# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 12:29:20 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 8-fluoro-2-(3-piperidin-1-ylpropanoyl)-1,3,4,5-tetrahydrobenzo[c][1,6]naphthyridin-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc2C3=C(CCN(C3)C(=O)CCN4CCCCC4)NC(=O)c2c1
#
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
 G9L  G9L  8-fluoro-2-(3-piperidin-1-ylpropanoyl)-1,3,4,5-tetrahydrobenzo[c][1,6]naphthyridin-6-one  ligand  50  26  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G9L
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
 G9L  N11   N  NT    0  -0.424  -5.2196   0.3488  -0.1305
 G9L  N12   N  NT    0  -0.478  -0.4367   0.3412   0.9469
 G9L  N13   N  NR16  0  -0.737   2.6164  -2.2789   0.0261
 G9L  OAA   O  O     0  -0.500  -1.3740   2.0265  -0.2176
 G9L  CAD   C  CR16  0  -0.382   4.9295   2.1274  -0.0496
 G9L  CAE   C  CR16  0  -0.329   3.6471   1.7307   0.2553
 G9L  CAF   C  CR16  0  -0.450   5.5376  -0.1582  -0.5309
 G9L  CAG   C  CH2   0  -0.439  -7.8672  -0.5895  -0.8806
 G9L  CAH   C  CH2   0  -0.437  -7.6554   0.6110   0.0319
 G9L  CAI   C  CH2   0  -0.435  -6.6688  -1.5255  -0.7932
 G9L  CAJ   C  CH2   0  -0.626  -2.8203   0.2242   0.3930
 G9L  CAK   C  CH2   0  -0.511   0.3214  -1.9584   0.7796
 G9L  CAL   C  CH2   0  -0.277  -6.3240   1.2855  -0.2613
 G9L  CAM   C  CH2   0  -0.285  -5.3741  -0.7680  -1.0486
 G9L  CAN   C  CH2   0  -0.242  -3.9364   1.0109  -0.2814
 G9L  CAO   C  CH2   0  -0.342  -0.4713  -0.9524   1.5959
 G9L  CAP   C  CH2   0  -0.333   0.8803   0.9364   0.8994
 G9L  CAR   C  C     0   0.582  -1.4880   0.9436   0.3411
 G9L  CAS   C  CR6   0   0.537   5.8591   1.1699  -0.4407
 G9L  CAT   C  CR6   0   0.346   1.6553  -1.3836   0.4247
 G9L  CAU   C  CR6   0  -0.112   1.9305  -0.0635   0.4931
 G9L  CAV   C  CR6   0   0.523   3.9023  -1.9797  -0.3152
 G9L  CAW   C  CR66  0   0.269   3.2646   0.3795   0.1792
 G9L  CAX   C  CR66  0  -0.167   4.2351  -0.5571  -0.2191
 G9L  HN13  H  HNR6  0   0.418   2.3626  -3.2578  -0.0104
 G9L  HAD   H  HCR6  0   0.291   5.2133   3.1700   0.0107
 G9L  HAE   H  HCR6  0   0.273   2.9340   2.4852   0.5580
 G9L  HAF   H  HCR6  0   0.285   6.2765  -0.8872  -0.8367
 G9L  HAG   H  HCH2  0   0.230  -8.7898  -1.1136  -0.6217
 G9L  HAGA  H  HCH2  0   0.210  -7.9822  -0.2430  -1.9134
 G9L  HAH   H  HCH2  0   0.229  -8.4621   1.3377  -0.0872
 G9L  HAHA  H  HCH2  0   0.213  -7.6684   0.2868   1.0769
 G9L  HAI   H  HCH2  0   0.214  -6.6274  -1.9834   0.1999
 G9L  HAIA  H  HCH2  0   0.229  -6.7571  -2.3392  -1.5165
 G9L  HAJ   H  HCH2  0   0.272  -3.1042   0.0447   1.4339
 G9L  HAJA  H  HCH2  0   0.269  -2.7064  -0.7642  -0.0615
 G9L  HAK   H  HCH2  0   0.275   0.4520  -2.8779   1.3556
 G9L  HAKA  H  HCH2  0   0.278  -0.2236  -2.2297  -0.1302
 G9L  HAL   H  HCH2  0   0.232  -6.1665   2.1070   0.4416
 G9L  HALA  H  HCH2  0   0.181  -6.3594   1.7336  -1.2713
 G9L  HAM   H  HCH2  0   0.184  -5.3578  -0.4193  -2.0978
 G9L  HAMA  H  HCH2  0   0.233  -4.5279  -1.4489  -0.9368
 G9L  HAN   H  HCH2  0   0.200  -3.6938   1.1955  -1.3394
 G9L  HANA  H  HCH2  0   0.234  -4.0062   1.9911   0.1935
 G9L  HAO   H  HCH2  0   0.268  -0.0297  -0.8527   2.5916
 G9L  HAOA  H  HCH2  0   0.289  -1.4904  -1.2965   1.7380
 G9L  HAP   H  HCH2  0   0.272   0.8593   1.7638   0.1919
 G9L  HAPA  H  HCH2  0   0.261   1.1294   1.3650   1.8782
 G9L  OAB   O  O     0  -0.476   4.6908  -2.8498  -0.6615
 G9L  FAC   F  F     0  -0.312   7.1044   1.5688  -0.7396

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
 G9L  CAM  N11   single    1.454  0.020  1.454
 G9L  N11  CAL   single    1.454  0.020  1.454
 G9L  N11  CAN   single    1.452  0.020  1.452
 G9L  CAR  N12   single    1.355  0.020  1.355
 G9L  N12  CAO   single    1.448  0.020  1.448
 G9L  N12  CAP   single    1.446  0.020  1.446
 G9L  CAT  N13   single    1.373  0.020  1.373
 G9L  N13  CAV   single    1.364  0.020  1.364
 G9L  N13  HN13  single    0.860  0.020  1.020
 G9L  OAA  CAR   double    1.224  0.020  1.224
 G9L  CAV  OAB   double    1.224  0.020  1.224
 G9L  CAS  FAC   single    1.341  0.020  1.341
 G9L  CAE  CAD   aromatic  1.377  0.020  1.377
 G9L  CAD  CAS   aromatic  1.391  0.020  1.391
 G9L  CAD  HAD   single    0.930  0.020  1.080
 G9L  CAE  CAW   aromatic  1.406  0.020  1.406
 G9L  CAE  HAE   single    0.930  0.020  1.080
 G9L  CAX  CAF   aromatic  1.398  0.020  1.398
 G9L  CAS  CAF   aromatic  1.369  0.020  1.369
 G9L  CAF  HAF   single    0.930  0.020  1.080
 G9L  CAI  CAG   single    1.523  0.020  1.523
 G9L  CAG  CAH   single    1.523  0.020  1.523
 G9L  CAG  HAG   single    0.970  0.020  1.090
 G9L  CAG  HAGA  single    0.970  0.020  1.090
 G9L  CAH  CAL   single    1.521  0.020  1.521
 G9L  CAH  HAH   single    0.970  0.020  1.090
 G9L  CAH  HAHA  single    0.970  0.020  1.090
 G9L  CAI  CAM   single    1.522  0.020  1.522
 G9L  CAI  HAI   single    0.970  0.020  1.090
 G9L  CAI  HAIA  single    0.970  0.020  1.090
 G9L  CAN  CAJ   single    1.523  0.020  1.523
 G9L  CAJ  CAR   single    1.515  0.020  1.515
 G9L  CAJ  HAJ   single    0.970  0.020  1.090
 G9L  CAJ  HAJA  single    0.970  0.020  1.090
 G9L  CAO  CAK   single    1.519  0.020  1.519
 G9L  CAK  CAT   single    1.495  0.020  1.495
 G9L  CAK  HAK   single    0.970  0.020  1.090
 G9L  CAK  HAKA  single    0.970  0.020  1.090
 G9L  CAL  HAL   single    0.970  0.020  1.090
 G9L  CAL  HALA  single    0.970  0.020  1.090
 G9L  CAM  HAM   single    0.970  0.020  1.090
 G9L  CAM  HAMA  single    0.970  0.020  1.090
 G9L  CAN  HAN   single    0.970  0.020  1.090
 G9L  CAN  HANA  single    0.970  0.020  1.090
 G9L  CAO  HAO   single    0.970  0.020  1.090
 G9L  CAO  HAOA  single    0.970  0.020  1.090
 G9L  CAP  CAU   single    1.506  0.020  1.506
 G9L  CAP  HAP   single    0.970  0.020  1.090
 G9L  CAP  HAPA  single    0.970  0.020  1.090
 G9L  CAU  CAT   double    1.350  0.020  1.350
 G9L  CAU  CAW   single    1.440  0.020  1.440
 G9L  CAX  CAV   single    1.464  0.020  1.464
 G9L  CAW  CAX   aromatic  1.406  0.020  1.406

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
 G9L  CAN   N11  CAM  112.24  3.000
 G9L  CAN   N11  CAL  111.61  3.000
 G9L  CAM   N11  CAL  110.94  3.000
 G9L  CAR   N12  CAP  120.60  3.000
 G9L  CAP   N12  CAO  113.85  3.000
 G9L  CAR   N12  CAO  125.40  3.000
 G9L  HN13  N13  CAV  116.09  3.000
 G9L  HN13  N13  CAT  117.76  3.000
 G9L  CAV   N13  CAT  126.14  3.000
 G9L  HAD   CAD  CAS  120.24  3.000
 G9L  HAD   CAD  CAE  120.64  3.000
 G9L  CAS   CAD  CAE  119.12  3.000
 G9L  HAE   CAE  CAW  120.41  3.000
 G9L  HAE   CAE  CAD  118.38  3.000
 G9L  CAW   CAE  CAD  121.22  3.000
 G9L  HAF   CAF  CAX  120.48  3.000
 G9L  HAF   CAF  CAS  120.78  3.000
 G9L  CAX   CAF  CAS  118.74  3.000
 G9L  HAGA  CAG  HAG  106.66  3.000
 G9L  HAGA  CAG  CAI  109.34  3.000
 G9L  HAG   CAG  CAI  110.86  3.000
 G9L  HAGA  CAG  CAH  109.29  3.000
 G9L  HAG   CAG  CAH  110.71  3.000
 G9L  CAI   CAG  CAH  109.92  3.000
 G9L  HAHA  CAH  HAH  107.00  3.000
 G9L  HAHA  CAH  CAL  109.02  3.000
 G9L  HAH   CAH  CAL  109.29  3.000
 G9L  HAHA  CAH  CAG  109.70  3.000
 G9L  HAH   CAH  CAG  110.88  3.000
 G9L  CAL   CAH  CAG  110.84  3.000
 G9L  HAIA  CAI  HAI  106.99  3.000
 G9L  HAIA  CAI  CAM  109.18  3.000
 G9L  HAI   CAI  CAM  109.17  3.000
 G9L  HAIA  CAI  CAG  110.87  3.000
 G9L  HAI   CAI  CAG  109.82  3.000
 G9L  CAM   CAI  CAG  110.73  3.000
 G9L  HAJA  CAJ  HAJ  105.92  3.000
 G9L  HAJA  CAJ  CAR  108.86  3.000
 G9L  HAJ   CAJ  CAR  109.81  3.000
 G9L  HAJA  CAJ  CAN  111.04  3.000
 G9L  HAJ   CAJ  CAN  108.42  3.000
 G9L  CAR   CAJ  CAN  112.58  3.000
 G9L  HAKA  CAK  HAK  106.80  3.000
 G9L  HAKA  CAK  CAT  110.00  3.000
 G9L  HAK   CAK  CAT  110.00  3.000
 G9L  HAKA  CAK  CAO  110.55  3.000
 G9L  HAK   CAK  CAO  109.66  3.000
 G9L  CAT   CAK  CAO  109.80  3.000
 G9L  HALA  CAL  HAL  106.71  3.000
 G9L  HALA  CAL  CAH  109.14  3.000
 G9L  HAL   CAL  CAH  109.61  3.000
 G9L  HALA  CAL  N11  111.57  3.000
 G9L  HAL   CAL  N11  108.48  3.000
 G9L  CAH   CAL  N11  111.21  3.000
 G9L  HAMA  CAM  HAM  106.40  3.000
 G9L  HAMA  CAM  CAI  109.38  3.000
 G9L  HAM   CAM  CAI  109.19  3.000
 G9L  HAMA  CAM  N11  109.39  3.000
 G9L  HAM   CAM  N11  110.82  3.000
 G9L  CAI   CAM  N11  111.52  3.000
 G9L  HANA  CAN  HAN  106.36  3.000
 G9L  HANA  CAN  CAJ  108.55  3.000
 G9L  HAN   CAN  CAJ  110.53  3.000
 G9L  HANA  CAN  N11  107.92  3.000
 G9L  HAN   CAN  N11  111.78  3.000
 G9L  CAJ   CAN  N11  111.48  3.000
 G9L  HAOA  CAO  HAO  106.80  3.000
 G9L  HAOA  CAO  CAK  110.52  3.000
 G9L  HAO   CAO  CAK  109.81  3.000
 G9L  HAOA  CAO  N12  111.38  3.000
 G9L  HAO   CAO  N12  108.48  3.000
 G9L  CAK   CAO  N12  109.78  3.000
 G9L  HAPA  CAP  HAP  106.69  3.000
 G9L  HAPA  CAP  CAU  109.98  3.000
 G9L  HAP   CAP  CAU  110.04  3.000
 G9L  HAPA  CAP  N12  109.77  3.000
 G9L  HAP   CAP  N12  108.46  3.000
 G9L  CAU   CAP  N12  111.76  3.000
 G9L  CAJ   CAR  OAA  121.19  3.000
 G9L  CAJ   CAR  N12  117.13  3.000
 G9L  OAA   CAR  N12  121.69  3.000
 G9L  CAF   CAS  CAD  121.96  3.000
 G9L  CAF   CAS  FAC  119.45  3.000
 G9L  CAD   CAS  FAC  118.59  3.000
 G9L  CAU   CAT  CAK  123.07  3.000
 G9L  CAU   CAT  N13  120.64  3.000
 G9L  CAK   CAT  N13  116.29  3.000
 G9L  CAW   CAU  CAT  118.59  3.000
 G9L  CAW   CAU  CAP  120.03  3.000
 G9L  CAT   CAU  CAP  121.38  3.000
 G9L  CAX   CAV  OAB  124.24  3.000
 G9L  CAX   CAV  N13  114.27  3.000
 G9L  OAB   CAV  N13  121.48  3.000
 G9L  CAX   CAW  CAU  119.73  3.000
 G9L  CAX   CAW  CAE  117.87  3.000
 G9L  CAU   CAW  CAE  122.39  3.000
 G9L  CAW   CAX  CAV  120.59  3.000
 G9L  CAW   CAX  CAF  121.08  3.000
 G9L  CAV   CAX  CAF  118.33  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
 G9L  CONST_01  CAX   CAW  CAE  CAD     0.00   0.0  0
 G9L  CONST_02  CAX   CAF  CAS  CAD     0.00   0.0  0
 G9L  CONST_03  CAF   CAS  CAD  CAE     0.00   0.0  0
 G9L  CONST_04  CAF   CAX  CAW  CAE     0.00   0.0  0
 G9L  CONST_05  CAW   CAE  CAD  CAS     0.00   0.0  0
 G9L  CONST_06  CAW   CAX  CAF  CAS     0.00   0.0  0
 G9L  CONST_07  CAX   CAV  N13  CAT     0.00   0.0  0
 G9L  CONST_08  CAE   CAD  CAS  FAC   180.00   0.0  0
 G9L  CONST_09  CAX   CAF  CAS  FAC   180.00   0.0  0
 G9L  CONST_10  CAT   N13  CAV  OAB   180.00   0.0  0
 G9L  CONST_11  HAF   CAF  CAS  CAD   180.00   0.0  0
 G9L  CONST_12  HAD   CAD  CAS  CAF   180.00   0.0  0
 G9L  CONST_13  HAE   CAE  CAD  CAS   180.00   0.0  0
 G9L  CONST_14  HN13  N13  CAV  CAX   180.00   0.0  0
 G9L  CONST_15  CAO   N12  CAR  OAA   180.00   0.0  0
 G9L  CONST_16  CAP   N12  CAR  OAA     0.00   0.0  0
 G9L  CONST_17  CAO   N12  CAR  CAJ     0.00   0.0  0
 G9L  CONST_18  CAP   N12  CAR  CAJ   180.00   0.0  0
 G9L  Var_01    CAG   CAI  CAM  N11    56.36  30.0  1
 G9L  Var_02    CAG   CAH  CAL  N11   -56.80  30.0  1
 G9L  Var_03    CAT   CAK  CAO  N12    48.57  30.0  1
 G9L  Var_04    CAT   CAU  CAP  N12   -10.58  30.0  1
 G9L  Var_05    CAO   CAK  CAT  N13   162.27  30.0  1
 G9L  Var_06    CAM   CAI  CAG  CAH   -52.87  30.0  1
 G9L  Var_07    CAM   N11  CAL  CAH    59.56  30.0  1
 G9L  Var_08    CAL   CAH  CAG  CAI    53.20  30.0  1
 G9L  Var_09    CAL   N11  CAM  CAI   -59.46  30.0  1
 G9L  Var_10    CAP   N12  CAO  CAK   -65.48  30.0  1
 G9L  Var_11    CAU   CAP  N12  CAO    44.54  30.0  1
 G9L  Var_12    CAR   CAJ  CAN  N11  -175.69  30.0  3
 G9L  Var_13    CAN   CAJ  CAR  N12   178.26  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
 G9L  plan-1  N12   0.020
 G9L  plan-1  OAA   0.020
 G9L  plan-1  CAJ   0.020
 G9L  plan-1  CAO   0.020
 G9L  plan-1  CAP   0.020
 G9L  plan-1  CAR   0.020
 G9L  plan-2  N13   0.020
 G9L  plan-2  CAD   0.020
 G9L  plan-2  CAE   0.020
 G9L  plan-2  CAF   0.020
 G9L  plan-2  CAK   0.020
 G9L  plan-2  CAP   0.020
 G9L  plan-2  CAS   0.020
 G9L  plan-2  CAT   0.020
 G9L  plan-2  CAU   0.020
 G9L  plan-2  CAV   0.020
 G9L  plan-2  CAW   0.020
 G9L  plan-2  CAX   0.020
 G9L  plan-2  HN13  0.020
 G9L  plan-2  HAD   0.020
 G9L  plan-2  HAE   0.020
 G9L  plan-2  HAF   0.020
 G9L  plan-2  OAB   0.020
 G9L  plan-2  FAC   0.020

