# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 20:42:24 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: methyl 2-deoxy-2-(2-hydroxyethyl)-alpha-D-mannopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]1CCO
#
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
 H1M  H1M  'methyl 2-deoxy-2-(2-hydroxyethyl)-alpha-D-mannopyranoside'  D-saccharide  33  15  .  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_H1M
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
 H1M  C9   C  CH3   0  -0.411   1.0748   2.7302   1.6624
 H1M  O1   O  O2    0  -0.498   0.3391   1.5254   1.6951
 H1M  C1   C  CH1   0   0.304  -0.2577   1.1846   0.4842
 H1M  C2   C  CH1   0  -0.338  -1.1430  -0.0417   0.7074
 H1M  C7   C  CH2   0  -0.478  -2.0592  -0.2842  -0.4969
 H1M  C8   C  CH2   0  -0.137  -3.2141   0.6996  -0.5608
 H1M  O8   O  OH1   0  -0.674  -4.0031   0.3864  -1.6884
 H1M  C3   C  CH1   0   0.053  -0.2379  -1.2331   1.0252
 H1M  O3   O  OH1   0  -0.671  -1.0293  -2.3813   1.2132
 H1M  C4   C  CH1   0  -0.017   0.7918  -1.4334  -0.0815
 H1M  O4   O  OH1   0  -0.676   1.6622  -2.4677   0.3334
 H1M  C5   C  CH1   0  -0.006   1.5666  -0.1311  -0.3172
 H1M  O5   O  O2    0  -0.500   0.6807   0.9540  -0.5304
 H1M  C6   C  CH2   0  -0.162   2.4598  -0.2200  -1.5359
 H1M  O6   O  OH1   0  -0.668   3.2456   0.9449  -1.6146
 H1M  H9   H  HCH3  0   0.235   1.3471   2.9730   2.6881
 H1M  H9A  H  HCH3  0   0.218   1.9910   2.6473   1.0717
 H1M  H9B  H  HCH3  0   0.210   0.4784   3.5556   1.2579
 H1M  H1   H  HCH1  0   0.225  -0.8511   2.0311   0.1121
 H1M  H2   H  HCH1  0   0.253  -1.7718   0.1509   1.5844
 H1M  H7   H  HCH2  0   0.229  -1.4886  -0.2317  -1.4281
 H1M  H7A  H  HCH2  0   0.247  -2.4729  -1.2925  -0.4390
 H1M  H8   H  HCH2  0   0.193  -3.7965   0.6317   0.3682
 H1M  H8A  H  HCH2  0   0.191  -2.8393   1.7298  -0.6196
 H1M  HO8  H  HOH1  0   0.453  -4.7291   1.0148  -1.7312
 H1M  H3   H  HCH1  0   0.219   0.3136  -1.0048   1.9493
 H1M  HO3  H  HOH1  0   0.448  -0.4337  -3.1214   1.3725
 H1M  H4   H  HCH1  0   0.227   0.2714  -1.7190  -1.0060
 H1M  HO4  H  HOH1  0   0.461   1.9272  -2.9849  -0.4314
 H1M  H5   H  HCH1  0   0.221   2.1992   0.0508   0.5642
 H1M  H6   H  HCH2  0   0.198   3.0834  -1.1176  -1.4463
 H1M  H6A  H  HCH2  0   0.198   1.8336  -0.3505  -2.4293
 H1M  HO6  H  HOH1  0   0.455   3.7928   0.8819  -2.4020

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
 H1M  O1  C9   single  1.412  0.020  1.412
 H1M  C9  H9   single  0.970  0.020  1.090
 H1M  C9  H9A  single  0.970  0.020  1.090
 H1M  C9  H9B  single  0.970  0.020  1.090
 H1M  C1  O1   single  1.392  0.020  1.392
 H1M  C2  C1   single  1.529  0.020  1.529
 H1M  C1  O5   single  1.401  0.020  1.401
 H1M  C1  H1   single  0.970  0.020  1.090
 H1M  C3  C2   single  1.530  0.020  1.530
 H1M  C7  C2   single  1.533  0.020  1.533
 H1M  C2  H2   single  0.970  0.020  1.090
 H1M  C7  C8   single  1.518  0.020  1.518
 H1M  C7  H7   single  0.970  0.020  1.090
 H1M  C7  H7A  single  0.970  0.020  1.090
 H1M  O8  C8   single  1.411  0.020  1.411
 H1M  C8  H8   single  0.970  0.020  1.090
 H1M  C8  H8A  single  0.970  0.020  1.090
 H1M  O8  HO8  single  0.850  0.020  0.980
 H1M  O3  C3   single  1.407  0.020  1.407
 H1M  C3  C4   single  1.525  0.020  1.525
 H1M  C3  H3   single  0.970  0.020  1.090
 H1M  O3  HO3  single  0.850  0.020  0.980
 H1M  O4  C4   single  1.414  0.020  1.414
 H1M  C4  C5   single  1.534  0.020  1.534
 H1M  C4  H4   single  0.970  0.020  1.090
 H1M  O4  HO4  single  0.850  0.020  0.980
 H1M  C5  C6   single  1.514  0.020  1.514
 H1M  C5  O5   single  1.417  0.020  1.417
 H1M  C5  H5   single  0.970  0.020  1.090
 H1M  O6  C6   single  1.407  0.020  1.407
 H1M  C6  H6   single  0.970  0.020  1.090
 H1M  C6  H6A  single  0.970  0.020  1.090
 H1M  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
 H1M  H9B  C9  H9A  108.29  3.000
 H1M  H9B  C9  H9   108.42  3.000
 H1M  H9A  C9  H9   108.44  3.000
 H1M  H9B  C9  O1   111.57  3.000
 H1M  H9A  C9  O1   112.61  3.000
 H1M  H9   C9  O1   107.39  3.000
 H1M  C1   O1  C9   114.33  3.000
 H1M  H1   C1  O5   104.08  3.000
 H1M  H1   C1  C2   110.78  3.000
 H1M  O5   C1  C2   111.19  3.000
 H1M  H1   C1  O1   109.72  3.000
 H1M  O5   C1  O1   112.52  3.000
 H1M  C2   C1  O1   108.51  3.000
 H1M  H2   C2  C3   108.07  3.000
 H1M  H2   C2  C7   108.27  3.000
 H1M  C3   C2  C7   113.19  3.000
 H1M  H2   C2  C1   107.94  3.000
 H1M  C7   C2  C1   111.00  3.000
 H1M  C3   C2  C1   108.21  3.000
 H1M  H7A  C7  H7   106.70  3.000
 H1M  H7A  C7  C8   108.21  3.000
 H1M  H7   C7  C8   109.27  3.000
 H1M  H7A  C7  C2   109.33  3.000
 H1M  H7   C7  C2   110.47  3.000
 H1M  C8   C7  C2   112.66  3.000
 H1M  H8A  C8  H8   106.52  3.000
 H1M  H8A  C8  O8   110.87  3.000
 H1M  H8   C8  O8   111.44  3.000
 H1M  H8A  C8  C7   110.53  3.000
 H1M  H8   C8  C7   109.12  3.000
 H1M  O8   C8  C7   108.36  3.000
 H1M  HO8  O8  C8   108.22  3.000
 H1M  H3   C3  C4   107.35  3.000
 H1M  H3   C3  O3   109.82  3.000
 H1M  C4   C3  O3   111.69  3.000
 H1M  H3   C3  C2   108.03  3.000
 H1M  C4   C3  C2   110.56  3.000
 H1M  O3   C3  C2   109.30  3.000
 H1M  HO3  O3  C3   107.54  3.000
 H1M  H4   C4  C5   109.31  3.000
 H1M  H4   C4  O4   110.39  3.000
 H1M  C5   C4  O4   110.81  3.000
 H1M  H4   C4  C3   108.96  3.000
 H1M  C5   C4  C3   109.95  3.000
 H1M  O4   C4  C3   107.38  3.000
 H1M  HO4  O4  C4   109.27  3.000
 H1M  H5   C5  C6   108.39  3.000
 H1M  H5   C5  O5   110.71  3.000
 H1M  C6   C5  O5   107.02  3.000
 H1M  H5   C5  C4   107.93  3.000
 H1M  O5   C5  C4   110.95  3.000
 H1M  C6   C5  C4   111.84  3.000
 H1M  C5   O5  C1   115.84  3.000
 H1M  H6A  C6  H6   107.06  3.000
 H1M  H6A  C6  O6   111.77  3.000
 H1M  H6   C6  O6   111.38  3.000
 H1M  H6A  C6  C5   108.99  3.000
 H1M  H6   C6  C5   108.54  3.000
 H1M  O6   C6  C5   109.02  3.000
 H1M  HO6  O6  C6   108.03  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
 H1M  Var_01  O8  C8  C7  C2  -179.36  30.0  3
 H1M  Var_02  H9  C9  O1  C1   170.69  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
 H1M  chir_01  C1  O1  C2  O5  positiv
 H1M  chir_02  C2  C7  C3  C1  negativ
 H1M  chir_03  C3  O3  C2  C4  positiv
 H1M  chir_04  C4  O4  C5  C3  positiv
 H1M  chir_05  C5  O5  C4  C6  negativ

