# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:48:13 2022
#   Inital geometry file: a 53 line input string
#   Ligand name: 3-deoxy-beta-D-ribo-hexopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](O)[C@H](O)C[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
 3DO  3DO  3-deoxy-beta-D-ribo-hexopyranose  D-saccharide  23  11  .  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_3DO
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
 3DO  C2   C  CH1   0   0.005  25.6921  32.0049  32.5048
 3DO  C3   C  CH2   0  -0.480  25.6006  30.4763  32.5305
 3DO  C4   C  CH1   0  -0.024  24.7229  29.9479  33.6509
 3DO  C5   C  CH1   0   0.007  25.2491  30.4758  35.0029
 3DO  C6   C  CH2   0  -0.188  26.2024  29.4917  35.6622
 3DO  O1   O  OH1   0  -0.658  26.0459  33.7901  34.0212
 3DO  O6   O  OH1   0  -0.667  25.4578  28.3659  36.0646
 3DO  O5   O  O2    0  -0.510  25.9732  31.6843  34.8630
 3DO  O4   O  OH1   0  -0.666  23.3923  30.3481  33.3917
 3DO  O2   O  OH1   0  -0.666  24.7877  32.5280  31.5578
 3DO  C1   C  CH1   0   0.263  25.4243  32.5607  33.9053
 3DO  H2   H  HCH1  0   0.214  26.7237  32.2760  32.2381
 3DO  H3   H  HCH2  0   0.256  25.2450  30.1086  31.5660
 3DO  H3A  H  HCH2  0   0.249  26.6015  30.0601  32.6612
 3DO  H4   H  HCH1  0   0.232  24.7868  28.8527  33.6628
 3DO  H5   H  HCH1  0   0.224  24.3927  30.6324  35.6793
 3DO  H61  H  HCH2  0   0.204  26.9975  29.2238  34.9536
 3DO  H62  H  HCH2  0   0.211  26.6853  29.9839  36.5161
 3DO  HO1  H  HOH1  0   0.459  25.6720  34.2696  34.7684
 3DO  HO6  H  HOH1  0   0.457  26.0728  27.6747  36.3244
 3DO  HO4  H  HOH1  0   0.446  22.8305  30.0027  34.0928
 3DO  HO2  H  HOH1  0   0.446  24.9606  33.4705  31.4662
 3DO  H1   H  HCH1  0   0.187  24.3377  32.6477  34.0640

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
 3DO  O2  C2   single  1.410  0.020  1.410
 3DO  C3  C2   single  1.532  0.020  1.532
 3DO  C3  C4   single  1.518  0.020  1.518
 3DO  C2  C1   single  1.530  0.020  1.530
 3DO  O4  C4   single  1.413  0.020  1.413
 3DO  C4  C5   single  1.544  0.020  1.544
 3DO  C1  O1   single  1.382  0.020  1.382
 3DO  C1  O5   single  1.409  0.020  1.409
 3DO  O5  C5   single  1.416  0.020  1.416
 3DO  C5  C6   single  1.520  0.020  1.520
 3DO  C6  O6   single  1.408  0.020  1.408
 3DO  C2  H2   single  0.970  0.020  1.090
 3DO  C3  H3   single  0.970  0.020  1.090
 3DO  C3  H3A  single  0.970  0.020  1.090
 3DO  C4  H4   single  0.970  0.020  1.090
 3DO  C5  H5   single  0.970  0.020  1.090
 3DO  C6  H61  single  0.970  0.020  1.090
 3DO  C6  H62  single  0.970  0.020  1.090
 3DO  O1  HO1  single  0.850  0.020  0.980
 3DO  O6  HO6  single  0.850  0.020  0.980
 3DO  O4  HO4  single  0.850  0.020  0.980
 3DO  O2  HO2  single  0.850  0.020  0.980
 3DO  C1  H1   single  0.970  0.020  1.090

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
 3DO  H2   C2  C1   107.26  3.000
 3DO  H2   C2  O2   110.33  3.000
 3DO  C1   C2  O2   111.57  3.000
 3DO  H2   C2  C3   107.83  3.000
 3DO  C1   C2  C3   109.68  3.000
 3DO  O2   C2  C3   110.07  3.000
 3DO  H3A  C3  H3   106.02  3.000
 3DO  H3A  C3  C4   108.00  3.000
 3DO  H3   C3  C4   110.27  3.000
 3DO  H3A  C3  C2   109.13  3.000
 3DO  H3   C3  C2   109.92  3.000
 3DO  C4   C3  C2   113.22  3.000
 3DO  H4   C4  O4   109.85  3.000
 3DO  H4   C4  C5   108.17  3.000
 3DO  O4   C4  C5   112.62  3.000
 3DO  H4   C4  C3   108.77  3.000
 3DO  C5   C4  C3   109.28  3.000
 3DO  O4   C4  C3   108.08  3.000
 3DO  H5   C5  O5   109.67  3.000
 3DO  H5   C5  C6   108.24  3.000
 3DO  O5   C5  C6   105.95  3.000
 3DO  H5   C5  C4   108.73  3.000
 3DO  C6   C5  C4   111.85  3.000
 3DO  O5   C5  C4   112.31  3.000
 3DO  H62  C6  H61  107.03  3.000
 3DO  H62  C6  O6   111.64  3.000
 3DO  H61  C6  O6   111.84  3.000
 3DO  H62  C6  C5   108.85  3.000
 3DO  H61  C6  C5   109.39  3.000
 3DO  O6   C6  C5   108.05  3.000
 3DO  HO1  O1  C1   109.46  3.000
 3DO  HO6  O6  C6   108.30  3.000
 3DO  C1   O5  C5   113.50  3.000
 3DO  HO4  O4  C4   108.32  3.000
 3DO  HO2  O2  C2   108.17  3.000
 3DO  H1   C1  O5   109.59  3.000
 3DO  H1   C1  O1   111.18  3.000
 3DO  O5   C1  O1   108.72  3.000
 3DO  H1   C1  C2   109.46  3.000
 3DO  O5   C1  C2   109.14  3.000
 3DO  O1   C1  C2   108.73  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
 3DO  chir_01  C2  O2  C3  C1  positiv
 3DO  chir_02  C4  O4  C5  C3  positiv
 3DO  chir_03  C5  O5  C4  C6  negativ
 3DO  chir_04  C1  O5  O1  C2  negativ

