# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 11:22:00 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: L-ribulose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H](O)[C@H](O)C(=O)CO
#
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
 QDK  QDK  'L-ribulose               '  L-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 OK (reasonable std)
;

data_comp_QDK
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
 QDK  C1   C  CH2   0  -0.256  -2.1486  -0.7181  -0.6171
 QDK  O1   O  OH1   0  -0.657  -3.3103  -1.0132   0.0935
 QDK  C2   C  C     0   0.363  -1.2957   0.2406   0.1561
 QDK  O2   O  O     0  -0.391  -1.6456   0.7490   1.1934
 QDK  C3   C  CH1   0  -0.105   0.0584   0.5969  -0.4550
 QDK  O3   O  OH1   0  -0.651   0.2416   1.9871  -0.4592
 QDK  C4   C  CH1   0  -0.021   1.1639  -0.1373   0.3249
 QDK  O4   O  OH1   0  -0.660   0.8233  -1.4931   0.5036
 QDK  C5   C  CH2   0  -0.167   2.5115   0.0434  -0.3488
 QDK  O5   O  OH1   0  -0.669   3.5080  -0.5100   0.4762
 QDK  H1   H  HCH2  0   0.234  -1.5392  -1.6039  -0.8446
 QDK  H1A  H  HCH2  0   0.244  -2.3451  -0.2406  -1.5906
 QDK  HO1  H  HOH1  0   0.464  -3.8315  -1.6281  -0.4307
 QDK  H3   H  HCH1  0   0.259   0.0852   0.2792  -1.5037
 QDK  HO3  H  HOH1  0   0.449   0.1480   2.3103   0.4449
 QDK  H4   H  HCH1  0   0.242   1.2078   0.2960   1.3311
 QDK  HO4  H  HOH1  0   0.451   1.0082  -1.9746  -0.3104
 QDK  H5   H  HCH2  0   0.197   2.4805  -0.4452  -1.3352
 QDK  H5A  H  HCH2  0   0.213   2.6770   1.1113  -0.5283
 QDK  HO5  H  HOH1  0   0.457   4.3569  -0.3833   0.0435

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
 QDK  C1  O1   single  1.393  0.020  1.393
 QDK  C1  C2   single  1.498  0.020  1.498
 QDK  C2  O2   double  1.207  0.020  1.207
 QDK  C2  C3   single  1.528  0.020  1.528
 QDK  C3  O3   single  1.402  0.020  1.402
 QDK  C3  C4   single  1.539  0.020  1.539
 QDK  C4  O4   single  1.409  0.020  1.409
 QDK  C4  C5   single  1.517  0.020  1.517
 QDK  C5  O5   single  1.407  0.020  1.407
 QDK  C1  H1   single  0.970  0.020  1.090
 QDK  C1  H1A  single  0.970  0.020  1.090
 QDK  O1  HO1  single  0.850  0.020  0.980
 QDK  C3  H3   single  0.970  0.020  1.090
 QDK  O3  HO3  single  0.850  0.020  0.980
 QDK  C4  H4   single  0.970  0.020  1.090
 QDK  O4  HO4  single  0.850  0.020  0.980
 QDK  C5  H5   single  0.970  0.020  1.090
 QDK  C5  H5A  single  0.970  0.020  1.090
 QDK  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
 QDK  H1A  C1  H1  105.38  3.000
 QDK  H1A  C1  C2  106.27  3.000
 QDK  H1   C1  C2  107.88  3.000
 QDK  H1A  C1  O1  113.18  3.000
 QDK  H1   C1  O1  113.40  3.000
 QDK  C2   C1  O1  110.30  3.000
 QDK  HO1  O1  C1  108.02  3.000
 QDK  C3   C2  O2  120.16  3.000
 QDK  C3   C2  C1  116.58  3.000
 QDK  O2   C2  C1  123.24  3.000
 QDK  H3   C3  C4  109.21  3.000
 QDK  H3   C3  O3  106.34  3.000
 QDK  C4   C3  O3  112.37  3.000
 QDK  H3   C3  C2  109.68  3.000
 QDK  C4   C3  C2  108.82  3.000
 QDK  O3   C3  C2  110.38  3.000
 QDK  HO3  O3  C3  108.46  3.000
 QDK  H4   C4  C5  108.95  3.000
 QDK  H4   C4  O4  105.87  3.000
 QDK  C5   C4  O4  112.67  3.000
 QDK  H4   C4  C3  107.78  3.000
 QDK  C5   C4  C3  110.86  3.000
 QDK  O4   C4  C3  110.46  3.000
 QDK  HO4  O4  C4  109.10  3.000
 QDK  H5A  C5  H5  106.85  3.000
 QDK  H5A  C5  O5  111.87  3.000
 QDK  H5   C5  O5  111.75  3.000
 QDK  H5A  C5  C4  108.85  3.000
 QDK  H5   C5  C4  108.65  3.000
 QDK  O5   C5  C4  108.78  3.000
 QDK  HO5  O5  C5  108.04  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
 QDK  Var_01  O2  C2  C1  O1  -5.48  30.0  3

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
 QDK  chir_01  C3  C2  O3  C4  negativ
 QDK  chir_02  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
 QDK  plan-1  C1  0.020
 QDK  plan-1  C2  0.020
 QDK  plan-1  O2  0.020
 QDK  plan-1  C3  0.020

