# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 05:08:17 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 1-(1,2,3-benzothiadiazol-6-yl)-3-[2-(cyclohex-1-en-1-yl)ethyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCCC1=CCCCC1)Nc2ccc3nnsc3c2
#
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
 TDU  TDU  1-(1,2,3-benzothiadiazol-6-yl)-3-[2-(cyclohex-1-en-1-yl)ethyl]urea  ligand  39  21  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_TDU
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
 TDU  OAA   O  O     0  -0.516   0.0870   0.8047   0.3714
 TDU  CAB   C  C1    0  -0.288  -5.6481   0.1930  -1.2202
 TDU  CAC   C  CR16  0  -0.358   3.2059  -2.0756  -0.3506
 TDU  CAD   C  CR16  0  -0.257   4.5689  -1.9707  -0.2981
 TDU  CAE   C  CR16  0  -0.360   2.9019   0.2529   0.2916
 TDU  CAF   C  CH2   0  -0.463  -6.9422   0.9449  -1.1248
 TDU  CAG   C  CH2   0  -0.443  -7.5962   0.7919   0.2437
 TDU  CAH   C  CH2   0  -0.441  -6.5630   0.9468   1.3516
 TDU  CAI   C  CH2   0  -0.223  -2.4837  -0.1509  -0.0760
 TDU  CAJ   C  CH2   0  -0.487  -5.4836  -0.1225   1.2366
 TDU  CAK   C  CH2   0  -0.553  -3.6905  -1.0451  -0.3430
 TDU  NAL   N  N     0  -0.319   6.7157   0.7343   0.4809
 TDU  NAM   N  N     0  -0.230   6.4609  -0.4474   0.1515
 TDU  NAN   N  NH1   0  -0.693  -1.2607  -0.9178  -0.1909
 TDU  NAO   N  NH1   0  -0.792   1.0005  -1.2310  -0.1599
 TDU  SAP   S  S2    0   0.380   5.3012   1.6715   0.7203
 TDU  CAQ   C  C     0   0.115  -4.9834  -0.2960  -0.1726
 TDU  CAR   C  C     0   0.758  -0.0547  -0.3601   0.0306
 TDU  CAS   C  CR6   0   0.401   2.3543  -0.9766  -0.0603
 TDU  CAT   C  CR56  0   0.284   5.1281  -0.7375   0.0526
 TDU  CAU   C  CR56  0  -0.228   4.2893   0.3459   0.3398
 TDU  HAC   H  HCR6  0   0.285   2.7598  -3.0232  -0.6260
 TDU  HAD   H  HCR6  0   0.286   5.2011  -2.8183  -0.5251
 TDU  HAE   H  HCR6  0   0.301   2.2823   1.1039   0.5172
 TDU  HAF   H  HCH2  0   0.229  -6.7615   2.0052  -1.3381
 TDU  HAFA  H  HCH2  0   0.235  -7.6231   0.6035  -1.9097
 TDU  HAG   H  HCH2  0   0.230  -8.4003   1.5213   0.3600
 TDU  HAGA  H  HCH2  0   0.216  -8.0578  -0.1977   0.3177
 TDU  HAH   H  HCH2  0   0.218  -6.1023   1.9375   1.2822
 TDU  HAHA  H  HCH2  0   0.231  -7.0383   0.8943   2.3334
 TDU  HAI   H  HCH2  0   0.236  -2.4852   0.6763  -0.7910
 TDU  HAIA  H  HCH2  0   0.234  -2.5524   0.2876   0.9224
 TDU  HAJ   H  HCH2  0   0.236  -4.6494   0.1179   1.9032
 TDU  HAJA  H  HCH2  0   0.235  -5.8669  -1.0867   1.5920
 TDU  HAK   H  HCH2  0   0.250  -3.6190  -1.4505  -1.3559
 TDU  HAKA  H  HCH2  0   0.244  -3.6654  -1.8966   0.3463
 TDU  HNAN  H  HNH1  0   0.404  -1.3284  -1.8687  -0.5163
 TDU  HNAO  H  HNH1  0   0.416   0.7659  -2.1744  -0.4287
 TDU  HAB   H  H     0   0.226  -5.2411   0.0429  -2.2167

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
 TDU  OAA  CAR   double    1.222  0.020  1.222
 TDU  CAB  CAF   single    1.500  0.020  1.500
 TDU  CAB  CAQ   double    1.334  0.020  1.334
 TDU  CAC  CAD   aromatic  1.368  0.020  1.368
 TDU  CAC  CAS   aromatic  1.420  0.020  1.420
 TDU  CAD  CAT   aromatic  1.399  0.020  1.399
 TDU  CAE  CAS   aromatic  1.391  0.020  1.391
 TDU  CAE  CAU   aromatic  1.391  0.020  1.391
 TDU  CAF  CAG   single    1.524  0.020  1.524
 TDU  CAG  CAH   single    1.523  0.020  1.523
 TDU  CAH  CAJ   single    1.524  0.020  1.524
 TDU  CAI  CAK   single    1.525  0.020  1.525
 TDU  CAI  NAN   single    1.448  0.020  1.448
 TDU  CAJ  CAQ   single    1.505  0.020  1.505
 TDU  CAK  CAQ   single    1.504  0.020  1.504
 TDU  NAL  NAM   aromatic  1.253  0.020  1.253
 TDU  NAL  SAP   aromatic  1.714  0.020  1.714
 TDU  NAM  CAT   aromatic  1.368  0.020  1.368
 TDU  NAN  CAR   single    1.347  0.020  1.347
 TDU  NAO  CAR   single    1.381  0.020  1.381
 TDU  NAO  CAS   single    1.381  0.020  1.381
 TDU  SAP  CAU   aromatic  1.711  0.020  1.711
 TDU  CAT  CAU   aromatic  1.400  0.020  1.400
 TDU  CAB  HAB   single    0.930  0.020  1.080
 TDU  CAC  HAC   single    0.930  0.020  1.080
 TDU  CAD  HAD   single    0.930  0.020  1.080
 TDU  CAE  HAE   single    0.930  0.020  1.080
 TDU  CAF  HAF   single    0.970  0.020  1.090
 TDU  CAF  HAFA  single    0.970  0.020  1.090
 TDU  CAG  HAG   single    0.970  0.020  1.090
 TDU  CAG  HAGA  single    0.970  0.020  1.090
 TDU  CAH  HAH   single    0.970  0.020  1.090
 TDU  CAH  HAHA  single    0.970  0.020  1.090
 TDU  CAI  HAI   single    0.970  0.020  1.090
 TDU  CAI  HAIA  single    0.970  0.020  1.090
 TDU  CAJ  HAJ   single    0.970  0.020  1.090
 TDU  CAJ  HAJA  single    0.970  0.020  1.090
 TDU  CAK  HAK   single    0.970  0.020  1.090
 TDU  CAK  HAKA  single    0.970  0.020  1.090
 TDU  NAN  HNAN  single    0.860  0.020  1.020
 TDU  NAO  HNAO  single    0.860  0.020  1.020

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
 TDU  HAB   CAB  CAQ  118.88  3.000
 TDU  HAB   CAB  CAF  116.79  3.000
 TDU  CAQ   CAB  CAF  124.33  3.000
 TDU  HAC   CAC  CAS  118.82  3.000
 TDU  HAC   CAC  CAD  119.16  3.000
 TDU  CAS   CAC  CAD  122.02  3.000
 TDU  HAD   CAD  CAT  120.66  3.000
 TDU  HAD   CAD  CAC  120.95  3.000
 TDU  CAT   CAD  CAC  118.39  3.000
 TDU  HAE   CAE  CAU  120.92  3.000
 TDU  HAE   CAE  CAS  121.67  3.000
 TDU  CAU   CAE  CAS  117.41  3.000
 TDU  HAFA  CAF  HAF  105.36  3.000
 TDU  HAFA  CAF  CAG  110.23  3.000
 TDU  HAF   CAF  CAG  110.02  3.000
 TDU  HAFA  CAF  CAB  109.57  3.000
 TDU  HAF   CAF  CAB  109.28  3.000
 TDU  CAG   CAF  CAB  112.14  3.000
 TDU  HAGA  CAG  HAG  106.63  3.000
 TDU  HAGA  CAG  CAH  109.20  3.000
 TDU  HAG   CAG  CAH  110.75  3.000
 TDU  HAGA  CAG  CAF  109.42  3.000
 TDU  HAG   CAG  CAF  110.15  3.000
 TDU  CAH   CAG  CAF  110.60  3.000
 TDU  HAHA  CAH  HAH  106.48  3.000
 TDU  HAHA  CAH  CAJ  110.02  3.000
 TDU  HAH   CAH  CAJ  109.40  3.000
 TDU  HAHA  CAH  CAG  110.72  3.000
 TDU  HAH   CAH  CAG  109.35  3.000
 TDU  CAJ   CAH  CAG  110.75  3.000
 TDU  HAIA  CAI  HAI  107.08  3.000
 TDU  HAIA  CAI  NAN  109.76  3.000
 TDU  HAI   CAI  NAN  110.48  3.000
 TDU  HAIA  CAI  CAK  110.21  3.000
 TDU  HAI   CAI  CAK  109.14  3.000
 TDU  NAN   CAI  CAK  110.11  3.000
 TDU  HAJA  CAJ  HAJ  105.19  3.000
 TDU  HAJA  CAJ  CAQ  108.55  3.000
 TDU  HAJ   CAJ  CAQ  110.01  3.000
 TDU  HAJA  CAJ  CAH  110.18  3.000
 TDU  HAJ   CAJ  CAH  109.87  3.000
 TDU  CAQ   CAJ  CAH  112.76  3.000
 TDU  HAKA  CAK  HAK  107.04  3.000
 TDU  HAKA  CAK  CAQ  109.60  3.000
 TDU  HAK   CAK  CAQ  110.24  3.000
 TDU  HAKA  CAK  CAI  109.10  3.000
 TDU  HAK   CAK  CAI  109.13  3.000
 TDU  CAQ   CAK  CAI  111.61  3.000
 TDU  SAP   NAL  NAM  112.62  3.000
 TDU  CAT   NAM  NAL  114.66  3.000
 TDU  HNAN  NAN  CAR  120.28  3.000
 TDU  HNAN  NAN  CAI  117.95  3.000
 TDU  CAR   NAN  CAI  121.59  3.000
 TDU  HNAO  NAO  CAS  114.81  3.000
 TDU  HNAO  NAO  CAR  116.67  3.000
 TDU  CAS   NAO  CAR  128.51  3.000
 TDU  CAU   SAP  NAL   91.92  3.000
 TDU  CAK   CAQ  CAJ  116.69  3.000
 TDU  CAK   CAQ  CAB  121.48  3.000
 TDU  CAJ   CAQ  CAB  121.84  3.000
 TDU  NAO   CAR  NAN  113.59  3.000
 TDU  NAO   CAR  OAA  123.43  3.000
 TDU  NAN   CAR  OAA  122.98  3.000
 TDU  NAO   CAS  CAE  124.54  3.000
 TDU  NAO   CAS  CAC  115.49  3.000
 TDU  CAE   CAS  CAC  119.97  3.000
 TDU  CAU   CAT  NAM  113.89  3.000
 TDU  CAU   CAT  CAD  119.62  3.000
 TDU  NAM   CAT  CAD  126.49  3.000
 TDU  CAT   CAU  SAP  106.91  3.000
 TDU  CAT   CAU  CAE  122.59  3.000
 TDU  SAP   CAU  CAE  130.50  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
 TDU  CONST_01  NAM   CAT  CAD  CAC   180.00   0.0  0
 TDU  CONST_02  CAU   CAT  CAD  CAC     0.00   0.0  0
 TDU  CONST_03  CAU   CAE  CAS  CAC     0.00   0.0  0
 TDU  CONST_04  CAE   CAS  CAC  CAD     0.00   0.0  0
 TDU  CONST_05  NAL   NAM  CAT  CAD   180.00   0.0  0
 TDU  CONST_06  CAE   CAU  CAT  CAD     0.00   0.0  0
 TDU  CONST_07  SAP   CAU  CAT  CAD   180.00   0.0  0
 TDU  CONST_08  NAL   SAP  CAU  CAE   180.00   0.0  0
 TDU  CONST_09  NAM   CAT  CAU  CAE   180.00   0.0  0
 TDU  CONST_10  CAU   CAT  NAM  NAL     0.00   0.0  0
 TDU  CONST_11  CAT   CAU  SAP  NAL     0.00   0.0  0
 TDU  CONST_12  CAU   SAP  NAL  NAM     0.00   0.0  0
 TDU  CONST_13  SAP   CAU  CAT  NAM     0.00   0.0  0
 TDU  CONST_14  CAT   NAM  NAL  SAP     0.00   0.0  0
 TDU  CONST_15  CAS   CAE  CAU  SAP   180.00   0.0  0
 TDU  CONST_16  CAT   CAD  CAC  CAS     0.00   0.0  0
 TDU  CONST_17  CAT   CAU  CAE  CAS     0.00   0.0  0
 TDU  CONST_18  NAO   CAS  CAC  CAD   180.00   0.0  0
 TDU  CONST_19  CAU   CAE  CAS  NAO   180.00   0.0  0
 TDU  CONST_20  HAE   CAE  CAS  CAC   180.00   0.0  0
 TDU  CONST_21  HAC   CAC  CAS  CAE   180.00   0.0  0
 TDU  CONST_22  HAD   CAD  CAT  NAM     0.00   0.0  0
 TDU  CONST_23  CAR   NAO  CAS  CAC   180.00   0.0  0
 TDU  CONST_24  CAR   NAO  CAS  CAE     0.00   0.0  0
 TDU  CONST_25  HNAO  NAO  CAS  CAC     0.00   0.0  0
 TDU  CONST_26  CAS   NAO  CAR  OAA     0.00   0.0  0
 TDU  CONST_27  CAS   NAO  CAR  NAN   180.00   0.0  0
 TDU  CONST_28  CAI   NAN  CAR  OAA     0.00   0.0  0
 TDU  CONST_29  NAO   CAR  NAN  CAI   180.00   0.0  0
 TDU  CONST_30  HNAN  NAN  CAR  OAA   180.00   0.0  0
 TDU  Var_01    CAH   CAG  CAF  CAB    44.27  30.0  1
 TDU  Var_02    CAH   CAJ  CAQ  CAB   -15.41  30.0  1
 TDU  Var_03    CAJ   CAQ  CAB  CAF    -0.44  30.0  1
 TDU  Var_04    CAJ   CAH  CAG  CAF   -60.89  30.0  1
 TDU  Var_05    CAQ   CAB  CAF  CAG   -14.42  30.0  1
 TDU  Var_06    CAQ   CAJ  CAH  CAG    45.50  30.0  1
 TDU  Var_07    CAI   CAK  CAQ  CAB    99.04  30.0  2
 TDU  Var_08    CAQ   CAK  CAI  NAN   177.48  30.0  3
 TDU  Var_09    CAR   NAN  CAI  CAK  -178.44  30.0  3

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
 TDU  plan-1  CAC   0.020
 TDU  plan-1  CAD   0.020
 TDU  plan-1  CAE   0.020
 TDU  plan-1  NAL   0.020
 TDU  plan-1  NAM   0.020
 TDU  plan-1  NAO   0.020
 TDU  plan-1  SAP   0.020
 TDU  plan-1  CAS   0.020
 TDU  plan-1  CAT   0.020
 TDU  plan-1  CAU   0.020
 TDU  plan-1  HAC   0.020
 TDU  plan-1  HAD   0.020
 TDU  plan-1  HAE   0.020
 TDU  plan-2  OAA   0.020
 TDU  plan-2  CAI   0.020
 TDU  plan-2  NAN   0.020
 TDU  plan-2  NAO   0.020
 TDU  plan-2  CAR   0.020
 TDU  plan-2  CAS   0.020
 TDU  plan-2  HNAN  0.020
 TDU  plan-2  HNAO  0.020

