# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 03:44:33 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: N-{(3S)-1-[3-(pyridin-4-yl)-1H-pyrazol-5-yl]piperidin-3-yl}-1H-indole-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(N[C@H]1CCCN(C1)c2[nH]nc(c2)c3ccncc3)c4[nH]c5ccccc5c4
#
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
 9WO  9WO  N-{(3S)-1-[3-(pyridin-4-yl)-1H-pyrazol-5-yl]piperidin-3-yl}-1H-indole-2-carboxamide  ligand  51  29  .  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_9WO
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
 9WO  CAK  C  CR15  0  -0.399   5.1304   0.2387   0.0215
 9WO  CAZ  C  CR56  0   0.067   5.2980  -1.1744   0.0658
 9WO  CAH  C  CR16  0  -0.338   6.3915  -2.0335  -0.1147
 9WO  CAB  C  CR16  0  -0.270   6.1986  -3.3910   0.0238
 9WO  CAC  C  CR16  0  -0.277   4.9314  -3.9168   0.3393
 9WO  CAI  C  CR16  0  -0.310   3.8355  -3.0986   0.5177
 9WO  CBA  C  CR56  0   0.347   4.0332  -1.7248   0.3705
 9WO  NAT  N  NR15  0  -0.741   3.1488  -0.6944   0.4795
 9WO  CAX  C  CR5   0   0.220   3.8113   0.4930   0.2814
 9WO  CAU  C  C     0   0.525   3.1682   1.8218   0.3241
 9WO  OAA  O  O     0  -0.486   3.8413   2.8314   0.4840
 9WO  NAR  N  NH1   0  -0.653   1.8308   1.8363   0.1845
 9WO  CBB  C  CH1   0  -0.114   1.0475   3.0583   0.2102
 9WO  CAO  C  CH2   0  -0.335  -0.3628   2.7124   0.6698
 9WO  CAM  C  CH2   0  -0.439   1.0035   3.7445  -1.1542
 9WO  CAL  C  CH2   0  -0.457   0.2631   2.8773  -2.1621
 9WO  CAN  C  CH2   0  -0.301  -1.1076   2.4739  -1.6443
 9WO  NBC  N  NT    0  -0.537  -1.0099   1.8669  -0.3182
 9WO  CAY  C  CR5   0   0.687  -2.0810   1.1021   0.0747
 9WO  CAJ  C  CR15  0  -0.614  -2.9126   0.2753  -0.6626
 9WO  NAS  N  NR15  0  -0.518  -2.5049   0.9956   1.3537
 9WO  NAQ  N  N     0  -0.307  -3.5334   0.1591   1.5041
 9WO  CAW  C  CR5   0   0.295  -3.7916  -0.2819   0.2865
 9WO  CAV  C  CR6   0   0.156  -4.8735  -1.2379   0.0548
 9WO  CAF  C  CR16  0  -0.405  -5.1094  -1.7761  -1.2081
 9WO  CAD  C  CR16  0  -0.059  -6.1458  -2.6803  -1.3760
 9WO  NAP  N  N     0  -0.410  -6.9470  -3.0756  -0.3938
 9WO  CAE  C  CR16  0  -0.062  -6.7219  -2.5612   0.8116
 9WO  CAG  C  CR16  0  -0.360  -5.7145  -1.6534   1.0871
 9WO  H1   H  HCR5  0   0.259   5.8840   0.9787  -0.1963
 9WO  H2   H  HCR6  0   0.252   7.3692  -1.6357  -0.3559
 9WO  H3   H  HCR6  0   0.251   7.0311  -4.0692  -0.1100
 9WO  H4   H  HCR6  0   0.255   4.8149  -4.9879   0.4421
 9WO  H5   H  HCR6  0   0.264   2.8622  -3.5055   0.7604
 9WO  H6   H  HNR5  0   0.411   2.2064  -0.7937   0.8207
 9WO  H7   H  HNH1  0   0.395   1.3537   1.0075  -0.1377
 9WO  H8   H  HCH1  0   0.277   1.4892   3.7277   0.9490
 9WO  H9   H  HCH2  0   0.266  -0.2898   2.1849   1.6217
 9WO  H10  H  HCH2  0   0.253  -0.9226   3.6409   0.8451
 9WO  H11  H  HCH2  0   0.235   0.4906   4.7043  -1.0388
 9WO  H12  H  HCH2  0   0.253   2.0150   3.9676  -1.4970
 9WO  H13  H  HCH2  0   0.252   0.1358   3.4131  -3.1041
 9WO  H14  H  HCH2  0   0.231   0.8443   1.9795  -2.3902
 9WO  H15  H  HCH2  0   0.226  -1.7688   3.3508  -1.6072
 9WO  H16  H  HCH2  0   0.266  -1.5588   1.7590  -2.3297
 9WO  H17  H  HCR5  0   0.273  -2.8779   0.0930  -1.7231
 9WO  H18  H  HNR5  0   0.426  -2.1521   1.4786   2.1642
 9WO  H19  H  HCR6  0   0.261  -4.4982  -1.5072  -2.0593
 9WO  H20  H  HCR6  0   0.264  -6.3325  -3.1057  -2.3560
 9WO  H21  H  HCR6  0   0.263  -7.3814  -2.8881   1.6081
 9WO  H22  H  HCR6  0   0.264  -5.5914  -1.2757   2.0925

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
 9WO  CAD  NAP  aromatic  1.328  0.020  1.328
 9WO  CAD  CAF  aromatic  1.386  0.020  1.386
 9WO  NAP  CAE  aromatic  1.330  0.020  1.330
 9WO  CAF  CAV  aromatic  1.393  0.020  1.393
 9WO  CAE  CAG  aromatic  1.384  0.020  1.384
 9WO  CAV  CAG  aromatic  1.395  0.020  1.395
 9WO  CAV  CAW  single    1.462  0.020  1.462
 9WO  CAW  NAQ  aromatic  1.320  0.020  1.320
 9WO  CAW  CAJ  aromatic  1.409  0.020  1.409
 9WO  NAQ  NAS  aromatic  1.334  0.020  1.334
 9WO  NAS  CAY  aromatic  1.352  0.020  1.352
 9WO  CAJ  CAY  aromatic  1.385  0.020  1.385
 9WO  CAY  NBC  single    1.373  0.020  1.373
 9WO  NBC  CAO  single    1.453  0.020  1.453
 9WO  NBC  CAN  single    1.462  0.020  1.462
 9WO  OAA  CAU  double    1.224  0.020  1.224
 9WO  CAO  CBB  single    1.523  0.020  1.523
 9WO  CAU  CAX  single    1.477  0.020  1.477
 9WO  CAU  NAR  single    1.345  0.020  1.345
 9WO  CAN  CAL  single    1.520  0.020  1.520
 9WO  CBB  NAR  single    1.452  0.020  1.452
 9WO  CBB  CAM  single    1.528  0.020  1.528
 9WO  CAX  NAT  aromatic  1.374  0.020  1.374
 9WO  CAX  CAK  aromatic  1.368  0.020  1.368
 9WO  NAT  CBA  aromatic  1.362  0.020  1.362
 9WO  CAK  CAZ  aromatic  1.424  0.020  1.424
 9WO  CAL  CAM  single    1.522  0.020  1.522
 9WO  CBA  CAZ  aromatic  1.413  0.020  1.413
 9WO  CBA  CAI  aromatic  1.396  0.020  1.396
 9WO  CAZ  CAH  aromatic  1.402  0.020  1.402
 9WO  CAI  CAC  aromatic  1.379  0.020  1.379
 9WO  CAH  CAB  aromatic  1.378  0.020  1.378
 9WO  CAC  CAB  aromatic  1.408  0.020  1.408
 9WO  CAK  H1   single    0.930  0.020  1.080
 9WO  CAH  H2   single    0.930  0.020  1.080
 9WO  CAB  H3   single    0.930  0.020  1.080
 9WO  CAC  H4   single    0.930  0.020  1.080
 9WO  CAI  H5   single    0.930  0.020  1.080
 9WO  NAT  H6   single    0.860  0.020  1.020
 9WO  NAR  H7   single    0.860  0.020  1.020
 9WO  CBB  H8   single    0.970  0.020  1.090
 9WO  CAO  H9   single    0.970  0.020  1.090
 9WO  CAO  H10  single    0.970  0.020  1.090
 9WO  CAM  H11  single    0.970  0.020  1.090
 9WO  CAM  H12  single    0.970  0.020  1.090
 9WO  CAL  H13  single    0.970  0.020  1.090
 9WO  CAL  H14  single    0.970  0.020  1.090
 9WO  CAN  H15  single    0.970  0.020  1.090
 9WO  CAN  H16  single    0.970  0.020  1.090
 9WO  CAJ  H17  single    0.930  0.020  1.080
 9WO  NAS  H18  single    0.860  0.020  1.020
 9WO  CAF  H19  single    0.930  0.020  1.080
 9WO  CAD  H20  single    0.930  0.020  1.080
 9WO  CAE  H21  single    0.930  0.020  1.080
 9WO  CAG  H22  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
 9WO  H1   CAK  CAX  125.77  3.000
 9WO  H1   CAK  CAZ  127.24  3.000
 9WO  CAX  CAK  CAZ  106.98  3.000
 9WO  CBA  CAZ  CAH  119.16  3.000
 9WO  CAH  CAZ  CAK  134.09  3.000
 9WO  CBA  CAZ  CAK  106.74  3.000
 9WO  H2   CAH  CAB  120.71  3.000
 9WO  H2   CAH  CAZ  120.52  3.000
 9WO  CAB  CAH  CAZ  118.77  3.000
 9WO  H3   CAB  CAC  119.09  3.000
 9WO  H3   CAB  CAH  119.81  3.000
 9WO  CAC  CAB  CAH  121.10  3.000
 9WO  H4   CAC  CAI  119.30  3.000
 9WO  H4   CAC  CAB  119.19  3.000
 9WO  CAI  CAC  CAB  121.51  3.000
 9WO  H5   CAI  CBA  121.40  3.000
 9WO  H5   CAI  CAC  121.36  3.000
 9WO  CBA  CAI  CAC  117.24  3.000
 9WO  NAT  CBA  CAI  130.09  3.000
 9WO  CAI  CBA  CAZ  122.21  3.000
 9WO  NAT  CBA  CAZ  107.69  3.000
 9WO  H6   NAT  CAX  125.81  3.000
 9WO  H6   NAT  CBA  124.06  3.000
 9WO  CAX  NAT  CBA  109.21  3.000
 9WO  CAU  CAX  NAT  124.29  3.000
 9WO  NAT  CAX  CAK  109.37  3.000
 9WO  CAU  CAX  CAK  126.34  3.000
 9WO  NAR  CAU  OAA  123.48  3.000
 9WO  NAR  CAU  CAX  116.09  3.000
 9WO  OAA  CAU  CAX  120.43  3.000
 9WO  H7   NAR  CBB  116.22  3.000
 9WO  H7   NAR  CAU  119.64  3.000
 9WO  CBB  NAR  CAU  122.95  3.000
 9WO  H8   CBB  CAM  109.94  3.000
 9WO  H8   CBB  CAO  108.06  3.000
 9WO  CAM  CBB  CAO  110.17  3.000
 9WO  H8   CBB  NAR  108.07  3.000
 9WO  CAM  CBB  NAR  112.20  3.000
 9WO  CAO  CBB  NAR  108.29  3.000
 9WO  H10  CAO  H9   107.68  3.000
 9WO  H10  CAO  NBC  111.94  3.000
 9WO  H9   CAO  NBC  110.00  3.000
 9WO  H10  CAO  CBB  109.15  3.000
 9WO  H9   CAO  CBB  108.13  3.000
 9WO  NBC  CAO  CBB  109.84  3.000
 9WO  H12  CAM  H11  106.76  3.000
 9WO  H12  CAM  CAL  111.06  3.000
 9WO  H11  CAM  CAL  109.97  3.000
 9WO  H12  CAM  CBB  110.23  3.000
 9WO  H11  CAM  CBB  108.26  3.000
 9WO  CAL  CAM  CBB  110.46  3.000
 9WO  H14  CAL  H13  106.56  3.000
 9WO  H14  CAL  CAN  109.42  3.000
 9WO  H13  CAL  CAN  108.62  3.000
 9WO  H14  CAL  CAM  110.33  3.000
 9WO  H13  CAL  CAM  110.41  3.000
 9WO  CAN  CAL  CAM  111.37  3.000
 9WO  H16  CAN  H15  107.22  3.000
 9WO  H16  CAN  NBC  109.04  3.000
 9WO  H15  CAN  NBC  109.94  3.000
 9WO  H16  CAN  CAL  109.49  3.000
 9WO  H15  CAN  CAL  110.02  3.000
 9WO  NBC  CAN  CAL  111.04  3.000
 9WO  CAY  NBC  CAN  116.02  3.000
 9WO  CAN  NBC  CAO  113.90  3.000
 9WO  CAY  NBC  CAO  118.48  3.000
 9WO  NAS  CAY  CAJ  105.57  3.000
 9WO  CAJ  CAY  NBC  130.41  3.000
 9WO  NAS  CAY  NBC  124.00  3.000
 9WO  H17  CAJ  CAW  128.09  3.000
 9WO  H17  CAJ  CAY  127.30  3.000
 9WO  CAW  CAJ  CAY  104.60  3.000
 9WO  H18  NAS  NAQ  118.68  3.000
 9WO  H18  NAS  CAY  127.86  3.000
 9WO  NAQ  NAS  CAY  113.44  3.000
 9WO  CAW  NAQ  NAS  104.85  3.000
 9WO  CAV  CAW  NAQ  120.61  3.000
 9WO  NAQ  CAW  CAJ  111.54  3.000
 9WO  CAV  CAW  CAJ  127.85  3.000
 9WO  CAG  CAV  CAF  116.98  3.000
 9WO  CAG  CAV  CAW  121.58  3.000
 9WO  CAF  CAV  CAW  121.44  3.000
 9WO  H19  CAF  CAD  119.31  3.000
 9WO  H19  CAF  CAV  121.44  3.000
 9WO  CAD  CAF  CAV  119.25  3.000
 9WO  H20  CAD  NAP  116.60  3.000
 9WO  H20  CAD  CAF  119.61  3.000
 9WO  NAP  CAD  CAF  123.78  3.000
 9WO  CAE  NAP  CAD  116.95  3.000
 9WO  H21  CAE  CAG  119.62  3.000
 9WO  H21  CAE  NAP  116.50  3.000
 9WO  CAG  CAE  NAP  123.88  3.000
 9WO  H22  CAG  CAE  119.82  3.000
 9WO  H22  CAG  CAV  121.03  3.000
 9WO  CAE  CAG  CAV  119.15  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
 9WO  CONST_01  CBA  NAT  CAX  CAK    0.00   0.0  0
 9WO  CONST_02  NAT  CBA  CAZ  CAK    0.00   0.0  0
 9WO  CONST_03  CAI  CBA  CAZ  CAK  180.00   0.0  0
 9WO  CONST_04  CAB  CAH  CAZ  CAK  180.00   0.0  0
 9WO  CONST_05  NAT  CAX  CAK  CAZ    0.00   0.0  0
 9WO  CONST_06  CAX  NAT  CBA  CAZ    0.00   0.0  0
 9WO  CONST_07  CAC  CAI  CBA  CAZ    0.00   0.0  0
 9WO  CONST_08  CAC  CAB  CAH  CAZ    0.00   0.0  0
 9WO  CONST_09  CAX  CAK  CAZ  CAH  180.00   0.0  0
 9WO  CONST_10  NAT  CBA  CAZ  CAH  180.00   0.0  0
 9WO  CONST_11  CAI  CBA  CAZ  CAH    0.00   0.0  0
 9WO  CONST_12  CAI  CAC  CAB  CAH    0.00   0.0  0
 9WO  CONST_13  CBA  CAZ  CAH  CAB    0.00   0.0  0
 9WO  CONST_14  CBA  CAI  CAC  CAB    0.00   0.0  0
 9WO  CONST_15  NAT  CBA  CAI  CAC  180.00   0.0  0
 9WO  CONST_16  CAX  NAT  CBA  CAI  180.00   0.0  0
 9WO  CONST_17  CAX  CAK  CAZ  CBA    0.00   0.0  0
 9WO  CONST_18  CAW  NAQ  NAS  CAY    0.00   0.0  0
 9WO  CONST_19  CAV  CAW  CAJ  CAY  180.00   0.0  0
 9WO  CONST_20  NAQ  CAW  CAJ  CAY    0.00   0.0  0
 9WO  CONST_21  CAF  CAV  CAW  CAJ    0.00   0.0  0
 9WO  CONST_22  CAG  CAV  CAW  CAJ  180.00   0.0  0
 9WO  CONST_23  NAS  NAQ  CAW  CAJ    0.00   0.0  0
 9WO  CONST_24  NAQ  NAS  CAY  CAJ    0.00   0.0  0
 9WO  CONST_25  CAV  CAW  NAQ  NAS  180.00   0.0  0
 9WO  CONST_26  CAW  CAJ  CAY  NAS    0.00   0.0  0
 9WO  CONST_27  CAF  CAV  CAW  NAQ  180.00   0.0  0
 9WO  CONST_28  CAG  CAV  CAW  NAQ    0.00   0.0  0
 9WO  CONST_29  CAD  CAF  CAV  CAW  180.00   0.0  0
 9WO  CONST_30  CAE  CAG  CAV  CAW  180.00   0.0  0
 9WO  CONST_31  NAP  CAD  CAF  CAV    0.00   0.0  0
 9WO  CONST_32  NAP  CAE  CAG  CAV    0.00   0.0  0
 9WO  CONST_33  CAE  NAP  CAD  CAF    0.00   0.0  0
 9WO  CONST_34  CAE  CAG  CAV  CAF    0.00   0.0  0
 9WO  CONST_35  CAG  CAE  NAP  CAD    0.00   0.0  0
 9WO  CONST_36  CAG  CAV  CAF  CAD    0.00   0.0  0
 9WO  CONST_37  NAQ  NAS  CAY  NBC  180.00   0.0  0
 9WO  CONST_38  CAW  CAJ  CAY  NBC  180.00   0.0  0
 9WO  CONST_39  CAU  CAX  CAK  CAZ  180.00   0.0  0
 9WO  CONST_40  CAU  CAX  NAT  CBA  180.00   0.0  0
 9WO  CONST_41  H6   NAT  CAX  CAK  180.00   0.0  0
 9WO  CONST_42  H2   CAH  CAZ  CAK    0.00   0.0  0
 9WO  CONST_43  H5   CAI  CBA  CAZ  180.00   0.0  0
 9WO  CONST_44  H3   CAB  CAH  CAZ  180.00   0.0  0
 9WO  CONST_45  H1   CAK  CAZ  CAH    0.00   0.0  0
 9WO  CONST_46  H4   CAC  CAB  CAH  180.00   0.0  0
 9WO  CONST_47  H18  NAS  CAY  NBC    0.00   0.0  0
 9WO  CONST_48  H17  CAJ  CAY  NBC    0.00   0.0  0
 9WO  CONST_49  H19  CAF  CAV  CAW    0.00   0.0  0
 9WO  CONST_50  H22  CAG  CAV  CAW    0.00   0.0  0
 9WO  CONST_51  H20  CAD  CAF  CAV  180.00   0.0  0
 9WO  CONST_52  H21  CAE  CAG  CAV  180.00   0.0  0
 9WO  CONST_53  CBB  NAR  CAU  CAX  180.00   0.0  0
 9WO  CONST_54  CBB  NAR  CAU  OAA    0.00   0.0  0
 9WO  CONST_55  H7   NAR  CAU  CAX    0.00   0.0  0
 9WO  Var_01    CAY  NBC  CAO  CBB  159.22  30.0  1
 9WO  Var_02    CAN  CAL  CAM  CBB   53.02  30.0  1
 9WO  Var_03    NAS  CAY  NBC  CAO   -5.96  30.0  3
 9WO  Var_04    CAL  CAN  NBC  CAO   56.57  30.0  1
 9WO  Var_05    NBC  CAN  CAL  CAM  -52.63  30.0  1
 9WO  Var_06    OAA  CAU  CAX  CAK  -20.14  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
 9WO  chir_01  CBB  CAO  NAR  CAM  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
 9WO  plan-1  NBC  0.020
 9WO  plan-1  CAY  0.020
 9WO  plan-1  CAJ  0.020
 9WO  plan-1  NAS  0.020
 9WO  plan-1  NAQ  0.020
 9WO  plan-1  CAW  0.020
 9WO  plan-1  CAV  0.020
 9WO  plan-1  H17  0.020
 9WO  plan-1  H18  0.020
 9WO  plan-2  CAW  0.020
 9WO  plan-2  CAV  0.020
 9WO  plan-2  CAF  0.020
 9WO  plan-2  CAD  0.020
 9WO  plan-2  NAP  0.020
 9WO  plan-2  CAE  0.020
 9WO  plan-2  CAG  0.020
 9WO  plan-2  H19  0.020
 9WO  plan-2  H20  0.020
 9WO  plan-2  H21  0.020
 9WO  plan-2  H22  0.020
 9WO  plan-3  CAK  0.020
 9WO  plan-3  CAZ  0.020
 9WO  plan-3  CAH  0.020
 9WO  plan-3  CAB  0.020
 9WO  plan-3  CAC  0.020
 9WO  plan-3  CAI  0.020
 9WO  plan-3  CBA  0.020
 9WO  plan-3  NAT  0.020
 9WO  plan-3  CAX  0.020
 9WO  plan-3  CAU  0.020
 9WO  plan-3  H1   0.020
 9WO  plan-3  H2   0.020
 9WO  plan-3  H3   0.020
 9WO  plan-3  H4   0.020
 9WO  plan-3  H5   0.020
 9WO  plan-3  H6   0.020
 9WO  plan-4  CAX  0.020
 9WO  plan-4  CAU  0.020
 9WO  plan-4  OAA  0.020
 9WO  plan-4  NAR  0.020
 9WO  plan-4  CBB  0.020
 9WO  plan-4  H7   0.020

