# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 17:30:20 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: D-ribose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@@H](O)[C@@H](O)C=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
 RB5  RB5  'D-ribose                 '  D-saccharide  20  10  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RB5
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
 RB5  C1   C  CH2   0  -0.158  -2.4352   0.4605  -0.5194
 RB5  O1   O  OH1   0  -0.671  -3.6585   0.1353   0.0954
 RB5  C2   C  CH1   0  -0.015  -1.2951  -0.0599   0.3424
 RB5  O2   O  OH1   0  -0.656  -1.3274  -1.4585   0.4712
 RB5  C3   C  CH1   0  -0.029   0.0468   0.4756  -0.1888
 RB5  O3   O  OH1   0  -0.657   0.1628   1.8584   0.0613
 RB5  C4   C  CH1   0  -0.103   1.2640  -0.3178   0.3441
 RB5  O4   O  OH1   0  -0.655   1.4052  -1.5445  -0.3129
 RB5  C5   C  C1    0   0.164   2.5087   0.5307   0.1922
 RB5  O5   O  O     0  -0.378   3.3559   0.2806  -0.6285
 RB5  H1   H  HCH2  0   0.195  -2.3493   0.0116  -1.5207
 RB5  H1A  H  HCH2  0   0.203  -2.3204   1.5435  -0.6467
 RB5  HO1  H  HOH1  0   0.455  -4.3684   0.4715  -0.4584
 RB5  H2   H  HCH1  0   0.232  -1.4219   0.3242   1.3630
 RB5  HO2  H  HOH1  0   0.443  -1.0811  -1.8577  -0.3700
 RB5  H3   H  HCH1  0   0.247   0.0737   0.3763  -1.2812
 RB5  HO3  H  HOH1  0   0.453   0.0334   2.0231   1.0024
 RB5  H4   H  HCH1  0   0.269   1.1397  -0.5102   1.4178
 RB5  HO4  H  HOH1  0   0.446   1.9553  -1.4035  -1.0937
 RB5  H5   H  H     0   0.216   2.6077   1.3834   0.8790

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
 RB5  C1  O1   single  1.407  0.020  1.407
 RB5  C1  C2   single  1.521  0.020  1.521
 RB5  C2  O2   single  1.405  0.020  1.405
 RB5  C2  C3   single  1.539  0.020  1.539
 RB5  C3  O3   single  1.410  0.020  1.410
 RB5  C3  C4   single  1.548  0.020  1.548
 RB5  C4  O4   single  1.399  0.020  1.399
 RB5  C4  C5   single  1.514  0.020  1.514
 RB5  C5  O5   double  1.206  0.020  1.206
 RB5  C1  H1   single  0.970  0.020  1.090
 RB5  C1  H1A  single  0.970  0.020  1.090
 RB5  O1  HO1  single  0.850  0.020  0.980
 RB5  C2  H2   single  0.970  0.020  1.090
 RB5  O2  HO2  single  0.850  0.020  0.980
 RB5  C3  H3   single  0.970  0.020  1.090
 RB5  O3  HO3  single  0.850  0.020  0.980
 RB5  C4  H4   single  0.970  0.020  1.090
 RB5  O4  HO4  single  0.850  0.020  0.980
 RB5  C5  H5   single  0.930  0.020  1.080

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
 RB5  H1A  C1  H1  106.80  3.000
 RB5  H1A  C1  C2  108.98  3.000
 RB5  H1   C1  C2  108.51  3.000
 RB5  H1A  C1  O1  111.71  3.000
 RB5  H1   C1  O1  111.77  3.000
 RB5  C2   C1  O1  108.97  3.000
 RB5  HO1  O1  C1  108.04  3.000
 RB5  H2   C2  C3  107.45  3.000
 RB5  H2   C2  O2  105.09  3.000
 RB5  C3   C2  O2  113.45  3.000
 RB5  H2   C2  C1  108.69  3.000
 RB5  C3   C2  C1  109.81  3.000
 RB5  O2   C2  C1  112.04  3.000
 RB5  HO2  O2  C2  109.06  3.000
 RB5  H3   C3  C4  106.09  3.000
 RB5  H3   C3  O3  105.27  3.000
 RB5  C4   C3  O3  112.15  3.000
 RB5  H3   C3  C2  109.48  3.000
 RB5  C4   C3  C2  112.86  3.000
 RB5  O3   C3  C2  110.59  3.000
 RB5  HO3  O3  C3  109.25  3.000
 RB5  H4   C4  C5  106.82  3.000
 RB5  H4   C4  O4  108.49  3.000
 RB5  C5   C4  O4  111.19  3.000
 RB5  H4   C4  C3  109.73  3.000
 RB5  C5   C4  C3  108.95  3.000
 RB5  O4   C4  C3  111.55  3.000
 RB5  HO4  O4  C4  108.02  3.000
 RB5  H5   C5  O5  121.52  3.000
 RB5  H5   C5  C4  116.49  3.000
 RB5  O5   C5  C4  121.99  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
 RB5  chir_01  C2  C1  O2  C3  negativ
 RB5  chir_02  C3  O3  C2  C4  positiv
 RB5  chir_03  C4  O4  C3  C5  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 RB5  plan-1  C4  0.020
 RB5  plan-1  C5  0.020
 RB5  plan-1  O5  0.020
 RB5  plan-1  H5  0.020

