# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 22:10:41 2022
#   Inital geometry file: a 81 line input string
#   Ligand name: 2-deoxy-3-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](O)[C@H](N[S](O)(=O)=O)[C@@H](O[S](O)(=O)=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
 GNX  GNX  2-deoxy-3-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose  D-saccharide  31  20  .  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_GNX
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
 GNX  N2    N  NC1    0  -0.754  26.3575   -8.6219  -22.5225
 GNX  C1    C  CH1    0   0.250  26.5981   -6.2773  -21.6912
 GNX  O1    O  OH1    0  -0.665  27.4953   -6.7209  -20.7212
 GNX  S1    S  S      0   1.501  24.7410   -9.1004  -22.3991
 GNX  C2    C  CH1    0  -0.148  26.6599   -7.2542  -22.8684
 GNX  C3    C  CH1    0   0.039  28.0341   -7.1559  -23.5412
 GNX  O3    O  OC2    0  -0.624  28.0473   -7.9821  -24.6890
 GNX  C4    C  CH1    0   0.015  28.2922   -5.7122  -23.9616
 GNX  O4    O  OH1    0  -0.665  29.6003   -5.6093  -24.4706
 GNX  C5    C  CH1    0  -0.007  28.1237   -4.7798  -22.7523
 GNX  O5    O  O2     0  -0.498  26.8702   -4.9729  -22.1246
 GNX  C6    C  CH2    0  -0.162  28.1959   -3.3243  -23.1652
 GNX  O6    O  OH1    0  -0.666  28.1872   -2.5171  -22.0118
 GNX  O12   O  OS    -1  -0.735  28.1682  -10.1979  -25.6071
 GNX  S12   S  S      0   1.558  28.9809   -9.3440  -24.7421
 GNX  O1S   O  OS     0  -0.756  24.1735   -8.7449  -23.7086
 GNX  O22   O  OS     0  -0.738  30.2480   -8.9165  -25.3394
 GNX  O2S   O  OS     0  -0.755  24.8525  -10.5435  -22.1500
 GNX  O32   O  OS     0  -0.733  29.1222   -9.8191  -23.3631
 GNX  O3S   O  OS    -1  -0.752  24.0975   -8.3779  -21.2849
 GNX  HN21  H  HNC1   0   0.369  26.9049   -8.9626  -21.7403
 GNX  H1    H  HCH1   0   0.233  25.5783   -6.2352  -21.2985
 GNX  HO1   H  HOH1   0   0.460  27.3061   -6.2803  -19.8860
 GNX  H2    H  HCH1   0   0.258  25.9147   -6.9250  -23.5988
 GNX  H3    H  HCH1   0   0.233  28.8147   -7.4551  -22.8332
 GNX  H4    H  HCH1   0   0.222  27.5452   -5.4396  -24.7212
 GNX  HO4   H  HOH1   0   0.457  29.5915   -5.0579  -25.2567
 GNX  H5    H  HCH1   0   0.216  28.9443   -4.9870  -22.0503
 GNX  H61   H  HCH2   0   0.200  29.1094   -3.1748  -23.7521
 GNX  H62   H  HCH2   0   0.194  27.3473   -3.1020  -23.8277
 GNX  HO6   H  HOH1   0   0.453  28.2389   -1.5988  -22.2908

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
 GNX  N2   S1    single  1.690  0.020  1.690
 GNX  N2   C2    single  1.443  0.020  1.443
 GNX  C1   O1    single  1.394  0.020  1.394
 GNX  C1   C2    single  1.531  0.020  1.531
 GNX  C1   O5    single  1.401  0.020  1.401
 GNX  S1   O1S   deloc   1.471  0.020  1.471
 GNX  S1   O2S   deloc   1.469  0.020  1.469
 GNX  S1   O3S   deloc   1.476  0.020  1.476
 GNX  C2   C3    single  1.533  0.020  1.533
 GNX  C3   O3    single  1.414  0.020  1.414
 GNX  C3   C4    single  1.526  0.020  1.526
 GNX  O3   S12   single  1.652  0.020  1.652
 GNX  C4   O4    single  1.407  0.020  1.407
 GNX  C4   C5    single  1.536  0.020  1.536
 GNX  C5   O5    single  1.415  0.020  1.415
 GNX  C5   C6    single  1.515  0.020  1.515
 GNX  C6   O6    single  1.408  0.020  1.408
 GNX  O12  S12   deloc   1.462  0.020  1.462
 GNX  S12  O22   deloc   1.465  0.020  1.465
 GNX  S12  O32   deloc   1.465  0.020  1.465
 GNX  N2   HN21  single  0.890  0.020  1.040
 GNX  C1   H1    single  0.970  0.020  1.090
 GNX  O1   HO1   single  0.850  0.020  0.980
 GNX  C2   H2    single  0.970  0.020  1.090
 GNX  C3   H3    single  0.970  0.020  1.090
 GNX  C4   H4    single  0.970  0.020  1.090
 GNX  O4   HO4   single  0.850  0.020  0.980
 GNX  C5   H5    single  0.970  0.020  1.090
 GNX  C6   H61   single  0.970  0.020  1.090
 GNX  C6   H62   single  0.970  0.020  1.090
 GNX  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
 GNX  HN21  N2   C2   112.98  3.000
 GNX  HN21  N2   S1   111.41  3.000
 GNX  C2    N2   S1   119.09  3.000
 GNX  H1    C1   O5   104.86  3.000
 GNX  H1    C1   C2   109.77  3.000
 GNX  O5    C1   C2   110.39  3.000
 GNX  H1    C1   O1   111.26  3.000
 GNX  O5    C1   O1   112.74  3.000
 GNX  C2    C1   O1   107.82  3.000
 GNX  HO1   O1   C1   109.37  3.000
 GNX  O3S   S1   O2S  112.71  3.000
 GNX  O3S   S1   O1S  112.68  3.000
 GNX  O2S   S1   O1S  114.69  3.000
 GNX  O3S   S1   N2   109.49  3.000
 GNX  O2S   S1   N2   102.59  3.000
 GNX  O1S   S1   N2   103.63  3.000
 GNX  H2    C2   C3   107.35  3.000
 GNX  H2    C2   C1   107.08  3.000
 GNX  C3    C2   C1   109.43  3.000
 GNX  H2    C2   N2   107.61  3.000
 GNX  C3    C2   N2   110.72  3.000
 GNX  C1    C2   N2   114.34  3.000
 GNX  H3    C3   C4   108.42  3.000
 GNX  H3    C3   O3   110.99  3.000
 GNX  C4    C3   O3   109.12  3.000
 GNX  H3    C3   C2   109.73  3.000
 GNX  C4    C3   C2   109.47  3.000
 GNX  O3    C3   C2   109.08  3.000
 GNX  S12   O3   C3   120.86  3.000
 GNX  H4    C4   C5   108.59  3.000
 GNX  H4    C4   O4   111.31  3.000
 GNX  C5    C4   O4   110.01  3.000
 GNX  H4    C4   C3   108.06  3.000
 GNX  C5    C4   C3   109.81  3.000
 GNX  O4    C4   C3   109.03  3.000
 GNX  HO4   O4   C4   109.24  3.000
 GNX  H5    C5   C6   108.63  3.000
 GNX  H5    C5   O5   110.62  3.000
 GNX  C6    C5   O5   107.12  3.000
 GNX  H5    C5   C4   107.84  3.000
 GNX  C6    C5   C4   111.31  3.000
 GNX  O5    C5   C4   111.31  3.000
 GNX  C5    O5   C1   115.87  3.000
 GNX  H62   C6   H61  107.05  3.000
 GNX  H62   C6   O6   111.90  3.000
 GNX  H61   C6   O6   111.45  3.000
 GNX  H62   C6   C5   108.77  3.000
 GNX  H61   C6   C5   108.47  3.000
 GNX  O6    C6   C5   109.10  3.000
 GNX  HO6   O6   C6   108.03  3.000
 GNX  O32   S12  O22  113.26  3.000
 GNX  O32   S12  O12  114.90  3.000
 GNX  O22   S12  O12  114.21  3.000
 GNX  O32   S12  O3   106.95  3.000
 GNX  O22   S12  O3   105.15  3.000
 GNX  O12   S12  O3   100.74  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
 GNX  Var_01  O1S  S1   N2  C2   55.89  30.0  3
 GNX  Var_02  O12  S12  O3  C3  148.69  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
 GNX  chir_01  C1  O1  C2  O5  positiv
 GNX  chir_02  C2  N2  C3  C1  positiv
 GNX  chir_03  C3  O3  C4  C2  negativ
 GNX  chir_04  C4  O4  C3  C5  negativ
 GNX  chir_05  C5  O5  C4  C6  negativ

