# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 05:14:23 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 5-[(5-methoxy-1H-pyrrolo[2,3-b]pyridin-3-yl)methyl]-N-[4-(trifluoromethyl)benzyl]pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cnc2[nH]cc(Cc3ccc(NCc4ccc(cc4)C(F)(F)F)nc3)c2c1
#
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
 64M  64M  5-[(5-methoxy-1H-pyrrolo[2,3-b]pyridin-3-yl)methyl]-N-[4-(trifluoromethyl)benzyl]pyridin-2-amine  ligand  49  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_64M
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
 64M  C1   C  CR6   0   0.317   5.3021  -1.8914   0.2237
 64M  C2   C  CR16  0  -0.211   6.1447  -1.7839   1.3431
 64M  N4   N  N     0  -0.416   6.5094  -0.6240   1.8784
 64M  C5   C  CR16  0  -0.360   4.8074  -0.7382  -0.3739
 64M  N7   N  NR15  0  -0.674   6.2669   1.7505   1.6680
 64M  C9   C  CR15  0  -0.053   5.5895   2.5800   0.8170
 64M  C11  C  CR5   0  -0.026   4.9083   1.8571  -0.1219
 64M  C12  C  CR56  0   0.023   5.1787   0.4835   0.1720
 64M  C13  C  CR56  0   0.452   6.0329   0.4582   1.2988
 64M  O14  O  O2    0  -0.479   4.9287  -3.0693  -0.3253
 64M  C15  C  CH2   0  -0.617   4.0404   2.3825  -1.2188
 64M  C18  C  CR6   0   0.031   2.6036   1.9422  -1.0903
 64M  C19  C  CR16  0  -0.090   1.8484   2.2599   0.0310
 64M  N21  N  N     0  -0.459   0.5853   1.9090   0.2149
 64M  C22  C  CR6   0   0.481  -0.0273   1.1921  -0.7302
 64M  C23  C  CR16  0  -0.395   0.6327   0.8215  -1.9102
 64M  C25  C  CR16  0  -0.213   1.9519   1.2028  -2.0713
 64M  C27  C  CH3   0  -0.436   5.4161  -4.2655   0.2453
 64M  N31  N  NH1   0  -0.656  -1.3167   0.8297  -0.4564
 64M  C33  C  CH2   0  -0.336  -2.2092   0.3180  -1.4704
 64M  C36  C  CR6   0   0.090  -3.5164  -0.0820  -0.8442
 64M  C37  C  CR16  0  -0.293  -4.6936   0.5864  -1.1573
 64M  C39  C  CR16  0  -0.255  -5.8939   0.2266  -0.5632
 64M  C41  C  CR6   0  -0.208  -5.9248  -0.8111   0.3600
 64M  C42  C  CR16  0  -0.265  -4.7534  -1.4902   0.6781
 64M  C44  C  CR16  0  -0.265  -3.5600  -1.1221   0.0801
 64M  C46  C  CT    0   1.050  -7.2305  -1.2115   0.9697
 64M  F47  F  F     0  -0.315  -7.9504  -1.9848   0.1412
 64M  F48  F  F     0  -0.305  -7.0762  -1.9031   2.1034
 64M  F49  F  F     0  -0.310  -7.9957  -0.1504   1.2582
 64M  H1   H  HCR6  0   0.270   6.5389  -2.6683   1.8286
 64M  H2   H  HCR6  0   0.260   4.1513  -0.8056  -1.2340
 64M  H3   H  HNR5  0   0.408   6.8308   2.0459   2.4473
 64M  H4   H  HCR5  0   0.289   5.6397   3.6504   0.9429
 64M  H5   H  HCH2  0   0.263   4.0985   3.4745  -1.2257
 64M  H6   H  HCH2  0   0.257   4.4222   2.0555  -2.1907
 64M  H7   H  HCR6  0   0.246   2.2987   2.8376   0.8341
 64M  H8   H  HCR6  0   0.270   0.1338   0.2549  -2.6839
 64M  H9   H  HCR6  0   0.260   2.4766   0.9224  -2.9777
 64M  H10  H  HCH3  0   0.226   6.5077  -4.3233   0.2112
 64M  H11  H  HCH3  0   0.226   5.0905  -4.3900   1.2817
 64M  H12  H  HCH3  0   0.258   5.0065  -5.0800  -0.3473
 64M  H13  H  HNH1  0   0.380  -1.7466   1.3734   0.2765
 64M  H14  H  HCH2  0   0.246  -2.3855   1.0442  -2.2733
 64M  H15  H  HCH2  0   0.257  -1.7561  -0.5613  -1.9356
 64M  H16  H  HCR6  0   0.267  -4.6779   1.4012  -1.8700
 64M  H17  H  HCR6  0   0.275  -6.7935   0.7689  -0.8232
 64M  H18  H  HCR6  0   0.273  -4.7552  -2.3044   1.3897
 64M  H19  H  HCR6  0   0.264  -2.6518  -1.6540   0.3357

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
 64M  N4   C2   aromatic  1.329  0.020  1.329
 64M  N4   C13  aromatic  1.317  0.020  1.317
 64M  C2   C1   aromatic  1.405  0.020  1.405
 64M  N7   C13  aromatic  1.364  0.020  1.364
 64M  N7   C9   aromatic  1.368  0.020  1.368
 64M  C13  C12  aromatic  1.414  0.020  1.414
 64M  C1   O14  single    1.352  0.020  1.352
 64M  C1   C5   aromatic  1.390  0.020  1.390
 64M  C25  C23  aromatic  1.383  0.020  1.383
 64M  C25  C18  aromatic  1.391  0.020  1.391
 64M  C23  C22  aromatic  1.402  0.020  1.402
 64M  C9   C11  aromatic  1.367  0.020  1.367
 64M  O14  C27  single    1.412  0.020  1.412
 64M  C12  C5   aromatic  1.389  0.020  1.389
 64M  C12  C11  aromatic  1.430  0.020  1.430
 64M  C11  C15  single    1.494  0.020  1.494
 64M  N31  C22  single    1.367  0.020  1.367
 64M  N31  C33  single    1.445  0.020  1.445
 64M  C18  C15  single    1.508  0.020  1.508
 64M  C18  C19  aromatic  1.389  0.020  1.389
 64M  C22  N21  aromatic  1.335  0.020  1.335
 64M  C33  C36  single    1.504  0.020  1.504
 64M  C19  N21  aromatic  1.324  0.020  1.324
 64M  C36  C37  aromatic  1.389  0.020  1.389
 64M  C36  C44  aromatic  1.392  0.020  1.392
 64M  C37  C39  aromatic  1.387  0.020  1.387
 64M  C44  C42  aromatic  1.385  0.020  1.385
 64M  C39  C41  aromatic  1.389  0.020  1.389
 64M  C42  C41  aromatic  1.391  0.020  1.391
 64M  C41  C46  single    1.496  0.020  1.496
 64M  F49  C46  single    1.340  0.020  1.340
 64M  C46  F47  single    1.343  0.020  1.343
 64M  C46  F48  single    1.337  0.020  1.337
 64M  C2   H1   single    0.930  0.020  1.080
 64M  C5   H2   single    0.930  0.020  1.080
 64M  N7   H3   single    0.860  0.020  1.020
 64M  C9   H4   single    0.930  0.020  1.080
 64M  C15  H5   single    0.970  0.020  1.090
 64M  C15  H6   single    0.970  0.020  1.090
 64M  C19  H7   single    0.930  0.020  1.080
 64M  C23  H8   single    0.930  0.020  1.080
 64M  C25  H9   single    0.930  0.020  1.080
 64M  C27  H10  single    0.970  0.020  1.090
 64M  C27  H11  single    0.970  0.020  1.090
 64M  C27  H12  single    0.970  0.020  1.090
 64M  N31  H13  single    0.890  0.020  1.040
 64M  C33  H14  single    0.970  0.020  1.090
 64M  C33  H15  single    0.970  0.020  1.090
 64M  C37  H16  single    0.930  0.020  1.080
 64M  C39  H17  single    0.930  0.020  1.080
 64M  C42  H18  single    0.930  0.020  1.080
 64M  C44  H19  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
 64M  O14  C1   C5   116.74  3.000
 64M  C5   C1   C2   119.51  3.000
 64M  O14  C1   C2   123.76  3.000
 64M  H1   C2   N4   115.62  3.000
 64M  H1   C2   C1   120.85  3.000
 64M  N4   C2   C1   123.53  3.000
 64M  C13  N4   C2   116.15  3.000
 64M  H2   C5   C12  121.90  3.000
 64M  H2   C5   C1   120.34  3.000
 64M  C12  C5   C1   117.76  3.000
 64M  H3   N7   C13  125.72  3.000
 64M  H3   N7   C9   125.54  3.000
 64M  C13  N7   C9   108.73  3.000
 64M  H4   C9   C11  128.90  3.000
 64M  H4   C9   N7   120.40  3.000
 64M  C11  C9   N7   110.70  3.000
 64M  C15  C11  C12  126.75  3.000
 64M  C15  C11  C9   127.43  3.000
 64M  C12  C11  C9   105.81  3.000
 64M  C13  C12  C11  107.16  3.000
 64M  C11  C12  C5   135.52  3.000
 64M  C13  C12  C5   117.32  3.000
 64M  C12  C13  N7   107.60  3.000
 64M  C12  C13  N4   125.73  3.000
 64M  N7   C13  N4   126.67  3.000
 64M  C27  O14  C1   118.59  3.000
 64M  H6   C15  H5   105.92  3.000
 64M  H6   C15  C18  108.71  3.000
 64M  H5   C15  C18  110.04  3.000
 64M  H6   C15  C11  110.13  3.000
 64M  H5   C15  C11  108.97  3.000
 64M  C18  C15  C11  112.84  3.000
 64M  C25  C18  C19  115.87  3.000
 64M  C19  C18  C15  121.33  3.000
 64M  C25  C18  C15  122.79  3.000
 64M  H7   C19  N21  115.69  3.000
 64M  H7   C19  C18  119.53  3.000
 64M  N21  C19  C18  124.77  3.000
 64M  C22  N21  C19  118.81  3.000
 64M  N31  C22  C23  122.86  3.000
 64M  N31  C22  N21  115.68  3.000
 64M  C23  C22  N21  121.45  3.000
 64M  H8   C23  C25  120.10  3.000
 64M  H8   C23  C22  121.58  3.000
 64M  C25  C23  C22  118.32  3.000
 64M  H9   C25  C23  119.20  3.000
 64M  H9   C25  C18  120.03  3.000
 64M  C23  C25  C18  120.77  3.000
 64M  H12  C27  H11  108.60  3.000
 64M  H12  C27  H10  108.62  3.000
 64M  H11  C27  H10  108.71  3.000
 64M  H12  C27  O14  106.52  3.000
 64M  H11  C27  O14  112.13  3.000
 64M  H10  C27  O14  112.13  3.000
 64M  H13  N31  C33  115.95  3.000
 64M  H13  N31  C22  113.87  3.000
 64M  C33  N31  C22  122.41  3.000
 64M  H15  C33  H14  106.72  3.000
 64M  H15  C33  C36  108.88  3.000
 64M  H14  C33  C36  109.95  3.000
 64M  H15  C33  N31  109.12  3.000
 64M  H14  C33  N31  112.25  3.000
 64M  C36  C33  N31  109.82  3.000
 64M  C44  C36  C37  118.85  3.000
 64M  C44  C36  C33  120.17  3.000
 64M  C37  C36  C33  120.98  3.000
 64M  H16  C37  C39  119.33  3.000
 64M  H16  C37  C36  119.88  3.000
 64M  C39  C37  C36  120.79  3.000
 64M  H17  C39  C41  121.03  3.000
 64M  H17  C39  C37  119.11  3.000
 64M  C41  C39  C37  119.85  3.000
 64M  C46  C41  C42  120.75  3.000
 64M  C46  C41  C39  119.36  3.000
 64M  C42  C41  C39  119.87  3.000
 64M  H18  C42  C44  119.06  3.000
 64M  H18  C42  C41  121.12  3.000
 64M  C44  C42  C41  119.82  3.000
 64M  H19  C44  C42  119.36  3.000
 64M  H19  C44  C36  119.82  3.000
 64M  C42  C44  C36  120.82  3.000
 64M  F49  C46  F48  107.04  3.000
 64M  F48  C46  F47  106.69  3.000
 64M  F49  C46  F47  106.43  3.000
 64M  F48  C46  C41  112.54  3.000
 64M  F47  C46  C41  111.76  3.000
 64M  F49  C46  C41  111.99  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
 64M  CONST_01  C13  N4   C2   C1      0.00   0.0  0
 64M  CONST_02  C13  C12  C5   C1      0.00   0.0  0
 64M  CONST_03  C11  C12  C5   C1    180.00   0.0  0
 64M  CONST_04  N7   C13  N4   C2    180.00   0.0  0
 64M  CONST_05  C12  C13  N4   C2      0.00   0.0  0
 64M  CONST_06  C12  C5   C1   C2      0.00   0.0  0
 64M  CONST_07  C5   C1   C2   N4      0.00   0.0  0
 64M  CONST_08  C9   N7   C13  N4    180.00   0.0  0
 64M  CONST_09  C5   C12  C13  N4      0.00   0.0  0
 64M  CONST_10  C11  C12  C13  N4    180.00   0.0  0
 64M  CONST_11  N7   C13  C12  C5    180.00   0.0  0
 64M  CONST_12  C9   C11  C12  C5    180.00   0.0  0
 64M  CONST_13  C11  C12  C13  N7      0.00   0.0  0
 64M  CONST_14  C12  C11  C9   N7      0.00   0.0  0
 64M  CONST_15  C12  C13  N7   C9      0.00   0.0  0
 64M  CONST_16  C13  C12  C11  C9      0.00   0.0  0
 64M  CONST_17  C13  N7   C9   C11     0.00   0.0  0
 64M  CONST_18  C22  C23  C25  C18     0.00   0.0  0
 64M  CONST_19  C22  N21  C19  C18     0.00   0.0  0
 64M  CONST_20  C23  C25  C18  C19     0.00   0.0  0
 64M  CONST_21  C23  C22  N21  C19     0.00   0.0  0
 64M  CONST_22  C25  C23  C22  N21     0.00   0.0  0
 64M  CONST_23  C25  C18  C19  N21     0.00   0.0  0
 64M  CONST_24  C41  C39  C37  C36     0.00   0.0  0
 64M  CONST_25  C41  C42  C44  C36     0.00   0.0  0
 64M  CONST_26  C42  C44  C36  C37     0.00   0.0  0
 64M  CONST_27  C42  C41  C39  C37     0.00   0.0  0
 64M  CONST_28  C44  C36  C37  C39     0.00   0.0  0
 64M  CONST_29  C44  C42  C41  C39     0.00   0.0  0
 64M  CONST_30  O14  C1   C2   N4    180.00   0.0  0
 64M  CONST_31  C15  C11  C12  C5      0.00   0.0  0
 64M  CONST_32  C15  C11  C9   N7    180.00   0.0  0
 64M  CONST_33  O14  C1   C5   C12   180.00   0.0  0
 64M  CONST_34  C15  C11  C12  C13   180.00   0.0  0
 64M  CONST_35  C23  C25  C18  C15   180.00   0.0  0
 64M  CONST_36  N21  C19  C18  C15   180.00   0.0  0
 64M  CONST_37  N31  C22  N21  C19   180.00   0.0  0
 64M  CONST_38  N31  C22  C23  C25   180.00   0.0  0
 64M  CONST_39  C39  C37  C36  C33   180.00   0.0  0
 64M  CONST_40  C42  C44  C36  C33   180.00   0.0  0
 64M  CONST_41  C46  C41  C39  C37   180.00   0.0  0
 64M  CONST_42  C46  C41  C42  C44   180.00   0.0  0
 64M  CONST_43  H2   C5   C1   C2    180.00   0.0  0
 64M  CONST_44  H3   N7   C13  N4      0.00   0.0  0
 64M  CONST_45  H1   C2   C1   C5    180.00   0.0  0
 64M  CONST_46  H4   C9   C11  C12   180.00   0.0  0
 64M  CONST_47  H8   C23  C25  C18   180.00   0.0  0
 64M  CONST_48  H9   C25  C18  C19   180.00   0.0  0
 64M  CONST_49  H7   C19  N21  C22   180.00   0.0  0
 64M  CONST_50  H17  C39  C37  C36   180.00   0.0  0
 64M  CONST_51  H18  C42  C44  C36   180.00   0.0  0
 64M  CONST_52  H19  C44  C36  C37   180.00   0.0  0
 64M  CONST_53  H16  C37  C39  C41   180.00   0.0  0
 64M  CONST_54  C33  N31  C22  N21   180.00   0.0  0
 64M  Var_01    C18  C15  C11  C9   -117.22  30.0  2
 64M  Var_02    C25  C18  C15  C11  -120.47  30.0  2
 64M  Var_03    C36  C33  N31  C22   175.92  30.0  3
 64M  Var_04    C37  C36  C33  N31   114.68  30.0  2
 64M  Var_05    F49  C46  C41  C39   -39.97  30.0  2
 64M  Var_06    H10  C27  O14  C1    -60.78  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
 64M  plan-1  C15  0.020
 64M  plan-1  C18  0.020
 64M  plan-1  C19  0.020
 64M  plan-1  N21  0.020
 64M  plan-1  C22  0.020
 64M  plan-1  C23  0.020
 64M  plan-1  C25  0.020
 64M  plan-1  N31  0.020
 64M  plan-1  H7   0.020
 64M  plan-1  H8   0.020
 64M  plan-1  H9   0.020
 64M  plan-2  C33  0.020
 64M  plan-2  C36  0.020
 64M  plan-2  C37  0.020
 64M  plan-2  C39  0.020
 64M  plan-2  C41  0.020
 64M  plan-2  C42  0.020
 64M  plan-2  C44  0.020
 64M  plan-2  C46  0.020
 64M  plan-2  H16  0.020
 64M  plan-2  H17  0.020
 64M  plan-2  H18  0.020
 64M  plan-2  H19  0.020
 64M  plan-3  C1   0.020
 64M  plan-3  C2   0.020
 64M  plan-3  N4   0.020
 64M  plan-3  C5   0.020
 64M  plan-3  N7   0.020
 64M  plan-3  C9   0.020
 64M  plan-3  C11  0.020
 64M  plan-3  C12  0.020
 64M  plan-3  C13  0.020
 64M  plan-3  O14  0.020
 64M  plan-3  C15  0.020
 64M  plan-3  H1   0.020
 64M  plan-3  H2   0.020
 64M  plan-3  H3   0.020
 64M  plan-3  H4   0.020
 64M  plan-4  C22  0.020
 64M  plan-4  N31  0.020
 64M  plan-4  C33  0.020
 64M  plan-4  H13  0.020

