# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 18:30:59 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 3-(4-methoxy-3-methylphenyl)-1-(piperidin-4-ylmethyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1C)c2nn(CC3CCNCC3)c4ncnc(N)c24
#
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
 C88  C88  3-(4-methoxy-3-methylphenyl)-1-(piperidin-4-ylmethyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine  ligand  50  26  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_C88
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
 C88  CAJ  C  CH2   0  -0.419   3.7138  -0.5108   0.9222
 C88  CAH  C  CH2   0  -0.290   4.3726  -1.5482   1.8209
 C88  NAP  N  NH1   0  -0.596   5.6197  -1.9984   1.2295
 C88  CAI  C  CH2   0  -0.292   5.4059  -2.6392  -0.0552
 C88  CAK  C  CH2   0  -0.417   4.7817  -1.6509  -1.0297
 C88  CAY  C  CH1   0  -0.261   3.4764  -1.0880  -0.4714
 C88  CAL  C  CH2   0  -0.282   2.8923  -0.0658  -1.4390
 C88  NAZ  N  NR5   0  -0.373   1.6315   0.4733  -0.9839
 C88  NAO  N  N     0  -0.278   0.5521  -0.3168  -0.8786
 C88  C4   C  CR56  0   0.576   1.3658   1.7240  -0.5691
 C88  N3   N  N     0  -0.463   2.2109   2.7590  -0.5318
 C88  C2   C  CR16  0   0.052   1.6440   3.8447  -0.0497
 C88  N1   N  N     0  -0.479   0.4013   4.0011   0.4062
 C88  C6   C  CR6   0   0.431  -0.4322   2.9584   0.3787
 C88  NAC  N  NH2   0  -0.817  -1.6621   3.1276   0.8704
 C88  C5   C  CR56  0  -0.265   0.0265   1.7386  -0.1700
 C88  CAV  C  CR5   0   0.260  -0.4303   0.4109  -0.3990
 C88  CAS  C  CR6   0   0.029  -1.7556  -0.1707  -0.1692
 C88  CAG  C  CR16  0  -0.373  -2.9116   0.4900  -0.5939
 C88  CAR  C  CR6   0   0.026  -4.1781  -0.0373  -0.4030
 C88  CAB  C  CH3   0  -0.712  -5.4017   0.6890  -0.8759
 C88  CAU  C  CR6   0   0.349  -4.2902  -1.2830   0.2363
 C88  OAQ  O  O2    0  -0.461  -5.5415  -1.7468   0.3969
 C88  CAA  C  CH3   0  -0.438  -5.7300  -2.9869   1.0494
 C88  CAE  C  CR16  0  -0.372  -3.1489  -1.9615   0.6545
 C88  CAD  C  CR16  0  -0.291  -1.8935  -1.4066   0.4488
 C88  H1   H  HCH2  0   0.232   2.7734  -0.1846   1.3737
 C88  H2   H  HCH2  0   0.214   4.3619   0.3694   0.8513
 C88  H3   H  HCH2  0   0.232   4.5819  -1.1144   2.8007
 C88  H4   H  HCH2  0   0.185   3.6604  -2.3753   1.9828
 C88  H5   H  HNH1  0   0.351   6.0786  -2.6450   1.8573
 C88  H7   H  HCH2  0   0.231   6.3661  -2.9858  -0.4418
 C88  H8   H  HCH2  0   0.186   4.7525  -3.5251   0.0178
 C88  H9   H  HCH2  0   0.216   5.4875  -0.8326  -1.2086
 C88  H10  H  HCH2  0   0.232   4.6058  -2.1418  -1.9901
 C88  H11  H  HCH1  0   0.229   2.7610  -1.9149  -0.3802
 C88  H12  H  HCH2  0   0.256   3.5726   0.7781  -1.5600
 C88  H13  H  HCH2  0   0.265   2.7435  -0.5147  -2.4235
 C88  H14  H  HCR6  0   0.253   2.2681   4.7314  -0.0055
 C88  H15  H  HNH2  0   0.405  -1.8843   3.9880   1.3427
 C88  H16  H  HNH2  0   0.414  -2.2768   2.3461   1.0199
 C88  H17  H  HCR6  0   0.264  -2.8238   1.4350  -1.1191
 C88  H18  H  HCH3  0   0.245  -5.9687   0.0977  -1.5969
 C88  H19  H  HCH3  0   0.245  -6.0775   0.9195  -0.0506
 C88  H20  H  HCH3  0   0.244  -5.1307   1.6278  -1.3566
 C88  H21  H  HCH3  0   0.261  -6.8025  -3.1623   1.0743
 C88  H22  H  HCH3  0   0.230  -5.2512  -3.8086   0.5108
 C88  H23  H  HCH3  0   0.230  -5.3520  -2.9693   2.0747
 C88  H24  H  HCR6  0   0.282  -3.2173  -2.9220   1.1475
 C88  H25  H  HCR6  0   0.255  -1.0166  -1.9424   0.7888

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
 C88  CAI  NAP  single    1.451  0.020  1.451
 C88  CAI  CAK  single    1.522  0.020  1.522
 C88  NAP  CAH  single    1.452  0.020  1.452
 C88  CAH  CAJ  single    1.522  0.020  1.522
 C88  CAK  CAY  single    1.527  0.020  1.527
 C88  CAY  CAJ  single    1.527  0.020  1.527
 C88  CAY  CAL  single    1.524  0.020  1.524
 C88  CAL  NAZ  single    1.445  0.020  1.445
 C88  N3   C2   aromatic  1.316  0.020  1.316
 C88  N3   C4   aromatic  1.337  0.020  1.337
 C88  C2   N1   aromatic  1.333  0.020  1.333
 C88  NAZ  C4   aromatic  1.344  0.020  1.344
 C88  NAZ  NAO  aromatic  1.342  0.020  1.342
 C88  C4   C5   aromatic  1.398  0.020  1.398
 C88  N1   C6   aromatic  1.335  0.020  1.335
 C88  CAD  CAE  aromatic  1.388  0.020  1.388
 C88  CAD  CAS  aromatic  1.389  0.020  1.389
 C88  NAO  CAV  aromatic  1.313  0.020  1.313
 C88  C5   C6   aromatic  1.414  0.020  1.414
 C88  C5   CAV  aromatic  1.423  0.020  1.423
 C88  C6   NAC  single    1.335  0.020  1.335
 C88  CAV  CAS  single    1.465  0.020  1.465
 C88  CAE  CAU  aromatic  1.392  0.020  1.392
 C88  CAS  CAG  aromatic  1.398  0.020  1.398
 C88  CAA  OAQ  single    1.414  0.020  1.414
 C88  CAU  OAQ  single    1.344  0.020  1.344
 C88  CAU  CAR  aromatic  1.405  0.020  1.405
 C88  CAG  CAR  aromatic  1.385  0.020  1.385
 C88  CAR  CAB  single    1.499  0.020  1.499
 C88  CAJ  H1   single    0.970  0.020  1.090
 C88  CAJ  H2   single    0.970  0.020  1.090
 C88  CAH  H3   single    0.970  0.020  1.090
 C88  CAH  H4   single    0.970  0.020  1.090
 C88  NAP  H5   single    0.890  0.020  1.040
 C88  CAI  H7   single    0.970  0.020  1.090
 C88  CAI  H8   single    0.970  0.020  1.090
 C88  CAK  H9   single    0.970  0.020  1.090
 C88  CAK  H10  single    0.970  0.020  1.090
 C88  CAY  H11  single    0.970  0.020  1.090
 C88  CAL  H12  single    0.970  0.020  1.090
 C88  CAL  H13  single    0.970  0.020  1.090
 C88  C2   H14  single    0.930  0.020  1.080
 C88  NAC  H15  single    0.860  0.020  1.020
 C88  NAC  H16  single    0.860  0.020  1.020
 C88  CAG  H17  single    0.930  0.020  1.080
 C88  CAB  H18  single    0.970  0.020  1.090
 C88  CAB  H19  single    0.970  0.020  1.090
 C88  CAB  H20  single    0.970  0.020  1.090
 C88  CAA  H21  single    0.970  0.020  1.090
 C88  CAA  H22  single    0.970  0.020  1.090
 C88  CAA  H23  single    0.970  0.020  1.090
 C88  CAE  H24  single    0.930  0.020  1.080
 C88  CAD  H25  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
 C88  H2   CAJ  H1   107.22  3.000
 C88  H2   CAJ  CAY  109.67  3.000
 C88  H1   CAJ  CAY  110.86  3.000
 C88  H2   CAJ  CAH  109.25  3.000
 C88  H1   CAJ  CAH  109.38  3.000
 C88  CAY  CAJ  CAH  110.39  3.000
 C88  H4   CAH  H3   106.85  3.000
 C88  H4   CAH  NAP  112.45  3.000
 C88  H3   CAH  NAP  108.91  3.000
 C88  H4   CAH  CAJ  108.55  3.000
 C88  H3   CAH  CAJ  110.00  3.000
 C88  NAP  CAH  CAJ  110.03  3.000
 C88  H5   NAP  CAI  109.51  3.000
 C88  H5   NAP  CAH  109.59  3.000
 C88  CAI  NAP  CAH  111.77  3.000
 C88  H8   CAI  H7   106.83  3.000
 C88  H8   CAI  CAK  108.72  3.000
 C88  H7   CAI  CAK  109.89  3.000
 C88  H8   CAI  NAP  112.53  3.000
 C88  H7   CAI  NAP  108.91  3.000
 C88  CAK  CAI  NAP  109.91  3.000
 C88  H10  CAK  H9   107.20  3.000
 C88  H10  CAK  CAY  110.44  3.000
 C88  H9   CAK  CAY  109.58  3.000
 C88  H10  CAK  CAI  109.70  3.000
 C88  H9   CAK  CAI  108.99  3.000
 C88  CAY  CAK  CAI  110.85  3.000
 C88  H11  CAY  CAL  107.96  3.000
 C88  H11  CAY  CAK  108.05  3.000
 C88  CAL  CAY  CAK  110.05  3.000
 C88  H11  CAY  CAJ  108.08  3.000
 C88  CAL  CAY  CAJ  112.67  3.000
 C88  CAK  CAY  CAJ  109.88  3.000
 C88  H13  CAL  H12  107.63  3.000
 C88  H13  CAL  NAZ  108.57  3.000
 C88  H12  CAL  NAZ  106.90  3.000
 C88  H13  CAL  CAY  110.41  3.000
 C88  H12  CAL  CAY  110.51  3.000
 C88  NAZ  CAL  CAY  112.63  3.000
 C88  C4   NAZ  NAO  111.39  3.000
 C88  NAO  NAZ  CAL  120.47  3.000
 C88  C4   NAZ  CAL  128.08  3.000
 C88  CAV  NAO  NAZ  107.71  3.000
 C88  C5   C4   N3   126.14  3.000
 C88  C5   C4   NAZ  106.69  3.000
 C88  N3   C4   NAZ  127.16  3.000
 C88  C2   N3   C4   112.12  3.000
 C88  H14  C2   N1   115.24  3.000
 C88  H14  C2   N3   116.18  3.000
 C88  N1   C2   N3   128.58  3.000
 C88  C6   N1   C2   118.90  3.000
 C88  C5   C6   NAC  123.44  3.000
 C88  NAC  C6   N1   117.93  3.000
 C88  C5   C6   N1   118.63  3.000
 C88  H16  NAC  H15  117.37  3.000
 C88  H16  NAC  C6   121.29  3.000
 C88  H15  NAC  C6   118.98  3.000
 C88  CAV  C5   C6   139.76  3.000
 C88  CAV  C5   C4   104.60  3.000
 C88  C6   C5   C4   115.51  3.000
 C88  CAS  CAV  C5   129.46  3.000
 C88  CAS  CAV  NAO  120.92  3.000
 C88  C5   CAV  NAO  109.61  3.000
 C88  CAD  CAS  CAG  118.29  3.000
 C88  CAG  CAS  CAV  120.84  3.000
 C88  CAD  CAS  CAV  120.85  3.000
 C88  H17  CAG  CAR  118.19  3.000
 C88  H17  CAG  CAS  119.48  3.000
 C88  CAR  CAG  CAS  122.30  3.000
 C88  CAU  CAR  CAB  120.53  3.000
 C88  CAB  CAR  CAG  121.22  3.000
 C88  CAU  CAR  CAG  118.25  3.000
 C88  H20  CAB  H19  107.81  3.000
 C88  H20  CAB  H18  107.74  3.000
 C88  H19  CAB  H18  106.99  3.000
 C88  H20  CAB  CAR  110.72  3.000
 C88  H19  CAB  CAR  111.66  3.000
 C88  H18  CAB  CAR  111.71  3.000
 C88  CAE  CAU  OAQ  124.00  3.000
 C88  OAQ  CAU  CAR  115.76  3.000
 C88  CAE  CAU  CAR  120.24  3.000
 C88  CAA  OAQ  CAU  118.80  3.000
 C88  H23  CAA  H22  108.84  3.000
 C88  H23  CAA  H21  108.80  3.000
 C88  H22  CAA  H21  108.80  3.000
 C88  H23  CAA  OAQ  111.88  3.000
 C88  H22  CAA  OAQ  111.94  3.000
 C88  H21  CAA  OAQ  106.48  3.000
 C88  H24  CAE  CAD  118.66  3.000
 C88  H24  CAE  CAU  121.19  3.000
 C88  CAD  CAE  CAU  120.15  3.000
 C88  H25  CAD  CAE  119.24  3.000
 C88  H25  CAD  CAS  119.99  3.000
 C88  CAE  CAD  CAS  120.77  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
 C88  CONST_01  C2   N3   C4   NAZ  180.00   0.0  0
 C88  CONST_02  C6   C5   C4   NAZ  180.00   0.0  0
 C88  CONST_03  CAV  C5   C4   NAZ    0.00   0.0  0
 C88  CONST_04  C5   CAV  NAO  NAZ    0.00   0.0  0
 C88  CONST_05  CAS  CAV  NAO  NAZ  180.00   0.0  0
 C88  CONST_06  N3   C4   NAZ  NAO  180.00   0.0  0
 C88  CONST_07  C5   C4   NAZ  NAO    0.00   0.0  0
 C88  CONST_08  C4   C5   CAV  NAO    0.00   0.0  0
 C88  CONST_09  C6   C5   CAV  NAO  180.00   0.0  0
 C88  CONST_12  N1   C2   N3   C4     0.00   0.0  0
 C88  CONST_13  CAV  NAO  NAZ  C4     0.00   0.0  0
 C88  CONST_14  N1   C6   C5   C4     0.00   0.0  0
 C88  CONST_15  CAS  CAV  C5   C4   180.00   0.0  0
 C88  CONST_16  C6   N1   C2   N3     0.00   0.0  0
 C88  CONST_17  C6   C5   C4   N3     0.00   0.0  0
 C88  CONST_18  CAV  C5   C4   N3   180.00   0.0  0
 C88  CONST_19  C5   C4   N3   C2     0.00   0.0  0
 C88  CONST_20  C5   C6   N1   C2     0.00   0.0  0
 C88  CONST_21  CAV  C5   C6   N1   180.00   0.0  0
 C88  CONST_22  CAS  CAV  C5   C6     0.00   0.0  0
 C88  CONST_25  CAE  CAD  CAS  CAV  180.00   0.0  0
 C88  CONST_26  CAR  CAG  CAS  CAV  180.00   0.0  0
 C88  CONST_27  CAU  CAE  CAD  CAS    0.00   0.0  0
 C88  CONST_28  CAU  CAR  CAG  CAS    0.00   0.0  0
 C88  CONST_29  CAE  CAD  CAS  CAG    0.00   0.0  0
 C88  CONST_30  CAE  CAU  CAR  CAG    0.00   0.0  0
 C88  CONST_31  CAD  CAE  CAU  CAR    0.00   0.0  0
 C88  CONST_32  CAD  CAS  CAG  CAR    0.00   0.0  0
 C88  CONST_33  N3   C4   NAZ  CAL    0.00   0.0  0
 C88  CONST_34  C5   C4   NAZ  CAL  180.00   0.0  0
 C88  CONST_35  CAV  NAO  NAZ  CAL  180.00   0.0  0
 C88  CONST_36  NAC  C6   C5   C4   180.00   0.0  0
 C88  CONST_37  NAC  C6   N1   C2   180.00   0.0  0
 C88  CONST_38  CAV  C5   C6   NAC    0.00   0.0  0
 C88  CONST_39  CAB  CAR  CAG  CAS  180.00   0.0  0
 C88  CONST_40  OAQ  CAU  CAR  CAG  180.00   0.0  0
 C88  CONST_41  CAE  CAU  CAR  CAB  180.00   0.0  0
 C88  CONST_42  CAD  CAE  CAU  OAQ  180.00   0.0  0
 C88  CONST_43  H14  C2   N3   C4   180.00   0.0  0
 C88  CONST_44  H25  CAD  CAS  CAV    0.00   0.0  0
 C88  CONST_45  H17  CAG  CAS  CAV    0.00   0.0  0
 C88  CONST_46  H24  CAE  CAD  CAS  180.00   0.0  0
 C88  CONST_47  H15  NAC  C6   N1     0.00   0.0  0
 C88  CONST_48  H16  NAC  C6   N1   180.00   0.0  0
 C88  Var_01    CAI  NAP  CAH  CAJ  -61.79  30.0  1
 C88  Var_02    CAK  CAI  NAP  CAH   61.31  30.0  1
 C88  Var_03    CAY  CAK  CAI  NAP  -56.77  30.0  1
 C88  Var_04    CAY  CAJ  CAH  NAP   57.38  30.0  1
 C88  Var_05    C4   NAZ  CAL  CAY  111.54  30.0  2
 C88  Var_06    CAE  CAU  OAQ  CAA    1.16  30.0  2
 C88  Var_07    H18  CAB  CAR  CAG  120.11  30.0  2
 C88  Var_08    H21  CAA  OAQ  CAU  179.69  30.0  3

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
 C88  chir_01  CAY  CAK  CAJ  CAL  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
 C88  plan-1  CAV  0.020
 C88  plan-1  CAS  0.020
 C88  plan-1  CAG  0.020
 C88  plan-1  CAR  0.020
 C88  plan-1  CAB  0.020
 C88  plan-1  CAU  0.020
 C88  plan-1  OAQ  0.020
 C88  plan-1  CAE  0.020
 C88  plan-1  CAD  0.020
 C88  plan-1  H17  0.020
 C88  plan-1  H24  0.020
 C88  plan-1  H25  0.020
 C88  plan-2  CAL  0.020
 C88  plan-2  NAZ  0.020
 C88  plan-2  NAO  0.020
 C88  plan-2  C4   0.020
 C88  plan-2  N3   0.020
 C88  plan-2  C2   0.020
 C88  plan-2  N1   0.020
 C88  plan-2  C6   0.020
 C88  plan-2  NAC  0.020
 C88  plan-2  C5   0.020
 C88  plan-2  CAV  0.020
 C88  plan-2  CAS  0.020
 C88  plan-2  H14  0.020
 C88  plan-3  C6   0.020
 C88  plan-3  NAC  0.020
 C88  plan-3  H15  0.020
 C88  plan-3  H16  0.020

