# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 14:39:27 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: (3~{a}~{S},4~{R},5~{S},6~{R},7~{R},7~{a}~{R})-7-(hydroxymethyl)-2,2-bis(oxidanylidene)-3~{a},4,5,6,7,7~{a}-hexahydrobenzo[d][1,3,2]dioxathiole-4,5,6-triol
#   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]2O[S](=O)(=O)O[C@H]12
#
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
 9FQ  9FQ  (3~{a}~{S},4~{R},5~{S},6~{R},7~{R},7~{a}~{R})-7-(hydroxymethyl)-2,2-bis(oxidanylidene)-3~{a},4,5,6,7,7~{a}-hexahydrobenzo[d][1,3,2]dioxathiole-4,5,6-triol  ligand  28  16  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9FQ
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
 9FQ  C1   C  CR15  0  -0.036  -0.6976  -0.5061   1.0595
 9FQ  C2   C  CH1   0   0.046  -0.2089  -1.6481   0.1858
 9FQ  C3   C  CH1   0  -0.029   1.3166  -1.6669   0.1664
 9FQ  C4   C  CH1   0   0.069   1.8544  -0.3547  -0.4056
 9FQ  C5   C  CH1   0  -0.355   1.4588   0.8056   0.5037
 9FQ  C6   C  CH2   0  -0.128   1.9233   2.1811   0.0228
 9FQ  C7   C  CR15  0  -0.048  -0.0355   0.8345   0.7609
 9FQ  O8   O  O     0  -0.573  -2.0995  -0.2515   0.8166
 9FQ  O9   O  OH1   0  -0.665  -0.7552  -2.8273   0.7088
 9FQ  O10  O  OH1   0  -0.677   1.7384  -2.7397  -0.6494
 9FQ  O11  O  OH1   0  -0.660   3.2518  -0.3911  -0.5078
 9FQ  O12  O  OH1   0  -0.661   3.2798   2.3625   0.3421
 9FQ  O13  O  O     0  -0.575  -0.7517   1.2779  -0.4220
 9FQ  S14  S  S     0   1.653  -2.2999   0.9004  -0.2820
 9FQ  O15  O  OS    0  -0.604  -2.7390   0.3510  -1.5341
 9FQ  O16  O  OS    0  -0.608  -3.0414   1.9715   0.3240
 9FQ  H1   H  HCR5  0   0.322  -0.6028  -0.7587   2.1166
 9FQ  H2   H  HCH1  0   0.228  -0.5481  -1.4892  -0.8498
 9FQ  H3   H  HCH1  0   0.241   1.6921  -1.7881   1.1921
 9FQ  H4   H  HCH1  0   0.210   1.4007  -0.1968  -1.3983
 9FQ  H5   H  HCH1  0   0.283   1.8993   0.6334   1.4947
 9FQ  H6   H  HCH2  0   0.206   1.7429   2.2678  -1.0564
 9FQ  H7   H  HCH2  0   0.213   1.3059   2.9495   0.5081
 9FQ  H8   H  HCR5  0   0.319  -0.2412   1.5424   1.5694
 9FQ  H9   H  HOH1  0   0.456  -0.5061  -3.5543   0.1279
 9FQ  H10  H  HOH1  0   0.468   2.2514  -3.3573  -0.1221
 9FQ  H11  H  HOH1  0   0.446   3.4774  -1.1477  -1.0605
 9FQ  H12  H  HOH1  0   0.455   3.5390   3.2340   0.0294

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
 9FQ  O10  C3   single  1.412  0.020  1.412
 9FQ  O11  C4   single  1.402  0.020  1.402
 9FQ  C4   C3   single  1.529  0.020  1.529
 9FQ  C4   C5   single  1.526  0.020  1.526
 9FQ  C3   C2   single  1.526  0.020  1.526
 9FQ  C2   O9   single  1.401  0.020  1.401
 9FQ  C2   C1   single  1.519  0.020  1.519
 9FQ  C6   C5   single  1.529  0.020  1.529
 9FQ  C6   O12  single  1.405  0.020  1.405
 9FQ  C5   C7   single  1.517  0.020  1.517
 9FQ  O15  S14  double  1.436  0.020  1.436
 9FQ  O13  C7   single  1.452  0.020  1.452
 9FQ  O13  S14  single  1.600  0.020  1.600
 9FQ  C7   C1   single  1.525  0.020  1.525
 9FQ  C1   O8   single  1.445  0.020  1.445
 9FQ  S14  O8   single  1.604  0.020  1.604
 9FQ  S14  O16  double  1.437  0.020  1.437
 9FQ  C1   H1   single  0.970  0.020  1.090
 9FQ  C2   H2   single  0.970  0.020  1.090
 9FQ  C3   H3   single  0.970  0.020  1.090
 9FQ  C4   H4   single  0.970  0.020  1.090
 9FQ  C5   H5   single  0.970  0.020  1.090
 9FQ  C6   H6   single  0.970  0.020  1.090
 9FQ  C6   H7   single  0.970  0.020  1.090
 9FQ  C7   H8   single  0.970  0.020  1.090
 9FQ  O9   H9   single  0.850  0.020  0.980
 9FQ  O10  H10  single  0.850  0.020  0.980
 9FQ  O11  H11  single  0.850  0.020  0.980
 9FQ  O12  H12  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
 9FQ  H1   C1   O8   106.73  3.000
 9FQ  H1   C1   C7   110.83  3.000
 9FQ  O8   C1   C7   103.50  3.000
 9FQ  H1   C1   C2   110.81  3.000
 9FQ  O8   C1   C2   110.36  3.000
 9FQ  C7   C1   C2   114.13  3.000
 9FQ  H2   C2   O9   110.63  3.000
 9FQ  H2   C2   C3   107.33  3.000
 9FQ  O9   C2   C3   112.60  3.000
 9FQ  H2   C2   C1   109.47  3.000
 9FQ  O9   C2   C1   107.02  3.000
 9FQ  C3   C2   C1   109.77  3.000
 9FQ  H3   C3   O10  110.69  3.000
 9FQ  H3   C3   C4   108.88  3.000
 9FQ  O10  C3   C4   109.32  3.000
 9FQ  H3   C3   C2   109.34  3.000
 9FQ  C4   C3   C2   110.24  3.000
 9FQ  O10  C3   C2   108.38  3.000
 9FQ  H4   C4   O11  110.38  3.000
 9FQ  H4   C4   C5   108.71  3.000
 9FQ  O11  C4   C5   108.76  3.000
 9FQ  H4   C4   C3   108.36  3.000
 9FQ  C5   C4   C3   109.77  3.000
 9FQ  O11  C4   C3   110.83  3.000
 9FQ  H5   C5   C7   104.19  3.000
 9FQ  H5   C5   C6   107.64  3.000
 9FQ  C7   C5   C6   109.60  3.000
 9FQ  H5   C5   C4   108.33  3.000
 9FQ  C7   C5   C4   111.77  3.000
 9FQ  C6   C5   C4   114.69  3.000
 9FQ  H7   C6   H6   106.67  3.000
 9FQ  H7   C6   O12  110.60  3.000
 9FQ  H6   C6   O12  111.83  3.000
 9FQ  H7   C6   C5   108.63  3.000
 9FQ  H6   C6   C5   109.29  3.000
 9FQ  O12  C6   C5   109.74  3.000
 9FQ  H8   C7   O13  108.16  3.000
 9FQ  H8   C7   C5   108.84  3.000
 9FQ  O13  C7   C5   110.71  3.000
 9FQ  H8   C7   C1   110.03  3.000
 9FQ  O13  C7   C1   102.34  3.000
 9FQ  C5   C7   C1   116.38  3.000
 9FQ  S14  O8   C1   111.26  3.000
 9FQ  H9   O9   C2   108.01  3.000
 9FQ  H10  O10  C3   109.32  3.000
 9FQ  H11  O11  C4   107.19  3.000
 9FQ  H12  O12  C6   107.65  3.000
 9FQ  S14  O13  C7   109.51  3.000
 9FQ  O16  S14  O15  119.68  3.000
 9FQ  O16  S14  O13  111.13  3.000
 9FQ  O15  S14  O13  108.05  3.000
 9FQ  O16  S14  O8   108.12  3.000
 9FQ  O13  S14  O8    96.23  3.000
 9FQ  O15  S14  O8   111.14  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
 9FQ  Var_01  O13  S14  O8   C1   -5.74  30.0  1
 9FQ  Var_02  O8   S14  O13  C7  -20.99  30.0  1

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
 9FQ  chir_01  C1  C2   C7  O8  negativ
 9FQ  chir_02  C2  O9   C1  C3  negativ
 9FQ  chir_03  C3  O10  C4  C2  negativ
 9FQ  chir_04  C4  O11  C5  C3  positiv
 9FQ  chir_05  C5  C7   C6  C4  positiv
 9FQ  chir_06  C7  O13  C1  C5  negativ

