# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 12:47:50 2022
#   Inital geometry file: a 47 line input string
#   Ligand name: beta-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
 BDR  BDR  'beta-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 PERFECT
;

data_comp_BDR
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
 BDR  C4   C  CR15  0  -0.011  -4.3655  -2.6258  4.5932
 BDR  O4   O  O     0  -0.485  -3.1791  -1.9926  4.1559
 BDR  C1   C  CR15  0   0.278  -2.0543  -2.8277  4.2890
 BDR  O1   O  OH1   0  -0.626  -1.0846  -2.2334  5.0771
 BDR  C2   C  CR15  0   0.009  -2.5699  -4.0976  4.9648
 BDR  O2   O  OH1   0  -0.667  -1.8392  -5.2134  4.5148
 BDR  C3   C  CR15  0  -0.102  -4.0556  -4.1221  4.6201
 BDR  O3   O  OH1   0  -0.682  -4.3043  -4.6890  3.3636
 BDR  C5   C  CH2   0  -0.195  -4.7925  -2.0655  5.9508
 BDR  O5   O  OH1   0  -0.632  -6.0610  -2.5408  6.3386
 BDR  H4   H  HCR5  0   0.264  -5.1687  -2.4248  3.8729
 BDR  H1   H  HCR5  0   0.125  -1.6588  -3.0435  3.2864
 BDR  HO1  H  HOH1  0   0.467  -0.4358  -1.7940  4.5184
 BDR  H2   H  HCR5  0   0.247  -2.4621  -3.9695  6.0497
 BDR  HO2  H  HOH1  0   0.464  -2.0464  -5.9541  5.0952
 BDR  H3   H  HCR5  0   0.193  -4.6188  -4.6384  5.4087
 BDR  HO3  H  HOH1  0   0.446  -3.5918  -5.3016  3.1479
 BDR  H51  H  HCH2  0   0.220  -4.7542  -0.9701  5.9022
 BDR  H52  H  HCH2  0   0.256  -4.0973  -2.3723  6.7366
 BDR  HO5  H  HOH1  0   0.430  -6.7107  -2.1924  5.7202

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
 BDR  C4  O4   single  1.414  0.020  1.414
 BDR  C4  C3   single  1.528  0.020  1.528
 BDR  C4  C5   single  1.529  0.020  1.529
 BDR  C4  H4   single  0.970  0.020  1.090
 BDR  O4  C1   single  1.407  0.020  1.407
 BDR  C1  O1   single  1.384  0.020  1.384
 BDR  C1  C2   single  1.528  0.020  1.528
 BDR  C1  H1   single  0.970  0.020  1.090
 BDR  O1  HO1  single  0.850  0.020  0.980
 BDR  C2  O2   single  1.408  0.020  1.408
 BDR  C2  C3   single  1.525  0.020  1.525
 BDR  C2  H2   single  0.970  0.020  1.090
 BDR  O2  HO2  single  0.850  0.020  0.980
 BDR  C3  O3   single  1.401  0.020  1.401
 BDR  C3  H3   single  0.970  0.020  1.090
 BDR  O3  HO3  single  0.850  0.020  0.980
 BDR  C5  O5   single  1.409  0.020  1.409
 BDR  C5  H51  single  0.970  0.020  1.090
 BDR  C5  H52  single  0.970  0.020  1.090
 BDR  O5  HO5  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
 BDR  H4   C4  C5   108.13  3.000
 BDR  H4   C4  C3   109.84  3.000
 BDR  C5   C4  C3   113.56  3.000
 BDR  H4   C4  O4   109.21  3.000
 BDR  C5   C4  O4   110.16  3.000
 BDR  C3   C4  O4   105.89  3.000
 BDR  C1   O4  C4   112.06  3.000
 BDR  H1   C1  C2   111.20  3.000
 BDR  H1   C1  O1   110.59  3.000
 BDR  C2   C1  O1   109.97  3.000
 BDR  H1   C1  O4   108.53  3.000
 BDR  C2   C1  O4   105.38  3.000
 BDR  O1   C1  O4   111.04  3.000
 BDR  HO1  O1  C1   109.75  3.000
 BDR  H2   C2  C3   108.71  3.000
 BDR  H2   C2  O2   110.94  3.000
 BDR  C3   C2  O2   114.87  3.000
 BDR  H2   C2  C1   107.88  3.000
 BDR  C3   C2  C1   104.01  3.000
 BDR  O2   C2  C1   110.01  3.000
 BDR  HO2  O2  C2   107.77  3.000
 BDR  H3   C3  O3   111.27  3.000
 BDR  H3   C3  C2   110.18  3.000
 BDR  O3   C3  C2   112.47  3.000
 BDR  H3   C3  C4   111.65  3.000
 BDR  O3   C3  C4   110.15  3.000
 BDR  C2   C3  C4   100.71  3.000
 BDR  HO3  O3  C3   109.07  3.000
 BDR  H52  C5  H51  106.85  3.000
 BDR  H52  C5  O5   106.26  3.000
 BDR  H51  C5  O5   112.36  3.000
 BDR  H52  C5  C4   110.96  3.000
 BDR  H51  C5  C4   108.46  3.000
 BDR  O5   C5  C4   111.84  3.000
 BDR  HO5  O5  C5   107.98  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
 BDR  chir_01  C4  O4  C3  C5  negativ
 BDR  chir_02  C1  O1  O4  C2  positiv
 BDR  chir_03  C2  O2  C1  C3  negativ
 BDR  chir_04  C3  O3  C2  C4  negativ

