# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 28 23:51:16 2022
#   Inital geometry file: a 65 line input string
#   Ligand name: (2~{R},3~{S},4~{R},5~{S},6~{S})-2-(hydroxymethyl)-6-methoxy-5-methyl-oxane-3,4-diol
#   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]1C
#
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
 5II  5II  "methyl 2-deoxy-2-methyl-alpha-D-mannopyranoside"  D-saccharide  29  13  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5II
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
 5II  C9   C  CH3   0  -0.408  -80.5252  20.7115  -46.7697
 5II  O1   O  O2    0  -0.495  -80.4681  19.3086  -46.9099
 5II  C1   C  CH1   0   0.307  -80.7375  18.6004  -45.7409
 5II  C2   C  CH1   0  -0.348  -80.4930  17.1164  -45.9991
 5II  C7   C  CH3   0  -0.666  -80.4055  16.3599  -44.6761
 5II  C3   C  CH1   0   0.053  -81.5709  16.5710  -46.9479
 5II  O3   O  OH1   0  -0.664  -81.4846  15.1748  -47.1113
 5II  C4   C  CH1   0   0.009  -82.9662  16.8953  -46.4354
 5II  O4   O  OH1   0  -0.668  -83.8970  16.5236  -47.4277
 5II  C5   C  CH1   0  -0.014  -83.0725  18.3979  -46.1371
 5II  O5   O  O2    0  -0.500  -82.0368  18.8213  -45.2676
 5II  C6   C  CH2   0  -0.162  -84.3835  18.7490  -45.4651
 5II  O6   O  OH1   0  -0.665  -84.4813  20.1496  -45.3591
 5II  H1   H  HCH3  0   0.234  -80.1295  21.1464  -47.6862
 5II  H2   H  HCH3  0   0.213  -81.5448  21.0799  -46.6263
 5II  H3   H  HCH3  0   0.208  -79.9137  21.0595  -45.9295
 5II  H4   H  HCH1  0   0.220  -80.0848  18.9542  -44.9291
 5II  H5   H  HCH1  0   0.249  -79.5221  17.0270  -46.4991
 5II  H6   H  HCH3  0   0.233  -79.5891  16.7575  -44.0715
 5II  H7   H  HCH3  0   0.225  -81.3179  16.4392  -44.0845
 5II  H8   H  HCH3  0   0.237  -80.2045  15.3022  -44.8366
 5II  H9   H  HCH1  0   0.215  -81.4539  17.0735  -47.9200
 5II  H10  H  HOH1  0   0.448  -80.6212  14.9685  -47.4836
 5II  H11  H  HCH1  0   0.220  -83.1442  16.3370  -45.5050
 5II  H12  H  HOH1  0   0.454  -84.7137  16.2454  -47.0058
 5II  H13  H  HCH1  0   0.219  -83.0204  18.9377  -47.0943
 5II  H14  H  HCH2  0   0.198  -85.2049  18.3365  -46.0625
 5II  H15  H  HCH2  0   0.196  -84.4220  18.2592  -44.4820
 5II  H16  H  HOH1  0   0.453  -85.3135  20.3588  -44.9260

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
 5II  O4  C4   single  1.410  0.020  1.410
 5II  O3  C3   single  1.408  0.020  1.408
 5II  C3  C4   single  1.521  0.020  1.521
 5II  C3  C2   single  1.536  0.020  1.536
 5II  O1  C9   single  1.411  0.020  1.411
 5II  O1  C1   single  1.393  0.020  1.393
 5II  C4  C5   single  1.536  0.020  1.536
 5II  C5  C6   single  1.514  0.020  1.514
 5II  C5  O5   single  1.417  0.020  1.417
 5II  C2  C1   single  1.526  0.020  1.526
 5II  C2  C7   single  1.527  0.020  1.527
 5II  C1  O5   single  1.400  0.020  1.400
 5II  C6  O6   single  1.408  0.020  1.408
 5II  C9  H1   single  0.970  0.020  1.090
 5II  C9  H2   single  0.970  0.020  1.090
 5II  C9  H3   single  0.970  0.020  1.090
 5II  C1  H4   single  0.970  0.020  1.090
 5II  C2  H5   single  0.970  0.020  1.090
 5II  C7  H6   single  0.970  0.020  1.090
 5II  C7  H7   single  0.970  0.020  1.090
 5II  C7  H8   single  0.970  0.020  1.090
 5II  C3  H9   single  0.970  0.020  1.090
 5II  O3  H10  single  0.850  0.020  0.980
 5II  C4  H11  single  0.970  0.020  1.090
 5II  O4  H12  single  0.850  0.020  0.980
 5II  C5  H13  single  0.970  0.020  1.090
 5II  C6  H14  single  0.970  0.020  1.090
 5II  C6  H15  single  0.970  0.020  1.090
 5II  O6  H16  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
 5II  H3   C9  H2   108.22  3.000
 5II  H3   C9  H1   108.40  3.000
 5II  H2   C9  H1   108.34  3.000
 5II  H3   C9  O1   111.67  3.000
 5II  H2   C9  O1   112.69  3.000
 5II  H1   C9  O1   107.39  3.000
 5II  C1   O1  C9   114.47  3.000
 5II  H4   C1  O5   104.50  3.000
 5II  H4   C1  C2   110.03  3.000
 5II  O5   C1  C2   111.05  3.000
 5II  H4   C1  O1   109.94  3.000
 5II  O5   C1  O1   112.51  3.000
 5II  C2   C1  O1   108.75  3.000
 5II  H5   C2  C3   108.12  3.000
 5II  H5   C2  C7   107.71  3.000
 5II  C3   C2  C7   113.55  3.000
 5II  H5   C2  C1   107.37  3.000
 5II  C7   C2  C1   110.15  3.000
 5II  C3   C2  C1   109.72  3.000
 5II  H8   C7  H7   107.77  3.000
 5II  H8   C7  H6   107.32  3.000
 5II  H7   C7  H6   107.39  3.000
 5II  H8   C7  C2   111.37  3.000
 5II  H7   C7  C2   112.72  3.000
 5II  H6   C7  C2   110.03  3.000
 5II  H9   C3  C4   107.32  3.000
 5II  H9   C3  O3   110.10  3.000
 5II  C4   C3  O3   107.85  3.000
 5II  H9   C3  C2   107.99  3.000
 5II  C4   C3  C2   111.09  3.000
 5II  O3   C3  C2   112.37  3.000
 5II  H10  O3  C3   108.20  3.000
 5II  H11  C4  C5   108.74  3.000
 5II  H11  C4  O4   110.77  3.000
 5II  C5   C4  O4   110.42  3.000
 5II  H11  C4  C3   108.98  3.000
 5II  C5   C4  C3   109.73  3.000
 5II  O4   C4  C3   108.18  3.000
 5II  H12  O4  C4   109.17  3.000
 5II  H13  C5  C6   108.26  3.000
 5II  H13  C5  O5   110.65  3.000
 5II  C6   C5  O5   106.93  3.000
 5II  H13  C5  C4   107.93  3.000
 5II  O5   C5  C4   111.16  3.000
 5II  C6   C5  C4   111.90  3.000
 5II  C5   O5  C1   115.07  3.000
 5II  H15  C6  H14  107.07  3.000
 5II  H15  C6  O6   111.94  3.000
 5II  H14  C6  O6   111.30  3.000
 5II  H15  C6  C5   108.90  3.000
 5II  H14  C6  C5   108.64  3.000
 5II  O6   C6  C5   108.92  3.000
 5II  H16  O6  C6   108.09  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
 5II  Var_01  H1  C9  O1  C1  170.17  30.0  3
 5II  Var_02  H2  C9  O1  C1  -70.60  30.0  3
 5II  Var_03  H3  C9  O1  C1   51.46  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
 5II  chir_01  C1  O1  C2  O5  positiv
 5II  chir_02  C2  C3  C1  C7  negativ
 5II  chir_03  C3  O3  C2  C4  positiv
 5II  chir_04  C4  O4  C5  C3  positiv
 5II  chir_05  C5  O5  C4  C6  negativ

