# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 20:18:18 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: (2S)-1-(1H-indol-3-yl)-3-[(2-pyridin-4-yl-1,7-naphthyridin-5-yl)oxy]propan-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](COc1cncc2nc(ccc12)c3ccncc3)Cc4c[nH]c5ccccc45
#
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
 6EA  6EA  (2S)-1-(1H-indol-3-yl)-3-[(2-pyridin-4-yl-1,7-naphthyridin-5-yl)oxy]propan-2-amine  ligand  51  30  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6EA
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
 6EA  N1    N  N     0  -0.401   8.4329   2.1112  -0.0762
 6EA  C2    C  CR16  0  -0.058   8.1642   0.9888  -0.7353
 6EA  C3    C  CR16  0  -0.350   6.9271   0.3679  -0.7208
 6EA  C4    C  CR6   0   0.158   5.8906   0.9429   0.0110
 6EA  C5    C  CR16  0  -0.387   6.1712   2.1169   0.7034
 6EA  C6    C  CR16  0  -0.059   7.4483   2.6525   0.6293
 6EA  C11   C  CR6   0   0.223   4.5528   0.3119   0.0414
 6EA  C12   C  CR16  0  -0.312   3.3939   1.0759   0.3297
 6EA  C13   C  CR16  0  -0.156   2.1720   0.4686   0.3358
 6EA  C14   C  CR66  0   0.030   2.0968  -0.9116   0.0554
 6EA  C15   C  CR66  0   0.138   3.3016  -1.5854  -0.2233
 6EA  N16   N  N     0  -0.453   4.4976  -0.9681  -0.2281
 6EA  C19   C  CR6   0   0.310   0.8910  -1.6609   0.0251
 6EA  C20   C  CR16  0  -0.220   0.9618  -3.0037  -0.2682
 6EA  N21   N  N     0  -0.378   2.1253  -3.6367  -0.5314
 6EA  C22   C  CR16  0  -0.118   3.2435  -2.9717  -0.5124
 6EA  O25   O  O2    0  -0.467  -0.2268  -0.9811   0.2894
 6EA  C26   C  CH2   0  -0.178  -1.4845  -1.6381   0.2009
 6EA  C27   C  CH1   0  -0.127  -2.5749  -0.5861   0.3817
 6EA  N30   N  NH2   0  -0.774  -2.5337   0.4856  -0.5921
 6EA  C31   C  CH2   0  -0.553  -3.9378  -1.2855   0.3500
 6EA  C33   C  CR5   0   0.045  -5.0862  -0.3988   0.7032
 6EA  C36   C  CR15  0  -0.090  -5.6204  -0.2240   1.9491
 6EA  N37   N  NR15  0  -0.687  -6.6604   0.6626   1.8997
 6EA  C38   C  CR56  0   0.349  -6.8385   1.0746   0.6122
 6EA  C39   C  CR56  0   0.032  -5.8579   0.4295  -0.1751
 6EA  C43   C  CR16  0  -0.308  -7.7732   1.9536   0.0649
 6EA  C44   C  CR16  0  -0.286  -7.7162   2.1783  -1.2969
 6EA  C45   C  CR16  0  -0.272  -6.7513   1.5453  -2.0998
 6EA  C46   C  CR16  0  -0.370  -5.8250   0.6800  -1.5518
 6EA  H2    H  HCR6  0   0.268   8.9759   0.5582  -1.3109
 6EA  H3    H  HCR6  0   0.270   6.7714  -0.5441  -1.2796
 6EA  H5    H  HCR6  0   0.272   5.4289   2.6139   1.3129
 6EA  H6    H  HCR6  0   0.269   7.6801   3.5632   1.1700
 6EA  H12   H  HCR6  0   0.282   3.4696   2.1368   0.5221
 6EA  H13   H  HCR6  0   0.279   1.2793   1.0418   0.5440
 6EA  H20   H  HCR6  0   0.283   0.0745  -3.6233  -0.3016
 6EA  H22   H  HCR6  0   0.269   4.1650  -3.5026  -0.7284
 6EA  H261  H  HCH2  0   0.231  -1.5572  -2.4102   0.9749
 6EA  H262  H  HCH2  0   0.226  -1.5888  -2.1229  -0.7778
 6EA  H27   H  HCH1  0   0.239  -2.4500  -0.1413   1.3751
 6EA  H301  H  HNH2  0   0.347  -1.6283   0.9374  -0.5834
 6EA  H302  H  HNH2  0   0.337  -2.6539   0.1094  -1.5258
 6EA  H311  H  HCH2  0   0.238  -4.0925  -1.7138  -0.6470
 6EA  H312  H  HCH2  0   0.250  -3.9107  -2.1326   1.0407
 6EA  H36   H  HCR5  0   0.278  -5.3331  -0.6780   2.8851
 6EA  H37   H  HNR5  0   0.406  -7.2321   0.9240   2.6850
 6EA  H43   H  HCR6  0   0.256  -8.5174   2.4399   0.6831
 6EA  H44   H  HCR6  0   0.246  -8.4290   2.8523  -1.7547
 6EA  H45   H  HCR6  0   0.243  -6.7357   1.7456  -3.1636
 6EA  H46   H  HCR6  0   0.231  -5.0862   0.2006  -2.1817

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
 6EA  N1   C2    aromatic  1.329  0.020  1.329
 6EA  N1   C6    aromatic  1.327  0.020  1.327
 6EA  C2   C3    aromatic  1.384  0.020  1.384
 6EA  C2   H2    single    0.930  0.020  1.080
 6EA  C3   C4    aromatic  1.393  0.020  1.393
 6EA  C3   H3    single    0.930  0.020  1.080
 6EA  C4   C5    aromatic  1.392  0.020  1.392
 6EA  C4   C11   single    1.479  0.020  1.479
 6EA  C5   C6    aromatic  1.387  0.020  1.387
 6EA  C5   H5    single    0.930  0.020  1.080
 6EA  C6   H6    single    0.930  0.020  1.080
 6EA  C11  C12   aromatic  1.418  0.020  1.418
 6EA  C11  N16   aromatic  1.309  0.020  1.309
 6EA  C12  C13   aromatic  1.364  0.020  1.364
 6EA  C12  H12   single    0.930  0.020  1.080
 6EA  C13  C14   aromatic  1.410  0.020  1.410
 6EA  C13  H13   single    0.930  0.020  1.080
 6EA  C14  C15   aromatic  1.408  0.020  1.408
 6EA  C14  C19   aromatic  1.420  0.020  1.420
 6EA  C15  N16   aromatic  1.346  0.020  1.346
 6EA  C15  C22   aromatic  1.417  0.020  1.417
 6EA  C19  C20   aromatic  1.376  0.020  1.376
 6EA  C19  O25   single    1.335  0.020  1.335
 6EA  C20  N21   aromatic  1.350  0.020  1.350
 6EA  C20  H20   single    0.930  0.020  1.080
 6EA  N21  C22   aromatic  1.301  0.020  1.301
 6EA  C22  H22   single    0.930  0.020  1.080
 6EA  O25  C26   single    1.422  0.020  1.422
 6EA  C26  C27   single    1.526  0.020  1.526
 6EA  C26  H261  single    0.970  0.020  1.090
 6EA  C26  H262  single    0.970  0.020  1.090
 6EA  C27  N30   single    1.449  0.020  1.449
 6EA  C27  C31   single    1.532  0.020  1.532
 6EA  C27  H27   single    0.970  0.020  1.090
 6EA  N30  H301  single    0.890  0.020  1.040
 6EA  N30  H302  single    0.890  0.020  1.040
 6EA  C31  C33   single    1.493  0.020  1.493
 6EA  C31  H311  single    0.970  0.020  1.090
 6EA  C31  H312  single    0.970  0.020  1.090
 6EA  C33  C36   aromatic  1.367  0.020  1.367
 6EA  C33  C39   aromatic  1.433  0.020  1.433
 6EA  C36  N37   aromatic  1.368  0.020  1.368
 6EA  C36  H36   single    0.930  0.020  1.080
 6EA  N37  C38   aromatic  1.363  0.020  1.363
 6EA  N37  H37   single    0.860  0.020  1.020
 6EA  C38  C39   aromatic  1.413  0.020  1.413
 6EA  C38  C43   aromatic  1.395  0.020  1.395
 6EA  C39  C46   aromatic  1.400  0.020  1.400
 6EA  C43  C44   aromatic  1.381  0.020  1.381
 6EA  C43  H43   single    0.930  0.020  1.080
 6EA  C44  C45   aromatic  1.406  0.020  1.406
 6EA  C44  H44   single    0.930  0.020  1.080
 6EA  C45  C46   aromatic  1.381  0.020  1.381
 6EA  C45  H45   single    0.930  0.020  1.080
 6EA  C46  H46   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
 6EA  C6    N1   C2    117.27  3.000
 6EA  H2    C2   C3    119.76  3.000
 6EA  H2    C2   N1    116.58  3.000
 6EA  C3    C2   N1    123.66  3.000
 6EA  H3    C3   C4    120.85  3.000
 6EA  H3    C3   C2    120.12  3.000
 6EA  C4    C3   C2    119.03  3.000
 6EA  C11   C4   C5    122.14  3.000
 6EA  C11   C4   C3    120.50  3.000
 6EA  C5    C4   C3    117.37  3.000
 6EA  H5    C5   C6    118.99  3.000
 6EA  H5    C5   C4    121.99  3.000
 6EA  C6    C5   C4    119.01  3.000
 6EA  H6    C6   C5    119.65  3.000
 6EA  H6    C6   N1    116.70  3.000
 6EA  C5    C6   N1    123.66  3.000
 6EA  N16   C11  C12   122.29  3.000
 6EA  N16   C11  C4    116.80  3.000
 6EA  C12   C11  C4    120.90  3.000
 6EA  H12   C12  C13   119.92  3.000
 6EA  H12   C12  C11   120.52  3.000
 6EA  C13   C12  C11   119.55  3.000
 6EA  H13   C13  C14   120.86  3.000
 6EA  H13   C13  C12   120.29  3.000
 6EA  C14   C13  C12   118.84  3.000
 6EA  C19   C14  C15   118.02  3.000
 6EA  C19   C14  C13   124.47  3.000
 6EA  C15   C14  C13   117.51  3.000
 6EA  C22   C15  N16   118.97  3.000
 6EA  C22   C15  C14   118.25  3.000
 6EA  N16   C15  C14   122.78  3.000
 6EA  C15   N16  C11   119.02  3.000
 6EA  O25   C19  C20   125.61  3.000
 6EA  O25   C19  C14   115.99  3.000
 6EA  C20   C19  C14   118.40  3.000
 6EA  H20   C20  N21   115.58  3.000
 6EA  H20   C20  C19   121.51  3.000
 6EA  N21   C20  C19   122.90  3.000
 6EA  C22   N21  C20   119.87  3.000
 6EA  H22   C22  N21   118.48  3.000
 6EA  H22   C22  C15   118.97  3.000
 6EA  N21   C22  C15   122.56  3.000
 6EA  C26   O25  C19   119.55  3.000
 6EA  H262  C26  H261  108.21  3.000
 6EA  H262  C26  C27   110.02  3.000
 6EA  H261  C26  C27   110.77  3.000
 6EA  H262  C26  O25   110.11  3.000
 6EA  H261  C26  O25   109.90  3.000
 6EA  C27   C26  O25   107.83  3.000
 6EA  H27   C27  C31   107.78  3.000
 6EA  H27   C27  N30   107.82  3.000
 6EA  C31   C27  N30   110.43  3.000
 6EA  H27   C27  C26   107.81  3.000
 6EA  C31   C27  C26   108.57  3.000
 6EA  N30   C27  C26   114.21  3.000
 6EA  H302  N30  H301  106.24  3.000
 6EA  H302  N30  C27   109.95  3.000
 6EA  H301  N30  C27   110.49  3.000
 6EA  H312  C31  H311  105.99  3.000
 6EA  H312  C31  C33   109.25  3.000
 6EA  H311  C31  C33   109.79  3.000
 6EA  H312  C31  C27   108.58  3.000
 6EA  H311  C31  C27   108.83  3.000
 6EA  C33   C31  C27   114.09  3.000
 6EA  C39   C33  C36   105.92  3.000
 6EA  C39   C33  C31   127.77  3.000
 6EA  C36   C33  C31   126.31  3.000
 6EA  H36   C36  N37   120.43  3.000
 6EA  H36   C36  C33   129.25  3.000
 6EA  N37   C36  C33   110.32  3.000
 6EA  H37   N37  C38   125.76  3.000
 6EA  H37   N37  C36   124.93  3.000
 6EA  C38   N37  C36   109.23  3.000
 6EA  C43   C38  C39   122.27  3.000
 6EA  C43   C38  N37   130.42  3.000
 6EA  C39   C38  N37   107.30  3.000
 6EA  C46   C39  C38   118.85  3.000
 6EA  C46   C39  C33   133.93  3.000
 6EA  C38   C39  C33   107.22  3.000
 6EA  H43   C43  C44   121.20  3.000
 6EA  H43   C43  C38   121.30  3.000
 6EA  C44   C43  C38   117.49  3.000
 6EA  H44   C44  C45   119.39  3.000
 6EA  H44   C44  C43   119.41  3.000
 6EA  C45   C44  C43   121.21  3.000
 6EA  H45   C45  C46   119.75  3.000
 6EA  H45   C45  C44   119.20  3.000
 6EA  C46   C45  C44   121.05  3.000
 6EA  H46   C46  C45   120.29  3.000
 6EA  H46   C46  C39   120.59  3.000
 6EA  C45   C46  C39   119.12  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
 6EA  CONST_01  C4   C3   C2   N1      0.00   0.0  0
 6EA  CONST_02  C4   C5   C6   N1      0.00   0.0  0
 6EA  CONST_03  C5   C6   N1   C2      0.00   0.0  0
 6EA  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 6EA  CONST_05  C11  C4   C3   C2    180.00   0.0  0
 6EA  CONST_06  C6   N1   C2   C3      0.00   0.0  0
 6EA  CONST_07  C6   C5   C4   C3      0.00   0.0  0
 6EA  CONST_10  C13  C12  C11  C4    180.00   0.0  0
 6EA  CONST_11  C15  N16  C11  C4    180.00   0.0  0
 6EA  CONST_14  C11  C4   C5   C6    180.00   0.0  0
 6EA  CONST_15  C14  C13  C12  C11     0.00   0.0  0
 6EA  CONST_16  C14  C15  N16  C11     0.00   0.0  0
 6EA  CONST_17  C22  C15  N16  C11   180.00   0.0  0
 6EA  CONST_18  C15  N16  C11  C12     0.00   0.0  0
 6EA  CONST_19  C15  C14  C13  C12     0.00   0.0  0
 6EA  CONST_20  C19  C14  C13  C12   180.00   0.0  0
 6EA  CONST_21  N16  C11  C12  C13     0.00   0.0  0
 6EA  CONST_22  N16  C15  C14  C13     0.00   0.0  0
 6EA  CONST_23  C22  C15  C14  C13   180.00   0.0  0
 6EA  CONST_24  C20  C19  C14  C13   180.00   0.0  0
 6EA  CONST_25  N21  C22  C15  C14     0.00   0.0  0
 6EA  CONST_26  N21  C20  C19  C14     0.00   0.0  0
 6EA  CONST_27  C20  C19  C14  C15     0.00   0.0  0
 6EA  CONST_28  C20  N21  C22  C15     0.00   0.0  0
 6EA  CONST_29  C19  C14  C15  N16   180.00   0.0  0
 6EA  CONST_30  N21  C22  C15  N16   180.00   0.0  0
 6EA  CONST_31  C22  C15  C14  C19     0.00   0.0  0
 6EA  CONST_32  C22  N21  C20  C19     0.00   0.0  0
 6EA  CONST_33  C38  N37  C36  C33     0.00   0.0  0
 6EA  CONST_34  N37  C38  C39  C33     0.00   0.0  0
 6EA  CONST_35  C43  C38  C39  C33   180.00   0.0  0
 6EA  CONST_36  C45  C46  C39  C33   180.00   0.0  0
 6EA  CONST_37  C38  C39  C33  C36     0.00   0.0  0
 6EA  CONST_38  C46  C39  C33  C36   180.00   0.0  0
 6EA  CONST_39  C39  C38  N37  C36     0.00   0.0  0
 6EA  CONST_40  C43  C38  N37  C36   180.00   0.0  0
 6EA  CONST_41  C39  C33  C36  N37     0.00   0.0  0
 6EA  CONST_42  C46  C39  C38  N37   180.00   0.0  0
 6EA  CONST_43  C44  C43  C38  N37   180.00   0.0  0
 6EA  CONST_44  C45  C46  C39  C38     0.00   0.0  0
 6EA  CONST_45  C45  C44  C43  C38     0.00   0.0  0
 6EA  CONST_46  C44  C43  C38  C39     0.00   0.0  0
 6EA  CONST_47  C44  C45  C46  C39     0.00   0.0  0
 6EA  CONST_48  C46  C39  C38  C43     0.00   0.0  0
 6EA  CONST_49  C46  C45  C44  C43     0.00   0.0  0
 6EA  CONST_50  O25  C19  C14  C13     0.00   0.0  0
 6EA  CONST_51  O25  C19  C14  C15   180.00   0.0  0
 6EA  CONST_52  O25  C19  C20  N21   180.00   0.0  0
 6EA  CONST_53  N37  C36  C33  C31   180.00   0.0  0
 6EA  CONST_54  C38  C39  C33  C31   180.00   0.0  0
 6EA  CONST_55  C46  C39  C33  C31     0.00   0.0  0
 6EA  CONST_56  H3   C3   C2   N1    180.00   0.0  0
 6EA  CONST_57  H5   C5   C6   N1    180.00   0.0  0
 6EA  CONST_58  H6   C6   N1   C2    180.00   0.0  0
 6EA  CONST_59  H2   C2   C3   C4    180.00   0.0  0
 6EA  CONST_60  H12  C12  C11  C4      0.00   0.0  0
 6EA  CONST_61  H13  C13  C12  C11   180.00   0.0  0
 6EA  CONST_62  H22  C22  C15  C14   180.00   0.0  0
 6EA  CONST_63  H20  C20  C19  C14   180.00   0.0  0
 6EA  CONST_64  H37  N37  C36  C33   180.00   0.0  0
 6EA  CONST_65  H46  C46  C39  C33     0.00   0.0  0
 6EA  CONST_66  H43  C43  C38  N37     0.00   0.0  0
 6EA  CONST_67  H36  C36  N37  C38   180.00   0.0  0
 6EA  CONST_68  H44  C44  C43  C38   180.00   0.0  0
 6EA  CONST_69  H45  C45  C46  C39   180.00   0.0  0
 6EA  Var_01    C36  C33  C31  C27   -92.25  30.0  2
 6EA  Var_02    C27  C26  O25  C19  -173.05  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
 6EA  chir_01  C27  C26  N30  C31  negativ

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
 6EA  plan-1  N1   0.020
 6EA  plan-1  C2   0.020
 6EA  plan-1  C3   0.020
 6EA  plan-1  C4   0.020
 6EA  plan-1  C5   0.020
 6EA  plan-1  C6   0.020
 6EA  plan-1  C11  0.020
 6EA  plan-1  H2   0.020
 6EA  plan-1  H3   0.020
 6EA  plan-1  H5   0.020
 6EA  plan-1  H6   0.020
 6EA  plan-2  C31  0.020
 6EA  plan-2  C33  0.020
 6EA  plan-2  C36  0.020
 6EA  plan-2  N37  0.020
 6EA  plan-2  C38  0.020
 6EA  plan-2  C39  0.020
 6EA  plan-2  C43  0.020
 6EA  plan-2  C44  0.020
 6EA  plan-2  C45  0.020
 6EA  plan-2  C46  0.020
 6EA  plan-2  H36  0.020
 6EA  plan-2  H37  0.020
 6EA  plan-2  H43  0.020
 6EA  plan-2  H44  0.020
 6EA  plan-2  H45  0.020
 6EA  plan-2  H46  0.020
 6EA  plan-3  C4   0.020
 6EA  plan-3  C11  0.020
 6EA  plan-3  C12  0.020
 6EA  plan-3  C13  0.020
 6EA  plan-3  C14  0.020
 6EA  plan-3  C15  0.020
 6EA  plan-3  N16  0.020
 6EA  plan-3  C19  0.020
 6EA  plan-3  C20  0.020
 6EA  plan-3  N21  0.020
 6EA  plan-3  C22  0.020
 6EA  plan-3  O25  0.020
 6EA  plan-3  H12  0.020
 6EA  plan-3  H13  0.020
 6EA  plan-3  H20  0.020
 6EA  plan-3  H22  0.020

