# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 02:08:26 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 1-cyclopentyl-3-(1H-pyrrolo[2,3-b]pyridin-5-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(nc(c3cnc4[nH]ccc4c3)c12)C5CCCC5
#
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
 KS1  KS1  1-cyclopentyl-3-(1H-pyrrolo[2,3-b]pyridin-5-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine  ligand  41  24  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KS1
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
 KS1  CAI   C  CH2   0  -0.449  -3.6417  -1.5010   1.3962
 KS1  CAG   C  CH2   0  -0.449  -4.5600  -2.6735   0.9907
 KS1  CAH   C  CH2   0  -0.456  -4.9454  -2.4135  -0.4740
 KS1  CAJ   C  CH2   0  -0.440  -3.7638  -1.6283  -1.0288
 KS1  CAW   C  CH1   0  -0.084  -3.4611  -0.6646   0.1163
 KS1  NAX   N  NR5   0  -0.386  -2.1725  -0.0146   0.0201
 KS1  NAN   N  N     0  -0.278  -1.0399  -0.7300  -0.0077
 KS1  C4    C  CR56  0   0.579  -1.9177   1.3056  -0.0212
 KS1  N3    N  N     0  -0.466  -2.8103   2.3002  -0.0011
 KS1  C2    C  CR16  0   0.056  -2.2375   3.4830  -0.0760
 KS1  N1    N  N     0  -0.478  -0.9425   3.7721  -0.1967
 KS1  C6    C  CR6   0   0.432  -0.0581   2.7725  -0.2330
 KS1  NAA   N  NH2   0  -0.816   1.2305   3.0848  -0.3907
 KS1  C5    C  CR56  0  -0.271  -0.5290   1.4460  -0.0978
 KS1  CAR   C  CR5   0   0.268  -0.0349   0.1126  -0.0745
 KS1  CAP   C  CR6   0  -0.075   1.3464  -0.3742  -0.1033
 KS1  CAF   C  CR16  0  -0.298   2.3302   0.1962   0.6957
 KS1  CAS   C  CR56  0   0.028   3.6136  -0.3349   0.6325
 KS1  CAD   C  CR15  0  -0.446   4.8700  -0.0700   1.2548
 KS1  CAB   C  CR15  0   0.004   5.7473  -0.9862   0.7515
 KS1  NAO   N  NR15  0  -0.661   5.1130  -1.8042  -0.1434
 KS1  CAT   C  CR56  0   0.469   3.8097  -1.4338  -0.2376
 KS1  NAM   N  N     0  -0.419   2.8883  -2.0001  -1.0004
 KS1  CAE   C  CR16  0  -0.100   1.6821  -1.4668  -0.9247
 KS1  HAI   H  HCH2  0   0.244  -4.0643  -0.8976   2.1997
 KS1  HAIA  H  HCH2  0   0.243  -2.6745  -1.8659   1.7428
 KS1  HAG   H  HCH2  0   0.231  -4.0184  -3.6172   1.0696
 KS1  HAGA  H  HCH2  0   0.236  -5.4348  -2.7562   1.6353
 KS1  HAH   H  HCH2  0   0.239  -5.1454  -3.3315  -1.0271
 KS1  HAHA  H  HCH2  0   0.226  -5.8502  -1.8019  -0.5252
 KS1  HAJ   H  HCH2  0   0.233  -2.9106  -2.2919  -1.1924
 KS1  HAJA  H  HCH2  0   0.245  -3.9768  -1.1118  -1.9656
 KS1  HAW   H  HCH1  0   0.270  -4.1938   0.1442   0.0995
 KS1  H2    H  HCR6  0   0.254  -2.9027   4.3397  -0.0462
 KS1  HNAA  H  HNH2  0   0.405   1.4791   4.0419  -0.5777
 KS1  HNAB  H  HNH2  0   0.414   1.9182   2.3824  -0.6007
 KS1  HAF   H  HCR6  0   0.277   2.1006   1.0146   1.3683
 KS1  HAD   H  HCR5  0   0.256   5.0956   0.6990   1.9756
 KS1  HAB   H  HCR5  0   0.292   6.7951  -1.1222   0.9644
 KS1  HNAO  H  HNR5  0   0.414   5.5436  -2.5625  -0.6475
 KS1  HAE   H  HCR6  0   0.257   0.9174  -1.9120  -1.5513

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
 KS1  CAI  CAG   single    1.544  0.020  1.544
 KS1  CAI  CAW   single    1.540  0.020  1.540
 KS1  CAG  CAH   single    1.537  0.020  1.537
 KS1  CAH  CAJ   single    1.523  0.020  1.523
 KS1  CAJ  CAW   single    1.527  0.020  1.527
 KS1  CAW  NAX   single    1.446  0.020  1.446
 KS1  NAX  NAN   aromatic  1.340  0.020  1.340
 KS1  NAX  C4    aromatic  1.345  0.020  1.345
 KS1  NAN  CAR   aromatic  1.313  0.020  1.313
 KS1  C4   N3    aromatic  1.337  0.020  1.337
 KS1  C4   C5    aromatic  1.398  0.020  1.398
 KS1  N3   C2    aromatic  1.316  0.020  1.316
 KS1  C2   N1    aromatic  1.332  0.020  1.332
 KS1  N1   C6    aromatic  1.335  0.020  1.335
 KS1  C6   NAA   single    1.335  0.020  1.335
 KS1  C6   C5    aromatic  1.414  0.020  1.414
 KS1  C5   CAR   aromatic  1.422  0.020  1.422
 KS1  CAR  CAP   single    1.465  0.020  1.465
 KS1  CAP  CAF   aromatic  1.390  0.020  1.390
 KS1  CAP  CAE   aromatic  1.407  0.020  1.407
 KS1  CAF  CAS   aromatic  1.390  0.020  1.390
 KS1  CAS  CAD   aromatic  1.427  0.020  1.427
 KS1  CAS  CAT   aromatic  1.415  0.020  1.415
 KS1  CAD  CAB   aromatic  1.365  0.020  1.365
 KS1  CAB  NAO   aromatic  1.368  0.020  1.368
 KS1  NAO  CAT   aromatic  1.358  0.020  1.358
 KS1  CAT  NAM   aromatic  1.323  0.020  1.323
 KS1  NAM  CAE   aromatic  1.321  0.020  1.321
 KS1  CAI  HAI   single    0.970  0.020  1.090
 KS1  CAI  HAIA  single    0.970  0.020  1.090
 KS1  CAG  HAG   single    0.970  0.020  1.090
 KS1  CAG  HAGA  single    0.970  0.020  1.090
 KS1  CAH  HAH   single    0.970  0.020  1.090
 KS1  CAH  HAHA  single    0.970  0.020  1.090
 KS1  CAJ  HAJ   single    0.970  0.020  1.090
 KS1  CAJ  HAJA  single    0.970  0.020  1.090
 KS1  CAW  HAW   single    0.970  0.020  1.090
 KS1  C2   H2    single    0.930  0.020  1.080
 KS1  NAA  HNAA  single    0.860  0.020  1.020
 KS1  NAA  HNAB  single    0.860  0.020  1.020
 KS1  CAF  HAF   single    0.930  0.020  1.080
 KS1  CAD  HAD   single    0.930  0.020  1.080
 KS1  CAB  HAB   single    0.930  0.020  1.080
 KS1  NAO  HNAO  single    0.860  0.020  1.020
 KS1  CAE  HAE   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
 KS1  HAIA  CAI  HAI   107.15  3.000
 KS1  HAIA  CAI  CAW   110.00  3.000
 KS1  HAI   CAI  CAW   110.95  3.000
 KS1  HAIA  CAI  CAG   110.92  3.000
 KS1  HAI   CAI  CAG   112.55  3.000
 KS1  CAW   CAI  CAG   105.32  3.000
 KS1  HAGA  CAG  HAG   106.87  3.000
 KS1  HAGA  CAG  CAH   112.04  3.000
 KS1  HAG   CAG  CAH   109.86  3.000
 KS1  HAGA  CAG  CAI   112.32  3.000
 KS1  HAG   CAG  CAI   110.05  3.000
 KS1  CAH   CAG  CAI   105.73  3.000
 KS1  HAHA  CAH  HAH   107.18  3.000
 KS1  HAHA  CAH  CAJ   109.67  3.000
 KS1  HAH   CAH  CAJ   113.05  3.000
 KS1  HAHA  CAH  CAG   110.30  3.000
 KS1  HAH   CAH  CAG   112.77  3.000
 KS1  CAJ   CAH  CAG   103.87  3.000
 KS1  HAJA  CAJ  HAJ   108.15  3.000
 KS1  HAJA  CAJ  CAW   112.58  3.000
 KS1  HAJ   CAJ  CAW   109.91  3.000
 KS1  HAJA  CAJ  CAH   113.92  3.000
 KS1  HAJ   CAJ  CAH   110.30  3.000
 KS1  CAW   CAJ  CAH   101.89  3.000
 KS1  HAW   CAW  NAX   105.31  3.000
 KS1  HAW   CAW  CAJ   108.85  3.000
 KS1  NAX   CAW  CAJ   114.23  3.000
 KS1  HAW   CAW  CAI   109.67  3.000
 KS1  NAX   CAW  CAI   113.82  3.000
 KS1  CAJ   CAW  CAI   104.91  3.000
 KS1  C4    NAX  NAN   111.30  3.000
 KS1  C4    NAX  CAW   127.72  3.000
 KS1  NAN   NAX  CAW   120.97  3.000
 KS1  CAR   NAN  NAX   107.78  3.000
 KS1  C5    C4   N3    126.12  3.000
 KS1  C5    C4   NAX   106.77  3.000
 KS1  N3    C4   NAX   127.11  3.000
 KS1  C2    N3   C4    112.16  3.000
 KS1  H2    C2   N1    115.28  3.000
 KS1  H2    C2   N3    116.18  3.000
 KS1  N1    C2   N3    128.54  3.000
 KS1  C6    N1   C2    118.94  3.000
 KS1  C5    C6   NAA   123.51  3.000
 KS1  C5    C6   N1    118.63  3.000
 KS1  NAA   C6   N1    117.86  3.000
 KS1  HNAB  NAA  HNAA  117.17  3.000
 KS1  HNAB  NAA  C6    121.43  3.000
 KS1  HNAA  NAA  C6    118.87  3.000
 KS1  CAR   C5   C6    139.94  3.000
 KS1  CAR   C5   C4    104.48  3.000
 KS1  C6    C5   C4    115.49  3.000
 KS1  CAP   CAR  C5    129.70  3.000
 KS1  CAP   CAR  NAN   120.63  3.000
 KS1  C5    CAR  NAN   109.67  3.000
 KS1  CAE   CAP  CAF   119.03  3.000
 KS1  CAE   CAP  CAR   119.63  3.000
 KS1  CAF   CAP  CAR   121.32  3.000
 KS1  HAF   CAF  CAS   120.80  3.000
 KS1  HAF   CAF  CAP   121.11  3.000
 KS1  CAS   CAF  CAP   118.07  3.000
 KS1  CAT   CAS  CAD   106.87  3.000
 KS1  CAT   CAS  CAF   116.90  3.000
 KS1  CAD   CAS  CAF   136.23  3.000
 KS1  HAD   CAD  CAB   126.22  3.000
 KS1  HAD   CAD  CAS   127.48  3.000
 KS1  CAB   CAD  CAS   106.30  3.000
 KS1  HAB   CAB  NAO   120.29  3.000
 KS1  HAB   CAB  CAD   129.56  3.000
 KS1  NAO   CAB  CAD   110.15  3.000
 KS1  HNAO  NAO  CAT   125.51  3.000
 KS1  HNAO  NAO  CAB   125.40  3.000
 KS1  CAT   NAO  CAB   109.09  3.000
 KS1  NAM   CAT  NAO   126.26  3.000
 KS1  NAM   CAT  CAS   126.16  3.000
 KS1  NAO   CAT  CAS   107.59  3.000
 KS1  CAE   NAM  CAT   115.47  3.000
 KS1  HAE   CAE  NAM   116.43  3.000
 KS1  HAE   CAE  CAP   119.20  3.000
 KS1  NAM   CAE  CAP   124.38  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
 KS1  CONST_01  C5    CAR  NAN  NAX    0.00   0.0  0
 KS1  CONST_02  CAP   CAR  NAN  NAX  180.00   0.0  0
 KS1  CONST_03  C2    N3   C4   NAX  180.00   0.0  0
 KS1  CONST_04  C6    C5   C4   NAX  180.00   0.0  0
 KS1  CONST_05  CAR   C5   C4   NAX    0.00   0.0  0
 KS1  CONST_06  N3    C4   NAX  NAN  180.00   0.0  0
 KS1  CONST_07  C5    C4   NAX  NAN    0.00   0.0  0
 KS1  CONST_08  C4    C5   CAR  NAN    0.00   0.0  0
 KS1  CONST_09  C6    C5   CAR  NAN  180.00   0.0  0
 KS1  CONST_12  CAR   NAN  NAX  C4     0.00   0.0  0
 KS1  CONST_13  N1    C2   N3   C4     0.00   0.0  0
 KS1  CONST_14  N1    C6   C5   C4     0.00   0.0  0
 KS1  CONST_15  CAP   CAR  C5   C4   180.00   0.0  0
 KS1  CONST_16  C6    C5   C4   N3     0.00   0.0  0
 KS1  CONST_17  CAR   C5   C4   N3   180.00   0.0  0
 KS1  CONST_18  C6    N1   C2   N3     0.00   0.0  0
 KS1  CONST_19  C5    C4   N3   C2     0.00   0.0  0
 KS1  CONST_20  C5    C6   N1   C2     0.00   0.0  0
 KS1  CONST_21  CAR   C5   C6   N1   180.00   0.0  0
 KS1  CONST_22  CAP   CAR  C5   C6     0.00   0.0  0
 KS1  CONST_25  CAS   CAF  CAP  CAR  180.00   0.0  0
 KS1  CONST_26  NAM   CAE  CAP  CAR  180.00   0.0  0
 KS1  CONST_27  CAD   CAS  CAF  CAP  180.00   0.0  0
 KS1  CONST_28  CAT   CAS  CAF  CAP    0.00   0.0  0
 KS1  CONST_29  CAT   NAM  CAE  CAP    0.00   0.0  0
 KS1  CONST_30  NAM   CAE  CAP  CAF    0.00   0.0  0
 KS1  CONST_31  CAB   CAD  CAS  CAF  180.00   0.0  0
 KS1  CONST_32  NAO   CAT  CAS  CAF  180.00   0.0  0
 KS1  CONST_33  NAM   CAT  CAS  CAF    0.00   0.0  0
 KS1  CONST_34  CAE   CAP  CAF  CAS    0.00   0.0  0
 KS1  CONST_35  NAO   CAB  CAD  CAS    0.00   0.0  0
 KS1  CONST_36  CAB   NAO  CAT  CAS    0.00   0.0  0
 KS1  CONST_37  CAE   NAM  CAT  CAS    0.00   0.0  0
 KS1  CONST_38  NAO   CAT  CAS  CAD    0.00   0.0  0
 KS1  CONST_39  NAM   CAT  CAS  CAD  180.00   0.0  0
 KS1  CONST_40  CAT   NAO  CAB  CAD    0.00   0.0  0
 KS1  CONST_41  CAT   CAS  CAD  CAB    0.00   0.0  0
 KS1  CONST_42  NAM   CAT  NAO  CAB  180.00   0.0  0
 KS1  CONST_43  CAE   NAM  CAT  NAO  180.00   0.0  0
 KS1  CONST_44  CAR   NAN  NAX  CAW  180.00   0.0  0
 KS1  CONST_45  N3    C4   NAX  CAW    0.00   0.0  0
 KS1  CONST_46  C5    C4   NAX  CAW  180.00   0.0  0
 KS1  CONST_47  NAA   C6   C5   C4   180.00   0.0  0
 KS1  CONST_48  NAA   C6   N1   C2   180.00   0.0  0
 KS1  CONST_49  CAR   C5   C6   NAA    0.00   0.0  0
 KS1  CONST_50  H2    C2   N3   C4   180.00   0.0  0
 KS1  CONST_51  HAF   CAF  CAP  CAR    0.00   0.0  0
 KS1  CONST_52  HAE   CAE  CAP  CAR    0.00   0.0  0
 KS1  CONST_53  HAD   CAD  CAS  CAF    0.00   0.0  0
 KS1  CONST_54  HAB   CAB  CAD  CAS  180.00   0.0  0
 KS1  CONST_55  HNAO  NAO  CAT  CAS  180.00   0.0  0
 KS1  CONST_56  HNAA  NAA  C6   N1     0.00   0.0  0
 KS1  CONST_57  HNAB  NAA  C6   N1   180.00   0.0  0
 KS1  Var_01    CAJ   CAH  CAG  CAI   28.36  30.0  1
 KS1  Var_02    CAW   CAJ  CAH  CAG  -41.90  30.0  1
 KS1  Var_03    CAW   CAI  CAG  CAH   -3.70  30.0  1

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
 KS1  chir_01  CAW  CAI  CAJ  NAX  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
 KS1  plan-1  CAW   0.020
 KS1  plan-1  NAX   0.020
 KS1  plan-1  NAN   0.020
 KS1  plan-1  C4    0.020
 KS1  plan-1  N3    0.020
 KS1  plan-1  C2    0.020
 KS1  plan-1  N1    0.020
 KS1  plan-1  C6    0.020
 KS1  plan-1  NAA   0.020
 KS1  plan-1  C5    0.020
 KS1  plan-1  CAR   0.020
 KS1  plan-1  CAP   0.020
 KS1  plan-1  H2    0.020
 KS1  plan-2  CAR   0.020
 KS1  plan-2  CAP   0.020
 KS1  plan-2  CAF   0.020
 KS1  plan-2  CAS   0.020
 KS1  plan-2  CAD   0.020
 KS1  plan-2  CAB   0.020
 KS1  plan-2  NAO   0.020
 KS1  plan-2  CAT   0.020
 KS1  plan-2  NAM   0.020
 KS1  plan-2  CAE   0.020
 KS1  plan-2  HAF   0.020
 KS1  plan-2  HAD   0.020
 KS1  plan-2  HAB   0.020
 KS1  plan-2  HNAO  0.020
 KS1  plan-2  HAE   0.020
 KS1  plan-3  C6    0.020
 KS1  plan-3  NAA   0.020
 KS1  plan-3  HNAA  0.020
 KS1  plan-3  HNAB  0.020

