# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 22:38:55 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: (2~{S},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-5-oxidanylsulfanyloxy-oxane-2,3,4-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](O)[C@H](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
 5TK  5TK  (2~{S},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-5-oxidanylsulfanyloxy-oxane-2,3,4-triol  D-saccharide  26  14  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_5TK
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
 5TK  SA   S  S2    0   0.526  -2.8866   0.8559   0.0600
 5TK  C1   C  CH1   0   0.222   2.5089  -0.0974  -0.1632
 5TK  C2   C  CH1   0  -0.017   1.8554   1.2540  -0.4615
 5TK  O2S  O  OH1   0  -0.732  -3.6508  -0.4444  -0.5877
 5TK  C3   C  CH1   0   0.018   0.5242   1.3700   0.2717
 5TK  C4   C  CH1   0   0.019  -0.3503   0.1826  -0.0883
 5TK  C5   C  CH1   0  -0.005   0.3816  -1.1336   0.1782
 5TK  C6   C  CH2   0  -0.159  -0.4103  -2.3242  -0.3216
 5TK  O2   O  OH1   0  -0.669   2.6589   2.3390  -0.0742
 5TK  O3   O  OH1   0  -0.666  -0.1722   2.5367  -0.0854
 5TK  O4   O  O2    0  -0.588  -1.5284   0.2156   0.7194
 5TK  O5   O  O2    0  -0.502   1.6217  -1.1320  -0.5075
 5TK  O1   O  OH1   0  -0.662   2.8831  -0.1277   1.1726
 5TK  H1   H  HCH1  0   0.236   3.3719  -0.2466  -0.8232
 5TK  H2   H  HCH1  0   0.232   1.6530   1.2788  -1.5412
 5TK  H3   H  HOH1  0   0.484  -4.1854  -0.8825   0.0893
 5TK  H4   H  HCH1  0   0.221   0.7115   1.3441   1.3557
 5TK  H5   H  HCH1  0   0.241  -0.6173   0.2403  -1.1521
 5TK  H6   H  HCH1  0   0.230   0.5363  -1.2420   1.2606
 5TK  H7   H  HCH2  0   0.211  -1.4107  -2.2865   0.1212
 5TK  H8   H  HCH2  0   0.196  -0.5353  -2.2390  -1.4102
 5TK  H9   H  HOH1  0   0.460   3.3192   2.4959  -0.7557
 5TK  H10  H  HOH1  0   0.453   0.3691   3.2940   0.1609
 5TK  H11  H  HOH1  0   0.457  -0.2978  -4.2487  -0.1689
 5TK  H12  H  HOH1  0   0.463   3.4651  -0.8810   1.3198
 5TK  O6   O  OH1   0  -0.671   0.2718  -3.5023   0.0361

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
 5TK  C1   C2   single  1.530  0.020  1.530
 5TK  C1   O5   single  1.406  0.020  1.406
 5TK  C2   O2   single  1.405  0.020  1.405
 5TK  C2   C3   single  1.524  0.020  1.524
 5TK  O6   C6   single  1.408  0.020  1.408
 5TK  O3   C3   single  1.405  0.020  1.405
 5TK  O5   C5   single  1.417  0.020  1.417
 5TK  C6   C5   single  1.515  0.020  1.515
 5TK  C3   C4   single  1.518  0.020  1.518
 5TK  C5   C4   single  1.529  0.020  1.529
 5TK  C4   O4   single  1.429  0.020  1.429
 5TK  O4   SA   single  1.640  0.020  1.640
 5TK  SA   O2S  single  1.641  0.020  1.641
 5TK  C1   O1   single  1.388  0.020  1.388
 5TK  C1   H1   single  0.970  0.020  1.090
 5TK  C2   H2   single  0.970  0.020  1.090
 5TK  O2S  H3   single  0.850  0.020  0.980
 5TK  C3   H4   single  0.970  0.020  1.090
 5TK  C4   H5   single  0.970  0.020  1.090
 5TK  C5   H6   single  0.970  0.020  1.090
 5TK  C6   H7   single  0.970  0.020  1.090
 5TK  C6   H8   single  0.970  0.020  1.090
 5TK  O2   H9   single  0.850  0.020  0.980
 5TK  O3   H10  single  0.850  0.020  0.980
 5TK  O6   H11  single  0.850  0.020  0.980
 5TK  O1   H12  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
 5TK  O4   SA   O2S  103.59  3.000
 5TK  H1   C1   O1   111.36  3.000
 5TK  H1   C1   O5   104.43  3.000
 5TK  O1   C1   O5   112.95  3.000
 5TK  H1   C1   C2   109.80  3.000
 5TK  O1   C1   C2   108.79  3.000
 5TK  O5   C1   C2   109.43  3.000
 5TK  H2   C2   O2   111.03  3.000
 5TK  H2   C2   C3   108.07  3.000
 5TK  O2   C2   C3   107.95  3.000
 5TK  H2   C2   C1   106.87  3.000
 5TK  C3   C2   C1   110.27  3.000
 5TK  O2   C2   C1   112.58  3.000
 5TK  H3   O2S  SA   109.87  3.000
 5TK  H4   C3   O3   110.75  3.000
 5TK  H4   C3   C4   108.25  3.000
 5TK  O3   C3   C4   107.68  3.000
 5TK  H4   C3   C2   108.88  3.000
 5TK  C4   C3   C2   109.24  3.000
 5TK  O3   C3   C2   111.96  3.000
 5TK  H5   C4   O4   110.23  3.000
 5TK  H5   C4   C5   109.29  3.000
 5TK  O4   C4   C5   108.42  3.000
 5TK  H5   C4   C3   109.19  3.000
 5TK  O4   C4   C3   108.84  3.000
 5TK  C5   C4   C3   110.86  3.000
 5TK  H6   C5   O5   110.71  3.000
 5TK  H6   C5   C6   108.73  3.000
 5TK  O5   C5   C6   107.38  3.000
 5TK  H6   C5   C4   108.90  3.000
 5TK  C6   C5   C4   111.64  3.000
 5TK  O5   C5   C4   109.48  3.000
 5TK  H8   C6   H7   107.10  3.000
 5TK  H8   C6   O6   111.82  3.000
 5TK  H7   C6   O6   111.65  3.000
 5TK  H8   C6   C5   108.99  3.000
 5TK  H7   C6   C5   108.49  3.000
 5TK  O6   C6   C5   108.70  3.000
 5TK  H9   O2   C2   108.87  3.000
 5TK  H10  O3   C3   108.03  3.000
 5TK  C4   O4   SA   117.69  3.000
 5TK  C5   O5   C1   115.76  3.000
 5TK  H12  O1   C1   109.09  3.000
 5TK  H11  O6   C6   107.98  3.000

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
 5TK  chir_01  C1  C2  O5  O1  positiv
 5TK  chir_02  C2  O2  C1  C3  negativ
 5TK  chir_03  C3  O3  C2  C4  positiv
 5TK  chir_04  C4  O4  C5  C3  positiv
 5TK  chir_05  C5  O5  C4  C6  negativ

