# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 13:05:10 2022
#   Inital geometry file: a 68 line input string
#   Ligand name: 2-O-sulfo-alpha-L-idopyranuronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[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
 IDS  IDS  '2-O-sulfo-alpha-L-idopyranuronic acid'  L-saccharide  25  17  .  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 (reasonable std)
;

data_comp_IDS
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
 IDS  C1   C  CH1    0   0.274  3.9702   7.1685   3.5440
 IDS  C2   C  CH1    0  -0.101  2.7598   8.0555   3.8722
 IDS  C3   C  CH1    0   0.066  1.4669   7.3129   3.5365
 IDS  C4   C  CH1    0   0.028  1.4402   7.0133   2.0348
 IDS  C5   C  CH1    0  -0.164  2.8656   6.7959   1.4980
 IDS  C6   C  C      0   0.420  2.9257   5.8894   0.2463
 IDS  O1   O  OH1    0  -0.661  5.0401   8.0139   3.2575
 IDS  O2   O  OC2    0  -0.626  2.8706   8.3395   5.2654
 IDS  O3   O  OH1    0  -0.700  0.3007   8.0287   3.8485
 IDS  O4   O  OH1    0  -0.695  0.5886   5.9176   1.8203
 IDS  O5   O  O2     0  -0.495  3.7020   6.2706   2.5111
 IDS  O6A  O  O      0  -0.612  1.8898   5.9004  -0.4668
 IDS  O6B  O  OC    -1  -0.560  3.9737   5.2756   0.0299
 IDS  S    S  S      0   1.580  2.4393   9.8086   5.8693
 IDS  O1S  O  OS     0  -0.711  3.0320   9.7515   7.1983
 IDS  O2S  O  OS     0  -0.719  3.0034  10.8102   4.9672
 IDS  O3S  O  OS    -1  -0.740  0.9639   9.7882   5.8756
 IDS  H1   H  HCH1   0   0.217  4.1886   6.5372   4.4142
 IDS  H2   H  HCH1   0   0.249  2.8109   8.9822   3.2865
 IDS  H3   H  HCH1   0   0.192  1.4915   6.3521   4.0764
 IDS  H4   H  HCH1   0   0.187  1.0514   7.9162   1.5391
 IDS  H5   H  HCH1   0   0.230  3.2473   7.7767   1.1711
 IDS  HO1  H  HOH1   0   0.455  5.8558   7.5014   3.2742
 IDS  HO3  H  HOH1   0   0.446  0.4189   8.5336   4.6711
 IDS  HO4  H  HOH1   0   0.440  0.7065   5.7273   0.8690

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
 IDS  C1  C2   single  1.536  0.020  1.536
 IDS  C1  O1   single  1.393  0.020  1.393
 IDS  C1  O5   single  1.395  0.020  1.395
 IDS  C1  H1   single  0.970  0.020  1.090
 IDS  C2  C3   single  1.528  0.020  1.528
 IDS  C2  O2   single  1.426  0.020  1.426
 IDS  C2  H2   single  0.970  0.020  1.090
 IDS  C3  C4   single  1.531  0.020  1.531
 IDS  C3  O3   single  1.403  0.020  1.403
 IDS  C3  H3   single  0.970  0.020  1.090
 IDS  C4  C5   single  1.539  0.020  1.539
 IDS  C4  O4   single  1.404  0.020  1.404
 IDS  C4  H4   single  0.970  0.020  1.090
 IDS  C5  C6   single  1.547  0.020  1.547
 IDS  C5  O5   single  1.415  0.020  1.415
 IDS  C5  H5   single  0.970  0.020  1.090
 IDS  C6  O6A  deloc   1.258  0.020  1.258
 IDS  C6  O6B  deloc   1.234  0.020  1.234
 IDS  O1  HO1  single  0.850  0.020  0.980
 IDS  O2  S    single  1.646  0.020  1.646
 IDS  O3  HO3  single  0.850  0.020  0.980
 IDS  O4  HO4  single  0.850  0.020  0.980
 IDS  S   O1S  deloc   1.456  0.020  1.456
 IDS  S   O2S  deloc   1.461  0.020  1.461
 IDS  S   O3S  deloc   1.476  0.020  1.476

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
 IDS  H1   C1  O5   104.79  3.000
 IDS  H1   C1  O1   111.06  3.000
 IDS  O5   C1  O1   112.70  3.000
 IDS  H1   C1  C2   108.64  3.000
 IDS  O5   C1  C2   112.24  3.000
 IDS  O1   C1  C2   107.38  3.000
 IDS  H2   C2  O2   110.46  3.000
 IDS  H2   C2  C3   109.41  3.000
 IDS  O2   C2  C3   112.15  3.000
 IDS  H2   C2  C1   109.69  3.000
 IDS  O2   C2  C1   105.22  3.000
 IDS  C3   C2  C1   109.82  3.000
 IDS  H3   C3  O3   110.74  3.000
 IDS  H3   C3  C4   108.07  3.000
 IDS  O3   C3  C4   107.66  3.000
 IDS  H3   C3  C2   107.28  3.000
 IDS  O3   C3  C2   113.97  3.000
 IDS  C4   C3  C2   108.97  3.000
 IDS  H4   C4  O4   110.91  3.000
 IDS  H4   C4  C5   106.61  3.000
 IDS  O4   C4  C5   113.47  3.000
 IDS  H4   C4  C3   106.69  3.000
 IDS  O4   C4  C3   108.24  3.000
 IDS  C5   C4  C3   110.71  3.000
 IDS  H5   C5  O5   109.76  3.000
 IDS  H5   C5  C6   105.56  3.000
 IDS  O5   C5  C6   109.81  3.000
 IDS  H5   C5  C4   107.38  3.000
 IDS  O5   C5  C4   110.50  3.000
 IDS  C6   C5  C4   113.65  3.000
 IDS  O6B  C6  O6A  127.20  3.000
 IDS  O6B  C6  C5   117.82  3.000
 IDS  O6A  C6  C5   114.94  3.000
 IDS  HO1  O1  C1   108.89  3.000
 IDS  S    O2  C2   121.06  3.000
 IDS  HO3  O3  C3   110.61  3.000
 IDS  HO4  O4  C4   103.15  3.000
 IDS  C5   O5  C1   113.89  3.000
 IDS  O3S  S   O2S  113.46  3.000
 IDS  O3S  S   O1S  113.74  3.000
 IDS  O2S  S   O1S  115.67  3.000
 IDS  O3S  S   O2   104.55  3.000
 IDS  O2S  S   O2   106.51  3.000
 IDS  O1S  S   O2   101.14  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
 IDS  Var_01  O1S  S  O2  C2  -166.01  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
 IDS  chir_01  C1  C2  O1  O5  positiv
 IDS  chir_02  C2  O2  C3  C1  positiv
 IDS  chir_03  C3  O3  C2  C4  positiv
 IDS  chir_04  C4  O4  C3  C5  negativ
 IDS  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
 IDS  plan-1  C5   0.020
 IDS  plan-1  C6   0.020
 IDS  plan-1  O6A  0.020
 IDS  plan-1  O6B  0.020

