# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 07:55:43 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 3-(3-chlorophenoxy)-1-[(piperidin-4-yl)methyl]-1H-pyrazolo[3,4-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(CC3CCNCC3)nc(Oc4cccc(Cl)c4)c12
#
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
 9XJ  9XJ  3-(3-chlorophenoxy)-1-[(piperidin-4-yl)methyl]-1H-pyrazolo[3,4-d]pyrimidin-4-amine  ligand  44  25  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9XJ
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
 9XJ  CAH  C   CH2   0  -0.419   4.2356  -2.1322   1.0876
 9XJ  CAI  C   CH2   0  -0.292   5.0290  -2.9576   0.0866
 9XJ  NAJ  N   NH1   0  -0.595   4.1242  -3.7450  -0.7318
 9XJ  CAK  C   CH2   0  -0.292   3.2219  -2.9019  -1.4959
 9XJ  CAL  C   CH2   0  -0.410   2.3538  -2.0725  -0.5588
 9XJ  CAG  C   CH1   0  -0.268   3.2243  -1.2356   0.3757
 9XJ  CAF  C   CH2   0  -0.284   2.4196  -0.4592   1.4136
 9XJ  NAE  N   NR5   0  -0.393   1.4713   0.4696   0.8431
 9XJ  NAM  N   N     0  -0.281   0.1652   0.1354   0.7017
 9XJ  C6   C   CR56  0   0.607   1.7248   1.6761   0.3148
 9XJ  N1   N   N     0  -0.468   2.8998   2.3128   0.2728
 9XJ  C2   C   CR16  0   0.058   2.8062   3.4897  -0.3133
 9XJ  N3   N   N     0  -0.484   1.7335   4.0806  -0.8387
 9XJ  C4   C   CR6   0   0.484   0.5604   3.4415  -0.7940
 9XJ  NAA  N   NH2   0  -0.814  -0.5094   4.0359  -1.3159
 9XJ  C5   C   CR56  0  -0.301   0.5181   2.1660  -0.1937
 9XJ  CAN  C   CR5   0   0.479  -0.4025   1.1332   0.0921
 9XJ  OAO  O   O2    0  -0.521  -1.7097   1.1829  -0.2109
 9XJ  CAP  C   CR6   0   0.344  -2.4633   0.0474  -0.0156
 9XJ  CAV  C   CR16  0  -0.270  -3.3911   0.0551   1.0114
 9XJ  CAT  C   CR6   0  -0.036  -4.2006  -1.0596   1.1732
 9XJ  CL   CL  CL    0  -0.120  -5.3740  -1.0632   2.4473
 9XJ  CAS  C   CR16  0  -0.216  -4.0889  -2.1648   0.3458
 9XJ  CAR  C   CR16  0  -0.263  -3.1447  -2.1429  -0.6723
 9XJ  CAQ  C   CR16  0  -0.283  -2.3258  -1.0411  -0.8628
 9XJ  H1   H   HCH2  0   0.216   3.7098  -2.8060   1.7734
 9XJ  H2   H   HCH2  0   0.232   4.9197  -1.5295   1.6907
 9XJ  H3   H   HCH2  0   0.186   5.6562  -2.2766  -0.5127
 9XJ  H4   H   HCH2  0   0.231   5.7079  -3.6319   0.6128
 9XJ  H5   H   HNH1  0   0.350   4.6616  -4.3224  -1.3651
 9XJ  H7   H   HCH2  0   0.185   3.7586  -2.2172  -2.1745
 9XJ  H8   H   HCH2  0   0.231   2.5912  -3.5355  -2.1225
 9XJ  H9   H   HCH2  0   0.232   1.6952  -1.4337  -1.1511
 9XJ  H10  H   HCH2  0   0.213   1.7131  -2.7381   0.0296
 9XJ  H11  H   HCH1  0   0.229   3.7829  -0.5118  -0.2323
 9XJ  H12  H   HCH2  0   0.262   1.8542  -1.1424   2.0483
 9XJ  H13  H   HCH2  0   0.264   3.0965   0.1029   2.0598
 9XJ  H14  H   HCR6  0   0.255   3.7259   4.0617  -0.3822
 9XJ  H15  H   HNH2  0   0.411  -1.4145   3.5999  -1.3164
 9XJ  H16  H   HNH2  0   0.407  -0.4196   4.9397  -1.7487
 9XJ  H17  H   HCR6  0   0.293  -3.4838   0.9146   1.6620
 9XJ  H18  H   HCR6  0   0.284  -4.7268  -3.0261   0.4871
 9XJ  H19  H   HCR6  0   0.278  -3.0503  -2.9984  -1.3270
 9XJ  H20  H   HCR6  0   0.279  -1.5974  -1.0294  -1.6626

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
 9XJ  CAI  NAJ  single    1.452  0.020  1.452
 9XJ  CAI  CAH  single    1.521  0.020  1.521
 9XJ  NAJ  CAK  single    1.452  0.020  1.452
 9XJ  CAK  CAL  single    1.523  0.020  1.523
 9XJ  CAH  CAG  single    1.528  0.020  1.528
 9XJ  CAG  CAL  single    1.527  0.020  1.527
 9XJ  CAG  CAF  single    1.526  0.020  1.526
 9XJ  OAO  CAN  single    1.343  0.020  1.343
 9XJ  OAO  CAP  single    1.377  0.020  1.377
 9XJ  NAA  C4   single    1.330  0.020  1.330
 9XJ  CAN  C5   aromatic  1.413  0.020  1.413
 9XJ  CAN  NAM  aromatic  1.300  0.020  1.300
 9XJ  C4   C5   aromatic  1.410  0.020  1.410
 9XJ  C4   N3   aromatic  1.337  0.020  1.337
 9XJ  C5   C6   aromatic  1.398  0.020  1.398
 9XJ  N3   C2   aromatic  1.333  0.020  1.333
 9XJ  NAM  NAE  aromatic  1.356  0.020  1.356
 9XJ  C6   NAE  aromatic  1.341  0.020  1.341
 9XJ  C6   N1   aromatic  1.337  0.020  1.337
 9XJ  NAE  CAF  single    1.445  0.020  1.445
 9XJ  C2   N1   aromatic  1.318  0.020  1.318
 9XJ  CAV  CAP  aromatic  1.384  0.020  1.384
 9XJ  CAV  CAT  aromatic  1.387  0.020  1.387
 9XJ  CAP  CAQ  aromatic  1.386  0.020  1.386
 9XJ  CL   CAT  single    1.732  0.020  1.732
 9XJ  CAT  CAS  aromatic  1.385  0.020  1.385
 9XJ  CAQ  CAR  aromatic  1.386  0.020  1.386
 9XJ  CAS  CAR  aromatic  1.389  0.020  1.389
 9XJ  CAH  H1   single    0.970  0.020  1.090
 9XJ  CAH  H2   single    0.970  0.020  1.090
 9XJ  CAI  H3   single    0.970  0.020  1.090
 9XJ  CAI  H4   single    0.970  0.020  1.090
 9XJ  NAJ  H5   single    0.890  0.020  1.040
 9XJ  CAK  H7   single    0.970  0.020  1.090
 9XJ  CAK  H8   single    0.970  0.020  1.090
 9XJ  CAL  H9   single    0.970  0.020  1.090
 9XJ  CAL  H10  single    0.970  0.020  1.090
 9XJ  CAG  H11  single    0.970  0.020  1.090
 9XJ  CAF  H12  single    0.970  0.020  1.090
 9XJ  CAF  H13  single    0.970  0.020  1.090
 9XJ  C2   H14  single    0.930  0.020  1.080
 9XJ  NAA  H15  single    0.860  0.020  1.020
 9XJ  NAA  H16  single    0.860  0.020  1.020
 9XJ  CAV  H17  single    0.930  0.020  1.080
 9XJ  CAS  H18  single    0.930  0.020  1.080
 9XJ  CAR  H19  single    0.930  0.020  1.080
 9XJ  CAQ  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
 9XJ  H2   CAH  H1   107.10  3.000
 9XJ  H2   CAH  CAG  110.35  3.000
 9XJ  H1   CAH  CAG  109.56  3.000
 9XJ  H2   CAH  CAI  109.63  3.000
 9XJ  H1   CAH  CAI  109.18  3.000
 9XJ  CAG  CAH  CAI  110.93  3.000
 9XJ  H4   CAI  H3   106.83  3.000
 9XJ  H4   CAI  NAJ  108.91  3.000
 9XJ  H3   CAI  NAJ  112.52  3.000
 9XJ  H4   CAI  CAH  110.01  3.000
 9XJ  H3   CAI  CAH  108.62  3.000
 9XJ  NAJ  CAI  CAH  109.89  3.000
 9XJ  H5   NAJ  CAK  109.40  3.000
 9XJ  H5   NAJ  CAI  109.35  3.000
 9XJ  CAK  NAJ  CAI  111.65  3.000
 9XJ  H8   CAK  H7   106.75  3.000
 9XJ  H8   CAK  CAL  109.87  3.000
 9XJ  H7   CAK  CAL  108.53  3.000
 9XJ  H8   CAK  NAJ  108.90  3.000
 9XJ  H7   CAK  NAJ  112.44  3.000
 9XJ  CAL  CAK  NAJ  110.28  3.000
 9XJ  H10  CAL  H9   107.10  3.000
 9XJ  H10  CAL  CAG  109.74  3.000
 9XJ  H9   CAL  CAG  110.81  3.000
 9XJ  H10  CAL  CAK  109.45  3.000
 9XJ  H9   CAL  CAK  109.18  3.000
 9XJ  CAG  CAL  CAK  110.49  3.000
 9XJ  H11  CAG  CAF  108.03  3.000
 9XJ  H11  CAG  CAL  108.20  3.000
 9XJ  CAF  CAG  CAL  113.24  3.000
 9XJ  H11  CAG  CAH  107.95  3.000
 9XJ  CAF  CAG  CAH  109.32  3.000
 9XJ  CAL  CAG  CAH  109.94  3.000
 9XJ  H13  CAF  H12  107.43  3.000
 9XJ  H13  CAF  NAE  108.04  3.000
 9XJ  H12  CAF  NAE  106.99  3.000
 9XJ  H13  CAF  CAG  109.74  3.000
 9XJ  H12  CAF  CAG  110.53  3.000
 9XJ  NAE  CAF  CAG  113.88  3.000
 9XJ  C6   NAE  NAM  111.27  3.000
 9XJ  C6   NAE  CAF  127.57  3.000
 9XJ  NAM  NAE  CAF  121.00  3.000
 9XJ  CAN  NAM  NAE  106.29  3.000
 9XJ  C5   C6   N1   125.47  3.000
 9XJ  N1   C6   NAE  127.36  3.000
 9XJ  C5   C6   NAE  107.18  3.000
 9XJ  C2   N1   C6   112.13  3.000
 9XJ  H14  C2   N3   115.05  3.000
 9XJ  H14  C2   N1   116.02  3.000
 9XJ  N3   C2   N1   128.93  3.000
 9XJ  C4   N3   C2   118.77  3.000
 9XJ  C5   C4   NAA  123.16  3.000
 9XJ  C5   C4   N3   118.22  3.000
 9XJ  NAA  C4   N3   118.62  3.000
 9XJ  H16  NAA  H15  118.04  3.000
 9XJ  H16  NAA  C4   119.89  3.000
 9XJ  H15  NAA  C4   122.05  3.000
 9XJ  CAN  C5   C4   140.06  3.000
 9XJ  C4   C5   C6   116.48  3.000
 9XJ  CAN  C5   C6   103.46  3.000
 9XJ  OAO  CAN  C5   124.17  3.000
 9XJ  C5   CAN  NAM  111.80  3.000
 9XJ  OAO  CAN  NAM  124.02  3.000
 9XJ  CAP  OAO  CAN  118.05  3.000
 9XJ  CAQ  CAP  CAV  121.63  3.000
 9XJ  CAQ  CAP  OAO  120.44  3.000
 9XJ  CAV  CAP  OAO  117.88  3.000
 9XJ  H17  CAV  CAT  121.22  3.000
 9XJ  H17  CAV  CAP  120.53  3.000
 9XJ  CAT  CAV  CAP  118.25  3.000
 9XJ  CAS  CAT  CL   119.50  3.000
 9XJ  CAS  CAT  CAV  121.63  3.000
 9XJ  CL   CAT  CAV  118.87  3.000
 9XJ  H18  CAS  CAR  120.64  3.000
 9XJ  H18  CAS  CAT  120.67  3.000
 9XJ  CAR  CAS  CAT  118.70  3.000
 9XJ  H19  CAR  CAQ  119.61  3.000
 9XJ  H19  CAR  CAS  119.39  3.000
 9XJ  CAQ  CAR  CAS  121.00  3.000
 9XJ  H20  CAQ  CAR  120.53  3.000
 9XJ  H20  CAQ  CAP  120.67  3.000
 9XJ  CAR  CAQ  CAP  118.79  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
 9XJ  CONST_01  C5   CAN  NAM  NAE    0.00   0.0  0
 9XJ  CONST_02  CAN  C5   C6   NAE    0.00   0.0  0
 9XJ  CONST_03  C4   C5   C6   NAE  180.00   0.0  0
 9XJ  CONST_04  C2   N1   C6   NAE  180.00   0.0  0
 9XJ  CONST_05  C4   C5   CAN  NAM  180.00   0.0  0
 9XJ  CONST_06  C6   C5   CAN  NAM    0.00   0.0  0
 9XJ  CONST_07  C5   C6   NAE  NAM    0.00   0.0  0
 9XJ  CONST_08  N1   C6   NAE  NAM  180.00   0.0  0
 9XJ  CONST_09  N3   C4   C5   C6     0.00   0.0  0
 9XJ  CONST_10  CAN  NAM  NAE  C6     0.00   0.0  0
 9XJ  CONST_11  N3   C2   N1   C6     0.00   0.0  0
 9XJ  CONST_12  CAN  C5   C6   N1   180.00   0.0  0
 9XJ  CONST_13  C4   C5   C6   N1     0.00   0.0  0
 9XJ  CONST_14  C4   N3   C2   N1     0.00   0.0  0
 9XJ  CONST_15  C5   C4   N3   C2     0.00   0.0  0
 9XJ  CONST_16  C5   C6   N1   C2     0.00   0.0  0
 9XJ  CONST_17  CAN  C5   C4   N3   180.00   0.0  0
 9XJ  CONST_18  CAS  CAT  CAV  CAP    0.00   0.0  0
 9XJ  CONST_19  CAS  CAR  CAQ  CAP    0.00   0.0  0
 9XJ  CONST_20  CAR  CAQ  CAP  CAV    0.00   0.0  0
 9XJ  CONST_21  CAR  CAS  CAT  CAV    0.00   0.0  0
 9XJ  CONST_22  CAQ  CAP  CAV  CAT    0.00   0.0  0
 9XJ  CONST_23  CAQ  CAR  CAS  CAT    0.00   0.0  0
 9XJ  CONST_24  CAN  NAM  NAE  CAF  180.00   0.0  0
 9XJ  CONST_25  C5   C6   NAE  CAF  180.00   0.0  0
 9XJ  CONST_26  N1   C6   NAE  CAF    0.00   0.0  0
 9XJ  CONST_27  OAO  CAN  NAM  NAE  180.00   0.0  0
 9XJ  CONST_28  OAO  CAN  C5   C6   180.00   0.0  0
 9XJ  CONST_29  NAA  C4   C5   C6   180.00   0.0  0
 9XJ  CONST_30  NAA  C4   N3   C2   180.00   0.0  0
 9XJ  CONST_31  OAO  CAN  C5   C4     0.00   0.0  0
 9XJ  CONST_32  CAN  C5   C4   NAA    0.00   0.0  0
 9XJ  CONST_33  CAT  CAV  CAP  OAO  180.00   0.0  0
 9XJ  CONST_34  CAR  CAQ  CAP  OAO  180.00   0.0  0
 9XJ  CONST_35  CL   CAT  CAV  CAP  180.00   0.0  0
 9XJ  CONST_36  CAR  CAS  CAT  CL   180.00   0.0  0
 9XJ  CONST_37  H14  C2   N1   C6   180.00   0.0  0
 9XJ  CONST_38  H19  CAR  CAQ  CAP  180.00   0.0  0
 9XJ  CONST_39  H20  CAQ  CAP  CAV  180.00   0.0  0
 9XJ  CONST_40  H18  CAS  CAT  CAV  180.00   0.0  0
 9XJ  CONST_41  H17  CAV  CAT  CAS  180.00   0.0  0
 9XJ  CONST_42  H15  NAA  C4   N3   180.00   0.0  0
 9XJ  CONST_43  H16  NAA  C4   N3     0.00   0.0  0
 9XJ  Var_01    CAK  NAJ  CAI  CAH   61.40  30.0  1
 9XJ  Var_02    CAL  CAK  NAJ  CAI  -61.59  30.0  1
 9XJ  Var_03    CAG  CAH  CAI  NAJ  -57.00  30.0  1
 9XJ  Var_04    CAG  CAL  CAK  NAJ   56.93  30.0  1
 9XJ  Var_05    NAM  NAE  CAF  CAG   97.57  30.0  2
 9XJ  Var_06    CAV  CAP  OAO  CAN  109.89  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
 9XJ  chir_01  CAG  CAH  CAL  CAF  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
 9XJ  plan-1  OAO  0.020
 9XJ  plan-1  CAP  0.020
 9XJ  plan-1  CAV  0.020
 9XJ  plan-1  CAT  0.020
 9XJ  plan-1  CL   0.020
 9XJ  plan-1  CAS  0.020
 9XJ  plan-1  CAR  0.020
 9XJ  plan-1  CAQ  0.020
 9XJ  plan-1  H17  0.020
 9XJ  plan-1  H18  0.020
 9XJ  plan-1  H19  0.020
 9XJ  plan-1  H20  0.020
 9XJ  plan-2  CAF  0.020
 9XJ  plan-2  NAE  0.020
 9XJ  plan-2  NAM  0.020
 9XJ  plan-2  C6   0.020
 9XJ  plan-2  N1   0.020
 9XJ  plan-2  C2   0.020
 9XJ  plan-2  N3   0.020
 9XJ  plan-2  C4   0.020
 9XJ  plan-2  NAA  0.020
 9XJ  plan-2  C5   0.020
 9XJ  plan-2  CAN  0.020
 9XJ  plan-2  OAO  0.020
 9XJ  plan-2  H14  0.020
 9XJ  plan-3  C4   0.020
 9XJ  plan-3  NAA  0.020
 9XJ  plan-3  H15  0.020
 9XJ  plan-3  H16  0.020

