# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 03:01:34 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: [(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-2,5-bis(oxidanyl)-4-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](OSO)[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
 5TM  5TM  '[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-2,5-bis(oxidanyl)-4-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 PERFECT
;

data_comp_5TM
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
 5TM  C1   C  CH1    0   0.192  -0.5761  -1.6464   0.5647
 5TM  C2   C  CH1    0  -0.057   0.1575  -0.4826  -0.0977
 5TM  C3   C  CH1    0   0.038  -0.6725   0.7888  -0.0082
 5TM  C4   C  CH1    0  -0.038  -2.0595   0.5530  -0.5888
 5TM  C5   C  CH1    0  -0.010  -2.6970  -0.6790   0.0688
 5TM  C6   C  CH2    0  -0.150  -3.9990  -1.0571  -0.6040
 5TM  O2   O  OC2    0  -0.543   1.4129  -0.3142   0.5381
 5TM  O3   O  O2     0  -0.508  -0.0110   1.7811  -0.7836
 5TM  O4   O  OH1    0  -0.658  -2.8187   1.7148  -0.3605
 5TM  O5   O  O2     0  -0.434  -1.8311  -1.7975  -0.0388
 5TM  O6   O  OH1    0  -0.664  -4.5800  -2.1295   0.0973
 5TM  O1S  O  OS    -1  -0.942   3.0788   1.1692  -0.5735
 5TM  O2S  O  OS     0  -0.638   3.7500  -0.8455   0.6447
 5TM  O3S  O  OS     0  -0.703   2.5996  -1.0350  -1.5342
 5TM  O3X  O  OH1    0  -0.775   1.5994   2.8155   0.9513
 5TM  S    S  S      0   1.526   2.8199  -0.2607  -0.3131
 5TM  S'   S  S2     0   0.468   0.3910   3.2082  -0.0795
 5TM  O1   O  OH1    0  -0.673  -0.6554  -1.3977   1.9270
 5TM  H1   H  HCH1   0   0.302  -0.0452  -2.5827   0.3558
 5TM  H2   H  HCH1   0   0.324   0.2849  -0.7445  -1.1525
 5TM  H3   H  HCH1   0   0.311  -0.7711   1.1133   1.0351
 5TM  H4   H  HCH1   0   0.254  -1.9498   0.3550  -1.6651
 5TM  H5   H  HCH1   0   0.258  -2.8988  -0.4461   1.1230
 5TM  H6   H  HCH2   0   0.168  -4.6537  -0.1778  -0.6074
 5TM  H7   H  HCH2   0   0.163  -3.7997  -1.3159  -1.6536
 5TM  H8   H  HOH1   0   0.446  -3.4039   1.8586  -1.1085
 5TM  H9   H  HOH1   0   0.468  -5.4257  -2.3304  -0.3135
 5TM  H10  H  HOH1   0   0.506   2.3275   2.3928   0.4411
 5TM  H11  H  HOH1   0   0.369  -0.9397  -2.1999   2.3789

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
 5TM  O3S  S    deloc   1.463  0.020  1.463
 5TM  O2S  S    deloc   1.458  0.020  1.458
 5TM  O1S  S    deloc   1.476  0.020  1.476
 5TM  S    O2   single  1.645  0.020  1.645
 5TM  O2   C2   single  1.417  0.020  1.417
 5TM  C2   C3   single  1.521  0.020  1.521
 5TM  C2   C1   single  1.527  0.020  1.527
 5TM  O4   C4   single  1.406  0.020  1.406
 5TM  C3   C4   single  1.522  0.020  1.522
 5TM  C3   O3   single  1.422  0.020  1.422
 5TM  C1   O5   single  1.401  0.020  1.401
 5TM  S'   O3   single  1.641  0.020  1.641
 5TM  S'   O3X  single  1.636  0.020  1.636
 5TM  C4   C5   single  1.535  0.020  1.535
 5TM  O5   C5   single  1.419  0.020  1.419
 5TM  C5   C6   single  1.513  0.020  1.513
 5TM  C6   O6   single  1.407  0.020  1.407
 5TM  C1   O1   single  1.387  0.020  1.387
 5TM  C1   H1   single  0.970  0.020  1.090
 5TM  C2   H2   single  0.970  0.020  1.090
 5TM  C3   H3   single  0.970  0.020  1.090
 5TM  C4   H4   single  0.970  0.020  1.090
 5TM  C5   H5   single  0.970  0.020  1.090
 5TM  C6   H6   single  0.970  0.020  1.090
 5TM  C6   H7   single  0.970  0.020  1.090
 5TM  O4   H8   single  0.850  0.020  0.980
 5TM  O6   H9   single  0.850  0.020  0.980
 5TM  O3X  H10  single  0.850  0.020  0.980
 5TM  O1   H11  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
 5TM  H1   C1   O1   111.58  3.000
 5TM  H1   C1   O5   105.05  3.000
 5TM  O1   C1   O5   113.03  3.000
 5TM  H1   C1   C2   109.61  3.000
 5TM  O1   C1   C2   108.47  3.000
 5TM  O5   C1   C2   109.02  3.000
 5TM  H2   C2   O2   110.96  3.000
 5TM  H2   C2   C3   108.68  3.000
 5TM  O2   C2   C3   110.96  3.000
 5TM  H2   C2   C1   106.96  3.000
 5TM  C3   C2   C1   110.45  3.000
 5TM  O2   C2   C1   108.76  3.000
 5TM  H3   C3   O3   110.72  3.000
 5TM  H3   C3   C4   109.07  3.000
 5TM  O3   C3   C4   108.90  3.000
 5TM  H3   C3   C2   110.62  3.000
 5TM  O3   C3   C2   107.29  3.000
 5TM  C4   C3   C2   110.20  3.000
 5TM  H4   C4   O4   111.19  3.000
 5TM  H4   C4   C5   108.42  3.000
 5TM  O4   C4   C5   111.67  3.000
 5TM  H4   C4   C3   108.08  3.000
 5TM  C5   C4   C3   109.84  3.000
 5TM  O4   C4   C3   107.58  3.000
 5TM  H5   C5   O5   110.62  3.000
 5TM  H5   C5   C6   108.76  3.000
 5TM  O5   C5   C6   107.12  3.000
 5TM  H5   C5   C4   108.49  3.000
 5TM  C6   C5   C4   111.55  3.000
 5TM  O5   C5   C4   110.29  3.000
 5TM  H7   C6   H6   107.11  3.000
 5TM  H7   C6   O6   111.80  3.000
 5TM  H6   C6   O6   111.48  3.000
 5TM  H7   C6   C5   109.11  3.000
 5TM  H6   C6   C5   108.35  3.000
 5TM  O6   C6   C5   108.91  3.000
 5TM  S    O2   C2   121.95  3.000
 5TM  S'   O3   C3   119.12  3.000
 5TM  H8   O4   C4   109.04  3.000
 5TM  C5   O5   C1   115.41  3.000
 5TM  H9   O6   C6   108.03  3.000
 5TM  H10  O3X  S'   108.83  3.000
 5TM  O3S  S    O2S  115.62  3.000
 5TM  O2S  S    O1S  113.12  3.000
 5TM  O3S  S    O1S  113.07  3.000
 5TM  O1S  S    O2   105.82  3.000
 5TM  O2S  S    O2   101.10  3.000
 5TM  O3S  S    O2   106.61  3.000
 5TM  O3X  S'   O3   104.03  3.000
 5TM  H11  O1   C1   109.16  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
 5TM  Var_01  O3S  S  O2  C2  -27.34  30.0  2

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

