# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 16:21:08 2020
#   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
 2SI  2SI  '2-O-sulfo-alpha-L-idopyranuronic acid'  L-peptide  25  17  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_2SI
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
 2SI  C1    C  CH1    0   0.240   3.6867  -2.9075   0.2053
 2SI  C2    C  CH1    0  -0.037   3.8673  -2.9585   1.7227
 2SI  C3    C  CH1    0  -0.016   3.3541  -1.6733   2.3875
 2SI  C4    C  CH1    0   0.026   1.9574  -1.2876   1.8814
 2SI  C5    C  CH1    0  -0.163   1.9041  -1.3363   0.3553
 2SI  C6    C  C      0   0.451   0.4863  -1.1668  -0.2470
 2SI  O1    O  OH1    0  -0.677   4.6166  -1.9787  -0.2787
 2SI  O2    O  OC2    0  -0.612   3.1368  -4.0877   2.1735
 2SI  O3    O  OH1    0  -0.681   4.2746  -0.6168   2.2094
 2SI  O5    O  O2     0  -0.503   2.3769  -2.5845  -0.1493
 2SI  O61   O  OC    -1  -0.606  -0.4922  -1.3751   0.5153
 2SI  O62   O  O      0  -0.575   0.4305  -0.8531  -1.4409
 2SI  S     S  S      0   1.570   3.8706  -5.0930   3.2424
 2SI  O1S   O  OS     0  -0.743   5.0919  -5.5564   2.5773
 2SI  O2S   O  OS     0  -0.740   4.1281  -4.2898   4.4409
 2SI  O3S   O  OS    -1  -0.734   2.8385  -6.1142   3.4003
 2SI  O4    O  OH1    0  -0.704   1.0077  -2.1276   2.4776
 2SI  H1    H  HCH1   0   0.241   3.8643  -3.9014  -0.2213
 2SI  H2    H  HCH1   0   0.255   4.9365  -3.0681   1.9387
 2SI  H3    H  HCH1   0   0.248   3.2945  -1.8486   3.4652
 2SI  H4    H  HCH1   0   0.196   1.7943  -0.2339   2.1667
 2SI  H5    H  HCH1   0   0.212   2.5179  -0.5140  -0.0341
 2SI  H1O1  H  HOH1   0   0.468   4.5517  -1.9337  -1.2399
 2SI  H3O1  H  HOH1   0   0.446   4.5365  -0.5820   1.2818
 2SI  H4O1  H  HOH1   0   0.438   0.2081  -1.9782   1.9217

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
 2SI  C1  C2    single  1.529  0.020  1.529
 2SI  C1  O1    single  1.401  0.020  1.401
 2SI  C1  O5    single  1.395  0.020  1.395
 2SI  C1  H1    single  0.970  0.020  1.090
 2SI  C2  C3    single  1.535  0.020  1.535
 2SI  C2  O2    single  1.418  0.020  1.418
 2SI  C2  H2    single  0.970  0.020  1.090
 2SI  C3  C4    single  1.535  0.020  1.535
 2SI  C3  O3    single  1.412  0.020  1.412
 2SI  C3  H3    single  0.970  0.020  1.090
 2SI  C4  C5    single  1.528  0.020  1.528
 2SI  C4  O4    single  1.401  0.020  1.401
 2SI  C4  H4    single  0.970  0.020  1.090
 2SI  C5  C6    single  1.550  0.020  1.550
 2SI  C5  O5    single  1.427  0.020  1.427
 2SI  C5  H5    single  0.970  0.020  1.090
 2SI  C6  O61   deloc   1.258  0.020  1.258
 2SI  C6  O62   deloc   1.236  0.020  1.236
 2SI  O1  H1O1  single  0.850  0.020  0.980
 2SI  O2  S     single  1.641  0.020  1.641
 2SI  O3  H3O1  single  0.850  0.020  0.980
 2SI  S   O1S   deloc   1.466  0.020  1.466
 2SI  S   O2S   deloc   1.466  0.020  1.466
 2SI  S   O3S   deloc   1.460  0.020  1.460
 2SI  O4  H4O1  single  0.850  0.020  0.980

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
 2SI  H1    C1  O5   105.26  3.000
 2SI  H1    C1  O1   111.06  3.000
 2SI  O5    C1  O1   112.46  3.000
 2SI  H1    C1  C2   109.68  3.000
 2SI  O5    C1  C2   111.77  3.000
 2SI  O1    C1  C2   106.66  3.000
 2SI  H2    C2  O2   111.11  3.000
 2SI  H2    C2  C3   108.93  3.000
 2SI  O2    C2  C3   110.89  3.000
 2SI  H2    C2  C1   108.31  3.000
 2SI  O2    C2  C1   106.32  3.000
 2SI  C3    C2  C1   111.24  3.000
 2SI  H3    C3  O3   106.24  3.000
 2SI  H3    C3  C4   108.40  3.000
 2SI  O3    C3  C4   111.31  3.000
 2SI  H3    C3  C2   108.11  3.000
 2SI  O3    C3  C2   110.71  3.000
 2SI  C4    C3  C2   111.83  3.000
 2SI  H4    C4  O4   111.24  3.000
 2SI  H4    C4  C5   106.47  3.000
 2SI  O4    C4  C5   112.48  3.000
 2SI  H4    C4  C3   106.81  3.000
 2SI  O4    C4  C3   109.02  3.000
 2SI  C5    C4  C3   110.68  3.000
 2SI  H5    C5  O5   110.15  3.000
 2SI  H5    C5  C6   106.96  3.000
 2SI  O5    C5  C6   105.15  3.000
 2SI  H5    C5  C4   108.13  3.000
 2SI  O5    C5  C4   111.69  3.000
 2SI  C6    C5  C4   114.62  3.000
 2SI  O62   C6  O61  126.33  3.000
 2SI  O62   C6  C5   116.40  3.000
 2SI  O61   C6  C5   117.26  3.000
 2SI  H1O1  O1  C1   109.31  3.000
 2SI  S     O2  C2   117.68  3.000
 2SI  H3O1  O3  C3   108.98  3.000
 2SI  C5    O5  C1   115.07  3.000
 2SI  O3S   S   O2S  114.77  3.000
 2SI  O3S   S   O1S  114.63  3.000
 2SI  O2S   S   O1S  113.45  3.000
 2SI  O3S   S   O2   100.53  3.000
 2SI  O2S   S   O2   106.00  3.000
 2SI  O1S   S   O2   105.71  3.000
 2SI  H4O1  O4  C4   102.66  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
 2SI  Var_01  O1S  S  O2  C2  -58.35  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
 2SI  chir_01  C1  C2  O1  O5  positiv
 2SI  chir_02  C2  O2  C3  C1  positiv
 2SI  chir_03  C3  O3  C2  C4  positiv
 2SI  chir_04  C4  O4  C3  C5  negativ
 2SI  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
 2SI  plan-1  C5   0.020
 2SI  plan-1  C6   0.020
 2SI  plan-1  O61  0.020
 2SI  plan-1  O62  0.020

