# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 02:16:46 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: 2-(acetylamino)-2-deoxy-alpha-L-glucopyranose
#   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
 NGZ  NGZ  2-(acetylamino)-2-deoxy-alpha-L-glucopyranose  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 OK
;

data_comp_NGZ
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
 NGZ  C1   C  CH1   0   0.309  14.5860  -17.5272  -2.5758
 NGZ  C2   C  CH1   0  -0.207  13.4951  -17.8129  -1.5205
 NGZ  C3   C  CH1   0   0.071  13.7048  -19.2184  -0.9592
 NGZ  C4   C  CH1   0  -0.010  15.0008  -19.1947  -0.1559
 NGZ  C5   C  CH1   0  -0.046  16.1079  -18.4374  -0.9262
 NGZ  C6   C  CH2   0  -0.182  16.5106  -17.1572  -0.2087
 NGZ  C7   C  C     0   0.493  11.1139  -17.0719  -1.4389
 NGZ  C8   C  CH3   0  -0.814  11.3405  -16.4418  -0.0869
 NGZ  N2   N  NH1   0  -0.609  12.1885  -17.5936  -2.0732
 NGZ  O3   O  OH1   0  -0.659  12.5996  -19.5575  -0.1637
 NGZ  O4   O  OH1   0  -0.671  15.3410  -20.5322   0.1293
 NGZ  O5   O  O2    0  -0.491  15.7683  -18.2300  -2.2825
 NGZ  O6   O  OH1   0  -0.662  17.5464  -16.5410  -0.9294
 NGZ  O7   O  O     0  -0.489  10.0092  -17.0866  -1.9624
 NGZ  O1   O  OH1   0  -0.660  14.1470  -17.9776  -3.8091
 NGZ  H1   H  HCH1  0   0.218  14.7832  -16.4463  -2.6055
 NGZ  H2   H  HCH1  0   0.280  13.6347  -17.0978  -0.7068
 NGZ  H3   H  HCH1  0   0.220  13.8136  -19.9310  -1.7908
 NGZ  H4   H  HCH1  0   0.226  14.7849  -18.6516   0.7772
 NGZ  H5   H  HCH1  0   0.258  16.9912  -19.0816  -0.9654
 NGZ  H61  H  HCH2  0   0.206  15.6491  -16.4855  -0.0848
 NGZ  H62  H  HCH2  0   0.214  16.8243  -17.4408   0.8056
 NGZ  H81  H  HCH3  0   0.266  10.4021  -16.0347   0.2802
 NGZ  H82  H  HCH3  0   0.265  11.7131  -17.1680   0.6342
 NGZ  H83  H  HCH3  0   0.263  12.0698  -15.6318  -0.1406
 NGZ  HN2  H  HNH1  0   0.384  11.9968  -18.0279  -2.9651
 NGZ  HO3  H  HOH1  0   0.452  12.7376  -20.4472   0.1779
 NGZ  HO4  H  HOH1  0   0.454  15.9787  -20.5437   0.8499
 NGZ  HO6  H  HOH1  0   0.455  17.7934  -15.7331  -0.4707
 NGZ  HO1  H  HOH1  0   0.468  14.5641  -17.4656  -4.5090

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
 NGZ  C1  C2   single  1.545  0.020  1.545
 NGZ  C1  O5   single  1.406  0.020  1.406
 NGZ  C1  O1   single  1.384  0.020  1.384
 NGZ  C1  H1   single  0.970  0.020  1.090
 NGZ  C2  C3   single  1.528  0.020  1.528
 NGZ  C2  N2   single  1.436  0.020  1.436
 NGZ  C2  H2   single  0.970  0.020  1.090
 NGZ  C3  C4   single  1.525  0.020  1.525
 NGZ  C3  O3   single  1.403  0.020  1.403
 NGZ  C3  H3   single  0.970  0.020  1.090
 NGZ  C4  C5   single  1.547  0.020  1.547
 NGZ  C4  O4   single  1.409  0.020  1.409
 NGZ  C4  H4   single  0.970  0.020  1.090
 NGZ  C5  C6   single  1.522  0.020  1.522
 NGZ  C5  O5   single  1.413  0.020  1.413
 NGZ  C5  H5   single  0.970  0.020  1.090
 NGZ  C6  O6   single  1.404  0.020  1.404
 NGZ  C6  H61  single  0.970  0.020  1.090
 NGZ  C6  H62  single  0.970  0.020  1.090
 NGZ  C7  C8   single  1.509  0.020  1.509
 NGZ  C7  N2   single  1.352  0.020  1.352
 NGZ  C7  O7   double  1.223  0.020  1.223
 NGZ  C8  H81  single  0.970  0.020  1.090
 NGZ  C8  H82  single  0.970  0.020  1.090
 NGZ  C8  H83  single  0.970  0.020  1.090
 NGZ  N2  HN2  single  0.860  0.020  1.020
 NGZ  O3  HO3  single  0.850  0.020  0.980
 NGZ  O4  HO4  single  0.850  0.020  0.980
 NGZ  O6  HO6  single  0.850  0.020  0.980
 NGZ  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
 NGZ  H1   C1  O1   110.66  3.000
 NGZ  H1   C1  O5   110.26  3.000
 NGZ  O1   C1  O5   106.85  3.000
 NGZ  H1   C1  C2   109.09  3.000
 NGZ  O1   C1  C2   108.94  3.000
 NGZ  O5   C1  C2   111.03  3.000
 NGZ  H2   C2  N2   107.65  3.000
 NGZ  H2   C2  C3   108.12  3.000
 NGZ  N2   C2  C3   114.01  3.000
 NGZ  H2   C2  C1   107.32  3.000
 NGZ  N2   C2  C1   110.58  3.000
 NGZ  C3   C2  C1   108.92  3.000
 NGZ  H3   C3  O3   110.48  3.000
 NGZ  H3   C3  C4   108.91  3.000
 NGZ  O3   C3  C4   111.99  3.000
 NGZ  H3   C3  C2   109.37  3.000
 NGZ  O3   C3  C2   108.81  3.000
 NGZ  C4   C3  C2   107.21  3.000
 NGZ  H4   C4  O4   110.11  3.000
 NGZ  H4   C4  C5   108.72  3.000
 NGZ  O4   C4  C5   113.12  3.000
 NGZ  H4   C4  C3   106.70  3.000
 NGZ  O4   C4  C3   107.28  3.000
 NGZ  C5   C4  C3   110.71  3.000
 NGZ  H5   C5  O5   104.25  3.000
 NGZ  H5   C5  C6   107.38  3.000
 NGZ  O5   C5  C6   113.11  3.000
 NGZ  H5   C5  C4   107.90  3.000
 NGZ  O5   C5  C4   112.19  3.000
 NGZ  C6   C5  C4   111.50  3.000
 NGZ  H62  C6  H61  106.10  3.000
 NGZ  H62  C6  O6   112.11  3.000
 NGZ  H61  C6  O6   111.58  3.000
 NGZ  H62  C6  C5   107.07  3.000
 NGZ  H61  C6  C5   111.08  3.000
 NGZ  O6   C6  C5   108.80  3.000
 NGZ  O7   C7  N2   120.83  3.000
 NGZ  O7   C7  C8   121.63  3.000
 NGZ  N2   C7  C8   117.52  3.000
 NGZ  H83  C8  H82  107.39  3.000
 NGZ  H83  C8  H81  108.40  3.000
 NGZ  H82  C8  H81  108.76  3.000
 NGZ  H83  C8  C7   111.49  3.000
 NGZ  H82  C8  C7   111.48  3.000
 NGZ  H81  C8  C7   109.23  3.000
 NGZ  HN2  N2  C7   115.41  3.000
 NGZ  HN2  N2  C2   116.55  3.000
 NGZ  C7   N2  C2   126.98  3.000
 NGZ  HO3  O3  C3   108.15  3.000
 NGZ  HO4  O4  C4   108.84  3.000
 NGZ  C5   O5  C1   118.39  3.000
 NGZ  HO6  O6  C6   108.27  3.000
 NGZ  HO1  O1  C1   109.72  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
 NGZ  CONST_01  C8   C7  N2  C2    0.00   0.0  0
 NGZ  CONST_02  O7   C7  N2  C2  180.00   0.0  0
 NGZ  CONST_03  HN2  N2  C7  C8  180.00   0.0  0
 NGZ  Var_01    H81  C8  C7  N2  177.80  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
 NGZ  chir_01  C1  C2  O5  O1  negativ
 NGZ  chir_02  C2  N2  C3  C1  negativ
 NGZ  chir_03  C3  O3  C2  C4  negativ
 NGZ  chir_04  C4  O4  C5  C3  negativ
 NGZ  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
 NGZ  plan-1  C2   0.020
 NGZ  plan-1  C7   0.020
 NGZ  plan-1  C8   0.020
 NGZ  plan-1  N2   0.020
 NGZ  plan-1  O7   0.020
 NGZ  plan-1  HN2  0.020

