# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 21:07:22 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 4-[6,6-dimethyl-4-oxo-3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl]-2-{[2-(methylsulfanyl)ethyl]amino}benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCCNc1cc(ccc1C(N)=O)n2nc(c3C(=O)CC(C)(C)Cc23)C(F)(F)F
#
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
 D1U  D1U  4-[6,6-dimethyl-4-oxo-3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl]-2-{[2-(methylsulfanyl)ethyl]amino}benzamide  ligand  53  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 PERFECT
;

data_comp_D1U
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
 D1U  CAA   C  CH3   0  -0.763   6.8489  -3.4913  -1.3961
 D1U  CAB   C  CH3   0  -0.644  -4.1959   3.3511  -1.9997
 D1U  CAC   C  CH3   0  -0.637  -3.2609   1.1960  -2.8236
 D1U  NAD   N  NH2   0  -0.803   3.9793   4.1986   1.5887
 D1U  OAE   O  O     0  -0.500   4.8584   2.8362   0.0350
 D1U  OAF   O  O     0  -0.401  -5.2667  -1.0540  -0.2430
 D1U  FAG   F  F     0  -0.309  -3.8553  -2.5322   2.0696
 D1U  FAH   F  F     0  -0.305  -1.8391  -3.2513   1.8392
 D1U  FAI   F  F     0  -0.310  -3.1985  -3.3081   0.1720
 D1U  CAJ   C  CR16  0  -0.318   0.1962   2.4457   0.9923
 D1U  CAK   C  CR16  0  -0.284   1.4254   3.0800   1.0115
 D1U  CAL   C  CR16  0  -0.414   1.3208   0.4087   0.3279
 D1U  CAM   C  CH2   0  -0.260   3.6809  -1.0173  -0.3940
 D1U  CAN   C  CH2   0  -0.583   5.1021  -1.4740  -0.6766
 D1U  CAO   C  CH2   0  -0.547  -4.8577   1.2241  -0.8771
 D1U  CAP   C  CH2   0  -0.494  -2.5271   2.1339  -0.6066
 D1U  NAQ   N  N     0  -0.265  -1.1464  -0.8365   1.0544
 D1U  NAR   N  NH1   0  -0.704   3.6952   0.3578   0.0396
 D1U  SAS   S  S2    0  -0.035   5.0801  -3.2235  -1.1495
 D1U  CAT   C  C     0   0.517   3.9072   3.1589   0.7455
 D1U  CAU   C  C     0   0.346  -4.4867  -0.1256  -0.3068
 D1U  CAV   C  CR6   0   0.363   0.1694   1.1033   0.6437
 D1U  CAW   C  CR6   0   0.402   2.5708   1.0494   0.3426
 D1U  CAX   C  CR6   0  -0.132   2.6130   2.4226   0.7096
 D1U  CAY   C  CR5   0   0.513  -2.2294   0.8395   0.0532
 D1U  CAZ   C  CR5   0   0.011  -2.3742  -1.2202   0.8244
 D1U  CBA   C  CR5   0  -0.319  -3.1215  -0.2037   0.1932
 D1U  NBB   N  NR5   0  -0.490  -1.0671   0.4162   0.5879
 D1U  CBC   C  CT    0  -0.147  -3.7090   1.9671  -1.5798
 D1U  HAA   H  HCH3  0   0.264   7.4101  -3.2321  -0.4995
 D1U  HAAA  H  HCH3  0   0.276   6.9910  -4.5499  -1.6010
 D1U  HAAB  H  HCH3  0   0.264   7.2245  -2.9128  -2.2385
 D1U  HAB   H  HCH3  0   0.236  -3.3959   3.9165  -2.4814
 D1U  HABA  H  HCH3  0   0.238  -5.0213   3.2721  -2.7088
 D1U  HABB  H  HCH3  0   0.232  -4.5454   3.9288  -1.1419
 D1U  HAC   H  HCH3  0   0.234  -2.8890   0.1962  -2.5925
 D1U  HACA  H  HCH3  0   0.238  -4.0893   1.0838  -3.5255
 D1U  HACB  H  HCH3  0   0.237  -2.4609   1.7309  -3.3393
 D1U  HNAD  H  HNH2  0   0.407   4.8392   4.7184   1.6595
 D1U  HNAA  H  HNH2  0   0.414   3.2768   4.3841   2.2827
 D1U  HAJ   H  HCR6  0   0.278  -0.7010   2.9820   1.2641
 D1U  HAK   H  HCR6  0   0.269   1.4448   4.1322   1.2637
 D1U  HAL   H  HCR6  0   0.295   1.2435  -0.6318   0.0471
 D1U  HAM   H  HCH2  0   0.238   3.0679  -1.1496  -1.2944
 D1U  HAMA  H  HCH2  0   0.243   3.2431  -1.6486   0.3854
 D1U  HAN   H  HCH2  0   0.271   5.5353  -0.8827  -1.4868
 D1U  HANA  H  HCH2  0   0.273   5.7263  -1.3493   0.2101
 D1U  HAO   H  HCH2  0   0.271  -5.7044   1.1044  -1.5565
 D1U  HAOA  H  HCH2  0   0.282  -5.2153   1.8285  -0.0332
 D1U  HAP   H  HCH2  0   0.287  -2.7796   2.8770   0.1574
 D1U  HAPA  H  HCH2  0   0.284  -1.6521   2.5180  -1.1362
 D1U  HNAR  H  HNH1  0   0.403   4.5039   0.9186  -0.1849
 D1U  CBD   C  CT    0   1.077  -2.8183  -2.5837   1.2288

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
 D1U  CAA  SAS   single    1.806  0.020  1.806
 D1U  CAA  HAA   single    0.970  0.020  1.090
 D1U  CAA  HAAA  single    0.970  0.020  1.090
 D1U  CAA  HAAB  single    0.970  0.020  1.090
 D1U  CBC  CAB   single    1.526  0.020  1.526
 D1U  CAB  HAB   single    0.970  0.020  1.090
 D1U  CAB  HABA  single    0.970  0.020  1.090
 D1U  CAB  HABB  single    0.970  0.020  1.090
 D1U  CBC  CAC   single    1.530  0.020  1.530
 D1U  CAC  HAC   single    0.970  0.020  1.090
 D1U  CAC  HACA  single    0.970  0.020  1.090
 D1U  CAC  HACB  single    0.970  0.020  1.090
 D1U  NAD  CAT   single    1.341  0.020  1.341
 D1U  NAD  HNAD  single    0.860  0.020  1.020
 D1U  NAD  HNAA  single    0.860  0.020  1.020
 D1U  CAT  OAE   double    1.230  0.020  1.230
 D1U  CAU  OAF   double    1.214  0.020  1.214
 D1U  CBD  FAG   single    1.336  0.020  1.336
 D1U  FAH  CBD   single    1.333  0.020  1.333
 D1U  FAI  CBD   single    1.336  0.020  1.336
 D1U  CAK  CAJ   aromatic  1.383  0.020  1.383
 D1U  CAJ  CAV   aromatic  1.387  0.020  1.387
 D1U  CAJ  HAJ   single    0.930  0.020  1.080
 D1U  CAX  CAK   aromatic  1.391  0.020  1.391
 D1U  CAK  HAK   single    0.930  0.020  1.080
 D1U  CAW  CAL   aromatic  1.405  0.020  1.405
 D1U  CAL  CAV   aromatic  1.381  0.020  1.381
 D1U  CAL  HAL   single    0.930  0.020  1.080
 D1U  NAR  CAM   single    1.442  0.020  1.442
 D1U  CAN  CAM   single    1.519  0.020  1.519
 D1U  CAM  HAM   single    0.970  0.020  1.090
 D1U  CAM  HAMA  single    0.970  0.020  1.090
 D1U  SAS  CAN   single    1.812  0.020  1.812
 D1U  CAN  HAN   single    0.970  0.020  1.090
 D1U  CAN  HANA  single    0.970  0.020  1.090
 D1U  CAU  CAO   single    1.511  0.020  1.511
 D1U  CBC  CAO   single    1.538  0.020  1.538
 D1U  CAO  HAO   single    0.970  0.020  1.090
 D1U  CAO  HAOA  single    0.970  0.020  1.090
 D1U  CAY  CAP   single    1.483  0.020  1.483
 D1U  CAP  CBC   single    1.540  0.020  1.540
 D1U  CAP  HAP   single    0.970  0.020  1.090
 D1U  CAP  HAPA  single    0.970  0.020  1.090
 D1U  NAQ  NBB   aromatic  1.339  0.020  1.339
 D1U  NAQ  CAZ   aromatic  1.307  0.020  1.307
 D1U  NAR  CAW   single    1.354  0.020  1.354
 D1U  NAR  HNAR  single    0.890  0.020  1.040
 D1U  CAT  CAX   single    1.489  0.020  1.489
 D1U  CBA  CAU   single    1.456  0.020  1.456
 D1U  CAV  NBB   single    1.416  0.020  1.416
 D1U  CAX  CAW   aromatic  1.422  0.020  1.422
 D1U  NBB  CAY   aromatic  1.348  0.020  1.348
 D1U  CAY  CBA   aromatic  1.380  0.020  1.380
 D1U  CBD  CAZ   single    1.490  0.020  1.490
 D1U  CAZ  CBA   aromatic  1.411  0.020  1.411

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
 D1U  HAAB  CAA  HAAA  109.05  3.000
 D1U  HAAB  CAA  HAA   109.44  3.000
 D1U  HAAA  CAA  HAA   108.63  3.000
 D1U  HAAB  CAA  SAS   111.39  3.000
 D1U  HAAA  CAA  SAS   107.34  3.000
 D1U  HAA   CAA  SAS   110.92  3.000
 D1U  HABB  CAB  HABA  107.87  3.000
 D1U  HABB  CAB  HAB   107.89  3.000
 D1U  HABA  CAB  HAB   107.77  3.000
 D1U  HABB  CAB  CBC   111.46  3.000
 D1U  HABA  CAB  CBC   110.77  3.000
 D1U  HAB   CAB  CBC   110.94  3.000
 D1U  HACB  CAC  HACA  107.62  3.000
 D1U  HACB  CAC  HAC   107.40  3.000
 D1U  HACA  CAC  HAC   107.49  3.000
 D1U  HACB  CAC  CBC   110.58  3.000
 D1U  HACA  CAC  CBC   110.62  3.000
 D1U  HAC   CAC  CBC   112.91  3.000
 D1U  HNAA  NAD  HNAD  116.94  3.000
 D1U  HNAA  NAD  CAT   122.68  3.000
 D1U  HNAD  NAD  CAT   119.36  3.000
 D1U  HAJ   CAJ  CAV   121.85  3.000
 D1U  HAJ   CAJ  CAK   120.46  3.000
 D1U  CAV   CAJ  CAK   117.67  3.000
 D1U  HAK   CAK  CAX   119.66  3.000
 D1U  HAK   CAK  CAJ   117.71  3.000
 D1U  CAX   CAK  CAJ   122.62  3.000
 D1U  HAL   CAL  CAW   120.37  3.000
 D1U  HAL   CAL  CAV   118.95  3.000
 D1U  CAW   CAL  CAV   120.67  3.000
 D1U  HAMA  CAM  HAM   106.95  3.000
 D1U  HAMA  CAM  NAR   109.87  3.000
 D1U  HAM   CAM  NAR   111.55  3.000
 D1U  HAMA  CAM  CAN   109.47  3.000
 D1U  HAM   CAM  CAN   109.49  3.000
 D1U  NAR   CAM  CAN   109.47  3.000
 D1U  HANA  CAN  HAN   108.29  3.000
 D1U  HANA  CAN  SAS   109.22  3.000
 D1U  HAN   CAN  SAS   109.50  3.000
 D1U  HANA  CAN  CAM   110.46  3.000
 D1U  HAN   CAN  CAM   110.25  3.000
 D1U  SAS   CAN  CAM   109.10  3.000
 D1U  HAOA  CAO  HAO   106.62  3.000
 D1U  HAOA  CAO  CBC   109.18  3.000
 D1U  HAO   CAO  CBC   110.35  3.000
 D1U  HAOA  CAO  CAU   106.35  3.000
 D1U  HAO   CAO  CAU   109.10  3.000
 D1U  CBC   CAO  CAU   114.87  3.000
 D1U  HAPA  CAP  HAP   106.51  3.000
 D1U  HAPA  CAP  CBC   110.27  3.000
 D1U  HAP   CAP  CBC   109.72  3.000
 D1U  HAPA  CAP  CAY   111.21  3.000
 D1U  HAP   CAP  CAY   109.15  3.000
 D1U  CBC   CAP  CAY   109.92  3.000
 D1U  NBB   NAQ  CAZ   105.60  3.000
 D1U  HNAR  NAR  CAW   115.54  3.000
 D1U  HNAR  NAR  CAM   118.09  3.000
 D1U  CAW   NAR  CAM   123.09  3.000
 D1U  CAN   SAS  CAA    99.61  3.000
 D1U  CAX   CAT  OAE   121.88  3.000
 D1U  CAX   CAT  NAD   116.45  3.000
 D1U  OAE   CAT  NAD   121.68  3.000
 D1U  CBA   CAU  CAO   114.05  3.000
 D1U  CBA   CAU  OAF   122.91  3.000
 D1U  CAO   CAU  OAF   123.02  3.000
 D1U  NBB   CAV  CAL   118.36  3.000
 D1U  NBB   CAV  CAJ   119.77  3.000
 D1U  CAL   CAV  CAJ   121.87  3.000
 D1U  CAX   CAW  NAR   121.75  3.000
 D1U  CAX   CAW  CAL   118.00  3.000
 D1U  NAR   CAW  CAL   120.23  3.000
 D1U  CAW   CAX  CAT   120.62  3.000
 D1U  CAW   CAX  CAK   119.16  3.000
 D1U  CAT   CAX  CAK   120.21  3.000
 D1U  NBB   CAY  CBA   106.26  3.000
 D1U  CBA   CAY  CAP   125.12  3.000
 D1U  NBB   CAY  CAP   128.59  3.000
 D1U  CBD   CAZ  CBA   128.53  3.000
 D1U  CBA   CAZ  NAQ   111.40  3.000
 D1U  CBD   CAZ  NAQ   120.07  3.000
 D1U  CAZ   CBA  CAY   104.34  3.000
 D1U  CAZ   CBA  CAU   133.55  3.000
 D1U  CAY   CBA  CAU   122.06  3.000
 D1U  CAY   NBB  CAV   128.06  3.000
 D1U  CAY   NBB  NAQ   112.39  3.000
 D1U  CAV   NBB  NAQ   119.47  3.000
 D1U  CAP   CBC  CAO   109.68  3.000
 D1U  CAP   CBC  CAC   110.09  3.000
 D1U  CAO   CBC  CAC   110.28  3.000
 D1U  CAP   CBC  CAB   108.69  3.000
 D1U  CAO   CBC  CAB   109.00  3.000
 D1U  CAC   CBC  CAB   109.07  3.000
 D1U  CAZ   CBD  FAI   111.48  3.000
 D1U  CAZ   CBD  FAH   111.32  3.000
 D1U  FAI   CBD  FAH   107.43  3.000
 D1U  CAZ   CBD  FAG   111.52  3.000
 D1U  FAI   CBD  FAG   107.32  3.000
 D1U  FAH   CBD  FAG   107.53  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
 D1U  CONST_01  CAW   CAX  CAK  CAJ     0.00   0.0  0
 D1U  CONST_02  CAW   CAL  CAV  CAJ     0.00   0.0  0
 D1U  CONST_05  CAL   CAV  CAJ  CAK     0.00   0.0  0
 D1U  CONST_06  NBB   CAV  CAJ  CAK   180.00   0.0  0
 D1U  CONST_07  CAL   CAW  CAX  CAK     0.00   0.0  0
 D1U  CONST_10  CBA   CAY  NBB  NAQ     0.00   0.0  0
 D1U  CONST_11  CAY   CBA  CAZ  NAQ     0.00   0.0  0
 D1U  CONST_12  CAX   CAK  CAJ  CAV     0.00   0.0  0
 D1U  CONST_13  CAX   CAW  CAL  CAV     0.00   0.0  0
 D1U  CONST_14  CAZ   NAQ  NBB  CAV   180.00   0.0  0
 D1U  CONST_15  CBA   CAY  NBB  CAV   180.00   0.0  0
 D1U  CONST_16  NBB   CAV  CAL  CAW   180.00   0.0  0
 D1U  CONST_17  CAZ   NAQ  NBB  CAY     0.00   0.0  0
 D1U  CONST_18  NBB   CAY  CBA  CAZ     0.00   0.0  0
 D1U  CONST_19  NBB   NAQ  CAZ  CBA     0.00   0.0  0
 D1U  CONST_20  CAV   NBB  CAY  CAP     0.00   0.0  0
 D1U  CONST_21  CAT   CAX  CAK  CAJ   180.00   0.0  0
 D1U  CONST_22  NAR   CAW  CAX  CAK   180.00   0.0  0
 D1U  CONST_23  CAT   CAX  CAW  CAL   180.00   0.0  0
 D1U  CONST_24  CAV   CAL  CAW  NAR   180.00   0.0  0
 D1U  CONST_25  CBD   CAZ  CBA  CAU     0.00   0.0  0
 D1U  CONST_26  CBD   CAZ  CBA  CAY   180.00   0.0  0
 D1U  CONST_27  CBD   CAZ  NAQ  NBB   180.00   0.0  0
 D1U  CONST_28  HAL   CAL  CAV  CAJ   180.00   0.0  0
 D1U  CONST_29  HAJ   CAJ  CAV  CAL   180.00   0.0  0
 D1U  CONST_30  HAK   CAK  CAJ  CAV   180.00   0.0  0
 D1U  CONST_31  CAM   NAR  CAW  CAL     0.00   0.0  0
 D1U  CONST_32  CAX   CAW  NAR  CAM   180.00   0.0  0
 D1U  CONST_34  HNAD  NAD  CAT  CAX   180.00   0.0  0
 D1U  CONST_35  HNAA  NAD  CAT  CAX     0.00   0.0  0
 D1U  Var_01    CAY   CBA  CAU  CAO    -4.82  30.0  1
 D1U  Var_02    CAY   CAP  CBC  CAO    48.23  30.0  1
 D1U  Var_03    CAU   CAO  CBC  CAP   -56.49  30.0  1
 D1U  Var_04    CBC   CAO  CAU  CBA    33.74  30.0  1
 D1U  Var_05    CBC   CAP  CAY  CBA   -22.61  30.0  1
 D1U  Var_06    CAK   CAX  CAT  NAD    28.30  30.0  2
 D1U  Var_07    NAQ   CAZ  CBD  FAG   121.73  30.0  2
 D1U  Var_08    HAB   CAB  CBC  CAO   178.62  30.0  3
 D1U  Var_09    HAC   CAC  CBC  CAO   -60.94  30.0  3
 D1U  Var_10    CAW   NAR  CAM  CAN   178.80  30.0  1
 D1U  Var_11    CAM   CAN  SAS  CAA  -179.28  30.0  3
 D1U  Var_12    SAS   CAN  CAM  NAR   177.51  30.0  1
 D1U  Var_13    HAA   CAA  SAS  CAN    56.35  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
 D1U  plan-1  CAJ   0.020
 D1U  plan-1  CAK   0.020
 D1U  plan-1  CAL   0.020
 D1U  plan-1  NAR   0.020
 D1U  plan-1  CAT   0.020
 D1U  plan-1  CAV   0.020
 D1U  plan-1  CAW   0.020
 D1U  plan-1  CAX   0.020
 D1U  plan-1  NBB   0.020
 D1U  plan-1  HAJ   0.020
 D1U  plan-1  HAK   0.020
 D1U  plan-1  HAL   0.020
 D1U  plan-2  CAP   0.020
 D1U  plan-2  NAQ   0.020
 D1U  plan-2  CAU   0.020
 D1U  plan-2  CAV   0.020
 D1U  plan-2  CAY   0.020
 D1U  plan-2  CAZ   0.020
 D1U  plan-2  CBA   0.020
 D1U  plan-2  NBB   0.020
 D1U  plan-2  CBD   0.020
 D1U  plan-3  NAD   0.020
 D1U  plan-3  OAE   0.020
 D1U  plan-3  CAT   0.020
 D1U  plan-3  CAX   0.020
 D1U  plan-3  HNAD  0.020
 D1U  plan-3  HNAA  0.020
 D1U  plan-4  CAM   0.020
 D1U  plan-4  NAR   0.020
 D1U  plan-4  CAW   0.020
 D1U  plan-4  HNAR  0.020
 D1U  plan-5  OAF   0.020
 D1U  plan-5  CAO   0.020
 D1U  plan-5  CAU   0.020
 D1U  plan-5  CBA   0.020

