# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 12:29:06 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 2-{4-[(3S)-piperidin-3-yl]phenyl}-2H-indazole-7-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cccc2cn(nc12)c3ccc(cc3)[C@@H]4CCCNC4
#
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
 3JD  3JD  2-{4-[(3S)-piperidin-3-yl]phenyl}-2H-indazole-7-carboxamide  ligand  44  24  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3JD
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
 3JD  CAM  C  CH2   0  -0.418  -4.9143  -0.7957   1.1827
 3JD  CAK  C  CH2   0  -0.446  -6.4329  -0.9361   1.1894
 3JD  CAL  C  CH2   0  -0.314  -6.9576  -1.1303  -0.2299
 3JD  NAP  N  NH1   0  -0.578  -6.5296  -0.0931  -1.1560
 3JD  CAN  C  CH2   0  -0.283  -5.0888   0.0740  -1.1673
 3JD  CAW  C  CH1   0  -0.361  -4.4722   0.3146   0.2222
 3JD  CAR  C  CR6   0   0.198  -2.9761   0.4426   0.1417
 3JD  CAF  C  CR16  0  -0.312  -2.1786  -0.6245  -0.2746
 3JD  CAH  C  CR16  0  -0.270  -0.8022  -0.5073  -0.3652
 3JD  CAE  C  CR16  0  -0.335  -2.3413   1.6365   0.4715
 3JD  CAG  C  CR16  0  -0.286  -0.9628   1.7696   0.3993
 3JD  CAS  C  CR6   0   0.347  -0.1952   0.6963  -0.0286
 3JD  NAX  N  NR5   0  -0.382   1.2101   0.8229  -0.1241
 3JD  CAJ  C  CR15  0   0.004   1.8895   1.9472  -0.4001
 3JD  NAO  N  N     0  -0.310   1.9768  -0.2511   0.0561
 3JD  CAV  C  CR56  0   0.272   3.2200   0.1945  -0.1086
 3JD  CAU  C  CR56  0  -0.139   3.2299   1.5904  -0.3966
 3JD  CAI  C  CR16  0  -0.316   4.4394   2.2856  -0.6033
 3JD  CAC  C  CR16  0  -0.269   5.6048   1.5808  -0.4997
 3JD  CAD  C  CR16  0  -0.294   5.6019   0.1953  -0.1901
 3JD  CAT  C  CR6   0  -0.085   4.4458  -0.5167   0.0084
 3JD  CAQ  C  C     0   0.479   4.4562  -1.9842   0.2751
 3JD  OAB  O  O     0  -0.475   3.6066  -2.7251  -0.1966
 3JD  NAA  N  NH2   0  -0.803   5.4681  -2.4216   1.0429
 3JD  H1   H  HCH2  0   0.238  -4.5411  -0.5874   2.1884
 3JD  H2   H  HCH2  0   0.219  -4.4654  -1.7464   0.8733
 3JD  H3   H  HCH2  0   0.229  -6.7331  -1.7771   1.8194
 3JD  H4   H  HCH2  0   0.215  -6.8867  -0.0389   1.6244
 3JD  H5   H  HCH2  0   0.214  -6.6057  -2.0942  -0.6154
 3JD  H6   H  HCH2  0   0.235  -8.0489  -1.1722  -0.2353
 3JD  H7   H  HNH1  0   0.339  -6.9648   0.7843  -0.8939
 3JD  H9   H  HCH2  0   0.215  -4.6447  -0.8278  -1.6052
 3JD  H10  H  HCH2  0   0.240  -4.8370   0.9018  -1.8343
 3JD  H11  H  HCH1  0   0.239  -4.8711   1.2643   0.5994
 3JD  H12  H  HCR6  0   0.257  -2.6328  -1.5709  -0.5414
 3JD  H13  H  HCR6  0   0.277  -0.2052  -1.3445  -0.6990
 3JD  H14  H  HCR6  0   0.258  -2.9295   2.4806   0.8099
 3JD  H15  H  HCR6  0   0.280  -0.5001   2.7014   0.6969
 3JD  H16  H  HCR5  0   0.311   1.4012   2.8861  -0.6015
 3JD  H17  H  HCR6  0   0.263   4.4419   3.3429  -0.8340
 3JD  H18  H  HCR6  0   0.263   6.5542   2.0747  -0.6561
 3JD  H19  H  HCR6  0   0.267   6.5583  -0.3096  -0.1347
 3JD  H20  H  HNH2  0   0.410   6.0622  -1.7898   1.5510
 3JD  H21  H  HNH2  0   0.403   5.5351  -3.4001   1.2720

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
 3JD  CAC  CAI  aromatic  1.366  0.020  1.366
 3JD  CAC  CAD  aromatic  1.420  0.020  1.420
 3JD  CAI  CAU  aromatic  1.410  0.020  1.410
 3JD  CAD  CAT  aromatic  1.372  0.020  1.372
 3JD  CAU  CAJ  aromatic  1.387  0.020  1.387
 3JD  CAU  CAV  aromatic  1.425  0.020  1.425
 3JD  CAJ  NAX  aromatic  1.342  0.020  1.342
 3JD  CAT  CAV  aromatic  1.422  0.020  1.422
 3JD  CAT  CAQ  single    1.492  0.020  1.492
 3JD  CAV  NAO  aromatic  1.331  0.020  1.331
 3JD  OAB  CAQ  double    1.222  0.020  1.222
 3JD  NAX  NAO  aromatic  1.332  0.020  1.332
 3JD  NAX  CAS  single    1.414  0.020  1.414
 3JD  CAQ  NAA  single    1.343  0.020  1.343
 3JD  CAH  CAS  aromatic  1.389  0.020  1.389
 3JD  CAH  CAF  aromatic  1.384  0.020  1.384
 3JD  CAS  CAG  aromatic  1.387  0.020  1.387
 3JD  CAF  CAR  aromatic  1.396  0.020  1.396
 3JD  CAG  CAE  aromatic  1.387  0.020  1.387
 3JD  CAR  CAE  aromatic  1.392  0.020  1.392
 3JD  CAR  CAW  single    1.504  0.020  1.504
 3JD  CAW  CAM  single    1.533  0.020  1.533
 3JD  CAW  CAN  single    1.539  0.020  1.539
 3JD  CAM  CAK  single    1.525  0.020  1.525
 3JD  CAN  NAP  single    1.450  0.020  1.450
 3JD  NAP  CAL  single    1.455  0.020  1.455
 3JD  CAK  CAL  single    1.526  0.020  1.526
 3JD  CAM  H1   single    0.970  0.020  1.090
 3JD  CAM  H2   single    0.970  0.020  1.090
 3JD  CAK  H3   single    0.970  0.020  1.090
 3JD  CAK  H4   single    0.970  0.020  1.090
 3JD  CAL  H5   single    0.970  0.020  1.090
 3JD  CAL  H6   single    0.970  0.020  1.090
 3JD  NAP  H7   single    0.890  0.020  1.040
 3JD  CAN  H9   single    0.970  0.020  1.090
 3JD  CAN  H10  single    0.970  0.020  1.090
 3JD  CAW  H11  single    0.970  0.020  1.090
 3JD  CAF  H12  single    0.930  0.020  1.080
 3JD  CAH  H13  single    0.930  0.020  1.080
 3JD  CAE  H14  single    0.930  0.020  1.080
 3JD  CAG  H15  single    0.930  0.020  1.080
 3JD  CAJ  H16  single    0.930  0.020  1.080
 3JD  CAI  H17  single    0.930  0.020  1.080
 3JD  CAC  H18  single    0.930  0.020  1.080
 3JD  CAD  H19  single    0.930  0.020  1.080
 3JD  NAA  H20  single    0.860  0.020  1.020
 3JD  NAA  H21  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
 3JD  H2   CAM  H1   106.58  3.000
 3JD  H2   CAM  CAW  109.46  3.000
 3JD  H1   CAM  CAW  109.88  3.000
 3JD  H2   CAM  CAK  109.22  3.000
 3JD  H1   CAM  CAK  110.71  3.000
 3JD  CAW  CAM  CAK  110.89  3.000
 3JD  H4   CAK  H3   106.71  3.000
 3JD  H4   CAK  CAL  109.34  3.000
 3JD  H3   CAK  CAL  110.11  3.000
 3JD  H4   CAK  CAM  109.80  3.000
 3JD  H3   CAK  CAM  110.30  3.000
 3JD  CAL  CAK  CAM  110.50  3.000
 3JD  H6   CAL  H5   106.58  3.000
 3JD  H6   CAL  NAP  108.56  3.000
 3JD  H5   CAL  NAP  107.97  3.000
 3JD  H6   CAL  CAK  110.68  3.000
 3JD  H5   CAL  CAK  109.19  3.000
 3JD  NAP  CAL  CAK  113.60  3.000
 3JD  H7   NAP  CAN  109.19  3.000
 3JD  H7   NAP  CAL  109.03  3.000
 3JD  CAN  NAP  CAL  112.29  3.000
 3JD  H10  CAN  H9   106.62  3.000
 3JD  H10  CAN  CAW  109.90  3.000
 3JD  H9   CAN  CAW  109.08  3.000
 3JD  H10  CAN  NAP  108.72  3.000
 3JD  H9   CAN  NAP  108.10  3.000
 3JD  CAW  CAN  NAP  114.14  3.000
 3JD  H11  CAW  CAR  107.85  3.000
 3JD  H11  CAW  CAN  107.47  3.000
 3JD  CAR  CAW  CAN  111.32  3.000
 3JD  H11  CAW  CAM  107.86  3.000
 3JD  CAN  CAW  CAM  109.69  3.000
 3JD  CAR  CAW  CAM  112.46  3.000
 3JD  CAE  CAR  CAF  117.76  3.000
 3JD  CAE  CAR  CAW  120.94  3.000
 3JD  CAF  CAR  CAW  121.29  3.000
 3JD  H12  CAF  CAH  118.35  3.000
 3JD  H12  CAF  CAR  120.12  3.000
 3JD  CAH  CAF  CAR  121.53  3.000
 3JD  H13  CAH  CAS  120.29  3.000
 3JD  H13  CAH  CAF  120.24  3.000
 3JD  CAS  CAH  CAF  119.46  3.000
 3JD  H14  CAE  CAG  118.77  3.000
 3JD  H14  CAE  CAR  119.66  3.000
 3JD  CAG  CAE  CAR  121.56  3.000
 3JD  H15  CAG  CAS  120.96  3.000
 3JD  H15  CAG  CAE  119.57  3.000
 3JD  CAS  CAG  CAE  119.46  3.000
 3JD  NAX  CAS  CAG  120.09  3.000
 3JD  CAG  CAS  CAH  120.21  3.000
 3JD  NAX  CAS  CAH  119.69  3.000
 3JD  NAO  NAX  CAJ  114.33  3.000
 3JD  NAO  NAX  CAS  119.38  3.000
 3JD  CAJ  NAX  CAS  126.29  3.000
 3JD  H16  CAJ  CAU  131.50  3.000
 3JD  H16  CAJ  NAX  122.62  3.000
 3JD  CAU  CAJ  NAX  105.85  3.000
 3JD  CAV  NAO  NAX  104.54  3.000
 3JD  CAT  CAV  CAU  120.03  3.000
 3JD  CAT  CAV  NAO  128.88  3.000
 3JD  CAU  CAV  NAO  111.06  3.000
 3JD  CAI  CAU  CAV  121.22  3.000
 3JD  CAV  CAU  CAJ  104.23  3.000
 3JD  CAI  CAU  CAJ  134.55  3.000
 3JD  H17  CAI  CAC  121.22  3.000
 3JD  H17  CAI  CAU  120.99  3.000
 3JD  CAC  CAI  CAU  117.79  3.000
 3JD  H18  CAC  CAD  118.62  3.000
 3JD  H18  CAC  CAI  120.16  3.000
 3JD  CAD  CAC  CAI  121.22  3.000
 3JD  H19  CAD  CAT  119.65  3.000
 3JD  H19  CAD  CAC  117.67  3.000
 3JD  CAT  CAD  CAC  122.66  3.000
 3JD  CAQ  CAT  CAD  122.04  3.000
 3JD  CAQ  CAT  CAV  120.85  3.000
 3JD  CAD  CAT  CAV  117.06  3.000
 3JD  NAA  CAQ  OAB  123.15  3.000
 3JD  NAA  CAQ  CAT  115.33  3.000
 3JD  OAB  CAQ  CAT  121.51  3.000
 3JD  H21  NAA  H20  117.15  3.000
 3JD  H21  NAA  CAQ  119.77  3.000
 3JD  H20  NAA  CAQ  121.97  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
 3JD  CONST_01  CAS  CAH  CAF  CAR    0.00   0.0  0
 3JD  CONST_02  CAS  CAG  CAE  CAR    0.00   0.0  0
 3JD  CONST_03  NAX  CAS  CAH  CAF  180.00   0.0  0
 3JD  CONST_04  CAG  CAS  CAH  CAF    0.00   0.0  0
 3JD  CONST_05  CAG  CAE  CAR  CAF    0.00   0.0  0
 3JD  CONST_08  CAE  CAG  CAS  CAH    0.00   0.0  0
 3JD  CONST_09  CAE  CAR  CAF  CAH    0.00   0.0  0
 3JD  CONST_10  NAX  CAS  CAG  CAE  180.00   0.0  0
 3JD  CONST_13  CAU  CAJ  NAX  CAS  180.00   0.0  0
 3JD  CONST_14  CAV  NAO  NAX  CAS  180.00   0.0  0
 3JD  CONST_15  CAI  CAU  CAJ  NAX  180.00   0.0  0
 3JD  CONST_16  CAV  CAU  CAJ  NAX    0.00   0.0  0
 3JD  CONST_17  CAU  CAV  NAO  NAX    0.00   0.0  0
 3JD  CONST_18  CAT  CAV  NAO  NAX  180.00   0.0  0
 3JD  CONST_19  CAC  CAI  CAU  CAJ  180.00   0.0  0
 3JD  CONST_20  CAT  CAV  CAU  CAJ  180.00   0.0  0
 3JD  CONST_21  NAO  CAV  CAU  CAJ    0.00   0.0  0
 3JD  CONST_22  CAV  NAO  NAX  CAJ    0.00   0.0  0
 3JD  CONST_23  CAI  CAU  CAV  NAO  180.00   0.0  0
 3JD  CONST_24  CAD  CAT  CAV  NAO  180.00   0.0  0
 3JD  CONST_25  CAU  CAJ  NAX  NAO    0.00   0.0  0
 3JD  CONST_26  CAC  CAI  CAU  CAV    0.00   0.0  0
 3JD  CONST_27  CAC  CAD  CAT  CAV    0.00   0.0  0
 3JD  CONST_28  CAD  CAC  CAI  CAU    0.00   0.0  0
 3JD  CONST_29  CAD  CAT  CAV  CAU    0.00   0.0  0
 3JD  CONST_30  CAT  CAD  CAC  CAI    0.00   0.0  0
 3JD  CONST_31  CAT  CAV  CAU  CAI    0.00   0.0  0
 3JD  CONST_32  CAH  CAF  CAR  CAW  180.00   0.0  0
 3JD  CONST_33  CAG  CAE  CAR  CAW  180.00   0.0  0
 3JD  CONST_34  CAQ  CAT  CAV  NAO    0.00   0.0  0
 3JD  CONST_35  CAQ  CAT  CAV  CAU  180.00   0.0  0
 3JD  CONST_36  CAQ  CAT  CAD  CAC  180.00   0.0  0
 3JD  CONST_37  H12  CAF  CAR  CAW    0.00   0.0  0
 3JD  CONST_38  H14  CAE  CAR  CAW    0.00   0.0  0
 3JD  CONST_39  H13  CAH  CAF  CAR  180.00   0.0  0
 3JD  CONST_40  H15  CAG  CAE  CAR  180.00   0.0  0
 3JD  CONST_41  H16  CAJ  NAX  CAS    0.00   0.0  0
 3JD  CONST_42  H17  CAI  CAU  CAJ    0.00   0.0  0
 3JD  CONST_43  H19  CAD  CAT  CAV  180.00   0.0  0
 3JD  CONST_44  H18  CAC  CAI  CAU  180.00   0.0  0
 3JD  CONST_45  H20  NAA  CAQ  CAT    0.00   0.0  0
 3JD  CONST_46  H21  NAA  CAQ  CAT  180.00   0.0  0
 3JD  Var_01    NAP  CAL  CAK  CAM  -54.25  30.0  1
 3JD  Var_02    CAN  NAP  CAL  CAK   53.79  30.0  1
 3JD  Var_03    CAW  CAN  NAP  CAL  -53.65  30.0  1
 3JD  Var_04    CAW  CAM  CAK  CAL   53.84  30.0  1
 3JD  Var_05    OAB  CAQ  CAT  CAV   35.50  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
 3JD  chir_01  CAW  CAR  CAM  CAN  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
 3JD  plan-1  CAW  0.020
 3JD  plan-1  CAR  0.020
 3JD  plan-1  CAF  0.020
 3JD  plan-1  CAH  0.020
 3JD  plan-1  CAE  0.020
 3JD  plan-1  CAG  0.020
 3JD  plan-1  CAS  0.020
 3JD  plan-1  NAX  0.020
 3JD  plan-1  H12  0.020
 3JD  plan-1  H13  0.020
 3JD  plan-1  H14  0.020
 3JD  plan-1  H15  0.020
 3JD  plan-2  CAS  0.020
 3JD  plan-2  NAX  0.020
 3JD  plan-2  CAJ  0.020
 3JD  plan-2  NAO  0.020
 3JD  plan-2  CAV  0.020
 3JD  plan-2  CAU  0.020
 3JD  plan-2  CAI  0.020
 3JD  plan-2  CAC  0.020
 3JD  plan-2  CAD  0.020
 3JD  plan-2  CAT  0.020
 3JD  plan-2  CAQ  0.020
 3JD  plan-2  H16  0.020
 3JD  plan-2  H17  0.020
 3JD  plan-2  H18  0.020
 3JD  plan-2  H19  0.020
 3JD  plan-3  CAT  0.020
 3JD  plan-3  CAQ  0.020
 3JD  plan-3  OAB  0.020
 3JD  plan-3  NAA  0.020
 3JD  plan-3  H20  0.020
 3JD  plan-3  H21  0.020

