# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 11:19:29 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 1-methyl-2-[4-(piperazin-1-yl)phenyl]-1H-pyrrolo[2,3-b]pyridine-4-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1c(cc2c(ccnc12)C#N)c3ccc(cc3)N4CCNCC4
#
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
 7LK  7LK  1-methyl-2-[4-(piperazin-1-yl)phenyl]-1H-pyrrolo[2,3-b]pyridine-4-carbonitrile  ligand  43  24  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_7LK
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
 7LK  CAA  C  CR16  0  -0.350   5.9580   0.0620   0.1396
 7LK  CAB  C  CR16  0  -0.087   5.6870   1.3924  -0.1739
 7LK  CAD  C  CR6   0   0.037   4.9003  -0.8254   0.3115
 7LK  CAF  C  CR5   0   0.388   1.4260   0.1770  -0.0078
 7LK  CAG  C  CR15  0  -0.506   2.2883  -0.8677   0.2427
 7LK  CAH  C  CR56  0   0.095   3.5966  -0.3455   0.1632
 7LK  CAI  C  CR56  0   0.485   3.4742   1.0332  -0.1448
 7LK  CAJ  C  CSP   0   0.022   5.1353  -2.1946   0.6289
 7LK  CAL  C  CR6   0   0.011  -0.0315   0.1252  -0.0198
 7LK  CAM  C  CR16  0  -0.273  -0.8292   1.1181   0.5459
 7LK  CAN  C  CR16  0  -0.353  -2.2092   1.0201   0.5598
 7LK  CAO  C  CR6   0   0.385  -2.8713  -0.0940   0.0171
 7LK  CAP  C  CR16  0  -0.328  -2.0595  -1.0953  -0.5482
 7LK  CAQ  C  CR16  0  -0.287  -0.6849  -0.9849  -0.5623
 7LK  CAS  C  CH2   0  -0.315  -5.0255   0.8233   0.6932
 7LK  CAT  C  CH2   0  -0.321  -6.4340   0.3391   1.0169
 7LK  CAV  C  CH2   0  -0.324  -6.3348  -1.2795  -0.7105
 7LK  CAW  C  CH2   0  -0.311  -4.9258  -0.8354  -1.0792
 7LK  NAC  N  N     0  -0.421   4.4616   1.8860  -0.3151
 7LK  NAE  N  NR5   0  -0.563   2.1464   1.3265  -0.2474
 7LK  NAK  N  NS    0  -0.240   5.3114  -3.3036   0.8874
 7LK  NAR  N  NT    0  -0.514  -4.2468  -0.2278   0.0610
 7LK  NAU  N  NH1   0  -0.576  -7.1410  -0.2333  -0.1117
 7LK  H1   H  HCR6  0   0.287   6.9814  -0.2682   0.2463
 7LK  H2   H  HCR6  0   0.270   6.5075   2.0850  -0.3132
 7LK  H3   H  HCR5  0   0.264   1.9959  -1.8745   0.4943
 7LK  H4   H  HCR6  0   0.260  -0.3793   1.9881   1.0059
 7LK  H5   H  HCR6  0   0.271  -2.7609   1.8359   1.0026
 7LK  H6   H  HCR6  0   0.267  -2.4972  -1.9873  -0.9723
 7LK  H7   H  HCR6  0   0.255  -0.1067  -1.7811  -1.0141
 7LK  H8   H  HCH2  0   0.217  -5.0770   1.7196   0.0556
 7LK  H9   H  HCH2  0   0.251  -4.5511   1.1159   1.6299
 7LK  H10  H  HCH2  0   0.226  -6.3724  -0.4217   1.8012
 7LK  H11  H  HCH2  0   0.245  -7.0067   1.1741   1.4227
 7LK  H12  H  HCH2  0   0.244  -6.8303  -1.6548  -1.6073
 7LK  H13  H  HCH2  0   0.226  -6.2731  -2.1121  -0.0027
 7LK  H14  H  HCH2  0   0.255  -4.3748  -1.7047  -1.4301
 7LK  H15  H  HCH2  0   0.220  -4.9721  -0.1213  -1.9154
 7LK  H16  H  HCH3  0   0.259   1.3459   3.2263   0.1963
 7LK  H17  H  HCH3  0   0.274   2.4177   3.1415  -1.2035
 7LK  H18  H  HCH3  0   0.266   0.7807   2.4888  -1.3144
 7LK  H19  H  HNH1  0   0.342  -7.3135   0.4912  -0.8005
 7LK  CAX  C  CH3   0  -0.550   1.6379   2.6170  -0.6581

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
 7LK  NAU  CAV  single    1.450  0.020  1.450
 7LK  NAU  CAT  single    1.450  0.020  1.450
 7LK  CAV  CAW  single    1.523  0.020  1.523
 7LK  CAT  CAS  single    1.524  0.020  1.524
 7LK  CAW  NAR  single    1.459  0.020  1.459
 7LK  CAS  NAR  single    1.453  0.020  1.453
 7LK  NAR  CAO  single    1.383  0.020  1.383
 7LK  CAO  CAP  aromatic  1.408  0.020  1.408
 7LK  CAO  CAN  aromatic  1.405  0.020  1.405
 7LK  CAP  CAQ  aromatic  1.379  0.020  1.379
 7LK  CAN  CAM  aromatic  1.384  0.020  1.384
 7LK  CAQ  CAL  aromatic  1.398  0.020  1.398
 7LK  CAM  CAL  aromatic  1.394  0.020  1.394
 7LK  CAL  CAF  single    1.458  0.020  1.458
 7LK  CAF  CAG  aromatic  1.378  0.020  1.378
 7LK  CAF  NAE  aromatic  1.378  0.020  1.378
 7LK  CAG  CAH  aromatic  1.411  0.020  1.411
 7LK  NAE  CAX  single    1.447  0.020  1.447
 7LK  NAE  CAI  aromatic  1.364  0.020  1.364
 7LK  CAH  CAI  aromatic  1.418  0.020  1.418
 7LK  CAH  CAD  aromatic  1.397  0.020  1.397
 7LK  CAI  NAC  aromatic  1.316  0.020  1.316
 7LK  NAK  CAJ  triple    1.152  0.020  1.152
 7LK  CAJ  CAD  single    1.425  0.020  1.425
 7LK  CAD  CAA  aromatic  1.391  0.020  1.391
 7LK  NAC  CAB  aromatic  1.329  0.020  1.329
 7LK  CAA  CAB  aromatic  1.393  0.020  1.393
 7LK  CAA  H1   single    0.930  0.020  1.080
 7LK  CAB  H2   single    0.930  0.020  1.080
 7LK  CAG  H3   single    0.930  0.020  1.080
 7LK  CAM  H4   single    0.930  0.020  1.080
 7LK  CAN  H5   single    0.930  0.020  1.080
 7LK  CAP  H6   single    0.930  0.020  1.080
 7LK  CAQ  H7   single    0.930  0.020  1.080
 7LK  CAS  H8   single    0.970  0.020  1.090
 7LK  CAS  H9   single    0.970  0.020  1.090
 7LK  CAT  H10  single    0.970  0.020  1.090
 7LK  CAT  H11  single    0.970  0.020  1.090
 7LK  CAV  H12  single    0.970  0.020  1.090
 7LK  CAV  H13  single    0.970  0.020  1.090
 7LK  CAW  H14  single    0.970  0.020  1.090
 7LK  CAW  H15  single    0.970  0.020  1.090
 7LK  CAX  H16  single    0.970  0.020  1.090
 7LK  CAX  H17  single    0.970  0.020  1.090
 7LK  CAX  H18  single    0.970  0.020  1.090
 7LK  NAU  H19  single    0.890  0.020  1.040

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
 7LK  H1   CAA  CAD  120.85  3.000
 7LK  H1   CAA  CAB  119.88  3.000
 7LK  CAD  CAA  CAB  119.27  3.000
 7LK  H2   CAB  NAC  116.59  3.000
 7LK  H2   CAB  CAA  119.49  3.000
 7LK  NAC  CAB  CAA  123.92  3.000
 7LK  CAJ  CAD  CAH  120.50  3.000
 7LK  CAJ  CAD  CAA  121.00  3.000
 7LK  CAH  CAD  CAA  118.50  3.000
 7LK  NAE  CAF  CAL  123.42  3.000
 7LK  NAE  CAF  CAG  109.69  3.000
 7LK  CAL  CAF  CAG  126.88  3.000
 7LK  H3   CAG  CAH  127.61  3.000
 7LK  H3   CAG  CAF  125.51  3.000
 7LK  CAH  CAG  CAF  106.83  3.000
 7LK  CAI  CAH  CAG  106.98  3.000
 7LK  CAI  CAH  CAD  115.95  3.000
 7LK  CAG  CAH  CAD  137.06  3.000
 7LK  NAE  CAI  NAC  125.56  3.000
 7LK  NAC  CAI  CAH  126.41  3.000
 7LK  NAE  CAI  CAH  108.03  3.000
 7LK  NAK  CAJ  CAD  180.00  3.000
 7LK  CAQ  CAL  CAM  117.11  3.000
 7LK  CAM  CAL  CAF  122.92  3.000
 7LK  CAQ  CAL  CAF  119.90  3.000
 7LK  H4   CAM  CAN  117.87  3.000
 7LK  H4   CAM  CAL  120.49  3.000
 7LK  CAN  CAM  CAL  121.64  3.000
 7LK  H5   CAN  CAO  121.11  3.000
 7LK  H5   CAN  CAM  117.40  3.000
 7LK  CAO  CAN  CAM  121.49  3.000
 7LK  NAR  CAO  CAP  121.17  3.000
 7LK  CAP  CAO  CAN  116.58  3.000
 7LK  NAR  CAO  CAN  122.23  3.000
 7LK  H6   CAP  CAQ  117.77  3.000
 7LK  H6   CAP  CAO  120.75  3.000
 7LK  CAQ  CAP  CAO  121.47  3.000
 7LK  H7   CAQ  CAP  118.53  3.000
 7LK  H7   CAQ  CAL  119.76  3.000
 7LK  CAP  CAQ  CAL  121.71  3.000
 7LK  H9   CAS  H8   107.43  3.000
 7LK  H9   CAS  NAR  109.57  3.000
 7LK  H8   CAS  NAR  111.22  3.000
 7LK  H9   CAS  CAT  107.76  3.000
 7LK  H8   CAS  CAT  109.78  3.000
 7LK  NAR  CAS  CAT  110.97  3.000
 7LK  H11  CAT  H10  107.16  3.000
 7LK  H11  CAT  NAU  109.62  3.000
 7LK  H10  CAT  NAU  108.12  3.000
 7LK  H11  CAT  CAS  108.72  3.000
 7LK  H10  CAT  CAS  108.72  3.000
 7LK  NAU  CAT  CAS  114.26  3.000
 7LK  H13  CAV  H12  107.18  3.000
 7LK  H13  CAV  NAU  108.25  3.000
 7LK  H12  CAV  NAU  109.58  3.000
 7LK  H13  CAV  CAW  109.04  3.000
 7LK  H12  CAV  CAW  108.75  3.000
 7LK  NAU  CAV  CAW  113.83  3.000
 7LK  H15  CAW  H14  107.15  3.000
 7LK  H15  CAW  NAR  110.07  3.000
 7LK  H14  CAW  NAR  110.44  3.000
 7LK  H15  CAW  CAV  109.53  3.000
 7LK  H14  CAW  CAV  108.29  3.000
 7LK  NAR  CAW  CAV  111.27  3.000
 7LK  CAI  NAC  CAB  115.95  3.000
 7LK  CAX  NAE  CAI  123.75  3.000
 7LK  CAI  NAE  CAF  108.46  3.000
 7LK  CAX  NAE  CAF  127.58  3.000
 7LK  CAW  NAR  CAS  113.07  3.000
 7LK  CAS  NAR  CAO  118.48  3.000
 7LK  CAW  NAR  CAO  118.57  3.000
 7LK  H19  NAU  CAV  109.23  3.000
 7LK  H19  NAU  CAT  109.24  3.000
 7LK  CAV  NAU  CAT  109.58  3.000
 7LK  H18  CAX  H17  108.65  3.000
 7LK  H18  CAX  H16  109.15  3.000
 7LK  H17  CAX  H16  108.42  3.000
 7LK  H18  CAX  NAE  110.08  3.000
 7LK  H17  CAX  NAE  108.71  3.000
 7LK  H16  CAX  NAE  111.75  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
 7LK  CONST_01  CAG  CAH  CAD  CAA   180.00   0.0  0
 7LK  CONST_02  CAI  CAH  CAD  CAA     0.00   0.0  0
 7LK  CONST_03  CAI  NAC  CAB  CAA     0.00   0.0  0
 7LK  CONST_04  NAE  CAI  NAC  CAB   180.00   0.0  0
 7LK  CONST_05  CAH  CAI  NAC  CAB     0.00   0.0  0
 7LK  CONST_06  CAH  CAD  CAA  CAB     0.00   0.0  0
 7LK  CONST_07  CAF  CAG  CAH  CAD   180.00   0.0  0
 7LK  CONST_08  NAE  CAI  CAH  CAD   180.00   0.0  0
 7LK  CONST_09  NAC  CAI  CAH  CAD     0.00   0.0  0
 7LK  CONST_10  NAC  CAB  CAA  CAD     0.00   0.0  0
 7LK  CONST_11  CAP  CAQ  CAL  CAF   180.00   0.0  0
 7LK  CONST_12  CAN  CAM  CAL  CAF   180.00   0.0  0
 7LK  CONST_13  CAI  CAH  CAG  CAF     0.00   0.0  0
 7LK  CONST_14  CAH  CAI  NAE  CAF     0.00   0.0  0
 7LK  CONST_15  NAC  CAI  NAE  CAF   180.00   0.0  0
 7LK  CONST_18  CAI  NAE  CAF  CAG     0.00   0.0  0
 7LK  CONST_19  NAE  CAI  CAH  CAG     0.00   0.0  0
 7LK  CONST_20  NAC  CAI  CAH  CAG   180.00   0.0  0
 7LK  CONST_21  CAL  CAF  CAG  CAH   180.00   0.0  0
 7LK  CONST_22  NAE  CAF  CAG  CAH     0.00   0.0  0
 7LK  CONST_23  CAL  CAF  NAE  CAI   180.00   0.0  0
 7LK  CONST_24  CAO  CAP  CAQ  CAL     0.00   0.0  0
 7LK  CONST_25  CAO  CAN  CAM  CAL     0.00   0.0  0
 7LK  CONST_26  CAP  CAO  CAN  CAM     0.00   0.0  0
 7LK  CONST_27  CAP  CAQ  CAL  CAM     0.00   0.0  0
 7LK  CONST_29  CAQ  CAP  CAO  CAN     0.00   0.0  0
 7LK  CONST_30  CAQ  CAL  CAM  CAN     0.00   0.0  0
 7LK  CONST_32  NAR  CAO  CAN  CAM   180.00   0.0  0
 7LK  CONST_33  NAR  CAO  CAP  CAQ   180.00   0.0  0
 7LK  CONST_34  CAJ  CAD  CAA  CAB   180.00   0.0  0
 7LK  CONST_35  CAX  NAE  CAF  CAG   180.00   0.0  0
 7LK  CONST_36  CAJ  CAD  CAH  CAG     0.00   0.0  0
 7LK  CONST_37  CAX  NAE  CAI  CAH   180.00   0.0  0
 7LK  CONST_38  CAJ  CAD  CAH  CAI   180.00   0.0  0
 7LK  CONST_39  CAX  NAE  CAF  CAL     0.00   0.0  0
 7LK  CONST_40  NAC  CAI  NAE  CAX     0.00   0.0  0
 7LK  CONST_41  H3   CAG  CAH  CAD     0.00   0.0  0
 7LK  CONST_42  H2   CAB  CAA  CAD   180.00   0.0  0
 7LK  CONST_43  H7   CAQ  CAL  CAF     0.00   0.0  0
 7LK  CONST_44  H4   CAM  CAL  CAF     0.00   0.0  0
 7LK  CONST_45  H1   CAA  CAD  CAH   180.00   0.0  0
 7LK  CONST_46  H6   CAP  CAQ  CAL   180.00   0.0  0
 7LK  CONST_47  H5   CAN  CAM  CAL   180.00   0.0  0
 7LK  Var_01    CAW  NAR  CAO  CAN   143.35  30.0  2
 7LK  Var_02    CAV  CAW  NAR  CAO   163.08  30.0  1
 7LK  Var_03    CAT  CAS  NAR  CAO  -163.30  30.0  1
 7LK  Var_04    CAV  NAU  CAT  CAS    53.58  30.0  1
 7LK  Var_05    CAW  CAV  NAU  CAT   -53.44  30.0  1
 7LK  Var_06    NAU  CAV  CAW  NAR    53.19  30.0  1
 7LK  Var_07    NAU  CAT  CAS  NAR   -53.19  30.0  1
 7LK  Var_08    H16  CAX  NAE  CAF    87.21  30.0  2

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
 7LK  plan-1  CAF  0.020
 7LK  plan-1  CAL  0.020
 7LK  plan-1  CAM  0.020
 7LK  plan-1  CAN  0.020
 7LK  plan-1  CAO  0.020
 7LK  plan-1  CAP  0.020
 7LK  plan-1  CAQ  0.020
 7LK  plan-1  NAR  0.020
 7LK  plan-1  H4   0.020
 7LK  plan-1  H5   0.020
 7LK  plan-1  H6   0.020
 7LK  plan-1  H7   0.020
 7LK  plan-2  CAA  0.020
 7LK  plan-2  CAB  0.020
 7LK  plan-2  CAD  0.020
 7LK  plan-2  CAF  0.020
 7LK  plan-2  CAG  0.020
 7LK  plan-2  CAH  0.020
 7LK  plan-2  CAI  0.020
 7LK  plan-2  CAJ  0.020
 7LK  plan-2  CAL  0.020
 7LK  plan-2  NAC  0.020
 7LK  plan-2  NAE  0.020
 7LK  plan-2  NAK  0.020
 7LK  plan-2  H1   0.020
 7LK  plan-2  H2   0.020
 7LK  plan-2  H3   0.020
 7LK  plan-2  CAX  0.020

