# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:48:30 2022
#   Inital geometry file: a 61 line input string
#   Ligand name: 2-deoxy-beta-L-galacto-heptopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H](O)[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
 293  293  2-deoxy-beta-L-galacto-heptopyranose  D-saccharide  27  13  .  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_293
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
 293  C1   C  CH1   0   0.247  27.6886  -17.3836  10.5394
 293  C2   C  CH2   0  -0.542  26.4096  -17.6452   9.7554
 293  C3   C  CH1   0   0.013  26.0307  -16.4872   8.8333
 293  C4   C  CH1   0   0.030  26.0057  -15.1925   9.6403
 293  C5   C  CH1   0  -0.022  27.3540  -15.0265  10.3581
 293  C6   C  CH1   0  -0.053  27.4277  -13.7816  11.2372
 293  C7   C  CH2   0  -0.161  28.8193  -13.5960  11.8374
 293  O1   O  OH1   0  -0.657  28.8487  -17.5076   9.7761
 293  O3   O  OH1   0  -0.656  24.8234  -16.7362   8.1571
 293  O4   O  OH1   0  -0.666  25.7699  -14.1175   8.7659
 293  O5   O  O2    0  -0.506  27.6169  -16.1395  11.1914
 293  O6   O  OH1   0  -0.662  26.4329  -13.7640  12.2388
 293  O7   O  OH1   0  -0.662  28.9456  -12.3690  12.5153
 293  H1   H  HCH1  0   0.238  27.7830  -18.1112  11.3477
 293  H2   H  HCH2  0   0.262  26.5050  -18.5725   9.1863
 293  H2A  H  HCH2  0   0.245  25.6001  -17.7969  10.4771
 293  H3   H  HCH1  0   0.226  26.7797  -16.3763   8.0390
 293  H4   H  HCH1  0   0.213  25.2104  -15.2801  10.3957
 293  H5   H  HCH1  0   0.220  28.1343  -14.9183   9.5874
 293  H6   H  HCH1  0   0.239  27.2294  -12.9140  10.6000
 293  H71  H  HCH2  0   0.200  29.0604  -14.4428  12.4927
 293  H72  H  HCH2  0   0.219  29.5585  -13.5917  11.0328
 293  HO1  H  HOH1  0   0.454  28.7060  -17.1985   8.8754
 293  HO3  H  HOH1  0   0.441  24.1345  -16.9001   8.8112
 293  HO4  H  HOH1  0   0.456  25.3493  -13.4033   9.2526
 293  HO6  H  HOH1  0   0.444  26.5249  -14.5615  12.7733
 293  HO7  H  HOH1  0   0.441  28.3093  -12.3645  13.2374

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
 293  C2  C1   single  1.523  0.020  1.523
 293  O1  C1   single  1.394  0.020  1.394
 293  C1  O5   single  1.406  0.020  1.406
 293  C1  H1   single  0.970  0.020  1.090
 293  C3  C2   single  1.528  0.020  1.528
 293  C2  H2   single  0.970  0.020  1.090
 293  C2  H2A  single  0.970  0.020  1.090
 293  O3  C3   single  1.406  0.020  1.406
 293  C3  C4   single  1.526  0.020  1.526
 293  C3  H3   single  0.970  0.020  1.090
 293  O4  C4   single  1.406  0.020  1.406
 293  C4  C5   single  1.536  0.020  1.536
 293  C4  H4   single  0.970  0.020  1.090
 293  C5  C6   single  1.526  0.020  1.526
 293  C5  O5   single  1.415  0.020  1.415
 293  C5  H5   single  0.970  0.020  1.090
 293  C6  C7   single  1.527  0.020  1.527
 293  C6  O6   single  1.412  0.020  1.412
 293  C6  H6   single  0.970  0.020  1.090
 293  C7  O7   single  1.408  0.020  1.408
 293  C7  H71  single  0.970  0.020  1.090
 293  C7  H72  single  0.970  0.020  1.090
 293  O1  HO1  single  0.850  0.020  0.980
 293  O3  HO3  single  0.850  0.020  0.980
 293  O4  HO4  single  0.850  0.020  0.980
 293  O6  HO6  single  0.850  0.020  0.980
 293  O7  HO7  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
 293  H1   C1  O5   104.52  3.000
 293  H1   C1  O1   105.91  3.000
 293  O5   C1  O1   112.02  3.000
 293  H1   C1  C2   109.84  3.000
 293  O5   C1  C2   110.35  3.000
 293  O1   C1  C2   113.68  3.000
 293  H2A  C2  H2   106.88  3.000
 293  H2A  C2  C3   108.63  3.000
 293  H2   C2  C3   110.53  3.000
 293  H2A  C2  C1   107.78  3.000
 293  H2   C2  C1   109.92  3.000
 293  C3   C2  C1   112.88  3.000
 293  H3   C3  O3   104.83  3.000
 293  H3   C3  C4   107.96  3.000
 293  O3   C3  C4   112.99  3.000
 293  H3   C3  C2   110.13  3.000
 293  C4   C3  C2   109.14  3.000
 293  O3   C3  C2   111.65  3.000
 293  H4   C4  O4   111.52  3.000
 293  H4   C4  C5   108.79  3.000
 293  O4   C4  C5   110.80  3.000
 293  H4   C4  C3   107.90  3.000
 293  C5   C4  C3   108.93  3.000
 293  O4   C4  C3   108.82  3.000
 293  H5   C5  O5   110.94  3.000
 293  H5   C5  C6   106.78  3.000
 293  O5   C5  C6   107.06  3.000
 293  H5   C5  C4   107.78  3.000
 293  O5   C5  C4   110.68  3.000
 293  C6   C5  C4   113.56  3.000
 293  H6   C6  O6   105.99  3.000
 293  H6   C6  C7   107.31  3.000
 293  O6   C6  C7   111.21  3.000
 293  H6   C6  C5   107.61  3.000
 293  O6   C6  C5   112.64  3.000
 293  C7   C6  C5   111.70  3.000
 293  H72  C7  H71  107.11  3.000
 293  H72  C7  O7   106.89  3.000
 293  H71  C7  O7   111.43  3.000
 293  H72  C7  C6   109.12  3.000
 293  H71  C7  C6   109.95  3.000
 293  O7   C7  C6   112.15  3.000
 293  HO1  O1  C1   111.12  3.000
 293  HO3  O3  C3   108.51  3.000
 293  HO4  O4  C4   109.06  3.000
 293  C5   O5  C1   115.61  3.000
 293  HO6  O6  C6   108.40  3.000
 293  HO7  O7  C7   107.82  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
 293  chir_01  C1  C2  O1  O5  negativ
 293  chir_02  C3  O3  C4  C2  negativ
 293  chir_03  C4  O4  C3  C5  negativ
 293  chir_04  C5  O5  C6  C4  positiv
 293  chir_05  C6  O6  C5  C7  positiv

