# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 09:08:10 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 1-[(2,6-difluorophenyl)sulfonyl]-4-(2,3-dihydro-1,4-benzodioxin-6-ylsulfonyl)piperazine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cccc(F)c1[S](=O)(=O)N2CCN(CC2)[S](=O)(=O)c3ccc4OCCOc4c3
#
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
 DYY  DYY  1-[(2,6-difluorophenyl)sulfonyl]-4-(2,3-dihydro-1,4-benzodioxin-6-ylsulfonyl)piperazine  ligand  48  30  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DYY
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
 DYY  CAY   C  CR16  0  -0.346  -2.7503   0.3527   0.6619
 DYY  CAZ   C  CR6   0   0.340  -3.1979  -0.9485   0.5076
 DYY  OBA   O  O2    0  -0.474  -3.6850  -1.5957   1.5871
 DYY  CBB   C  CH2   0  -0.232  -4.4728  -2.7355   1.2711
 DYY  CAO   C  CH2   0  -0.232  -3.7643  -3.5799   0.2423
 DYY  OAN   O  O2    0  -0.471  -3.5408  -2.8284  -0.9454
 DYY  CAM   C  CR6   0   0.341  -3.1465  -1.5571  -0.7543
 DYY  CAL   C  CR16  0  -0.344  -2.6750  -0.8413  -1.8479
 DYY  CAK   C  CR16  0  -0.242  -2.2361   0.4611  -1.7017
 DYY  CAX   C  CR6   0  -0.223  -2.2636   1.0444  -0.4397
 DYY  SAW   S  S     0   1.381  -1.6029   2.6655  -0.2137
 DYY  OBD   O  OS    0  -0.647  -1.7187   3.3926  -1.4655
 DYY  OAJ   O  OS    0  -0.646  -2.1655   3.2292   1.0010
 DYY  NAV   N  N     0  -0.564   0.0266   2.4517   0.0694
 DYY  CAU   C  CH2   0  -0.310   0.8086   1.9977  -1.0826
 DYY  CAT   C  CH2   0  -0.335   2.2907   2.1132  -0.7684
 DYY  CAI   C  CH2   0  -0.315   0.3449   1.7333   1.3048
 DYY  CAH   C  CH2   0  -0.331   1.8308   1.8506   1.5932
 DYY  NAG   N  N     0  -0.560   2.6456   1.4203   0.4642
 DYY  SAF   S  S     0   1.408   3.3090  -0.0770   0.4195
 DYY  OAS   O  OS    0  -0.628   4.2931  -0.0790  -0.6416
 DYY  OAB   O  OS    0  -0.629   3.7197  -0.4079   1.7675
 DYY  CAE   C  CR6   0  -0.609   2.0177  -1.2288  -0.0455
 DYY  CAD   C  CR6   0   0.623   1.1993  -1.8330   0.9098
 DYY  FAA   F  F     0  -0.287   1.3425  -1.5172   2.1945
 DYY  CAC   C  CR16  0  -0.421   0.2080  -2.7312   0.5762
 DYY  CAP   C  CR16  0  -0.202   0.0139  -3.0461  -0.7585
 DYY  CAQ   C  CR16  0  -0.409   0.7904  -2.4622  -1.7448
 DYY  CAR   C  CR6   0   0.615   1.7741  -1.5684  -1.3771
 DYY  FBC   F  F     0  -0.285   2.4808  -0.9947  -2.3466
 DYY  HAY   H  HCR6  0   0.297  -2.8009   0.8094   1.6420
 DYY  HBB   H  HCH2  0   0.270  -4.6110  -3.2967   2.1932
 DYY  HBBA  H  HCH2  0   0.253  -5.4549  -2.4224   0.9024
 DYY  HAO   H  HCH2  0   0.246  -2.8102  -3.9435   0.6376
 DYY  HAOA  H  HCH2  0   0.273  -4.3694  -4.4416  -0.0337
 DYY  HAL   H  HCR6  0   0.283  -2.6534  -1.3177  -2.8194
 DYY  HAK   H  HCR6  0   0.289  -1.8802   1.0033  -2.5665
 DYY  HAU   H  HCH2  0   0.238   0.5525   0.9655  -1.3532
 DYY  HAUA  H  HCH2  0   0.296   0.5960   2.6310  -1.9410
 DYY  HAT   H  HCH2  0   0.297   2.8759   1.7448  -1.6078
 DYY  HATA  H  HCH2  0   0.284   2.5545   3.1640  -0.6305
 DYY  HAI   H  HCH2  0   0.296  -0.1968   2.1761   2.1380
 DYY  HAIA  H  HCH2  0   0.238   0.0478   0.6797   1.2364
 DYY  HAH   H  HCH2  0   0.283   2.0828   2.8955   1.7856
 DYY  HAHA  H  HCH2  0   0.296   2.0826   1.2894   2.4893
 DYY  HAC   H  HCR6  0   0.298  -0.3949  -3.1746   1.3570
 DYY  HAP   H  HCR6  0   0.295  -0.7566  -3.7511  -1.0376
 DYY  HAQ   H  HCR6  0   0.302   0.6373  -2.6906  -2.7905

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
 DYY  CAZ  CAY   aromatic  1.385  0.020  1.385
 DYY  CAY  CAX   aromatic  1.389  0.020  1.389
 DYY  CAY  HAY   single    0.930  0.020  1.080
 DYY  OBA  CAZ   single    1.350  0.020  1.350
 DYY  CAZ  CAM   aromatic  1.402  0.020  1.402
 DYY  CBB  OBA   single    1.421  0.020  1.421
 DYY  CAO  CBB   single    1.508  0.020  1.508
 DYY  CBB  HBB   single    0.970  0.020  1.090
 DYY  CBB  HBBA  single    0.970  0.020  1.090
 DYY  CAO  OAN   single    1.423  0.020  1.423
 DYY  CAO  HAO   single    0.970  0.020  1.090
 DYY  CAO  HAOA  single    0.970  0.020  1.090
 DYY  OAN  CAM   single    1.345  0.020  1.345
 DYY  CAM  CAL   aromatic  1.389  0.020  1.389
 DYY  CAL  CAK   aromatic  1.382  0.020  1.382
 DYY  CAL  HAL   single    0.930  0.020  1.080
 DYY  CAX  CAK   aromatic  1.391  0.020  1.391
 DYY  CAK  HAK   single    0.930  0.020  1.080
 DYY  CAX  SAW   single    1.765  0.020  1.765
 DYY  NAV  SAW   single    1.668  0.020  1.668
 DYY  OBD  SAW   double    1.452  0.020  1.452
 DYY  SAW  OAJ   double    1.453  0.020  1.453
 DYY  CAI  NAV   single    1.464  0.020  1.464
 DYY  NAV  CAU   single    1.464  0.020  1.464
 DYY  CAT  CAU   single    1.519  0.020  1.519
 DYY  CAU  HAU   single    0.970  0.020  1.090
 DYY  CAU  HAUA  single    0.970  0.020  1.090
 DYY  NAG  CAT   single    1.458  0.020  1.458
 DYY  CAT  HAT   single    0.970  0.020  1.090
 DYY  CAT  HATA  single    0.970  0.020  1.090
 DYY  CAH  CAI   single    1.518  0.020  1.518
 DYY  CAI  HAI   single    0.970  0.020  1.090
 DYY  CAI  HAIA  single    0.970  0.020  1.090
 DYY  CAH  NAG   single    1.457  0.020  1.457
 DYY  CAH  HAH   single    0.970  0.020  1.090
 DYY  CAH  HAHA  single    0.970  0.020  1.090
 DYY  SAF  NAG   single    1.638  0.020  1.638
 DYY  OAB  SAF   double    1.447  0.020  1.447
 DYY  SAF  OAS   double    1.447  0.020  1.447
 DYY  SAF  CAE   single    1.792  0.020  1.792
 DYY  CAD  CAE   aromatic  1.395  0.020  1.395
 DYY  CAE  CAR   aromatic  1.396  0.020  1.396
 DYY  FAA  CAD   single    1.331  0.020  1.331
 DYY  CAD  CAC   aromatic  1.379  0.020  1.379
 DYY  CAC  CAP   aromatic  1.385  0.020  1.385
 DYY  CAC  HAC   single    0.930  0.020  1.080
 DYY  CAP  CAQ   aromatic  1.384  0.020  1.384
 DYY  CAP  HAP   single    0.930  0.020  1.080
 DYY  CAR  CAQ   aromatic  1.379  0.020  1.379
 DYY  CAQ  HAQ   single    0.930  0.020  1.080
 DYY  CAR  FBC   single    1.330  0.020  1.330

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
 DYY  HAY   CAY  CAX  121.63  3.000
 DYY  HAY   CAY  CAZ  118.83  3.000
 DYY  CAX   CAY  CAZ  119.53  3.000
 DYY  CAM   CAZ  OBA  121.67  3.000
 DYY  CAM   CAZ  CAY  119.77  3.000
 DYY  OBA   CAZ  CAY  118.57  3.000
 DYY  CBB   OBA  CAZ  114.01  3.000
 DYY  HBBA  CBB  HBB  108.60  3.000
 DYY  HBBA  CBB  CAO  110.60  3.000
 DYY  HBB   CBB  CAO  110.43  3.000
 DYY  HBBA  CBB  OBA  110.04  3.000
 DYY  HBB   CBB  OBA  107.19  3.000
 DYY  CAO   CBB  OBA  109.90  3.000
 DYY  HAOA  CAO  HAO  108.24  3.000
 DYY  HAOA  CAO  OAN  107.08  3.000
 DYY  HAO   CAO  OAN  109.87  3.000
 DYY  HAOA  CAO  CBB  110.80  3.000
 DYY  HAO   CAO  CBB  110.43  3.000
 DYY  OAN   CAO  CBB  110.34  3.000
 DYY  CAM   OAN  CAO  115.26  3.000
 DYY  CAL   CAM  OAN  118.34  3.000
 DYY  CAL   CAM  CAZ  119.81  3.000
 DYY  OAN   CAM  CAZ  121.84  3.000
 DYY  HAL   CAL  CAK  120.22  3.000
 DYY  HAL   CAL  CAM  119.11  3.000
 DYY  CAK   CAL  CAM  120.66  3.000
 DYY  HAK   CAK  CAX  121.47  3.000
 DYY  HAK   CAK  CAL  119.51  3.000
 DYY  CAX   CAK  CAL  119.01  3.000
 DYY  SAW   CAX  CAK  119.61  3.000
 DYY  SAW   CAX  CAY  119.14  3.000
 DYY  CAK   CAX  CAY  121.19  3.000
 DYY  NAV   SAW  OAJ  106.64  3.000
 DYY  OAJ   SAW  OBD  119.71  3.000
 DYY  NAV   SAW  OBD  106.76  3.000
 DYY  OAJ   SAW  CAX  108.57  3.000
 DYY  OBD   SAW  CAX  108.64  3.000
 DYY  NAV   SAW  CAX  105.65  3.000
 DYY  CAI   NAV  CAU  113.30  3.000
 DYY  CAU   NAV  SAW  115.34  3.000
 DYY  CAI   NAV  SAW  114.74  3.000
 DYY  HAUA  CAU  HAU  107.90  3.000
 DYY  HAUA  CAU  CAT  108.03  3.000
 DYY  HAU   CAU  CAT  110.49  3.000
 DYY  HAUA  CAU  NAV  109.63  3.000
 DYY  HAU   CAU  NAV  111.16  3.000
 DYY  CAT   CAU  NAV  109.55  3.000
 DYY  HATA  CAT  HAT  107.06  3.000
 DYY  HATA  CAT  NAG  106.96  3.000
 DYY  HAT   CAT  NAG  111.14  3.000
 DYY  HATA  CAT  CAU  109.56  3.000
 DYY  HAT   CAT  CAU  109.85  3.000
 DYY  NAG   CAT  CAU  112.10  3.000
 DYY  HAIA  CAI  HAI  107.69  3.000
 DYY  HAIA  CAI  CAH  110.56  3.000
 DYY  HAI   CAI  CAH  108.08  3.000
 DYY  HAIA  CAI  NAV  111.09  3.000
 DYY  HAI   CAI  NAV  109.77  3.000
 DYY  CAH   CAI  NAV  109.58  3.000
 DYY  HAHA  CAH  HAH  107.18  3.000
 DYY  HAHA  CAH  NAG  110.90  3.000
 DYY  HAH   CAH  NAG  106.86  3.000
 DYY  HAHA  CAH  CAI  110.09  3.000
 DYY  HAH   CAH  CAI  109.47  3.000
 DYY  NAG   CAH  CAI  112.16  3.000
 DYY  SAF   NAG  CAH  121.16  3.000
 DYY  SAF   NAG  CAT  120.66  3.000
 DYY  CAH   NAG  CAT  112.24  3.000
 DYY  CAE   SAF  OAB  107.41  3.000
 DYY  CAE   SAF  OAS  107.39  3.000
 DYY  OAB   SAF  OAS  119.31  3.000
 DYY  CAE   SAF  NAG  107.63  3.000
 DYY  OAS   SAF  NAG  107.26  3.000
 DYY  OAB   SAF  NAG  107.37  3.000
 DYY  CAR   CAE  CAD  116.45  3.000
 DYY  CAR   CAE  SAF  121.99  3.000
 DYY  CAD   CAE  SAF  121.55  3.000
 DYY  CAC   CAD  FAA  117.75  3.000
 DYY  CAC   CAD  CAE  122.56  3.000
 DYY  FAA   CAD  CAE  119.67  3.000
 DYY  HAC   CAC  CAP  121.62  3.000
 DYY  HAC   CAC  CAD  119.56  3.000
 DYY  CAP   CAC  CAD  118.82  3.000
 DYY  HAP   CAP  CAQ  119.40  3.000
 DYY  HAP   CAP  CAC  119.80  3.000
 DYY  CAQ   CAP  CAC  120.80  3.000
 DYY  HAQ   CAQ  CAR  119.72  3.000
 DYY  HAQ   CAQ  CAP  121.36  3.000
 DYY  CAR   CAQ  CAP  118.92  3.000
 DYY  FBC   CAR  CAQ  117.67  3.000
 DYY  FBC   CAR  CAE  119.86  3.000
 DYY  CAQ   CAR  CAE  122.45  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
 DYY  CONST_01  CAL  CAM  CAZ  CAY    0.00   0.0  0
 DYY  CONST_02  CAL  CAK  CAX  CAY    0.00   0.0  0
 DYY  CONST_03  CAK  CAX  CAY  CAZ    0.00   0.0  0
 DYY  CONST_04  CAK  CAL  CAM  CAZ    0.00   0.0  0
 DYY  CONST_05  CAX  CAY  CAZ  CAM    0.00   0.0  0
 DYY  CONST_06  CAX  CAK  CAL  CAM    0.00   0.0  0
 DYY  CONST_07  CAP  CAC  CAD  CAE    0.00   0.0  0
 DYY  CONST_08  CAP  CAQ  CAR  CAE    0.00   0.0  0
 DYY  CONST_09  CAQ  CAR  CAE  CAD    0.00   0.0  0
 DYY  CONST_10  CAQ  CAP  CAC  CAD    0.00   0.0  0
 DYY  CONST_11  CAR  CAE  CAD  CAC    0.00   0.0  0
 DYY  CONST_12  CAR  CAQ  CAP  CAC    0.00   0.0  0
 DYY  CONST_13  SAW  CAX  CAY  CAZ  180.00   0.0  0
 DYY  CONST_14  SAW  CAX  CAK  CAL  180.00   0.0  0
 DYY  CONST_15  CAC  CAD  CAE  SAF  180.00   0.0  0
 DYY  CONST_16  CAQ  CAR  CAE  SAF  180.00   0.0  0
 DYY  CONST_17  FBC  CAR  CAE  CAD  180.00   0.0  0
 DYY  CONST_18  CAR  CAE  CAD  FAA  180.00   0.0  0
 DYY  CONST_19  CAP  CAC  CAD  FAA  180.00   0.0  0
 DYY  CONST_20  FBC  CAR  CAQ  CAP  180.00   0.0  0
 DYY  CONST_21  HAK  CAK  CAX  CAY  180.00   0.0  0
 DYY  CONST_22  HAL  CAL  CAM  CAZ  180.00   0.0  0
 DYY  CONST_23  HAY  CAY  CAZ  OBA    0.00   0.0  0
 DYY  CONST_24  HAC  CAC  CAD  CAE  180.00   0.0  0
 DYY  CONST_25  HAQ  CAQ  CAR  CAE  180.00   0.0  0
 DYY  CONST_26  HAP  CAP  CAC  CAD  180.00   0.0  0
 DYY  Var_01    CAO  CBB  OBA  CAZ   47.04  30.0  1
 DYY  Var_02    OAN  CAO  CBB  OBA  -59.81  30.0  1
 DYY  Var_03    CAM  CAZ  OBA  CBB  -17.47  30.0  1
 DYY  Var_04    CAL  CAM  OAN  CAO  168.36  30.0  1
 DYY  Var_05    NAG  CAH  CAI  NAV  -53.93  30.0  1
 DYY  Var_06    NAG  CAT  CAU  NAV   53.97  30.0  1
 DYY  Var_07    CAH  CAI  NAV  CAU   56.17  30.0  1
 DYY  Var_08    CAH  NAG  CAT  CAU  -53.91  30.0  1
 DYY  Var_09    CAI  NAV  CAU  CAT  -56.19  30.0  1
 DYY  Var_10    CAI  CAH  NAG  CAT   53.91  30.0  1
 DYY  Var_11    NAV  SAW  CAX  CAY   90.86  30.0  2
 DYY  Var_12    CAE  SAF  NAG  CAT  -72.70  30.0  1
 DYY  Var_13    CAD  CAE  SAF  NAG  -88.66  30.0  2

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
 DYY  plan-1  SAF  0.020
 DYY  plan-1  CAE  0.020
 DYY  plan-1  CAD  0.020
 DYY  plan-1  FAA  0.020
 DYY  plan-1  CAC  0.020
 DYY  plan-1  CAP  0.020
 DYY  plan-1  CAQ  0.020
 DYY  plan-1  CAR  0.020
 DYY  plan-1  FBC  0.020
 DYY  plan-1  HAC  0.020
 DYY  plan-1  HAP  0.020
 DYY  plan-1  HAQ  0.020
 DYY  plan-2  CAY  0.020
 DYY  plan-2  CAZ  0.020
 DYY  plan-2  OBA  0.020
 DYY  plan-2  OAN  0.020
 DYY  plan-2  CAM  0.020
 DYY  plan-2  CAL  0.020
 DYY  plan-2  CAK  0.020
 DYY  plan-2  CAX  0.020
 DYY  plan-2  SAW  0.020
 DYY  plan-2  HAY  0.020
 DYY  plan-2  HAL  0.020
 DYY  plan-2  HAK  0.020

