# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 06:28:41 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: N-(6-oxo-5H-benzo[h][1,5]naphthyridin-2-yl)-2-(4-pyrrolidin-1-ylpiperidin-1-yl)ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(CN1CCC(CC1)N2CCCC2)Nc3ccc4NC(=O)c5ccccc5c4n3
#
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
 G9M  G9M  N-(6-oxo-5H-benzo[h][1,5]naphthyridin-2-yl)-2-(4-pyrrolidin-1-ylpiperidin-1-yl)ethanamide  ligand  57  30  .  2021-08-10  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_G9M
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
 G9M  C     C  C     0   0.513   0.2570  -1.2570  -0.5089
 G9M  O     O  O     0  -0.422   0.1333  -0.1349  -0.9430
 G9M  CA    C  CH2   0  -0.417   1.5623  -2.0393  -0.6106
 G9M  N11   N  NT    0  -0.434   6.4356   0.7267   0.1656
 G9M  N12   N  NT    0  -0.406   2.7064  -1.1740  -0.5619
 G9M  N13   N  NH1   0  -0.739  -0.7411  -1.9845   0.0787
 G9M  N14   N  NR16  0  -0.766  -6.0194  -0.6773   0.8453
 G9M  N15   N  N     0  -0.437  -2.5261  -0.4901  -0.1379
 G9M  OAB   O  O     0  -0.466  -7.7494   0.7529   0.6525
 G9M  CAC   C  CR16  0  -0.248  -5.2702   3.5870  -1.2306
 G9M  CAD   C  CR16  0  -0.233  -3.9277   3.2570  -1.4280
 G9M  CAE   C  CR16  0  -0.390  -2.9051  -2.5969   0.9021
 G9M  CAF   C  CR16  0  -0.281  -6.1182   2.6880  -0.6174
 G9M  CAG   C  CR16  0  -0.295  -3.4406   2.0344  -1.0150
 G9M  CAH   C  CR16  0  -0.198  -4.2260  -2.2868   1.1019
 G9M  CAI   C  CH2   0  -0.464   8.7175   1.2928  -0.0120
 G9M  CAJ   C  CH2   0  -0.463   8.1098   2.0147   1.2066
 G9M  CAK   C  CH2   0  -0.458   5.0535  -0.8179  -1.1670
 G9M  CAL   C  CH2   0  -0.457   4.0908   0.3263   0.8042
 G9M  CAM   C  CH2   0  -0.282   7.6924   0.2145  -0.3632
 G9M  CAN   C  CH2   0  -0.282   6.7963   1.2776   1.4641
 G9M  CAO   C  CH2   0  -0.281   3.8924  -1.7977  -1.1167
 G9M  CAP   C  CH2   0  -0.281   2.9560  -0.6840   0.7801
 G9M  CAV   C  CR6   0   0.501  -2.0779  -1.6516   0.2674
 G9M  CAW   C  CR6   0   0.498  -6.5677   0.5080   0.4591
 G9M  CAX   C  CR66  0   0.325  -4.7040  -1.0468   0.6710
 G9M  CAY   C  CR66  0  -0.155  -5.6381   1.4470  -0.1933
 G9M  CAZ   C  CR66  0   0.193  -4.2914   1.1146  -0.3931
 G9M  CBA   C  CR66  0   0.114  -3.8084  -0.1792   0.0538
 G9M  CBB   C  CH1   0  -0.030   5.3723  -0.2598   0.2179
 G9M  HA    H  HCH2  0   0.225   1.5960  -2.8394   0.1492
 G9M  HAA   H  HCH2  0   0.288   1.5378  -2.5487  -1.5803
 G9M  HN13  H  HNH1  0   0.418  -0.4758  -2.8907   0.4332
 G9M  HN14  H  HNR6  0   0.418  -6.6413  -1.3354   1.2964
 G9M  HAC   H  HCR6  0   0.268  -5.6448   4.5468  -1.5598
 G9M  HAD   H  HCR6  0   0.269  -3.2649   3.9648  -1.9084
 G9M  HAE   H  HCR6  0   0.290  -2.5123  -3.5503   1.2300
 G9M  HAF   H  HCR6  0   0.267  -7.1586   2.9394  -0.4629
 G9M  HAG   H  HCR6  0   0.269  -2.4017   1.7702  -1.1633
 G9M  HAH   H  HCR6  0   0.295  -4.8862  -2.9935   1.5886
 G9M  HAI   H  HCH2  0   0.233   8.8515   1.9843  -0.8446
 G9M  HAIA  H  HCH2  0   0.233   9.6922   0.8558   0.2029
 G9M  HAJ   H  HCH2  0   0.233   8.7596   1.9845   2.0806
 G9M  HAJA  H  HCH2  0   0.233   7.9239   3.0651   0.9808
 G9M  HAK   H  HCH2  0   0.243   5.9155  -1.3345  -1.5924
 G9M  HAKA  H  HCH2  0   0.220   4.8074   0.0096  -1.8398
 G9M  HAL   H  HCH2  0   0.221   3.8050   1.2128   0.2296
 G9M  HALA  H  HCH2  0   0.242   4.2387   0.6444   1.8376
 G9M  HAM   H  HCH2  0   0.188   7.9649  -0.7424   0.1146
 G9M  HAMA  H  HCH2  0   0.234   7.6337   0.0333  -1.4368
 G9M  HAN   H  HCH2  0   0.234   6.0196   1.9370   1.8528
 G9M  HANA  H  HCH2  0   0.188   6.9465   0.4776   2.2107
 G9M  HAO   H  HCH2  0   0.190   4.1940  -2.6893  -0.5384
 G9M  HAOA  H  HCH2  0   0.242   3.6658  -2.1443  -2.1277
 G9M  HAP   H  HCH2  0   0.245   2.0517  -0.2100   1.1671
 G9M  HAPA  H  HCH2  0   0.186   3.1916  -1.5161   1.4686
 G9M  HBB   H  HCH1  0   0.169   5.6823  -1.1097   0.8612

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
 G9M  O    C     double    1.209  0.020  1.209
 G9M  CA   C     single    1.525  0.020  1.525
 G9M  C    N13   single    1.368  0.020  1.368
 G9M  N12  CA    single    1.435  0.020  1.435
 G9M  CA   HA    single    0.970  0.020  1.090
 G9M  CA   HAA   single    0.970  0.020  1.090
 G9M  CAM  N11   single    1.457  0.020  1.457
 G9M  CAN  N11   single    1.456  0.020  1.456
 G9M  N11  CBB   single    1.451  0.020  1.451
 G9M  CAO  N12   single    1.450  0.020  1.450
 G9M  CAP  N12   single    1.450  0.020  1.450
 G9M  N13  CAV   single    1.391  0.020  1.391
 G9M  N13  HN13  single    0.860  0.020  1.020
 G9M  CAX  N14   single    1.377  0.020  1.377
 G9M  N14  CAW   single    1.362  0.020  1.362
 G9M  N14  HN14  single    0.860  0.020  1.020
 G9M  CAV  N15   aromatic  1.309  0.020  1.309
 G9M  N15  CBA   aromatic  1.333  0.020  1.333
 G9M  CAW  OAB   double    1.222  0.020  1.222
 G9M  CAD  CAC   aromatic  1.397  0.020  1.397
 G9M  CAF  CAC   aromatic  1.380  0.020  1.380
 G9M  CAC  HAC   single    0.930  0.020  1.080
 G9M  CAG  CAD   aromatic  1.379  0.020  1.379
 G9M  CAD  HAD   single    0.930  0.020  1.080
 G9M  CAE  CAV   aromatic  1.407  0.020  1.407
 G9M  CAE  CAH   aromatic  1.372  0.020  1.372
 G9M  CAE  HAE   single    0.930  0.020  1.080
 G9M  CAY  CAF   aromatic  1.397  0.020  1.397
 G9M  CAF  HAF   single    0.930  0.020  1.080
 G9M  CAZ  CAG   aromatic  1.399  0.020  1.399
 G9M  CAG  HAG   single    0.930  0.020  1.080
 G9M  CAH  CAX   aromatic  1.397  0.020  1.397
 G9M  CAH  HAH   single    0.930  0.020  1.080
 G9M  CAI  CAJ   single    1.541  0.020  1.541
 G9M  CAI  CAM   single    1.529  0.020  1.529
 G9M  CAI  HAI   single    0.970  0.020  1.090
 G9M  CAI  HAIA  single    0.970  0.020  1.090
 G9M  CAJ  CAN   single    1.528  0.020  1.528
 G9M  CAJ  HAJ   single    0.970  0.020  1.090
 G9M  CAJ  HAJA  single    0.970  0.020  1.090
 G9M  CBB  CAK   single    1.527  0.020  1.527
 G9M  CAK  CAO   single    1.520  0.020  1.520
 G9M  CAK  HAK   single    0.970  0.020  1.090
 G9M  CAK  HAKA  single    0.970  0.020  1.090
 G9M  CBB  CAL   single    1.526  0.020  1.526
 G9M  CAL  CAP   single    1.520  0.020  1.520
 G9M  CAL  HAL   single    0.970  0.020  1.090
 G9M  CAL  HALA  single    0.970  0.020  1.090
 G9M  CAM  HAM   single    0.970  0.020  1.090
 G9M  CAM  HAMA  single    0.970  0.020  1.090
 G9M  CAN  HAN   single    0.970  0.020  1.090
 G9M  CAN  HANA  single    0.970  0.020  1.090
 G9M  CAO  HAO   single    0.970  0.020  1.090
 G9M  CAO  HAOA  single    0.970  0.020  1.090
 G9M  CAP  HAP   single    0.970  0.020  1.090
 G9M  CAP  HAPA  single    0.970  0.020  1.090
 G9M  CAW  CAY   single    1.474  0.020  1.474
 G9M  CAX  CBA   aromatic  1.391  0.020  1.391
 G9M  CAZ  CAY   aromatic  1.401  0.020  1.401
 G9M  CBA  CAZ   aromatic  1.452  0.020  1.452
 G9M  CBB  HBB   single    0.970  0.020  1.090

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
 G9M  N13   C    CA   112.35  3.000
 G9M  N13   C    O    124.96  3.000
 G9M  CA    C    O    122.65  3.000
 G9M  HAA   CA   HA   105.83  3.000
 G9M  HAA   CA   N12  109.16  3.000
 G9M  HA    CA   N12  112.91  3.000
 G9M  HAA   CA   C    106.16  3.000
 G9M  HA    CA   C    110.61  3.000
 G9M  N12   CA   C    111.76  3.000
 G9M  CBB   N11  CAN  113.99  3.000
 G9M  CBB   N11  CAM  113.97  3.000
 G9M  CAN   N11  CAM  104.07  3.000
 G9M  CAP   N12  CAO  111.01  3.000
 G9M  CAP   N12  CA   111.86  3.000
 G9M  CAO   N12  CA   112.31  3.000
 G9M  HN13  N13  CAV  114.85  3.000
 G9M  HN13  N13  C    115.91  3.000
 G9M  CAV   N13  C    129.24  3.000
 G9M  HN14  N14  CAX  117.97  3.000
 G9M  HN14  N14  CAW  116.43  3.000
 G9M  CAX   N14  CAW  125.59  3.000
 G9M  CBA   N15  CAV  119.44  3.000
 G9M  HAC   CAC  CAF  120.04  3.000
 G9M  HAC   CAC  CAD  119.97  3.000
 G9M  CAF   CAC  CAD  119.98  3.000
 G9M  HAD   CAD  CAG  119.77  3.000
 G9M  HAD   CAD  CAC  119.80  3.000
 G9M  CAG   CAD  CAC  120.44  3.000
 G9M  HAE   CAE  CAV  121.01  3.000
 G9M  HAE   CAE  CAH  120.31  3.000
 G9M  CAV   CAE  CAH  118.67  3.000
 G9M  HAF   CAF  CAY  119.60  3.000
 G9M  HAF   CAF  CAC  120.23  3.000
 G9M  CAY   CAF  CAC  120.18  3.000
 G9M  HAG   CAG  CAZ  118.97  3.000
 G9M  HAG   CAG  CAD  120.96  3.000
 G9M  CAZ   CAG  CAD  120.08  3.000
 G9M  HAH   CAH  CAX  120.62  3.000
 G9M  HAH   CAH  CAE  120.34  3.000
 G9M  CAX   CAH  CAE  119.04  3.000
 G9M  HAIA  CAI  HAI  107.15  3.000
 G9M  HAIA  CAI  CAM  111.24  3.000
 G9M  HAI   CAI  CAM  110.74  3.000
 G9M  HAIA  CAI  CAJ  112.63  3.000
 G9M  HAI   CAI  CAJ  110.80  3.000
 G9M  CAM   CAI  CAJ  104.34  3.000
 G9M  HAJA  CAJ  HAJ  107.13  3.000
 G9M  HAJA  CAJ  CAN  110.67  3.000
 G9M  HAJ   CAJ  CAN  111.35  3.000
 G9M  HAJA  CAJ  CAI  110.78  3.000
 G9M  HAJ   CAJ  CAI  112.71  3.000
 G9M  CAN   CAJ  CAI  104.26  3.000
 G9M  HAKA  CAK  HAK  107.21  3.000
 G9M  HAKA  CAK  CBB  109.16  3.000
 G9M  HAK   CAK  CBB  111.20  3.000
 G9M  HAKA  CAK  CAO  109.62  3.000
 G9M  HAK   CAK  CAO  108.13  3.000
 G9M  CBB   CAK  CAO  111.41  3.000
 G9M  HALA  CAL  HAL  107.24  3.000
 G9M  HALA  CAL  CBB  111.22  3.000
 G9M  HAL   CAL  CBB  109.19  3.000
 G9M  HALA  CAL  CAP  108.06  3.000
 G9M  HAL   CAL  CAP  109.58  3.000
 G9M  CBB   CAL  CAP  111.45  3.000
 G9M  HAMA  CAM  HAM  107.18  3.000
 G9M  HAMA  CAM  CAI  112.31  3.000
 G9M  HAM   CAM  CAI  110.28  3.000
 G9M  HAMA  CAM  N11  111.68  3.000
 G9M  HAM   CAM  N11  111.14  3.000
 G9M  CAI   CAM  N11  104.31  3.000
 G9M  HANA  CAN  HAN  107.09  3.000
 G9M  HANA  CAN  CAJ  110.27  3.000
 G9M  HAN   CAN  CAJ  112.38  3.000
 G9M  HANA  CAN  N11  111.25  3.000
 G9M  HAN   CAN  N11  111.73  3.000
 G9M  CAJ   CAN  N11  104.19  3.000
 G9M  HAOA  CAO  HAO  106.56  3.000
 G9M  HAOA  CAO  CAK  109.41  3.000
 G9M  HAO   CAO  CAK  109.20  3.000
 G9M  HAOA  CAO  N12  108.71  3.000
 G9M  HAO   CAO  N12  111.72  3.000
 G9M  CAK   CAO  N12  111.11  3.000
 G9M  HAPA  CAP  HAP  106.40  3.000
 G9M  HAPA  CAP  CAL  109.36  3.000
 G9M  HAP   CAP  CAL  108.92  3.000
 G9M  HAPA  CAP  N12  111.02  3.000
 G9M  HAP   CAP  N12  109.40  3.000
 G9M  CAL   CAP  N12  111.59  3.000
 G9M  CAE   CAV  N15  122.30  3.000
 G9M  CAE   CAV  N13  117.74  3.000
 G9M  N15   CAV  N13  119.96  3.000
 G9M  CAY   CAW  OAB  123.52  3.000
 G9M  CAY   CAW  N14  115.23  3.000
 G9M  OAB   CAW  N14  121.25  3.000
 G9M  CBA   CAX  CAH  118.04  3.000
 G9M  CBA   CAX  N14  120.24  3.000
 G9M  CAH   CAX  N14  121.72  3.000
 G9M  CAZ   CAY  CAW  121.21  3.000
 G9M  CAZ   CAY  CAF  119.85  3.000
 G9M  CAW   CAY  CAF  118.94  3.000
 G9M  CBA   CAZ  CAY  119.16  3.000
 G9M  CBA   CAZ  CAG  121.37  3.000
 G9M  CAY   CAZ  CAG  119.47  3.000
 G9M  CAZ   CBA  CAX  118.57  3.000
 G9M  CAZ   CBA  N15  118.92  3.000
 G9M  CAX   CBA  N15  122.51  3.000
 G9M  HBB   CBB  CAL  107.81  3.000
 G9M  HBB   CBB  CAK  107.70  3.000
 G9M  CAL   CBB  CAK  108.27  3.000
 G9M  HBB   CBB  N11  109.68  3.000
 G9M  CAL   CBB  N11  111.59  3.000
 G9M  CAK   CBB  N11  111.64  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
 G9M  CONST_01  CAH   CAE  CAV  N15    0.00   0.0  0
 G9M  CONST_02  CAH   CAX  CBA  N15    0.00   0.0  0
 G9M  CONST_03  CAG   CAZ  CBA  N15    0.00   0.0  0
 G9M  CONST_04  CAY   CAZ  CBA  N15  180.00   0.0  0
 G9M  CONST_05  CAZ   CAG  CAD  CAC    0.00   0.0  0
 G9M  CONST_06  CAZ   CAY  CAF  CAC    0.00   0.0  0
 G9M  CONST_07  CAY   CAF  CAC  CAD    0.00   0.0  0
 G9M  CONST_08  CAY   CAZ  CAG  CAD    0.00   0.0  0
 G9M  CONST_09  CBA   CAZ  CAG  CAD  180.00   0.0  0
 G9M  CONST_10  CBA   N15  CAV  CAE    0.00   0.0  0
 G9M  CONST_11  CBA   CAX  CAH  CAE    0.00   0.0  0
 G9M  CONST_12  CAG   CAD  CAC  CAF    0.00   0.0  0
 G9M  CONST_13  CAG   CAZ  CAY  CAF    0.00   0.0  0
 G9M  CONST_14  CBA   CAZ  CAY  CAF  180.00   0.0  0
 G9M  CONST_15  CAX   CBA  CAZ  CAG  180.00   0.0  0
 G9M  CONST_16  CAZ   CBA  CAX  CAH  180.00   0.0  0
 G9M  CONST_17  CAX   CBA  N15  CAV    0.00   0.0  0
 G9M  CONST_18  CAZ   CBA  N15  CAV  180.00   0.0  0
 G9M  CONST_19  CAX   CAH  CAE  CAV    0.00   0.0  0
 G9M  CONST_20  CAY   CAZ  CBA  CAX    0.00   0.0  0
 G9M  CONST_21  CAY   CAW  N14  CAX    0.00   0.0  0
 G9M  CONST_22  CBA   N15  CAV  N13  180.00   0.0  0
 G9M  CONST_23  CAH   CAE  CAV  N13  180.00   0.0  0
 G9M  CONST_24  CAX   N14  CAW  OAB  180.00   0.0  0
 G9M  CONST_25  HAH   CAH  CAX  N14    0.00   0.0  0
 G9M  CONST_26  HAE   CAE  CAV  N15  180.00   0.0  0
 G9M  CONST_27  HAG   CAG  CAD  CAC  180.00   0.0  0
 G9M  CONST_28  HAF   CAF  CAC  CAD  180.00   0.0  0
 G9M  CONST_29  HAD   CAD  CAC  CAF  180.00   0.0  0
 G9M  CONST_30  HAC   CAC  CAD  CAG  180.00   0.0  0
 G9M  CONST_31  HN14  N14  CAW  CAY  180.00   0.0  0
 G9M  CONST_32  N15   CAV  N13  C      0.00   0.0  0
 G9M  CONST_33  CAE   CAV  N13  C    180.00   0.0  0
 G9M  CONST_34  HN13  N13  CAV  N15  180.00   0.0  0
 G9M  CONST_35  CAV   N13  C    O      0.00   0.0  0
 G9M  CONST_36  CAV   N13  C    CA   180.00   0.0  0
 G9M  Var_01    CAJ   CAI  CAM  N11   24.66  30.0  1
 G9M  Var_02    CAI   CAJ  CAN  N11  -25.92  30.0  1
 G9M  Var_03    CBB   CAK  CAO  N12   57.63  30.0  1
 G9M  Var_04    CBB   CAL  CAP  N12  -56.70  30.0  1
 G9M  Var_05    CAN   N11  CAM  CAI  -42.04  30.0  1
 G9M  Var_06    CAM   N11  CAN  CAJ   42.54  30.0  1
 G9M  Var_07    CAP   N12  CAO  CAK  -59.06  30.0  1
 G9M  Var_08    CAO   N12  CAP  CAL   58.73  30.0  1
 G9M  Var_09    CAN   CAJ  CAI  CAM    0.76  30.0  1
 G9M  Var_10    N12   CA   C    O     31.67  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
 G9M  chir_01  CBB  N11  CAK  CAL  positiv

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
 G9M  plan-1  C     0.020
 G9M  plan-1  O     0.020
 G9M  plan-1  CA    0.020
 G9M  plan-1  N13   0.020
 G9M  plan-1  CAV   0.020
 G9M  plan-1  HN13  0.020
 G9M  plan-2  N13   0.020
 G9M  plan-2  N14   0.020
 G9M  plan-2  N15   0.020
 G9M  plan-2  OAB   0.020
 G9M  plan-2  CAC   0.020
 G9M  plan-2  CAD   0.020
 G9M  plan-2  CAE   0.020
 G9M  plan-2  CAF   0.020
 G9M  plan-2  CAG   0.020
 G9M  plan-2  CAH   0.020
 G9M  plan-2  CAV   0.020
 G9M  plan-2  CAW   0.020
 G9M  plan-2  CAX   0.020
 G9M  plan-2  CAY   0.020
 G9M  plan-2  CAZ   0.020
 G9M  plan-2  CBA   0.020
 G9M  plan-2  HN14  0.020
 G9M  plan-2  HAC   0.020
 G9M  plan-2  HAD   0.020
 G9M  plan-2  HAE   0.020
 G9M  plan-2  HAF   0.020
 G9M  plan-2  HAG   0.020
 G9M  plan-2  HAH   0.020

