# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 00:30:48 2022
#   Inital geometry file: a 47 line input string
#   Ligand name: alpha-D-ribofuranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](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
 RIB  RIB  'alpha-D-ribofuranose     '  D-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 OK
;

data_comp_RIB
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
 RIB  O5   O  OH1   0  -0.664  -22.5696  15.0841  44.1854
 RIB  C5   C  CH2   0  -0.154  -21.6041  14.5382  45.0494
 RIB  C4   C  CH1   0  -0.003  -20.5433  13.8482  44.2154
 RIB  O4   O  O2    0  -0.503  -19.9107  14.7873  43.3435
 RIB  C3   C  CH1   0  -0.073  -19.4356  13.2474  45.0758
 RIB  O3   O  OH1   0  -0.662  -18.9816  12.0601  44.4621
 RIB  C2   C  CH1   0  -0.030  -18.3791  14.3487  45.0205
 RIB  O2   O  OH1   0  -0.657  -17.1253  13.8475  45.3721
 RIB  C1   C  CH1   0   0.233  -18.5246  14.8434  43.5714
 RIB  O1   O  OH1   0  -0.656  -17.7905  14.1114  42.6490
 RIB  HO5  H  HOH1  0   0.454  -23.2126  15.5614  44.7172
 RIB  H51  H  HCH2  0   0.198  -21.1362  15.3063  45.6807
 RIB  H52  H  HCH2  0   0.200  -22.0392  13.7905  45.7260
 RIB  H4   H  HCH1  0   0.246  -21.0225  13.0652  43.6158
 RIB  H3   H  HCH1  0   0.252  -19.7745  13.0529  46.1006
 RIB  HO3  H  HOH1  0   0.456  -18.2186  11.7366  44.9541
 RIB  H2   H  HCH1  0   0.231  -18.6958  15.1637  45.6858
 RIB  HO2  H  HOH1  0   0.460  -16.4748  14.5546  45.3149
 RIB  H1   H  HCH1  0   0.233  -18.2109  15.8830  43.4449
 RIB  HO1  H  HOH1  0   0.438  -17.9002  13.1698  42.8353

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
 RIB  O5  C5   single  1.406  0.020  1.406
 RIB  O5  HO5  single  0.850  0.020  0.980
 RIB  C5  C4   single  1.516  0.020  1.516
 RIB  C5  H51  single  0.970  0.020  1.090
 RIB  C5  H52  single  0.970  0.020  1.090
 RIB  C4  O4   single  1.429  0.020  1.429
 RIB  C4  C3   single  1.526  0.020  1.526
 RIB  C4  H4   single  0.970  0.020  1.090
 RIB  O4  C1   single  1.406  0.020  1.406
 RIB  C3  O3   single  1.412  0.020  1.412
 RIB  C3  C2   single  1.527  0.020  1.527
 RIB  C3  H3   single  0.970  0.020  1.090
 RIB  O3  HO3  single  0.850  0.020  0.980
 RIB  C2  O2   single  1.395  0.020  1.395
 RIB  C2  C1   single  1.538  0.020  1.538
 RIB  C2  H2   single  0.970  0.020  1.090
 RIB  O2  HO2  single  0.850  0.020  0.980
 RIB  C1  O1   single  1.388  0.020  1.388
 RIB  C1  H1   single  0.970  0.020  1.090
 RIB  O1  HO1  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
 RIB  HO5  O5  C5   108.19  3.000
 RIB  H52  C5  H51  106.89  3.000
 RIB  H52  C5  C4   107.84  3.000
 RIB  H51  C5  C4   109.66  3.000
 RIB  H52  C5  O5   111.77  3.000
 RIB  H51  C5  O5   111.97  3.000
 RIB  C4   C5  O5   108.62  3.000
 RIB  H4   C4  C3   110.15  3.000
 RIB  H4   C4  O4   109.22  3.000
 RIB  C3   C4  O4   106.35  3.000
 RIB  H4   C4  C5   108.67  3.000
 RIB  C3   C4  C5   112.15  3.000
 RIB  O4   C4  C5   110.27  3.000
 RIB  C1   O4  C4   111.33  3.000
 RIB  H3   C3  C2   112.05  3.000
 RIB  H3   C3  O3   110.89  3.000
 RIB  C2   C3  O3   111.61  3.000
 RIB  H3   C3  C4   111.87  3.000
 RIB  C2   C3  C4   101.41  3.000
 RIB  O3   C3  C4   108.63  3.000
 RIB  HO3  O3  C3   108.36  3.000
 RIB  H2   C2  C1   107.74  3.000
 RIB  H2   C2  O2   111.89  3.000
 RIB  C1   C2  O2   115.97  3.000
 RIB  H2   C2  C3   108.28  3.000
 RIB  C1   C2  C3   101.57  3.000
 RIB  O2   C2  C3   110.70  3.000
 RIB  HO2  O2  C2   109.18  3.000
 RIB  H1   C1  O1   105.84  3.000
 RIB  H1   C1  C2   112.81  3.000
 RIB  O1   C1  C2   113.99  3.000
 RIB  H1   C1  O4   107.59  3.000
 RIB  O1   C1  O4   113.13  3.000
 RIB  C2   C1  O4   103.48  3.000
 RIB  HO1  O1  C1   109.02  3.000

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
 RIB  chir_01  C4  C5  O4  C3  negativ
 RIB  chir_02  C3  O3  C4  C2  positiv
 RIB  chir_03  C2  O2  C3  C1  positiv
 RIB  chir_04  C1  O4  O1  C2  positiv

