# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 13:10:21 2022
#   Inital geometry file: a 74 line input string
#   Ligand name: methyl 2-O-sulfo-alpha-L-idopyranosiduronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1O[C@H]([C@@H](O)[C@H](O)[C@H]1O[S](O)(=O)=O)C(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
 IDY  IDY  'methyl 2-O-sulfo-alpha-L-idopyranosiduronic acid'  L-saccharide  28  18  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_IDY
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
 IDY  S    S  S      0   1.560  -26.9572   -8.7950  60.8594
 IDY  C1   C  CH1    0   0.273  -27.8735  -11.5624  62.9253
 IDY  O1   O  O2     0  -0.491  -28.0667  -11.2126  64.2662
 IDY  C2   C  CH1    0  -0.048  -26.5858  -10.9599  62.3010
 IDY  O2   O  OC2    0  -0.621  -26.9404  -10.4342  61.0238
 IDY  C3   C  CH1    0   0.020  -25.4085  -11.9183  62.0934
 IDY  O3   O  OH1    0  -0.663  -24.6797  -11.9478  63.3006
 IDY  C4   C  CH1    0  -0.008  -25.8778  -13.3182  61.6989
 IDY  O4   O  OH1    0  -0.699  -26.3692  -13.2855  60.3900
 IDY  C5   C  CH1    0  -0.141  -26.9308  -13.7982  62.6889
 IDY  O5   O  O2     0  -0.507  -28.0565  -12.9230  62.6872
 IDY  C6   C  C      0   0.448  -27.5068  -15.1894  62.3274
 IDY  C7   C  CH3    0  -0.432  -27.3333  -11.8825  65.2684
 IDY  O6A  O  O      0  -0.563  -27.7455  -15.9661  63.2582
 IDY  O6B  O  OC    -1  -0.604  -27.7010  -15.3993  61.1010
 IDY  OS1  O  OS     0  -0.726  -27.3668   -8.6687  59.4637
 IDY  OS2  O  OS     0  -0.738  -25.5859   -8.3603  61.1393
 IDY  OS3  O  OS    -1  -0.738  -27.9362   -8.3090  61.8367
 IDY  H2   H  HCH1   0   0.253  -26.2434  -10.1577  62.9636
 IDY  H3   H  HCH1   0   0.229  -24.7929  -11.5052  61.2830
 IDY  HO3  H  HOH1   0   0.453  -23.9899  -12.6154  63.2267
 IDY  H4   H  HCH1   0   0.201  -25.0136  -14.0033  61.7853
 IDY  HO4  H  HOH1   0   0.437  -26.9441  -14.0869  60.3458
 IDY  H5   H  HCH1   0   0.210  -26.4752  -13.8579  63.6819
 IDY  H7   H  HCH3   0   0.233  -27.5431  -11.3681  66.2059
 IDY  H7A  H  HCH3   0   0.212  -27.6448  -12.9247  65.3858
 IDY  H7B  H  HCH3   0   0.218  -26.2552  -11.8590  65.0979
 IDY  H1   H  HCH1   0   0.234  -28.7051  -11.0669  62.4189

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
 IDY  S   O2   single  1.647  0.020  1.647
 IDY  S   OS1  deloc   1.460  0.020  1.460
 IDY  S   OS2  deloc   1.466  0.020  1.466
 IDY  S   OS3  deloc   1.466  0.020  1.466
 IDY  C1  O1   single  1.399  0.020  1.399
 IDY  C1  C2   single  1.553  0.020  1.553
 IDY  C1  O5   single  1.393  0.020  1.393
 IDY  O1  C7   single  1.411  0.020  1.411
 IDY  C2  O2   single  1.426  0.020  1.426
 IDY  C2  C3   single  1.532  0.020  1.532
 IDY  C3  O3   single  1.410  0.020  1.410
 IDY  C3  C4   single  1.528  0.020  1.528
 IDY  C4  O4   single  1.399  0.020  1.399
 IDY  C4  C5   single  1.523  0.020  1.523
 IDY  C5  O5   single  1.426  0.020  1.426
 IDY  C5  C6   single  1.548  0.020  1.548
 IDY  C6  O6A  deloc   1.236  0.020  1.236
 IDY  C6  O6B  deloc   1.259  0.020  1.259
 IDY  C1  H1   single  0.970  0.020  1.090
 IDY  C2  H2   single  0.970  0.020  1.090
 IDY  C3  H3   single  0.970  0.020  1.090
 IDY  O3  HO3  single  0.850  0.020  0.980
 IDY  C4  H4   single  0.970  0.020  1.090
 IDY  O4  HO4  single  0.850  0.020  0.980
 IDY  C5  H5   single  0.970  0.020  1.090
 IDY  C7  H7   single  0.970  0.020  1.090
 IDY  C7  H7A  single  0.970  0.020  1.090
 IDY  C7  H7B  single  0.970  0.020  1.090

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
 IDY  OS3  S   OS2  113.53  3.000
 IDY  OS3  S   OS1  114.91  3.000
 IDY  OS2  S   OS1  114.80  3.000
 IDY  OS3  S   O2   105.67  3.000
 IDY  OS2  S   O2   105.46  3.000
 IDY  OS1  S   O2   100.62  3.000
 IDY  H1   C1  O5   105.29  3.000
 IDY  H1   C1  C2   105.60  3.000
 IDY  O5   C1  C2   114.78  3.000
 IDY  H1   C1  O1   103.05  3.000
 IDY  O5   C1  O1   112.94  3.000
 IDY  C2   C1  O1   113.75  3.000
 IDY  C7   O1  C1   119.36  3.000
 IDY  H2   C2  C3   107.45  3.000
 IDY  H2   C2  O2   110.46  3.000
 IDY  C3   C2  O2   107.48  3.000
 IDY  H2   C2  C1   107.47  3.000
 IDY  C3   C2  C1   116.68  3.000
 IDY  O2   C2  C1   107.28  3.000
 IDY  C2   O2  S    117.31  3.000
 IDY  H3   C3  C4   109.03  3.000
 IDY  H3   C3  O3   110.47  3.000
 IDY  C4   C3  O3   111.13  3.000
 IDY  H3   C3  C2   107.18  3.000
 IDY  C4   C3  C2   111.84  3.000
 IDY  O3   C3  C2   107.11  3.000
 IDY  HO3  O3  C3   108.60  3.000
 IDY  H4   C4  C5   107.11  3.000
 IDY  H4   C4  O4   111.23  3.000
 IDY  C5   C4  O4   111.89  3.000
 IDY  H4   C4  C3   107.89  3.000
 IDY  C5   C4  C3   109.46  3.000
 IDY  O4   C4  C3   109.15  3.000
 IDY  HO4  O4  C4   103.15  3.000
 IDY  H5   C5  C6   108.53  3.000
 IDY  H5   C5  O5   111.30  3.000
 IDY  C6   C5  O5   104.92  3.000
 IDY  H5   C5  C4   108.62  3.000
 IDY  C6   C5  C4   112.87  3.000
 IDY  O5   C5  C4   110.59  3.000
 IDY  C5   O5  C1   119.70  3.000
 IDY  O6B  C6  O6A  126.80  3.000
 IDY  O6B  C6  C5   115.75  3.000
 IDY  O6A  C6  C5   117.44  3.000
 IDY  H7B  C7  H7A  108.56  3.000
 IDY  H7B  C7  H7   108.32  3.000
 IDY  H7A  C7  H7   107.61  3.000
 IDY  H7B  C7  O1   113.08  3.000
 IDY  H7A  C7  O1   112.36  3.000
 IDY  H7   C7  O1   106.67  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
 IDY  Var_01  OS1  S   O2  C2  -179.47  30.0  2
 IDY  Var_02  H7   C7  O1  C1   172.83  30.0  3

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
 IDY  chir_01  C1  O1  C2  O5  negativ
 IDY  chir_02  C2  O2  C3  C1  positiv
 IDY  chir_03  C3  O3  C2  C4  positiv
 IDY  chir_04  C4  O4  C3  C5  negativ
 IDY  chir_05  C5  O5  C4  C6  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 IDY  plan-1  C5   0.020
 IDY  plan-1  C6   0.020
 IDY  plan-1  O6A  0.020
 IDY  plan-1  O6B  0.020

