# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 26 00:54:24 2022
#   Inital geometry file: a 83 line input string
#   Ligand name: 1,5-anhydro-3-O-methyl-2,6-di-O-sulfo-D-glucitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1[C@H](O)[C@@H](CO[S](O)(=O)=O)OC[C@@H]1O[S](O)(=O)=O
#
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
 YYB  YYB  1,5-anhydro-3-O-methyl-2,6-di-O-sulfo-D-glucitol  D-saccharide  32  20  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_YYB
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
 YYB  C1    C  CH2    0  -0.198  24.6959  -3.3654  65.5766
 YYB  C2    C  CH1    0   0.004  25.7799  -3.2184  64.5120
 YYB  C3    C  CH1    0   0.030  26.3043  -1.7878  64.4734
 YYB  C4    C  CH1    0   0.017  25.1464  -0.7966  64.3996
 YYB  C5    C  CH1    0   0.009  24.1318  -1.1000  65.5120
 YYB  C6    C  CH2    0  -0.235  22.9427  -0.1592  65.5242
 YYB  O1S2  O  OS    -1  -0.736  27.1768  -5.2286  62.6590
 YYB  O1S6  O  OS    -1  -0.714  21.6170   0.9959  62.2309
 YYB  O2    O  OC2    0  -0.622  26.8752  -4.0651  64.8315
 YYB  O2S2  O  OS     0  -0.735  25.7497  -6.2376  64.3793
 YYB  O2S6  O  OS     0  -0.747  23.5616   1.8985  63.4371
 YYB  O3    O  O2     0  -0.492  27.1508  -1.6561  63.3582
 YYB  O3S2  O  OS     0  -0.728  28.1775  -6.0681  64.7478
 YYB  O3S6  O  OS     0  -0.722  21.3223   2.1718  64.3839
 YYB  O4    O  OH1    0  -0.696  25.6587   0.5028  64.5164
 YYB  O5    O  O2     0  -0.486  23.6657  -2.4261  65.3896
 YYB  O6    O  OC2    0  -0.606  22.3189  -0.0968  64.2441
 YYB  S2    S  S      0   1.564  26.9970  -5.5276  64.0811
 YYB  S6    S  S      0   1.587  22.1849   1.3684  63.5194
 YYB  H11   H  HCH2   0   0.246  24.2485  -4.3573  65.5211
 YYB  H12   H  HCH2   0   0.205  25.1512  -3.2560  66.5722
 YYB  H2    H  HCH1   0   0.235  25.3595  -3.4614  63.5280
 YYB  H3    H  HCH1   0   0.213  26.8569  -1.6032  65.4089
 YYB  H3M1  H  HCH3   0   0.225  28.9380  -1.0172  62.6662
 YYB  H3M2  H  HCH3   0   0.203  28.9457  -1.4256  64.3869
 YYB  H3M3  H  HCH3   0   0.207  28.1999   0.0856  63.8364
 YYB  H4    H  HCH1   0   0.207  24.6454  -0.9448  63.4318
 YYB  H4O   H  HOH1   0   0.459  24.9956   1.1085  64.1374
 YYB  H5    H  HCH1   0   0.216  24.6335  -0.9677  66.4866
 YYB  H61   H  HCH2   0   0.239  23.2766   0.8219  65.8701
 YYB  H62   H  HCH2   0   0.253  22.2068  -0.5138  66.2504
 YYB  C3M   C  CH3    0  -0.403  28.3547  -0.9669  63.5859

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
 YYB  C1    O5    single  1.407  0.020  1.407
 YYB  C1    C2    single  1.526  0.020  1.526
 YYB  C1    H12   single  0.970  0.020  1.090
 YYB  C1    H11   single  0.970  0.020  1.090
 YYB  C2    C3    single  1.524  0.020  1.524
 YYB  C2    O2    single  1.421  0.020  1.421
 YYB  C2    H2    single  0.970  0.020  1.090
 YYB  C3    C4    single  1.526  0.020  1.526
 YYB  C3    O3    single  1.406  0.020  1.406
 YYB  C3    H3    single  0.970  0.020  1.090
 YYB  C3M   O3    single  1.406  0.020  1.406
 YYB  C3M   H3M1  single  0.970  0.020  1.090
 YYB  C3M   H3M3  single  0.970  0.020  1.090
 YYB  C3M   H3M2  single  0.970  0.020  1.090
 YYB  C4    H4    single  0.970  0.020  1.090
 YYB  C4    O4    single  1.402  0.020  1.402
 YYB  C4    C5    single  1.536  0.020  1.536
 YYB  C5    C6    single  1.516  0.020  1.516
 YYB  C5    O5    single  1.411  0.020  1.411
 YYB  C5    H5    single  0.970  0.020  1.090
 YYB  C6    H62   single  0.970  0.020  1.090
 YYB  C6    H61   single  0.970  0.020  1.090
 YYB  C6    O6    single  1.425  0.020  1.425
 YYB  O1S2  S2    deloc   1.464  0.020  1.464
 YYB  O1S6  S6    deloc   1.457  0.020  1.457
 YYB  O2    S2    single  1.648  0.020  1.648
 YYB  O2S2  S2    deloc   1.466  0.020  1.466
 YYB  O2S6  S6    deloc   1.477  0.020  1.477
 YYB  O3S2  S2    deloc   1.460  0.020  1.460
 YYB  O3S6  S6    deloc   1.462  0.020  1.462
 YYB  O4    H4O   single  0.850  0.020  0.980
 YYB  O6    S6    single  1.640  0.020  1.640

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
 YYB  H12   C1   H11   107.85  3.000
 YYB  H11   C1   O5    107.48  3.000
 YYB  H12   C1   O5    110.91  3.000
 YYB  H11   C1   C2    110.11  3.000
 YYB  H12   C1   C2    109.13  3.000
 YYB  O5    C1   C2    111.29  3.000
 YYB  H2    C2   O2    111.41  3.000
 YYB  H2    C2   C3    108.48  3.000
 YYB  O2    C2   C3    107.45  3.000
 YYB  H2    C2   C1    109.39  3.000
 YYB  O2    C2   C1    109.47  3.000
 YYB  C3    C2   C1    110.63  3.000
 YYB  H3    C3   O3    110.83  3.000
 YYB  H3    C3   C4    108.22  3.000
 YYB  O3    C3   C4    110.95  3.000
 YYB  H3    C3   C2    107.96  3.000
 YYB  O3    C3   C2    108.36  3.000
 YYB  C4    C3   C2    110.48  3.000
 YYB  H4    C4   O4    111.39  3.000
 YYB  O4    C4   C5    111.36  3.000
 YYB  H4    C4   C5    108.05  3.000
 YYB  C5    C4   C3    109.75  3.000
 YYB  O4    C4   C3    108.71  3.000
 YYB  H4    C4   C3    107.50  3.000
 YYB  H5    C5   O5    109.84  3.000
 YYB  H5    C5   C6    105.96  3.000
 YYB  O5    C5   C6    108.95  3.000
 YYB  H5    C5   C4    108.39  3.000
 YYB  O5    C5   C4    109.94  3.000
 YYB  C6    C5   C4    113.66  3.000
 YYB  H62   C6   H61   106.66  3.000
 YYB  H61   C6   O6    112.26  3.000
 YYB  H62   C6   O6    108.43  3.000
 YYB  O6    C6   C5    111.30  3.000
 YYB  H61   C6   C5    108.66  3.000
 YYB  H62   C6   C5    109.39  3.000
 YYB  S2    O2   C2    118.91  3.000
 YYB  C3M   O3   C3    115.66  3.000
 YYB  H4O   O4   C4    107.16  3.000
 YYB  C5    O5   C1    111.97  3.000
 YYB  S6    O6   C6    118.14  3.000
 YYB  O3S2  S2   O2S2  114.58  3.000
 YYB  O3S2  S2   O2    100.39  3.000
 YYB  O2S2  S2   O2    105.92  3.000
 YYB  O3S2  S2   O1S2  114.83  3.000
 YYB  O2S2  S2   O1S2  113.64  3.000
 YYB  O2    S2   O1S2  105.66  3.000
 YYB  O6    S6   O3S6  106.13  3.000
 YYB  O6    S6   O2S6  105.61  3.000
 YYB  O3S6  S6   O2S6  112.68  3.000
 YYB  O6    S6   O1S6  101.20  3.000
 YYB  O3S6  S6   O1S6  115.70  3.000
 YYB  O2S6  S6   O1S6  113.94  3.000
 YYB  H3M3  C3M  H3M2  108.17  3.000
 YYB  H3M2  C3M  H3M1  107.98  3.000
 YYB  H3M3  C3M  H3M1  108.28  3.000
 YYB  H3M2  C3M  O3    112.02  3.000
 YYB  H3M3  C3M  O3    112.83  3.000
 YYB  H3M1  C3M  O3    107.39  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
 YYB  Var_01  H12   C1   O5  C5   59.31  30.0  1
 YYB  Var_02  O1S2  S2   O2  C2   63.51  30.0  3
 YYB  Var_03  H3M1  C3M  O3  C3  175.29  30.0  3
 YYB  Var_04  O1S6  S6   O6  C6  175.48  30.0  3
 YYB  Var_05  H62   C6   O6  S6  116.96  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
 YYB  chir_01  C2  C1  C3  O2  negativ
 YYB  chir_02  C3  O3  C4  C2  negativ
 YYB  chir_03  C4  O4  C5  C3  positiv
 YYB  chir_04  C5  O5  C6  C4  positiv

