# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 23:57:34 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: 2-(acetylamino)-2-deoxy-beta-D-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
 NAG  NAG  2-(acetylamino)-2-deoxy-beta-D-glucopyranose  D-saccharide  30  15  .  2012-04-09  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NAG
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
 NAG  C1   C  CH1   0   0.309  7.2919  28.0647  26.6198
 NAG  C2   C  CH1   0  -0.158  6.9354  29.1741  27.6146
 NAG  C3   C  CH1   0   0.038  7.7086  28.9708  28.9142
 NAG  C4   C  CH1   0   0.010  7.5041  27.5522  29.4330
 NAG  C5   C  CH1   0  -0.013  7.8612  26.5509  28.3297
 NAG  C6   C  CH2   0  -0.193  7.6866  25.1036  28.7357
 NAG  C7   C  C     0   0.517  6.2721  31.3779  26.7284
 NAG  C8   C  CH3   0  -0.778  6.8018  32.6671  26.1499
 NAG  N2   N  NH1   0  -0.628  7.2119  30.4706  27.0544
 NAG  O1   O  OH1   0  -0.648  6.4915  28.1976  25.5084
 NAG  O3   O  OH1   0  -0.660  7.2725  29.9353  29.8347
 NAG  O4   O  OH1   0  -0.672  8.3298  27.3971  30.5647
 NAG  O5   O  O2    0  -0.496  7.0550  26.8050  27.1973
 NAG  O6   O  OH1   0  -0.667  6.3684  24.8897  29.1807
 NAG  O7   O  O     0  -0.494  5.0742  31.1947  26.8884
 NAG  H1   H  HCH1  0   0.183  8.3639  28.1455  26.3623
 NAG  H2   H  HCH1  0   0.270  5.8640  29.1143  27.8229
 NAG  H3   H  HCH1  0   0.206  8.7845  29.0940  28.6965
 NAG  H4   H  HCH1  0   0.225  6.4450  27.4337  29.6958
 NAG  H5   H  HCH1  0   0.223  8.9268  26.6803  28.0747
 NAG  H61  H  HCH2  0   0.218  7.9368  24.4691  27.8753
 NAG  H62  H  HCH2  0   0.208  8.4269  24.8802  29.5133
 NAG  H81  H  HCH3  0   0.263  6.3518  32.8352  25.1716
 NAG  H82  H  HCH3  0   0.264  6.5018  33.4973  26.7895
 NAG  H83  H  HCH3  0   0.247  7.8843  32.6912  26.0401
 NAG  HN2  H  HNH1  0   0.399  8.1793  30.7040  26.8910
 NAG  HO1  H  HOH1  0   0.463  6.8770  27.7069  24.7747
 NAG  HO3  H  HOH1  0   0.449  7.7850  29.8255  30.6426
 NAG  HO4  H  HOH1  0   0.459  7.9504  26.7257  31.1389
 NAG  HO6  H  HOH1  0   0.457  6.3077  23.9934  29.5225

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
 NAG  C1  C2   single  1.532  0.020  1.532
 NAG  C1  O1   single  1.376  0.020  1.376
 NAG  C1  O5   single  1.406  0.020  1.406
 NAG  C1  H1   single  0.970  0.020  1.090
 NAG  C2  C3   single  1.526  0.020  1.526
 NAG  C2  N2   single  1.439  0.020  1.439
 NAG  C2  H2   single  0.970  0.020  1.090
 NAG  C3  C4   single  1.524  0.020  1.524
 NAG  C3  O3   single  1.403  0.020  1.403
 NAG  C3  H3   single  0.970  0.020  1.090
 NAG  C4  C5   single  1.532  0.020  1.532
 NAG  C4  O4   single  1.409  0.020  1.409
 NAG  C4  H4   single  0.970  0.020  1.090
 NAG  C5  C6   single  1.513  0.020  1.513
 NAG  C5  O5   single  1.413  0.020  1.413
 NAG  C5  H5   single  0.970  0.020  1.090
 NAG  C6  O6   single  1.408  0.020  1.408
 NAG  C6  H61  single  0.970  0.020  1.090
 NAG  C6  H62  single  0.970  0.020  1.090
 NAG  C7  C8   single  1.509  0.020  1.509
 NAG  C7  N2   single  1.346  0.020  1.346
 NAG  C7  O7   double  1.222  0.020  1.222
 NAG  C8  H81  single  0.970  0.020  1.090
 NAG  C8  H82  single  0.970  0.020  1.090
 NAG  C8  H83  single  0.970  0.020  1.090
 NAG  N2  HN2  single  0.860  0.020  1.020
 NAG  O1  HO1  single  0.850  0.020  0.980
 NAG  O3  HO3  single  0.850  0.020  0.980
 NAG  O4  HO4  single  0.850  0.020  0.980
 NAG  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
 NAG  H1   C1  O5   108.94  3.000
 NAG  H1   C1  O1   111.64  3.000
 NAG  O5   C1  O1   108.68  3.000
 NAG  H1   C1  C2   108.90  3.000
 NAG  O5   C1  C2   110.06  3.000
 NAG  O1   C1  C2   108.61  3.000
 NAG  H2   C2  N2   108.16  3.000
 NAG  H2   C2  C3   109.09  3.000
 NAG  N2   C2  C3   110.74  3.000
 NAG  H2   C2  C1   108.19  3.000
 NAG  N2   C2  C1   110.79  3.000
 NAG  C3   C2  C1   109.80  3.000
 NAG  H3   C3  O3   110.82  3.000
 NAG  H3   C3  C4   107.55  3.000
 NAG  O3   C3  C4   112.02  3.000
 NAG  H3   C3  C2   108.11  3.000
 NAG  O3   C3  C2   108.05  3.000
 NAG  C4   C3  C2   110.24  3.000
 NAG  H4   C4  O4   111.17  3.000
 NAG  H4   C4  C5   109.07  3.000
 NAG  O4   C4  C5   111.70  3.000
 NAG  H4   C4  C3   108.14  3.000
 NAG  O4   C4  C3   107.29  3.000
 NAG  C5   C4  C3   109.38  3.000
 NAG  H5   C5  O5   110.16  3.000
 NAG  H5   C5  C6   106.60  3.000
 NAG  O5   C5  C6   108.73  3.000
 NAG  H5   C5  C4   108.36  3.000
 NAG  O5   C5  C4   109.06  3.000
 NAG  C6   C5  C4   113.89  3.000
 NAG  H62  C6  H61  106.50  3.000
 NAG  H62  C6  O6   112.15  3.000
 NAG  H61  C6  O6   111.92  3.000
 NAG  H62  C6  C5   107.89  3.000
 NAG  H61  C6  C5   108.43  3.000
 NAG  O6   C6  C5   109.77  3.000
 NAG  O7   C7  N2   123.46  3.000
 NAG  O7   C7  C8   121.48  3.000
 NAG  N2   C7  C8   115.06  3.000
 NAG  H83  C8  H82  108.42  3.000
 NAG  H83  C8  H81  108.46  3.000
 NAG  H82  C8  H81  107.19  3.000
 NAG  H83  C8  C7   114.00  3.000
 NAG  H82  C8  C7   109.22  3.000
 NAG  H81  C8  C7   109.32  3.000
 NAG  HN2  N2  C7   118.32  3.000
 NAG  HN2  N2  C2   117.12  3.000
 NAG  C7   N2  C2   124.56  3.000
 NAG  HO1  O1  C1   109.47  3.000
 NAG  HO3  O3  C3   107.86  3.000
 NAG  HO4  O4  C4   108.98  3.000
 NAG  C5   O5  C1   113.21  3.000
 NAG  HO6  O6  C6   108.26  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
 NAG  CONST_01  C8   C7  N2  C2  180.00   0.0  0
 NAG  CONST_02  O7   C7  N2  C2    0.00   0.0  0
 NAG  CONST_03  HN2  N2  C7  C8    0.00   0.0  0
 NAG  Var_01    H81  C8  C7  N2  123.30  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
 NAG  chir_01  C1  C2  O1  O5  positiv
 NAG  chir_02  C2  N2  C3  C1  positiv
 NAG  chir_03  C3  O3  C2  C4  positiv
 NAG  chir_04  C4  O4  C3  C5  negativ
 NAG  chir_05  C5  O5  C4  C6  negativ

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
 NAG  plan-1  C2   0.020
 NAG  plan-1  C7   0.020
 NAG  plan-1  C8   0.020
 NAG  plan-1  N2   0.020
 NAG  plan-1  O7   0.020
 NAG  plan-1  HN2  0.020

