# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 26 21:43:08 2022
#   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  36  28  .  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_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  -0.207  27.4013  15.3377   8.7503
 YYJ  C2    C  CR5    0   0.501  26.4213  16.1180   7.8711
 YYJ  C3    C  CR15   0  -0.126  25.0408  15.4053   7.7594
 YYJ  C4    C  CR15   0   0.013  25.1086  14.7230   6.3889
 YYJ  C5    C  CR15   0  -0.036  26.0366  15.6496   5.6059
 YYJ  C6    C  CH2    0  -0.209  25.3723  16.8491   4.9183
 YYJ  O1    O  OC2    0  -0.617  26.8941  15.2764  10.0743
 YYJ  O1S1  O  OS    -1  -0.738  28.1193  17.1474  11.1521
 YYJ  O1S3  O  OS    -1  -0.717  22.6223  15.4646   9.5961
 YYJ  O1S4  O  OS    -1  -0.726  25.2930  12.2586   8.5567
 YYJ  O1S6  O  OS    -1  -0.727  23.3234  16.1509   1.8926
 YYJ  O2    O  OH1    0  -0.683  26.3326  17.4406   8.2673
 YYJ  O2S1  O  OS     0  -0.730  27.0440  15.3607  12.4601
 YYJ  O2S3  O  OS     0  -0.708  22.1998  17.6782   8.5893
 YYJ  O2S4  O  OS     0  -0.721  25.6752  11.0629   6.4466
 YYJ  O2S6  O  OS     0  -0.732  23.8963  14.3426   3.4491
 YYJ  O3    O  OC2    0  -0.619  23.9693  16.3318   7.6981
 YYJ  O3S1  O  OS     0  -0.739  29.0895  14.8969  11.1604
 YYJ  O3S3  O  OS     0  -0.742  24.2081  17.2929   9.9694
 YYJ  O3S4  O  OS     0  -0.731  23.5812  12.3255   6.7977
 YYJ  O3S6  O  OS     0  -0.736  22.5883  16.2643   4.2471
 YYJ  O4    O  OC2    0  -0.627  25.7627  13.4650   6.4358
 YYJ  O5    O  O      0  -0.516  26.9661  16.1071   6.5753
 YYJ  O6    O  OC2    0  -0.609  24.9612  16.5826   3.5863
 YYJ  S1    S  S      0   1.564  27.8816  15.7120  11.3167
 YYJ  S3    S  S      0   1.585  23.1732  16.7174   9.0877
 YYJ  S4    S  S      0   1.566  25.0000  12.1657   7.1232
 YYJ  S6    S  S      0   1.571  23.5675  15.7617   3.2789
 YYJ  H11   H  HCH2   0   0.222  27.5269  14.3203   8.3723
 YYJ  H12   H  HCH2   0   0.234  28.3757  15.8335   8.6994
 YYJ  HO2   H  HOH1   0   0.454  25.7243  17.5107   9.0276
 YYJ  H3    H  HCR5   0   0.280  24.8833  14.6860   8.5659
 YYJ  H4    H  HCR5   0   0.265  24.1164  14.6290   5.9501
 YYJ  H5    H  HCR5   0   0.256  26.5927  15.0898   4.8482
 YYJ  H61   H  HCH2   0   0.234  24.5514  17.2590   5.5083
 YYJ  H62   H  HCH2   0   0.250  26.1300  17.6287   4.8245

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  1.530  0.020  1.530
 YYJ  C1    O1   single  1.419  0.020  1.419
 YYJ  C1    H11  single  0.970  0.020  1.090
 YYJ  C1    H12  single  0.970  0.020  1.090
 YYJ  C2    C3   single  1.558  0.020  1.558
 YYJ  C2    O2   single  1.384  0.020  1.384
 YYJ  C2    O5   single  1.406  0.020  1.406
 YYJ  C3    C4   single  1.533  0.020  1.533
 YYJ  C3    O3   single  1.418  0.020  1.418
 YYJ  C3    H3   single  0.970  0.020  1.090
 YYJ  C4    C5   single  1.527  0.020  1.527
 YYJ  C4    O4   single  1.419  0.020  1.419
 YYJ  C4    H4   single  0.970  0.020  1.090
 YYJ  C5    C6   single  1.534  0.020  1.534
 YYJ  C5    O5   single  1.419  0.020  1.419
 YYJ  C5    H5   single  0.970  0.020  1.090
 YYJ  C6    O6   single  1.419  0.020  1.419
 YYJ  C6    H61  single  0.970  0.020  1.090
 YYJ  C6    H62  single  0.970  0.020  1.090
 YYJ  O1    S1   single  1.646  0.020  1.646
 YYJ  O1S1  S1   deloc   1.464  0.020  1.464
 YYJ  O1S3  S3   deloc   1.460  0.020  1.460
 YYJ  O1S4  S4   deloc   1.466  0.020  1.466
 YYJ  O1S6  S6   deloc   1.460  0.020  1.460
 YYJ  O2    HO2  single  0.850  0.020  0.980
 YYJ  O2S1  S1   deloc   1.460  0.020  1.460
 YYJ  O2S3  S3   deloc   1.456  0.020  1.456
 YYJ  O2S4  S4   deloc   1.459  0.020  1.459
 YYJ  O2S6  S6   deloc   1.467  0.020  1.467
 YYJ  O3    S3   single  1.647  0.020  1.647
 YYJ  O3S1  S1   deloc   1.466  0.020  1.466
 YYJ  O3S3  S3   deloc   1.476  0.020  1.476
 YYJ  O3S4  S4   deloc   1.464  0.020  1.464
 YYJ  O3S6  S6   deloc   1.466  0.020  1.466
 YYJ  O4    S4   single  1.656  0.020  1.656
 YYJ  O6    S6   single  1.646  0.020  1.646

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   107.66  3.000
 YYJ  H12   C1  O1    112.41  3.000
 YYJ  H11   C1  O1    108.88  3.000
 YYJ  H12   C1  C2    108.21  3.000
 YYJ  H11   C1  C2    110.46  3.000
 YYJ  O1    C1  C2    109.22  3.000
 YYJ  O5    C2  O2    107.23  3.000
 YYJ  O5    C2  C3    105.90  3.000
 YYJ  O2    C2  C3    113.65  3.000
 YYJ  O5    C2  C1    106.11  3.000
 YYJ  O2    C2  C1    111.34  3.000
 YYJ  C3    C2  C1    112.05  3.000
 YYJ  H3    C3  O3    110.69  3.000
 YYJ  H3    C3  C4    111.93  3.000
 YYJ  O3    C3  C4    106.60  3.000
 YYJ  H3    C3  C2    112.10  3.000
 YYJ  O3    C3  C2    111.96  3.000
 YYJ  C4    C3  C2    103.22  3.000
 YYJ  H4    C4  O4    110.91  3.000
 YYJ  H4    C4  C5    113.54  3.000
 YYJ  O4    C4  C5    105.95  3.000
 YYJ  H4    C4  C3    111.01  3.000
 YYJ  O4    C4  C3    112.68  3.000
 YYJ  C5    C4  C3    102.43  3.000
 YYJ  H5    C5  O5    107.77  3.000
 YYJ  H5    C5  C6    108.05  3.000
 YYJ  O5    C5  C6    109.75  3.000
 YYJ  H5    C5  C4    110.70  3.000
 YYJ  O5    C5  C4    104.09  3.000
 YYJ  C6    C5  C4    116.17  3.000
 YYJ  H62   C6  H61   107.50  3.000
 YYJ  H62   C6  O6    104.75  3.000
 YYJ  H61   C6  O6    111.11  3.000
 YYJ  H62   C6  C5    107.24  3.000
 YYJ  H61   C6  C5    112.17  3.000
 YYJ  O6    C6  C5    113.54  3.000
 YYJ  S1    O1  C1    118.58  3.000
 YYJ  HO2   O2  C2    109.37  3.000
 YYJ  S3    O3  C3    118.79  3.000
 YYJ  S4    O4  C4    119.81  3.000
 YYJ  C5    O5  C2    112.24  3.000
 YYJ  S6    O6  C6    120.93  3.000
 YYJ  O3S1  S1  O2S1  114.99  3.000
 YYJ  O3S1  S1  O1S1  113.55  3.000
 YYJ  O2S1  S1  O1S1  114.64  3.000
 YYJ  O3S1  S1  O1    105.47  3.000
 YYJ  O2S1  S1  O1    100.56  3.000
 YYJ  O1S1  S1  O1    105.79  3.000
 YYJ  O3S3  S3  O3    104.85  3.000
 YYJ  O3S3  S3  O2S3  114.57  3.000
 YYJ  O3    S3  O2S3  100.88  3.000
 YYJ  O3S3  S3  O1S3  113.02  3.000
 YYJ  O3    S3  O1S3  105.98  3.000
 YYJ  O2S3  S3  O1S3  115.67  3.000
 YYJ  O4    S4  O3S4  105.57  3.000
 YYJ  O4    S4  O2S4  100.80  3.000
 YYJ  O3S4  S4  O2S4  115.32  3.000
 YYJ  O4    S4  O1S4  105.31  3.000
 YYJ  O3S4  S4  O1S4  113.83  3.000
 YYJ  O2S4  S4  O1S4  114.12  3.000
 YYJ  O6    S6  O3S6  105.73  3.000
 YYJ  O6    S6  O2S6  105.72  3.000
 YYJ  O3S6  S6  O2S6  113.88  3.000
 YYJ  O6    S6  O1S6  100.71  3.000
 YYJ  O3S6  S6  O1S6  115.09  3.000
 YYJ  O2S6  S6  O1S6  113.92  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  -59.85  30.0  3
 YYJ  Var_02  O1S4  S4  O4  C4  -85.68  30.0  3
 YYJ  Var_03  O1S1  S1  O1  C1   66.61  30.0  3
 YYJ  Var_04  O1S6  S6  O6  C6  160.35  30.0  3
 YYJ  Var_05  H11   C1  O1  S1  109.98  30.0  1
 YYJ  Var_06  H61   C6  O6  S6  -48.15  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

