# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 14:48:23 2020
#   Inital geometry file: a 49 line input string
#   Ligand name: (1~{R},3~{S},4~{R},5~{S},8~{S})-2,6-dioxabicyclo[3.2.1]octane-3,4,8-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1O[C@@H]2CO[C@H]([C@H]1O)[C@H]2O
#
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
 9RN  9RN  (1~{R},3~{S},4~{R},5~{S},8~{S})-2,6-dioxabicyclo[3.2.1]octane-3,4,8-triol  ligand  21  11  .  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_9RN
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
 9RN  C2   C  CH1   0  -0.026  -0.9138  -0.7940  -0.6782
 9RN  C4   C  CH1   0   0.017   1.2046  -0.5637   0.6047
 9RN  C5   C  CH1   0  -0.096   0.7843   0.8953   0.8025
 9RN  C6   C  CH2   0  -0.200   1.1880   1.4867  -0.5425
 9RN  O4   O  OH1   0  -0.667   2.5966  -0.7220   0.5244
 9RN  O5   O  O2    0  -0.500  -0.6092   0.9354   1.0450
 9RN  O3   O  O2    0  -0.502   0.9884   0.4347  -1.4876
 9RN  C3   C  CH1   0  -0.059   0.6109  -0.7421  -0.7838
 9RN  O2   O  OH1   0  -0.668  -1.2475  -1.9365   0.0665
 9RN  C1   C  CH1   0   0.272  -1.4204   0.5087  -0.0364
 9RN  O1   O  OH1   0  -0.665  -2.6932   0.2852   0.4485
 9RN  H1   H  HCH1  0   0.239  -1.3402  -0.8456  -1.6903
 9RN  H2   H  HCH1  0   0.251   0.7563  -1.2231   1.3536
 9RN  H3   H  HCH1  0   0.273   1.2694   1.3923   1.6444
 9RN  H4   H  HCH2  0   0.243   0.5951   2.3635  -0.8167
 9RN  H5   H  HCH2  0   0.240   2.2397   1.7859  -0.5304
 9RN  H6   H  HOH1  0   0.456   2.9732  -0.5307   1.3892
 9RN  H7   H  HCH1  0   0.267   0.9958  -1.6150  -1.3179
 9RN  H8   H  HOH1  0   0.455  -2.2063  -1.9829   0.1397
 9RN  H9   H  HCH1  0   0.202  -1.4333   1.2910  -0.8088
 9RN  H10  H  HOH1  0   0.469  -3.1521   1.1246   0.5570

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
 9RN  O4  C4   single  1.403  0.020  1.403
 9RN  C6  C5   single  1.524  0.020  1.524
 9RN  C6  O3   single  1.428  0.020  1.428
 9RN  C5  C4   single  1.531  0.020  1.531
 9RN  C5  O5   single  1.415  0.020  1.415
 9RN  C4  C3   single  1.521  0.020  1.521
 9RN  O3  C3   single  1.422  0.020  1.422
 9RN  O5  C1   single  1.418  0.020  1.418
 9RN  C3  C2   single  1.529  0.020  1.529
 9RN  C1  C2   single  1.538  0.020  1.538
 9RN  C1  O1   single  1.380  0.020  1.380
 9RN  C2  O2   single  1.404  0.020  1.404
 9RN  C2  H1   single  0.970  0.020  1.090
 9RN  C4  H2   single  0.970  0.020  1.090
 9RN  C5  H3   single  0.970  0.020  1.090
 9RN  C6  H4   single  0.970  0.020  1.090
 9RN  C6  H5   single  0.970  0.020  1.090
 9RN  O4  H6   single  0.850  0.020  0.980
 9RN  C3  H7   single  0.970  0.020  1.090
 9RN  O2  H8   single  0.850  0.020  0.980
 9RN  C1  H9   single  0.970  0.020  1.090
 9RN  O1  H10  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
 9RN  H1   C2  C1  107.23  3.000
 9RN  H1   C2  O2  110.97  3.000
 9RN  C1   C2  O2  112.93  3.000
 9RN  H1   C2  C3  108.95  3.000
 9RN  O2   C2  C3  107.53  3.000
 9RN  C1   C2  C3  109.17  3.000
 9RN  H2   C4  C3  113.23  3.000
 9RN  H2   C4  O4  112.19  3.000
 9RN  C3   C4  O4  108.77  3.000
 9RN  H2   C4  C5  111.93  3.000
 9RN  C3   C4  C5   97.05  3.000
 9RN  O4   C4  C5  112.78  3.000
 9RN  H3   C5  O5  107.02  3.000
 9RN  H3   C5  C6  112.73  3.000
 9RN  O5   C5  C6  113.65  3.000
 9RN  H3   C5  C4  114.31  3.000
 9RN  O5   C5  C4  108.63  3.000
 9RN  C6   C5  C4  100.55  3.000
 9RN  H5   C6  H4  107.75  3.000
 9RN  H5   C6  O3  110.08  3.000
 9RN  H4   C6  O3  110.42  3.000
 9RN  H5   C6  C5  110.56  3.000
 9RN  H4   C6  C5  112.88  3.000
 9RN  O3   C6  C5  105.14  3.000
 9RN  H6   O4  C4  108.32  3.000
 9RN  C1   O5  C5  115.11  3.000
 9RN  C3   O3  C6  108.61  3.000
 9RN  H7   C3  O3  108.99  3.000
 9RN  H7   C3  C4  113.72  3.000
 9RN  O3   C3  C4  104.55  3.000
 9RN  H7   C3  C2  110.95  3.000
 9RN  O3   C3  C2  109.08  3.000
 9RN  C4   C3  C2  109.28  3.000
 9RN  H8   O2  C2  108.44  3.000
 9RN  H9   C1  O1  110.56  3.000
 9RN  H9   C1  O5  109.17  3.000
 9RN  O1   C1  O5  107.97  3.000
 9RN  H9   C1  C2  108.26  3.000
 9RN  O1   C1  C2  108.25  3.000
 9RN  O5   C1  C2  112.63  3.000
 9RN  H10  O1  C1  109.75  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
 9RN  Var_01  H4  C6  O3  C3  -126.82  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
 9RN  chir_01  C2  C3  C1  O2  positiv
 9RN  chir_02  C4  O4  C5  C3  negativ
 9RN  chir_03  C5  O5  C4  C6  negativ
 9RN  chir_04  C3  O3  C2  C4  positiv
 9RN  chir_05  C1  O1  O5  C2  negativ

