# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 19:34:34 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: 1,5-anhydro-3-O-methyl-D-mannitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1[C@H](O)CO[C@H](CO)[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
 3HD  3HD  1,5-anhydro-3-O-methyl-D-mannitol  D-saccharide  26  12  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3HD
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
 3HD  C1   C  CH2   0  -0.220  -0.1299   1.7692  -0.8417
 3HD  C2   C  CH1   0  -0.019   1.1815   1.2099  -0.3137
 3HD  O2   O  OH1   0  -0.668   1.4071   1.5437   1.0349
 3HD  C3   C  CH1   0   0.041   1.1419  -0.3150  -0.4174
 3HD  O3   O  O2    0  -0.487   2.2508  -0.9369   0.1723
 3HD  CH3  C  CH3   0  -0.408   3.4622  -0.7304  -0.5102
 3HD  C4   C  CH1   0   0.005  -0.1139  -0.8750   0.2421
 3HD  O4   O  OH1   0  -0.670  -0.1801  -2.2519  -0.0518
 3HD  C5   C  CH1   0  -0.007  -1.3573  -0.1478  -0.2995
 3HD  O5   O  O2    0  -0.481  -1.2348   1.2474  -0.1483
 3HD  C6   C  CH2   0  -0.161  -2.6134  -0.5826   0.4251
 3HD  O6   O  OH1   0  -0.670  -3.7273   0.0254  -0.1834
 3HD  H1   H  HCH2  0   0.249  -0.1560   2.8552  -0.7221
 3HD  HC1  H  HCH2  0   0.209  -0.2021   1.5601  -1.9194
 3HD  H2   H  HCH1  0   0.227   1.9833   1.5984  -0.9591
 3HD  HO2  H  HOH1  0   0.452   1.4300   2.5027   1.1111
 3HD  H3   H  HCH1  0   0.213   1.0982  -0.5591  -1.4934
 3HD  H31  H  HCH3  0   0.236   4.2107  -1.3792  -0.0563
 3HD  H32  H  HCH3  0   0.205   3.3822  -0.9881  -1.5731
 3HD  H33  H  HCH3  0   0.209   3.8229   0.3013  -0.4398
 3HD  H4   H  HCH1  0   0.226  -0.0503  -0.7039   1.3252
 3HD  HO4  H  HOH1  0   0.457  -0.5933  -2.7095   0.6846
 3HD  H5   H  HCH1  0   0.208  -1.4581  -0.4030  -1.3689
 3HD  H61  H  HCH2  0   0.199  -2.6818  -1.6758   0.3813
 3HD  H62  H  HCH2  0   0.198  -2.5248  -0.3077   1.4856
 3HD  HO6  H  HOH1  0   0.456  -4.5169  -0.2769   0.2740

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
 3HD  C1   C2   single  1.520  0.020  1.520
 3HD  C1   O5   single  1.405  0.020  1.405
 3HD  C1   H1   single  0.970  0.020  1.090
 3HD  C1   HC1  single  0.970  0.020  1.090
 3HD  C2   O2   single  1.408  0.020  1.408
 3HD  C2   C3   single  1.529  0.020  1.529
 3HD  C2   H2   single  0.970  0.020  1.090
 3HD  O2   HO2  single  0.850  0.020  0.980
 3HD  C3   O3   single  1.401  0.020  1.401
 3HD  C3   C4   single  1.525  0.020  1.525
 3HD  C3   H3   single  0.970  0.020  1.090
 3HD  O3   CH3  single  1.406  0.020  1.406
 3HD  CH3  H31  single  0.970  0.020  1.090
 3HD  CH3  H32  single  0.970  0.020  1.090
 3HD  CH3  H33  single  0.970  0.020  1.090
 3HD  C4   O4   single  1.409  0.020  1.409
 3HD  C4   C5   single  1.539  0.020  1.539
 3HD  C4   H4   single  0.970  0.020  1.090
 3HD  O4   HO4  single  0.850  0.020  0.980
 3HD  C5   O5   single  1.409  0.020  1.409
 3HD  C5   C6   single  1.514  0.020  1.514
 3HD  C5   H5   single  0.970  0.020  1.090
 3HD  C6   O6   single  1.407  0.020  1.407
 3HD  C6   H61  single  0.970  0.020  1.090
 3HD  C6   H62  single  0.970  0.020  1.090
 3HD  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
 3HD  HC1  C1   H1   107.13  3.000
 3HD  HC1  C1   O5   111.18  3.000
 3HD  H1   C1   O5   107.24  3.000
 3HD  HC1  C1   C2   109.07  3.000
 3HD  H1   C1   C2   110.37  3.000
 3HD  O5   C1   C2   111.73  3.000
 3HD  H2   C2   C3   109.35  3.000
 3HD  H2   C2   O2   111.19  3.000
 3HD  C3   C2   O2   107.79  3.000
 3HD  H2   C2   C1   107.16  3.000
 3HD  C3   C2   C1   108.72  3.000
 3HD  O2   C2   C1   112.57  3.000
 3HD  HO2  O2   C2   108.42  3.000
 3HD  H3   C3   C4   107.92  3.000
 3HD  H3   C3   O3   110.07  3.000
 3HD  C4   C3   O3   107.86  3.000
 3HD  H3   C3   C2   106.71  3.000
 3HD  C4   C3   C2   110.99  3.000
 3HD  O3   C3   C2   113.17  3.000
 3HD  CH3  O3   C3   114.36  3.000
 3HD  H33  CH3  H32  107.92  3.000
 3HD  H33  CH3  H31  107.93  3.000
 3HD  H32  CH3  H31  108.29  3.000
 3HD  H33  CH3  O3   113.02  3.000
 3HD  H32  CH3  O3   111.92  3.000
 3HD  H31  CH3  O3   107.60  3.000
 3HD  H4   C4   C5   108.68  3.000
 3HD  H4   C4   O4   111.13  3.000
 3HD  C5   C4   O4   110.51  3.000
 3HD  H4   C4   C3   108.76  3.000
 3HD  C5   C4   C3   109.85  3.000
 3HD  O4   C4   C3   107.89  3.000
 3HD  HO4  O4   C4   109.02  3.000
 3HD  H5   C5   C6   108.75  3.000
 3HD  H5   C5   O5   109.93  3.000
 3HD  C6   C5   O5   107.77  3.000
 3HD  H5   C5   C4   107.79  3.000
 3HD  C6   C5   C4   111.48  3.000
 3HD  O5   C5   C4   111.10  3.000
 3HD  C5   O5   C1   112.54  3.000
 3HD  H62  C6   H61  107.04  3.000
 3HD  H62  C6   O6   111.90  3.000
 3HD  H61  C6   O6   111.35  3.000
 3HD  H62  C6   C5   108.85  3.000
 3HD  H61  C6   C5   108.61  3.000
 3HD  O6   C6   C5   109.01  3.000
 3HD  HO6  O6   C6   107.97  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 3HD  Var_01  H1   C1   O5  C5   176.27  30.0  1
 3HD  Var_02  H31  CH3  O3  C3  -171.29  30.0  3

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
 3HD  chir_01  C2  C1  O2  C3  negativ
 3HD  chir_02  C3  O3  C4  C2  negativ
 3HD  chir_03  C4  O4  C5  C3  positiv
 3HD  chir_04  C5  O5  C6  C4  positiv

