# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 11:37:11 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 2-(4-methylpiperazin-1-yl)-5H-benzo[c][1,5]naphthyridin-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)c2ccc3NC(=O)c4ccccc4c3n2
#
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
 G9G  G9G  2-(4-methylpiperazin-1-yl)-5H-benzo[c][1,5]naphthyridin-6-one  ligand  40  22  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_G9G
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
 G9G  N11   N  NT    0  -0.399   5.1287  -0.8292  -0.0411
 G9G  N12   N  NT    0  -0.510   2.4549   0.2886  -0.1173
 G9G  N13   N  NR16  0  -0.762  -2.7683   2.0101   0.1820
 G9G  N14   N  N     0  -0.500   0.1821  -0.1009  -0.0865
 G9G  CAA   C  CH3   0  -0.529   5.4711  -1.2271   1.3093
 G9G  OAB   O  O     0  -0.475  -4.9808   1.5817   0.1668
 G9G  CAC   C  CR16  0  -0.251  -4.2383  -2.5304  -0.3117
 G9G  CAD   C  CR16  0  -0.233  -2.9102  -2.9564  -0.3773
 G9G  CAE   C  CR16  0  -0.388   0.8960   2.1522   0.1589
 G9G  CAF   C  CR16  0  -0.280  -4.5225  -1.1897  -0.1558
 G9G  CAG   C  CR16  0  -0.299  -1.8788  -2.0452  -0.2876
 G9G  CAH   C  CR16  0  -0.204  -0.4070   2.5713   0.2199
 G9G  CAI   C  CH2   0  -0.330   4.0046  -1.5527  -0.6009
 G9G  CAJ   C  CH2   0  -0.323   4.8912   0.5907  -0.1918
 G9G  CAK   C  CH2   0  -0.304   2.6492  -1.1529  -0.0309
 G9G  CAL   C  CH2   0  -0.313   3.5684   1.0739   0.3950
 G9G  CAO   C  CR6   0   0.516   1.1725   0.7711  -0.0069
 G9G  CAP   C  CR6   0   0.491  -3.8304   1.1675   0.1026
 G9G  CAQ   C  CR66  0   0.301  -1.4402   1.6363   0.1218
 G9G  CAR   C  CR66  0  -0.156  -3.4874  -0.2561  -0.0638
 G9G  CAS   C  CR66  0   0.192  -2.1525  -0.6820  -0.1301
 G9G  CAT   C  CR66  0   0.120  -1.0875   0.3023  -0.0326
 G9G  HN13  H  HNR6  0   0.415  -2.9780   2.9926   0.2996
 G9G  HAA   H  HCH3  0   0.234   5.7201  -2.2894   1.3229
 G9G  HAAA  H  HCH3  0   0.234   6.3547  -0.6763   1.6351
 G9G  HAAB  H  HCH3  0   0.201   4.6885  -1.0644   2.0625
 G9G  HAC   H  HCR6  0   0.266  -5.0425  -3.2500  -0.3832
 G9G  HAD   H  HCR6  0   0.267  -2.6882  -4.0087  -0.4986
 G9G  HAE   H  HCR6  0   0.280   1.6800   2.8892   0.2337
 G9G  HAF   H  HCR6  0   0.265  -5.5491  -0.8538  -0.1021
 G9G  HAG   H  HCR6  0   0.266  -0.8495  -2.3728  -0.3394
 G9G  HAH   H  HCR6  0   0.287  -0.6296   3.6238   0.3448
 G9G  HAI   H  HCH2  0   0.234   3.9926  -1.3790  -1.6822
 G9G  HAIA  H  HCH2  0   0.243   4.1467  -2.6255  -0.4514
 G9G  HAJ   H  HCH2  0   0.245   5.7056   1.1509   0.2726
 G9G  HAJA  H  HCH2  0   0.236   4.9060   0.8295  -1.2606
 G9G  HAK   H  HCH2  0   0.218   2.5445  -1.4928   1.0090
 G9G  HAKA  H  HCH2  0   0.264   1.8707  -1.6558  -0.5993
 G9G  HAL   H  HCH2  0   0.259   3.4573   2.1195   0.1159
 G9G  HALA  H  HCH2  0   0.226   3.5944   1.0358   1.4927

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
 G9G  CAA  N11   single    1.449  0.020  1.449
 G9G  N11  CAI   single    1.449  0.020  1.449
 G9G  N11  CAJ   single    1.448  0.020  1.448
 G9G  CAL  N12   single    1.456  0.020  1.456
 G9G  CAK  N12   single    1.457  0.020  1.457
 G9G  N12  CAO   single    1.375  0.020  1.375
 G9G  CAQ  N13   single    1.381  0.020  1.381
 G9G  N13  CAP   single    1.358  0.020  1.358
 G9G  N13  HN13  single    0.860  0.020  1.020
 G9G  CAO  N14   aromatic  1.322  0.020  1.322
 G9G  N14  CAT   aromatic  1.333  0.020  1.333
 G9G  CAA  HAA   single    0.970  0.020  1.090
 G9G  CAA  HAAA  single    0.970  0.020  1.090
 G9G  CAA  HAAB  single    0.970  0.020  1.090
 G9G  CAP  OAB   double    1.224  0.020  1.224
 G9G  CAD  CAC   aromatic  1.396  0.020  1.396
 G9G  CAC  CAF   aromatic  1.379  0.020  1.379
 G9G  CAC  HAC   single    0.930  0.020  1.080
 G9G  CAG  CAD   aromatic  1.379  0.020  1.379
 G9G  CAD  HAD   single    0.930  0.020  1.080
 G9G  CAO  CAE   aromatic  1.418  0.020  1.418
 G9G  CAE  CAH   aromatic  1.370  0.020  1.370
 G9G  CAE  HAE   single    0.930  0.020  1.080
 G9G  CAR  CAF   aromatic  1.397  0.020  1.397
 G9G  CAF  HAF   single    0.930  0.020  1.080
 G9G  CAG  CAS   aromatic  1.399  0.020  1.399
 G9G  CAG  HAG   single    0.930  0.020  1.080
 G9G  CAH  CAQ   aromatic  1.397  0.020  1.397
 G9G  CAH  HAH   single    0.930  0.020  1.080
 G9G  CAI  CAK   single    1.524  0.020  1.524
 G9G  CAI  HAI   single    0.970  0.020  1.090
 G9G  CAI  HAIA  single    0.970  0.020  1.090
 G9G  CAJ  CAL   single    1.526  0.020  1.526
 G9G  CAJ  HAJ   single    0.970  0.020  1.090
 G9G  CAJ  HAJA  single    0.970  0.020  1.090
 G9G  CAK  HAK   single    0.970  0.020  1.090
 G9G  CAK  HAKA  single    0.970  0.020  1.090
 G9G  CAL  HAL   single    0.970  0.020  1.090
 G9G  CAL  HALA  single    0.970  0.020  1.090
 G9G  CAR  CAP   single    1.474  0.020  1.474
 G9G  CAT  CAQ   aromatic  1.388  0.020  1.388
 G9G  CAS  CAR   aromatic  1.403  0.020  1.403
 G9G  CAT  CAS   aromatic  1.453  0.020  1.453

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
 G9G  CAJ   N11  CAI   108.80  3.000
 G9G  CAJ   N11  CAA   113.91  3.000
 G9G  CAI   N11  CAA   113.97  3.000
 G9G  CAO   N12  CAL   119.74  3.000
 G9G  CAO   N12  CAK   117.83  3.000
 G9G  CAL   N12  CAK   114.25  3.000
 G9G  HN13  N13  CAQ   117.87  3.000
 G9G  HN13  N13  CAP   116.57  3.000
 G9G  CAQ   N13  CAP   125.56  3.000
 G9G  CAT   N14  CAO   120.76  3.000
 G9G  HAAB  CAA  HAAA  107.30  3.000
 G9G  HAAB  CAA  HAA   107.35  3.000
 G9G  HAAA  CAA  HAA   107.63  3.000
 G9G  HAAB  CAA  N11   115.48  3.000
 G9G  HAAA  CAA  N11   109.34  3.000
 G9G  HAA   CAA  N11   109.45  3.000
 G9G  HAC   CAC  CAF   120.06  3.000
 G9G  HAC   CAC  CAD   120.07  3.000
 G9G  CAF   CAC  CAD   119.86  3.000
 G9G  HAD   CAD  CAG   119.76  3.000
 G9G  HAD   CAD  CAC   119.80  3.000
 G9G  CAG   CAD  CAC   120.44  3.000
 G9G  HAE   CAE  CAO   122.13  3.000
 G9G  HAE   CAE  CAH   118.63  3.000
 G9G  CAO   CAE  CAH   119.24  3.000
 G9G  HAF   CAF  CAR   119.50  3.000
 G9G  HAF   CAF  CAC   120.21  3.000
 G9G  CAR   CAF  CAC   120.29  3.000
 G9G  HAG   CAG  CAS   119.12  3.000
 G9G  HAG   CAG  CAD   120.57  3.000
 G9G  CAS   CAG  CAD   120.31  3.000
 G9G  HAH   CAH  CAQ   120.44  3.000
 G9G  HAH   CAH  CAE   119.86  3.000
 G9G  CAQ   CAH  CAE   119.71  3.000
 G9G  HAIA  CAI  HAI   107.00  3.000
 G9G  HAIA  CAI  CAK   108.79  3.000
 G9G  HAI   CAI  CAK   108.54  3.000
 G9G  HAIA  CAI  N11   109.66  3.000
 G9G  HAI   CAI  N11   108.10  3.000
 G9G  CAK   CAI  N11   114.48  3.000
 G9G  HAJA  CAJ  HAJ   107.04  3.000
 G9G  HAJA  CAJ  CAL   108.54  3.000
 G9G  HAJ   CAJ  CAL   108.70  3.000
 G9G  HAJA  CAJ  N11   108.26  3.000
 G9G  HAJ   CAJ  N11   109.67  3.000
 G9G  CAL   CAJ  N11   114.38  3.000
 G9G  HAKA  CAK  HAK   106.46  3.000
 G9G  HAKA  CAK  CAI   108.67  3.000
 G9G  HAK   CAK  CAI   110.95  3.000
 G9G  HAKA  CAK  N12   109.34  3.000
 G9G  HAK   CAK  N12   110.45  3.000
 G9G  CAI   CAK  N12   110.85  3.000
 G9G  HALA  CAL  HAL   106.98  3.000
 G9G  HALA  CAL  CAJ   110.66  3.000
 G9G  HAL   CAL  CAJ   107.11  3.000
 G9G  HALA  CAL  N12   110.55  3.000
 G9G  HAL   CAL  N12   110.49  3.000
 G9G  CAJ   CAL  N12   110.92  3.000
 G9G  CAE   CAO  N14   120.23  3.000
 G9G  CAE   CAO  N12   122.21  3.000
 G9G  N14   CAO  N12   117.55  3.000
 G9G  CAR   CAP  OAB   123.47  3.000
 G9G  CAR   CAP  N13   115.08  3.000
 G9G  OAB   CAP  N13   121.45  3.000
 G9G  CAT   CAQ  CAH   117.58  3.000
 G9G  CAT   CAQ  N13   120.61  3.000
 G9G  CAH   CAQ  N13   121.81  3.000
 G9G  CAS   CAR  CAP   121.34  3.000
 G9G  CAS   CAR  CAF   119.94  3.000
 G9G  CAP   CAR  CAF   118.72  3.000
 G9G  CAT   CAS  CAR   119.24  3.000
 G9G  CAT   CAS  CAG   121.60  3.000
 G9G  CAR   CAS  CAG   119.16  3.000
 G9G  CAS   CAT  CAQ   118.16  3.000
 G9G  CAS   CAT  N14   119.36  3.000
 G9G  CAQ   CAT  N14   122.48  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
 G9G  CONST_01  CAH   CAE  CAO  N14     0.00   0.0  0
 G9G  CONST_02  CAH   CAQ  CAT  N14     0.00   0.0  0
 G9G  CONST_03  CAG   CAS  CAT  N14     0.00   0.0  0
 G9G  CONST_04  CAR   CAS  CAT  N14   180.00   0.0  0
 G9G  CONST_05  CAS   CAG  CAD  CAC     0.00   0.0  0
 G9G  CONST_06  CAS   CAR  CAF  CAC     0.00   0.0  0
 G9G  CONST_07  CAR   CAF  CAC  CAD     0.00   0.0  0
 G9G  CONST_08  CAR   CAS  CAG  CAD     0.00   0.0  0
 G9G  CONST_09  CAT   CAS  CAG  CAD   180.00   0.0  0
 G9G  CONST_10  CAT   N14  CAO  CAE     0.00   0.0  0
 G9G  CONST_11  CAT   CAQ  CAH  CAE     0.00   0.0  0
 G9G  CONST_12  CAG   CAD  CAC  CAF     0.00   0.0  0
 G9G  CONST_13  CAG   CAS  CAR  CAF     0.00   0.0  0
 G9G  CONST_14  CAT   CAS  CAR  CAF   180.00   0.0  0
 G9G  CONST_15  CAQ   CAT  CAS  CAG   180.00   0.0  0
 G9G  CONST_16  CAS   CAT  CAQ  CAH   180.00   0.0  0
 G9G  CONST_17  CAQ   CAT  N14  CAO     0.00   0.0  0
 G9G  CONST_18  CAS   CAT  N14  CAO   180.00   0.0  0
 G9G  CONST_19  CAQ   CAH  CAE  CAO     0.00   0.0  0
 G9G  CONST_20  CAR   CAS  CAT  CAQ     0.00   0.0  0
 G9G  CONST_21  CAT   N14  CAO  N12   180.00   0.0  0
 G9G  CONST_22  CAH   CAE  CAO  N12   180.00   0.0  0
 G9G  CONST_23  CAR   CAP  N13  CAQ     0.00   0.0  0
 G9G  CONST_24  CAQ   N13  CAP  OAB   180.00   0.0  0
 G9G  CONST_25  HAE   CAE  CAO  N12     0.00   0.0  0
 G9G  CONST_26  HAH   CAH  CAQ  N13     0.00   0.0  0
 G9G  CONST_27  HAG   CAG  CAD  CAC   180.00   0.0  0
 G9G  CONST_28  HAF   CAF  CAC  CAD   180.00   0.0  0
 G9G  CONST_29  HAD   CAD  CAC  CAF   180.00   0.0  0
 G9G  CONST_30  HAC   CAC  CAD  CAG   180.00   0.0  0
 G9G  CONST_31  HN13  N13  CAP  CAR   180.00   0.0  0
 G9G  Var_01    N12   CAK  CAI  N11    52.73  30.0  1
 G9G  Var_02    N12   CAL  CAJ  N11   -52.80  30.0  1
 G9G  Var_03    CAL   N12  CAO  N14  -159.41  30.0  3
 G9G  Var_04    CAL   CAJ  N11  CAI    54.65  30.0  1
 G9G  Var_05    CAK   CAI  N11  CAJ   -54.70  30.0  1
 G9G  Var_06    HAA   CAA  N11  CAI    59.34  30.0  3

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
 G9G  plan-1  N12   0.020
 G9G  plan-1  N13   0.020
 G9G  plan-1  N14   0.020
 G9G  plan-1  OAB   0.020
 G9G  plan-1  CAC   0.020
 G9G  plan-1  CAD   0.020
 G9G  plan-1  CAE   0.020
 G9G  plan-1  CAF   0.020
 G9G  plan-1  CAG   0.020
 G9G  plan-1  CAH   0.020
 G9G  plan-1  CAO   0.020
 G9G  plan-1  CAP   0.020
 G9G  plan-1  CAQ   0.020
 G9G  plan-1  CAR   0.020
 G9G  plan-1  CAS   0.020
 G9G  plan-1  CAT   0.020
 G9G  plan-1  HN13  0.020
 G9G  plan-1  HAC   0.020
 G9G  plan-1  HAD   0.020
 G9G  plan-1  HAE   0.020
 G9G  plan-1  HAF   0.020
 G9G  plan-1  HAG   0.020
 G9G  plan-1  HAH   0.020

