# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 17:20:54 2021
#   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  34  20  .  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_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  24.6642  -3.2120  65.9671
 YYB  C2    C  CH1   0  -0.071  25.6212  -3.3303  64.7880
 YYB  C3    C  CH1   0   0.051  26.2956  -1.9966  64.5033
 YYB  C4    C  CH1   0   0.011  25.2296  -0.9137  64.3393
 YYB  C5    C  CH1   0  -0.009  24.2925  -0.9442  65.5584
 YYB  C6    C  CH2   0  -0.239  23.1901   0.0823  65.4899
 YYB  O1S2  O  OS    0  -0.749  27.8515  -4.5568  63.0408
 YYB  O1S6  O  OS    0  -0.714  23.0368   1.5791  62.7947
 YYB  O2    O  OC2   0  -0.585  26.6194  -4.3020  65.1642
 YYB  O2S2  O  OS    0  -0.636  25.9311  -6.0269  63.5079
 YYB  O2S6  O  OS    0  -0.630  21.2198   2.0102  64.4158
 YYB  O3    O  O2    0  -0.553  27.0922  -2.1469  63.3353
 YYB  O3S2  O  OS    0  -0.625  28.0381  -6.2208  64.8189
 YYB  O3S6  O  OS    0  -0.614  20.9071   0.3843  62.5338
 YYB  O4    O  OH1   0  -0.660  25.8542   0.3415  64.2595
 YYB  O5    O  O2    0  -0.479  23.7104  -2.2166  65.7064
 YYB  O6    O  OC2   0  -0.572  22.3783  -0.1916  64.3233
 YYB  S2    S  S     0   1.645  27.0879  -5.4101  64.1096
 YYB  S6    S  S     0   1.662  21.7400   1.0071  63.5214
 YYB  H11   H  HCH2  0   0.276  24.1330  -4.1528  66.1097
 YYB  H12   H  HCH2  0   0.236  25.2307  -2.9929  66.8820
 YYB  H1S2  H  H     0   0.514  27.5546  -3.5809  63.0457
 YYB  H1S6  H  H     0   0.517  23.1358   2.5384  62.9165
 YYB  H2    H  HCH1  0   0.294  25.0662  -3.6700  63.9073
 YYB  H3    H  HCH1  0   0.261  26.9413  -1.7386  65.3553
 YYB  H3M1  H  HCH3  0   0.245  28.9072  -1.7169  62.5191
 YYB  H3M2  H  HCH3  0   0.233  28.6658  -1.0358  64.1386
 YYB  H3M3  H  HCH3  0   0.247  27.8626  -0.3025  62.7319
 YYB  H4    H  HCH1  0   0.256  24.6521  -1.1373  63.4343
 YYB  H4O   H  HOH1  0   0.462  25.4821   0.8367  63.5248
 YYB  H5    H  HCH1  0   0.257  24.8807  -0.6821  66.4532
 YYB  H61   H  HCH2  0   0.273  23.6289   1.0802  65.4530
 YYB  H62   H  HCH2  0   0.294  22.5507   0.0202  66.3701
 YYB  C3M   C  CH3   0  -0.401  28.1863  -1.2388  63.1795

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  1.403  0.020  1.403
 YYB  C1    C2    single  1.523  0.020  1.523
 YYB  C1    H12   single  0.970  0.020  1.090
 YYB  C1    H11   single  0.970  0.020  1.090
 YYB  C2    C3    single  1.521  0.020  1.521
 YYB  C2    O2    single  1.443  0.020  1.443
 YYB  C2    H2    single  0.970  0.020  1.090
 YYB  C3    C4    single  1.528  0.020  1.528
 YYB  C3    O3    single  1.422  0.020  1.422
 YYB  C3    H3    single  0.970  0.020  1.090
 YYB  C3M   O3    single  1.430  0.020  1.430
 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  1.404  0.020  1.404
 YYB  C4    C5    single  1.538  0.020  1.538
 YYB  C5    C6    single  1.508  0.020  1.508
 YYB  C5    O5    single  1.407  0.020  1.407
 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  1.447  0.020  1.447
 YYB  O1S2  H1S2  single  0.850  0.020  0.980
 YYB  O1S2  S2    single  1.566  0.020  1.566
 YYB  O1S6  H1S6  single  0.850  0.020  0.980
 YYB  O1S6  S6    single  1.593  0.020  1.593
 YYB  O2    S2    single  1.600  0.020  1.600
 YYB  O2S2  S2    double  1.442  0.020  1.442
 YYB  O2S6  S6    double  1.441  0.020  1.441
 YYB  O3S2  S2    double  1.436  0.020  1.436
 YYB  O3S6  S6    double  1.434  0.020  1.434
 YYB  O4    H4O   single  0.850  0.020  0.980
 YYB  O6    S6    single  1.577  0.020  1.577

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   108.34  3.000
 YYB  H11   C1    O5    107.78  3.000
 YYB  H12   C1    O5    111.34  3.000
 YYB  H11   C1    C2    109.91  3.000
 YYB  H12   C1    C2    109.65  3.000
 YYB  O5    C1    C2    109.78  3.000
 YYB  H2    C2    O2    110.57  3.000
 YYB  H2    C2    C3    110.25  3.000
 YYB  O2    C2    C3    109.42  3.000
 YYB  H2    C2    C1    109.16  3.000
 YYB  O2    C2    C1    106.57  3.000
 YYB  C3    C2    C1    110.81  3.000
 YYB  H3    C3    O3    109.40  3.000
 YYB  H3    C3    C4    109.05  3.000
 YYB  O3    C3    C4    112.18  3.000
 YYB  H3    C3    C2    108.72  3.000
 YYB  O3    C3    C2    108.02  3.000
 YYB  C4    C3    C2    109.40  3.000
 YYB  H4    C4    O4    111.69  3.000
 YYB  O4    C4    C5    109.50  3.000
 YYB  H4    C4    C5    109.22  3.000
 YYB  C5    C4    C3    109.01  3.000
 YYB  O4    C4    C3    109.22  3.000
 YYB  H4    C4    C3    108.14  3.000
 YYB  H5    C5    O5    110.51  3.000
 YYB  H5    C5    C6    105.37  3.000
 YYB  O5    C5    C6    108.54  3.000
 YYB  H5    C5    C4    108.28  3.000
 YYB  O5    C5    C4    110.70  3.000
 YYB  C6    C5    C4    113.32  3.000
 YYB  H62   C6    H61   108.39  3.000
 YYB  H61   C6    O6    111.81  3.000
 YYB  H62   C6    O6    108.13  3.000
 YYB  O6    C6    C5    108.53  3.000
 YYB  H61   C6    C5    109.28  3.000
 YYB  H62   C6    C5    110.70  3.000
 YYB  H1S2  O1S2  S2    112.09  3.000
 YYB  H1S6  O1S6  S6    112.34  3.000
 YYB  S2    O2    C2    119.81  3.000
 YYB  C3M   O3    C3    116.80  3.000
 YYB  H4O   O4    C4    109.38  3.000
 YYB  C5    O5    C1    112.33  3.000
 YYB  S6    O6    C6    119.54  3.000
 YYB  O3S2  S2    O2S2  119.68  3.000
 YYB  O3S2  S2    O2    105.02  3.000
 YYB  O2S2  S2    O2    109.65  3.000
 YYB  O3S2  S2    O1S2  108.78  3.000
 YYB  O2S2  S2    O1S2  109.83  3.000
 YYB  O2    S2    O1S2  102.43  3.000
 YYB  O6    S6    O3S6  104.78  3.000
 YYB  O6    S6    O2S6  111.08  3.000
 YYB  O3S6  S6    O2S6  121.34  3.000
 YYB  O6    S6    O1S6  100.10  3.000
 YYB  O3S6  S6    O1S6  108.33  3.000
 YYB  O2S6  S6    O1S6  109.09  3.000
 YYB  H3M3  C3M   H3M2  109.41  3.000
 YYB  H3M2  C3M   H3M1  108.91  3.000
 YYB  H3M3  C3M   H3M1  109.01  3.000
 YYB  H3M2  C3M   O3    111.01  3.000
 YYB  H3M3  C3M   O3    111.34  3.000
 YYB  H3M1  C3M   O3    107.09  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   58.95  30.0  1
 YYB  Var_02  O1S2  S2   O2  C2   68.21  30.0  3
 YYB  Var_03  H3M1  C3M  O3  C3  156.71  30.0  3
 YYB  Var_04  O1S6  S6   O6  C6   73.50  30.0  3
 YYB  Var_05  H62   C6   O6  S6   94.37  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

