# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 00:11:06 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: [(2~{R},3~{R},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-5,6-bis(oxidanyl)-3-oxidanylsulfanyloxy-oxan-4-yl] hydrogen sulfate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](O)[C@H](O)[C@@H](O[S](O)(=O)=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
 5TJ  5TJ  '[(2~{R},3~{R},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-5,6-bis(oxidanyl)-3-oxidanylsulfanyloxy-oxan-4-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_5TJ
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
 5TJ  C1   C  CH1    0   0.214   0.4079   2.7572  -0.3368
 5TJ  C2   C  CH1    0   0.006  -0.5802   1.6812  -0.7978
 5TJ  O2   O  OH1    0  -0.656  -1.9130   2.0716  -0.6306
 5TJ  C3   C  CH1    0   0.006  -0.3482   0.4006  -0.0087
 5TJ  O3   O  OC2    0  -0.619  -1.1693  -0.6149  -0.5681
 5TJ  C4   C  CH1    0   0.020   1.1155  -0.0172  -0.1044
 5TJ  O4   O  O2     0  -0.590   1.3057  -1.0866   0.8156
 5TJ  C5   C  CH1    0  -0.005   2.0466   1.1388   0.2707
 5TJ  O6   O  O2     0  -0.500   1.7226   2.2885  -0.4886
 5TJ  C51  C  CH2    0  -0.158   3.4930   0.7999  -0.0244
 5TJ  O52  O  OH1    0  -0.669   4.3057   1.8500   0.4398
 5TJ  S3   S  S      0   1.594  -2.2062  -1.4945   0.3474
 5TJ  S4   S  S2     0   0.506   1.8968  -2.5273   0.2790
 5TJ  O33  O  OS     0  -0.747  -1.4271  -2.6495   0.8443
 5TJ  O32  O  OS    -1  -0.718  -2.6700  -0.6246   1.4240
 5TJ  O31  O  OS     0  -0.722  -3.2087  -1.8652  -0.6443
 5TJ  O41  O  OH1    0  -0.764   0.7101  -3.1197  -0.6723
 5TJ  O1   O  OH1    0  -0.661   0.1046   3.1046   0.9717
 5TJ  H1   H  HCH1   0   0.240   0.3474   3.6248  -1.0056
 5TJ  H2   H  HCH1   0   0.230  -0.3506   1.4792  -1.8543
 5TJ  H3   H  HOH1   0   0.455  -2.1208   2.7388  -1.2919
 5TJ  H4   H  HCH1   0   0.255  -0.6019   0.5714   1.0426
 5TJ  H5   H  HCH1   0   0.246   1.3329  -0.3377  -1.1319
 5TJ  H6   H  HCH1   0   0.232   1.9414   1.3388   1.3457
 5TJ  H7   H  HCH2   0   0.204   3.7401  -0.1455   0.4714
 5TJ  H8   H  HCH2   0   0.201   3.6084   0.6366  -1.1049
 5TJ  H9   H  HOH1   0   0.457   5.2232   1.6002   0.2993
 5TJ  H10  H  HOH1   0   0.479  -0.1111  -3.2088  -0.1311
 5TJ  H11  H  HOH1   0   0.464   0.5891   3.9032   1.2072

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
 5TJ  O33  S3   deloc   1.479  0.020  1.479
 5TJ  O31  S3   deloc   1.458  0.020  1.458
 5TJ  C1   C2   single  1.532  0.020  1.532
 5TJ  C1   O6   single  1.404  0.020  1.404
 5TJ  O52  C51  single  1.407  0.020  1.407
 5TJ  S3   O3   single  1.639  0.020  1.639
 5TJ  S3   O32  deloc   1.460  0.020  1.460
 5TJ  C2   O2   single  1.399  0.020  1.399
 5TJ  C2   C3   single  1.522  0.020  1.522
 5TJ  O3   C3   single  1.421  0.020  1.421
 5TJ  O6   C5   single  1.415  0.020  1.415
 5TJ  C51  C5   single  1.515  0.020  1.515
 5TJ  C3   C4   single  1.525  0.020  1.525
 5TJ  C5   C4   single  1.531  0.020  1.531
 5TJ  C4   O4   single  1.423  0.020  1.423
 5TJ  O4   S4   single  1.647  0.020  1.647
 5TJ  S4   O41  single  1.632  0.020  1.632
 5TJ  C1   O1   single  1.387  0.020  1.387
 5TJ  C1   H1   single  0.970  0.020  1.090
 5TJ  C2   H2   single  0.970  0.020  1.090
 5TJ  O2   H3   single  0.850  0.020  0.980
 5TJ  C3   H4   single  0.970  0.020  1.090
 5TJ  C4   H5   single  0.970  0.020  1.090
 5TJ  C5   H6   single  0.970  0.020  1.090
 5TJ  C51  H7   single  0.970  0.020  1.090
 5TJ  C51  H8   single  0.970  0.020  1.090
 5TJ  O52  H9   single  0.850  0.020  0.980
 5TJ  O41  H10  single  0.850  0.020  0.980
 5TJ  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
 5TJ  H1   C1   O1   111.40  3.000
 5TJ  H1   C1   O6   104.46  3.000
 5TJ  O1   C1   O6   112.97  3.000
 5TJ  H1   C1   C2   109.66  3.000
 5TJ  O1   C1   C2   108.58  3.000
 5TJ  O6   C1   C2   109.70  3.000
 5TJ  H2   C2   C3   108.15  3.000
 5TJ  H2   C2   O2   111.41  3.000
 5TJ  C3   C2   O2   108.55  3.000
 5TJ  H2   C2   C1   106.46  3.000
 5TJ  C3   C2   C1   109.67  3.000
 5TJ  O2   C2   C1   112.50  3.000
 5TJ  H3   O2   C2   108.49  3.000
 5TJ  H4   C3   C4   108.99  3.000
 5TJ  H4   C3   O3   110.83  3.000
 5TJ  C4   C3   O3   109.52  3.000
 5TJ  H4   C3   C2   109.34  3.000
 5TJ  C4   C3   C2   110.14  3.000
 5TJ  O3   C3   C2   108.01  3.000
 5TJ  S3   O3   C3   121.96  3.000
 5TJ  H5   C4   C5   109.22  3.000
 5TJ  H5   C4   O4   111.04  3.000
 5TJ  C5   C4   O4   109.12  3.000
 5TJ  H5   C4   C3   109.19  3.000
 5TJ  O4   C4   C3   107.07  3.000
 5TJ  C5   C4   C3   111.19  3.000
 5TJ  S4   O4   C4   119.64  3.000
 5TJ  H6   C5   C51  108.84  3.000
 5TJ  H6   C5   O6   110.80  3.000
 5TJ  C51  C5   O6   107.21  3.000
 5TJ  H6   C5   C4   108.60  3.000
 5TJ  C51  C5   C4   111.35  3.000
 5TJ  O6   C5   C4   110.04  3.000
 5TJ  C5   O6   C1   115.31  3.000
 5TJ  H8   C51  H7   107.04  3.000
 5TJ  H8   C51  O52  112.01  3.000
 5TJ  H7   C51  O52  111.37  3.000
 5TJ  H8   C51  C5   108.97  3.000
 5TJ  H7   C51  C5   108.67  3.000
 5TJ  O52  C51  C5   108.69  3.000
 5TJ  H9   O52  C51  108.02  3.000
 5TJ  O31  S3   O32  115.77  3.000
 5TJ  O32  S3   O33  112.64  3.000
 5TJ  O31  S3   O33  113.08  3.000
 5TJ  O32  S3   O3   107.04  3.000
 5TJ  O31  S3   O3   101.04  3.000
 5TJ  O33  S3   O3   105.87  3.000
 5TJ  O41  S4   O4   104.26  3.000
 5TJ  H10  O41  S4   108.54  3.000
 5TJ  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
 5TJ  Var_01  O33  S3  O3  C3  -88.37  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
 5TJ  chir_01  C1  C2  O6  O1   positiv
 5TJ  chir_02  C2  O2  C1  C3   negativ
 5TJ  chir_03  C3  O3  C4  C2   negativ
 5TJ  chir_04  C4  O4  C5  C3   positiv
 5TJ  chir_05  C5  O6  C4  C51  negativ

