# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 19:46:00 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: 4-deoxy-2-O-sulfo-beta-D-erythro-hex-4-enopyranuronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1OC(=C[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
 IXD  IXD  '4-deoxy-2-O-sulfo-beta-D-erythro-hex-4-enopyranuronic acid'  D-saccharide  22  16  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IXD
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
 IXD  S    S  S      0   1.569  -2.9434   0.2316   0.4584
 IXD  C1   C  CH1    0   0.272   0.4591  -0.8032  -0.9594
 IXD  C2   C  CH1    0  -0.039  -0.3652   0.0694  -0.0188
 IXD  O2   O  OC2    0  -0.620  -1.6630   0.1666  -0.5704
 IXD  C3   C  CH1    0   0.006   0.3002   1.4329   0.1191
 IXD  O3   O  OH1    0  -0.667   0.0351   2.1707  -1.0620
 IXD  C4   C  C1     0  -0.403   1.7636   1.2290   0.3564
 IXD  O1   O  OH1    0  -0.649  -0.1340  -2.0347  -1.0880
 IXD  C5   C  C      0   0.174   2.3865   0.0759   0.1004
 IXD  O5   O  O2     0  -0.482   1.7570  -1.0022  -0.4154
 IXD  C6   C  C      0   0.377   3.8724  -0.1579   0.3714
 IXD  O1S  O  OS    -1  -0.736  -2.7662   1.4555   1.2444
 IXD  O2S  O  OS     0  -0.734  -4.0451   0.2743  -0.4992
 IXD  O3S  O  OS     0  -0.739  -2.8725  -0.9920   1.2598
 IXD  O61  O  OC    -1  -0.593   4.3208  -1.2648   0.0338
 IXD  O62  O  O      0  -0.588   4.4845   0.7864   0.9012
 IXD  H1   H  HCH1   0   0.209   0.5731  -0.2963  -1.9291
 IXD  H3   H  HCH1   0   0.223  -0.1318   1.9467   0.9864
 IXD  HO3  H  HOH1   0   0.449   0.6424   2.9166  -1.0862
 IXD  H4   H  H      0   0.253   2.3431   2.0455   0.7645
 IXD  HO1  H  HOH1   0   0.466   0.1854  -2.4627  -1.8891
 IXD  H2   H  HCH1   0   0.254  -0.3832  -0.4138   0.9665

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
 IXD  O2S  S    deloc   1.460  0.020  1.460
 IXD  O3S  S    deloc   1.464  0.020  1.464
 IXD  S    O1S  deloc   1.465  0.020  1.465
 IXD  S    O2   single  1.644  0.020  1.644
 IXD  C1   O5   single  1.421  0.020  1.421
 IXD  C1   C2   single  1.525  0.020  1.525
 IXD  C1   O1   single  1.373  0.020  1.373
 IXD  C1   H1   single  0.970  0.020  1.090
 IXD  O2   C2   single  1.414  0.020  1.414
 IXD  O1   HO1  single  0.850  0.020  0.980
 IXD  C2   C3   single  1.523  0.020  1.523
 IXD  C3   C4   single  1.496  0.020  1.496
 IXD  C3   O3   single  1.418  0.020  1.418
 IXD  C3   H3   single  0.970  0.020  1.090
 IXD  O3   HO3  single  0.850  0.020  0.980
 IXD  C5   C4   double  1.335  0.020  1.335
 IXD  C4   H4   single  0.930  0.020  1.080
 IXD  C2   H2   single  0.970  0.020  1.090
 IXD  O5   C5   single  1.351  0.020  1.351
 IXD  C5   C6   single  1.528  0.020  1.528
 IXD  C6   O62  deloc   1.244  0.020  1.244
 IXD  C6   O61  deloc   1.241  0.020  1.241

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
 IXD  O3S  S   O2S  114.82  3.000
 IXD  O3S  S   O1S  113.48  3.000
 IXD  O2S  S   O1S  114.74  3.000
 IXD  O1S  S   O2   105.94  3.000
 IXD  O3S  S   O2   105.77  3.000
 IXD  O2S  S   O2   100.28  3.000
 IXD  H1   C1  O5   107.89  3.000
 IXD  H1   C1  O1   112.06  3.000
 IXD  O5   C1  O1   107.74  3.000
 IXD  H1   C1  C2   109.64  3.000
 IXD  O1   C1  C2   109.73  3.000
 IXD  O5   C1  C2   109.73  3.000
 IXD  H2   C2  C3   108.66  3.000
 IXD  H2   C2  O2   111.44  3.000
 IXD  C3   C2  O2   112.01  3.000
 IXD  H2   C2  C1   108.10  3.000
 IXD  C3   C2  C1   109.38  3.000
 IXD  O2   C2  C1   107.15  3.000
 IXD  C2   O2  S    118.27  3.000
 IXD  H3   C3  C4   108.89  3.000
 IXD  H3   C3  O3   109.96  3.000
 IXD  C4   C3  O3   112.70  3.000
 IXD  H3   C3  C2   108.59  3.000
 IXD  O3   C3  C2   107.98  3.000
 IXD  C4   C3  C2   108.64  3.000
 IXD  HO3  O3  C3   107.84  3.000
 IXD  H4   C4  C5   118.33  3.000
 IXD  H4   C4  C3   118.76  3.000
 IXD  C5   C4  C3   122.91  3.000
 IXD  HO1  O1  C1   109.47  3.000
 IXD  C6   C5  O5   113.49  3.000
 IXD  C6   C5  C4   123.48  3.000
 IXD  O5   C5  C4   123.03  3.000
 IXD  C5   O5  C1   117.38  3.000
 IXD  O62  C6  O61  127.97  3.000
 IXD  O61  C6  C5   116.07  3.000
 IXD  O62  C6  C5   115.96  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
 IXD  Var_01  C4   C5  O5  C1    13.40  30.0  1
 IXD  Var_02  O5   C5  C4  C3     1.10  30.0  1
 IXD  Var_03  O62  C6  C5  C4     2.53  30.0  2
 IXD  Var_04  O2S  S   O2  C2  -178.03  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
 IXD  chir_01  C1  O5  C2  O1  positiv
 IXD  chir_02  C2  O2  C1  C3  negativ
 IXD  chir_03  C3  O3  C4  C2  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
 IXD  plan-1  C5   0.020
 IXD  plan-1  C6   0.020
 IXD  plan-1  O61  0.020
 IXD  plan-1  O62  0.020

