# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 05:23:52 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (2~{R},3~{S},4~{S},5~{S},6~{R})-2-(hydroxymethyl)-6-sulfanyl-oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](S)[C@@H](O)[C@@H](O)[C@@H]1O
#
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
 7K3  7K3  (2~{R},3~{S},4~{S},5~{S},6~{R})-2-(hydroxymethyl)-6-sulfanyl-oxane-3,4,5-triol  D-saccharide  24  12  .  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_7K3
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
 7K3  C7   C  CH1   0  -0.161  -0.3619  -1.3870   0.5178
 7K3  C9   C  CH1   0  -0.002   1.1211   0.3643  -0.1155
 7K3  C12  C  CH1   0   0.007  -1.5782  -0.4525   0.5312
 7K3  C13  C  CH2   0  -0.155   2.4293   0.9723   0.3437
 7K3  O17  O  OH1   0  -0.661  -1.7606   0.0850   1.8147
 7K3  C11  C  CH1   0   0.001  -1.3324   0.7023  -0.4367
 7K3  O16  O  OH1   0  -0.670  -2.3452   1.6765  -0.3843
 7K3  C10  C  CH1   0   0.031  -0.0101   1.3943  -0.1225
 7K3  O15  O  OH1   0  -0.675   0.2991   2.3608  -1.0977
 7K3  O14  O  OH1   0  -0.670   3.4447   0.0024   0.2431
 7K3  O8   O  O2    0  -0.458   0.8205  -0.7013   0.7668
 7K3  S1   S  S2    0  -0.264  -0.3518  -2.3288  -1.0659
 7K3  H1   H  HCH1  0   0.301  -0.4612  -2.1249   1.3154
 7K3  H2   H  HCH1  0   0.225   1.2456  -0.0232  -1.1377
 7K3  H3   H  HCH1  0   0.241  -2.4613  -1.0202   0.2070
 7K3  H4   H  HCH2  0   0.213   2.6410   1.8450  -0.2826
 7K3  H5   H  HCH2  0   0.195   2.3135   1.3366   1.3743
 7K3  H6   H  HOH1  0   0.458  -2.0479  -0.6189   2.4048
 7K3  H7   H  HCH1  0   0.228  -1.2558   0.2810  -1.4500
 7K3  H8   H  HOH1  0   0.459  -3.1029   1.3653  -0.8887
 7K3  H9   H  HCH1  0   0.214  -0.0757   1.8531   0.8755
 7K3  H10  H  HOH1  0   0.453  -0.4436   2.9716  -1.1515
 7K3  H11  H  HOH1  0   0.456   4.2833   0.4317   0.4330
 7K3  H12  H  HSH1  0   0.236   0.5329  -3.2528  -0.6776

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
 7K3  S1   C7   single  1.843  0.020  1.843
 7K3  C7   C12  single  1.534  0.020  1.534
 7K3  C7   O8   single  1.389  0.020  1.389
 7K3  C12  O17  single  1.403  0.020  1.403
 7K3  C12  C11  single  1.527  0.020  1.527
 7K3  O8   C9   single  1.416  0.020  1.416
 7K3  C9   C13  single  1.514  0.020  1.514
 7K3  C9   C10  single  1.530  0.020  1.530
 7K3  C11  O16  single  1.406  0.020  1.406
 7K3  C11  C10  single  1.525  0.020  1.525
 7K3  C13  O14  single  1.408  0.020  1.408
 7K3  C10  O15  single  1.407  0.020  1.407
 7K3  C7   H1   single  0.970  0.020  1.090
 7K3  C9   H2   single  0.970  0.020  1.090
 7K3  C12  H3   single  0.970  0.020  1.090
 7K3  C13  H4   single  0.970  0.020  1.090
 7K3  C13  H5   single  0.970  0.020  1.090
 7K3  O17  H6   single  0.850  0.020  0.980
 7K3  C11  H7   single  0.970  0.020  1.090
 7K3  O16  H8   single  0.850  0.020  0.980
 7K3  C10  H9   single  0.970  0.020  1.090
 7K3  O15  H10  single  0.850  0.020  0.980
 7K3  O14  H11  single  0.850  0.020  0.980
 7K3  S1   H12  single  1.200  0.020  1.300

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
 7K3  H1   C7   S1   106.45  3.000
 7K3  H1   C7   O8   106.27  3.000
 7K3  S1   C7   O8   113.68  3.000
 7K3  H1   C7   C12  109.48  3.000
 7K3  O8   C7   C12  111.87  3.000
 7K3  S1   C7   C12  108.86  3.000
 7K3  H2   C9   O8   109.75  3.000
 7K3  H2   C9   C10  108.46  3.000
 7K3  O8   C9   C10  110.65  3.000
 7K3  H2   C9   C13  108.99  3.000
 7K3  C10  C9   C13  111.71  3.000
 7K3  O8   C9   C13  107.26  3.000
 7K3  H3   C12  C11  109.46  3.000
 7K3  H3   C12  O17  111.30  3.000
 7K3  C11  C12  O17  108.12  3.000
 7K3  H3   C12  C7   108.66  3.000
 7K3  C11  C12  C7   109.12  3.000
 7K3  O17  C12  C7   110.15  3.000
 7K3  H5   C13  H4   107.01  3.000
 7K3  H5   C13  O14  111.80  3.000
 7K3  H4   C13  O14  111.65  3.000
 7K3  H5   C13  C9   109.05  3.000
 7K3  H4   C13  C9   108.28  3.000
 7K3  O14  C13  C9   108.96  3.000
 7K3  H6   O17  C12  108.62  3.000
 7K3  H7   C11  C10  107.64  3.000
 7K3  H7   C11  O16  110.47  3.000
 7K3  C10  C11  O16  107.60  3.000
 7K3  H7   C11  C12  107.79  3.000
 7K3  C10  C11  C12  110.62  3.000
 7K3  O16  C11  C12  112.61  3.000
 7K3  H8   O16  C11  108.88  3.000
 7K3  H9   C10  O15  110.80  3.000
 7K3  H9   C10  C11  108.92  3.000
 7K3  O15  C10  C11  111.06  3.000
 7K3  H9   C10  C9   108.70  3.000
 7K3  O15  C10  C9   107.65  3.000
 7K3  C11  C10  C9   109.67  3.000
 7K3  H10  O15  C10  107.75  3.000
 7K3  H11  O14  C13  107.91  3.000
 7K3  C9   O8   C7   116.14  3.000
 7K3  H12  S1   C7    96.16  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
 7K3  chir_01  C7   S1   C12  O8   positiv
 7K3  chir_02  C9   O8   C13  C10  positiv
 7K3  chir_03  C12  O17  C7   C11  positiv
 7K3  chir_04  C11  O16  C12  C10  positiv
 7K3  chir_05  C10  O15  C9   C11  positiv

