# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 22:29:10 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: (2R)-3-benzyl-2-(1H-indazol-5-yl)-1,3-thiazolidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1CS[C@@H](N1Cc2ccccc2)c3ccc4[nH]ncc4c3
#
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
 DLR  DLR  (2R)-3-benzyl-2-(1H-indazol-5-yl)-1,3-thiazolidin-4-one  ligand  37  22  .  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_DLR
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
 DLR  CAJ   C  CR16  0  -0.372  -1.4374  -0.4539  -0.8802
 DLR  CAS   C  CR56  0  -0.074  -2.7025  -0.9746  -0.5764
 DLR  CAI   C  CR15  0  -0.125  -3.5429  -1.9921  -1.1015
 DLR  NAM   N  N     0  -0.227  -4.6559  -2.0738  -0.4162
 DLR  NAN   N  NR15  0  -0.542  -4.5864  -1.1503   0.5449
 DLR  CAT   C  CR56  0   0.414  -3.4310  -0.4513   0.5047
 DLR  CAH   C  CR16  0  -0.277  -2.9347   0.5898   1.3017
 DLR  CAG   C  CR16  0  -0.275  -1.6975   1.0851   0.9757
 DLR  CAR   C  CR6   0   0.126  -0.9440   0.5710  -0.1068
 DLR  CAU   C  CH1   0  -0.297   0.4136   1.1374  -0.4068
 DLR  SAO   S  S2    0   0.038   0.2860   2.9099  -0.8486
 DLR  CAK   C  CH2   0  -0.674   1.7841   3.3305   0.0638
 DLR  CAP   C  C     0   0.573   2.0799   2.1738   0.9935
 DLR  OAA   O  O     0  -0.479   2.9404   2.2247   1.8525
 DLR  NAV   N  NT    0  -0.434   1.3058   1.0983   0.7332
 DLR  CAL   C  CH2   0  -0.399   1.5190  -0.1818   1.3858
 DLR  CAQ   C  CR6   0   0.116   2.1506  -1.1897   0.4594
 DLR  CAE   C  CR16  0  -0.293   3.4419  -0.9872  -0.0238
 DLR  CAC   C  CR16  0  -0.240   4.0208  -1.9016  -0.8908
 DLR  CAB   C  CR16  0  -0.265   3.3145  -3.0325  -1.2854
 DLR  CAD   C  CR16  0  -0.241   2.0300  -3.2432  -0.8054
 DLR  CAF   C  CR16  0  -0.298   1.4521  -2.3237   0.0621
 DLR  HAJ   H  HCR6  0   0.263  -0.8540  -0.8531  -1.7015
 DLR  HAI   H  HCR5  0   0.269  -3.3638  -2.6467  -1.9406
 DLR  HAN   H  HNR5  0   0.418  -5.3530  -1.0411   1.1885
 DLR  HAH   H  HCR6  0   0.273  -3.4999   0.9896   2.1328
 DLR  HAG   H  HCR6  0   0.259  -1.2821   1.8951   1.5625
 DLR  HAU   H  HCH1  0   0.299   0.8551   0.5850  -1.2421
 DLR  HAK1  H  HCH2  0   0.308   2.6395   3.4731  -0.5993
 DLR  HAK2  H  HCH2  0   0.312   1.6397   4.2455   0.6366
 DLR  HAL1  H  HCH2  0   0.288   2.1500  -0.0066   2.2560
 DLR  HAL2  H  HCH2  0   0.278   0.5619  -0.5574   1.7514
 DLR  HAE   H  HCR6  0   0.252   4.0025  -0.1133   0.2873
 DLR  HAF   H  HCR6  0   0.254   0.4476  -2.4924   0.4318
 DLR  HAC   H  HCR6  0   0.257   5.0254  -1.7341  -1.2570
 DLR  HAB   H  HCR6  0   0.257   3.7666  -3.7456  -1.9624
 DLR  HAD   H  HCR6  0   0.257   1.4738  -4.1209  -1.1088

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
 DLR  CAJ  CAS   aromatic  1.401  0.020  1.401
 DLR  CAJ  CAR   aromatic  1.376  0.020  1.376
 DLR  CAS  CAI   aromatic  1.420  0.020  1.420
 DLR  CAS  CAT   aromatic  1.405  0.020  1.405
 DLR  CAI  NAM   aromatic  1.310  0.020  1.310
 DLR  NAM  NAN   aromatic  1.335  0.020  1.335
 DLR  NAN  CAT   aromatic  1.351  0.020  1.351
 DLR  CAT  CAH   aromatic  1.402  0.020  1.402
 DLR  CAH  CAG   aromatic  1.372  0.020  1.372
 DLR  CAG  CAR   aromatic  1.416  0.020  1.416
 DLR  CAR  CAU   single    1.501  0.020  1.501
 DLR  CAU  SAO   single    1.831  0.020  1.831
 DLR  CAU  NAV   single    1.448  0.020  1.448
 DLR  SAO  CAK   single    1.804  0.020  1.804
 DLR  CAK  CAP   single    1.513  0.020  1.513
 DLR  CAP  OAA   double    1.217  0.020  1.217
 DLR  CAP  NAV   single    1.350  0.020  1.350
 DLR  NAV  CAL   single    1.453  0.020  1.453
 DLR  CAL  CAQ   single    1.508  0.020  1.508
 DLR  CAQ  CAE   aromatic  1.394  0.020  1.394
 DLR  CAQ  CAF   aromatic  1.390  0.020  1.390
 DLR  CAE  CAC   aromatic  1.387  0.020  1.387
 DLR  CAC  CAB   aromatic  1.391  0.020  1.391
 DLR  CAB  CAD   aromatic  1.387  0.020  1.387
 DLR  CAD  CAF   aromatic  1.390  0.020  1.390
 DLR  CAJ  HAJ   single    0.930  0.020  1.080
 DLR  CAI  HAI   single    0.930  0.020  1.080
 DLR  NAN  HAN   single    0.860  0.020  1.020
 DLR  CAH  HAH   single    0.930  0.020  1.080
 DLR  CAG  HAG   single    0.930  0.020  1.080
 DLR  CAU  HAU   single    0.970  0.020  1.090
 DLR  CAK  HAK1  single    0.970  0.020  1.090
 DLR  CAK  HAK2  single    0.970  0.020  1.090
 DLR  CAL  HAL1  single    0.970  0.020  1.090
 DLR  CAL  HAL2  single    0.970  0.020  1.090
 DLR  CAE  HAE   single    0.930  0.020  1.080
 DLR  CAF  HAF   single    0.930  0.020  1.080
 DLR  CAC  HAC   single    0.930  0.020  1.080
 DLR  CAB  HAB   single    0.930  0.020  1.080
 DLR  CAD  HAD   single    0.930  0.020  1.080

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
 DLR  HAJ   CAJ  CAR   120.49  3.000
 DLR  HAJ   CAJ  CAS   120.90  3.000
 DLR  CAR   CAJ  CAS   118.61  3.000
 DLR  CAT   CAS  CAI   104.15  3.000
 DLR  CAT   CAS  CAJ   119.77  3.000
 DLR  CAI   CAS  CAJ   136.07  3.000
 DLR  HAI   CAI  NAM   120.66  3.000
 DLR  HAI   CAI  CAS   128.59  3.000
 DLR  NAM   CAI  CAS   110.74  3.000
 DLR  NAN   NAM  CAI   106.82  3.000
 DLR  HAN   NAN  CAT   127.88  3.000
 DLR  HAN   NAN  NAM   119.71  3.000
 DLR  CAT   NAN  NAM   112.40  3.000
 DLR  CAH   CAT  NAN   132.07  3.000
 DLR  CAH   CAT  CAS   122.05  3.000
 DLR  NAN   CAT  CAS   105.88  3.000
 DLR  HAH   CAH  CAG   121.36  3.000
 DLR  HAH   CAH  CAT   121.76  3.000
 DLR  CAG   CAH  CAT   116.88  3.000
 DLR  HAG   CAG  CAR   118.80  3.000
 DLR  HAG   CAG  CAH   119.15  3.000
 DLR  CAR   CAG  CAH   122.05  3.000
 DLR  CAU   CAR  CAG   119.81  3.000
 DLR  CAU   CAR  CAJ   119.55  3.000
 DLR  CAG   CAR  CAJ   120.64  3.000
 DLR  HAU   CAU  NAV   109.79  3.000
 DLR  HAU   CAU  SAO   109.42  3.000
 DLR  NAV   CAU  SAO   105.01  3.000
 DLR  HAU   CAU  CAR   109.08  3.000
 DLR  NAV   CAU  CAR   112.93  3.000
 DLR  SAO   CAU  CAR   110.51  3.000
 DLR  CAK   SAO  CAU    92.62  3.000
 DLR  HAK2  CAK  HAK1  108.28  3.000
 DLR  HAK2  CAK  CAP   110.18  3.000
 DLR  HAK1  CAK  CAP   108.65  3.000
 DLR  HAK2  CAK  SAO   110.60  3.000
 DLR  HAK1  CAK  SAO   111.96  3.000
 DLR  CAP   CAK  SAO   107.15  3.000
 DLR  NAV   CAP  OAA   125.08  3.000
 DLR  NAV   CAP  CAK   112.23  3.000
 DLR  OAA   CAP  CAK   122.68  3.000
 DLR  CAL   NAV  CAP   122.08  3.000
 DLR  CAL   NAV  CAU   117.90  3.000
 DLR  CAP   NAV  CAU   118.91  3.000
 DLR  HAL2  CAL  HAL1  107.21  3.000
 DLR  HAL2  CAL  CAQ   110.07  3.000
 DLR  HAL1  CAL  CAQ   110.84  3.000
 DLR  HAL2  CAL  NAV   108.97  3.000
 DLR  HAL1  CAL  NAV   107.59  3.000
 DLR  CAQ   CAL  NAV   112.00  3.000
 DLR  CAF   CAQ  CAE   119.02  3.000
 DLR  CAF   CAQ  CAL   120.70  3.000
 DLR  CAE   CAQ  CAL   120.27  3.000
 DLR  HAE   CAE  CAC   119.68  3.000
 DLR  HAE   CAE  CAQ   119.80  3.000
 DLR  CAC   CAE  CAQ   120.52  3.000
 DLR  HAC   CAC  CAB   120.09  3.000
 DLR  HAC   CAC  CAE   119.80  3.000
 DLR  CAB   CAC  CAE   120.11  3.000
 DLR  HAB   CAB  CAD   120.21  3.000
 DLR  HAB   CAB  CAC   120.08  3.000
 DLR  CAD   CAB  CAC   119.71  3.000
 DLR  HAD   CAD  CAF   119.85  3.000
 DLR  HAD   CAD  CAB   120.13  3.000
 DLR  CAF   CAD  CAB   120.03  3.000
 DLR  HAF   CAF  CAD   119.70  3.000
 DLR  HAF   CAF  CAQ   119.69  3.000
 DLR  CAD   CAF  CAQ   120.61  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
 DLR  CONST_01  NAM  CAI  CAS  CAJ  180.00   0.0  0
 DLR  CONST_02  NAN  CAT  CAS  CAJ  180.00   0.0  0
 DLR  CONST_03  CAH  CAT  CAS  CAJ    0.00   0.0  0
 DLR  CONST_04  CAH  CAG  CAR  CAJ    0.00   0.0  0
 DLR  CONST_05  CAG  CAR  CAJ  CAS    0.00   0.0  0
 DLR  CONST_06  NAN  NAM  CAI  CAS    0.00   0.0  0
 DLR  CONST_07  NAM  NAN  CAT  CAS    0.00   0.0  0
 DLR  CONST_08  CAG  CAH  CAT  CAS    0.00   0.0  0
 DLR  CONST_09  CAR  CAJ  CAS  CAI  180.00   0.0  0
 DLR  CONST_10  NAN  CAT  CAS  CAI    0.00   0.0  0
 DLR  CONST_11  CAH  CAT  CAS  CAI  180.00   0.0  0
 DLR  CONST_12  CAT  NAN  NAM  CAI    0.00   0.0  0
 DLR  CONST_13  CAT  CAS  CAI  NAM    0.00   0.0  0
 DLR  CONST_14  CAH  CAT  NAN  NAM  180.00   0.0  0
 DLR  CONST_15  CAG  CAH  CAT  NAN  180.00   0.0  0
 DLR  CONST_16  CAR  CAJ  CAS  CAT    0.00   0.0  0
 DLR  CONST_17  CAR  CAG  CAH  CAT    0.00   0.0  0
 DLR  CONST_18  CAB  CAC  CAE  CAQ    0.00   0.0  0
 DLR  CONST_19  CAB  CAD  CAF  CAQ    0.00   0.0  0
 DLR  CONST_20  CAD  CAF  CAQ  CAE    0.00   0.0  0
 DLR  CONST_21  CAD  CAB  CAC  CAE    0.00   0.0  0
 DLR  CONST_22  CAF  CAQ  CAE  CAC    0.00   0.0  0
 DLR  CONST_23  CAF  CAD  CAB  CAC    0.00   0.0  0
 DLR  CONST_24  CAU  CAR  CAJ  CAS  180.00   0.0  0
 DLR  CONST_25  CAU  CAR  CAG  CAH  180.00   0.0  0
 DLR  CONST_26  CAK  CAP  NAV  CAU    0.00   0.0  0
 DLR  CONST_27  CAC  CAE  CAQ  CAL  180.00   0.0  0
 DLR  CONST_28  CAD  CAF  CAQ  CAL  180.00   0.0  0
 DLR  CONST_29  OAA  CAP  NAV  CAU  180.00   0.0  0
 DLR  CONST_30  CAL  NAV  CAP  CAK  180.00   0.0  0
 DLR  CONST_31  HAI  CAI  CAS  CAJ    0.00   0.0  0
 DLR  CONST_32  HAG  CAG  CAR  CAJ  180.00   0.0  0
 DLR  CONST_33  HAN  NAN  CAT  CAS  180.00   0.0  0
 DLR  CONST_34  HAH  CAH  CAT  CAS  180.00   0.0  0
 DLR  CONST_35  HAJ  CAJ  CAS  CAI    0.00   0.0  0
 DLR  CONST_36  HAC  CAC  CAE  CAQ  180.00   0.0  0
 DLR  CONST_37  HAD  CAD  CAF  CAQ  180.00   0.0  0
 DLR  CONST_38  HAF  CAF  CAQ  CAE  180.00   0.0  0
 DLR  CONST_39  HAB  CAB  CAC  CAE  180.00   0.0  0
 DLR  CONST_40  HAE  CAE  CAC  CAB  180.00   0.0  0
 DLR  CONST_41  CAL  NAV  CAP  OAA    0.00   0.0  0
 DLR  Var_01    CAP  CAK  SAO  CAU  -16.49  30.0  1
 DLR  Var_02    NAV  CAP  CAK  SAO   10.09  30.0  1
 DLR  Var_03    CAQ  CAL  NAV  CAU   62.15  30.0  3
 DLR  Var_04    CAE  CAQ  CAL  NAV   65.14  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
 DLR  chir_01  CAU  CAR  SAO  NAV  negativ

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
 DLR  plan-1  CAL  0.020
 DLR  plan-1  CAQ  0.020
 DLR  plan-1  CAE  0.020
 DLR  plan-1  CAC  0.020
 DLR  plan-1  CAB  0.020
 DLR  plan-1  CAD  0.020
 DLR  plan-1  CAF  0.020
 DLR  plan-1  HAE  0.020
 DLR  plan-1  HAF  0.020
 DLR  plan-1  HAC  0.020
 DLR  plan-1  HAB  0.020
 DLR  plan-1  HAD  0.020
 DLR  plan-2  CAJ  0.020
 DLR  plan-2  CAS  0.020
 DLR  plan-2  CAI  0.020
 DLR  plan-2  NAM  0.020
 DLR  plan-2  NAN  0.020
 DLR  plan-2  CAT  0.020
 DLR  plan-2  CAH  0.020
 DLR  plan-2  CAG  0.020
 DLR  plan-2  CAR  0.020
 DLR  plan-2  CAU  0.020
 DLR  plan-2  HAJ  0.020
 DLR  plan-2  HAI  0.020
 DLR  plan-2  HAN  0.020
 DLR  plan-2  HAH  0.020
 DLR  plan-2  HAG  0.020
 DLR  plan-3  CAU  0.020
 DLR  plan-3  CAK  0.020
 DLR  plan-3  CAP  0.020
 DLR  plan-3  OAA  0.020
 DLR  plan-3  NAV  0.020
 DLR  plan-3  CAL  0.020

