# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 07:54:50 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: [(2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-4,6-bis(oxidanyl)-5-sulfooxy-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]1O[S](O)(=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
 5LS  5LS  '[(2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-4,6-bis(oxidanyl)-5-sulfooxy-oxan-3-yl] hydrogen sulfate'  D-saccharide  30  20  .  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_5LS
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
 5LS  C1   C  CH1    0   0.247   1.2117  -1.7741   0.1308
 5LS  O1   O  OH1    0  -0.663   1.3291  -2.1564   1.4600
 5LS  C2   C  CH1    0  -0.042   1.3194  -0.2553   0.0465
 5LS  O2   O  OC2    0  -0.627   2.4756   0.2109   0.7250
 5LS  C3   C  CH1    0   0.022   0.1094   0.4282   0.6784
 5LS  C4   C  CH1    0   0.014  -1.1664  -0.1192   0.0494
 5LS  C5   C  CH1    0  -0.008  -1.1739  -1.6492   0.1521
 5LS  C6   C  CH2    0  -0.163  -2.3541  -2.2804  -0.5549
 5LS  O3   O  OH1    0  -0.655   0.1511   1.8154   0.4858
 5LS  O4   O  OC2    0  -0.628  -2.2749   0.4054   0.7648
 5LS  O5   O  O2     0  -0.502  -0.0016  -2.1737  -0.4499
 5LS  O11  O  OH1    0  -0.672  -2.2993  -3.6736  -0.3500
 5LS  S1   S  S      0   1.568   3.7936   0.6123  -0.1821
 5LS  S2   S  S      0   1.564  -3.3928   1.3389  -0.0106
 5LS  O7   O  OS    -1  -0.736   3.3674   1.7427  -1.0094
 5LS  O8   O  OS     0  -0.729   4.7479   0.9511   0.8690
 5LS  O9   O  OS     0  -0.733   4.1194  -0.5907  -0.9513
 5LS  O07  O  OS    -1  -0.732  -4.1579   0.4212  -0.8597
 5LS  O08  O  OS     0  -0.736  -4.1314   1.8570   1.1386
 5LS  O09  O  OS     0  -0.727  -2.6460   2.3417  -0.7676
 5LS  H1   H  HCH1   0   0.237   1.9856  -2.2376  -0.4894
 5LS  H2   H  HOH1   0   0.463   1.4567  -3.1103   1.5012
 5LS  H3   H  HCH1   0   0.253   1.3471   0.0163  -1.0158
 5LS  H4   H  HCH1   0   0.216   0.0864   0.1823   1.7513
 5LS  H5   H  HCH1   0   0.240  -1.1968   0.1720  -1.0089
 5LS  H6   H  HCH1   0   0.225  -1.2173  -1.9268   1.2145
 5LS  H7   H  HCH2   0   0.215  -3.2746  -1.8501  -0.1542
 5LS  H8   H  HCH2   0   0.191  -2.3171  -2.0226  -1.6223
 5LS  H13  H  HOH1   0   0.445   0.9861   2.1392   0.8404
 5LS  H9   H  HOH1   0   0.455  -3.1004  -4.0570  -0.7172

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
 5LS  C1   O5   single  1.403  0.020  1.403
 5LS  C1   O1   single  1.388  0.020  1.388
 5LS  C1   C2   single  1.525  0.020  1.525
 5LS  C2   O2   single  1.419  0.020  1.419
 5LS  C2   C3   single  1.527  0.020  1.527
 5LS  O2   S1   single  1.650  0.020  1.650
 5LS  C3   C4   single  1.524  0.020  1.524
 5LS  C3   O3   single  1.401  0.020  1.401
 5LS  C4   C5   single  1.533  0.020  1.533
 5LS  C4   O4   single  1.420  0.020  1.420
 5LS  C5   C6   single  1.514  0.020  1.514
 5LS  C5   O5   single  1.418  0.020  1.418
 5LS  C6   O11  single  1.409  0.020  1.409
 5LS  O4   S2   single  1.650  0.020  1.650
 5LS  S1   O8   deloc   1.460  0.020  1.460
 5LS  S1   O9   deloc   1.465  0.020  1.465
 5LS  S1   O7   deloc   1.464  0.020  1.464
 5LS  S2   O09  deloc   1.462  0.020  1.462
 5LS  S2   O08  deloc   1.461  0.020  1.461
 5LS  S2   O07  deloc   1.466  0.020  1.466
 5LS  C1   H1   single  0.970  0.020  1.090
 5LS  O1   H2   single  0.850  0.020  0.980
 5LS  C2   H3   single  0.970  0.020  1.090
 5LS  C3   H4   single  0.970  0.020  1.090
 5LS  C4   H5   single  0.970  0.020  1.090
 5LS  C5   H6   single  0.970  0.020  1.090
 5LS  C6   H7   single  0.970  0.020  1.090
 5LS  C6   H8   single  0.970  0.020  1.090
 5LS  O3   H13  single  0.850  0.020  0.980
 5LS  O11  H9   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
 5LS  H1   C1   O5   104.85  3.000
 5LS  H1   C1   C2   109.90  3.000
 5LS  O5   C1   C2   108.77  3.000
 5LS  H1   C1   O1   111.48  3.000
 5LS  C2   C1   O1   108.74  3.000
 5LS  O5   C1   O1   113.02  3.000
 5LS  H2   O1   C1   108.96  3.000
 5LS  H3   C2   C3   108.06  3.000
 5LS  H3   C2   O2   111.16  3.000
 5LS  C3   C2   O2   107.50  3.000
 5LS  H3   C2   C1   107.58  3.000
 5LS  C3   C2   C1   111.53  3.000
 5LS  O2   C2   C1   111.00  3.000
 5LS  S1   O2   C2   117.90  3.000
 5LS  H4   C3   O3   110.83  3.000
 5LS  H4   C3   C4   107.73  3.000
 5LS  O3   C3   C4   108.89  3.000
 5LS  H4   C3   C2   108.66  3.000
 5LS  O3   C3   C2   111.28  3.000
 5LS  C4   C3   C2   109.38  3.000
 5LS  H5   C4   O4   111.47  3.000
 5LS  H5   C4   C5   109.21  3.000
 5LS  O4   C4   C5   109.33  3.000
 5LS  H5   C4   C3   109.01  3.000
 5LS  O4   C4   C3   108.23  3.000
 5LS  C5   C4   C3   109.56  3.000
 5LS  H6   C5   O5   110.46  3.000
 5LS  H6   C5   C6   108.38  3.000
 5LS  O5   C5   C6   106.98  3.000
 5LS  H6   C5   C4   108.48  3.000
 5LS  O5   C5   C4   109.66  3.000
 5LS  C6   C5   C4   112.87  3.000
 5LS  H8   C6   H7   107.00  3.000
 5LS  H8   C6   O11  111.83  3.000
 5LS  H7   C6   O11  111.65  3.000
 5LS  H8   C6   C5   109.24  3.000
 5LS  H7   C6   C5   108.76  3.000
 5LS  O11  C6   C5   108.30  3.000
 5LS  H13  O3   C3   107.94  3.000
 5LS  S2   O4   C4   120.08  3.000
 5LS  C5   O5   C1   115.70  3.000
 5LS  H9   O11  C6   107.84  3.000
 5LS  O9   S1   O8   115.05  3.000
 5LS  O9   S1   O7   113.71  3.000
 5LS  O8   S1   O7   114.71  3.000
 5LS  O7   S1   O2   105.43  3.000
 5LS  O9   S1   O2   105.47  3.000
 5LS  O8   S1   O2   100.54  3.000
 5LS  O09  S2   O08  114.99  3.000
 5LS  O08  S2   O07  114.44  3.000
 5LS  O09  S2   O07  113.34  3.000
 5LS  O07  S2   O4   105.76  3.000
 5LS  O08  S2   O4    99.99  3.000
 5LS  O09  S2   O4   106.58  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
 5LS  Var_01  O8   S1  O2  C2  -176.85  30.0  3
 5LS  Var_02  O09  S2  O4  C4   -48.51  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
 5LS  chir_01  C1  O5  O1  C2  positiv
 5LS  chir_02  C2  O2  C3  C1  positiv
 5LS  chir_03  C3  O3  C2  C4  positiv
 5LS  chir_04  C4  O4  C3  C5  negativ
 5LS  chir_05  C5  O5  C4  C6  negativ

