# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 13:04:27 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: 2-(acetylamino)-2-deoxy-alpha-L-idopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H]1[C@H](O)O[C@@H](CO)[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
 HSQ  HSQ  2-(acetylamino)-2-deoxy-alpha-L-idopyranose  L-saccharide  30  15  .  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_HSQ
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
 HSQ  C1   C  CH1   0   0.282  32.3872  -25.2340   8.4579
 HSQ  C2   C  CH1   0  -0.167  30.8604  -25.3796   8.6976
 HSQ  C3   C  CH1   0   0.078  30.5746  -25.6497  10.1727
 HSQ  C4   C  CH1   0  -0.052  31.6539  -26.5656  10.7363
 HSQ  C5   C  CH1   0  -0.024  33.0166  -25.8355  10.6825
 HSQ  C6   C  CH2   0  -0.151  33.3200  -25.0679  11.9562
 HSQ  C8   C  CH3   0  -0.813  28.5699  -25.4706   6.8519
 HSQ  N2   N  NH1   0  -0.623  30.1459  -24.2134   8.2364
 HSQ  O3   O  OH1   0  -0.665  29.2930  -26.2150  10.2612
 HSQ  O4   O  OH1   0  -0.664  31.2706  -26.9137  12.0455
 HSQ  O5   O  O2    0  -0.495  33.0481  -24.8814   9.6222
 HSQ  O6   O  OH1   0  -0.667  34.5630  -24.4247  11.7933
 HSQ  O7   O  O     0  -0.488  28.4821  -23.1111   7.2166
 HSQ  O1   O  OH1   0  -0.663  32.9627  -26.4161   7.9794
 HSQ  H1   H  HCH1  0   0.237  32.5526  -24.4051   7.7574
 HSQ  H2   H  HCH1  0   0.284  30.5095  -26.2419   8.1286
 HSQ  H3   H  HCH1  0   0.217  30.6117  -24.6926  10.7174
 HSQ  H4   H  HCH1  0   0.241  31.7038  -27.4651  10.1090
 HSQ  H5   H  HCH1  0   0.234  33.8149  -26.5728  10.5315
 HSQ  H61  H  HCH2  0   0.194  32.5159  -24.3475  12.1614
 HSQ  H62  H  HCH2  0   0.204  33.3436  -25.7723  12.7928
 HSQ  H81  H  HCH3  0   0.268  27.6872  -25.2837   6.2464
 HSQ  H82  H  HCH3  0   0.265  29.3325  -25.9273   6.2192
 HSQ  H83  H  HCH3  0   0.264  28.3144  -26.1914   7.6280
 HSQ  HN2  H  HNH1  0   0.387  30.4132  -23.3291   8.6489
 HSQ  HO3  H  HOH1  0   0.450  29.1075  -26.3938  11.1893
 HSQ  HO4  H  HOH1  0   0.461  31.7110  -27.7309  12.2967
 HSQ  HO6  H  HOH1  0   0.452  34.7956  -24.0154  12.6311
 HSQ  HO1  H  HOH1  0   0.459  32.5484  -26.6596   7.1445
 HSQ  C7   C  C     0   0.495  29.0494  -24.1690   7.4462

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
 HSQ  C1  O5   single  1.385  0.020  1.385
 HSQ  C1  O1   single  1.399  0.020  1.399
 HSQ  C1  H1   single  0.970  0.020  1.090
 HSQ  C2  C1   single  1.552  0.020  1.552
 HSQ  C2  C3   single  1.527  0.020  1.527
 HSQ  C2  H2   single  0.970  0.020  1.090
 HSQ  C3  C4   single  1.524  0.020  1.524
 HSQ  C3  H3   single  0.970  0.020  1.090
 HSQ  C4  C5   single  1.547  0.020  1.547
 HSQ  C4  O4   single  1.408  0.020  1.408
 HSQ  C4  H4   single  0.970  0.020  1.090
 HSQ  C5  C6   single  1.518  0.020  1.518
 HSQ  C5  H5   single  0.970  0.020  1.090
 HSQ  C6  H61  single  0.970  0.020  1.090
 HSQ  C6  H62  single  0.970  0.020  1.090
 HSQ  C7  N2   single  1.352  0.020  1.352
 HSQ  C7  C8   single  1.509  0.020  1.509
 HSQ  C8  H81  single  0.970  0.020  1.090
 HSQ  C8  H82  single  0.970  0.020  1.090
 HSQ  C8  H83  single  0.970  0.020  1.090
 HSQ  N2  C2   single  1.443  0.020  1.443
 HSQ  N2  HN2  single  0.860  0.020  1.020
 HSQ  O3  C3   single  1.404  0.020  1.404
 HSQ  O3  HO3  single  0.850  0.020  0.980
 HSQ  O4  HO4  single  0.850  0.020  0.980
 HSQ  O5  C5   single  1.427  0.020  1.427
 HSQ  O6  C6   single  1.409  0.020  1.409
 HSQ  O6  HO6  single  0.850  0.020  0.980
 HSQ  O7  C7   double  1.222  0.020  1.222
 HSQ  O1  HO1  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
 HSQ  H1   C1  O1   110.96  3.000
 HSQ  H1   C1  O5   105.81  3.000
 HSQ  O1   C1  O5   107.85  3.000
 HSQ  H1   C1  C2   108.51  3.000
 HSQ  O1   C1  C2   112.22  3.000
 HSQ  O5   C1  C2   111.32  3.000
 HSQ  H2   C2  N2   108.23  3.000
 HSQ  N2   C2  C3   111.04  3.000
 HSQ  H2   C2  C3   107.69  3.000
 HSQ  N2   C2  C1   111.21  3.000
 HSQ  H2   C2  C1   108.06  3.000
 HSQ  C3   C2  C1   110.48  3.000
 HSQ  H3   C3  O3   110.46  3.000
 HSQ  O3   C3  C4   112.42  3.000
 HSQ  H3   C3  C4   108.38  3.000
 HSQ  O3   C3  C2   107.64  3.000
 HSQ  H3   C3  C2   108.53  3.000
 HSQ  C4   C3  C2   109.34  3.000
 HSQ  H4   C4  O4   109.95  3.000
 HSQ  H4   C4  C5   109.08  3.000
 HSQ  O4   C4  C5   112.89  3.000
 HSQ  H4   C4  C3   108.26  3.000
 HSQ  O4   C4  C3   107.44  3.000
 HSQ  C5   C4  C3   109.11  3.000
 HSQ  H5   C5  O5   109.33  3.000
 HSQ  O5   C5  C6   106.32  3.000
 HSQ  H5   C5  C6   108.06  3.000
 HSQ  O5   C5  C4   111.16  3.000
 HSQ  H5   C5  C4   109.18  3.000
 HSQ  C6   C5  C4   112.68  3.000
 HSQ  H62  C6  H61  107.17  3.000
 HSQ  H62  C6  O6   111.30  3.000
 HSQ  H61  C6  O6   111.58  3.000
 HSQ  O6   C6  C5   108.07  3.000
 HSQ  H62  C6  C5   108.69  3.000
 HSQ  H61  C6  C5   110.00  3.000
 HSQ  H83  C8  H82  107.45  3.000
 HSQ  H83  C8  H81  108.68  3.000
 HSQ  H82  C8  H81  108.46  3.000
 HSQ  H83  C8  C7   111.38  3.000
 HSQ  H82  C8  C7   111.55  3.000
 HSQ  H81  C8  C7   109.23  3.000
 HSQ  HN2  N2  C7   115.07  3.000
 HSQ  HN2  N2  C2   116.43  3.000
 HSQ  C7   N2  C2   127.92  3.000
 HSQ  HO3  O3  C3   108.14  3.000
 HSQ  HO4  O4  C4   109.17  3.000
 HSQ  C5   O5  C1   116.37  3.000
 HSQ  HO6  O6  C6   107.88  3.000
 HSQ  HO1  O1  C1   109.45  3.000
 HSQ  O7   C7  N2   120.97  3.000
 HSQ  O7   C7  C8   121.67  3.000
 HSQ  N2   C7  C8   117.36  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
 HSQ  CONST_01  C8   C7  N2  C2    0.00   0.0  0
 HSQ  CONST_02  O7   C7  N2  C2  180.00   0.0  0
 HSQ  CONST_03  HN2  N2  C7  C8  180.00   0.0  0
 HSQ  Var_01    H81  C8  C7  N2  179.91  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
 HSQ  chir_01  C1  O5  O1  C2  negativ
 HSQ  chir_02  C2  N2  C3  C1  positiv
 HSQ  chir_03  C3  O3  C2  C4  positiv
 HSQ  chir_04  C4  O4  C5  C3  positiv
 HSQ  chir_05  C5  O5  C4  C6  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
 HSQ  plan-1  C2   0.020
 HSQ  plan-1  C8   0.020
 HSQ  plan-1  N2   0.020
 HSQ  plan-1  O7   0.020
 HSQ  plan-1  HN2  0.020
 HSQ  plan-1  C7   0.020

