# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 23:27:15 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: [(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4-bis(oxidanyl)-5-oxidanylsulfanyloxy-oxan-3-yl] hydrogen sulfate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](O)[C@H](O[S](O)(=O)=O)[C@@H](O)[C@@H]1OSO
#
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
 5TH  5TH  '[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4-bis(oxidanyl)-5-oxidanylsulfanyloxy-oxan-3-yl] hydrogen sulfate'  D-saccharide  29  18  .  2023-02-15  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_5TH
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
 5TH  C1   C  CH1    0   0.244   0.6480   1.5921  -0.2514
 5TH  C2   C  CH1    0  -0.039   0.7485   0.0949   0.0126
 5TH  O2   O  OC2    0  -0.626   1.8502  -0.4632  -0.6846
 5TH  C3   C  CH1    0   0.022  -0.5079  -0.6418  -0.4416
 5TH  C4   C  CH1    0   0.020  -1.7368   0.0110   0.1827
 5TH  C5   C  CH1    0  -0.009  -1.7262   1.5259  -0.0531
 5TH  C6   C  CH2    0  -0.157  -2.8345   2.2129   0.7205
 5TH  O3   O  OH1    0  -0.680  -0.4501  -1.9929  -0.0274
 5TH  O4   O  O2     0  -0.589  -2.9485  -0.4688  -0.4050
 5TH  O5   O  O2     0  -0.499  -0.5019   2.0813   0.3883
 5TH  O11  O  OH1    0  -0.669  -2.8248   3.5814   0.3947
 5TH  S1   S  S      0   1.567   3.1835  -0.8837   0.1972
 5TH  S2   S  S2     0   0.515  -3.5296  -1.9173   0.1240
 5TH  O7   O  OS    -1  -0.734   2.7408  -1.9880   1.0516
 5TH  O8   O  OS     0  -0.724   4.1017  -1.2647  -0.8701
 5TH  O9   O  OS     0  -0.731   3.5560   0.3233   0.9380
 5TH  O07  O  OH1    0  -0.750  -2.8339  -3.0069  -0.8750
 5TH  H1   H  HCH1   0   0.243   1.4820   2.1101   0.2330
 5TH  H3   H  HCH1   0   0.262   0.8491  -0.0425   1.0960
 5TH  H4   H  HCH1   0   0.239  -0.5953  -0.5729  -1.5347
 5TH  H5   H  HCH1   0   0.244  -1.7391  -0.1937   1.2623
 5TH  H6   H  HCH1   0   0.235  -1.8721   1.7138  -1.1253
 5TH  H7   H  HCH2   0   0.214  -3.7875   1.7432   0.4572
 5TH  H8   H  HCH2   0   0.198  -2.6764   2.0454   1.7952
 5TH  H9   H  HOH1   0   0.463   0.3771  -2.3785  -0.3407
 5TH  H10  H  HOH1   0   0.457  -3.5770   3.9948   0.8273
 5TH  H11  H  HOH1   0   0.480  -1.8942  -3.0743  -0.6130
 5TH  O1   O  OH1    0  -0.661   0.6401   1.8031  -1.6212
 5TH  HO1  H  HOH1   0   0.466   0.7902   2.7382  -1.7974

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
 5TH  O9   S1   deloc   1.464  0.020  1.464
 5TH  O8   S1   deloc   1.459  0.020  1.459
 5TH  O3   C3   single  1.414  0.020  1.414
 5TH  S1   O7   deloc   1.465  0.020  1.465
 5TH  S1   O2   single  1.653  0.020  1.653
 5TH  C2   C3   single  1.526  0.020  1.526
 5TH  C2   C1   single  1.524  0.020  1.524
 5TH  C2   O2   single  1.418  0.020  1.418
 5TH  C4   O4   single  1.430  0.020  1.430
 5TH  C4   C3   single  1.525  0.020  1.525
 5TH  C4   C5   single  1.533  0.020  1.533
 5TH  C6   O11  single  1.407  0.020  1.407
 5TH  C6   C5   single  1.516  0.020  1.516
 5TH  O4   S2   single  1.648  0.020  1.648
 5TH  C1   O5   single  1.404  0.020  1.404
 5TH  C5   O5   single  1.415  0.020  1.415
 5TH  S2   O07  single  1.634  0.020  1.634
 5TH  C1   H1   single  0.970  0.020  1.090
 5TH  C2   H3   single  0.970  0.020  1.090
 5TH  C3   H4   single  0.970  0.020  1.090
 5TH  C4   H5   single  0.970  0.020  1.090
 5TH  C5   H6   single  0.970  0.020  1.090
 5TH  C6   H7   single  0.970  0.020  1.090
 5TH  C6   H8   single  0.970  0.020  1.090
 5TH  O3   H9   single  0.850  0.020  0.980
 5TH  O11  H10  single  0.850  0.020  0.980
 5TH  O07  H11  single  0.850  0.020  0.980
 5TH  C1   O1   single  1.386  0.020  1.386
 5TH  O1   HO1  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
 5TH  O1   C1   H1   111.69  3.000
 5TH  O1   C1   O5   113.12  3.000
 5TH  H1   C1   O5   104.92  3.000
 5TH  O1   C1   C2   108.73  3.000
 5TH  H1   C1   C2   109.76  3.000
 5TH  O5   C1   C2   108.51  3.000
 5TH  H3   C2   C3   108.01  3.000
 5TH  H3   C2   O2   111.41  3.000
 5TH  C3   C2   O2   107.66  3.000
 5TH  H3   C2   C1   107.48  3.000
 5TH  O2   C2   C1   110.66  3.000
 5TH  C3   C2   C1   111.63  3.000
 5TH  S1   O2   C2   117.68  3.000
 5TH  H4   C3   O3   110.76  3.000
 5TH  H4   C3   C4   108.44  3.000
 5TH  O3   C3   C4   108.78  3.000
 5TH  H4   C3   C2   109.36  3.000
 5TH  C4   C3   C2   109.57  3.000
 5TH  O3   C3   C2   109.90  3.000
 5TH  H5   C4   O4   109.85  3.000
 5TH  H5   C4   C5   109.58  3.000
 5TH  O4   C4   C5   105.92  3.000
 5TH  H5   C4   C3   108.92  3.000
 5TH  C5   C4   C3   110.76  3.000
 5TH  O4   C4   C3   111.78  3.000
 5TH  H6   C5   O5   110.63  3.000
 5TH  H6   C5   C6   108.87  3.000
 5TH  O5   C5   C6   107.19  3.000
 5TH  H6   C5   C4   108.56  3.000
 5TH  O5   C5   C4   110.23  3.000
 5TH  C6   C5   C4   111.36  3.000
 5TH  H8   C6   H7   107.16  3.000
 5TH  H8   C6   O11  111.94  3.000
 5TH  H7   C6   O11  111.58  3.000
 5TH  H8   C6   C5   108.95  3.000
 5TH  H7   C6   C5   108.62  3.000
 5TH  O11  C6   C5   108.52  3.000
 5TH  H9   O3   C3   108.76  3.000
 5TH  S2   O4   C4   117.51  3.000
 5TH  C5   O5   C1   115.46  3.000
 5TH  H10  O11  C6   107.99  3.000
 5TH  O9   S1   O8   115.17  3.000
 5TH  O8   S1   O7   114.84  3.000
 5TH  O9   S1   O7   113.78  3.000
 5TH  O7   S1   O2   105.02  3.000
 5TH  O8   S1   O2   100.59  3.000
 5TH  O9   S1   O2   105.39  3.000
 5TH  O07  S2   O4   103.87  3.000
 5TH  H11  O07  S2   106.94  3.000
 5TH  HO1  O1   C1   109.13  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
 5TH  Var_01  O9  S1  O2  C2  -54.26  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
 5TH  chir_01  C1  C2  O5  O1  positiv
 5TH  chir_02  C2  O2  C3  C1  positiv
 5TH  chir_03  C3  O3  C2  C4  positiv
 5TH  chir_04  C4  O4  C3  C5  negativ
 5TH  chir_05  C5  O5  C4  C6  negativ

