# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 04:21:37 2022
#   Inital geometry file: a 82 line input string
#   Ligand name: 2-(acetylamino)-2-deoxy-6-O-sulfo-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[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
 NGS  NGS  2-(acetylamino)-2-deoxy-6-O-sulfo-beta-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 PERFECT
;

data_comp_NGS
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
 NGS  C1   C  CH1    0   0.308   0.9391   0.1004   6.7962
 NGS  C2   C  CH1    0  -0.173  -0.0295  -1.0038   7.2107
 NGS  C3   C  CH1    0   0.037  -0.9140  -0.5333   8.3710
 NGS  C4   C  CH1    0   0.017  -0.0653   0.0205   9.5075
 NGS  C5   C  CH1    0  -0.028   0.9004   1.0708   8.9384
 NGS  C6   C  CH2    0  -0.170   1.8516   1.6161   9.9812
 NGS  O1   O  OH1    0  -0.647   1.8021  -0.3918   5.8436
 NGS  O3   O  OH1    0  -0.657  -1.6989  -1.5840   8.8673
 NGS  O5   O  O2     0  -0.491   1.6864   0.4989   7.9175
 NGS  O6   O  OC2    0  -0.614   2.5773   2.6797   9.3860
 NGS  N2   N  NH1    0  -0.643  -0.8521  -1.4194   6.1027
 NGS  C7   C  C      0   0.521  -0.6885  -2.5816   5.4334
 NGS  O7   O  O      0  -0.487   0.1062  -3.4429   5.7753
 NGS  C8   C  CH3    0  -0.779  -1.5674  -2.7522   4.2196
 NGS  S    S  S      0   1.565   4.0979   2.9727   9.9437
 NGS  O7A  O  OS     0  -0.738   4.8760   1.7753   9.6167
 NGS  O8   O  OS    -1  -0.740   3.9452   3.1992  11.3834
 NGS  O9   O  OS     0  -0.729   4.4437   4.1591   9.1657
 NGS  O4   O  OH1    0  -0.664  -0.9319   0.5823  10.4629
 NGS  H1   H  HCH1   0   0.185   0.3649   0.9663   6.4196
 NGS  H2   H  HCH1   0   0.270   0.5527  -1.8679   7.5403
 NGS  H3   H  HCH1   0   0.209  -1.5471   0.2925   8.0024
 NGS  H4   H  HCH1   0   0.226   0.5258  -0.8026   9.9352
 NGS  H5   H  HCH1   0   0.223   0.2984   1.9044   8.5392
 NGS  H61  H  HCH2   0   0.225   1.2917   1.9819  10.8456
 NGS  H62  H  HCH2   0   0.223   2.5093   0.8092  10.3225
 NGS  HO3  H  HOH1   0   0.450  -2.2802  -1.8823   8.1596
 NGS  HN2  H  HNH1   0   0.401  -1.4880  -0.7354   5.7203
 NGS  H81  H  HCH3   0   0.264  -2.0777  -3.7131   4.2714
 NGS  H82  H  HCH3   0   0.249  -2.3135  -1.9687   4.1011
 NGS  H83  H  HCH3   0   0.267  -0.9416  -2.7648   3.3265
 NGS  HO4  H  HOH1   0   0.458  -0.5264   0.5218  11.3321
 NGS  HO1  H  HOH1   0   0.463   2.2205   0.3425   5.3813

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
 NGS  C1  C2   single  1.526  0.020  1.526
 NGS  C1  O1   single  1.376  0.020  1.376
 NGS  C1  O5   single  1.405  0.020  1.405
 NGS  C1  H1   single  0.970  0.020  1.090
 NGS  C2  C3   single  1.533  0.020  1.533
 NGS  C2  N2   single  1.441  0.020  1.441
 NGS  C2  H2   single  0.970  0.020  1.090
 NGS  C3  C4   single  1.523  0.020  1.523
 NGS  C3  O3   single  1.402  0.020  1.402
 NGS  C3  H3   single  0.970  0.020  1.090
 NGS  C4  C5   single  1.536  0.020  1.536
 NGS  C4  O4   single  1.407  0.020  1.407
 NGS  C4  H4   single  0.970  0.020  1.090
 NGS  C5  C6   single  1.513  0.020  1.513
 NGS  C5  O5   single  1.410  0.020  1.410
 NGS  C5  H5   single  0.970  0.020  1.090
 NGS  C6  O6   single  1.418  0.020  1.418
 NGS  C6  H61  single  0.970  0.020  1.090
 NGS  C6  H62  single  0.970  0.020  1.090
 NGS  O3  HO3  single  0.850  0.020  0.980
 NGS  O6  S    single  1.646  0.020  1.646
 NGS  N2  C7   single  1.351  0.020  1.351
 NGS  N2  HN2  single  0.860  0.020  1.020
 NGS  C7  O7   double  1.221  0.020  1.221
 NGS  C7  C8   single  1.508  0.020  1.508
 NGS  C8  H81  single  0.970  0.020  1.090
 NGS  C8  H82  single  0.970  0.020  1.090
 NGS  C8  H83  single  0.970  0.020  1.090
 NGS  S   O7A  deloc   1.465  0.020  1.465
 NGS  S   O8   deloc   1.465  0.020  1.465
 NGS  S   O9   deloc   1.460  0.020  1.460
 NGS  O4  HO4  single  0.850  0.020  0.980
 NGS  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
 NGS  H1   C1  O5   109.03  3.000
 NGS  H1   C1  O1   111.72  3.000
 NGS  O5   C1  O1   108.68  3.000
 NGS  H1   C1  C2   109.25  3.000
 NGS  O5   C1  C2   109.02  3.000
 NGS  O1   C1  C2   109.09  3.000
 NGS  H2   C2  N2   107.93  3.000
 NGS  H2   C2  C3   108.77  3.000
 NGS  N2   C2  C3   109.94  3.000
 NGS  H2   C2  C1   108.42  3.000
 NGS  N2   C2  C1   111.23  3.000
 NGS  C3   C2  C1   110.47  3.000
 NGS  H3   C3  O3   110.96  3.000
 NGS  H3   C3  C4   107.26  3.000
 NGS  O3   C3  C4   108.69  3.000
 NGS  H3   C3  C2   107.92  3.000
 NGS  O3   C3  C2   111.16  3.000
 NGS  C4   C3  C2   110.79  3.000
 NGS  H4   C4  O4   111.45  3.000
 NGS  H4   C4  C5   108.53  3.000
 NGS  O4   C4  C5   111.45  3.000
 NGS  H4   C4  C3   108.52  3.000
 NGS  O4   C4  C3   107.99  3.000
 NGS  C5   C4  C3   108.82  3.000
 NGS  H5   C5  O5   110.41  3.000
 NGS  H5   C5  C6   108.67  3.000
 NGS  O5   C5  C6   107.15  3.000
 NGS  H5   C5  C4   107.92  3.000
 NGS  O5   C5  C4   109.96  3.000
 NGS  C6   C5  C4   112.73  3.000
 NGS  H62  C6  H61  107.92  3.000
 NGS  H62  C6  O6   112.07  3.000
 NGS  H61  C6  O6   110.06  3.000
 NGS  H62  C6  C5   109.07  3.000
 NGS  H61  C6  C5   110.10  3.000
 NGS  O6   C6  C5   107.62  3.000
 NGS  HO1  O1  C1   109.38  3.000
 NGS  HO3  O3  C3   108.05  3.000
 NGS  C5   O5  C1   113.36  3.000
 NGS  S    O6  C6   117.64  3.000
 NGS  HN2  N2  C7   118.15  3.000
 NGS  HN2  N2  C2   117.10  3.000
 NGS  C7   N2  C2   124.04  3.000
 NGS  C8   C7  O7   121.66  3.000
 NGS  C8   C7  N2   115.17  3.000
 NGS  O7   C7  N2   123.17  3.000
 NGS  H83  C8  H82  108.22  3.000
 NGS  H83  C8  H81  107.31  3.000
 NGS  H82  C8  H81  108.60  3.000
 NGS  H83  C8  C7   109.03  3.000
 NGS  H82  C8  C7   113.93  3.000
 NGS  H81  C8  C7   109.54  3.000
 NGS  O9   S   O8   115.00  3.000
 NGS  O9   S   O7A  114.80  3.000
 NGS  O8   S   O7A  113.64  3.000
 NGS  O9   S   O6   100.54  3.000
 NGS  O8   S   O6   105.32  3.000
 NGS  O7A  S   O6   105.64  3.000
 NGS  HO4  O4  C4   109.21  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
 NGS  CONST_01  O7   C7  N2  C2     0.00   0.0  0
 NGS  CONST_02  C8   C7  N2  C2   180.00   0.0  0
 NGS  CONST_03  HN2  N2  C7  O7   180.00   0.0  0
 NGS  Var_01    O7A  S   O6  C6    64.11  30.0  3
 NGS  Var_02    H81  C8  C7  N2  -128.96  30.0  3
 NGS  Var_03    H61  C6  O6  S     89.07  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
 NGS  chir_01  C1  C2  O1  O5  positiv
 NGS  chir_02  C2  N2  C3  C1  positiv
 NGS  chir_03  C3  O3  C2  C4  positiv
 NGS  chir_04  C4  O4  C3  C5  negativ
 NGS  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
 NGS  plan-1  C2   0.020
 NGS  plan-1  N2   0.020
 NGS  plan-1  C7   0.020
 NGS  plan-1  O7   0.020
 NGS  plan-1  C8   0.020
 NGS  plan-1  HN2  0.020

