# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 21:35:49 2022
#   Inital geometry file: a 65 line input string
#   Ligand name: [(2~{S},3~{S},4~{S},5~{R})-5-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxolan-2-yl]methanesulfonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@]1(O)O[C@H](C[S](O)(=O)=O)[C@@H](O)[C@@H]1O
#
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
 RB8  RB8  '[(2~{S},3~{S},4~{S},5~{R})-5-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxolan-2-yl]methanesulfonic acid'  ligand  26  15  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RB8
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
 RB8  O1   O  OS     0  -0.764  21.1336  30.4150  -29.3853
 RB8  S1   S  S      0   1.399  22.5209  30.3474  -28.8823
 RB8  O2   O  OS    -1  -0.760  22.6073  30.0229  -27.4470
 RB8  O3   O  OS     0  -0.762  23.3984  29.5044  -29.7187
 RB8  C1   C  CH2    0  -0.663  23.1773  32.0224  -29.0766
 RB8  C2   C  CH1    0   0.050  22.2762  33.1267  -28.5614
 RB8  O4   O  O2     0  -0.506  22.0885  33.0681  -27.1532
 RB8  C3   C  CT     0   0.417  22.5307  34.2554  -26.5334
 RB8  O5   O  OH1    0  -0.665  23.8703  34.1711  -26.1709
 RB8  C4   C  CH2    0  -0.177  21.6542  34.5317  -25.3210
 RB8  O6   O  OH1    0  -0.670  21.9150  33.5496  -24.3453
 RB8  C5   C  CH1    0  -0.017  22.3847  35.3100  -27.6402
 RB8  O7   O  OH1    0  -0.656  23.1396  36.4739  -27.4860
 RB8  C6   C  CH1    0  -0.018  22.8325  34.5213  -28.8612
 RB8  O8   O  OH1    0  -0.660  22.3321  34.9764  -30.0884
 RB8  H1   H  HCH2   0   0.262  24.1579  32.0582  -28.5967
 RB8  H2   H  HCH2   0   0.265  23.3243  32.1731  -30.1487
 RB8  H3   H  HCH1   0   0.232  21.2952  33.0363  -29.0418
 RB8  H4   H  HOH1   0   0.446  23.9269  33.6539  -25.3569
 RB8  H5   H  HCH2   0   0.215  21.8899  35.5370  -24.9507
 RB8  H6   H  HCH2   0   0.206  20.6017  34.5373  -25.6286
 RB8  H7   H  HOH1   0   0.463  21.6974  33.9067  -23.4802
 RB8  H8   H  HCH1   0   0.227  21.3119  35.5324  -27.7494
 RB8  H9   H  HOH1   0   0.456  22.6919  37.0620  -26.8703
 RB8  H10  H  HCH1   0   0.224  23.9318  34.4955  -28.8732
 RB8  H11  H  HOH1   0   0.455  22.8127  35.7716  -30.3374

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
 RB8  O8  C6   single  1.401  0.020  1.401
 RB8  O3  S1   deloc   1.477  0.020  1.477
 RB8  C1  S1   single  1.810  0.020  1.810
 RB8  C1  C2   single  1.516  0.020  1.516
 RB8  O1  S1   deloc   1.477  0.020  1.477
 RB8  C6  C2   single  1.531  0.020  1.531
 RB8  C6  C5   single  1.521  0.020  1.521
 RB8  S1  O2   deloc   1.474  0.020  1.474
 RB8  C2  O4   single  1.422  0.020  1.422
 RB8  C5  O7   single  1.396  0.020  1.396
 RB8  C5  C3   single  1.536  0.020  1.536
 RB8  O4  C3   single  1.410  0.020  1.410
 RB8  C3  O5   single  1.390  0.020  1.390
 RB8  C3  C4   single  1.521  0.020  1.521
 RB8  C4  O6   single  1.409  0.020  1.409
 RB8  C1  H1   single  0.970  0.020  1.090
 RB8  C1  H2   single  0.970  0.020  1.090
 RB8  C2  H3   single  0.970  0.020  1.090
 RB8  O5  H4   single  0.850  0.020  0.980
 RB8  C4  H5   single  0.970  0.020  1.090
 RB8  C4  H6   single  0.970  0.020  1.090
 RB8  O6  H7   single  0.850  0.020  0.980
 RB8  C5  H8   single  0.970  0.020  1.090
 RB8  O7  H9   single  0.850  0.020  0.980
 RB8  C6  H10  single  0.970  0.020  1.090
 RB8  O8  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
 RB8  C1   S1  O3  104.60  3.000
 RB8  C1   S1  O2  106.68  3.000
 RB8  O3   S1  O2  113.02  3.000
 RB8  O2   S1  O1  113.37  3.000
 RB8  C1   S1  O1  105.17  3.000
 RB8  O3   S1  O1  113.04  3.000
 RB8  H2   C1  H1  107.81  3.000
 RB8  H2   C1  C2  108.25  3.000
 RB8  H1   C1  C2  111.13  3.000
 RB8  H2   C1  S1  106.37  3.000
 RB8  H1   C1  S1  107.98  3.000
 RB8  C2   C1  S1  114.98  3.000
 RB8  H3   C2  C6  108.33  3.000
 RB8  H3   C2  O4  108.21  3.000
 RB8  C6   C2  O4  106.23  3.000
 RB8  H3   C2  C1  108.85  3.000
 RB8  O4   C2  C1  112.65  3.000
 RB8  C6   C2  C1  112.40  3.000
 RB8  C3   O4  C2  111.04  3.000
 RB8  C5   C3  C4  113.26  3.000
 RB8  C4   C3  O5  111.00  3.000
 RB8  C5   C3  O5  108.74  3.000
 RB8  C4   C3  O4  108.81  3.000
 RB8  O5   C3  O4  111.44  3.000
 RB8  C5   C3  O4  103.39  3.000
 RB8  H4   O5  C3  107.98  3.000
 RB8  H6   C4  H5  107.23  3.000
 RB8  H6   C4  O6  112.05  3.000
 RB8  H5   C4  O6  111.43  3.000
 RB8  H6   C4  C3  109.29  3.000
 RB8  H5   C4  C3  108.16  3.000
 RB8  O6   C4  C3  108.59  3.000
 RB8  H7   O6  C4  108.82  3.000
 RB8  H8   C5  C6  108.18  3.000
 RB8  H8   C5  O7  111.69  3.000
 RB8  C6   C5  O7  111.21  3.000
 RB8  H8   C5  C3  107.63  3.000
 RB8  O7   C5  C3  116.20  3.000
 RB8  C6   C5  C3  101.22  3.000
 RB8  H9   O7  C5  109.19  3.000
 RB8  H10  C6  O8  110.81  3.000
 RB8  H10  C6  C5  108.38  3.000
 RB8  O8   C6  C5  115.44  3.000
 RB8  H10  C6  C2  110.11  3.000
 RB8  C5   C6  C2  102.01  3.000
 RB8  O8   C6  C2  109.73  3.000
 RB8  H11  O8  C6  108.46  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
 RB8  Var_01  C2  C1  S1  O1  47.90  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
 RB8  chir_01  C2  C1  C6  O4  positiv
 RB8  chir_02  C3  O4  C4  C5  positiv
 RB8  chir_03  C5  O7  C3  C6  positiv
 RB8  chir_04  C6  O8  C2  C5  positiv

