# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 10:29:53 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: (1R,2S,8S,8aS)-1,2,8-trihydroxyoctahydrothieno[1,2-a]thiopyranium (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1CCC[S@+]2C[C@@H](O)[C@@H](O)[C@H]12
#
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
 NK1  NK1  '(1R,2S,8S,8aS)-1,2,8-trihydroxyoctahydrothieno[1,2-a]thiopyranium (non-preferred name)'  ligand  27  12  .  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_NK1
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
 NK1  O7   O  OH1   0  -0.640   1.6333  -3.6445  -3.7051
 NK1  C7   C  CR15  0   0.040   2.0527  -2.4718  -3.0843
 NK1  C6   C  CR15  0  -0.463   1.5188  -2.4966  -1.6521
 NK1  C5   C  CH1   0   0.059   0.0184  -2.3198  -1.4502
 NK1  O5   O  OH1   0  -0.659  -0.1801  -2.4733  -0.0644
 NK1  C4   C  CH2   0  -0.505  -0.5166  -0.9824  -1.9522
 NK1  C3   C  CH2   0  -0.452   0.1111   0.2199  -1.2584
 NK1  C2   C  CH2   0  -0.574   1.6115   0.3058  -1.4745
 NK1  S1   S  S3    1   0.413   2.4301  -1.1743  -0.7987
 NK1  C9   C  CH2   0  -0.607   3.9029  -1.3256  -1.8646
 NK1  C8   C  CR15  0   0.014   3.5902  -2.3163  -3.0038
 NK1  O8   O  OH1   0  -0.639   4.2647  -3.5283  -2.8608
 NK1  HO7  H  HOH1  0   0.469   1.7805  -3.5690  -4.6537
 NK1  H7   H  HCR5  0   0.253   1.6641  -1.5844  -3.5989
 NK1  H6   H  HCR5  0   0.353   1.8306  -3.4194  -1.1501
 NK1  H5   H  HCH1  0   0.273  -0.4630  -3.1277  -2.0156
 NK1  HO5  H  HOH1  0   0.465  -1.1209  -2.3885   0.1246
 NK1  H41  H  HCH2  0   0.279  -1.5971  -0.9670  -1.7926
 NK1  H42  H  HCH2  0   0.255  -0.3799  -0.9109  -3.0342
 NK1  H31  H  HCH2  0   0.292  -0.3130   1.1394  -1.6640
 NK1  H32  H  HCH2  0   0.265  -0.1153   0.2201  -0.1914
 NK1  H21  H  HCH2  0   0.318   1.8662   0.3903  -2.5306
 NK1  H22  H  HCH2  0   0.346   2.0597   1.1422  -0.9399
 NK1  H91  H  HCH2  0   0.351   4.7235  -1.6708  -1.2384
 NK1  H92  H  HCH2  0   0.344   4.1415  -0.3235  -2.2181
 NK1  H8   H  HCR5  0   0.299   3.9529  -1.8817  -3.9364
 NK1  HO8  H  HOH1  0   0.453   3.9152  -4.0282  -2.1152

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
 NK1  O7  C7   single  1.392  0.020  1.392
 NK1  O7  HO7  single  0.850  0.020  0.980
 NK1  C7  C6   single  1.529  0.020  1.529
 NK1  C7  C8   single  1.547  0.020  1.547
 NK1  C7  H7   single  0.970  0.020  1.090
 NK1  C6  C5   single  1.524  0.020  1.524
 NK1  C6  S1   single  1.819  0.020  1.819
 NK1  C6  H6   single  0.970  0.020  1.090
 NK1  C5  O5   single  1.408  0.020  1.408
 NK1  C5  C4   single  1.525  0.020  1.525
 NK1  C5  H5   single  0.970  0.020  1.090
 NK1  O5  HO5  single  0.850  0.020  0.980
 NK1  C4  C3   single  1.523  0.020  1.523
 NK1  C4  H41  single  0.970  0.020  1.090
 NK1  C4  H42  single  0.970  0.020  1.090
 NK1  C3  C2   single  1.518  0.020  1.518
 NK1  C3  H31  single  0.970  0.020  1.090
 NK1  C3  H32  single  0.970  0.020  1.090
 NK1  C2  S1   single  1.821  0.020  1.821
 NK1  C2  H21  single  0.970  0.020  1.090
 NK1  C2  H22  single  0.970  0.020  1.090
 NK1  S1  C9   single  1.824  0.020  1.824
 NK1  C9  C8   single  1.542  0.020  1.542
 NK1  C9  H91  single  0.970  0.020  1.090
 NK1  C9  H92  single  0.970  0.020  1.090
 NK1  C8  O8   single  1.394  0.020  1.394
 NK1  C8  H8   single  0.970  0.020  1.090
 NK1  O8  HO8  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
 NK1  HO7  O7  C7   109.11  3.000
 NK1  H7   C7  C8   107.17  3.000
 NK1  H7   C7  C6   109.20  3.000
 NK1  C8   C7  C6   107.45  3.000
 NK1  H7   C7  O7   111.44  3.000
 NK1  C8   C7  O7   114.04  3.000
 NK1  C6   C7  O7   107.40  3.000
 NK1  H6   C6  S1   104.75  3.000
 NK1  H6   C6  C5   108.49  3.000
 NK1  S1   C6  C5   110.29  3.000
 NK1  H6   C6  C7   110.09  3.000
 NK1  S1   C6  C7   104.65  3.000
 NK1  C5   C6  C7   117.78  3.000
 NK1  H5   C5  C4   108.79  3.000
 NK1  H5   C5  O5   111.41  3.000
 NK1  C4   C5  O5   111.71  3.000
 NK1  H5   C5  C6   106.15  3.000
 NK1  C4   C5  C6   113.79  3.000
 NK1  O5   C5  C6   104.86  3.000
 NK1  HO5  O5  C5   108.73  3.000
 NK1  H42  C4  H41  105.51  3.000
 NK1  H42  C4  C3   110.34  3.000
 NK1  H41  C4  C3   109.27  3.000
 NK1  H42  C4  C5   109.83  3.000
 NK1  H41  C4  C5   108.13  3.000
 NK1  C3   C4  C5   113.43  3.000
 NK1  H32  C3  H31  106.43  3.000
 NK1  H32  C3  C2   110.14  3.000
 NK1  H31  C3  C2   106.48  3.000
 NK1  H32  C3  C4   111.10  3.000
 NK1  H31  C3  C4   109.62  3.000
 NK1  C2   C3  C4   112.77  3.000
 NK1  H22  C2  H21  108.66  3.000
 NK1  H22  C2  S1   104.89  3.000
 NK1  H21  C2  S1   108.52  3.000
 NK1  H22  C2  C3   112.35  3.000
 NK1  H21  C2  C3   111.92  3.000
 NK1  S1   C2  C3   110.20  3.000
 NK1  C9   S1  C2   102.32  3.000
 NK1  C9   S1  C6    94.02  3.000
 NK1  C2   S1  C6   101.04  3.000
 NK1  H92  C9  H91  108.26  3.000
 NK1  H92  C9  C8   113.32  3.000
 NK1  H91  C9  C8   111.98  3.000
 NK1  H92  C9  S1   106.87  3.000
 NK1  H91  C9  S1   107.38  3.000
 NK1  C8   C9  S1   108.74  3.000
 NK1  H8   C8  O8   105.85  3.000
 NK1  H8   C8  C9   107.95  3.000
 NK1  O8   C8  C9   112.62  3.000
 NK1  H8   C8  C7   109.02  3.000
 NK1  O8   C8  C7   113.49  3.000
 NK1  C9   C8  C7   107.73  3.000
 NK1  HO8  O8  C8   110.78  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
 NK1  Var_01  C3  C2  S1  C6   54.44  30.0  1
 NK1  Var_02  C8  C9  S1  C6    6.75  30.0  1
 NK1  Var_03  C2  C3  C4  C5   61.47  30.0  1
 NK1  Var_04  S1  C2  C3  C4  -60.90  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
 NK1  chir_01  C7  O7  C6  C8  negativ
 NK1  chir_02  C6  S1  C5  C7  negativ
 NK1  chir_03  C5  O5  C6  C4  positiv
 NK1  chir_04  C8  O8  C9  C7  positiv

