# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:47:00 2022
#   Inital geometry file: a 63 line input string
#   Ligand name: D-glycero-alpha-D-manno-heptopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@H]1O[C@H](O)[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
 289  289  D-glycero-alpha-D-manno-heptopyranose  D-saccharide  28  14  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_289
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
 289  O7   O  OH1   0  -0.664  33.1113  -12.7036  10.8163
 289  C7   C  CH2   0  -0.175  31.7789  -13.0888  10.5747
 289  C6   C  CH1   0  -0.021  30.8590  -11.8755  10.4467
 289  O6   O  OH1   0  -0.664  31.3348  -10.9997   9.4438
 289  C5   C  CH1   0  -0.036  29.3953  -12.2339  10.1954
 289  O5   O  O2    0  -0.505  29.3428  -12.9264   8.9606
 289  C1   C  CH1   0   0.230  28.0595  -13.2216   8.4742
 289  O1   O  OH1   0  -0.654  27.3811  -12.0956   8.0180
 289  C2   C  CH1   0  -0.061  27.2628  -14.0365   9.5053
 289  O2   O  OH1   0  -0.669  27.8270  -15.3184   9.6629
 289  C3   C  CH1   0  -0.020  27.2999  -13.3738  10.8824
 289  O3   O  OH1   0  -0.661  26.6329  -14.1436  11.8511
 289  C4   C  CH1   0   0.027  28.7425  -13.0731  11.2921
 289  O4   O  OH1   0  -0.668  28.7974  -12.3364  12.4879
 289  HO7  H  HOH1  0   0.439  33.3674  -12.0973  10.1133
 289  H71  H  HCH2  0   0.198  31.6981  -13.7168   9.6773
 289  H72  H  HCH2  0   0.223  31.4701  -13.7014  11.4237
 289  H6   H  HCH1  0   0.244  30.9060  -11.3077  11.3797
 289  HO6  H  HOH1  0   0.443  31.1884  -11.4164   8.5862
 289  H5   H  HCH1  0   0.231  28.8456  -11.2813  10.1275
 289  H1   H  HCH1  0   0.244  28.2330  -13.8409   7.5902
 289  HO1  H  HOH1  0   0.455  26.9261  -11.6362   8.7315
 289  H2   H  HCH1  0   0.247  26.2214  -14.1038   9.1646
 289  HO2  H  HOH1  0   0.463  27.5600  -15.8731   8.9234
 289  H3   H  HCH1  0   0.243  26.7571  -12.4217  10.8392
 289  HO3  H  HOH1  0   0.444  26.9589  -15.0493  11.7825
 289  H4   H  HCH1  0   0.217  29.2819  -14.0264  11.3919
 289  HO4  H  HOH1  0   0.450  28.3112  -12.8251  13.1607

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
 289  C7  O7   single  1.408  0.020  1.408
 289  O7  HO7  single  0.850  0.020  0.980
 289  C6  C7   single  1.528  0.020  1.528
 289  C7  H71  single  0.970  0.020  1.090
 289  C7  H72  single  0.970  0.020  1.090
 289  O6  C6   single  1.414  0.020  1.414
 289  C5  C6   single  1.528  0.020  1.528
 289  C6  H6   single  0.970  0.020  1.090
 289  O6  HO6  single  0.850  0.020  0.980
 289  O5  C5   single  1.417  0.020  1.417
 289  C5  C4   single  1.527  0.020  1.527
 289  C5  H5   single  0.970  0.020  1.090
 289  C1  O5   single  1.404  0.020  1.404
 289  O1  C1   single  1.391  0.020  1.391
 289  C1  C2   single  1.537  0.020  1.537
 289  C1  H1   single  0.970  0.020  1.090
 289  O1  HO1  single  0.850  0.020  0.980
 289  C2  O2   single  1.409  0.020  1.409
 289  C2  C3   single  1.529  0.020  1.529
 289  C2  H2   single  0.970  0.020  1.090
 289  O2  HO2  single  0.850  0.020  0.980
 289  C3  C4   single  1.529  0.020  1.529
 289  C3  O3   single  1.406  0.020  1.406
 289  C3  H3   single  0.970  0.020  1.090
 289  O3  HO3  single  0.850  0.020  0.980
 289  C4  O4   single  1.406  0.020  1.406
 289  C4  H4   single  0.970  0.020  1.090
 289  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
 289  HO7  O7  C7   107.38  3.000
 289  H72  C7  H71  107.08  3.000
 289  H72  C7  C6   109.91  3.000
 289  H71  C7  C6   109.96  3.000
 289  H72  C7  O7   106.73  3.000
 289  H71  C7  O7   111.49  3.000
 289  C6   C7  O7   111.52  3.000
 289  H6   C6  C5   107.66  3.000
 289  H6   C6  O6   105.62  3.000
 289  C5   C6  O6   110.55  3.000
 289  H6   C6  C7   108.36  3.000
 289  C5   C6  C7   113.85  3.000
 289  O6   C6  C7   110.41  3.000
 289  HO6  O6  C6   108.18  3.000
 289  H5   C5  C4   107.81  3.000
 289  H5   C5  O5   110.51  3.000
 289  C4   C5  O5   109.96  3.000
 289  H5   C5  C6   106.58  3.000
 289  C4   C5  C6   114.85  3.000
 289  O5   C5  C6   107.07  3.000
 289  C1   O5  C5   116.02  3.000
 289  H1   C1  C2   108.93  3.000
 289  H1   C1  O1   105.70  3.000
 289  C2   C1  O1   113.35  3.000
 289  H1   C1  O5   104.72  3.000
 289  C2   C1  O5   110.67  3.000
 289  O1   C1  O5   112.90  3.000
 289  HO1  O1  C1   111.93  3.000
 289  H2   C2  C3   109.22  3.000
 289  H2   C2  O2   111.02  3.000
 289  C3   C2  O2   106.49  3.000
 289  H2   C2  C1   108.42  3.000
 289  C3   C2  C1   111.21  3.000
 289  O2   C2  C1   110.47  3.000
 289  HO2  O2  C2   109.11  3.000
 289  H3   C3  C4   107.86  3.000
 289  H3   C3  O3   105.52  3.000
 289  C4   C3  O3   111.76  3.000
 289  H3   C3  C2   109.19  3.000
 289  O3   C3  C2   111.83  3.000
 289  C4   C3  C2   110.46  3.000
 289  HO3  O3  C3   107.74  3.000
 289  H4   C4  O4   110.98  3.000
 289  H4   C4  C3   108.45  3.000
 289  O4   C4  C3   111.58  3.000
 289  H4   C4  C5   109.37  3.000
 289  O4   C4  C5   107.83  3.000
 289  C3   C4  C5   108.59  3.000
 289  HO4  O4  C4   107.97  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
 289  chir_01  C6  C7  O6  C5  negativ
 289  chir_02  C5  O5  C4  C6  negativ
 289  chir_03  C1  O5  O1  C2  positiv
 289  chir_04  C2  O2  C1  C3  positiv
 289  chir_05  C3  O3  C2  C4  positiv
 289  chir_06  C4  O4  C3  C5  negativ

