# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 03:40:15 2022
#   Inital geometry file: a 82 line input string
#   Ligand name: 2-(acetylamino)-2-deoxy-6-O-sulfo-alpha-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[S](O)(=O)=O)[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
 NGY  NGY  2-(acetylamino)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose  D-saccharide  33  19  .  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_NGY
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
 NGY  O1   O  OH1    0  -0.662  17.7145   7.9749   4.2405
 NGY  C1   C  CH1    0   0.264  18.5377   6.9100   3.8914
 NGY  C2   C  CH1    0  -0.154  19.1038   7.1858   2.4972
 NGY  C3   C  CH1    0   0.044  17.9966   7.1063   1.4507
 NGY  C4   C  CH1    0   0.018  17.2577   5.7764   1.5718
 NGY  C5   C  CH1    0  -0.021  16.7785   5.5566   3.0127
 NGY  C6   C  CH2    0  -0.188  16.2442   4.1518   3.2653
 NGY  O3   O  OH1    0  -0.661  18.5893   7.2571   0.1862
 NGY  O4   O  OH1    0  -0.677  16.1997   5.8286   0.6469
 NGY  O5   O  O2     0  -0.503  17.8674   5.6804   3.9122
 NGY  O6   O  OC2    0  -0.632  15.1216   3.9468   2.4213
 NGY  N2   N  NH1    0  -0.626  19.7791   8.4567   2.4688
 NGY  C7   C  C      0   0.518  21.0412   8.6397   2.0337
 NGY  O7   O  O      0  -0.494  21.7660   7.7287   1.6618
 NGY  C8   C  CH3    0  -0.778  21.5172  10.0722   2.0388
 NGY  S    S  S      0   1.579  14.2310   2.5674   2.6495
 NGY  O7A  O  OS     0  -0.723  13.2550   2.7019   1.5741
 NGY  O8   O  OS     0  -0.734  15.1791   1.4641   2.4918
 NGY  O9   O  OS    -1  -0.734  13.6837   2.6907   4.0009
 NGY  H1   H  HCH1   0   0.245  19.3625   6.7925   4.6028
 NGY  H2   H  HCH1   0   0.275  19.8439   6.4112   2.2851
 NGY  H3   H  HCH1   0   0.211  17.2709   7.9127   1.6384
 NGY  H4   H  HCH1   0   0.202  17.9675   4.9685   1.3269
 NGY  H5   H  HCH1   0   0.230  15.9930   6.2884   3.2432
 NGY  H61  H  HCH2   0   0.224  17.0302   3.4186   3.0543
 NGY  H62  H  HCH2   0   0.238  15.9639   4.0616   4.3196
 NGY  HO3  H  HOH1   0   0.450  17.8867   7.2801  -0.4715
 NGY  HN2  H  HNH1   0   0.397  19.2443   9.2656   2.7436
 NGY  H81  H  HCH3   0   0.247  20.7933  10.7771   2.4432
 NGY  H82  H  HCH3   0   0.263  22.4360  10.1467   2.6197
 NGY  H83  H  HCH3   0   0.264  21.7552  10.3735   1.0184
 NGY  HO4  H  HOH1   0   0.453  15.6774   5.0224   0.7297
 NGY  HO1  H  HOH1   0   0.465  17.5439   7.9524   5.1884

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
 NGY  O1  C1   single  1.391  0.020  1.391
 NGY  C1  C2   single  1.530  0.020  1.530
 NGY  C1  O5   single  1.401  0.020  1.401
 NGY  C1  H1   single  0.970  0.020  1.090
 NGY  C2  C3   single  1.526  0.020  1.526
 NGY  C2  N2   single  1.439  0.020  1.439
 NGY  C2  H2   single  0.970  0.020  1.090
 NGY  C3  C4   single  1.526  0.020  1.526
 NGY  C3  O3   single  1.405  0.020  1.405
 NGY  C3  H3   single  0.970  0.020  1.090
 NGY  C4  C5   single  1.534  0.020  1.534
 NGY  C4  O4   single  1.406  0.020  1.406
 NGY  C4  H4   single  0.970  0.020  1.090
 NGY  C5  C6   single  1.524  0.020  1.524
 NGY  C5  O5   single  1.418  0.020  1.418
 NGY  C5  H5   single  0.970  0.020  1.090
 NGY  C6  O6   single  1.419  0.020  1.419
 NGY  C6  H61  single  0.970  0.020  1.090
 NGY  C6  H62  single  0.970  0.020  1.090
 NGY  O3  HO3  single  0.850  0.020  0.980
 NGY  O4  HO4  single  0.850  0.020  0.980
 NGY  O6  S    single  1.658  0.020  1.658
 NGY  N2  C7   single  1.347  0.020  1.347
 NGY  N2  HN2  single  0.860  0.020  1.020
 NGY  C7  O7   double  1.222  0.020  1.222
 NGY  C7  C8   single  1.510  0.020  1.510
 NGY  C8  H81  single  0.970  0.020  1.090
 NGY  C8  H82  single  0.970  0.020  1.090
 NGY  C8  H83  single  0.970  0.020  1.090
 NGY  S   O7A  deloc   1.459  0.020  1.459
 NGY  S   O8   deloc   1.463  0.020  1.463
 NGY  S   O9   deloc   1.463  0.020  1.463
 NGY  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
 NGY  HO1  O1  C1   109.51  3.000
 NGY  H1   C1  O5   104.87  3.000
 NGY  H1   C1  C2   109.42  3.000
 NGY  O5   C1  C2   110.42  3.000
 NGY  H1   C1  O1   111.40  3.000
 NGY  O5   C1  O1   112.66  3.000
 NGY  C2   C1  O1   108.04  3.000
 NGY  H2   C2  N2   107.72  3.000
 NGY  H2   C2  C3   108.76  3.000
 NGY  N2   C2  C3   111.90  3.000
 NGY  H2   C2  C1   107.45  3.000
 NGY  N2   C2  C1   110.54  3.000
 NGY  C3   C2  C1   110.32  3.000
 NGY  H3   C3  O3   110.67  3.000
 NGY  H3   C3  C4   107.79  3.000
 NGY  O3   C3  C4   111.67  3.000
 NGY  H3   C3  C2   108.86  3.000
 NGY  O3   C3  C2   107.80  3.000
 NGY  C4   C3  C2   110.02  3.000
 NGY  H4   C4  O4   111.43  3.000
 NGY  H4   C4  C5   107.73  3.000
 NGY  O4   C4  C5   112.83  3.000
 NGY  H4   C4  C3   108.00  3.000
 NGY  O4   C4  C3   106.24  3.000
 NGY  C5   C4  C3   110.52  3.000
 NGY  H5   C5  O5   110.98  3.000
 NGY  H5   C5  C6   109.19  3.000
 NGY  O5   C5  C6   104.16  3.000
 NGY  H5   C5  C4   108.97  3.000
 NGY  O5   C5  C4   110.09  3.000
 NGY  C6   C5  C4   113.40  3.000
 NGY  H62  C6  H61  108.31  3.000
 NGY  H62  C6  O6   110.99  3.000
 NGY  H61  C6  O6   110.87  3.000
 NGY  H62  C6  C5   108.99  3.000
 NGY  H61  C6  C5   109.48  3.000
 NGY  O6   C6  C5   108.17  3.000
 NGY  HO3  O3  C3   108.04  3.000
 NGY  HO4  O4  C4   108.67  3.000
 NGY  C5   O5  C1   115.78  3.000
 NGY  S    O6  C6   117.60  3.000
 NGY  HN2  N2  C7   118.43  3.000
 NGY  HN2  N2  C2   117.02  3.000
 NGY  C7   N2  C2   124.45  3.000
 NGY  C8   C7  O7   121.42  3.000
 NGY  C8   C7  N2   115.03  3.000
 NGY  O7   C7  N2   123.54  3.000
 NGY  H83  C8  H82  107.22  3.000
 NGY  H83  C8  H81  108.30  3.000
 NGY  H82  C8  H81  108.57  3.000
 NGY  H83  C8  C7   109.14  3.000
 NGY  H82  C8  C7   109.43  3.000
 NGY  H81  C8  C7   113.96  3.000
 NGY  O9   S   O8   113.92  3.000
 NGY  O9   S   O7A  115.02  3.000
 NGY  O8   S   O7A  115.07  3.000
 NGY  O9   S   O6   104.95  3.000
 NGY  O8   S   O6   105.34  3.000
 NGY  O7A  S   O6   100.44  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
 NGY  CONST_01  O7   C7  N2  C2     0.00   0.0  0
 NGY  CONST_02  C8   C7  N2  C2   180.00   0.0  0
 NGY  CONST_03  HN2  N2  C7  O7   180.00   0.0  0
 NGY  Var_01    O7A  S   O6  C6  -177.09  30.0  3
 NGY  Var_02    H81  C8  C7  N2     2.93  30.0  3
 NGY  Var_03    H61  C6  O6  S     68.01  30.0  1

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
 NGY  chir_01  C1  O1  C2  O5  positiv
 NGY  chir_02  C2  N2  C3  C1  positiv
 NGY  chir_03  C3  O3  C2  C4  positiv
 NGY  chir_04  C4  O4  C3  C5  negativ
 NGY  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
 NGY  plan-1  C2   0.020
 NGY  plan-1  N2   0.020
 NGY  plan-1  C7   0.020
 NGY  plan-1  O7   0.020
 NGY  plan-1  C8   0.020
 NGY  plan-1  HN2  0.020

