# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 05:09:07 2022
#   Inital geometry file: a 82 line input string
#   Ligand name: 2-(acetylamino)-2-deoxy-6-O-sulfo-beta-D-galactopyranose
#   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
 NG6  NG6  2-(acetylamino)-2-deoxy-6-O-sulfo-beta-D-galactopyranose  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_NG6
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
 NG6  C1   C  CH1    0   0.308  33.4925  27.5651  45.5152
 NG6  C2   C  CH1    0  -0.155  32.6942  27.9081  46.7783
 NG6  C3   C  CH1    0   0.049  31.1986  27.7438  46.5077
 NG6  C4   C  CH1    0  -0.032  30.7886  28.5299  45.2613
 NG6  C5   C  CH1    0  -0.011  31.6788  28.0714  44.1044
 NG6  C6   C  CH2    0  -0.177  31.3535  28.7787  42.8083
 NG6  C7   C  C      0   0.516  33.6785  27.5124  49.0043
 NG6  C8   C  CH3    0  -0.779  34.0322  26.4393  50.0053
 NG6  N2   N  NH1    0  -0.628  33.1116  27.0660  47.8684
 NG6  O1   O  OH1    0  -0.649  34.8146  27.8800  45.7365
 NG6  O3   O  OH1    0  -0.658  30.5038  28.1314  47.6608
 NG6  O4   O  OH1    0  -0.669  30.9242  29.9047  45.5234
 NG6  O5   O  O2     0  -0.492  33.0337  28.3101  44.4161
 NG6  O6   O  OC2    0  -0.615  32.0566  28.1302  41.7601
 NG6  O7   O  O      0  -0.496  33.8978  28.6940  49.2299
 NG6  S    S  S      0   1.570  31.5046  28.3753  40.2267
 NG6  O1S  O  OS     0  -0.728  32.4358  27.5525  39.4609
 NG6  O2S  O  OS     0  -0.740  30.1245  27.8856  40.2275
 NG6  O3S  O  OS    -1  -0.741  31.6218  29.8175  39.9996
 NG6  H1   H  HCH1   0   0.183  33.3621  26.4888  45.2974
 NG6  H2   H  HCH1   0   0.271  32.9034  28.9442  47.0525
 NG6  H3   H  HCH1   0   0.216  31.0153  26.6818  46.2776
 NG6  H4   H  HCH1   0   0.241  29.7482  28.2690  45.0189
 NG6  H5   H  HCH1   0   0.223  31.4992  26.9937  43.9573
 NG6  H61  H  HCH2   0   0.227  30.2711  28.7234  42.6517
 NG6  H62  H  HCH2   0   0.223  31.6338  29.8350  42.8677
 NG6  H81  H  HCH3   0   0.263  35.0910  26.5117  50.2527
 NG6  H82  H  HCH3   0   0.264  33.4729  26.6053  50.9262
 NG6  H83  H  HCH3   0   0.247  33.8284  25.4282  49.6573
 NG6  HN2  H  HNH1   0   0.398  32.9483  26.0753  47.7742
 NG6  HO1  H  HOH1   0   0.462  35.3659  27.4176  45.0962
 NG6  HO3  H  HOH1   0   0.452  29.5831  27.8673  47.5661
 NG6  HO4  H  HOH1   0   0.457  30.3258  30.3952  44.9531

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
 NG6  C1  C2   single  1.533  0.020  1.533
 NG6  C1  O1   single  1.377  0.020  1.377
 NG6  C1  O5   single  1.405  0.020  1.405
 NG6  C1  H1   single  0.970  0.020  1.090
 NG6  C2  C3   single  1.529  0.020  1.529
 NG6  C2  N2   single  1.439  0.020  1.439
 NG6  C2  H2   single  0.970  0.020  1.090
 NG6  C3  C4   single  1.530  0.020  1.530
 NG6  C3  O3   single  1.401  0.020  1.401
 NG6  C3  H3   single  0.970  0.020  1.090
 NG6  C4  C5   single  1.530  0.020  1.530
 NG6  C4  O4   single  1.406  0.020  1.406
 NG6  C4  H4   single  0.970  0.020  1.090
 NG6  C5  C6   single  1.512  0.020  1.512
 NG6  C5  O5   single  1.411  0.020  1.411
 NG6  C5  H5   single  0.970  0.020  1.090
 NG6  C6  O6   single  1.419  0.020  1.419
 NG6  C6  H61  single  0.970  0.020  1.090
 NG6  C6  H62  single  0.970  0.020  1.090
 NG6  C7  C8   single  1.510  0.020  1.510
 NG6  C7  N2   single  1.346  0.020  1.346
 NG6  C7  O7   double  1.223  0.020  1.223
 NG6  C8  H81  single  0.970  0.020  1.090
 NG6  C8  H82  single  0.970  0.020  1.090
 NG6  C8  H83  single  0.970  0.020  1.090
 NG6  N2  HN2  single  0.860  0.020  1.020
 NG6  O1  HO1  single  0.850  0.020  0.980
 NG6  O3  HO3  single  0.850  0.020  0.980
 NG6  O4  HO4  single  0.850  0.020  0.980
 NG6  O6  S    single  1.648  0.020  1.648
 NG6  S   O1S  deloc   1.460  0.020  1.460
 NG6  S   O2S  deloc   1.464  0.020  1.464
 NG6  S   O3S  deloc   1.465  0.020  1.465

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
 NG6  H1   C1  O5   108.87  3.000
 NG6  H1   C1  O1   111.56  3.000
 NG6  O5   C1  O1   108.54  3.000
 NG6  H1   C1  C2   108.58  3.000
 NG6  O5   C1  C2   110.85  3.000
 NG6  O1   C1  C2   108.45  3.000
 NG6  H2   C2  N2   108.02  3.000
 NG6  H2   C2  C3   109.50  3.000
 NG6  N2   C2  C3   110.79  3.000
 NG6  H2   C2  C1   108.63  3.000
 NG6  N2   C2  C1   110.00  3.000
 NG6  C3   C2  C1   109.85  3.000
 NG6  H3   C3  O3   110.85  3.000
 NG6  H3   C3  C4   106.29  3.000
 NG6  O3   C3  C4   113.30  3.000
 NG6  H3   C3  C2   107.65  3.000
 NG6  O3   C3  C2   108.05  3.000
 NG6  C4   C3  C2   110.56  3.000
 NG6  H4   C4  O4   111.36  3.000
 NG6  H4   C4  C5   108.22  3.000
 NG6  O4   C4  C5   112.20  3.000
 NG6  H4   C4  C3   108.14  3.000
 NG6  O4   C4  C3   108.95  3.000
 NG6  C5   C4  C3   107.83  3.000
 NG6  H5   C5  O5   110.57  3.000
 NG6  H5   C5  C6   107.93  3.000
 NG6  O5   C5  C6   108.48  3.000
 NG6  H5   C5  C4   107.40  3.000
 NG6  O5   C5  C4   109.94  3.000
 NG6  C6   C5  C4   112.51  3.000
 NG6  H62  C6  H61  108.04  3.000
 NG6  H62  C6  O6   110.75  3.000
 NG6  H61  C6  O6   111.16  3.000
 NG6  H62  C6  C5   110.48  3.000
 NG6  H61  C6  C5   108.16  3.000
 NG6  O6   C6  C5   108.23  3.000
 NG6  O7   C7  N2   123.49  3.000
 NG6  O7   C7  C8   121.51  3.000
 NG6  N2   C7  C8   115.00  3.000
 NG6  H83  C8  H82  108.39  3.000
 NG6  H83  C8  H81  108.44  3.000
 NG6  H82  C8  H81  107.25  3.000
 NG6  H83  C8  C7   113.86  3.000
 NG6  H82  C8  C7   109.37  3.000
 NG6  H81  C8  C7   109.33  3.000
 NG6  HN2  N2  C7   118.22  3.000
 NG6  HN2  N2  C2   117.20  3.000
 NG6  C7   N2  C2   124.57  3.000
 NG6  HO1  O1  C1   109.45  3.000
 NG6  HO3  O3  C3   108.51  3.000
 NG6  HO4  O4  C4   109.17  3.000
 NG6  C5   O5  C1   113.38  3.000
 NG6  S    O6  C6   116.96  3.000
 NG6  O3S  S   O2S  113.88  3.000
 NG6  O3S  S   O1S  115.00  3.000
 NG6  O2S  S   O1S  114.39  3.000
 NG6  O3S  S   O6   105.30  3.000
 NG6  O2S  S   O6   105.39  3.000
 NG6  O1S  S   O6   100.99  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
 NG6  CONST_01  C8   C7  N2  C2   180.00   0.0  0
 NG6  CONST_02  O7   C7  N2  C2     0.00   0.0  0
 NG6  CONST_03  HN2  N2  C7  C8     0.00   0.0  0
 NG6  Var_01    O1S  S   O6  C6  -178.93  30.0  3
 NG6  Var_02    H81  C8  C7  N2   124.40  30.0  3
 NG6  Var_03    H61  C6  O6  S     41.73  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
 NG6  chir_01  C1  C2  O1  O5  positiv
 NG6  chir_02  C2  N2  C3  C1  positiv
 NG6  chir_03  C3  O3  C2  C4  positiv
 NG6  chir_04  C4  O4  C5  C3  negativ
 NG6  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
 NG6  plan-1  C2   0.020
 NG6  plan-1  C7   0.020
 NG6  plan-1  C8   0.020
 NG6  plan-1  N2   0.020
 NG6  plan-1  O7   0.020
 NG6  plan-1  HN2  0.020

