# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 09:19:49 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: (1R,2S,8aS)-1,2-dihydroxyoctahydrothieno[1,2-a]thiopyranium (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1C[S@@+]2CCCC[C@H]2[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
 NK2  NK2  '(1R,2S,8aS)-1,2-dihydroxyoctahydrothieno[1,2-a]thiopyranium (non-preferred name)'  ligand  26  11  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NK2
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
 NK2  O7   O  OH1   0  -0.642   4.6993   0.5607  -0.2255
 NK2  C7   C  CH1   0   0.061   4.1945  -0.3494   0.6959
 NK2  C6   C  CH1   0  -0.425   3.2382  -1.3608   0.0420
 NK2  C5   C  CH2   0  -0.443   1.9286  -0.8237  -0.5120
 NK2  C4   C  CH2   0  -0.457   0.9655  -0.2700   0.5289
 NK2  C3   C  CH2   0  -0.457   0.5491  -1.3246   1.5458
 NK2  C2   C  CH2   0  -0.566   1.7137  -1.8078   2.3917
 NK2  S1   S  S3    1   0.393   2.9705  -2.6133   1.3451
 NK2  C9   C  CH2   0  -0.577   4.5286  -2.2318   2.2403
 NK2  C8   C  CH1   0  -0.008   5.2644  -1.1827   1.4073
 NK2  O8   O  OH1   0  -0.664   6.0479  -1.7644   0.4017
 NK2  HO7  H  HOH1  0   0.454   5.3196   0.1021  -0.8058
 NK2  H7   H  HCH1  0   0.270   3.6541   0.2347   1.4476
 NK2  H6   H  HCH1  0   0.349   3.7617  -1.9121  -0.7437
 NK2  H51  H  HCH2  0   0.270   1.4356  -1.6167  -1.0799
 NK2  H52  H  HCH2  0   0.281   2.1933  -0.0513  -1.2369
 NK2  H41  H  HCH2  0   0.269   0.0786   0.1006   0.0142
 NK2  H42  H  HCH2  0   0.241   1.4021   0.5901   1.0446
 NK2  H31  H  HCH2  0   0.288  -0.1859  -0.9119   2.2388
 NK2  H32  H  HCH2  0   0.262   0.0692  -2.1694   1.0454
 NK2  H21  H  HCH2  0   0.314   2.1913  -0.9884   2.9293
 NK2  H22  H  HCH2  0   0.341   1.4170  -2.5707   3.1099
 NK2  H91  H  HCH2  0   0.346   5.0845  -3.1597   2.3533
 NK2  H92  H  HCH2  0   0.335   4.2483  -1.8624   3.2254
 NK2  H8   H  HCH1  0   0.292   5.8580  -0.5552   2.0801
 NK2  HO8  H  HOH1  0   0.474   6.8818  -2.0656   0.7757

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
 NK2  O7  C7   single  1.390  0.020  1.390
 NK2  O7  HO7  single  0.850  0.020  0.980
 NK2  C7  C6   single  1.538  0.020  1.538
 NK2  C7  C8   single  1.531  0.020  1.531
 NK2  C7  H7   single  0.970  0.020  1.090
 NK2  C6  C5   single  1.520  0.020  1.520
 NK2  C6  S1   single  1.827  0.020  1.827
 NK2  C6  H6   single  0.970  0.020  1.090
 NK2  C5  C4   single  1.522  0.020  1.522
 NK2  C5  H51  single  0.970  0.020  1.090
 NK2  C5  H52  single  0.970  0.020  1.090
 NK2  C4  C3   single  1.523  0.020  1.523
 NK2  C4  H41  single  0.970  0.020  1.090
 NK2  C4  H42  single  0.970  0.020  1.090
 NK2  C3  C2   single  1.518  0.020  1.518
 NK2  C3  H31  single  0.970  0.020  1.090
 NK2  C3  H32  single  0.970  0.020  1.090
 NK2  C2  S1   single  1.823  0.020  1.823
 NK2  C2  H21  single  0.970  0.020  1.090
 NK2  C2  H22  single  0.970  0.020  1.090
 NK2  S1  C9   single  1.837  0.020  1.837
 NK2  C9  C8   single  1.528  0.020  1.528
 NK2  C9  H91  single  0.970  0.020  1.090
 NK2  C9  H92  single  0.970  0.020  1.090
 NK2  C8  O8   single  1.401  0.020  1.401
 NK2  C8  H8   single  0.970  0.020  1.090
 NK2  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
 NK2  HO7  O7  C7   108.72  3.000
 NK2  H7   C7  C8   108.44  3.000
 NK2  H7   C7  C6   109.63  3.000
 NK2  C8   C7  C6   105.91  3.000
 NK2  H7   C7  O7   106.57  3.000
 NK2  C8   C7  O7   114.24  3.000
 NK2  C6   C7  O7   112.00  3.000
 NK2  H6   C6  S1   103.71  3.000
 NK2  H6   C6  C5   109.20  3.000
 NK2  S1   C6  C5   112.08  3.000
 NK2  H6   C6  C7   109.84  3.000
 NK2  S1   C6  C7   103.81  3.000
 NK2  C5   C6  C7   117.28  3.000
 NK2  H52  C5  H51  106.12  3.000
 NK2  H52  C5  C4   110.49  3.000
 NK2  H51  C5  C4   109.50  3.000
 NK2  H52  C5  C6   106.44  3.000
 NK2  H51  C5  C6   108.76  3.000
 NK2  C4   C5  C6   115.11  3.000
 NK2  H42  C4  H41  106.26  3.000
 NK2  H42  C4  C3   109.80  3.000
 NK2  H41  C4  C3   109.15  3.000
 NK2  H42  C4  C5   110.85  3.000
 NK2  H41  C4  C5   108.39  3.000
 NK2  C3   C4  C5   112.19  3.000
 NK2  H32  C3  H31  106.70  3.000
 NK2  H32  C3  C2   110.23  3.000
 NK2  H31  C3  C2   106.45  3.000
 NK2  H32  C3  C4   110.47  3.000
 NK2  H31  C3  C4   110.26  3.000
 NK2  C2   C3  C4   112.50  3.000
 NK2  H22  C2  H21  108.70  3.000
 NK2  H22  C2  S1   104.88  3.000
 NK2  H21  C2  S1   108.25  3.000
 NK2  H22  C2  C3   112.42  3.000
 NK2  H21  C2  C3   111.81  3.000
 NK2  S1   C2  C3   110.46  3.000
 NK2  C9   S1  C2   102.31  3.000
 NK2  C9   S1  C6    94.64  3.000
 NK2  C2   S1  C6   101.98  3.000
 NK2  H92  C9  H91  109.09  3.000
 NK2  H92  C9  C8   112.59  3.000
 NK2  H91  C9  C8   113.34  3.000
 NK2  H92  C9  S1   107.04  3.000
 NK2  H91  C9  S1   107.88  3.000
 NK2  C8   C9  S1   106.58  3.000
 NK2  H8   C8  O8   112.07  3.000
 NK2  H8   C8  C9   108.63  3.000
 NK2  O8   C8  C9   112.05  3.000
 NK2  H8   C8  C7   110.63  3.000
 NK2  O8   C8  C7   106.45  3.000
 NK2  C9   C8  C7   106.88  3.000
 NK2  HO8  O8  C8   109.61  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
 NK2  Var_01  C3  C4  C5  C6  -60.51  30.0  1
 NK2  Var_02  C3  C2  S1  C6   51.09  30.0  1
 NK2  Var_03  C8  C9  S1  C6   -4.09  30.0  1
 NK2  Var_04  S1  C2  C3  C4  -62.51  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
 NK2  chir_01  C7  O7  C6  C8  negativ
 NK2  chir_02  C6  S1  C5  C7  negativ
 NK2  chir_03  C8  O8  C7  C9  negativ

