# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 04:24:51 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: [(1~{S},2~{S},3~{S},4~{S})-2-(hydroxymethyl)-3,4-bis(oxidanyl)cyclopentyl] hydrogen sulfate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1[C@H](O)[C@@H](O)C[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
 LX5  LX5  '[(1~{S},2~{S},3~{S},4~{S})-2-(hydroxymethyl)-3,4-bis(oxidanyl)cyclopentyl] hydrogen sulfate'  ligand  25  14  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LX5
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
 LX5  C1   C  CR15   0   0.043  -0.0324   0.0633   0.4182
 LX5  C2   C  CH2    0  -0.506  -0.4749   1.5300   0.5629
 LX5  C6   C  CH2    0  -0.138  -1.3024  -2.1069   0.4121
 LX5  C5   C  CR15   0  -0.331  -1.2408  -0.7011  -0.1496
 LX5  C3   C  CR15   0   0.025  -1.8417   1.5968  -0.1124
 LX5  C4   C  CR15   0   0.064  -2.4230   0.2126   0.1529
 LX5  O7   O  OH1    0  -0.667  -2.3215  -2.8409  -0.2234
 LX5  O8   O  OH1    0  -0.664  -3.5432  -0.1016  -0.6302
 LX5  O9   O  OH1    0  -0.673  -2.7103   2.5904   0.3740
 LX5  O10  O  OC2    0  -0.620   1.0631  -0.1189  -0.4743
 LX5  S11  S  S      0   1.566   2.5698  -0.1714   0.1716
 LX5  O12  O  OS    -1  -0.743   2.5764  -1.3330   1.0656
 LX5  O13  O  OS     0  -0.737   3.3749  -0.3314  -1.0372
 LX5  O14  O  OS     0  -0.740   2.7568   1.1026   0.8718
 LX5  H1   H  HCR5   0   0.238   0.2229  -0.3437   1.4022
 LX5  H21  H  HCH2   0   0.238  -0.5855   1.7778   1.6210
 LX5  H2   H  HCH2   0   0.255   0.2526   2.2219   0.1398
 LX5  H6   H  HCH2   0   0.204  -0.3205  -2.5783   0.2693
 LX5  H61  H  HCH2   0   0.187  -1.4668  -2.0442   1.4979
 LX5  H5   H  HCR5   0   0.250  -1.1282  -0.7537  -1.2395
 LX5  H3   H  HCR5   0   0.204  -1.7068   1.6977  -1.1996
 LX5  H4   H  HCR5   0   0.193  -2.6599   0.1445   1.2293
 LX5  HO7  H  HOH1   0   0.452  -2.2815  -3.7442   0.1029
 LX5  HO8  H  HOH1   0   0.446  -4.2304   0.5433  -0.4329
 LX5  HO9  H  HOH1   0   0.455  -2.4166   3.4436   0.0412

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
 LX5  O13  S11  deloc   1.461  0.020  1.461
 LX5  O14  S11  deloc   1.466  0.020  1.466
 LX5  S11  O10  single  1.640  0.020  1.640
 LX5  S11  O12  deloc   1.466  0.020  1.466
 LX5  O10  C1   single  1.425  0.020  1.425
 LX5  C2   C1   single  1.539  0.020  1.539
 LX5  C2   C3   single  1.526  0.020  1.526
 LX5  C1   C5   single  1.538  0.020  1.538
 LX5  C3   O9   single  1.407  0.020  1.407
 LX5  C3   C4   single  1.525  0.020  1.525
 LX5  C5   C4   single  1.524  0.020  1.524
 LX5  C5   C6   single  1.515  0.020  1.515
 LX5  C4   O8   single  1.402  0.020  1.402
 LX5  O7   C6   single  1.408  0.020  1.408
 LX5  C1   H1   single  0.970  0.020  1.090
 LX5  C2   H21  single  0.970  0.020  1.090
 LX5  C2   H2   single  0.970  0.020  1.090
 LX5  C6   H6   single  0.970  0.020  1.090
 LX5  C6   H61  single  0.970  0.020  1.090
 LX5  C5   H5   single  0.970  0.020  1.090
 LX5  C3   H3   single  0.970  0.020  1.090
 LX5  C4   H4   single  0.970  0.020  1.090
 LX5  O7   HO7  single  0.850  0.020  0.980
 LX5  O8   HO8  single  0.850  0.020  0.980
 LX5  O9   HO9  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
 LX5  H1   C1   O10  109.64  3.000
 LX5  H1   C1   C5   109.27  3.000
 LX5  O10  C1   C5   108.02  3.000
 LX5  H1   C1   C2   109.68  3.000
 LX5  C5   C1   C2   106.40  3.000
 LX5  O10  C1   C2   113.70  3.000
 LX5  H2   C2   H21  107.44  3.000
 LX5  H2   C2   C3   113.48  3.000
 LX5  H21  C2   C3   109.14  3.000
 LX5  H2   C2   C1   112.14  3.000
 LX5  H21  C2   C1   109.66  3.000
 LX5  C3   C2   C1   104.93  3.000
 LX5  H61  C6   H6   106.64  3.000
 LX5  H61  C6   O7   111.54  3.000
 LX5  H6   C6   O7   111.38  3.000
 LX5  H61  C6   C5   108.61  3.000
 LX5  H6   C6   C5   108.28  3.000
 LX5  O7   C6   C5   110.24  3.000
 LX5  H5   C5   C4   107.78  3.000
 LX5  H5   C5   C6   109.15  3.000
 LX5  C4   C5   C6   116.81  3.000
 LX5  H5   C5   C1   108.05  3.000
 LX5  C6   C5   C1   110.86  3.000
 LX5  C4   C5   C1   103.77  3.000
 LX5  H3   C3   O9   110.65  3.000
 LX5  H3   C3   C4   107.58  3.000
 LX5  O9   C3   C4   110.23  3.000
 LX5  H3   C3   C2   109.36  3.000
 LX5  C4   C3   C2   102.99  3.000
 LX5  O9   C3   C2   115.53  3.000
 LX5  H4   C4   O8   111.04  3.000
 LX5  H4   C4   C3   107.90  3.000
 LX5  O8   C4   C3   114.26  3.000
 LX5  H4   C4   C5   108.83  3.000
 LX5  O8   C4   C5   111.98  3.000
 LX5  C3   C4   C5   102.36  3.000
 LX5  HO7  O7   C6   107.86  3.000
 LX5  HO8  O8   C4   107.79  3.000
 LX5  HO9  O9   C3   108.57  3.000
 LX5  S11  O10  C1   117.63  3.000
 LX5  O14  S11  O13  114.84  3.000
 LX5  O14  S11  O12  113.38  3.000
 LX5  O13  S11  O12  114.54  3.000
 LX5  O12  S11  O10  105.65  3.000
 LX5  O14  S11  O10  106.11  3.000
 LX5  O13  S11  O10  100.60  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
 LX5  Var_01  O13  S11  O10  C1  -178.72  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
 LX5  chir_01  C1  O10  C2  C5  negativ
 LX5  chir_02  C5  C1   C4  C6  positiv
 LX5  chir_03  C3  O9   C4  C2  positiv
 LX5  chir_04  C4  O8   C3  C5  positiv

