# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 12:05:01 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 1-(piperidin-4-ylmethyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(CC3CCNCC3)ncc12
#
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
 B5A  B5A  1-(piperidin-4-ylmethyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine  ligand  33  17  .  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_B5A
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
 B5A  CAF  C  CH2   0  -0.412   2.3370   1.0354   0.3784
 B5A  CAD  C  CH2   0  -0.292   3.4126   0.8895   1.4453
 B5A  NAL  N  NH1   0  -0.595   4.5959   0.2675   0.8789
 B5A  CAE  C  CH2   0  -0.293   4.3096  -1.0686   0.3888
 B5A  CAG  C  CH2   0  -0.417   3.2756  -1.0017  -0.7249
 B5A  CAP  C  CH1   0  -0.267   1.9967  -0.3193  -0.2404
 B5A  CAH  C  CH2   0  -0.287   1.0049  -0.2070  -1.3942
 B5A  NAQ  N  NR5   0  -0.370  -0.2719   0.3470  -1.0024
 B5A  NAK  N  N     0  -0.250  -0.5428   1.6567  -1.1435
 B5A  CAC  C  CR15  0  -0.102  -1.7322   1.8642  -0.6366
 B5A  C5   C  CR56  0  -0.235  -2.2706   0.6555  -0.1381
 B5A  C4   C  CR56  0   0.584  -1.2847  -0.2979  -0.3954
 B5A  N3   N  N     0  -0.466  -1.3523  -1.6004  -0.0968
 B5A  C2   C  CR16  0   0.055  -2.4900  -1.9142   0.4878
 B5A  N1   N  N     0  -0.484  -3.5159  -1.1206   0.7986
 B5A  C6   C  CR6   0   0.468  -3.4383   0.1782   0.4978
 B5A  NAA  N  NH2   0  -0.813  -4.4646   0.9674   0.8089
 B5A  H1   H  HCH2  0   0.233   1.4525   1.4978   0.8207
 B5A  H2   H  HCH2  0   0.212   2.6956   1.7111  -0.4055
 B5A  H3   H  HCH2  0   0.231   3.6826   1.8719   1.8382
 B5A  H4   H  HCH2  0   0.185   2.9991   0.3117   2.2892
 B5A  H5   H  HNH1  0   0.350   5.3220   0.2205   1.5815
 B5A  H7   H  HCH2  0   0.232   5.2333  -1.5156   0.0155
 B5A  H8   H  HCH2  0   0.185   3.9303  -1.7344   1.1826
 B5A  H9   H  HCH2  0   0.216   3.6898  -0.4412  -1.5699
 B5A  H10  H  HCH2  0   0.232   3.0563  -2.0106  -1.0839
 B5A  H11  H  HCH1  0   0.229   1.5466  -0.9541   0.5338
 B5A  H12  H  HCH2  0   0.262   1.4033   0.4331  -2.1826
 B5A  H13  H  HCH2  0   0.264   0.8237  -1.1911  -1.8296
 B5A  H14  H  HCR5  0   0.272  -2.1635   2.8537  -0.6452
 B5A  H15  H  HCR6  0   0.252  -2.6172  -2.9579   0.7567
 B5A  H16  H  HNH2  0   0.413  -4.4525   1.9542   0.6211
 B5A  H17  H  HNH2  0   0.406  -5.2673   0.5874   1.2809

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
 B5A  CAE  NAL  single    1.452  0.020  1.452
 B5A  CAE  CAG  single    1.521  0.020  1.521
 B5A  NAL  CAD  single    1.452  0.020  1.452
 B5A  CAD  CAF  single    1.522  0.020  1.522
 B5A  CAG  CAP  single    1.528  0.020  1.528
 B5A  CAP  CAF  single    1.528  0.020  1.528
 B5A  CAP  CAH  single    1.526  0.020  1.526
 B5A  CAH  NAQ  single    1.446  0.020  1.446
 B5A  NAQ  NAK  aromatic  1.345  0.020  1.345
 B5A  NAQ  C4   aromatic  1.345  0.020  1.345
 B5A  NAK  CAC  aromatic  1.309  0.020  1.309
 B5A  C4   N3   aromatic  1.338  0.020  1.338
 B5A  C4   C5   aromatic  1.395  0.020  1.395
 B5A  N3   C2   aromatic  1.317  0.020  1.317
 B5A  CAC  C5   aromatic  1.414  0.020  1.414
 B5A  C5   C6   aromatic  1.413  0.020  1.413
 B5A  C2   N1   aromatic  1.334  0.020  1.334
 B5A  C6   N1   aromatic  1.335  0.020  1.335
 B5A  C6   NAA  single    1.331  0.020  1.331
 B5A  CAF  H1   single    0.970  0.020  1.090
 B5A  CAF  H2   single    0.970  0.020  1.090
 B5A  CAD  H3   single    0.970  0.020  1.090
 B5A  CAD  H4   single    0.970  0.020  1.090
 B5A  NAL  H5   single    0.890  0.020  1.040
 B5A  CAE  H7   single    0.970  0.020  1.090
 B5A  CAE  H8   single    0.970  0.020  1.090
 B5A  CAG  H9   single    0.970  0.020  1.090
 B5A  CAG  H10  single    0.970  0.020  1.090
 B5A  CAP  H11  single    0.970  0.020  1.090
 B5A  CAH  H12  single    0.970  0.020  1.090
 B5A  CAH  H13  single    0.970  0.020  1.090
 B5A  CAC  H14  single    0.930  0.020  1.080
 B5A  C2   H15  single    0.930  0.020  1.080
 B5A  NAA  H16  single    0.860  0.020  1.020
 B5A  NAA  H17  single    0.860  0.020  1.020

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
 B5A  H2   CAF  H1   107.09  3.000
 B5A  H2   CAF  CAP  109.28  3.000
 B5A  H1   CAF  CAP  111.05  3.000
 B5A  H2   CAF  CAD  109.24  3.000
 B5A  H1   CAF  CAD  109.22  3.000
 B5A  CAP  CAF  CAD  110.88  3.000
 B5A  H4   CAD  H3   106.78  3.000
 B5A  H4   CAD  NAL  112.31  3.000
 B5A  H3   CAD  NAL  108.92  3.000
 B5A  H4   CAD  CAF  108.76  3.000
 B5A  H3   CAD  CAF  109.92  3.000
 B5A  NAL  CAD  CAF  110.09  3.000
 B5A  H5   NAL  CAE  109.47  3.000
 B5A  H5   NAL  CAD  109.51  3.000
 B5A  CAE  NAL  CAD  111.42  3.000
 B5A  H8   CAE  H7   106.84  3.000
 B5A  H8   CAE  CAG  108.63  3.000
 B5A  H7   CAE  CAG  110.04  3.000
 B5A  H8   CAE  NAL  112.35  3.000
 B5A  H7   CAE  NAL  108.99  3.000
 B5A  CAG  CAE  NAL  109.92  3.000
 B5A  H10  CAG  H9   107.15  3.000
 B5A  H10  CAG  CAP  110.39  3.000
 B5A  H9   CAG  CAP  109.42  3.000
 B5A  H10  CAG  CAE  109.65  3.000
 B5A  H9   CAG  CAE  109.28  3.000
 B5A  CAP  CAG  CAE  110.88  3.000
 B5A  H11  CAP  CAH  108.02  3.000
 B5A  H11  CAP  CAG  107.97  3.000
 B5A  CAH  CAP  CAG  109.70  3.000
 B5A  H11  CAP  CAF  108.57  3.000
 B5A  CAH  CAP  CAF  112.70  3.000
 B5A  CAG  CAP  CAF  109.75  3.000
 B5A  H13  CAH  H12  107.55  3.000
 B5A  H13  CAH  NAQ  107.88  3.000
 B5A  H12  CAH  NAQ  107.07  3.000
 B5A  H13  CAH  CAP  110.08  3.000
 B5A  H12  CAH  CAP  110.63  3.000
 B5A  NAQ  CAH  CAP  113.41  3.000
 B5A  C4   NAQ  NAK  111.25  3.000
 B5A  C4   NAQ  CAH  127.11  3.000
 B5A  NAK  NAQ  CAH  121.51  3.000
 B5A  CAC  NAK  NAQ  107.26  3.000
 B5A  H14  CAC  C5   129.37  3.000
 B5A  H14  CAC  NAK  120.34  3.000
 B5A  C5   CAC  NAK  110.30  3.000
 B5A  C6   C5   C4   115.86  3.000
 B5A  C6   C5   CAC  139.66  3.000
 B5A  C4   C5   CAC  104.48  3.000
 B5A  N3   C4   C5   126.03  3.000
 B5A  C5   C4   NAQ  106.72  3.000
 B5A  N3   C4   NAQ  127.25  3.000
 B5A  C2   N3   C4   112.00  3.000
 B5A  H15  C2   N1   115.12  3.000
 B5A  H15  C2   N3   116.12  3.000
 B5A  N1   C2   N3   128.76  3.000
 B5A  C6   N1   C2   118.79  3.000
 B5A  NAA  C6   N1   118.62  3.000
 B5A  NAA  C6   C5   122.82  3.000
 B5A  N1   C6   C5   118.56  3.000
 B5A  H17  NAA  H16  117.94  3.000
 B5A  H17  NAA  C6   120.05  3.000
 B5A  H16  NAA  C6   121.96  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
 B5A  CONST_01  C5   CAC  NAK  NAQ    0.00   0.0  0
 B5A  CONST_02  C2   N3   C4   NAQ  180.00   0.0  0
 B5A  CONST_03  CAC  C5   C4   NAQ    0.00   0.0  0
 B5A  CONST_04  C6   C5   C4   NAQ  180.00   0.0  0
 B5A  CONST_05  N3   C4   NAQ  NAK  180.00   0.0  0
 B5A  CONST_06  C5   C4   NAQ  NAK    0.00   0.0  0
 B5A  CONST_07  C4   C5   CAC  NAK    0.00   0.0  0
 B5A  CONST_08  C6   C5   CAC  NAK  180.00   0.0  0
 B5A  CONST_09  C4   NAQ  NAK  CAC    0.00   0.0  0
 B5A  CONST_10  N3   C4   C5   CAC  180.00   0.0  0
 B5A  CONST_11  N1   C6   C5   CAC  180.00   0.0  0
 B5A  CONST_12  C2   N3   C4   C5     0.00   0.0  0
 B5A  CONST_13  C2   N1   C6   C5     0.00   0.0  0
 B5A  CONST_14  N1   C2   N3   C4     0.00   0.0  0
 B5A  CONST_15  N1   C6   C5   C4     0.00   0.0  0
 B5A  CONST_16  C6   C5   C4   N3     0.00   0.0  0
 B5A  CONST_17  C6   N1   C2   N3     0.00   0.0  0
 B5A  CONST_18  CAC  NAK  NAQ  CAH  180.00   0.0  0
 B5A  CONST_19  N3   C4   NAQ  CAH    0.00   0.0  0
 B5A  CONST_20  C5   C4   NAQ  CAH  180.00   0.0  0
 B5A  CONST_21  NAA  C6   C5   CAC    0.00   0.0  0
 B5A  CONST_22  NAA  C6   C5   C4   180.00   0.0  0
 B5A  CONST_23  NAA  C6   N1   C2   180.00   0.0  0
 B5A  CONST_24  H14  CAC  NAK  NAQ  180.00   0.0  0
 B5A  CONST_25  H15  C2   N3   C4   180.00   0.0  0
 B5A  CONST_26  H16  NAA  C6   C5     0.00   0.0  0
 B5A  CONST_27  H17  NAA  C6   C5   180.00   0.0  0
 B5A  Var_01    CAE  NAL  CAD  CAF  -61.79  30.0  1
 B5A  Var_02    CAG  CAE  NAL  CAD   61.94  30.0  1
 B5A  Var_03    CAP  CAG  CAE  NAL  -57.31  30.0  1
 B5A  Var_04    CAP  CAF  CAD  NAL   56.93  30.0  1
 B5A  Var_05    NAK  NAQ  CAH  CAP   95.46  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
 B5A  chir_01  CAP  CAG  CAF  CAH  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
 B5A  plan-1  CAH  0.020
 B5A  plan-1  NAQ  0.020
 B5A  plan-1  NAK  0.020
 B5A  plan-1  CAC  0.020
 B5A  plan-1  C5   0.020
 B5A  plan-1  C4   0.020
 B5A  plan-1  N3   0.020
 B5A  plan-1  C2   0.020
 B5A  plan-1  N1   0.020
 B5A  plan-1  C6   0.020
 B5A  plan-1  NAA  0.020
 B5A  plan-1  H14  0.020
 B5A  plan-1  H15  0.020
 B5A  plan-2  C6   0.020
 B5A  plan-2  NAA  0.020
 B5A  plan-2  H16  0.020
 B5A  plan-2  H17  0.020

