# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 08:06:53 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 8-[[(3R,4R)-3-(cyclohexylmethoxy)piperidin-4-yl]amino]-3-methyl-1H-1,7-naphthyridin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=Cc2ccnc(N[C@@H]3CCNC[C@H]3OCC4CCCCC4)c2NC1=O
#
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
 78J  78J  8-[[(3R,4R)-3-(cyclohexylmethoxy)piperidin-4-yl]amino]-3-methyl-1H-1,7-naphthyridin-2-one  ligand  57  27  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_78J
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
 78J  C01   C  CH3   0  -0.712   5.2239   3.3501  -0.5332
 78J  C05   C  CR6   0  -0.112   4.3195   2.2059  -0.2205
 78J  C06   C  CR16  0  -0.193   4.5187   1.3690   0.8195
 78J  C08   C  CR66  0   0.128   3.6365   0.2746   1.1012
 78J  C09   C  CR16  0  -0.428   3.7938  -0.5872   2.2023
 78J  C11   C  CR16  0  -0.080   2.8615  -1.5728   2.3831
 78J  N13   N  N     0  -0.465   1.8414  -1.7959   1.5421
 78J  C14   C  CR6   0   0.507   1.6823  -1.0217   0.4885
 78J  N15   N  NH1   0  -0.690   0.6395  -1.2416  -0.3609
 78J  C17   C  CH1   0  -0.101  -0.3237  -2.3041  -0.1647
 78J  C19   C  CH2   0  -0.453   0.1397  -3.6366  -0.7559
 78J  C22   C  CH2   0  -0.321  -0.9490  -4.6994  -0.6430
 78J  N25   N  NH1   0  -0.576  -2.2221  -4.2913  -1.2132
 78J  C27   C  CH2   0  -0.340  -2.6767  -3.0320  -0.6566
 78J  C30   C  CH1   0   0.081  -1.6599  -1.8893  -0.7761
 78J  O32   O  O2    0  -0.494  -2.1070  -0.7323  -0.1162
 78J  C33   C  CH2   0  -0.112  -2.9607   0.0919  -0.8736
 78J  C36   C  CH1   0  -0.279  -3.2797   1.3548  -0.0937
 78J  C38   C  CH2   0  -0.424  -4.1282   2.2918  -0.9535
 78J  C41   C  CH2   0  -0.429  -4.4823   3.5783  -0.2146
 78J  C44   C  CH2   0  -0.429  -5.1785   3.2819   1.1096
 78J  C47   C  CH2   0  -0.434  -4.3380   2.3490   1.9740
 78J  C50   C  CH2   0  -0.411  -3.9855   1.0633   1.2313
 78J  C53   C  CR66  0   0.213   2.5570   0.0779   0.2535
 78J  N54   N  NR16  0  -0.748   2.3544   0.9563  -0.7818
 78J  C56   C  CR6   0   0.516   3.1538   2.0238  -1.0872
 78J  O57   O  O     0  -0.479   2.8830   2.7671  -2.0223
 78J  H011  H  HCH3  0   0.252   5.6537   3.2523  -1.5313
 78J  H012  H  HCH3  0   0.251   4.6837   4.2977  -0.5129
 78J  H013  H  HCH3  0   0.248   6.0401   3.4072   0.1844
 78J  H06   H  HCR6  0   0.271   5.3704   1.5152   1.4744
 78J  H09   H  HCR6  0   0.262   4.6188  -0.4608   2.8896
 78J  H11   H  HCR6  0   0.256   2.9257  -2.2424   3.2328
 78J  H15   H  HNH1  0   0.381   0.7860  -0.9991  -1.3290
 78J  H17   H  HCH1  0   0.247  -0.4631  -2.4273   0.9128
 78J  H191  H  HCH2  0   0.220   0.3998  -3.4938  -1.8107
 78J  H192  H  HCH2  0   0.242   1.0481  -3.9648  -0.2455
 78J  H30   H  HCH1  0   0.196  -1.4996  -1.6781  -1.8477
 78J  H221  H  HCH2  0   0.242  -0.6250  -5.6222  -1.1271
 78J  H222  H  HCH2  0   0.221  -1.1124  -4.9418   0.4125
 78J  H25   H  HNH1  0   0.342  -2.1268  -4.2018  -2.2182
 78J  H271  H  HCH2  0   0.241  -3.6133  -2.7485  -1.1423
 78J  H272  H  HCH2  0   0.222  -2.9044  -3.1821   0.4048
 78J  H331  H  HCH2  0   0.203  -2.4795   0.3585  -1.8266
 78J  H332  H  HCH2  0   0.186  -3.8986  -0.4241  -1.1279
 78J  H36   H  HCH1  0   0.213  -2.3315   1.8642   0.1260
 78J  H381  H  HCH2  0   0.226  -3.6016   2.5258  -1.8835
 78J  H382  H  HCH2  0   0.208  -5.0522   1.7760  -1.2418
 78J  H501  H  HCH2  0   0.201  -4.9037   0.4978   1.0285
 78J  H502  H  HCH2  0   0.228  -3.3616   0.4277   1.8628
 78J  H411  H  HCH2  0   0.209  -3.5678   4.1507  -0.0247
 78J  H412  H  HCH2  0   0.226  -5.1163   4.2073  -0.8445
 78J  H441  H  HCH2  0   0.225  -5.3889   4.2116   1.6443
 78J  H442  H  HCH2  0   0.207  -6.1479   2.8122   0.9089
 78J  H471  H  HCH2  0   0.208  -3.4144   2.8607   2.2666
 78J  H472  H  HCH2  0   0.225  -4.8659   2.1115   2.9010
 78J  H54   H  HNR6  0   0.405   1.5151   0.8816  -1.3397

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
 78J  C01  C05   single    1.492  0.020  1.492
 78J  C05  C06   double    1.350  0.020  1.350
 78J  C05  C56   single    1.464  0.020  1.464
 78J  C06  C08   single    1.434  0.020  1.434
 78J  C08  C09   aromatic  1.407  0.020  1.407
 78J  C08  C53   aromatic  1.387  0.020  1.387
 78J  C09  C11   aromatic  1.369  0.020  1.369
 78J  C11  N13   aromatic  1.341  0.020  1.341
 78J  N13  C14   aromatic  1.317  0.020  1.317
 78J  C14  N15   single    1.363  0.020  1.363
 78J  C14  C53   aromatic  1.425  0.020  1.425
 78J  N15  C17   single    1.447  0.020  1.447
 78J  C17  C19   single    1.530  0.020  1.530
 78J  C17  C30   single    1.527  0.020  1.527
 78J  C19  C22   single    1.526  0.020  1.526
 78J  C22  N25   single    1.453  0.020  1.453
 78J  N25  C27   single    1.450  0.020  1.450
 78J  C27  C30   single    1.534  0.020  1.534
 78J  C30  O32   single    1.405  0.020  1.405
 78J  O32  C33   single    1.408  0.020  1.408
 78J  C33  C36   single    1.518  0.020  1.518
 78J  C36  C38   single    1.529  0.020  1.529
 78J  C36  C50   single    1.529  0.020  1.529
 78J  C38  C41   single    1.525  0.020  1.525
 78J  C41  C44   single    1.525  0.020  1.525
 78J  C44  C47   single    1.524  0.020  1.524
 78J  C47  C50   single    1.526  0.020  1.526
 78J  C53  N54   single    1.373  0.020  1.373
 78J  N54  C56   single    1.368  0.020  1.368
 78J  C56  O57   double    1.225  0.020  1.225
 78J  C01  H011  single    0.970  0.020  1.090
 78J  C01  H012  single    0.970  0.020  1.090
 78J  C01  H013  single    0.970  0.020  1.090
 78J  C06  H06   single    0.930  0.020  1.080
 78J  C09  H09   single    0.930  0.020  1.080
 78J  C11  H11   single    0.930  0.020  1.080
 78J  N15  H15   single    0.890  0.020  1.040
 78J  C17  H17   single    0.970  0.020  1.090
 78J  C19  H191  single    0.970  0.020  1.090
 78J  C19  H192  single    0.970  0.020  1.090
 78J  C30  H30   single    0.970  0.020  1.090
 78J  C22  H221  single    0.970  0.020  1.090
 78J  C22  H222  single    0.970  0.020  1.090
 78J  N25  H25   single    0.890  0.020  1.040
 78J  C27  H271  single    0.970  0.020  1.090
 78J  C27  H272  single    0.970  0.020  1.090
 78J  C33  H331  single    0.970  0.020  1.090
 78J  C33  H332  single    0.970  0.020  1.090
 78J  C36  H36   single    0.970  0.020  1.090
 78J  C38  H381  single    0.970  0.020  1.090
 78J  C38  H382  single    0.970  0.020  1.090
 78J  C50  H501  single    0.970  0.020  1.090
 78J  C50  H502  single    0.970  0.020  1.090
 78J  C41  H411  single    0.970  0.020  1.090
 78J  C41  H412  single    0.970  0.020  1.090
 78J  C44  H441  single    0.970  0.020  1.090
 78J  C44  H442  single    0.970  0.020  1.090
 78J  C47  H471  single    0.970  0.020  1.090
 78J  C47  H472  single    0.970  0.020  1.090
 78J  N54  H54   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
 78J  H013  C01  H012  108.27  3.000
 78J  H013  C01  H011  108.21  3.000
 78J  H012  C01  H011  106.85  3.000
 78J  H013  C01  C05   110.91  3.000
 78J  H012  C01  C05   111.23  3.000
 78J  H011  C01  C05   111.21  3.000
 78J  C56   C05  C06   119.78  3.000
 78J  C56   C05  C01   117.01  3.000
 78J  C06   C05  C01   123.20  3.000
 78J  H06   C06  C08   117.88  3.000
 78J  H06   C06  C05   119.85  3.000
 78J  C08   C06  C05   122.27  3.000
 78J  C53   C08  C09   118.59  3.000
 78J  C53   C08  C06   117.86  3.000
 78J  C09   C08  C06   123.54  3.000
 78J  H09   C09  C11   121.33  3.000
 78J  H09   C09  C08   120.74  3.000
 78J  C11   C09  C08   117.93  3.000
 78J  H11   C11  N13   115.73  3.000
 78J  H11   C11  C09   120.54  3.000
 78J  N13   C11  C09   123.72  3.000
 78J  C14   N13  C11   119.73  3.000
 78J  C53   C14  N15   119.44  3.000
 78J  C53   C14  N13   120.76  3.000
 78J  N15   C14  N13   119.75  3.000
 78J  H15   N15  C17   113.77  3.000
 78J  H15   N15  C14   116.63  3.000
 78J  C17   N15  C14   122.90  3.000
 78J  H17   C17  C30   108.28  3.000
 78J  H17   C17  C19   108.74  3.000
 78J  C30   C17  C19   110.31  3.000
 78J  H17   C17  N15   107.52  3.000
 78J  C30   C17  N15   109.19  3.000
 78J  C19   C17  N15   112.67  3.000
 78J  H192  C19  H191  106.95  3.000
 78J  H192  C19  C22   110.46  3.000
 78J  H191  C19  C22   109.35  3.000
 78J  H192  C19  C17   109.46  3.000
 78J  H191  C19  C17   109.30  3.000
 78J  C22   C19  C17   111.22  3.000
 78J  H222  C22  H221  106.54  3.000
 78J  H222  C22  N25   108.03  3.000
 78J  H221  C22  N25   108.87  3.000
 78J  H222  C22  C19   109.39  3.000
 78J  H221  C22  C19   110.14  3.000
 78J  N25   C22  C19   113.60  3.000
 78J  H25   N25  C27   109.48  3.000
 78J  H25   N25  C22   109.36  3.000
 78J  C27   N25  C22   111.59  3.000
 78J  H272  C27  H271  106.74  3.000
 78J  H272  C27  C30   108.37  3.000
 78J  H271  C27  C30   109.90  3.000
 78J  H272  C27  N25   108.54  3.000
 78J  H271  C27  N25   108.88  3.000
 78J  C30   C27  N25   114.15  3.000
 78J  H30   C30  O32   110.15  3.000
 78J  H30   C30  C27   108.32  3.000
 78J  O32   C30  C27   111.46  3.000
 78J  H30   C30  C17   108.27  3.000
 78J  O32   C30  C17   108.31  3.000
 78J  C27   C30  C17   110.27  3.000
 78J  C33   O32  C30   114.99  3.000
 78J  H332  C33  H331  106.63  3.000
 78J  H332  C33  C36   109.25  3.000
 78J  H331  C33  C36   109.59  3.000
 78J  H332  C33  O32   111.51  3.000
 78J  H331  C33  O32   110.04  3.000
 78J  C36   C33  O32   109.76  3.000
 78J  H36   C36  C50   108.27  3.000
 78J  H36   C36  C38   107.90  3.000
 78J  C50   C36  C38   110.36  3.000
 78J  H36   C36  C33   107.89  3.000
 78J  C50   C36  C33   112.55  3.000
 78J  C38   C36  C33   109.73  3.000
 78J  H382  C38  H381  106.42  3.000
 78J  H382  C38  C41   109.18  3.000
 78J  H381  C38  C41   110.07  3.000
 78J  H382  C38  C36   109.09  3.000
 78J  H381  C38  C36   110.00  3.000
 78J  C41   C38  C36   111.92  3.000
 78J  H412  C41  H411  106.47  3.000
 78J  H412  C41  C44   110.33  3.000
 78J  H411  C41  C44   109.40  3.000
 78J  H412  C41  C38   109.93  3.000
 78J  H411  C41  C38   109.33  3.000
 78J  C44   C41  C38   111.26  3.000
 78J  H442  C44  H441  106.50  3.000
 78J  H442  C44  C47   109.23  3.000
 78J  H441  C44  C47   110.44  3.000
 78J  H442  C44  C41   109.16  3.000
 78J  H441  C44  C41   110.32  3.000
 78J  C47   C44  C41   111.08  3.000
 78J  H472  C47  H471  106.39  3.000
 78J  H472  C47  C50   109.96  3.000
 78J  H471  C47  C50   109.19  3.000
 78J  H472  C47  C44   110.34  3.000
 78J  H471  C47  C44   109.29  3.000
 78J  C50   C47  C44   111.53  3.000
 78J  H502  C50  H501  106.56  3.000
 78J  H502  C50  C47   109.93  3.000
 78J  H501  C50  C47   109.32  3.000
 78J  H502  C50  C36   110.38  3.000
 78J  H501  C50  C36   108.93  3.000
 78J  C47   C50  C36   111.57  3.000
 78J  N54   C53  C14   121.85  3.000
 78J  N54   C53  C08   119.02  3.000
 78J  C14   C53  C08   119.12  3.000
 78J  H54   N54  C56   114.81  3.000
 78J  H54   N54  C53   119.45  3.000
 78J  C56   N54  C53   125.55  3.000
 78J  O57   C56  N54   120.98  3.000
 78J  O57   C56  C05   123.54  3.000
 78J  N54   C56  C05   115.48  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
 78J  CONST_01  N13   C11  C09  C08     0.00   0.0  0
 78J  CONST_02  N13   C14  C53  C08     0.00   0.0  0
 78J  CONST_03  C14   C53  C08  C09     0.00   0.0  0
 78J  CONST_04  C14   N13  C11  C09     0.00   0.0  0
 78J  CONST_05  C53   C08  C09  C11     0.00   0.0  0
 78J  CONST_06  C53   C14  N13  C11     0.00   0.0  0
 78J  CONST_07  C53   N54  C56  C05     0.00   0.0  0
 78J  CONST_08  N15   C14  C53  C08   180.00   0.0  0
 78J  CONST_09  N15   C14  N13  C11   180.00   0.0  0
 78J  CONST_10  N54   C53  C14  N15     0.00   0.0  0
 78J  CONST_11  C17   N15  C14  N13     0.00   0.0  0
 78J  CONST_12  C53   C14  N15  C17   180.00   0.0  0
 78J  CONST_13  O57   C56  N54  C53   180.00   0.0  0
 78J  CONST_14  H09   C09  C08  C06     0.00   0.0  0
 78J  CONST_15  H11   C11  C09  C08   180.00   0.0  0
 78J  CONST_16  H54   N54  C56  C05   180.00   0.0  0
 78J  Var_01    N25   C22  C19  C17    53.90  30.0  1
 78J  Var_02    C27   N25  C22  C19   -54.05  30.0  1
 78J  Var_03    C30   C27  N25  C22    54.61  30.0  1
 78J  Var_04    C44   C41  C38  C36   -55.52  30.0  1
 78J  Var_05    C44   C47  C50  C36    55.63  30.0  1
 78J  Var_06    C47   C44  C41  C38    54.91  30.0  1
 78J  Var_07    C50   C47  C44  C41   -55.14  30.0  1
 78J  Var_08    C36   C33  O32  C30  -175.46  30.0  3
 78J  Var_09    H011  C01  C05  C06   120.26  30.0  3

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
 78J  chir_01  C17  N15  C19  C30  positiv
 78J  chir_02  C30  O32  C17  C27  negativ
 78J  chir_03  C36  C50  C38  C33  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
 78J  plan-1  C14  0.020
 78J  plan-1  N15  0.020
 78J  plan-1  C17  0.020
 78J  plan-1  H15  0.020
 78J  plan-2  C01  0.020
 78J  plan-2  C05  0.020
 78J  plan-2  C06  0.020
 78J  plan-2  C08  0.020
 78J  plan-2  C09  0.020
 78J  plan-2  C11  0.020
 78J  plan-2  N13  0.020
 78J  plan-2  C14  0.020
 78J  plan-2  N15  0.020
 78J  plan-2  C53  0.020
 78J  plan-2  N54  0.020
 78J  plan-2  C56  0.020
 78J  plan-2  O57  0.020
 78J  plan-2  H06  0.020
 78J  plan-2  H09  0.020
 78J  plan-2  H11  0.020
 78J  plan-2  H54  0.020

