# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 16:55:14 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: [(1~{S},2~{R},3~{S},4~{S},5~{R},6~{S})-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
 HF8  HF8  '[(1~{S},2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-3,4,5,6-tetrakis(oxidanyl)cyclohexyl] hydrogen sulfate'  ligand  30  17  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HF8
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
 HF8  C1   C  CH1    0   0.023  -2.7832   0.2978   0.3706
 HF8  C2   C  CH1    0   0.017  -2.1532  -1.0005  -0.1189
 HF8  C3   C  CH1    0  -0.348  -0.7493  -1.1653   0.4630
 HF8  C4   C  CH1    0   0.057   0.1335   0.0338   0.0923
 HF8  C5   C  CH1    0   0.027  -0.5098   1.3236   0.5958
 HF8  C7   C  CH1    0  -0.012  -1.9116   1.4900   0.0104
 HF8  C8   C  CH2    0  -0.124  -0.1277  -2.4988   0.0662
 HF8  O9   O  OH1    0  -0.676  -0.9935  -3.5328   0.4892
 HF8  O10  O  OC2    0  -0.630   1.4031  -0.0970   0.7252
 HF8  O11  O  OH1    0  -0.673  -2.0605  -1.0314  -1.5261
 HF8  O12  O  OH1    0  -0.680  -4.0666   0.3958  -0.2021
 HF8  O13  O  OH1    0  -0.683  -2.5386   2.6507   0.5260
 HF8  S15  S  S      0   1.563   2.7683  -0.1540  -0.1902
 HF8  O18  O  OS     0  -0.741   3.7787  -0.2340   0.8636
 HF8  O19  O  OS     0  -0.737   2.6481  -1.3612  -1.0141
 HF8  O1   O  OS    -1  -0.731   2.8031   1.0783  -0.9767
 HF8  O2   O  OH1    0  -0.661   0.3124   2.4092   0.2542
 HF8  H1   H  HCH1   0   0.207  -2.8538   0.2377   1.4689
 HF8  H2   H  HCH1   0   0.235  -2.7765  -1.8280   0.2445
 HF8  H3   H  HCH1   0   0.245  -0.8602  -1.1667   1.5552
 HF8  H4   H  HCH1   0   0.233   0.2463   0.0864  -0.9967
 HF8  H5   H  HCH1   0   0.205  -0.6051   1.2394   1.6908
 HF8  H6   H  HCH1   0   0.223  -1.8324   1.5575  -1.0823
 HF8  H7   H  HCH2   0   0.193   0.0339  -2.5298  -1.0172
 HF8  H8   H  HCH2   0   0.209   0.8535  -2.5976   0.5379
 HF8  H9   H  HOH1   0   0.454  -0.5975  -4.3709   0.2360
 HF8  H10  H  HOH1   0   0.449  -2.9326  -0.8328  -1.8838
 HF8  H11  H  HOH1   0   0.450  -4.3893   1.2920  -0.0556
 HF8  H12  H  HOH1   0   0.460  -2.3703   3.3879  -0.0671
 HF8  H13  H  HOH1   0   0.448   0.0189   3.1735   0.7594

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
 HF8  O19  S15  deloc   1.466  0.020  1.466
 HF8  O18  S15  deloc   1.462  0.020  1.462
 HF8  S15  O1   deloc   1.462  0.020  1.462
 HF8  S15  O10  single  1.645  0.020  1.645
 HF8  O9   C8   single  1.413  0.020  1.413
 HF8  C8   C3   single  1.524  0.020  1.524
 HF8  C3   C2   single  1.529  0.020  1.529
 HF8  C3   C4   single  1.534  0.020  1.534
 HF8  O10  C4   single  1.425  0.020  1.425
 HF8  C2   C1   single  1.524  0.020  1.524
 HF8  C2   O11  single  1.411  0.020  1.411
 HF8  C4   C5   single  1.527  0.020  1.527
 HF8  C1   O12  single  1.409  0.020  1.409
 HF8  C1   C7   single  1.520  0.020  1.520
 HF8  C5   C7   single  1.528  0.020  1.528
 HF8  C7   O13  single  1.416  0.020  1.416
 HF8  C5   O2   single  1.404  0.020  1.404
 HF8  C1   H1   single  0.970  0.020  1.090
 HF8  C2   H2   single  0.970  0.020  1.090
 HF8  C3   H3   single  0.970  0.020  1.090
 HF8  C4   H4   single  0.970  0.020  1.090
 HF8  C5   H5   single  0.970  0.020  1.090
 HF8  C7   H6   single  0.970  0.020  1.090
 HF8  C8   H7   single  0.970  0.020  1.090
 HF8  C8   H8   single  0.970  0.020  1.090
 HF8  O9   H9   single  0.850  0.020  0.980
 HF8  O11  H10  single  0.850  0.020  0.980
 HF8  O12  H11  single  0.850  0.020  0.980
 HF8  O13  H12  single  0.850  0.020  0.980
 HF8  O2   H13  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
 HF8  H1   C1   O12  110.52  3.000
 HF8  H1   C1   C7   108.39  3.000
 HF8  O12  C1   C7   111.81  3.000
 HF8  H1   C1   C2   107.46  3.000
 HF8  C7   C1   C2   110.80  3.000
 HF8  O12  C1   C2   107.78  3.000
 HF8  H2   C2   O11  110.55  3.000
 HF8  H2   C2   C3   108.31  3.000
 HF8  O11  C2   C3   108.49  3.000
 HF8  H2   C2   C1   107.53  3.000
 HF8  O11  C2   C1   111.49  3.000
 HF8  C3   C2   C1   110.44  3.000
 HF8  H3   C3   C8   107.41  3.000
 HF8  H3   C3   C4   107.43  3.000
 HF8  C8   C3   C4   112.72  3.000
 HF8  H3   C3   C2   106.63  3.000
 HF8  C4   C3   C2   110.62  3.000
 HF8  C8   C3   C2   111.70  3.000
 HF8  H4   C4   O10  110.74  3.000
 HF8  H4   C4   C5   109.30  3.000
 HF8  O10  C4   C5   107.85  3.000
 HF8  H4   C4   C3   109.68  3.000
 HF8  C5   C4   C3   109.76  3.000
 HF8  O10  C4   C3   109.49  3.000
 HF8  H5   C5   O2   110.57  3.000
 HF8  H5   C5   C7   108.03  3.000
 HF8  O2   C5   C7   111.09  3.000
 HF8  H5   C5   C4   107.43  3.000
 HF8  O2   C5   C4   109.04  3.000
 HF8  C7   C5   C4   110.61  3.000
 HF8  H6   C7   O13  110.12  3.000
 HF8  H6   C7   C5   108.78  3.000
 HF8  O13  C7   C5   110.85  3.000
 HF8  H6   C7   C1   108.99  3.000
 HF8  O13  C7   C1   107.61  3.000
 HF8  C5   C7   C1   110.48  3.000
 HF8  H8   C8   H7   106.96  3.000
 HF8  H8   C8   O9   110.76  3.000
 HF8  H7   C8   O9   111.44  3.000
 HF8  H8   C8   C3   109.44  3.000
 HF8  H7   C8   C3   110.03  3.000
 HF8  O9   C8   C3   108.20  3.000
 HF8  H9   O9   C8   107.86  3.000
 HF8  S15  O10  C4   119.71  3.000
 HF8  H10  O11  C2   107.85  3.000
 HF8  H11  O12  C1   107.94  3.000
 HF8  H12  O13  C7   109.05  3.000
 HF8  O1   S15  O19  113.17  3.000
 HF8  O1   S15  O18  114.66  3.000
 HF8  O19  S15  O18  114.62  3.000
 HF8  O1   S15  O10  106.85  3.000
 HF8  O18  S15  O10  100.04  3.000
 HF8  O19  S15  O10  105.85  3.000
 HF8  H13  O2   C5   107.93  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
 HF8  Var_01  O19  S15  O10  C4  -62.75  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
 HF8  chir_01  C1  C2   O12  C7  positiv
 HF8  chir_02  C2  O11  C1   C3  positiv
 HF8  chir_03  C3  C4   C2   C8  negativ
 HF8  chir_04  C4  O10  C5   C3  positiv
 HF8  chir_05  C5  O2   C4   C7  positiv
 HF8  chir_06  C7  O13  C5   C1  negativ

