# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 17:10:04 2022
#   Inital geometry file: a 55 line input string
#   Ligand name: 1,4-dithio-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](S)[C@H](O)[C@@H](O)[C@@H]1S
#
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
 MA1  MA1  1,4-dithio-alpha-D-glucopyranose  D-saccharide  24  12  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MA1
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
 MA1  C1   C  CH1   0  -0.135  18.0024  24.7097  18.7759
 MA1  C2   C  CH1   0   0.028  19.1702  25.1707  17.9078
 MA1  C3   C  CH1   0   0.054  20.4997  24.8813  18.5965
 MA1  C4   C  CH1   0  -0.466  20.4883  25.4597  20.0129
 MA1  C5   C  CH1   0   0.051  19.2654  24.9689  20.7875
 MA1  C6   C  CH2   0  -0.147  19.1176  25.6575  22.1277
 MA1  S1   S  S2    0  -0.257  17.9218  22.8688  18.7578
 MA1  O2   O  OH1   0  -0.653  19.0672  24.5417  16.6621
 MA1  O3   O  OH1   0  -0.660  21.5018  25.4510  17.7976
 MA1  S4   S  S2    0  -0.226  22.0500  24.9555  20.8241
 MA1  O5   O  O2    0  -0.457  18.0858  25.2492  20.0530
 MA1  O6   O  OH1   0  -0.664  18.0266  25.0890  22.8101
 MA1  H1   H  HCH1  0   0.299  17.0649  25.0764  18.3561
 MA1  H2   H  HCH1  0   0.244  19.0724  26.2639  17.8137
 MA1  H3   H  HCH1  0   0.224  20.6255  23.7893  18.6676
 MA1  H4   H  HCH1  0   0.299  20.4791  26.5519  19.9509
 MA1  H5   H  HCH1  0   0.230  19.3597  23.8852  20.9448
 MA1  H61  H  HCH2  0   0.206  20.0522  25.5314  22.6848
 MA1  H62  H  HCH2  0   0.199  18.9846  26.7357  21.9600
 MA1  HS1  H  HSH1  0   0.229  16.8102  22.7817  19.4980
 MA1  HO2  H  HOH1  0   0.455  19.7806  24.8645  16.1011
 MA1  HO3  H  HOH1  0   0.450  22.3594  25.2169  18.1716
 MA1  HS4  H  HSH1  0   0.240  22.3231  26.1111  21.4366
 MA1  HO6  H  HOH1  0   0.455  17.9703  25.5019  23.6765

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
 MA1  C1  C2   single  1.526  0.020  1.526
 MA1  C1  S1   single  1.843  0.020  1.843
 MA1  C1  O5   single  1.389  0.020  1.389
 MA1  C1  H1   single  0.970  0.020  1.090
 MA1  C2  C3   single  1.525  0.020  1.525
 MA1  C2  O2   single  1.399  0.020  1.399
 MA1  C2  H2   single  0.970  0.020  1.090
 MA1  C3  C4   single  1.530  0.020  1.530
 MA1  C3  O3   single  1.403  0.020  1.403
 MA1  C3  H3   single  0.970  0.020  1.090
 MA1  C4  C5   single  1.529  0.020  1.529
 MA1  C4  S4   single  1.831  0.020  1.831
 MA1  C4  H4   single  0.970  0.020  1.090
 MA1  C5  C6   single  1.514  0.020  1.514
 MA1  C5  O5   single  1.417  0.020  1.417
 MA1  C5  H5   single  0.970  0.020  1.090
 MA1  C6  O6   single  1.407  0.020  1.407
 MA1  C6  H61  single  0.970  0.020  1.090
 MA1  C6  H62  single  0.970  0.020  1.090
 MA1  S1  HS1  single  1.200  0.020  1.300
 MA1  O2  HO2  single  0.850  0.020  0.980
 MA1  O3  HO3  single  0.850  0.020  0.980
 MA1  S4  HS4  single  1.200  0.020  1.300
 MA1  O6  HO6  single  0.850  0.020  0.980

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
 MA1  H1   C1  O5   105.96  3.000
 MA1  H1   C1  S1   107.13  3.000
 MA1  O5   C1  S1   113.56  3.000
 MA1  H1   C1  C2   109.71  3.000
 MA1  O5   C1  C2   111.08  3.000
 MA1  S1   C1  C2   109.24  3.000
 MA1  H2   C2  O2   111.31  3.000
 MA1  H2   C2  C3   107.72  3.000
 MA1  O2   C2  C3   112.39  3.000
 MA1  H2   C2  C1   106.28  3.000
 MA1  O2   C2  C1   108.31  3.000
 MA1  C3   C2  C1   110.66  3.000
 MA1  H3   C3  O3   110.97  3.000
 MA1  H3   C3  C4   108.41  3.000
 MA1  O3   C3  C4   112.28  3.000
 MA1  H3   C3  C2   108.47  3.000
 MA1  O3   C3  C2   106.78  3.000
 MA1  C4   C3  C2   109.87  3.000
 MA1  H4   C4  S4   107.89  3.000
 MA1  H4   C4  C5   110.03  3.000
 MA1  S4   C4  C5   111.68  3.000
 MA1  H4   C4  C3   108.97  3.000
 MA1  S4   C4  C3   107.44  3.000
 MA1  C5   C4  C3   110.71  3.000
 MA1  H5   C5  O5   109.91  3.000
 MA1  H5   C5  C6   109.28  3.000
 MA1  O5   C5  C6   106.71  3.000
 MA1  H5   C5  C4   108.69  3.000
 MA1  O5   C5  C4   109.86  3.000
 MA1  C6   C5  C4   112.37  3.000
 MA1  H62  C6  H61  107.09  3.000
 MA1  H62  C6  O6   112.12  3.000
 MA1  H61  C6  O6   111.62  3.000
 MA1  H62  C6  C5   108.84  3.000
 MA1  H61  C6  C5   108.33  3.000
 MA1  O6   C6  C5   108.74  3.000
 MA1  HS1  S1  C1    95.50  3.000
 MA1  HO2  O2  C2   108.26  3.000
 MA1  HO3  O3  C3   108.41  3.000
 MA1  HS4  S4  C4    98.01  3.000
 MA1  C5   O5  C1   116.72  3.000
 MA1  HO6  O6  C6   108.00  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
 MA1  chir_01  C1  C2  S1  O5  negativ
 MA1  chir_02  C2  O2  C1  C3  negativ
 MA1  chir_03  C3  O3  C2  C4  positiv
 MA1  chir_04  C4  S4  C5  C3  positiv
 MA1  chir_05  C5  O5  C4  C6  negativ

