# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 23:28:44 2022
#   Inital geometry file: a 47 line input string
#   Ligand name: beta-D-ribopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CO[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
 RIP  RIP  'beta-D-ribopyranose      '  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_RIP
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
 RIP  C1   C  CH1   0   0.289  49.7239  33.6496  43.6239
 RIP  C2   C  CH1   0   0.005  49.0541  33.1364  44.8976
 RIP  C3   C  CH1   0  -0.057  48.7029  34.3060  45.8179
 RIP  C4   C  CH1   0   0.005  49.9550  35.1409  46.0690
 RIP  C5   C  CH2   0  -0.216  50.5723  35.5506  44.7342
 RIP  O1   O  OH1   0  -0.656  50.1368  32.5690  42.8741
 RIP  O2   O  OH1   0  -0.664  47.9247  32.3899  44.5293
 RIP  O3   O  OH1   0  -0.664  47.6877  35.0630  45.2035
 RIP  O4   O  OH1   0  -0.667  49.5703  36.2527  46.8416
 RIP  O5   O  O2    0  -0.495  50.8655  34.4056  43.9662
 RIP  H1   H  HCH1  0   0.188  49.0219  34.2886  43.0634
 RIP  H2   H  HCH1  0   0.217  49.7923  32.5141  45.4271
 RIP  H3   H  HCH1  0   0.231  48.3543  33.9001  46.7815
 RIP  H4   H  HCH1  0   0.215  50.6790  34.5122  46.6067
 RIP  H51  H  HCH2  0   0.209  49.8954  36.2317  44.2014
 RIP  H52  H  HCH2  0   0.244  51.5158  36.0782  44.8915
 RIP  HO1  H  HOH1  0   0.459  50.3490  32.8640  41.9820
 RIP  HO2  H  HOH1  0   0.451  47.5295  32.0222  45.3264
 RIP  HO3  H  HOH1  0   0.448  47.5510  35.8578  45.7299
 RIP  HO4  H  HOH1  0   0.458  50.3441  36.7964  47.0198

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
 RIP  C1  C2   single  1.528  0.020  1.528
 RIP  C1  O1   single  1.379  0.020  1.379
 RIP  C1  O5   single  1.411  0.020  1.411
 RIP  C1  H1   single  0.970  0.020  1.090
 RIP  C2  C3   single  1.529  0.020  1.529
 RIP  C2  O2   single  1.403  0.020  1.403
 RIP  C2  H2   single  0.970  0.020  1.090
 RIP  C3  C4   single  1.526  0.020  1.526
 RIP  C3  O3   single  1.408  0.020  1.408
 RIP  C3  H3   single  0.970  0.020  1.090
 RIP  C4  C5   single  1.527  0.020  1.527
 RIP  C4  O4   single  1.407  0.020  1.407
 RIP  C4  H4   single  0.970  0.020  1.090
 RIP  C5  O5   single  1.410  0.020  1.410
 RIP  C5  H51  single  0.970  0.020  1.090
 RIP  C5  H52  single  0.970  0.020  1.090
 RIP  O1  HO1  single  0.850  0.020  0.980
 RIP  O2  HO2  single  0.850  0.020  0.980
 RIP  O3  HO3  single  0.850  0.020  0.980
 RIP  O4  HO4  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
 RIP  H1   C1  O5   109.14  3.000
 RIP  H1   C1  O1   111.63  3.000
 RIP  O5   C1  O1   108.03  3.000
 RIP  H1   C1  C2   109.84  3.000
 RIP  O5   C1  C2   109.41  3.000
 RIP  O1   C1  C2   108.75  3.000
 RIP  H2   C2  O2   111.43  3.000
 RIP  H2   C2  C3   107.26  3.000
 RIP  O2   C2  C3   112.34  3.000
 RIP  H2   C2  C1   107.26  3.000
 RIP  O2   C2  C1   108.23  3.000
 RIP  C3   C2  C1   110.21  3.000
 RIP  H3   C3  O3   110.58  3.000
 RIP  H3   C3  C4   108.49  3.000
 RIP  O3   C3  C4   111.68  3.000
 RIP  H3   C3  C2   108.49  3.000
 RIP  O3   C3  C2   108.31  3.000
 RIP  C4   C3  C2   109.22  3.000
 RIP  H4   C4  O4   111.30  3.000
 RIP  H4   C4  C5   108.34  3.000
 RIP  O4   C4  C5   112.24  3.000
 RIP  H4   C4  C3   107.94  3.000
 RIP  O4   C4  C3   107.36  3.000
 RIP  C5   C4  C3   109.56  3.000
 RIP  H52  C5  H51  107.62  3.000
 RIP  H52  C5  O5   106.93  3.000
 RIP  H51  C5  O5   111.57  3.000
 RIP  H52  C5  C4   110.67  3.000
 RIP  H51  C5  C4   109.96  3.000
 RIP  O5   C5  C4   110.03  3.000
 RIP  HO1  O1  C1   109.25  3.000
 RIP  HO2  O2  C2   108.44  3.000
 RIP  HO3  O3  C3   107.91  3.000
 RIP  HO4  O4  C4   109.16  3.000
 RIP  C5   O5  C1   113.52  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
 RIP  Var_01  C4  C5  O5  C1  62.67  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
 RIP  chir_01  C1  C2  O1  O5  positiv
 RIP  chir_02  C2  O2  C1  C3  negativ
 RIP  chir_03  C3  O3  C2  C4  negativ
 RIP  chir_04  C4  O4  C3  C5  negativ

