# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:36:06 2022
#   Inital geometry file: a 76 line input string
#   Ligand name: methyl 2-(acetylamino)-2-deoxy-alpha-D-glucopyranoside
#   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]1NC(C)=O
#
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
 2F8  2F8  'methyl 2-(acetylamino)-2-deoxy-alpha-D-glucopyranoside'  D-saccharide  33  16  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2F8
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
 2F8  O6   O  OH1   0  -0.666  33.5260  43.5682   2.9051
 2F8  C6   C  CH2   0  -0.161  32.9601  42.5036   3.6328
 2F8  C5   C  CH1   0  -0.014  32.5653  43.0145   5.0024
 2F8  O5   O  O2    0  -0.499  31.5454  43.9830   4.8114
 2F8  C1   C  CH1   0   0.296  31.1059  44.6256   5.9715
 2F8  O1   O  O2    0  -0.497  32.1162  45.3364   6.6087
 2F8  CM   C  CH3   0  -0.406  32.5883  46.4575   5.8905
 2F8  C2   C  CH1   0  -0.162  30.5476  43.6068   6.9651
 2F8  N2   N  NH1   0  -0.629  30.1296  44.2457   8.1861
 2F8  C7   C  C     0   0.501  28.8564  44.2800   8.6392
 2F8  O7   O  O     0  -0.484  27.9294  43.7216   8.0748
 2F8  C8   C  CH3   0  -0.784  28.6807  45.0696   9.9148
 2F8  C3   C  CH1   0   0.018  31.5665  42.4961   7.2320
 2F8  O3   O  OH1   0  -0.666  31.0009  41.4460   7.9802
 2F8  C4   C  CH1   0   0.036  32.0551  41.9021   5.9157
 2F8  O4   O  OH1   0  -0.668  33.1078  40.9943   6.1245
 2F8  HO6  H  HOH1  0   0.454  33.8258  43.2253   2.0585
 2F8  H61  H  HCH2  0   0.195  32.0717  42.0912   3.1341
 2F8  H62  H  HCH2  0   0.211  33.6696  41.6798   3.7626
 2F8  H5   H  HCH1  0   0.226  33.4484  43.4717   5.4707
 2F8  H1   H  HCH1  0   0.236  30.3054  45.3018   5.6410
 2F8  H6   H  HCH3  0   0.238  33.2723  46.9970   6.5428
 2F8  H7   H  HCH3  0   0.218  33.1259  46.1729   4.9825
 2F8  H8   H  HCH3  0   0.214  31.7694  47.1291   5.6113
 2F8  H2   H  HCH1  0   0.275  29.6635  43.1588   6.5073
 2F8  HN2  H  HNH1  0   0.399  30.8273  44.7703   8.6915
 2F8  H81  H  HCH3  0   0.260  27.6336  45.0929  10.2040
 2F8  H82  H  HCH3  0   0.265  29.2587  44.6247  10.7260
 2F8  H83  H  HCH3  0   0.262  29.0336  46.0940   9.7895
 2F8  H3   H  HCH1  0   0.219  32.4361  42.9189   7.7564
 2F8  HO3  H  HOH1  0   0.456  30.9243  41.7268   8.8974
 2F8  H4   H  HCH1  0   0.208  31.1994  41.4121   5.4217
 2F8  HO4  H  HOH1  0   0.451  32.7972  40.3108   6.7280

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
 2F8  O6  C6   single  1.408  0.020  1.408
 2F8  C6  C5   single  1.514  0.020  1.514
 2F8  O5  C5   single  1.419  0.020  1.419
 2F8  O5  C1   single  1.397  0.020  1.397
 2F8  C5  C4   single  1.527  0.020  1.527
 2F8  CM  O1   single  1.413  0.020  1.413
 2F8  C4  O4   single  1.406  0.020  1.406
 2F8  C4  C3   single  1.525  0.020  1.525
 2F8  C1  O1   single  1.390  0.020  1.390
 2F8  C1  C2   single  1.529  0.020  1.529
 2F8  C2  C3   single  1.531  0.020  1.531
 2F8  C2  N2   single  1.440  0.020  1.440
 2F8  C3  O3   single  1.408  0.020  1.408
 2F8  N2  C7   single  1.352  0.020  1.352
 2F8  O7  C7   double  1.221  0.020  1.221
 2F8  C7  C8   single  1.510  0.020  1.510
 2F8  O6  HO6  single  0.850  0.020  0.980
 2F8  C6  H61  single  0.970  0.020  1.090
 2F8  C6  H62  single  0.970  0.020  1.090
 2F8  C5  H5   single  0.970  0.020  1.090
 2F8  C1  H1   single  0.970  0.020  1.090
 2F8  CM  H6   single  0.970  0.020  1.090
 2F8  CM  H7   single  0.970  0.020  1.090
 2F8  CM  H8   single  0.970  0.020  1.090
 2F8  C2  H2   single  0.970  0.020  1.090
 2F8  N2  HN2  single  0.860  0.020  1.020
 2F8  C8  H81  single  0.970  0.020  1.090
 2F8  C8  H82  single  0.970  0.020  1.090
 2F8  C8  H83  single  0.970  0.020  1.090
 2F8  C3  H3   single  0.970  0.020  1.090
 2F8  O3  HO3  single  0.850  0.020  0.980
 2F8  C4  H4   single  0.970  0.020  1.090
 2F8  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
 2F8  HO6  O6  C6   108.10  3.000
 2F8  H62  C6  H61  107.17  3.000
 2F8  H62  C6  C5   108.40  3.000
 2F8  H61  C6  C5   109.05  3.000
 2F8  H62  C6  O6   111.69  3.000
 2F8  H61  C6  O6   111.96  3.000
 2F8  C5   C6  O6   108.49  3.000
 2F8  H5   C5  C4   108.46  3.000
 2F8  H5   C5  O5   110.53  3.000
 2F8  C4   C5  O5   109.72  3.000
 2F8  H5   C5  C6   108.44  3.000
 2F8  C4   C5  C6   112.48  3.000
 2F8  O5   C5  C6   107.21  3.000
 2F8  C1   O5  C5   115.35  3.000
 2F8  H1   C1  C2   109.85  3.000
 2F8  H1   C1  O1   110.65  3.000
 2F8  C2   C1  O1   107.96  3.000
 2F8  H1   C1  O5   105.22  3.000
 2F8  C2   C1  O5   110.37  3.000
 2F8  O1   C1  O5   112.78  3.000
 2F8  CM   O1  C1   114.56  3.000
 2F8  H8   CM  H7   108.40  3.000
 2F8  H8   CM  H6   108.58  3.000
 2F8  H7   CM  H6   108.53  3.000
 2F8  H8   CM  O1   111.49  3.000
 2F8  H7   CM  O1   112.34  3.000
 2F8  H6   CM  O1   107.39  3.000
 2F8  H2   C2  C3   108.33  3.000
 2F8  H2   C2  N2   107.61  3.000
 2F8  C3   C2  N2   111.55  3.000
 2F8  H2   C2  C1   107.26  3.000
 2F8  N2   C2  C1   111.19  3.000
 2F8  C3   C2  C1   110.72  3.000
 2F8  HN2  N2  C7   118.05  3.000
 2F8  HN2  N2  C2   117.05  3.000
 2F8  C7   N2  C2   124.67  3.000
 2F8  C8   C7  O7   122.78  3.000
 2F8  C8   C7  N2   113.95  3.000
 2F8  O7   C7  N2   123.27  3.000
 2F8  H83  C8  H82  107.28  3.000
 2F8  H83  C8  H81  108.80  3.000
 2F8  H82  C8  H81  108.75  3.000
 2F8  H83  C8  C7   110.88  3.000
 2F8  H82  C8  C7   110.68  3.000
 2F8  H81  C8  C7   110.37  3.000
 2F8  H3   C3  C4   107.94  3.000
 2F8  H3   C3  O3   110.54  3.000
 2F8  C4   C3  O3   107.27  3.000
 2F8  H3   C3  C2   109.30  3.000
 2F8  O3   C3  C2   111.50  3.000
 2F8  C4   C3  C2   110.21  3.000
 2F8  HO3  O3  C3   108.72  3.000
 2F8  H4   C4  O4   111.14  3.000
 2F8  H4   C4  C3   108.13  3.000
 2F8  O4   C4  C3   111.31  3.000
 2F8  H4   C4  C5   108.36  3.000
 2F8  C3   C4  C5   109.86  3.000
 2F8  O4   C4  C5   108.00  3.000
 2F8  HO4  O4  C4   108.05  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
 2F8  CONST_01  O7   C7  N2  C2    0.00   0.0  0
 2F8  CONST_02  C8   C7  N2  C2  180.00   0.0  0
 2F8  CONST_03  HN2  N2  C7  O7  180.00   0.0  0
 2F8  Var_01    H6   CM  O1  C1  172.69  30.0  3
 2F8  Var_02    H81  C8  C7  N2  177.71  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
 2F8  chir_01  C5  C6  O5  C4  negativ
 2F8  chir_02  C1  O5  O1  C2  positiv
 2F8  chir_03  C2  N2  C3  C1  positiv
 2F8  chir_04  C3  O3  C2  C4  positiv
 2F8  chir_05  C4  O4  C5  C3  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 2F8  plan-1  C2   0.020
 2F8  plan-1  N2   0.020
 2F8  plan-1  C7   0.020
 2F8  plan-1  O7   0.020
 2F8  plan-1  C8   0.020
 2F8  plan-1  HN2  0.020

