# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 17:32:13 2022
#   Inital geometry file: a 55 line input string
#   Ligand name: alpha-D-mannopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[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
 MAN  MAN  'alpha-D-mannopyranose    '  D-saccharide  24  12  .  2012-04-12  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_MAN
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
 MAN  C1   C  CH1   0   0.231   99.7264  -29.3157  24.1658
 MAN  C2   C  CH1   0  -0.014  101.2061  -29.3887  24.5307
 MAN  C3   C  CH1   0   0.005  102.0170  -28.5078  23.5871
 MAN  C4   C  CH1   0  -0.003  101.7209  -28.8715  22.1373
 MAN  C5   C  CH1   0  -0.012  100.2105  -28.7935  21.8872
 MAN  C6   C  CH2   0  -0.160   99.8476  -29.2781  20.4996
 MAN  O1   O  OH1   0  -0.664   99.2731  -28.0470  24.5167
 MAN  O2   O  OH1   0  -0.668  101.5822  -30.7407  24.4346
 MAN  O3   O  OH1   0  -0.671  103.3768  -28.6822  23.9061
 MAN  O4   O  OH1   0  -0.671  102.4340  -27.9601  21.3275
 MAN  O5   O  O2    0  -0.496   99.5177  -29.6134  22.8144
 MAN  O6   O  OH1   0  -0.665   98.4688  -29.0907  20.2930
 MAN  H1   H  HCH1  0   0.234   99.1809  -30.0979  24.7078
 MAN  H2   H  HCH1  0   0.231  101.3268  -29.0199  25.5594
 MAN  H3   H  HCH1  0   0.214  101.7101  -27.4627  23.7435
 MAN  H4   H  HCH1  0   0.221  102.0577  -29.9011  21.9565
 MAN  H5   H  HCH1  0   0.219   99.8960  -27.7446  21.9871
 MAN  H61  H  HCH2  0   0.200  100.4407  -28.7141  19.7700
 MAN  H62  H  HCH2  0   0.196  100.1377  -30.3342  20.4033
 MAN  HO1  H  HOH1  0   0.460   98.3129  -28.0243  24.4407
 MAN  HO2  H  HOH1  0   0.450  102.5392  -30.7889  24.5331
 MAN  HO3  H  HOH1  0   0.450  103.9010  -28.2486  23.2238
 MAN  HO4  H  HOH1  0   0.459  102.6843  -28.3918  20.5062
 MAN  HO6  H  HOH1  0   0.453   98.2595  -29.3729  19.3984

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
 MAN  C1  C2   single  1.526  0.020  1.526
 MAN  C1  O1   single  1.392  0.020  1.392
 MAN  C1  O5   single  1.399  0.020  1.399
 MAN  C1  H1   single  0.970  0.020  1.090
 MAN  C2  C3   single  1.525  0.020  1.525
 MAN  C2  O2   single  1.407  0.020  1.407
 MAN  C2  H2   single  0.970  0.020  1.090
 MAN  C3  C4   single  1.524  0.020  1.524
 MAN  C3  O3   single  1.408  0.020  1.408
 MAN  C3  H3   single  0.970  0.020  1.090
 MAN  C4  C5   single  1.533  0.020  1.533
 MAN  C4  O4   single  1.412  0.020  1.412
 MAN  C4  H4   single  0.970  0.020  1.090
 MAN  C5  C6   single  1.514  0.020  1.514
 MAN  C5  O5   single  1.418  0.020  1.418
 MAN  C5  H5   single  0.970  0.020  1.090
 MAN  C6  O6   single  1.407  0.020  1.407
 MAN  C6  H61  single  0.970  0.020  1.090
 MAN  C6  H62  single  0.970  0.020  1.090
 MAN  O1  HO1  single  0.850  0.020  0.980
 MAN  O2  HO2  single  0.850  0.020  0.980
 MAN  O3  HO3  single  0.850  0.020  0.980
 MAN  O4  HO4  single  0.850  0.020  0.980
 MAN  O6  HO6  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
 MAN  H1   C1  O5   104.56  3.000
 MAN  H1   C1  O1   111.31  3.000
 MAN  O5   C1  O1   112.88  3.000
 MAN  H1   C1  C2   109.27  3.000
 MAN  O5   C1  C2   111.43  3.000
 MAN  O1   C1  C2   107.40  3.000
 MAN  H2   C2  O2   110.92  3.000
 MAN  H2   C2  C3   109.08  3.000
 MAN  O2   C2  C3   111.77  3.000
 MAN  H2   C2  C1   108.31  3.000
 MAN  O2   C2  C1   106.80  3.000
 MAN  C3   C2  C1   109.89  3.000
 MAN  H3   C3  O3   110.79  3.000
 MAN  H3   C3  C4   107.92  3.000
 MAN  O3   C3  C4   111.95  3.000
 MAN  H3   C3  C2   108.21  3.000
 MAN  O3   C3  C2   107.58  3.000
 MAN  C4   C3  C2   110.34  3.000
 MAN  H4   C4  O4   110.84  3.000
 MAN  H4   C4  C5   108.84  3.000
 MAN  O4   C4  C5   111.79  3.000
 MAN  H4   C4  C3   108.71  3.000
 MAN  O4   C4  C3   107.06  3.000
 MAN  C5   C4  C3   109.55  3.000
 MAN  H5   C5  O5   110.63  3.000
 MAN  H5   C5  C6   108.66  3.000
 MAN  O5   C5  C6   107.28  3.000
 MAN  H5   C5  C4   108.39  3.000
 MAN  O5   C5  C4   110.20  3.000
 MAN  C6   C5  C4   111.68  3.000
 MAN  H62  C6  H61  107.05  3.000
 MAN  H62  C6  O6   111.94  3.000
 MAN  H61  C6  O6   111.34  3.000
 MAN  H62  C6  C5   108.94  3.000
 MAN  H61  C6  C5   108.39  3.000
 MAN  O6   C6  C5   109.08  3.000
 MAN  HO1  O1  C1   109.03  3.000
 MAN  HO2  O2  C2   107.86  3.000
 MAN  HO3  O3  C3   108.02  3.000
 MAN  HO4  O4  C4   109.37  3.000
 MAN  C5   O5  C1   115.81  3.000
 MAN  HO6  O6  C6   108.12  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
 MAN  chir_01  C1  C2  O1  O5  negativ
 MAN  chir_02  C2  O2  C1  C3  positiv
 MAN  chir_03  C3  O3  C2  C4  positiv
 MAN  chir_04  C4  O4  C5  C3  positiv
 MAN  chir_05  C5  O5  C4  C6  negativ

