# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 19:45:54 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: (2S,3aR,5R,6R,7R,7aR)-5-(hydroxymethyl)-2-methyl-2,3a,5,6,7,7a-hexahydro-1H-pyrano[3,2-d][1,3]thiazole-6,7-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1N[C@@H]2[C@@H](O)[C@@H](O)[C@@H](CO)O[C@@H]2S1
#
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
 NSG  NSG  (2S,3aR,5R,6R,7R,7aR)-5-(hydroxymethyl)-2-methyl-2,3a,5,6,7,7a-hexahydro-1H-pyrano[3,2-d][1,3]thiazole-6,7-diol  ligand  29  14  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NSG
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
 NSG  C1   C  CR15  0  -0.078  -0.2809  -0.6332   1.0105
 NSG  S1   S  S2    0  -0.093  -1.2915  -1.7248  -0.0853
 NSG  C2   C  CR15  0  -0.180  -0.8170   0.7911   0.7270
 NSG  N2   N  NR15  0  -0.550  -2.2447   0.6926   0.5239
 NSG  C3   C  CH1   0   0.066  -0.1290   1.4113  -0.4855
 NSG  O3   O  OH1   0  -0.665  -0.5116   2.7593  -0.5473
 NSG  C4   C  CH1   0  -0.035   1.3812   1.2186  -0.4080
 NSG  O4   O  OH1   0  -0.669   1.8685   1.9290   0.7029
 NSG  C5   C  CH1   0   0.000   1.6581  -0.2814  -0.3160
 NSG  O5   O  O2    0  -0.462   1.0846  -0.8088   0.8635
 NSG  C6   C  CH2   0  -0.166   3.1373  -0.5959  -0.2966
 NSG  O6   O  OH1   0  -0.668   3.3124  -1.9897  -0.3766
 NSG  C7   C  CR15  0  -0.211  -2.5448  -0.3762  -0.3926
 NSG  C8   C  CH3   0  -0.664  -3.9566  -0.8916  -0.2314
 NSG  H1   H  HCR5  0   0.282  -0.5004  -0.9042   2.0440
 NSG  H2   H  HCR5  0   0.283  -0.6262   1.4211   1.5996
 NSG  HN2  H  HNR5  0   0.364  -2.6973   0.5129   1.4130
 NSG  H3   H  HCH1  0   0.222  -0.4509   0.8730  -1.3885
 NSG  HO3  H  HOH1  0   0.452  -0.1901   3.1283  -1.3761
 NSG  H4   H  HCH1  0   0.237   1.8250   1.5882  -1.3448
 NSG  HO4  H  HOH1  0   0.457   2.8227   2.0176   0.6255
 NSG  H5   H  HCH1  0   0.223   1.2156  -0.7616  -1.2025
 NSG  H6   H  HCH2  0   0.206   3.5964  -0.0790  -1.1501
 NSG  H6A  H  HCH2  0   0.200   3.5943  -0.1865   0.6138
 NSG  HO6  H  HOH1  0   0.457   4.2556  -2.1725  -0.3453
 NSG  H7   H  HCR5  0   0.272  -2.3973  -0.0392  -1.4196
 NSG  H8   H  HCH3  0   0.233  -4.1236  -1.2702   0.7777
 NSG  H8A  H  HCH3  0   0.244  -4.6691  -0.0880  -0.4254
 NSG  H8B  H  HCH3  0   0.248  -4.1611  -1.6960  -0.9360

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
 NSG  C1  S1   single  1.848  0.020  1.848
 NSG  C1  C2   single  1.548  0.020  1.548
 NSG  C1  O5   single  1.385  0.020  1.385
 NSG  S1  C7   single  1.867  0.020  1.867
 NSG  C2  N2   single  1.445  0.020  1.445
 NSG  C2  C3   single  1.526  0.020  1.526
 NSG  N2  C7   single  1.440  0.020  1.440
 NSG  C3  O3   single  1.403  0.020  1.403
 NSG  C3  C4   single  1.524  0.020  1.524
 NSG  C4  O4   single  1.406  0.020  1.406
 NSG  C4  C5   single  1.528  0.020  1.528
 NSG  C5  O5   single  1.414  0.020  1.414
 NSG  C5  C6   single  1.512  0.020  1.512
 NSG  C6  O6   single  1.407  0.020  1.407
 NSG  C7  C8   single  1.511  0.020  1.511
 NSG  C1  H1   single  0.970  0.020  1.090
 NSG  C2  H2   single  0.970  0.020  1.090
 NSG  N2  HN2  single  0.890  0.020  1.040
 NSG  C3  H3   single  0.970  0.020  1.090
 NSG  O3  HO3  single  0.850  0.020  0.980
 NSG  C4  H4   single  0.970  0.020  1.090
 NSG  O4  HO4  single  0.850  0.020  0.980
 NSG  C5  H5   single  0.970  0.020  1.090
 NSG  C6  H6   single  0.970  0.020  1.090
 NSG  C6  H6A  single  0.970  0.020  1.090
 NSG  O6  HO6  single  0.850  0.020  0.980
 NSG  C7  H7   single  0.970  0.020  1.090
 NSG  C8  H8   single  0.970  0.020  1.090
 NSG  C8  H8A  single  0.970  0.020  1.090
 NSG  C8  H8B  single  0.970  0.020  1.090

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
 NSG  H1   C1  O5   105.52  3.000
 NSG  H1   C1  C2   109.42  3.000
 NSG  O5   C1  C2   116.03  3.000
 NSG  H1   C1  S1   107.76  3.000
 NSG  O5   C1  S1   113.67  3.000
 NSG  C2   C1  S1   104.21  3.000
 NSG  C7   S1  C1    92.18  3.000
 NSG  H2   C2  C3   108.74  3.000
 NSG  H2   C2  N2   108.90  3.000
 NSG  C3   C2  N2   111.19  3.000
 NSG  H2   C2  C1   108.88  3.000
 NSG  C3   C2  C1   111.31  3.000
 NSG  N2   C2  C1   107.77  3.000
 NSG  HN2  N2  C7   109.49  3.000
 NSG  HN2  N2  C2   109.26  3.000
 NSG  C7   N2  C2   110.24  3.000
 NSG  H3   C3  C4   105.66  3.000
 NSG  H3   C3  O3   110.76  3.000
 NSG  C4   C3  O3   113.20  3.000
 NSG  H3   C3  C2   108.76  3.000
 NSG  C4   C3  C2   110.79  3.000
 NSG  O3   C3  C2   107.62  3.000
 NSG  HO3  O3  C3   108.38  3.000
 NSG  H4   C4  C5   107.93  3.000
 NSG  H4   C4  O4   111.30  3.000
 NSG  C5   C4  O4   112.68  3.000
 NSG  H4   C4  C3   108.29  3.000
 NSG  C5   C4  C3   107.86  3.000
 NSG  O4   C4  C3   108.65  3.000
 NSG  HO4  O4  C4   109.08  3.000
 NSG  H5   C5  C6   108.22  3.000
 NSG  H5   C5  O5   110.24  3.000
 NSG  C6   C5  O5   107.97  3.000
 NSG  H5   C5  C4   107.87  3.000
 NSG  C6   C5  C4   112.47  3.000
 NSG  O5   C5  C4   110.06  3.000
 NSG  C5   O5  C1   116.19  3.000
 NSG  H6A  C6  H6   107.15  3.000
 NSG  H6A  C6  O6   111.39  3.000
 NSG  H6   C6  O6   111.72  3.000
 NSG  H6A  C6  C5   109.89  3.000
 NSG  H6   C6  C5   107.51  3.000
 NSG  O6   C6  C5   109.08  3.000
 NSG  HO6  O6  C6   107.97  3.000
 NSG  H7   C7  C8   109.39  3.000
 NSG  H7   C7  N2   109.99  3.000
 NSG  C8   C7  N2   112.33  3.000
 NSG  H7   C7  S1   106.70  3.000
 NSG  C8   C7  S1   111.30  3.000
 NSG  N2   C7  S1   106.95  3.000
 NSG  H8B  C8  H8A  107.84  3.000
 NSG  H8B  C8  H8   108.27  3.000
 NSG  H8A  C8  H8   108.67  3.000
 NSG  H8B  C8  C7   111.00  3.000
 NSG  H8A  C8  C7   109.87  3.000
 NSG  H8   C8  C7   111.10  3.000

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
 NSG  chir_01  C1  S1  C2  O5  positiv
 NSG  chir_02  C2  N2  C3  C1  positiv
 NSG  chir_03  C3  O3  C2  C4  positiv
 NSG  chir_04  C4  O4  C5  C3  negativ
 NSG  chir_05  C5  O5  C4  C6  negativ
 NSG  chir_06  C7  S1  N2  C8  positiv

