# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 08:07:50 2022
#   Inital geometry file: a 47 line input string
#   Ligand name: alpha-L-ribulofuranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@]1(O)OC[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
 RUU  RUU  'alpha-L-ribulofuranose   '  L-saccharide  20  10  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RUU
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
 RUU  C1   C  CH2   0  -0.154  17.5587  6.8526  17.7411
 RUU  O1   O  OH1   0  -0.665  16.3044  6.2231  17.7777
 RUU  C2   C  CT    0   0.432  18.5199  6.0393  16.8902
 RUU  O2   O  OH1   0  -0.664  18.5886  4.7603  17.4282
 RUU  C3   C  CH1   0  -0.033  19.9087  6.7204  16.7770
 RUU  O3   O  OH1   0  -0.654  20.8186  6.4143  17.7883
 RUU  C4   C  CH1   0  -0.076  20.4005  6.1987  15.4310
 RUU  O4   O  OH1   0  -0.662  20.8421  4.8597  15.5225
 RUU  C5   C  CH2   0  -0.167  19.1124  6.2438  14.6349
 RUU  O5   O  O2    0  -0.508  18.0530  6.0096  15.5569
 RUU  H11  H  HCH2  0   0.198  17.9914  6.9594  18.7459
 RUU  H12  H  HCH2  0   0.200  17.5009  7.8614  17.3127
 RUU  HO1  H  HOH1  0   0.455  15.7246  6.7478  18.3369
 RUU  HO2  H  HOH1  0   0.440  19.3026  4.2825  16.9856
 RUU  H3   H  HCH1  0   0.229  19.7515  7.8047  16.6798
 RUU  HO3  H  HOH1  0   0.459  20.5260  6.8084  18.6161
 RUU  H4   H  HCH1  0   0.253  21.1704  6.8411  14.9899
 RUU  HO4  H  HOH1  0   0.457  21.6299  4.8355  16.0771
 RUU  H51  H  HCH2  0   0.223  18.9949  7.2286  14.1728
 RUU  H52  H  HCH2  0   0.238  19.0910  5.4944  13.8400

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
 RUU  C5  C4   single  1.515  0.020  1.515
 RUU  C5  O5   single  1.424  0.020  1.424
 RUU  C4  O4   single  1.413  0.020  1.413
 RUU  C4  C3   single  1.525  0.020  1.525
 RUU  O5  C2   single  1.413  0.020  1.413
 RUU  C3  C2   single  1.551  0.020  1.551
 RUU  C3  O3   single  1.394  0.020  1.394
 RUU  C2  O2   single  1.389  0.020  1.389
 RUU  C2  C1   single  1.520  0.020  1.520
 RUU  C1  O1   single  1.404  0.020  1.404
 RUU  C1  H11  single  0.970  0.020  1.090
 RUU  C1  H12  single  0.970  0.020  1.090
 RUU  O1  HO1  single  0.850  0.020  0.980
 RUU  O2  HO2  single  0.850  0.020  0.980
 RUU  C3  H3   single  0.970  0.020  1.090
 RUU  O3  HO3  single  0.850  0.020  0.980
 RUU  C4  H4   single  0.970  0.020  1.090
 RUU  O4  HO4  single  0.850  0.020  0.980
 RUU  C5  H51  single  0.970  0.020  1.090
 RUU  C5  H52  single  0.970  0.020  1.090

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
 RUU  H12  C1  H11  106.76  3.000
 RUU  H12  C1  C2   107.86  3.000
 RUU  H11  C1  C2   108.35  3.000
 RUU  H12  C1  O1   112.04  3.000
 RUU  H11  C1  O1   111.80  3.000
 RUU  C2   C1  O1   109.85  3.000
 RUU  HO1  O1  C1   108.01  3.000
 RUU  O5   C2  C3   103.66  3.000
 RUU  C3   C2  O2   112.84  3.000
 RUU  O5   C2  O2   111.25  3.000
 RUU  O2   C2  C1   107.89  3.000
 RUU  C3   C2  C1   111.85  3.000
 RUU  O5   C2  C1   109.31  3.000
 RUU  HO2  O2  C2   108.33  3.000
 RUU  H3   C3  C4   107.78  3.000
 RUU  H3   C3  O3   111.94  3.000
 RUU  C4   C3  O3   110.77  3.000
 RUU  H3   C3  C2   108.14  3.000
 RUU  O3   C3  C2   115.79  3.000
 RUU  C4   C3  C2   101.71  3.000
 RUU  HO3  O3  C3   109.61  3.000
 RUU  H4   C4  C5   111.62  3.000
 RUU  H4   C4  O4   111.23  3.000
 RUU  C5   C4  O4   109.15  3.000
 RUU  H4   C4  C3   112.42  3.000
 RUU  O4   C4  C3   111.58  3.000
 RUU  C5   C4  C3   100.34  3.000
 RUU  HO4  O4  C4   108.45  3.000
 RUU  H52  C5  H51  107.94  3.000
 RUU  H52  C5  O5   110.10  3.000
 RUU  H51  C5  O5   109.98  3.000
 RUU  H52  C5  C4   112.24  3.000
 RUU  H51  C5  C4   109.88  3.000
 RUU  O5   C5  C4   106.71  3.000
 RUU  C5   O5  C2   111.20  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
 RUU  Var_01  C4  C5  O5  C2  9.70  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
 RUU  chir_01  C2  C3  O5  C1  positiv
 RUU  chir_02  C3  O3  C2  C4  positiv
 RUU  chir_03  C4  O4  C3  C5  positiv

