# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 06:39:01 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 1-tert-butyl-3-[(1H-indol-3-yl)methyl]-1H-pyrazolo[3,4-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)n1nc(Cc2c[nH]c3ccccc23)c4c(N)ncnc14
#
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
 9YG  9YG  1-tert-butyl-3-[(1H-indol-3-yl)methyl]-1H-pyrazolo[3,4-d]pyrimidin-4-amine  ligand  44  24  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9YG
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
 9YG  C4   C  CR6   0   0.426  -1.1003   2.1386   0.4801
 9YG  C5   C  CR56  0  -0.249  -1.1171   0.8770  -0.1550
 9YG  C6   C  CR56  0   0.589  -2.0979  -0.0170   0.2857
 9YG  N1   N  N     0  -0.466  -3.0053   0.2362   1.2387
 9YG  N3   N  N     0  -0.481  -2.0105   2.3983   1.4212
 9YG  CAA  C  CH3   0  -0.648  -2.1820  -3.4144  -1.3277
 9YG  CAC  C  CH3   0  -0.649  -4.1828  -2.1320  -0.5828
 9YG  CAD  C  CH3   0  -0.646  -2.5032  -2.9647   1.1029
 9YG  NAE  N  NR5   0  -0.381  -1.9473  -1.1485  -0.4320
 9YG  NAX  N  N     0  -0.280  -0.9314  -1.0229  -1.3042
 9YG  C2   C  CR16  0   0.051  -2.8910   1.4489   1.7360
 9YG  NAK  N  NH2   0  -0.824  -0.2274   3.1013   0.1674
 9YG  CAM  C  CR5   0   0.312  -0.4160   0.1725  -1.1685
 9YG  CAN  C  CH2   0  -0.632   0.7464   0.5990  -2.0080
 9YG  CAO  C  CR5   0  -0.016   1.9668   0.9146  -1.2007
 9YG  CAS  C  CR56  0   0.035   2.5732   0.0953  -0.1922
 9YG  CAT  C  CR16  0  -0.367   2.2813  -1.1665   0.3418
 9YG  CAU  C  CR16  0  -0.268   3.0981  -1.6778   1.3304
 9YG  CAV  C  CR16  0  -0.281   4.2067  -0.9544   1.8024
 9YG  CAW  C  CR16  0  -0.303   4.5226   0.2893   1.2917
 9YG  CAR  C  CR56  0   0.353   3.6977   0.8013   0.2904
 9YG  NAQ  N  NR15  0  -0.681   3.7681   1.9776  -0.3958
 9YG  CAP  C  CR15  0  -0.106   2.7340   2.0446  -1.2849
 9YG  H1   H  HCH3  0   0.238  -1.1354  -3.6656  -1.1579
 9YG  H2   H  HCH3  0   0.237  -2.7675  -4.3296  -1.2342
 9YG  H3   H  HCH3  0   0.238  -2.2880  -3.0540  -2.3504
 9YG  H4   H  HCH3  0   0.233  -4.7512  -3.0590  -0.5008
 9YG  H5   H  HCH3  0   0.247  -4.6007  -1.4183   0.1248
 9YG  H6   H  HCH3  0   0.234  -4.3231  -1.7417  -1.5919
 9YG  H7   H  HCH3  0   0.233  -1.4456  -3.1532   1.2945
 9YG  H8   H  HCH3  0   0.245  -2.8765  -2.2811   1.8641
 9YG  H9   H  HCH3  0   0.234  -3.0380  -3.9090   1.2091
 9YG  H10  H  HCR6  0   0.251  -3.6040   1.7172   2.5093
 9YG  H11  H  HNH2  0   0.400  -0.2031   3.9321   0.7351
 9YG  H12  H  HNH2  0   0.416   0.5989   2.8883  -0.3669
 9YG  H13  H  HCH2  0   0.271   0.9497  -0.2060  -2.7194
 9YG  H14  H  HCH2  0   0.266   0.4718   1.4732  -2.6052
 9YG  H15  H  HCR6  0   0.240   1.4316  -1.7339  -0.0173
 9YG  H16  H  HCR6  0   0.247   2.8844  -2.6520   1.7509
 9YG  H17  H  HCR6  0   0.250   4.8264  -1.3820   2.5802
 9YG  H18  H  HCR6  0   0.260   5.3788   0.8434   1.6550
 9YG  H19  H  HNR5  0   0.410   4.4594   2.6961  -0.2623
 9YG  H20  H  HCR5  0   0.297   2.6204   2.9005  -1.9334
 9YG  CAB  C  CT    0   0.063  -2.7051  -2.4092  -0.3078

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
 9YG  CAA  CAB  single    1.525  0.020  1.525
 9YG  CAC  CAB  single    1.528  0.020  1.528
 9YG  CAB  NAE  single    1.476  0.020  1.476
 9YG  CAB  CAD  single    1.529  0.020  1.529
 9YG  NAE  NAX  aromatic  1.345  0.020  1.345
 9YG  NAE  C6   aromatic  1.348  0.020  1.348
 9YG  NAX  CAM  aromatic  1.309  0.020  1.309
 9YG  C6   N1   aromatic  1.340  0.020  1.340
 9YG  C6   C5   aromatic  1.398  0.020  1.398
 9YG  N1   C2   aromatic  1.316  0.020  1.316
 9YG  CAN  CAM  single    1.496  0.020  1.496
 9YG  CAN  CAO  single    1.497  0.020  1.497
 9YG  CAM  C5   aromatic  1.420  0.020  1.420
 9YG  C5   C4   aromatic  1.413  0.020  1.413
 9YG  C2   N3   aromatic  1.333  0.020  1.333
 9YG  C4   N3   aromatic  1.335  0.020  1.335
 9YG  C4   NAK  single    1.337  0.020  1.337
 9YG  CAT  CAU  aromatic  1.381  0.020  1.381
 9YG  CAT  CAS  aromatic  1.401  0.020  1.401
 9YG  CAO  CAS  aromatic  1.434  0.020  1.434
 9YG  CAO  CAP  aromatic  1.368  0.020  1.368
 9YG  CAU  CAV  aromatic  1.405  0.020  1.405
 9YG  CAS  CAR  aromatic  1.413  0.020  1.413
 9YG  CAP  NAQ  aromatic  1.365  0.020  1.365
 9YG  CAV  CAW  aromatic  1.381  0.020  1.381
 9YG  CAR  NAQ  aromatic  1.364  0.020  1.364
 9YG  CAR  CAW  aromatic  1.395  0.020  1.395
 9YG  CAA  H1   single    0.970  0.020  1.090
 9YG  CAA  H2   single    0.970  0.020  1.090
 9YG  CAA  H3   single    0.970  0.020  1.090
 9YG  CAC  H4   single    0.970  0.020  1.090
 9YG  CAC  H5   single    0.970  0.020  1.090
 9YG  CAC  H6   single    0.970  0.020  1.090
 9YG  CAD  H7   single    0.970  0.020  1.090
 9YG  CAD  H8   single    0.970  0.020  1.090
 9YG  CAD  H9   single    0.970  0.020  1.090
 9YG  C2   H10  single    0.930  0.020  1.080
 9YG  NAK  H11  single    0.890  0.020  1.040
 9YG  NAK  H12  single    0.890  0.020  1.040
 9YG  CAN  H13  single    0.970  0.020  1.090
 9YG  CAN  H14  single    0.970  0.020  1.090
 9YG  CAT  H15  single    0.930  0.020  1.080
 9YG  CAU  H16  single    0.930  0.020  1.080
 9YG  CAV  H17  single    0.930  0.020  1.080
 9YG  CAW  H18  single    0.930  0.020  1.080
 9YG  NAQ  H19  single    0.860  0.020  1.020
 9YG  CAP  H20  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
 9YG  NAK  C4   N3   118.04  3.000
 9YG  NAK  C4   C5   123.09  3.000
 9YG  N3   C4   C5   118.86  3.000
 9YG  CAM  C5   C6   104.73  3.000
 9YG  CAM  C5   C4   139.32  3.000
 9YG  C6   C5   C4   115.96  3.000
 9YG  NAE  C6   N1   127.79  3.000
 9YG  N1   C6   C5   125.33  3.000
 9YG  NAE  C6   C5   106.88  3.000
 9YG  C2   N1   C6   112.59  3.000
 9YG  C2   N3   C4   118.59  3.000
 9YG  H3   CAA  H2   107.82  3.000
 9YG  H3   CAA  H1   108.41  3.000
 9YG  H2   CAA  H1   107.99  3.000
 9YG  H3   CAA  CAB  112.12  3.000
 9YG  H2   CAA  CAB  108.17  3.000
 9YG  H1   CAA  CAB  112.16  3.000
 9YG  H6   CAC  H5   108.51  3.000
 9YG  H6   CAC  H4   107.86  3.000
 9YG  H5   CAC  H4   107.96  3.000
 9YG  H6   CAC  CAB  110.83  3.000
 9YG  H5   CAC  CAB  111.91  3.000
 9YG  H4   CAC  CAB  109.65  3.000
 9YG  H9   CAD  H8   107.90  3.000
 9YG  H9   CAD  H7   107.98  3.000
 9YG  H8   CAD  H7   108.53  3.000
 9YG  H9   CAD  CAB  109.86  3.000
 9YG  H8   CAD  CAB  111.80  3.000
 9YG  H7   CAD  CAB  110.65  3.000
 9YG  NAX  NAE  CAB  121.47  3.000
 9YG  NAX  NAE  C6   110.57  3.000
 9YG  CAB  NAE  C6   127.92  3.000
 9YG  CAM  NAX  NAE  108.39  3.000
 9YG  H10  C2   N3   115.22  3.000
 9YG  H10  C2   N1   116.10  3.000
 9YG  N3   C2   N1   128.67  3.000
 9YG  H12  NAK  H11  117.01  3.000
 9YG  H12  NAK  C4   120.51  3.000
 9YG  H11  NAK  C4   118.58  3.000
 9YG  CAN  CAM  NAX  120.54  3.000
 9YG  CAN  CAM  C5   130.02  3.000
 9YG  NAX  CAM  C5   109.44  3.000
 9YG  H14  CAN  H13  106.25  3.000
 9YG  H14  CAN  CAO  109.31  3.000
 9YG  H13  CAN  CAO  110.77  3.000
 9YG  H14  CAN  CAM  109.83  3.000
 9YG  H13  CAN  CAM  107.44  3.000
 9YG  CAO  CAN  CAM  113.01  3.000
 9YG  CAP  CAO  CAS  106.14  3.000
 9YG  CAP  CAO  CAN  126.73  3.000
 9YG  CAS  CAO  CAN  127.13  3.000
 9YG  CAR  CAS  CAT  119.06  3.000
 9YG  CAR  CAS  CAO  106.94  3.000
 9YG  CAT  CAS  CAO  133.99  3.000
 9YG  H15  CAT  CAU  120.50  3.000
 9YG  H15  CAT  CAS  120.60  3.000
 9YG  CAU  CAT  CAS  118.90  3.000
 9YG  H16  CAU  CAV  119.25  3.000
 9YG  H16  CAU  CAT  119.65  3.000
 9YG  CAV  CAU  CAT  121.10  3.000
 9YG  H17  CAV  CAW  119.37  3.000
 9YG  H17  CAV  CAU  119.31  3.000
 9YG  CAW  CAV  CAU  121.32  3.000
 9YG  H18  CAW  CAR  121.39  3.000
 9YG  H18  CAW  CAV  121.18  3.000
 9YG  CAR  CAW  CAV  117.44  3.000
 9YG  NAQ  CAR  CAW  130.35  3.000
 9YG  CAW  CAR  CAS  122.18  3.000
 9YG  NAQ  CAR  CAS  107.47  3.000
 9YG  H19  NAQ  CAP  124.88  3.000
 9YG  H19  NAQ  CAR  125.79  3.000
 9YG  CAP  NAQ  CAR  109.33  3.000
 9YG  H20  CAP  NAQ  120.64  3.000
 9YG  H20  CAP  CAO  129.23  3.000
 9YG  NAQ  CAP  CAO  110.12  3.000
 9YG  NAE  CAB  CAD  108.67  3.000
 9YG  CAD  CAB  CAC  111.06  3.000
 9YG  NAE  CAB  CAC  109.04  3.000
 9YG  CAD  CAB  CAA  109.40  3.000
 9YG  NAE  CAB  CAA  109.31  3.000
 9YG  CAC  CAB  CAA  109.32  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
 9YG  CONST_01  NAE  C6   C5   C4    180.00   0.0  0
 9YG  CONST_02  N1   C6   C5   C4      0.00   0.0  0
 9YG  CONST_03  NAX  CAM  C5   C4    180.00   0.0  0
 9YG  CONST_04  N1   C2   N3   C4      0.00   0.0  0
 9YG  CONST_05  NAX  NAE  C6   C5      0.00   0.0  0
 9YG  CONST_06  C2   N1   C6   C5      0.00   0.0  0
 9YG  CONST_07  NAE  NAX  CAM  C5      0.00   0.0  0
 9YG  CONST_08  C2   N3   C4   C5      0.00   0.0  0
 9YG  CONST_09  CAM  NAX  NAE  C6      0.00   0.0  0
 9YG  CONST_10  N3   C2   N1   C6      0.00   0.0  0
 9YG  CONST_11  NAX  CAM  C5   C6      0.00   0.0  0
 9YG  CONST_12  N3   C4   C5   C6      0.00   0.0  0
 9YG  CONST_13  NAX  NAE  C6   N1    180.00   0.0  0
 9YG  CONST_14  CAM  C5   C6   N1    180.00   0.0  0
 9YG  CONST_15  CAM  C5   C4   N3    180.00   0.0  0
 9YG  CONST_16  C2   N1   C6   NAE   180.00   0.0  0
 9YG  CONST_17  CAM  C5   C6   NAE     0.00   0.0  0
 9YG  CONST_18  CAU  CAT  CAS  CAO   180.00   0.0  0
 9YG  CONST_19  NAQ  CAR  CAS  CAO     0.00   0.0  0
 9YG  CONST_20  CAW  CAR  CAS  CAO   180.00   0.0  0
 9YG  CONST_21  CAR  NAQ  CAP  CAO     0.00   0.0  0
 9YG  CONST_22  CAV  CAU  CAT  CAS     0.00   0.0  0
 9YG  CONST_23  NAQ  CAP  CAO  CAS     0.00   0.0  0
 9YG  CONST_24  CAP  NAQ  CAR  CAS     0.00   0.0  0
 9YG  CONST_25  CAV  CAW  CAR  CAS     0.00   0.0  0
 9YG  CONST_26  CAW  CAV  CAU  CAT     0.00   0.0  0
 9YG  CONST_27  CAP  CAO  CAS  CAT   180.00   0.0  0
 9YG  CONST_28  NAQ  CAR  CAS  CAT   180.00   0.0  0
 9YG  CONST_29  CAW  CAR  CAS  CAT     0.00   0.0  0
 9YG  CONST_30  CAR  CAS  CAT  CAU     0.00   0.0  0
 9YG  CONST_31  CAR  CAW  CAV  CAU     0.00   0.0  0
 9YG  CONST_32  NAQ  CAR  CAW  CAV   180.00   0.0  0
 9YG  CONST_33  CAP  NAQ  CAR  CAW   180.00   0.0  0
 9YG  CONST_34  CAP  CAO  CAS  CAR     0.00   0.0  0
 9YG  CONST_35  CAN  CAM  C5   C4      0.00   0.0  0
 9YG  CONST_36  CAB  NAE  C6   C5    180.00   0.0  0
 9YG  CONST_37  CAN  CAM  C5   C6    180.00   0.0  0
 9YG  CONST_38  NAK  C4   C5   C6    180.00   0.0  0
 9YG  CONST_39  CAB  NAE  C6   N1      0.00   0.0  0
 9YG  CONST_40  CAM  NAX  NAE  CAB   180.00   0.0  0
 9YG  CONST_41  CAN  CAM  NAX  NAE   180.00   0.0  0
 9YG  CONST_42  NAK  C4   N3   C2    180.00   0.0  0
 9YG  CONST_43  CAM  C5   C4   NAK     0.00   0.0  0
 9YG  CONST_44  CAT  CAS  CAO  CAN     0.00   0.0  0
 9YG  CONST_45  CAR  CAS  CAO  CAN   180.00   0.0  0
 9YG  CONST_46  NAQ  CAP  CAO  CAN   180.00   0.0  0
 9YG  CONST_47  H10  C2   N3   C4    180.00   0.0  0
 9YG  CONST_48  H15  CAT  CAS  CAO     0.00   0.0  0
 9YG  CONST_49  H19  NAQ  CAP  CAO   180.00   0.0  0
 9YG  CONST_50  H16  CAU  CAT  CAS   180.00   0.0  0
 9YG  CONST_51  H20  CAP  CAO  CAS   180.00   0.0  0
 9YG  CONST_52  H18  CAW  CAR  CAS   180.00   0.0  0
 9YG  CONST_53  H17  CAV  CAU  CAT   180.00   0.0  0
 9YG  CONST_54  H11  NAK  C4   C5    180.00   0.0  0
 9YG  Var_01    CAO  CAN  CAM  C5     61.32  30.0  1
 9YG  Var_02    CAS  CAO  CAN  CAM    50.68  30.0  2
 9YG  Var_03    CAA  CAB  NAE  C6   -179.83  30.0  3
 9YG  Var_04    H1   CAA  CAB  NAE    62.18  30.0  3
 9YG  Var_05    H4   CAC  CAB  NAE   179.59  30.0  3
 9YG  Var_06    H7   CAD  CAB  NAE   -59.64  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
 9YG  plan-1  C4   0.020
 9YG  plan-1  C5   0.020
 9YG  plan-1  C6   0.020
 9YG  plan-1  N1   0.020
 9YG  plan-1  N3   0.020
 9YG  plan-1  NAE  0.020
 9YG  plan-1  NAX  0.020
 9YG  plan-1  C2   0.020
 9YG  plan-1  NAK  0.020
 9YG  plan-1  CAM  0.020
 9YG  plan-1  CAN  0.020
 9YG  plan-1  H10  0.020
 9YG  plan-1  CAB  0.020
 9YG  plan-2  CAN  0.020
 9YG  plan-2  CAO  0.020
 9YG  plan-2  CAS  0.020
 9YG  plan-2  CAT  0.020
 9YG  plan-2  CAU  0.020
 9YG  plan-2  CAV  0.020
 9YG  plan-2  CAW  0.020
 9YG  plan-2  CAR  0.020
 9YG  plan-2  NAQ  0.020
 9YG  plan-2  CAP  0.020
 9YG  plan-2  H15  0.020
 9YG  plan-2  H16  0.020
 9YG  plan-2  H17  0.020
 9YG  plan-2  H18  0.020
 9YG  plan-2  H19  0.020
 9YG  plan-2  H20  0.020
 9YG  plan-3  C4   0.020
 9YG  plan-3  NAK  0.020
 9YG  plan-3  H11  0.020
 9YG  plan-3  H12  0.020

