# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 12:38:05 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: [(1~{S},2~{R},3~{R},4~{S},5~{R})-2-(hydroxymethyl)-3,4,5,6-tetrakis(oxidanyl)cyclohexyl] hydrogen sulfate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1[C@@H](O)[C@H](O)[C@@H](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
 93Z  93Z  '[(1~{S},2~{R},3~{R},4~{S},5~{R})-2-(hydroxymethyl)-3,4,5,6-tetrakis(oxidanyl)cyclohexyl] hydrogen sulfate'  ligand  30  17  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_93Z
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
 93Z  C4   C  CH1    0   0.068  -2.1901   0.6548   0.3339
 93Z  C5   C  CH1    0  -0.340  -0.8575   1.0574  -0.3029
 93Z  C6   C  CH1    0   0.041   0.1883  -0.0379  -0.0325
 93Z  C3   C  CH1    0  -0.002  -2.6605  -0.7029  -0.1746
 93Z  C2   C  CH1    0  -0.021  -1.6138  -1.7638   0.1183
 93Z  C1   C  CH1    0   0.050  -0.2871  -1.3959  -0.5343
 93Z  C8   C  CH2    0  -0.131  -0.3698   2.4170   0.1961
 93Z  O7   O  OC2    0  -0.630   1.3883   0.2957  -0.7200
 93Z  O9   O  OH1    0  -0.668  -1.0832   3.4562  -0.4388
 93Z  O10  O  OH1    0  -0.664  -3.1548   1.6410   0.0692
 93Z  O11  O  OH1    0  -0.681  -3.8840  -0.9883   0.4715
 93Z  O12  O  OH1    0  -0.680  -1.9990  -3.0267  -0.3878
 93Z  S13  S  S      0   1.568   2.8163   0.4419   0.0935
 93Z  O14  O  OS     0  -0.742   3.5679   1.2701  -0.8485
 93Z  O15  O  OS     0  -0.740   2.4887   1.1018   1.3619
 93Z  O16  O  OS    -1  -0.723   3.3446  -0.9102   0.2552
 93Z  H1   H  HCH1   0   0.195  -2.0241   0.5640   1.4222
 93Z  H2   H  HCH1   0   0.239  -0.9938   1.1279  -1.3893
 93Z  H3   H  HCH1   0   0.234   0.3673  -0.1019   1.0478
 93Z  H4   H  HCH1   0   0.217  -2.8061  -0.6357  -1.2632
 93Z  H5   H  HCH1   0   0.222  -1.4610  -1.8214   1.2062
 93Z  H6   H  HCH1   0   0.202  -0.4506  -1.3159  -1.6228
 93Z  H8   H  HCH2   0   0.182  -0.4786   2.4575   1.2898
 93Z  H9   H  HCH2   0   0.211   0.6973   2.5169  -0.0120
 93Z  H10  H  HOH1   0   0.449  -0.6009   4.2721  -0.2802
 93Z  H11  H  HOH1   0   0.443  -3.9969   1.3059   0.3976
 93Z  H12  H  HOH1   0   0.458  -4.3661  -1.6395  -0.0463
 93Z  H13  H  HOH1   0   0.461  -2.4921  -3.4968   0.2902
 93Z  O1   O  OH1    0  -0.661   0.6947  -2.3532  -0.2455
 93Z  H14  H  HOH1   0   0.444   0.3133  -3.2172  -0.4381

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
 93Z  O12  C2   single  1.414  0.020  1.414
 93Z  O14  S13  deloc   1.462  0.020  1.462
 93Z  C1   C2   single  1.524  0.020  1.524
 93Z  C1   C6   single  1.524  0.020  1.524
 93Z  C2   C3   single  1.519  0.020  1.519
 93Z  O7   S13  single  1.650  0.020  1.650
 93Z  O7   C6   single  1.423  0.020  1.423
 93Z  S13  O15  deloc   1.467  0.020  1.467
 93Z  S13  O16  deloc   1.461  0.020  1.461
 93Z  C6   C5   single  1.538  0.020  1.538
 93Z  C3   O11  single  1.413  0.020  1.413
 93Z  C3   C4   single  1.524  0.020  1.524
 93Z  C5   C4   single  1.531  0.020  1.531
 93Z  C5   C8   single  1.528  0.020  1.528
 93Z  C4   O10  single  1.405  0.020  1.405
 93Z  C8   O9   single  1.411  0.020  1.411
 93Z  C4   H1   single  0.970  0.020  1.090
 93Z  C5   H2   single  0.970  0.020  1.090
 93Z  C6   H3   single  0.970  0.020  1.090
 93Z  C3   H4   single  0.970  0.020  1.090
 93Z  C2   H5   single  0.970  0.020  1.090
 93Z  C1   H6   single  0.970  0.020  1.090
 93Z  C8   H8   single  0.970  0.020  1.090
 93Z  C8   H9   single  0.970  0.020  1.090
 93Z  O9   H10  single  0.850  0.020  0.980
 93Z  O10  H11  single  0.850  0.020  0.980
 93Z  O11  H12  single  0.850  0.020  0.980
 93Z  O12  H13  single  0.850  0.020  0.980
 93Z  C1   O1   single  1.401  0.020  1.401
 93Z  O1   H14  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
 93Z  H1   C4   O10  110.28  3.000
 93Z  H1   C4   C3   107.57  3.000
 93Z  O10  C4   C3   110.53  3.000
 93Z  H1   C4   C5   107.49  3.000
 93Z  O10  C4   C5   109.56  3.000
 93Z  C3   C4   C5   111.35  3.000
 93Z  H2   C5   C8   107.81  3.000
 93Z  H2   C5   C6   107.71  3.000
 93Z  C8   C5   C6   111.04  3.000
 93Z  H2   C5   C4   108.71  3.000
 93Z  C8   C5   C4   112.08  3.000
 93Z  C6   C5   C4   109.36  3.000
 93Z  H3   C6   O7   110.61  3.000
 93Z  H3   C6   C1   108.86  3.000
 93Z  O7   C6   C1   108.24  3.000
 93Z  H3   C6   C5   109.00  3.000
 93Z  O7   C6   C5   108.76  3.000
 93Z  C1   C6   C5   111.38  3.000
 93Z  H4   C3   O11  110.50  3.000
 93Z  H4   C3   C2   108.94  3.000
 93Z  O11  C3   C2   111.57  3.000
 93Z  H4   C3   C4   108.45  3.000
 93Z  O11  C3   C4   107.14  3.000
 93Z  C2   C3   C4   110.19  3.000
 93Z  H5   C2   O12  110.19  3.000
 93Z  H5   C2   C1   108.38  3.000
 93Z  O12  C2   C1   107.43  3.000
 93Z  H5   C2   C3   108.84  3.000
 93Z  C1   C2   C3   110.41  3.000
 93Z  O12  C2   C3   111.53  3.000
 93Z  O1   C1   H6   110.89  3.000
 93Z  O1   C1   C2   110.90  3.000
 93Z  H6   C1   C2   108.12  3.000
 93Z  O1   C1   C6   108.80  3.000
 93Z  H6   C1   C6   107.85  3.000
 93Z  C2   C1   C6   110.23  3.000
 93Z  H9   C8   H8   106.43  3.000
 93Z  H9   C8   O9   109.93  3.000
 93Z  H8   C8   O9   111.73  3.000
 93Z  H9   C8   C5   109.33  3.000
 93Z  H8   C8   C5   109.02  3.000
 93Z  O9   C8   C5   110.30  3.000
 93Z  S13  O7   C6   120.83  3.000
 93Z  H10  O9   C8   107.29  3.000
 93Z  H11  O10  C4   106.96  3.000
 93Z  H12  O11  C3   108.95  3.000
 93Z  H13  O12  C2   108.91  3.000
 93Z  O16  S13  O15  113.68  3.000
 93Z  O16  S13  O14  114.19  3.000
 93Z  O15  S13  O14  114.65  3.000
 93Z  O16  S13  O7   106.59  3.000
 93Z  O15  S13  O7   105.84  3.000
 93Z  O14  S13  O7   100.22  3.000
 93Z  H14  O1   C1   107.09  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
 93Z  Var_01  O14  S13  O7  C6  -158.60  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
 93Z  chir_01  C4  C3   C5  O10  negativ
 93Z  chir_02  C5  C6   C4  C8   negativ
 93Z  chir_03  C6  O7   C1  C5   positiv
 93Z  chir_04  C3  O11  C4  C2   negativ
 93Z  chir_05  C2  O12  C3  C1   positiv
 93Z  chir_06  C1  O1   C2  C6   negativ

