# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  4 01:07:50 2021
#   Inital geometry file: a 103 line input string
#   Ligand name: 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@]1(CO[S](O)(=O)=O)O[C@H](CO[S](O)(=O)=O)[C@@H](O[S](O)(=O)=O)[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
 YYJ  YYJ  1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose  D-saccharide  40  28  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_YYJ
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
 YYJ  C1    C  CH2   0  -0.356  27.6403  16.3004   8.4990
 YYJ  C2    C  CT    0   0.526  26.2190  16.6248   8.0440
 YYJ  C3    C  CH1   0  -0.218  25.2533  15.4033   8.1907
 YYJ  C4    C  CH1   0  -0.086  24.7934  15.1223   6.7712
 YYJ  C5    C  CH1   0  -0.083  25.9260  15.7061   5.9339
 YYJ  C6    C  CH2   0  -0.272  25.5115  16.1410   4.5417
 YYJ  O1    O  OC2   0  -0.537  27.6391  15.7486   9.8209
 YYJ  O1S1  O  OS    0  -0.673  27.0082  17.5960  11.3806
 YYJ  O1S3  O  OS    0  -0.703  24.2389  13.6898  10.4131
 YYJ  O1S4  O  OS    0  -0.620  22.6946  13.2025   7.8047
 YYJ  O1S6  O  OS    0  -0.576  24.7518  15.7745   1.5622
 YYJ  O2    O  OH1   0  -0.558  25.8115  17.7489   8.6967
 YYJ  O2S1  O  OS    0  -0.734  28.2220  15.5623  12.1243
 YYJ  O2S3  O  OS    0  -0.595  22.5484  15.4945  10.7736
 YYJ  O2S4  O  OS    0  -0.609  23.4960  11.7077   5.9886
 YYJ  O2S6  O  OS    0  -0.784  23.5993  13.7354   2.3983
 YYJ  O3    O  OC2   0  -0.494  24.1016  15.7146   8.9753
 YYJ  O3S1  O  OS    0  -0.646  29.3072  17.3538  10.7534
 YYJ  O3S3  O  OS    0  -0.648  24.9774  15.7603  11.3135
 YYJ  O3S4  O  OS    0  -0.705  22.4147  13.9012   5.4515
 YYJ  O3S6  O  OS    0  -0.655  22.9326  16.0599   3.0861
 YYJ  O4    O  OC2   0  -0.485  24.6595  13.7220   6.5342
 YYJ  O5    O  O2    0  -0.504  26.2894  16.8651   6.6479
 YYJ  O6    O  OC2   0  -0.522  25.0117  14.9607   3.8915
 YYJ  S1    S  S     0   1.621  28.1579  16.5597  11.0927
 YYJ  S3    S  S     0   1.694  23.9247  15.2315  10.4840
 YYJ  S4    S  S     0   1.579  23.2277  13.0779   6.3058
 YYJ  S6    S  S     0   1.636  23.9308  15.0904   2.7323
 YYJ  H11   H  HCH2  0   0.348  28.0750  15.5294   7.8624
 YYJ  H12   H  HCH2  0   0.336  28.2664  17.1920   8.4249
 YYJ  H1S1  H  H     0   0.479  26.1327  17.1547  11.4537
 YYJ  H1S3  H  H     0   0.560  23.5488  13.1689   9.9622
 YYJ  H1S4  H  H     0   0.453  21.7229  13.2352   7.8410
 YYJ  H1S6  H  H     0   0.540  25.3744  15.1642   1.1301
 YYJ  HO2   H  HOH1  0   0.430  24.8808  17.9421   8.5246
 YYJ  H3    H  HCH1  0   0.403  25.7787  14.5308   8.5871
 YYJ  H4    H  HCH1  0   0.436  23.8611  15.6558   6.5574
 YYJ  H5    H  HCH1  0   0.364  26.7538  14.9861   5.8735
 YYJ  H61   H  HCH2  0   0.316  24.7420  16.9124   4.6124
 YYJ  H62   H  HCH2  0   0.342  26.3644  16.5307   3.9851

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
 YYJ  C1    C2    single  1.527  0.020  1.527
 YYJ  C1    O1    single  1.432  0.020  1.432
 YYJ  C1    H11   single  0.970  0.020  1.090
 YYJ  C1    H12   single  0.970  0.020  1.090
 YYJ  C2    C3    single  1.564  0.020  1.564
 YYJ  C2    O2    single  1.362  0.020  1.362
 YYJ  C2    O5    single  1.418  0.020  1.418
 YYJ  C3    C4    single  1.518  0.020  1.518
 YYJ  C3    O3    single  1.428  0.020  1.428
 YYJ  C3    H3    single  0.970  0.020  1.090
 YYJ  C4    C5    single  1.525  0.020  1.525
 YYJ  C4    O4    single  1.427  0.020  1.427
 YYJ  C4    H4    single  0.970  0.020  1.090
 YYJ  C5    C6    single  1.516  0.020  1.516
 YYJ  C5    O5    single  1.409  0.020  1.409
 YYJ  C5    H5    single  0.970  0.020  1.090
 YYJ  C6    O6    single  1.437  0.020  1.437
 YYJ  C6    H61   single  0.970  0.020  1.090
 YYJ  C6    H62   single  0.970  0.020  1.090
 YYJ  O1    S1    single  1.595  0.020  1.595
 YYJ  O1S1  S1    single  1.574  0.020  1.574
 YYJ  O1S1  H1S1  single  0.850  0.020  0.980
 YYJ  O1S3  H1S3  single  0.850  0.020  0.980
 YYJ  O1S3  S3    single  1.575  0.020  1.575
 YYJ  O1S4  S4    single  1.596  0.020  1.596
 YYJ  O1S4  H1S4  single  0.850  0.020  0.980
 YYJ  O1S6  H1S6  single  0.850  0.020  0.980
 YYJ  O1S6  S6    single  1.585  0.020  1.585
 YYJ  O2    HO2   single  0.850  0.020  0.980
 YYJ  O2S1  S1    double  1.436  0.020  1.436
 YYJ  O2S3  S3    double  1.431  0.020  1.431
 YYJ  O2S4  S4    double  1.432  0.020  1.432
 YYJ  O2S6  S6    double  1.434  0.020  1.434
 YYJ  O3    S3    single  1.594  0.020  1.594
 YYJ  O3S1  S1    double  1.438  0.020  1.438
 YYJ  O3S3  S3    double  1.441  0.020  1.441
 YYJ  O3S4  S4    double  1.438  0.020  1.438
 YYJ  O3S6  S6    double  1.436  0.020  1.436
 YYJ  O4    S4    single  1.587  0.020  1.587
 YYJ  O6    S6    single  1.590  0.020  1.590

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
 YYJ  H12   C1    H11   108.01  3.000
 YYJ  H12   C1    O1    112.19  3.000
 YYJ  H11   C1    O1    105.47  3.000
 YYJ  H12   C1    C2    109.88  3.000
 YYJ  H11   C1    C2    110.32  3.000
 YYJ  O1    C1    C2    110.85  3.000
 YYJ  O5    C2    O2    110.28  3.000
 YYJ  O5    C2    C3    104.79  3.000
 YYJ  O2    C2    C3    114.51  3.000
 YYJ  O5    C2    C1    106.44  3.000
 YYJ  O2    C2    C1    108.11  3.000
 YYJ  C3    C2    C1    112.39  3.000
 YYJ  H3    C3    O3    111.25  3.000
 YYJ  H3    C3    C4    109.69  3.000
 YYJ  O3    C3    C4    108.04  3.000
 YYJ  H3    C3    C2    111.14  3.000
 YYJ  O3    C3    C2    112.29  3.000
 YYJ  C4    C3    C2    104.11  3.000
 YYJ  H4    C4    O4    111.46  3.000
 YYJ  H4    C4    C5    109.79  3.000
 YYJ  O4    C4    C5    110.75  3.000
 YYJ  H4    C4    C3    110.50  3.000
 YYJ  O4    C4    C3    111.43  3.000
 YYJ  C5    C4    C3    102.56  3.000
 YYJ  H5    C5    O5    111.87  3.000
 YYJ  H5    C5    C6    110.09  3.000
 YYJ  O5    C5    C6    107.45  3.000
 YYJ  H5    C5    C4    109.82  3.000
 YYJ  O5    C5    C4    103.20  3.000
 YYJ  C6    C5    C4    114.27  3.000
 YYJ  H62   C6    H61   109.38  3.000
 YYJ  H62   C6    O6    109.54  3.000
 YYJ  H61   C6    O6    111.37  3.000
 YYJ  H62   C6    C5    110.94  3.000
 YYJ  H61   C6    C5    109.63  3.000
 YYJ  O6    C6    C5    105.95  3.000
 YYJ  S1    O1    C1    122.66  3.000
 YYJ  H1S1  O1S1  S1    111.62  3.000
 YYJ  H1S3  O1S3  S3    113.74  3.000
 YYJ  H1S4  O1S4  S4    111.80  3.000
 YYJ  H1S6  O1S6  S6    112.87  3.000
 YYJ  HO2   O2    C2    111.58  3.000
 YYJ  S3    O3    C3    122.92  3.000
 YYJ  S4    O4    C4    120.47  3.000
 YYJ  C5    O5    C2    110.28  3.000
 YYJ  S6    O6    C6    119.95  3.000
 YYJ  O3S1  S1    O2S1  121.15  3.000
 YYJ  O3S1  S1    O1S1  105.27  3.000
 YYJ  O2S1  S1    O1S1  111.00  3.000
 YYJ  O3S1  S1    O1    110.66  3.000
 YYJ  O2S1  S1    O1    103.54  3.000
 YYJ  O1S1  S1    O1    104.06  3.000
 YYJ  O3S3  S3    O3    110.64  3.000
 YYJ  O3S3  S3    O2S3  121.25  3.000
 YYJ  O3    S3    O2S3  104.04  3.000
 YYJ  O3S3  S3    O1S3  103.85  3.000
 YYJ  O3    S3    O1S3  103.41  3.000
 YYJ  O2S3  S3    O1S3  112.39  3.000
 YYJ  O4    S4    O3S4  111.30  3.000
 YYJ  O4    S4    O2S4  104.56  3.000
 YYJ  O3S4  S4    O2S4  121.48  3.000
 YYJ  O4    S4    O1S4   97.73  3.000
 YYJ  O3S4  S4    O1S4  108.93  3.000
 YYJ  O2S4  S4    O1S4  110.21  3.000
 YYJ  O6    S6    O3S6  110.36  3.000
 YYJ  O6    S6    O2S6  104.47  3.000
 YYJ  O3S6  S6    O2S6  122.31  3.000
 YYJ  O6    S6    O1S6  102.79  3.000
 YYJ  O3S6  S6    O1S6  104.52  3.000
 YYJ  O2S6  S6    O1S6  110.83  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
 YYJ  Var_01  O1S3  S3  O3  C3  -49.98  30.0  3
 YYJ  Var_02  O1S4  S4  O4  C4  -71.60  30.0  3
 YYJ  Var_03  O1S1  S1  O1  C1   74.71  30.0  3
 YYJ  Var_04  O1S6  S6  O6  C6   68.39  30.0  3
 YYJ  Var_05  H11   C1  O1  S1  132.82  30.0  2
 YYJ  Var_06  H61   C6  O6  S6   33.70  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
 YYJ  chir_01  C2  C3  O2  O5  positiv
 YYJ  chir_02  C3  O3  C4  C2  negativ
 YYJ  chir_03  C4  O4  C5  C3  positiv
 YYJ  chir_04  C5  O5  C4  C6  negativ

