# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 22:53:48 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 5-(1H-pyrrolo[2,3-b]pyridin-3-ylmethyl)-N-[4-(trifluoromethyl)benzyl]pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1ccc(CNc2ccc(Cc3c[nH]c4ncccc34)cn2)cc1
#
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
 647  647  5-(1H-pyrrolo[2,3-b]pyridin-3-ylmethyl)-N-[4-(trifluoromethyl)benzyl]pyridin-2-amine  ligand  45  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 PERFECT
;

data_comp_647
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
 647  C1   C  CR16  0  -0.345   5.6191   2.6256   0.7903
 647  C3   C  CR16  0  -0.091   6.5186   2.8527  -0.2570
 647  N5   N  N     0  -0.427   6.9698   1.9074  -1.0700
 647  C6   C  CR16  0  -0.240   5.1445   1.3461   1.0264
 647  N8   N  NR15  0  -0.670   6.8221  -0.4366  -1.5174
 647  C10  C  CR15  0  -0.058   6.1500  -1.4973  -0.9684
 647  C12  C  CR5   0  -0.010   5.3852  -1.0848   0.0849
 647  C13  C  CR56  0  -0.011   5.5959   0.3267   0.1925
 647  C14  C  CR56  0   0.465   6.5051   0.6918  -0.8291
 647  C15  C  CH2   0  -0.629   4.4868  -1.9232   0.9356
 647  C18  C  CR6   0   0.037   3.0285  -1.6050   0.7300
 647  C19  C  CR16  0  -0.128   2.2481  -1.0448   1.7272
 647  N21  N  N     0  -0.460   0.9611  -0.7429   1.6024
 647  C22  C  CR6   0   0.477   0.3549  -0.9928   0.4435
 647  C23  C  CR16  0  -0.390   1.0461  -1.5654  -0.6388
 647  C25  C  CR16  0  -0.180   2.3833  -1.8588  -0.4803
 647  N27  N  NH1   0  -0.652  -0.9623  -0.6404   0.3633
 647  C29  C  CH2   0  -0.340  -1.8267  -1.1346  -0.6870
 647  C32  C  CR6   0   0.085  -3.2239  -0.6249  -0.4713
 647  C33  C  CR16  0  -0.271  -3.5963   0.6361  -0.9240
 647  C35  C  CR16  0  -0.266  -4.8737   1.1237  -0.6967
 647  C37  C  CR6   0  -0.205  -5.7935   0.3504   0.0009
 647  C38  C  CR16  0  -0.257  -5.4326  -0.9115   0.4597
 647  C40  C  CR16  0  -0.279  -4.1541  -1.3904   0.2238
 647  C42  C  CT    0   1.050  -7.1903   0.8382   0.2212
 647  F43  F  F     0  -0.305  -7.2936   2.1664   0.1085
 647  F44  F  F     0  -0.315  -8.0456   0.3082  -0.6679
 647  F45  F  F     0  -0.310  -7.6521   0.5098   1.4347
 647  H1   H  HCR6  0   0.262   5.3046   3.4556   1.4079
 647  H2   H  HCR6  0   0.254   6.8886   3.8560  -0.4360
 647  H3   H  HCR6  0   0.252   4.4485   1.1547   1.8336
 647  H4   H  HNR5  0   0.408   7.4453  -0.4840  -2.3064
 647  H5   H  HCR5  0   0.289   6.2680  -2.4891  -1.3761
 647  H6   H  HCH2  0   0.264   4.6684  -2.9785   0.7150
 647  H7   H  HCH2  0   0.256   4.7369  -1.7884   1.9923
 647  H8   H  HCR6  0   0.248   2.6899  -0.8271   2.6963
 647  H9   H  HCR6  0   0.271   0.5508  -1.7784  -1.5760
 647  H10  H  HCR6  0   0.257   2.9324  -2.2958  -1.3067
 647  H11  H  HNH1  0   0.381  -1.3979  -0.4707   1.2572
 647  H12  H  HCH2  0   0.255  -1.4607  -0.7877  -1.6565
 647  H13  H  HCH2  0   0.245  -1.8348  -2.2309  -0.7247
 647  H14  H  HCR6  0   0.265  -2.8855   1.2448  -1.4686
 647  H15  H  HCR6  0   0.274  -5.1351   2.1049  -1.0688
 647  H16  H  HCR6  0   0.276  -6.1350  -1.5289   1.0039
 647  H17  H  HCR6  0   0.266  -3.8810  -2.3736   0.5863

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
 647  C40  C38  aromatic  1.385  0.020  1.385
 647  C40  C32  aromatic  1.391  0.020  1.391
 647  C29  N27  single    1.447  0.020  1.447
 647  C29  C32  single    1.503  0.020  1.503
 647  C38  C37  aromatic  1.390  0.020  1.390
 647  N27  C22  single    1.366  0.020  1.366
 647  N21  C22  aromatic  1.331  0.020  1.331
 647  N21  C19  aromatic  1.328  0.020  1.328
 647  C32  C33  aromatic  1.391  0.020  1.391
 647  C22  C23  aromatic  1.406  0.020  1.406
 647  C19  C18  aromatic  1.385  0.020  1.385
 647  C18  C25  aromatic  1.395  0.020  1.395
 647  C18  C15  single    1.507  0.020  1.507
 647  C23  C25  aromatic  1.378  0.020  1.378
 647  F45  C42  single    1.339  0.020  1.339
 647  C15  C12  single    1.495  0.020  1.495
 647  C37  C42  single    1.496  0.020  1.496
 647  C37  C35  aromatic  1.390  0.020  1.390
 647  C33  C35  aromatic  1.386  0.020  1.386
 647  C42  F44  single    1.343  0.020  1.343
 647  C42  F43  single    1.337  0.020  1.337
 647  C12  C13  aromatic  1.431  0.020  1.431
 647  C12  C10  aromatic  1.365  0.020  1.365
 647  C6   C13  aromatic  1.392  0.020  1.392
 647  C6   C1   aromatic  1.385  0.020  1.385
 647  C13  C14  aromatic  1.415  0.020  1.415
 647  C10  N8   aromatic  1.370  0.020  1.370
 647  C1   C3   aromatic  1.399  0.020  1.399
 647  C14  N8   aromatic  1.359  0.020  1.359
 647  C14  N5   aromatic  1.323  0.020  1.323
 647  C3   N5   aromatic  1.326  0.020  1.326
 647  C1   H1   single    0.930  0.020  1.080
 647  C3   H2   single    0.930  0.020  1.080
 647  C6   H3   single    0.930  0.020  1.080
 647  N8   H4   single    0.860  0.020  1.020
 647  C10  H5   single    0.930  0.020  1.080
 647  C15  H6   single    0.970  0.020  1.090
 647  C15  H7   single    0.970  0.020  1.090
 647  C19  H8   single    0.930  0.020  1.080
 647  C23  H9   single    0.930  0.020  1.080
 647  C25  H10  single    0.930  0.020  1.080
 647  N27  H11  single    0.890  0.020  1.040
 647  C29  H12  single    0.970  0.020  1.090
 647  C29  H13  single    0.970  0.020  1.090
 647  C33  H14  single    0.930  0.020  1.080
 647  C35  H15  single    0.930  0.020  1.080
 647  C38  H16  single    0.930  0.020  1.080
 647  C40  H17  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
 647  H1   C1   C6   120.81  3.000
 647  H1   C1   C3   119.34  3.000
 647  C6   C1   C3   119.86  3.000
 647  H2   C3   N5   116.25  3.000
 647  H2   C3   C1   119.55  3.000
 647  N5   C3   C1   124.20  3.000
 647  C14  N5   C3   115.07  3.000
 647  H3   C6   C13  121.70  3.000
 647  H3   C6   C1   120.70  3.000
 647  C13  C6   C1   117.60  3.000
 647  H4   N8   C14  125.48  3.000
 647  H4   N8   C10  125.54  3.000
 647  C14  N8   C10  108.98  3.000
 647  H5   C10  C12  129.09  3.000
 647  H5   C10  N8   120.44  3.000
 647  C12  C10  N8   110.48  3.000
 647  C15  C12  C13  126.79  3.000
 647  C13  C12  C10  105.87  3.000
 647  C15  C12  C10  127.32  3.000
 647  C14  C13  C12  107.14  3.000
 647  C14  C13  C6   116.85  3.000
 647  C12  C13  C6   136.01  3.000
 647  C13  C14  N8   107.52  3.000
 647  N8   C14  N5   126.05  3.000
 647  C13  C14  N5   126.43  3.000
 647  H7   C15  H6   106.01  3.000
 647  H7   C15  C18  109.09  3.000
 647  H6   C15  C18  109.70  3.000
 647  H7   C15  C12  110.07  3.000
 647  H6   C15  C12  109.08  3.000
 647  C18  C15  C12  112.68  3.000
 647  C25  C18  C19  115.96  3.000
 647  C25  C18  C15  121.85  3.000
 647  C19  C18  C15  122.19  3.000
 647  H8   C19  N21  115.61  3.000
 647  H8   C19  C18  119.60  3.000
 647  N21  C19  C18  124.79  3.000
 647  C22  N21  C19  118.71  3.000
 647  N27  C22  C23  122.27  3.000
 647  C23  C22  N21  121.51  3.000
 647  N27  C22  N21  116.21  3.000
 647  H9   C23  C25  120.16  3.000
 647  H9   C23  C22  121.48  3.000
 647  C25  C23  C22  118.37  3.000
 647  H10  C25  C23  119.31  3.000
 647  H10  C25  C18  120.03  3.000
 647  C23  C25  C18  120.66  3.000
 647  H11  N27  C29  116.27  3.000
 647  H11  N27  C22  114.07  3.000
 647  C29  N27  C22  122.04  3.000
 647  H13  C29  H12  106.81  3.000
 647  H13  C29  C32  109.70  3.000
 647  H12  C29  C32  109.33  3.000
 647  H13  C29  N27  111.75  3.000
 647  H12  C29  N27  109.59  3.000
 647  C32  C29  N27  109.59  3.000
 647  C40  C32  C33  118.86  3.000
 647  C33  C32  C29  120.65  3.000
 647  C40  C32  C29  120.45  3.000
 647  H14  C33  C35  119.32  3.000
 647  H14  C33  C32  119.85  3.000
 647  C35  C33  C32  120.83  3.000
 647  H15  C35  C37  121.17  3.000
 647  H15  C35  C33  119.05  3.000
 647  C37  C35  C33  119.77  3.000
 647  C42  C37  C38  119.32  3.000
 647  C42  C37  C35  120.70  3.000
 647  C38  C37  C35  119.93  3.000
 647  H16  C38  C40  119.17  3.000
 647  H16  C38  C37  121.02  3.000
 647  C40  C38  C37  119.81  3.000
 647  H17  C40  C38  119.32  3.000
 647  H17  C40  C32  119.89  3.000
 647  C38  C40  C32  120.79  3.000
 647  F45  C42  F44  106.48  3.000
 647  F44  C42  F43  106.69  3.000
 647  F45  C42  F43  107.06  3.000
 647  F43  C42  C37  112.56  3.000
 647  F44  C42  C37  111.63  3.000
 647  F45  C42  C37  112.05  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
 647  CONST_01  C12  C13  C6   C1    180.00   0.0  0
 647  CONST_02  C14  C13  C6   C1      0.00   0.0  0
 647  CONST_03  C14  N5   C3   C1      0.00   0.0  0
 647  CONST_04  C13  C6   C1   C3      0.00   0.0  0
 647  CONST_05  C13  C14  N5   C3      0.00   0.0  0
 647  CONST_06  N8   C14  N5   C3    180.00   0.0  0
 647  CONST_07  C12  C13  C14  N5    180.00   0.0  0
 647  CONST_08  C6   C13  C14  N5      0.00   0.0  0
 647  CONST_09  C10  N8   C14  N5    180.00   0.0  0
 647  CONST_10  C6   C1   C3   N5      0.00   0.0  0
 647  CONST_11  C10  C12  C13  C6    180.00   0.0  0
 647  CONST_12  N8   C14  C13  C6    180.00   0.0  0
 647  CONST_13  C13  C12  C10  N8      0.00   0.0  0
 647  CONST_14  C12  C13  C14  N8      0.00   0.0  0
 647  CONST_15  C14  C13  C12  C10     0.00   0.0  0
 647  CONST_16  C13  C14  N8   C10     0.00   0.0  0
 647  CONST_17  C14  N8   C10  C12     0.00   0.0  0
 647  CONST_18  C22  N21  C19  C18     0.00   0.0  0
 647  CONST_19  C22  C23  C25  C18     0.00   0.0  0
 647  CONST_20  C23  C22  N21  C19     0.00   0.0  0
 647  CONST_21  C23  C25  C18  C19     0.00   0.0  0
 647  CONST_22  C25  C23  C22  N21     0.00   0.0  0
 647  CONST_23  C25  C18  C19  N21     0.00   0.0  0
 647  CONST_24  C37  C38  C40  C32     0.00   0.0  0
 647  CONST_25  C37  C35  C33  C32     0.00   0.0  0
 647  CONST_26  C38  C40  C32  C33     0.00   0.0  0
 647  CONST_27  C38  C37  C35  C33     0.00   0.0  0
 647  CONST_28  C40  C38  C37  C35     0.00   0.0  0
 647  CONST_29  C40  C32  C33  C35     0.00   0.0  0
 647  CONST_30  C15  C12  C13  C6      0.00   0.0  0
 647  CONST_31  C15  C12  C10  N8    180.00   0.0  0
 647  CONST_32  C15  C12  C13  C14   180.00   0.0  0
 647  CONST_33  N21  C19  C18  C15   180.00   0.0  0
 647  CONST_34  C23  C25  C18  C15   180.00   0.0  0
 647  CONST_35  N27  C22  N21  C19   180.00   0.0  0
 647  CONST_36  N27  C22  C23  C25   180.00   0.0  0
 647  CONST_37  C38  C40  C32  C29   180.00   0.0  0
 647  CONST_38  C35  C33  C32  C29   180.00   0.0  0
 647  CONST_39  C42  C37  C35  C33   180.00   0.0  0
 647  CONST_40  C42  C37  C38  C40   180.00   0.0  0
 647  CONST_41  H3   C6   C1   C3    180.00   0.0  0
 647  CONST_42  H4   N8   C14  N5      0.00   0.0  0
 647  CONST_43  H1   C1   C3   N5    180.00   0.0  0
 647  CONST_44  H2   C3   C1   C6    180.00   0.0  0
 647  CONST_45  H5   C10  C12  C13   180.00   0.0  0
 647  CONST_46  H9   C23  C25  C18   180.00   0.0  0
 647  CONST_47  H10  C25  C18  C19   180.00   0.0  0
 647  CONST_48  H8   C19  N21  C22   180.00   0.0  0
 647  CONST_49  H16  C38  C40  C32   180.00   0.0  0
 647  CONST_50  H15  C35  C33  C32   180.00   0.0  0
 647  CONST_51  H17  C40  C32  C33   180.00   0.0  0
 647  CONST_52  H14  C33  C35  C37   180.00   0.0  0
 647  Var_01    C18  C15  C12  C10  -111.32  30.0  2
 647  Var_02    C19  C18  C15  C12  -113.90  30.0  2
 647  Var_03    C32  C29  N27  C22   177.37  30.0  1
 647  Var_04    C40  C32  C29  N27   -93.87  30.0  2
 647  Var_05    F45  C42  C37  C35  -141.99  30.0  2

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
 647  plan-1  C15  0.020
 647  plan-1  C18  0.020
 647  plan-1  C19  0.020
 647  plan-1  N21  0.020
 647  plan-1  C22  0.020
 647  plan-1  C23  0.020
 647  plan-1  C25  0.020
 647  plan-1  N27  0.020
 647  plan-1  H8   0.020
 647  plan-1  H9   0.020
 647  plan-1  H10  0.020
 647  plan-2  C29  0.020
 647  plan-2  C32  0.020
 647  plan-2  C33  0.020
 647  plan-2  C35  0.020
 647  plan-2  C37  0.020
 647  plan-2  C38  0.020
 647  plan-2  C40  0.020
 647  plan-2  C42  0.020
 647  plan-2  H14  0.020
 647  plan-2  H15  0.020
 647  plan-2  H16  0.020
 647  plan-2  H17  0.020
 647  plan-3  C1   0.020
 647  plan-3  C3   0.020
 647  plan-3  N5   0.020
 647  plan-3  C6   0.020
 647  plan-3  N8   0.020
 647  plan-3  C10  0.020
 647  plan-3  C12  0.020
 647  plan-3  C13  0.020
 647  plan-3  C14  0.020
 647  plan-3  C15  0.020
 647  plan-3  H1   0.020
 647  plan-3  H2   0.020
 647  plan-3  H3   0.020
 647  plan-3  H4   0.020
 647  plan-3  H5   0.020
 647  plan-4  C22  0.020
 647  plan-4  N27  0.020
 647  plan-4  C29  0.020
 647  plan-4  H11  0.020

