# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 15:19:29 2022
#   Inital geometry file: a 125 line input string
#   Ligand name: (8~{R})-4-[2,4-bis(fluoranyl)phenyl]-8-methyl-7-[(2-methylpyrazol-3-yl)methyl]-6,8-dihydro-5~{H}-1,7-naphthyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1N(CCc2c1nc(cc2c3ccc(F)cc3F)C(N)=O)Cc4ccnn4C
#
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
 J9U  J9U  (8~{R})-4-[2,4-bis(fluoranyl)phenyl]-8-methyl-7-[(2-methylpyrazol-3-yl)methyl]-6,8-dihydro-5~{H}-1,7-naphthyridine-2-carboxamide  ligand  50  29  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_J9U
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
 J9U  N1   N  NH2   0  -0.808  18.2064  -47.7912  39.2538
 J9U  N3   N  N     0  -0.282  15.3734  -54.7545  39.6942
 J9U  C4   C  C     0   0.487  17.3274  -47.0225  39.9020
 J9U  C5   C  CR16  0  -0.349  15.5394  -47.0604  41.6482
 J9U  C6   C  CR6   0   0.184  14.7879  -47.7570  42.5836
 J9U  C7   C  CR6   0  -0.207  13.8012  -47.0172  43.4016
 J9U  C8   C  CR16  0  -0.240  14.2308  -46.0605  44.3185
 J9U  C10  C  CR6   0   0.543  11.9885  -45.5930  44.9411
 J9U  C13  C  CR6   0   0.002  15.0312  -49.1195  42.7769
 J9U  C15  C  CH2   0  -0.301  14.9646  -51.2432  44.0977
 J9U  C17  C  CR5   0   0.415  15.8661  -53.9994  41.7327
 J9U  N    N  N     0  -0.453  16.7436  -49.0352  41.1155
 J9U  O    O  O     0  -0.467  17.1743  -45.8262  39.7028
 J9U  C1   C  CH1   0  -0.131  16.4310  -51.1606  42.1792
 J9U  C11  C  CR16  0  -0.554  11.5065  -46.5205  44.0371
 J9U  C12  C  CR6   0   0.559  12.4338  -47.2132  43.2832
 J9U  C14  C  CH2   0  -0.525  14.2674  -49.9330  43.7786
 J9U  C18  C  CR15  0  -0.532  16.9819  -54.6567  41.2598
 J9U  C19  C  CR15  0  -0.077  16.6130  -55.1058  39.9843
 J9U  C2   C  CR6   0   0.228  16.0389  -49.7113  42.0116
 J9U  C3   C  CR6   0   0.116  16.5042  -47.7468  40.9308
 J9U  C9   C  CR16  0  -0.409  13.3379  -45.3432  45.0976
 J9U  F    F  F     0  -0.305  11.1139  -44.9114  45.6878
 J9U  F1   F  F     0  -0.296  11.9848  -48.1039  42.3908
 J9U  N2   N  NT    0  -0.435  15.3746  -51.8870  42.8656
 J9U  N4   N  NR5   0  -0.309  14.9351  -54.0871  40.7590
 J9U  H1   H  HNH2  0   0.403  18.8077  -47.4009  38.5476
 J9U  H2   H  HNH2  0   0.408  18.2828  -48.7708  39.4725
 J9U  H3   H  HCR6  0   0.269  15.3710  -46.0054  41.4820
 J9U  H4   H  HCR6  0   0.280  15.2923  -45.8816  44.4293
 J9U  H5   H  HCH2  0   0.251  14.2654  -51.8991  44.6182
 J9U  H6   H  HCH2  0   0.216  15.8003  -51.0694  44.7919
 J9U  H7   H  HCH3  0   0.265  13.1134  -53.8026  39.8424
 J9U  H8   H  HCH3  0   0.252  13.0137  -54.0448  41.5930
 J9U  H9   H  HCH3  0   0.256  13.5868  -52.4989  40.9516
 J9U  H13  H  HCH1  0   0.269  16.5136  -51.5728  41.1686
 J9U  H14  H  HCR6  0   0.305  10.4451  -46.6951  43.9164
 J9U  H15  H  HCH2  0   0.255  14.1175  -49.3596  44.6960
 J9U  H16  H  HCH2  0   0.261  13.2729  -50.1502  43.3804
 J9U  H19  H  HCR5  0   0.258  17.9240  -54.7822  41.7684
 J9U  H20  H  HCR5  0   0.254  17.2003  -55.6657  39.2722
 J9U  H21  H  HCR6  0   0.288  13.6849  -44.6080  45.8106
 J9U  C    C  CH3   0  -0.680  17.8217  -51.2527  42.8253
 J9U  C16  C  CH2   0  -0.360  15.6318  -53.3059  43.0314
 J9U  C20  C  CH3   0  -0.522  13.5850  -53.5744  40.7929
 J9U  H10  H  HCH3  0   0.240  18.1838  -52.2806  42.8338
 J9U  H11  H  HCH3  0   0.243  18.5381  -50.6607  42.2575
 J9U  H12  H  HCH3  0   0.232  17.8214  -50.8829  43.8514
 J9U  H17  H  HCH2  0   0.269  14.7555  -53.7386  43.5241
 J9U  H18  H  HCH2  0   0.240  16.4856  -53.5219  43.6885

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
 J9U  N1   C4   single    1.335  0.020  1.335
 J9U  N3   C19  aromatic  1.321  0.020  1.321
 J9U  N3   N4   aromatic  1.331  0.020  1.331
 J9U  C4   O    double    1.222  0.020  1.222
 J9U  C4   C3   single    1.504  0.020  1.504
 J9U  C20  N4   single    1.445  0.020  1.445
 J9U  C19  C18  aromatic  1.402  0.020  1.402
 J9U  N4   C17  aromatic  1.350  0.020  1.350
 J9U  C3   N    aromatic  1.323  0.020  1.323
 J9U  C3   C5   aromatic  1.384  0.020  1.384
 J9U  N    C2   aromatic  1.325  0.020  1.325
 J9U  C18  C17  aromatic  1.379  0.020  1.379
 J9U  C17  C16  single    1.491  0.020  1.491
 J9U  C5   C6   aromatic  1.387  0.020  1.387
 J9U  C2   C1   single    1.511  0.020  1.511
 J9U  C2   C13  aromatic  1.397  0.020  1.397
 J9U  C1   N2   single    1.454  0.020  1.454
 J9U  C1   C    single    1.536  0.020  1.536
 J9U  C6   C13  aromatic  1.397  0.020  1.397
 J9U  C6   C7   single    1.480  0.020  1.480
 J9U  F1   C12  single    1.338  0.020  1.338
 J9U  N2   C16  single    1.451  0.020  1.451
 J9U  N2   C15  single    1.449  0.020  1.449
 J9U  C13  C14  single    1.500  0.020  1.500
 J9U  C12  C7   aromatic  1.386  0.020  1.386
 J9U  C12  C11  aromatic  1.381  0.020  1.381
 J9U  C7   C8   aromatic  1.393  0.020  1.393
 J9U  C14  C15  single    1.518  0.020  1.518
 J9U  C11  C10  aromatic  1.382  0.020  1.382
 J9U  C8   C9   aromatic  1.385  0.020  1.385
 J9U  C10  C9   aromatic  1.381  0.020  1.381
 J9U  C10  F    single    1.337  0.020  1.337
 J9U  N1   H1   single    0.860  0.020  1.020
 J9U  N1   H2   single    0.860  0.020  1.020
 J9U  C5   H3   single    0.930  0.020  1.080
 J9U  C8   H4   single    0.930  0.020  1.080
 J9U  C15  H5   single    0.970  0.020  1.090
 J9U  C15  H6   single    0.970  0.020  1.090
 J9U  C20  H7   single    0.970  0.020  1.090
 J9U  C20  H8   single    0.970  0.020  1.090
 J9U  C20  H9   single    0.970  0.020  1.090
 J9U  C    H10  single    0.970  0.020  1.090
 J9U  C    H11  single    0.970  0.020  1.090
 J9U  C    H12  single    0.970  0.020  1.090
 J9U  C1   H13  single    0.970  0.020  1.090
 J9U  C11  H14  single    0.930  0.020  1.080
 J9U  C14  H15  single    0.970  0.020  1.090
 J9U  C14  H16  single    0.970  0.020  1.090
 J9U  C16  H17  single    0.970  0.020  1.090
 J9U  C16  H18  single    0.970  0.020  1.090
 J9U  C18  H19  single    0.930  0.020  1.080
 J9U  C19  H20  single    0.930  0.020  1.080
 J9U  C9   H21  single    0.930  0.020  1.080

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
 J9U  H2   N1   H1   118.98  3.000
 J9U  H2   N1   C4   120.31  3.000
 J9U  H1   N1   C4   120.70  3.000
 J9U  N4   N3   C19  105.47  3.000
 J9U  C3   C4   O    120.95  3.000
 J9U  C3   C4   N1   114.53  3.000
 J9U  O    C4   N1   124.52  3.000
 J9U  H3   C5   C3   120.84  3.000
 J9U  H3   C5   C6   120.61  3.000
 J9U  C3   C5   C6   118.55  3.000
 J9U  C13  C6   C7   121.80  3.000
 J9U  C7   C6   C5   118.87  3.000
 J9U  C13  C6   C5   119.24  3.000
 J9U  C12  C7   C8   117.22  3.000
 J9U  C8   C7   C6   120.10  3.000
 J9U  C12  C7   C6   122.66  3.000
 J9U  H4   C8   C9   119.28  3.000
 J9U  H4   C8   C7   118.91  3.000
 J9U  C9   C8   C7   121.80  3.000
 J9U  F    C10  C9   118.93  3.000
 J9U  F    C10  C11  118.64  3.000
 J9U  C9   C10  C11  122.43  3.000
 J9U  C2   C13  C14  120.24  3.000
 J9U  C14  C13  C6   122.19  3.000
 J9U  C2   C13  C6   117.57  3.000
 J9U  H6   C15  H5   106.30  3.000
 J9U  H6   C15  N2   113.06  3.000
 J9U  H5   C15  N2   108.65  3.000
 J9U  H6   C15  C14  110.19  3.000
 J9U  H5   C15  C14  108.96  3.000
 J9U  N2   C15  C14  109.55  3.000
 J9U  N4   C17  C18  106.25  3.000
 J9U  C18  C17  C16  130.38  3.000
 J9U  N4   C17  C16  123.38  3.000
 J9U  C3   N    C2   119.66  3.000
 J9U  H13  C1   N2   107.60  3.000
 J9U  H13  C1   C2   106.17  3.000
 J9U  N2   C1   C2   110.06  3.000
 J9U  H13  C1   C    107.31  3.000
 J9U  N2   C1   C    115.41  3.000
 J9U  C2   C1   C    109.83  3.000
 J9U  H14  C11  C12  121.10  3.000
 J9U  H14  C11  C10  121.55  3.000
 J9U  C12  C11  C10  117.35  3.000
 J9U  F1   C12  C11  118.19  3.000
 J9U  C11  C12  C7   123.00  3.000
 J9U  F1   C12  C7   118.81  3.000
 J9U  H16  C14  H15  106.59  3.000
 J9U  H16  C14  C15  108.84  3.000
 J9U  H15  C14  C15  109.85  3.000
 J9U  H16  C14  C13  109.14  3.000
 J9U  H15  C14  C13  110.25  3.000
 J9U  C15  C14  C13  112.00  3.000
 J9U  H19  C18  C19  128.46  3.000
 J9U  H19  C18  C17  126.95  3.000
 J9U  C19  C18  C17  104.59  3.000
 J9U  H20  C19  C18  128.55  3.000
 J9U  H20  C19  N3   120.24  3.000
 J9U  C18  C19  N3   111.20  3.000
 J9U  C1   C2   N    115.24  3.000
 J9U  C1   C2   C13  122.20  3.000
 J9U  N    C2   C13  122.53  3.000
 J9U  N    C3   C5   122.44  3.000
 J9U  C5   C3   C4   119.82  3.000
 J9U  N    C3   C4   117.74  3.000
 J9U  H21  C9   C10  120.74  3.000
 J9U  H21  C9   C8   121.07  3.000
 J9U  C10  C9   C8   118.19  3.000
 J9U  C16  N2   C1   114.42  3.000
 J9U  C16  N2   C15  112.79  3.000
 J9U  C1   N2   C15  112.63  3.000
 J9U  C20  N4   C17  127.20  3.000
 J9U  C17  N4   N3   112.49  3.000
 J9U  C20  N4   N3   120.29  3.000
 J9U  H12  C    H11  107.84  3.000
 J9U  H12  C    H10  108.21  3.000
 J9U  H11  C    H10  107.34  3.000
 J9U  H12  C    C1   112.03  3.000
 J9U  H11  C    C1   110.10  3.000
 J9U  H10  C    C1   111.14  3.000
 J9U  H18  C16  H17  105.98  3.000
 J9U  H18  C16  N2   113.46  3.000
 J9U  H17  C16  N2   107.22  3.000
 J9U  H18  C16  C17  107.90  3.000
 J9U  H17  C16  C17  109.51  3.000
 J9U  N2   C16  C17  112.53  3.000
 J9U  H9   C20  H8   108.70  3.000
 J9U  H9   C20  H7   109.67  3.000
 J9U  H8   C20  H7   108.94  3.000
 J9U  H9   C20  N4   110.66  3.000
 J9U  H8   C20  N4   110.73  3.000
 J9U  H7   C20  N4   108.12  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
 J9U  CONST_01  C17  C18  C19  N3      0.00   0.0  0
 J9U  CONST_02  C18  C17  N4   N3      0.00   0.0  0
 J9U  CONST_03  C2   N    C3   C5      0.00   0.0  0
 J9U  CONST_04  C2   C13  C6   C5      0.00   0.0  0
 J9U  CONST_07  N    C3   C5   C6      0.00   0.0  0
 J9U  CONST_08  N    C2   C13  C6      0.00   0.0  0
 J9U  CONST_09  C11  C12  C7   C6    180.00   0.0  0
 J9U  CONST_10  C9   C8   C7   C6    180.00   0.0  0
 J9U  CONST_11  C3   C5   C6   C7    180.00   0.0  0
 J9U  CONST_12  C2   C13  C6   C7    180.00   0.0  0
 J9U  CONST_13  C10  C11  C12  C7      0.00   0.0  0
 J9U  CONST_14  C10  C9   C8   C7      0.00   0.0  0
 J9U  CONST_16  C11  C12  C7   C8      0.00   0.0  0
 J9U  CONST_17  C11  C10  C9   C8      0.00   0.0  0
 J9U  CONST_18  C3   N    C2   C13     0.00   0.0  0
 J9U  CONST_19  C3   C5   C6   C13     0.00   0.0  0
 J9U  CONST_21  C19  N3   N4   C17     0.00   0.0  0
 J9U  CONST_22  C9   C8   C7   C12     0.00   0.0  0
 J9U  CONST_23  C9   C10  C11  C12     0.00   0.0  0
 J9U  CONST_24  N4   N3   C19  C18     0.00   0.0  0
 J9U  CONST_25  N4   C17  C18  C19     0.00   0.0  0
 J9U  CONST_26  C14  C13  C6   C7      0.00   0.0  0
 J9U  CONST_27  C16  C17  N4   N3    180.00   0.0  0
 J9U  CONST_28  C2   N    C3   C4    180.00   0.0  0
 J9U  CONST_29  C6   C5   C3   C4    180.00   0.0  0
 J9U  CONST_30  F1   C12  C7   C6      0.00   0.0  0
 J9U  CONST_31  F1   C12  C7   C8    180.00   0.0  0
 J9U  CONST_32  F    C10  C9   C8    180.00   0.0  0
 J9U  CONST_33  F1   C12  C11  C10   180.00   0.0  0
 J9U  CONST_34  C19  N3   N4   C20   180.00   0.0  0
 J9U  CONST_35  C18  C17  N4   C20   180.00   0.0  0
 J9U  CONST_36  F    C10  C11  C12   180.00   0.0  0
 J9U  CONST_37  C19  C18  C17  C16   180.00   0.0  0
 J9U  CONST_38  H19  C18  C19  N3    180.00   0.0  0
 J9U  CONST_39  H4   C8   C7   C6      0.00   0.0  0
 J9U  CONST_40  H3   C5   C6   C7      0.00   0.0  0
 J9U  CONST_41  H14  C11  C12  C7    180.00   0.0  0
 J9U  CONST_42  H21  C9   C8   C7    180.00   0.0  0
 J9U  CONST_43  H20  C19  C18  C17   180.00   0.0  0
 J9U  CONST_44  H1   N1   C4   C3    180.00   0.0  0
 J9U  CONST_45  H2   N1   C4   C3      0.00   0.0  0
 J9U  Var_01    C15  C14  C13  C6   -163.13  30.0  1
 J9U  Var_02    N2   C15  C14  C13   -46.96  30.0  1
 J9U  Var_03    C14  C15  N2   C1     68.03  30.0  1
 J9U  Var_04    C17  C16  N2   C15   171.98  30.0  3
 J9U  Var_05    N2   C16  C17  C18   117.24  30.0  2
 J9U  Var_06    N    C3   C4   N1      1.57  30.0  2
 J9U  Var_07    H7   C20  N4   N3     -2.40  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
 J9U  chir_01  C1  C2  N2  C  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
 J9U  plan-1  N3   0.020
 J9U  plan-1  C17  0.020
 J9U  plan-1  C18  0.020
 J9U  plan-1  C19  0.020
 J9U  plan-1  N4   0.020
 J9U  plan-1  H19  0.020
 J9U  plan-1  H20  0.020
 J9U  plan-1  C16  0.020
 J9U  plan-1  C20  0.020
 J9U  plan-2  C6   0.020
 J9U  plan-2  C7   0.020
 J9U  plan-2  C8   0.020
 J9U  plan-2  C10  0.020
 J9U  plan-2  C11  0.020
 J9U  plan-2  C12  0.020
 J9U  plan-2  C9   0.020
 J9U  plan-2  F    0.020
 J9U  plan-2  F1   0.020
 J9U  plan-2  H4   0.020
 J9U  plan-2  H14  0.020
 J9U  plan-2  H21  0.020
 J9U  plan-3  C4   0.020
 J9U  plan-3  C5   0.020
 J9U  plan-3  C6   0.020
 J9U  plan-3  C7   0.020
 J9U  plan-3  C13  0.020
 J9U  plan-3  N    0.020
 J9U  plan-3  C1   0.020
 J9U  plan-3  C14  0.020
 J9U  plan-3  C2   0.020
 J9U  plan-3  C3   0.020
 J9U  plan-3  H3   0.020
 J9U  plan-4  N1   0.020
 J9U  plan-4  C4   0.020
 J9U  plan-4  O    0.020
 J9U  plan-4  C3   0.020
 J9U  plan-4  H1   0.020
 J9U  plan-4  H2   0.020

