# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 06:08:04 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: N-(3,3-dimethyl-2,3-dihydro-1H-indol-6-yl)-2-[(pyridin-4-ylmethyl)amino]pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)CNc2cc(NC(=O)c3cccnc3NCc4ccncc4)ccc12
#
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
 706  706  N-(3,3-dimethyl-2,3-dihydro-1H-indol-6-yl)-2-[(pyridin-4-ylmethyl)amino]pyridine-3-carboxamide  ligand  51  28  .  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_706
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
 706  C2    C  CH3   0  -0.649   6.1186   2.5904   0.2643
 706  C1    C  CR5   0  -0.151   5.9335   1.0848   0.1305
 706  C3    C  CH3   0  -0.635   6.8097   0.3478   1.1505
 706  C28   C  CH2   0  -0.261   6.2380   0.5902  -1.3015
 706  N27   N  NR15  0  -0.683   5.3501  -0.5545  -1.4794
 706  C26   C  CR56  0   0.362   4.2382  -0.3486  -0.6901
 706  C22   C  CR16  0  -0.455   3.0085  -0.9821  -0.7517
 706  C25   C  CR56  0   0.083   4.5012   0.6241   0.2790
 706  C23   C  CR16  0  -0.344   3.5318   0.9444   1.2008
 706  C24   C  CR16  0  -0.329   2.2831   0.3193   1.1646
 706  C13   C  CR6   0   0.378   2.0269  -0.6407   0.1872
 706  N12   N  NH1   0  -0.760   0.8180  -1.3490   0.0959
 706  C10   C  C     0   0.556  -0.4087  -0.9808   0.5391
 706  O11   O  O     0  -0.483  -0.6314   0.1089   1.0543
 706  C8    C  CR6   0  -0.218  -1.4773  -1.9956   0.3491
 706  C9    C  CR16  0  -0.182  -1.1912  -3.3529   0.3192
 706  C4    C  CR16  0  -0.360  -2.1972  -4.2896   0.1394
 706  C5    C  CR16  0  -0.045  -3.4856  -3.8089  -0.0049
 706  N6    N  N     0  -0.474  -3.8053  -2.5254   0.0511
 706  C7    C  CR6   0   0.537  -2.8475  -1.6165   0.2377
 706  N14   N  NH1   0  -0.687  -3.2296  -0.3211   0.2843
 706  C15   C  CH2   0  -0.305  -4.6122   0.0853   0.2906
 706  C16   C  CR6   0   0.163  -4.7535   1.5235  -0.1230
 706  C17   C  CR16  0  -0.363  -4.0257   2.0580  -1.1814
 706  C18   C  CR16  0  -0.058  -4.2329   3.3804  -1.5395
 706  N19   N  N     0  -0.410  -5.0964   4.1840  -0.9273
 706  C20   C  CR16  0  -0.059  -5.7888   3.6726   0.0831
 706  C21   C  CR16  0  -0.375  -5.6530   2.3636   0.5212
 706  H2    H  HCH3  0   0.232   7.1521   2.8746   0.0551
 706  H2A   H  HCH3  0   0.230   5.4738   3.1329  -0.4282
 706  H2B   H  HCH3  0   0.231   5.8871   2.9303   1.2759
 706  H3    H  HCH3  0   0.230   6.5259   0.6175   2.1690
 706  H3A   H  HCH3  0   0.232   6.7115  -0.7344   1.0511
 706  H3B   H  HCH3  0   0.227   7.8630   0.6034   1.0150
 706  H28   H  HCH2  0   0.227   6.0162   1.3813  -2.0292
 706  H28A  H  HCH2  0   0.234   7.2840   0.3065  -1.4282
 706  HN27  H  HNR5  0   0.376   5.2017  -0.8739  -2.4245
 706  H22   H  HCR6  0   0.264   2.8038  -1.7273  -1.5123
 706  H23   H  HCR6  0   0.244   3.7213   1.6891   1.9651
 706  H24   H  HCR6  0   0.262   1.5394   0.5806   1.8990
 706  HN12  H  HNH1  0   0.421   0.8615  -2.1775  -0.4772
 706  H9    H  HCR6  0   0.275  -0.1746  -3.6996   0.4586
 706  H4    H  HCR6  0   0.268  -1.9889  -5.3490   0.1196
 706  H5    H  HCR6  0   0.266  -4.3105  -4.4961  -0.1603
 706  HN14  H  HNH1  0   0.408  -2.5505   0.3198   0.6675
 706  H15   H  HCH2  0   0.272  -5.1687  -0.5393  -0.4096
 706  H15A  H  HCH2  0   0.250  -5.0748  -0.0654   1.2722
 706  H17   H  HCR6  0   0.267  -3.3072   1.4588  -1.7251
 706  H18   H  HCR6  0   0.264  -3.6726   3.8098  -2.3628
 706  H20   H  HCR6  0   0.264  -6.4886   4.3369   0.5780
 706  H21   H  HCR6  0   0.268  -6.2412   2.0120   1.3593

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
 706  C2   C1    single    1.523  0.020  1.523
 706  C1   C3    single    1.533  0.020  1.533
 706  C1   C28   single    1.545  0.020  1.545
 706  C1   C25   single    1.512  0.020  1.512
 706  C28  N27   single    1.460  0.020  1.460
 706  N27  C26   single    1.379  0.020  1.379
 706  C26  C22   aromatic  1.385  0.020  1.385
 706  C26  C25   aromatic  1.398  0.020  1.398
 706  C22  C13   aromatic  1.401  0.020  1.401
 706  C25  C23   aromatic  1.376  0.020  1.376
 706  C23  C24   aromatic  1.397  0.020  1.397
 706  C24  C13   aromatic  1.394  0.020  1.394
 706  C13  N12   single    1.404  0.020  1.404
 706  N12  C10   single    1.355  0.020  1.355
 706  C10  O11   double    1.226  0.020  1.226
 706  C10  C8    single    1.486  0.020  1.486
 706  C8   C9    aromatic  1.388  0.020  1.388
 706  C8   C7    aromatic  1.426  0.020  1.426
 706  C9   C4    aromatic  1.386  0.020  1.386
 706  C4   C5    aromatic  1.383  0.020  1.383
 706  C5   N6    aromatic  1.324  0.020  1.324
 706  N6   C7    aromatic  1.334  0.020  1.334
 706  C7   N14   single    1.351  0.020  1.351
 706  N14  C15   single    1.441  0.020  1.441
 706  C15  C16   single    1.503  0.020  1.503
 706  C16  C17   aromatic  1.391  0.020  1.391
 706  C16  C21   aromatic  1.389  0.020  1.389
 706  C17  C18   aromatic  1.386  0.020  1.386
 706  C18  N19   aromatic  1.329  0.020  1.329
 706  N19  C20   aromatic  1.327  0.020  1.327
 706  C20  C21   aromatic  1.387  0.020  1.387
 706  C2   H2    single    0.970  0.020  1.090
 706  C2   H2A   single    0.970  0.020  1.090
 706  C2   H2B   single    0.970  0.020  1.090
 706  C3   H3    single    0.970  0.020  1.090
 706  C3   H3A   single    0.970  0.020  1.090
 706  C3   H3B   single    0.970  0.020  1.090
 706  C28  H28   single    0.970  0.020  1.090
 706  C28  H28A  single    0.970  0.020  1.090
 706  N27  HN27  single    0.890  0.020  1.040
 706  C22  H22   single    0.930  0.020  1.080
 706  C23  H23   single    0.930  0.020  1.080
 706  C24  H24   single    0.930  0.020  1.080
 706  N12  HN12  single    0.860  0.020  1.020
 706  C9   H9    single    0.930  0.020  1.080
 706  C4   H4    single    0.930  0.020  1.080
 706  C5   H5    single    0.930  0.020  1.080
 706  N14  HN14  single    0.890  0.020  1.040
 706  C15  H15   single    0.970  0.020  1.090
 706  C15  H15A  single    0.970  0.020  1.090
 706  C17  H17   single    0.930  0.020  1.080
 706  C18  H18   single    0.930  0.020  1.080
 706  C20  H20   single    0.930  0.020  1.080
 706  C21  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
 706  H2B   C2   H2A  107.94  3.000
 706  H2B   C2   H2   107.28  3.000
 706  H2A   C2   H2   107.96  3.000
 706  H2B   C2   C1   111.31  3.000
 706  H2A   C2   C1   111.35  3.000
 706  H2    C2   C1   110.83  3.000
 706  C25   C1   C28  100.38  3.000
 706  C25   C1   C3   109.24  3.000
 706  C28   C1   C3   110.49  3.000
 706  C25   C1   C2   114.07  3.000
 706  C28   C1   C2   111.96  3.000
 706  C3    C1   C2   110.32  3.000
 706  H3B   C3   H3A  107.91  3.000
 706  H3B   C3   H3   107.98  3.000
 706  H3A   C3   H3   107.86  3.000
 706  H3B   C3   C1   110.86  3.000
 706  H3A   C3   C1   111.38  3.000
 706  H3    C3   C1   110.70  3.000
 706  H28A  C28  H28  107.71  3.000
 706  H28A  C28  N27  111.41  3.000
 706  H28   C28  N27  111.19  3.000
 706  H28A  C28  C1   112.31  3.000
 706  H28   C28  C1   110.11  3.000
 706  N27   C28  C1   104.13  3.000
 706  HN27  N27  C26  117.71  3.000
 706  HN27  N27  C28  116.88  3.000
 706  C26   N27  C28  107.68  3.000
 706  C25   C26  C22  121.08  3.000
 706  C25   C26  N27  110.42  3.000
 706  C22   C26  N27  128.49  3.000
 706  H22   C22  C13  120.36  3.000
 706  H22   C22  C26  120.88  3.000
 706  C13   C22  C26  118.76  3.000
 706  C23   C25  C26  119.61  3.000
 706  C23   C25  C1   131.49  3.000
 706  C26   C25  C1   108.79  3.000
 706  H23   C23  C24  118.82  3.000
 706  H23   C23  C25  120.62  3.000
 706  C24   C23  C25  120.55  3.000
 706  H24   C24  C13  121.20  3.000
 706  H24   C24  C23  119.40  3.000
 706  C13   C24  C23  119.39  3.000
 706  N12   C13  C24  123.46  3.000
 706  N12   C13  C22  115.91  3.000
 706  C24   C13  C22  120.60  3.000
 706  HN12  N12  C10  116.63  3.000
 706  HN12  N12  C13  114.47  3.000
 706  C10   N12  C13  128.38  3.000
 706  C8    C10  O11  122.02  3.000
 706  C8    C10  N12  115.06  3.000
 706  O11   C10  N12  122.92  3.000
 706  C7    C8   C9   117.17  3.000
 706  C7    C8   C10  121.29  3.000
 706  C9    C8   C10  121.50  3.000
 706  H9    C9   C4   118.79  3.000
 706  H9    C9   C8   120.26  3.000
 706  C4    C9   C8   120.94  3.000
 706  H4    C4   C5   121.26  3.000
 706  H4    C4   C9   121.68  3.000
 706  C5    C4   C9   117.06  3.000
 706  H5    C5   N6   115.88  3.000
 706  H5    C5   C4   120.22  3.000
 706  N6    C5   C4   123.89  3.000
 706  C7    N6   C5   119.56  3.000
 706  N14   C7   N6   117.07  3.000
 706  N14   C7   C8   121.59  3.000
 706  N6    C7   C8   121.32  3.000
 706  HN14  N14  C15  117.70  3.000
 706  HN14  N14  C7   115.56  3.000
 706  C15   N14  C7   122.80  3.000
 706  H15A  C15  H15  106.31  3.000
 706  H15A  C15  C16  109.78  3.000
 706  H15   C15  C16  108.85  3.000
 706  H15A  C15  N14  111.73  3.000
 706  H15   C15  N14  108.98  3.000
 706  C16   C15  N14  111.03  3.000
 706  C21   C16  C17  117.33  3.000
 706  C21   C16  C15  120.79  3.000
 706  C17   C16  C15  121.85  3.000
 706  H17   C17  C18  119.86  3.000
 706  H17   C17  C16  121.12  3.000
 706  C18   C17  C16  119.02  3.000
 706  H18   C18  N19  116.48  3.000
 706  H18   C18  C17  119.79  3.000
 706  N19   C18  C17  123.72  3.000
 706  C20   N19  C18  117.17  3.000
 706  H20   C20  C21  119.81  3.000
 706  H20   C20  N19  116.61  3.000
 706  C21   C20  N19  123.58  3.000
 706  H21   C21  C20  119.86  3.000
 706  H21   C21  C16  120.96  3.000
 706  C20   C21  C16  119.18  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
 706  CONST_01  C24   C13  C22  C26     0.00   0.0  0
 706  CONST_02  C24   C23  C25  C26     0.00   0.0  0
 706  CONST_03  C23   C25  C26  C22     0.00   0.0  0
 706  CONST_04  C23   C24  C13  C22     0.00   0.0  0
 706  CONST_05  C13   C22  C26  C25     0.00   0.0  0
 706  CONST_06  C13   C24  C23  C25     0.00   0.0  0
 706  CONST_07  C5    C4   C9   C8      0.00   0.0  0
 706  CONST_08  C5    N6   C7   C8      0.00   0.0  0
 706  CONST_09  N6    C7   C8   C9      0.00   0.0  0
 706  CONST_10  N6    C5   C4   C9      0.00   0.0  0
 706  CONST_11  C7    C8   C9   C4      0.00   0.0  0
 706  CONST_12  C7    N6   C5   C4      0.00   0.0  0
 706  CONST_13  N19   C18  C17  C16     0.00   0.0  0
 706  CONST_14  N19   C20  C21  C16     0.00   0.0  0
 706  CONST_15  C20   C21  C16  C17     0.00   0.0  0
 706  CONST_16  C20   N19  C18  C17     0.00   0.0  0
 706  CONST_17  C21   C16  C17  C18     0.00   0.0  0
 706  CONST_18  C21   C20  N19  C18     0.00   0.0  0
 706  CONST_19  N12   C13  C22  C26   180.00   0.0  0
 706  CONST_20  N12   C13  C24  C23   180.00   0.0  0
 706  CONST_21  C4    C9   C8   C10   180.00   0.0  0
 706  CONST_22  N6    C7   C8   C10   180.00   0.0  0
 706  CONST_23  N14   C7   C8   C9    180.00   0.0  0
 706  CONST_24  N14   C7   N6   C5    180.00   0.0  0
 706  CONST_25  C18   C17  C16  C15   180.00   0.0  0
 706  CONST_26  C20   C21  C16  C15   180.00   0.0  0
 706  CONST_27  H23   C23  C25  C1      0.00   0.0  0
 706  CONST_28  H22   C22  C26  N27     0.00   0.0  0
 706  CONST_29  H24   C24  C13  C22   180.00   0.0  0
 706  CONST_30  H4    C4   C9   C8    180.00   0.0  0
 706  CONST_31  H5    C5   C4   C9    180.00   0.0  0
 706  CONST_32  H9    C9   C4   C5    180.00   0.0  0
 706  CONST_33  H18   C18  C17  C16   180.00   0.0  0
 706  CONST_34  H20   C20  C21  C16   180.00   0.0  0
 706  CONST_35  H21   C21  C16  C17   180.00   0.0  0
 706  CONST_36  H17   C17  C18  N19   180.00   0.0  0
 706  CONST_37  C8    C10  N12  C13   180.00   0.0  0
 706  CONST_40  C15   N14  C7   C8    180.00   0.0  0
 706  CONST_41  C15   N14  C7   N6      0.00   0.0  0
 706  CONST_42  HN12  N12  C13  C22     0.00   0.0  0
 706  CONST_44  O11   C10  N12  C13     0.00   0.0  0
 706  Var_01    C26   N27  C28  C1     28.60  30.0  1
 706  Var_02    C26   C25  C1   C28    17.92  30.0  1
 706  Var_03    C22   C26  N27  C28   163.61  30.0  1
 706  Var_04    C25   C1   C28  N27   -27.34  30.0  1
 706  Var_05    C9    C8   C10  N12    28.17  30.0  2
 706  Var_06    C16   C15  N14  C7   -160.57  30.0  3
 706  Var_07    C17   C16  C15  N14    42.32  30.0  2
 706  Var_08    H2    C2   C1   C28   -61.50  30.0  3
 706  Var_09    H3    C3   C1   C28  -174.09  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
 706  plan-1  C10   0.020
 706  plan-1  C8    0.020
 706  plan-1  C9    0.020
 706  plan-1  C4    0.020
 706  plan-1  C5    0.020
 706  plan-1  N6    0.020
 706  plan-1  C7    0.020
 706  plan-1  N14   0.020
 706  plan-1  H9    0.020
 706  plan-1  H4    0.020
 706  plan-1  H5    0.020
 706  plan-2  C15   0.020
 706  plan-2  C16   0.020
 706  plan-2  C17   0.020
 706  plan-2  C18   0.020
 706  plan-2  N19   0.020
 706  plan-2  C20   0.020
 706  plan-2  C21   0.020
 706  plan-2  H17   0.020
 706  plan-2  H18   0.020
 706  plan-2  H20   0.020
 706  plan-2  H21   0.020
 706  plan-3  C1    0.020
 706  plan-3  N27   0.020
 706  plan-3  C26   0.020
 706  plan-3  C22   0.020
 706  plan-3  C25   0.020
 706  plan-3  C23   0.020
 706  plan-3  C24   0.020
 706  plan-3  C13   0.020
 706  plan-3  N12   0.020
 706  plan-3  H22   0.020
 706  plan-3  H23   0.020
 706  plan-3  H24   0.020
 706  plan-4  C13   0.020
 706  plan-4  N12   0.020
 706  plan-4  C10   0.020
 706  plan-4  O11   0.020
 706  plan-4  C8    0.020
 706  plan-4  HN12  0.020
 706  plan-5  C7    0.020
 706  plan-5  N14   0.020
 706  plan-5  C15   0.020
 706  plan-5  HN14  0.020

