBC  C2  C1   single  1.510  0.020  1.510
 DBC  C2  C3   single  1.529  0.020  1.529
 DBC  C2  H2   single  0.970  0.020  1.090
 DBC  C1  S1   single  1.824  0.020  1.824
 DBC  C1  H11  single  0.970  0.020  1.090
 DBC  C1  H12  single  0.970  0.020  1.090
 DBC  S1  HS1  single  1.200  0.020  1.300
 DBC  C3  C4   single  1.511  0.020  1.511
 DBC  C3  H3   single  0.970  0.020  1.090
 DBC  C4  S4   single  1.823  0.020  1.823
 DBC  C4  H41  single  0.970  0.020  1.090
 DBC  C4  H42  single  0.970  0.020  1.090
 DBC  S4  HS4  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
 DBC  HO4  O4  C5   109.85  3.000
 DBC  H5   C5  O2   110.67  3.000
 DBC  H5   C5  O3   109.35  3.000
 DBC  O2   C5  O3   106.65  3.000
 DBC  H5   C5  O4   111.08  3.000
 DBC  O2   C5  O4   109.78  3.000
 DBC  O3   C5  O4   109.19  3.000
 DBC  C3   O3  C5   110.42  3.000
 DBC  C2   O2  C5   108.96  3.000
 DBC  H2   C2  C3   110.33  3.000
 DBC  H2   C2  C1   109.32  3.000
 DBC  C3   C2  C1   114.11  3.000
 DBC  H2   C2  O2   110.49  3.000
 DBC  C3   C2  O2   102.23  3.000
 DBC  C1   C2  O2   110.18  3.000
 DBC  H12  C1  H11  108.56  3.000
 DBC  H12  C1  S1   110.34  3.000
 DBC  H11  C1  S1   108.97  3.000
 DBC  H12  C1  C2   110.70  3.000
 DBC  H11  C1  C2   108.95  3.000
 DBC  S1   C1  C2   109.28  3.000
 DBC  HS1  S1  C1    97.23  3.000
 DBC  H3   C3  C4   109.42  3.000
 DBC  H3   C3  C2   110.59  3.000
 DBC  C4   C3  C2   113.48  3.000
 DBC  H3   C3  O3   110.15  3.000
 DBC  C4   C3  O3   110.43  3.000
 DBC  C2   C3  O3   102.61  3.000
 DBC  H42  C4  H41  108.58  3.000
 DBC  H42  C4  S4   110.24  3.000
 DBC  H41  C4  S4   108.99  3.000
 DBC  H42  C4  C3   110.63  3.000
 DBC  H41  C4  C3   108.83  3.000
 DBC  S4   C4  C3   109.54  3.000
 DBC  HS4  S4  C4    97.09  3.000

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
 DBC  chir_01  C5  O4  O3  O2  negativ
 DBC  chir_02  C2  O2  C1  C3  positiv
 DBC  chir_03  C3  O3  C2  C4  negativ

