# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jun 13 02:37:50 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: (2S)-2,3-bis(nitrooxy)propyl ethyl[(4S,6S)-6-methyl-7,7-dioxido-2-sulfamoyl-5,6-dihydro-4H-thieno[2,3-b]thiopyran-4-yl]carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN([C@H]1C[C@H](C)[S](=O)(=O)c2sc(cc12)[S](N)(=O)=O)C(=O)OC[C@@H](CO[N+]([O-])=O)O[N+]([O-])=O
#
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
 NKX  NKX  '(2S)-2,3-bis(nitrooxy)propyl ethyl[(4S,6S)-6-methyl-7,7-dioxido-2-sulfamoyl-5,6-dihydro-4H-thieno[2,3-b]thiopyran-4-yl]carbamate'  ligand  53  33  .  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_NKX
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
 NKX  CAA   C  CH3    0  -0.718   4.3330  -3.1156   0.8841
 NKX  OAB   O  OS     0  -0.654   3.2894  -1.9025  -2.7493
 NKX  OAC   O  OS     0  -0.638   3.6851   4.2114  -0.7048
 NKX  CAD   C  CH1    0  -0.468   3.4436  -3.0381  -0.3465
 NKX  SAE   S  S      0   1.248   3.9992  -1.7628  -1.4823
 NKX  CAF   C  CR5    0  -0.553   3.4052  -0.3303  -0.6473
 NKX  SAG   S  S2     0   0.382   4.0720   1.2127  -0.9713
 NKX  CAH   C  CR5    0  -0.438   2.9725   1.9066   0.1424
 NKX  SAI   S  S      0   1.377   3.0163   3.6346   0.4477
 NKX  NAJ   N  NC2    0  -0.867   3.9476   3.7354   1.7978
 NKX  OAK   O  OS     0  -0.656   5.4547  -1.6621  -1.5273
 NKX  OAL   O  OS     0  -0.640   1.6852   4.0605   0.8339
 NKX  CAM   C  CH2    0  -0.465   1.9624  -2.7943  -0.0597
 NKX  CAN   C  CH1    0  -0.163   1.6921  -1.5433   0.7793
 NKX  CAO   C  CR5    0   0.350   2.3843  -0.3138   0.2584
 NKX  CAP   C  CR15   0  -0.152   2.1438   1.0022   0.7282
 NKX  NAQ   N  NT     0  -0.506   0.2692  -1.3307   0.9863
 NKX  CAR   C  CH2    0  -0.319  -0.3001  -1.7115   2.2766
 NKX  CAS   C  CH3    0  -0.664  -0.3140  -0.5750   3.2833
 NKX  OAT   O  O      0  -0.490  -0.0103  -0.5901  -1.1409
 NKX  CAU   C  C      0   0.792  -0.4561  -0.8453  -0.0440
 NKX  OAV   O  O2     0  -0.487  -1.7413  -0.6529   0.2868
 NKX  CAW   C  CH2    0  -0.136  -2.5929  -0.1842  -0.7418
 NKX  OAX   O  O      0  -0.354  -3.9422  -0.5938   2.4474
 NKX  CAY   C  CH1    0  -0.102  -3.9662  -0.0148  -0.1219
 NKX  OAZ   O  OC2    0  -0.381  -4.4109  -1.2765   0.4029
 NKX  NBA   N  N      1   0.756  -4.2848  -1.4911   1.7404
 NKX  OBB   O  O     -1  -0.363  -4.5607  -2.6087   2.0429
 NKX  CBC   C  CH2    0  -0.142  -4.9669   0.3874  -1.1832
 NKX  OBD   O  OC2    0  -0.384  -6.1862   0.6386  -0.4813
 NKX  NBE   N  N      1   0.771  -7.2358   1.0211  -1.2472
 NKX  OBF   O  O     -1  -0.361  -7.0665   1.1321  -2.4247
 NKX  OBG   O  O      0  -0.367  -8.2277   1.2043  -0.6160
 NKX  HAA   H  HCH3   0   0.252   4.3926  -2.1715   1.4264
 NKX  HAAA  H  HCH3   0   0.303   3.9159  -3.8623   1.5573
 NKX  HAAB  H  HCH3   0   0.295   5.3428  -3.4199   0.6204
 NKX  HAD   H  HCH1   0   0.372   3.5388  -3.9482  -0.9410
 NKX  HNAJ  H  HNC2   0   0.413   3.6139   4.4297   2.4553
 NKX  HNAA  H  HNC2   0   0.409   4.9379   3.8406   1.6145
 NKX  HAM   H  HCH2   0   0.292   1.4003  -2.7464  -0.9926
 NKX  HAMA  H  HCH2   0   0.291   1.5920  -3.6629   0.4871
 NKX  HAN   H  HCH1   0   0.303   2.1084  -1.7108   1.7777
 NKX  HAP   H  HCR5   0   0.296   1.3912   1.2580   1.4610
 NKX  HAR   H  HCH2   0   0.250  -1.3008  -2.1104   2.1299
 NKX  HARA  H  HCH2   0   0.261   0.2946  -2.5437   2.6554
 NKX  HAS   H  HCH3   0   0.228   0.6949  -0.2182   3.4972
 NKX  HASA  H  HCH3   0   0.237  -0.9083   0.2653   2.9248
 NKX  HASB  H  HCH3   0   0.246  -0.7474  -0.9151   4.2236
 NKX  HAW   H  HCH2   0   0.258  -2.2591   0.7817  -1.1269
 NKX  HAWA  H  HCH2   0   0.251  -2.6266  -0.8919  -1.5743
 NKX  HAY   H  HCH1   0   0.301  -3.9340   0.7431   0.6622
 NKX  HBC   H  HCH2   0   0.266  -4.6110   1.2904  -1.6822
 NKX  HBCA  H  HCH2   0   0.267  -5.0980  -0.4016  -1.9264

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
 NKX  CAA  CAD   single    1.520  0.020  1.520
 NKX  OAB  SAE   double    1.459  0.020  1.459
 NKX  OAC  SAI   double    1.452  0.020  1.452
 NKX  CAD  SAE   single    1.796  0.020  1.796
 NKX  CAD  CAM   single    1.528  0.020  1.528
 NKX  SAE  CAF   single    1.761  0.020  1.761
 NKX  SAE  OAK   double    1.460  0.020  1.460
 NKX  CAF  SAG   aromatic  1.712  0.020  1.712
 NKX  CAF  CAO   aromatic  1.365  0.020  1.365
 NKX  SAG  CAH   aromatic  1.712  0.020  1.712
 NKX  CAH  SAI   single    1.755  0.020  1.755
 NKX  CAH  CAP   aromatic  1.359  0.020  1.359
 NKX  SAI  NAJ   single    1.643  0.020  1.643
 NKX  SAI  OAL   double    1.450  0.020  1.450
 NKX  CAM  CAN   single    1.530  0.020  1.530
 NKX  CAN  CAO   single    1.504  0.020  1.504
 NKX  CAN  NAQ   single    1.454  0.020  1.454
 NKX  CAO  CAP   aromatic  1.418  0.020  1.418
 NKX  NAQ  CAR   single    1.461  0.020  1.461
 NKX  NAQ  CAU   single    1.350  0.020  1.350
 NKX  CAR  CAS   single    1.518  0.020  1.518
 NKX  OAT  CAU   double    1.211  0.020  1.211
 NKX  CAU  OAV   single    1.341  0.020  1.341
 NKX  OAV  CAW   single    1.415  0.020  1.415
 NKX  CAW  CAY   single    1.516  0.020  1.516
 NKX  OAX  NBA   double    1.193  0.020  1.193
 NKX  CAY  OAZ   single    1.437  0.020  1.437
 NKX  CAY  CBC   single    1.513  0.020  1.513
 NKX  OAZ  NBA   single    1.360  0.020  1.360
 NKX  NBA  OBB   single    1.190  0.020  1.190
 NKX  CBC  OBD   single    1.429  0.020  1.429
 NKX  OBD  NBE   single    1.354  0.020  1.354
 NKX  NBE  OBF   single    1.195  0.020  1.195
 NKX  NBE  OBG   double    1.190  0.020  1.190
 NKX  CAA  HAA   single    0.970  0.020  1.090
 NKX  CAA  HAAA  single    0.970  0.020  1.090
 NKX  CAA  HAAB  single    0.970  0.020  1.090
 NKX  CAD  HAD   single    0.970  0.020  1.090
 NKX  NAJ  HNAJ  single    0.890  0.020  1.040
 NKX  NAJ  HNAA  single    0.890  0.020  1.040
 NKX  CAM  HAM   single    0.970  0.020  1.090
 NKX  CAM  HAMA  single    0.970  0.020  1.090
 NKX  CAN  HAN   single    0.970  0.020  1.090
 NKX  CAP  HAP   single    0.930  0.020  1.080
 NKX  CAR  HAR   single    0.970  0.020  1.090
 NKX  CAR  HARA  single    0.970  0.020  1.090
 NKX  CAS  HAS   single    0.970  0.020  1.090
 NKX  CAS  HASA  single    0.970  0.020  1.090
 NKX  CAS  HASB  single    0.970  0.020  1.090
 NKX  CAW  HAW   single    0.970  0.020  1.090
 NKX  CAW  HAWA  single    0.970  0.020  1.090
 NKX  CAY  HAY   single    0.970  0.020  1.090
 NKX  CBC  HBC   single    0.970  0.020  1.090
 NKX  CBC  HBCA  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
 NKX  HAAB  CAA  HAAA  108.29  3.000
 NKX  HAAB  CAA  HAA   108.20  3.000
 NKX  HAAA  CAA  HAA   107.90  3.000
 NKX  HAAB  CAA  CAD   111.18  3.000
 NKX  HAAA  CAA  CAD   108.14  3.000
 NKX  HAA   CAA  CAD   112.98  3.000
 NKX  HAD   CAD  CAM   108.65  3.000
 NKX  HAD   CAD  SAE   102.75  3.000
 NKX  CAM   CAD  SAE   107.77  3.000
 NKX  HAD   CAD  CAA   110.33  3.000
 NKX  CAM   CAD  CAA   115.04  3.000
 NKX  SAE   CAD  CAA   111.54  3.000
 NKX  OAK   SAE  CAF   107.14  3.000
 NKX  OAK   SAE  CAD   112.14  3.000
 NKX  CAF   SAE  CAD    99.99  3.000
 NKX  OAK   SAE  OAB   117.71  3.000
 NKX  CAF   SAE  OAB   109.00  3.000
 NKX  CAD   SAE  OAB   109.31  3.000
 NKX  CAO   CAF  SAG   113.96  3.000
 NKX  CAO   CAF  SAE   125.22  3.000
 NKX  SAG   CAF  SAE   120.80  3.000
 NKX  CAH   SAG  CAF    89.55  3.000
 NKX  CAP   CAH  SAI   126.53  3.000
 NKX  CAP   CAH  SAG   113.72  3.000
 NKX  SAI   CAH  SAG   119.74  3.000
 NKX  OAL   SAI  NAJ   106.47  3.000
 NKX  OAL   SAI  CAH   108.22  3.000
 NKX  NAJ   SAI  CAH   102.55  3.000
 NKX  OAL   SAI  OAC   121.17  3.000
 NKX  NAJ   SAI  OAC   111.51  3.000
 NKX  CAH   SAI  OAC   105.34  3.000
 NKX  HNAA  NAJ  HNAJ  111.63  3.000
 NKX  HNAA  NAJ  SAI   114.32  3.000
 NKX  HNAJ  NAJ  SAI   112.87  3.000
 NKX  HAMA  CAM  HAM   106.79  3.000
 NKX  HAMA  CAM  CAN   108.43  3.000
 NKX  HAM   CAM  CAN   110.01  3.000
 NKX  HAMA  CAM  CAD   107.22  3.000
 NKX  HAM   CAM  CAD   110.25  3.000
 NKX  CAN   CAM  CAD   113.86  3.000
 NKX  HAN   CAN  NAQ   105.36  3.000
 NKX  HAN   CAN  CAO   105.43  3.000
 NKX  NAQ   CAN  CAO   112.35  3.000
 NKX  HAN   CAN  CAM   107.92  3.000
 NKX  NAQ   CAN  CAM   111.75  3.000
 NKX  CAO   CAN  CAM   113.40  3.000
 NKX  CAP   CAO  CAN   124.47  3.000
 NKX  CAP   CAO  CAF   110.97  3.000
 NKX  CAN   CAO  CAF   124.35  3.000
 NKX  HAP   CAP  CAO   124.21  3.000
 NKX  HAP   CAP  CAH   123.99  3.000
 NKX  CAO   CAP  CAH   111.80  3.000
 NKX  CAU   NAQ  CAR   123.94  3.000
 NKX  CAU   NAQ  CAN   118.02  3.000
 NKX  CAR   NAQ  CAN   117.98  3.000
 NKX  HARA  CAR  HAR   105.59  3.000
 NKX  HARA  CAR  CAS   110.23  3.000
 NKX  HAR   CAR  CAS   110.84  3.000
 NKX  HARA  CAR  NAQ   107.05  3.000
 NKX  HAR   CAR  NAQ   109.58  3.000
 NKX  CAS   CAR  NAQ   113.21  3.000
 NKX  HASB  CAS  HASA  107.91  3.000
 NKX  HASB  CAS  HAS   107.49  3.000
 NKX  HASA  CAS  HAS   108.45  3.000
 NKX  HASB  CAS  CAR   110.01  3.000
 NKX  HASA  CAS  CAR   111.35  3.000
 NKX  HAS   CAS  CAR   111.49  3.000
 NKX  OAV   CAU  OAT   123.09  3.000
 NKX  OAV   CAU  NAQ   112.22  3.000
 NKX  OAT   CAU  NAQ   124.68  3.000
 NKX  CAW   OAV  CAU   116.42  3.000
 NKX  HAWA  CAW  HAW   108.27  3.000
 NKX  HAWA  CAW  CAY   110.84  3.000
 NKX  HAW   CAW  CAY   108.79  3.000
 NKX  HAWA  CAW  OAV   110.95  3.000
 NKX  HAW   CAW  OAV   111.42  3.000
 NKX  CAY   CAW  OAV   106.55  3.000
 NKX  HAY   CAY  CBC   109.82  3.000
 NKX  HAY   CAY  OAZ   110.89  3.000
 NKX  CBC   CAY  OAZ   106.55  3.000
 NKX  HAY   CAY  CAW   110.16  3.000
 NKX  CBC   CAY  CAW   109.99  3.000
 NKX  OAZ   CAY  CAW   109.36  3.000
 NKX  NBA   OAZ  CAY   117.96  3.000
 NKX  OBB   NBA  OAZ   112.12  3.000
 NKX  OBB   NBA  OAX   128.49  3.000
 NKX  OAZ   NBA  OAX   119.39  3.000
 NKX  HBCA  CBC  HBC   109.02  3.000
 NKX  HBCA  CBC  OBD   111.03  3.000
 NKX  HBC   CBC  OBD   110.93  3.000
 NKX  HBCA  CBC  CAY   111.40  3.000
 NKX  HBC   CBC  CAY   108.97  3.000
 NKX  OBD   CBC  CAY   105.45  3.000
 NKX  NBE   OBD  CBC   115.66  3.000
 NKX  OBG   NBE  OBF   128.80  3.000
 NKX  OBG   NBE  OBD   112.92  3.000
 NKX  OBF   NBE  OBD   118.28  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
 NKX  CONST_01  CAP   CAH  SAG  CAF     0.00   0.0  0
 NKX  CONST_02  CAH   CAP  CAO  CAF     0.00   0.0  0
 NKX  CONST_03  CAP   CAO  CAF  SAG     0.00   0.0  0
 NKX  CONST_04  CAO   CAP  CAH  SAG     0.00   0.0  0
 NKX  CONST_05  CAO   CAF  SAG  CAH     0.00   0.0  0
 NKX  CONST_06  SAI   CAH  SAG  CAF   180.00   0.0  0
 NKX  CONST_07  CAO   CAP  CAH  SAI   180.00   0.0  0
 NKX  CONST_08  HAP   CAP  CAO  CAF   180.00   0.0  0
 NKX  Var_01    SAG   CAF  SAE  CAD   159.33  30.0  1
 NKX  Var_02    SAG   CAH  SAI  OAC    20.86  30.0  2
 NKX  Var_03    CAS   CAR  NAQ  CAN    91.97  30.0  3
 NKX  Var_04    OAT   CAU  NAQ  CAN     1.11  30.0  2
 NKX  Var_05    HNAJ  NAJ  SAI  CAH  -140.61  30.0  3
 NKX  Var_06    CAY   CAW  OAV  CAU  -178.64  30.0  3
 NKX  Var_07    OBB   NBA  OAZ  CAY  -173.15  30.0  3
 NKX  Var_08    OBF   NBE  OBD  CBC    -0.77  30.0  3
 NKX  Var_09    HAS   CAS  CAR  NAQ   -60.83  30.0  3
 NKX  Var_10    HBC   CBC  OBD  NBE    62.07  30.0  2

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
 NKX  chir_01  CAD  CAA  SAE  CAM  positiv
 NKX  chir_02  CAN  NAQ  CAO  CAM  positiv
 NKX  chir_03  CAY  OAZ  CBC  CAW  positiv

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
 NKX  plan-1  NAQ  0.020
 NKX  plan-1  OAT  0.020
 NKX  plan-1  CAU  0.020
 NKX  plan-1  OAV  0.020
 NKX  plan-2  SAE  0.020
 NKX  plan-2  CAF  0.020
 NKX  plan-2  SAG  0.020
 NKX  plan-2  CAH  0.020
 NKX  plan-2  SAI  0.020
 NKX  plan-2  CAN  0.020
 NKX  plan-2  CAO  0.020
 NKX  plan-2  CAP  0.020
 NKX  plan-2  HAP  0.020
 NKX  plan-3  OAX  0.020
 NKX  plan-3  OAZ  0.020
 NKX  plan-3  NBA  0.020
 NKX  plan-3  OBB  0.020
 NKX  plan-4  OBD  0.020
 NKX  plan-4  NBE  0.020
 NKX  plan-4  OBF  0.020
 NKX  plan-4  OBG  0.020

