# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 10:32:55 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: (2E)-N-methyl-N-[(1-methyl-1H-indol-3-yl)methyl]-3-(7-oxo-5,6,7,8-tetrahydro-1,8-naphthyridin-3-yl)prop-2-enamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(Cc1cn(C)c2ccccc12)C(=O)/C=C/c3cnc4NC(=O)CCc4c3
#
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
 IDN  IDN  (2E)-N-methyl-N-[(1-methyl-1H-indol-3-yl)methyl]-3-(7-oxo-5,6,7,8-tetrahydro-1,8-naphthyridin-3-yl)prop-2-enamide  ligand  50  28  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_IDN
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
 IDN  C01   C  CR66  0   0.477  -0.6547   0.1980  -4.1901
 IDN  C02   C  CR66  0   0.012   0.7080   0.3383  -4.4671
 IDN  C03   C  CR16  0  -0.260   1.5701   0.2489  -3.3967
 IDN  C04   C  CR6   0   0.065   1.0832   0.0468  -2.0998
 IDN  C05   C  CR16  0  -0.106  -0.3009  -0.0391  -1.9601
 IDN  N06   N  N     0  -0.428  -1.1485   0.0273  -2.9745
 IDN  C07   C  C1    0  -0.244   2.0190  -0.0519  -0.9886
 IDN  C08   C  C1    0  -0.408   1.7248  -0.3349   0.2855
 IDN  C09   C  C     0   0.562   2.8006  -0.3717   1.3063
 IDN  O10   O  O     0  -0.505   3.9449  -0.0124   1.0419
 IDN  N11   N  NT    0  -0.463   2.4663  -0.7931   2.5464
 IDN  C12   C  CH3   0  -0.527   3.4535  -0.7156   3.6057
 IDN  C13   C  CH2   0  -0.421   1.1868  -1.3865   2.8872
 IDN  C14   C  CR5   0  -0.029   0.1795  -0.3800   3.3424
 IDN  C15   C  CR15  0  -0.062   0.2882   0.9805   3.2913
 IDN  N16   N  NR5   0  -0.525  -0.8420   1.5708   3.7886
 IDN  C17   C  CR56  0   0.371  -1.7125   0.5914   4.1712
 IDN  C18   C  CR56  0   0.042  -1.1051  -0.6569   3.9080
 IDN  N19   N  NR16  0  -0.700  -1.5697   0.2578  -5.2267
 IDN  C20   C  CH3   0  -0.529  -1.0855   2.9885   3.8845
 IDN  C21   C  CR16  0  -0.270  -3.0587  -1.7355   4.7770
 IDN  C22   C  CR16  0  -0.280  -3.6452  -0.4848   5.0303
 IDN  C23   C  CR16  0  -0.314  -2.9851   0.6926   4.7315
 IDN  C24   C  CR16  0  -0.371  -1.7979  -1.8318   4.2198
 IDN  C25   C  C     0  -0.496   1.1178   0.6112  -5.8802
 IDN  C26   C  C     0  -0.596   0.1952  -0.1182  -6.8481
 IDN  C27   C  CR6   0   0.524  -1.2642   0.1170  -6.5517
 IDN  O28   O  O     0  -0.452  -2.1307   0.1402  -7.4028
 IDN  H03   H  HCR6  0   0.270   2.6381   0.3425  -3.5606
 IDN  H05   H  HCR6  0   0.262  -0.7532  -0.1681  -0.9831
 IDN  H07   H  H     0   0.262   3.0593   0.1204  -1.2458
 IDN  H08   H  H     0   0.267   0.7018  -0.5165   0.5849
 IDN  H121  H  HCH3  0   0.250   4.0436   0.1942   3.5264
 IDN  H122  H  HCH3  0   0.247   2.9390  -0.7024   4.5641
 IDN  H123  H  HCH3  0   0.243   4.1331  -1.5703   3.5916
 IDN  H131  H  HCH2  0   0.267   0.8066  -1.9691   2.0456
 IDN  H132  H  HCH2  0   0.280   1.3638  -2.1228   3.6754
 IDN  H15   H  HCR5  0   0.284   1.1056   1.5902   2.9369
 IDN  H19   H  HNR6  0   0.408  -2.5483   0.2959  -4.9715
 IDN  H201  H  HCH3  0   0.252  -1.9181   3.2893   3.2482
 IDN  H202  H  HCH3  0   0.252  -1.3091   3.2769   4.9115
 IDN  H203  H  HCH3  0   0.263  -0.1966   3.5251   3.5639
 IDN  H21   H  HCR6  0   0.247  -3.6059  -2.6365   5.0226
 IDN  H22   H  HCR6  0   0.250  -4.6344  -0.4415   5.4680
 IDN  H23   H  HCR6  0   0.264  -3.4454   1.6528   4.9280
 IDN  H24   H  HCR6  0   0.244  -1.3574  -2.8027   4.0280
 IDN  H251  H  H     0   0.276   2.1514   0.3099  -6.0474
 IDN  H252  H  H     0   0.272   1.0699   1.6888  -6.0669
 IDN  H261  H  H     0   0.289   0.3642  -1.1986  -6.7815
 IDN  H262  H  H     0   0.286   0.3919   0.1728  -7.8784

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
 IDN  C01  C02   aromatic  1.398  0.020  1.398
 IDN  C01  N06   aromatic  1.323  0.020  1.323
 IDN  C01  N19   single    1.384  0.020  1.384
 IDN  C02  C03   aromatic  1.377  0.020  1.377
 IDN  C02  C25   single    1.496  0.020  1.496
 IDN  C03  C04   aromatic  1.400  0.020  1.400
 IDN  C03  H03   single    0.930  0.020  1.080
 IDN  C04  C05   aromatic  1.394  0.020  1.394
 IDN  C04  C07   single    1.456  0.020  1.456
 IDN  C05  N06   aromatic  1.323  0.020  1.323
 IDN  C05  H05   single    0.930  0.020  1.080
 IDN  C07  C08   double    1.338  0.020  1.338
 IDN  C07  H07   single    0.930  0.020  1.080
 IDN  C08  C09   single    1.484  0.020  1.484
 IDN  C08  H08   single    0.930  0.020  1.080
 IDN  C09  O10   double    1.228  0.020  1.228
 IDN  C09  N11   single    1.352  0.020  1.352
 IDN  N11  C12   single    1.450  0.020  1.450
 IDN  N11  C13   single    1.451  0.020  1.451
 IDN  C12  H121  single    0.970  0.020  1.090
 IDN  C12  H122  single    0.970  0.020  1.090
 IDN  C12  H123  single    0.970  0.020  1.090
 IDN  C13  C14   single    1.495  0.020  1.495
 IDN  C13  H131  single    0.970  0.020  1.090
 IDN  C13  H132  single    0.970  0.020  1.090
 IDN  C14  C15   aromatic  1.366  0.020  1.366
 IDN  C14  C18   aromatic  1.431  0.020  1.431
 IDN  C15  N16   aromatic  1.369  0.020  1.369
 IDN  C15  H15   single    0.930  0.020  1.080
 IDN  N16  C17   aromatic  1.365  0.020  1.365
 IDN  N16  C20   single    1.442  0.020  1.442
 IDN  C17  C18   aromatic  1.413  0.020  1.413
 IDN  C17  C23   aromatic  1.394  0.020  1.394
 IDN  C18  C24   aromatic  1.399  0.020  1.399
 IDN  N19  C27   single    1.367  0.020  1.367
 IDN  N19  H19   single    0.860  0.020  1.020
 IDN  C20  H201  single    0.970  0.020  1.090
 IDN  C20  H202  single    0.970  0.020  1.090
 IDN  C20  H203  single    0.970  0.020  1.090
 IDN  C21  C22   aromatic  1.404  0.020  1.404
 IDN  C21  C24   aromatic  1.382  0.020  1.382
 IDN  C21  H21   single    0.930  0.020  1.080
 IDN  C22  C23   aromatic  1.382  0.020  1.382
 IDN  C22  H22   single    0.930  0.020  1.080
 IDN  C23  H23   single    0.930  0.020  1.080
 IDN  C24  H24   single    0.930  0.020  1.080
 IDN  C25  C26   single    1.523  0.020  1.523
 IDN  C25  H251  single    0.970  0.020  1.090
 IDN  C25  H252  single    0.970  0.020  1.090
 IDN  C26  C27   single    1.508  0.020  1.508
 IDN  C26  H261  single    0.970  0.020  1.090
 IDN  C26  H262  single    0.970  0.020  1.090
 IDN  C27  O28   double    1.215  0.020  1.215

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
 IDN  N19   C01  N06   116.55  3.000
 IDN  N19   C01  C02   119.46  3.000
 IDN  N06   C01  C02   123.98  3.000
 IDN  C25   C02  C03   125.05  3.000
 IDN  C25   C02  C01   118.20  3.000
 IDN  C03   C02  C01   116.72  3.000
 IDN  H03   C03  C04   119.66  3.000
 IDN  H03   C03  C02   119.57  3.000
 IDN  C04   C03  C02   120.77  3.000
 IDN  C07   C04  C05   123.89  3.000
 IDN  C07   C04  C03   119.55  3.000
 IDN  C05   C04  C03   116.55  3.000
 IDN  H05   C05  N06   115.43  3.000
 IDN  H05   C05  C04   120.78  3.000
 IDN  N06   C05  C04   123.79  3.000
 IDN  C05   N06  C01   118.14  3.000
 IDN  H07   C07  C08   118.03  3.000
 IDN  H07   C07  C04   115.11  3.000
 IDN  C08   C07  C04   126.85  3.000
 IDN  H08   C08  C09   119.43  3.000
 IDN  H08   C08  C07   120.48  3.000
 IDN  C09   C08  C07   120.07  3.000
 IDN  N11   C09  O10   121.28  3.000
 IDN  N11   C09  C08   117.36  3.000
 IDN  O10   C09  C08   121.35  3.000
 IDN  C13   N11  C12   116.78  3.000
 IDN  C13   N11  C09   124.13  3.000
 IDN  C12   N11  C09   119.02  3.000
 IDN  H123  C12  H122  108.37  3.000
 IDN  H123  C12  H121  108.43  3.000
 IDN  H122  C12  H121  108.10  3.000
 IDN  H123  C12  N11   111.87  3.000
 IDN  H122  C12  N11   108.80  3.000
 IDN  H121  C12  N11   111.15  3.000
 IDN  H132  C13  H131  104.64  3.000
 IDN  H132  C13  C14   110.07  3.000
 IDN  H131  C13  C14   111.06  3.000
 IDN  H132  C13  N11   107.58  3.000
 IDN  H131  C13  N11   110.13  3.000
 IDN  C14   C13  N11   112.98  3.000
 IDN  C18   C14  C15   106.20  3.000
 IDN  C18   C14  C13   126.52  3.000
 IDN  C15   C14  C13   127.27  3.000
 IDN  H15   C15  N16   120.06  3.000
 IDN  H15   C15  C14   129.43  3.000
 IDN  N16   C15  C14   110.51  3.000
 IDN  C20   N16  C17   125.40  3.000
 IDN  C20   N16  C15   126.00  3.000
 IDN  C17   N16  C15   108.60  3.000
 IDN  C23   C17  C18   122.10  3.000
 IDN  C23   C17  N16   129.99  3.000
 IDN  C18   C17  N16   107.91  3.000
 IDN  C24   C18  C17   119.18  3.000
 IDN  C24   C18  C14   134.04  3.000
 IDN  C17   C18  C14   106.78  3.000
 IDN  H19   N19  C27   117.67  3.000
 IDN  H19   N19  C01   116.87  3.000
 IDN  C27   N19  C01   125.01  3.000
 IDN  H203  C20  H202  108.37  3.000
 IDN  H203  C20  H201  108.43  3.000
 IDN  H202  C20  H201  108.68  3.000
 IDN  H203  C20  N16   109.13  3.000
 IDN  H202  C20  N16   110.95  3.000
 IDN  H201  C20  N16   111.19  3.000
 IDN  H21   C21  C24   119.65  3.000
 IDN  H21   C21  C22   119.29  3.000
 IDN  C24   C21  C22   121.06  3.000
 IDN  H22   C22  C23   119.32  3.000
 IDN  H22   C22  C21   119.35  3.000
 IDN  C23   C22  C21   121.33  3.000
 IDN  H23   C23  C22   120.86  3.000
 IDN  H23   C23  C17   121.69  3.000
 IDN  C22   C23  C17   117.45  3.000
 IDN  H24   C24  C21   120.32  3.000
 IDN  H24   C24  C18   120.79  3.000
 IDN  C21   C24  C18   118.89  3.000
 IDN  H252  C25  H251  106.71  3.000
 IDN  H252  C25  C26   109.66  3.000
 IDN  H251  C25  C26   110.16  3.000
 IDN  H252  C25  C02   109.18  3.000
 IDN  H251  C25  C02   110.75  3.000
 IDN  C26   C25  C02   110.29  3.000
 IDN  H262  C26  H261  107.05  3.000
 IDN  H262  C26  C27   108.62  3.000
 IDN  H261  C26  C27   106.93  3.000
 IDN  H262  C26  C25   111.34  3.000
 IDN  H261  C26  C25   109.89  3.000
 IDN  C27   C26  C25   112.75  3.000
 IDN  O28   C27  C26   123.76  3.000
 IDN  O28   C27  N19   121.18  3.000
 IDN  C26   C27  N19   115.02  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
 IDN  CONST_01  C04   C03  C02  C01     0.00   0.0  0
 IDN  CONST_02  C04   C05  N06  C01     0.00   0.0  0
 IDN  CONST_03  C05   N06  C01  C02     0.00   0.0  0
 IDN  CONST_04  C05   C04  C03  C02     0.00   0.0  0
 IDN  CONST_05  N06   C01  C02  C03     0.00   0.0  0
 IDN  CONST_06  N06   C05  C04  C03     0.00   0.0  0
 IDN  CONST_07  C17   N16  C15  C14     0.00   0.0  0
 IDN  CONST_08  N16   C17  C18  C14     0.00   0.0  0
 IDN  CONST_09  C23   C17  C18  C14   180.00   0.0  0
 IDN  CONST_10  C21   C24  C18  C14   180.00   0.0  0
 IDN  CONST_11  C17   C18  C14  C15     0.00   0.0  0
 IDN  CONST_12  C24   C18  C14  C15   180.00   0.0  0
 IDN  CONST_13  C18   C17  N16  C15     0.00   0.0  0
 IDN  CONST_14  C23   C17  N16  C15   180.00   0.0  0
 IDN  CONST_15  C18   C14  C15  N16     0.00   0.0  0
 IDN  CONST_16  C24   C18  C17  N16   180.00   0.0  0
 IDN  CONST_17  C22   C23  C17  N16   180.00   0.0  0
 IDN  CONST_18  C21   C24  C18  C17     0.00   0.0  0
 IDN  CONST_19  C21   C22  C23  C17     0.00   0.0  0
 IDN  CONST_20  C22   C23  C17  C18     0.00   0.0  0
 IDN  CONST_21  C22   C21  C24  C18     0.00   0.0  0
 IDN  CONST_22  C24   C18  C17  C23     0.00   0.0  0
 IDN  CONST_23  C24   C21  C22  C23     0.00   0.0  0
 IDN  CONST_24  C26   C27  N19  C01     0.00   0.0  0
 IDN  CONST_25  C07   C04  C03  C02   180.00   0.0  0
 IDN  CONST_26  C07   C04  C05  N06   180.00   0.0  0
 IDN  CONST_27  N16   C15  C14  C13   180.00   0.0  0
 IDN  CONST_28  C17   C18  C14  C13   180.00   0.0  0
 IDN  CONST_29  C24   C18  C14  C13     0.00   0.0  0
 IDN  CONST_30  C20   N16  C15  C14   180.00   0.0  0
 IDN  CONST_31  C20   N16  C17  C18   180.00   0.0  0
 IDN  CONST_32  C23   C17  N16  C20     0.00   0.0  0
 IDN  CONST_33  O28   C27  N19  C01   180.00   0.0  0
 IDN  CONST_34  H03   C03  C02  C01   180.00   0.0  0
 IDN  CONST_35  H05   C05  N06  C01   180.00   0.0  0
 IDN  CONST_36  H24   C24  C18  C14     0.00   0.0  0
 IDN  CONST_37  H23   C23  C17  N16     0.00   0.0  0
 IDN  CONST_38  H15   C15  N16  C17   180.00   0.0  0
 IDN  CONST_39  H22   C22  C23  C17   180.00   0.0  0
 IDN  CONST_40  H21   C21  C24  C18   180.00   0.0  0
 IDN  CONST_41  H19   N19  C27  C26   180.00   0.0  0
 IDN  CONST_42  C09   C08  C07  C04   180.00   0.0  0
 IDN  CONST_43  H08   C08  C07  C04     0.00   0.0  0
 IDN  CONST_44  C12   N11  C09  C08   180.00   0.0  0
 IDN  CONST_45  C13   N11  C09  C08     0.00   0.0  0
 IDN  CONST_46  C12   N11  C09  O10     0.00   0.0  0
 IDN  CONST_47  C13   N11  C09  O10   180.00   0.0  0
 IDN  CONST_48  H07   C07  C08  C09     0.00   0.0  0
 IDN  Var_01    C26   C25  C02  C01   -35.06  30.0  1
 IDN  Var_02    C27   N19  C01  C02    17.02  30.0  1
 IDN  Var_03    C27   C26  C25  C02    49.96  30.0  1
 IDN  Var_04    C25   C26  C27  N19   -33.92  30.0  1
 IDN  Var_05    C08   C07  C04  C03  -174.98  30.0  2
 IDN  Var_06    C15   C14  C13  N11     9.42  30.0  2
 IDN  Var_07    H201  C20  N16  C15   115.53  30.0  2
 IDN  Var_08    C14   C13  N11  C09   -91.28  30.0  3
 IDN  Var_09    O10   C09  C08  C07     7.66  30.0  2
 IDN  Var_10    H121  C12  N11  C09    38.63  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
 IDN  plan-1  C13  0.020
 IDN  plan-1  C14  0.020
 IDN  plan-1  C15  0.020
 IDN  plan-1  N16  0.020
 IDN  plan-1  C17  0.020
 IDN  plan-1  C18  0.020
 IDN  plan-1  C20  0.020
 IDN  plan-1  C21  0.020
 IDN  plan-1  C22  0.020
 IDN  plan-1  C23  0.020
 IDN  plan-1  C24  0.020
 IDN  plan-1  H15  0.020
 IDN  plan-1  H21  0.020
 IDN  plan-1  H22  0.020
 IDN  plan-1  H23  0.020
 IDN  plan-1  H24  0.020
 IDN  plan-2  C01  0.020
 IDN  plan-2  C02  0.020
 IDN  plan-2  C03  0.020
 IDN  plan-2  C04  0.020
 IDN  plan-2  C05  0.020
 IDN  plan-2  N06  0.020
 IDN  plan-2  C07  0.020
 IDN  plan-2  N19  0.020
 IDN  plan-2  C25  0.020
 IDN  plan-2  H03  0.020
 IDN  plan-2  H05  0.020
 IDN  plan-3  C08  0.020
 IDN  plan-3  C09  0.020
 IDN  plan-3  O10  0.020
 IDN  plan-3  N11  0.020
 IDN  plan-3  C12  0.020
 IDN  plan-3  C13  0.020
 IDN  plan-4  C01  0.020
 IDN  plan-4  N19  0.020
 IDN  plan-4  C26  0.020
 IDN  plan-4  C27  0.020
 IDN  plan-4  O28  0.020
 IDN  plan-4  H19  0.020
 IDN  plan-5  C04  0.020
 IDN  plan-5  C07  0.020
 IDN  plan-5  C08  0.020
 IDN  plan-5  C09  0.020
 IDN  plan-5  H07  0.020
 IDN  plan-5  H08  0.020

