# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 06:00:04 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 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: N#Cc1ccnc2[nH]c(cc12)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
 7GK  7GK  2-[4-(piperazin-1-yl)phenyl]-1H-pyrrolo[2,3-b]pyridine-4-carbonitrile  ligand  40  23  .  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_7GK
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
 7GK  CAR  C  CH2   0  -0.315  -4.7897   1.3572   0.0409
 7GK  CAS  C  CH2   0  -0.321  -6.2495   1.2991  -0.3938
 7GK  NAT  N  NH1   0  -0.576  -7.0301   0.2776   0.2759
 7GK  CAU  C  CH2   0  -0.323  -6.3706  -1.0067   0.1416
 7GK  CAV  C  CH2   0  -0.310  -4.9170  -1.0052   0.5927
 7GK  NAQ  N  NT    0  -0.512  -4.1580   0.0533  -0.0654
 7GK  CAN  C  CR6   0   0.385  -2.7786  -0.0140  -0.0375
 7GK  CAO  C  CR16  0  -0.328  -2.1067  -1.2446  -0.1600
 7GK  CAP  C  CR16  0  -0.286  -0.7297  -1.3179  -0.1587
 7GK  CAM  C  CR16  0  -0.343  -1.9741   1.1330   0.0873
 7GK  CAL  C  CR16  0  -0.308  -0.5958   1.0485   0.0828
 7GK  CAJ  C  CR6   0   0.029   0.0650  -0.1745  -0.0348
 7GK  CAH  C  CR5   0   0.419   1.5164  -0.2316  -0.0275
 7GK  CAI  C  CR15  0  -0.510   2.4261   0.7823  -0.2432
 7GK  CAE  C  CR56  0   0.087   3.7126   0.2101  -0.1261
 7GK  CAD  C  CR6   0   0.037   5.0364   0.6460  -0.2247
 7GK  CAK  C  CSP   0   0.020   5.3301   2.0090  -0.5183
 7GK  NAW  N  NS    0  -0.241   5.5542   3.1143  -0.7546
 7GK  CAA  C  CR16  0  -0.344   6.0562  -0.2805  -0.0254
 7GK  CAB  C  CR16  0  -0.087   5.7301  -1.6038   0.2615
 7GK  NAC  N  N     0  -0.412   4.4839  -2.0584   0.3568
 7GK  CAF  C  CR56  0   0.466   3.5356  -1.1680   0.1636
 7GK  NAG  N  NR15  0  -0.742   2.1969  -1.3991   0.2094
 7GK  H1   H  HCH2  0   0.252  -4.2759   2.0679  -0.6068
 7GK  H2   H  HCH2  0   0.217  -4.7264   1.7448   1.0694
 7GK  H3   H  HCH2  0   0.245  -6.7014   2.2770  -0.2196
 7GK  H4   H  HCH2  0   0.226  -6.2937   1.1123  -1.4715
 7GK  H5   H  HNH1  0   0.343  -7.1152   0.5112   1.2591
 7GK  H7   H  HCH2  0   0.245  -6.9145  -1.7595   0.7145
 7GK  H8   H  HCH2  0   0.226  -6.4171  -1.3080  -0.9097
 7GK  H9   H  HCH2  0   0.220  -4.8684  -0.8802   1.6847
 7GK  H10  H  HCH2  0   0.255  -4.4903  -1.9791   0.3639
 7GK  H11  H  HCR6  0   0.269  -2.6615  -2.1634  -0.2868
 7GK  H12  H  HCR6  0   0.248  -0.2801  -2.2956  -0.2844
 7GK  H13  H  HCR6  0   0.273  -2.4163   2.1099   0.2184
 7GK  H14  H  HCR6  0   0.256  -0.0255   1.9608   0.2061
 7GK  H15  H  HCR5  0   0.264   2.1887   1.8060  -0.4834
 7GK  H16  H  HCR6  0   0.287   7.0930   0.0164  -0.0920
 7GK  H17  H  HCR6  0   0.270   6.5218  -2.3250   0.4200
 7GK  H18  H  HNR5  0   0.419   1.7851  -2.2837   0.4612

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
 7GK  NAT  CAS  single    1.450  0.020  1.450
 7GK  NAT  CAU  single    1.450  0.020  1.450
 7GK  CAS  CAR  single    1.524  0.020  1.524
 7GK  CAU  CAV  single    1.522  0.020  1.522
 7GK  CAR  NAQ  single    1.453  0.020  1.453
 7GK  CAV  NAQ  single    1.459  0.020  1.459
 7GK  NAQ  CAN  single    1.381  0.020  1.381
 7GK  CAN  CAO  aromatic  1.407  0.020  1.407
 7GK  CAN  CAM  aromatic  1.407  0.020  1.407
 7GK  CAO  CAP  aromatic  1.379  0.020  1.379
 7GK  CAM  CAL  aromatic  1.381  0.020  1.381
 7GK  CAP  CAJ  aromatic  1.398  0.020  1.398
 7GK  CAL  CAJ  aromatic  1.395  0.020  1.395
 7GK  CAJ  CAH  single    1.452  0.020  1.452
 7GK  CAH  CAI  aromatic  1.379  0.020  1.379
 7GK  CAH  NAG  aromatic  1.372  0.020  1.372
 7GK  CAI  CAE  aromatic  1.413  0.020  1.413
 7GK  NAG  CAF  aromatic  1.359  0.020  1.359
 7GK  CAE  CAF  aromatic  1.419  0.020  1.419
 7GK  CAE  CAD  aromatic  1.397  0.020  1.397
 7GK  CAF  NAC  aromatic  1.315  0.020  1.315
 7GK  NAW  CAK  triple    1.152  0.020  1.152
 7GK  CAK  CAD  single    1.425  0.020  1.425
 7GK  CAD  CAA  aromatic  1.392  0.020  1.392
 7GK  NAC  CAB  aromatic  1.330  0.020  1.330
 7GK  CAA  CAB  aromatic  1.393  0.020  1.393
 7GK  CAR  H1   single    0.970  0.020  1.090
 7GK  CAR  H2   single    0.970  0.020  1.090
 7GK  CAS  H3   single    0.970  0.020  1.090
 7GK  CAS  H4   single    0.970  0.020  1.090
 7GK  NAT  H5   single    0.890  0.020  1.040
 7GK  CAU  H7   single    0.970  0.020  1.090
 7GK  CAU  H8   single    0.970  0.020  1.090
 7GK  CAV  H9   single    0.970  0.020  1.090
 7GK  CAV  H10  single    0.970  0.020  1.090
 7GK  CAO  H11  single    0.930  0.020  1.080
 7GK  CAP  H12  single    0.930  0.020  1.080
 7GK  CAM  H13  single    0.930  0.020  1.080
 7GK  CAL  H14  single    0.930  0.020  1.080
 7GK  CAI  H15  single    0.930  0.020  1.080
 7GK  CAA  H16  single    0.930  0.020  1.080
 7GK  CAB  H17  single    0.930  0.020  1.080
 7GK  NAG  H18  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
 7GK  H2   CAR  H1   107.37  3.000
 7GK  H2   CAR  NAQ  111.06  3.000
 7GK  H1   CAR  NAQ  109.67  3.000
 7GK  H2   CAR  CAS  109.57  3.000
 7GK  H1   CAR  CAS  107.87  3.000
 7GK  NAQ  CAR  CAS  111.18  3.000
 7GK  H4   CAS  H3   107.05  3.000
 7GK  H4   CAS  NAT  108.23  3.000
 7GK  H3   CAS  NAT  109.56  3.000
 7GK  H4   CAS  CAR  109.02  3.000
 7GK  H3   CAS  CAR  108.47  3.000
 7GK  NAT  CAS  CAR  114.26  3.000
 7GK  H5   NAT  CAU  109.39  3.000
 7GK  H5   NAT  CAS  109.31  3.000
 7GK  CAU  NAT  CAS  109.66  3.000
 7GK  H8   CAU  H7   107.05  3.000
 7GK  H8   CAU  CAV  109.00  3.000
 7GK  H7   CAU  CAV  108.73  3.000
 7GK  H8   CAU  NAT  108.27  3.000
 7GK  H7   CAU  NAT  109.62  3.000
 7GK  CAV  CAU  NAT  113.96  3.000
 7GK  H10  CAV  H9   107.05  3.000
 7GK  H10  CAV  NAQ  110.52  3.000
 7GK  H9   CAV  NAQ  110.01  3.000
 7GK  H10  CAV  CAU  108.15  3.000
 7GK  H9   CAV  CAU  109.66  3.000
 7GK  NAQ  CAV  CAU  111.33  3.000
 7GK  CAN  NAQ  CAV  118.35  3.000
 7GK  CAN  NAQ  CAR  118.46  3.000
 7GK  CAV  NAQ  CAR  113.07  3.000
 7GK  CAM  CAN  CAO  116.59  3.000
 7GK  CAM  CAN  NAQ  122.22  3.000
 7GK  CAO  CAN  NAQ  121.17  3.000
 7GK  H11  CAO  CAP  117.87  3.000
 7GK  H11  CAO  CAN  120.56  3.000
 7GK  CAP  CAO  CAN  121.55  3.000
 7GK  H12  CAP  CAJ  120.83  3.000
 7GK  H12  CAP  CAO  117.53  3.000
 7GK  CAJ  CAP  CAO  121.62  3.000
 7GK  H13  CAM  CAL  117.66  3.000
 7GK  H13  CAM  CAN  120.94  3.000
 7GK  CAL  CAM  CAN  121.38  3.000
 7GK  H14  CAL  CAJ  119.91  3.000
 7GK  H14  CAL  CAM  118.28  3.000
 7GK  CAJ  CAL  CAM  121.78  3.000
 7GK  CAH  CAJ  CAL  120.48  3.000
 7GK  CAH  CAJ  CAP  122.44  3.000
 7GK  CAL  CAJ  CAP  117.08  3.000
 7GK  NAG  CAH  CAI  108.99  3.000
 7GK  NAG  CAH  CAJ  122.00  3.000
 7GK  CAI  CAH  CAJ  129.01  3.000
 7GK  H15  CAI  CAE  127.13  3.000
 7GK  H15  CAI  CAH  125.99  3.000
 7GK  CAE  CAI  CAH  106.85  3.000
 7GK  CAF  CAE  CAD  115.82  3.000
 7GK  CAD  CAE  CAI  136.93  3.000
 7GK  CAF  CAE  CAI  107.25  3.000
 7GK  CAA  CAD  CAK  121.01  3.000
 7GK  CAA  CAD  CAE  118.45  3.000
 7GK  CAK  CAD  CAE  120.55  3.000
 7GK  NAW  CAK  CAD  180.00  3.000
 7GK  H16  CAA  CAB  119.89  3.000
 7GK  H16  CAA  CAD  120.75  3.000
 7GK  CAB  CAA  CAD  119.36  3.000
 7GK  H17  CAB  NAC  116.55  3.000
 7GK  H17  CAB  CAA  119.47  3.000
 7GK  NAC  CAB  CAA  123.98  3.000
 7GK  CAF  NAC  CAB  115.70  3.000
 7GK  NAG  CAF  NAC  126.16  3.000
 7GK  NAC  CAF  CAE  126.69  3.000
 7GK  NAG  CAF  CAE  107.14  3.000
 7GK  H18  NAG  CAF  124.06  3.000
 7GK  H18  NAG  CAH  125.98  3.000
 7GK  CAF  NAG  CAH  109.76  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
 7GK  CONST_01  CAJ  CAP  CAO  CAN     0.00   0.0  0
 7GK  CONST_02  CAJ  CAL  CAM  CAN     0.00   0.0  0
 7GK  CONST_03  CAL  CAM  CAN  CAO     0.00   0.0  0
 7GK  CONST_04  CAL  CAJ  CAP  CAO     0.00   0.0  0
 7GK  CONST_05  CAH  CAJ  CAP  CAO   180.00   0.0  0
 7GK  CONST_06  CAM  CAN  CAO  CAP     0.00   0.0  0
 7GK  CONST_07  CAM  CAL  CAJ  CAP     0.00   0.0  0
 7GK  CONST_10  CAH  CAJ  CAL  CAM   180.00   0.0  0
 7GK  CONST_13  CAE  CAI  CAH  CAJ   180.00   0.0  0
 7GK  CONST_14  CAF  NAG  CAH  CAJ   180.00   0.0  0
 7GK  CONST_15  CAF  CAE  CAI  CAH     0.00   0.0  0
 7GK  CONST_16  CAD  CAE  CAI  CAH   180.00   0.0  0
 7GK  CONST_17  CAE  CAF  NAG  CAH     0.00   0.0  0
 7GK  CONST_18  NAC  CAF  NAG  CAH   180.00   0.0  0
 7GK  CONST_19  CAF  NAG  CAH  CAI     0.00   0.0  0
 7GK  CONST_20  NAG  CAF  CAE  CAI     0.00   0.0  0
 7GK  CONST_21  NAC  CAF  CAE  CAI   180.00   0.0  0
 7GK  CONST_22  CAA  CAD  CAE  CAI   180.00   0.0  0
 7GK  CONST_23  NAG  CAH  CAI  CAE     0.00   0.0  0
 7GK  CONST_24  CAB  NAC  CAF  CAE     0.00   0.0  0
 7GK  CONST_25  CAB  CAA  CAD  CAE     0.00   0.0  0
 7GK  CONST_26  NAG  CAF  CAE  CAD   180.00   0.0  0
 7GK  CONST_27  NAC  CAF  CAE  CAD     0.00   0.0  0
 7GK  CONST_28  NAC  CAB  CAA  CAD     0.00   0.0  0
 7GK  CONST_29  CAF  CAE  CAD  CAA     0.00   0.0  0
 7GK  CONST_30  CAF  NAC  CAB  CAA     0.00   0.0  0
 7GK  CONST_31  NAG  CAF  NAC  CAB   180.00   0.0  0
 7GK  CONST_32  CAP  CAO  CAN  NAQ   180.00   0.0  0
 7GK  CONST_33  CAL  CAM  CAN  NAQ   180.00   0.0  0
 7GK  CONST_34  CAK  CAD  CAE  CAI     0.00   0.0  0
 7GK  CONST_35  CAF  CAE  CAD  CAK   180.00   0.0  0
 7GK  CONST_36  CAB  CAA  CAD  CAK   180.00   0.0  0
 7GK  CONST_37  H11  CAO  CAN  NAQ     0.00   0.0  0
 7GK  CONST_38  H13  CAM  CAN  NAQ     0.00   0.0  0
 7GK  CONST_39  H12  CAP  CAO  CAN   180.00   0.0  0
 7GK  CONST_40  H14  CAL  CAM  CAN   180.00   0.0  0
 7GK  CONST_41  H15  CAI  CAH  CAJ     0.00   0.0  0
 7GK  CONST_42  H18  NAG  CAH  CAJ     0.00   0.0  0
 7GK  CONST_43  H16  CAA  CAD  CAE   180.00   0.0  0
 7GK  CONST_44  H17  CAB  CAA  CAD   180.00   0.0  0
 7GK  Var_01    CAU  NAT  CAS  CAR   -53.25  30.0  1
 7GK  Var_02    CAU  CAV  NAQ  CAR    51.34  30.0  1
 7GK  Var_03    CAO  CAN  NAQ  CAR  -178.86  30.0  2
 7GK  Var_04    CAV  CAU  NAT  CAS    53.26  30.0  1
 7GK  Var_05    CAV  NAQ  CAR  CAS   -51.09  30.0  1
 7GK  Var_06    NAQ  CAR  CAS  NAT    52.88  30.0  1
 7GK  Var_07    NAQ  CAV  CAU  NAT   -53.03  30.0  1

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
 7GK  plan-1  NAQ  0.020
 7GK  plan-1  CAN  0.020
 7GK  plan-1  CAO  0.020
 7GK  plan-1  CAP  0.020
 7GK  plan-1  CAM  0.020
 7GK  plan-1  CAL  0.020
 7GK  plan-1  CAJ  0.020
 7GK  plan-1  CAH  0.020
 7GK  plan-1  H11  0.020
 7GK  plan-1  H12  0.020
 7GK  plan-1  H13  0.020
 7GK  plan-1  H14  0.020
 7GK  plan-2  CAJ  0.020
 7GK  plan-2  CAH  0.020
 7GK  plan-2  CAI  0.020
 7GK  plan-2  CAE  0.020
 7GK  plan-2  CAD  0.020
 7GK  plan-2  CAK  0.020
 7GK  plan-2  NAW  0.020
 7GK  plan-2  CAA  0.020
 7GK  plan-2  CAB  0.020
 7GK  plan-2  NAC  0.020
 7GK  plan-2  CAF  0.020
 7GK  plan-2  NAG  0.020
 7GK  plan-2  H15  0.020
 7GK  plan-2  H16  0.020
 7GK  plan-2  H17  0.020
 7GK  plan-2  H18  0.020

