# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 19:29:34 2022
#   Inital geometry file: a 51 line input string
#   Ligand name: 2,6-dideoxy-alpha-L-arabino-hexopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1O[C@@H](O)C[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
 RAE  RAE  2,6-dideoxy-alpha-L-arabino-hexopyranose  L-saccharide  22  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_RAE
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
 RAE  C1   C  CH1   0   0.244  -6.3351  21.9073  32.5199
 RAE  C2   C  CH2   0  -0.502  -7.4867  22.8386  32.1789
 RAE  C3   C  CH1   0   0.040  -7.6808  23.8993  33.2495
 RAE  O3   O  OH1   0  -0.667  -8.6812  24.7895  32.8118
 RAE  C4   C  CH1   0   0.012  -6.3583  24.6119  33.4939
 RAE  O4   O  OH1   0  -0.673  -6.5559  25.5223  34.5551
 RAE  C5   C  CH1   0   0.019  -5.2605  23.5964  33.8282
 RAE  O5   O  O2    0  -0.500  -5.1612  22.6270  32.7930
 RAE  C6   C  CH3   0  -0.695  -3.8952  24.2396  33.9679
 RAE  O1   O  OH1   0  -0.664  -6.7236  21.0999  33.5904
 RAE  H1   H  HCH1  0   0.225  -6.0816  21.2975  31.6450
 RAE  H21  H  HCH2  0   0.240  -7.2588  23.3261  31.2269
 RAE  H22  H  HCH2  0   0.253  -8.4010  22.2597  32.0323
 RAE  H3   H  HCH1  0   0.202  -7.9824  23.4148  34.1908
 RAE  HO3  H  HOH1  0   0.443  -8.7762  25.4763  33.4802
 RAE  H4   H  HCH1  0   0.208  -6.0766  25.1369  32.5679
 RAE  HO4  H  HOH1  0   0.456  -5.9159  26.2357  34.4804
 RAE  H5   H  HCH1  0   0.209  -5.5233  23.1115  34.7786
 RAE  H61  H  HCH3  0   0.242  -3.1335  23.4868  34.1726
 RAE  H62  H  HCH3  0   0.226  -3.6141  24.7736  33.0579
 RAE  H63  H  HCH3  0   0.231  -3.8810  24.9460  34.7971
 RAE  HO1  H  HOH1  0   0.454  -6.0484  20.4276  33.7343

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
 RAE  C1  C2   single  1.520  0.020  1.520
 RAE  C1  O5   single  1.404  0.020  1.404
 RAE  C1  O1   single  1.396  0.020  1.396
 RAE  C2  C3   single  1.520  0.020  1.520
 RAE  C3  O3   single  1.409  0.020  1.409
 RAE  C3  C4   single  1.522  0.020  1.522
 RAE  C4  O4   single  1.412  0.020  1.412
 RAE  C4  C5   single  1.532  0.020  1.532
 RAE  C5  O5   single  1.422  0.020  1.422
 RAE  C5  C6   single  1.516  0.020  1.516
 RAE  C1  H1   single  0.970  0.020  1.090
 RAE  C2  H21  single  0.970  0.020  1.090
 RAE  C2  H22  single  0.970  0.020  1.090
 RAE  C3  H3   single  0.970  0.020  1.090
 RAE  O3  HO3  single  0.850  0.020  0.980
 RAE  C4  H4   single  0.970  0.020  1.090
 RAE  O4  HO4  single  0.850  0.020  0.980
 RAE  C5  H5   single  0.970  0.020  1.090
 RAE  C6  H61  single  0.970  0.020  1.090
 RAE  C6  H62  single  0.970  0.020  1.090
 RAE  C6  H63  single  0.970  0.020  1.090
 RAE  O1  HO1  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
 RAE  H1   C1  O1   110.77  3.000
 RAE  H1   C1  O5   104.31  3.000
 RAE  O1   C1  O5   112.34  3.000
 RAE  H1   C1  C2   109.69  3.000
 RAE  O1   C1  C2   108.40  3.000
 RAE  O5   C1  C2   111.29  3.000
 RAE  H22  C2  H21  107.10  3.000
 RAE  H22  C2  C3   110.96  3.000
 RAE  H21  C2  C3   109.20  3.000
 RAE  H22  C2  C1   109.86  3.000
 RAE  H21  C2  C1   108.09  3.000
 RAE  C3   C2  C1   111.50  3.000
 RAE  H3   C3  C4   107.87  3.000
 RAE  H3   C3  O3   110.44  3.000
 RAE  C4   C3  O3   111.78  3.000
 RAE  H3   C3  C2   109.28  3.000
 RAE  C4   C3  C2   109.21  3.000
 RAE  O3   C3  C2   108.23  3.000
 RAE  HO3  O3  C3   107.76  3.000
 RAE  H4   C4  C5   108.43  3.000
 RAE  H4   C4  O4   111.13  3.000
 RAE  C5   C4  O4   111.32  3.000
 RAE  H4   C4  C3   108.08  3.000
 RAE  C5   C4  C3   110.32  3.000
 RAE  O4   C4  C3   107.52  3.000
 RAE  HO4  O4  C4   109.08  3.000
 RAE  H5   C5  C6   108.85  3.000
 RAE  H5   C5  O5   110.22  3.000
 RAE  C6   C5  O5   107.07  3.000
 RAE  H5   C5  C4   108.04  3.000
 RAE  C6   C5  C4   112.59  3.000
 RAE  O5   C5  C4   110.06  3.000
 RAE  C5   O5  C1   115.65  3.000
 RAE  H63  C6  H62  108.29  3.000
 RAE  H63  C6  H61  107.20  3.000
 RAE  H62  C6  H61  108.32  3.000
 RAE  H63  C6  C5   110.92  3.000
 RAE  H62  C6  C5   111.27  3.000
 RAE  H61  C6  C5   110.71  3.000
 RAE  HO1  O1  C1   108.85  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
 RAE  chir_01  C1  C2  O5  O1  negativ
 RAE  chir_02  C3  O3  C4  C2  positiv
 RAE  chir_03  C4  O4  C5  C3  negativ
 RAE  chir_04  C5  O5  C4  C6  positiv

