# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 20:53:11 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: N~2~-[2-(5-chloro-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-fluoropyrimidin-4-yl]-2-methyl-N-(2,2,2-trifluoroethyl)-D-alaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(Nc1nc(ncc1F)c2c[nH]c3ncc(Cl)cc23)C(=O)NCC(F)(F)F
#
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
 467  467  N~2~-[2-(5-chloro-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-fluoropyrimidin-4-yl]-2-methyl-N-(2,2,2-trifluoroethyl)-D-alaninamide  ligand  44  29  .  2022-07-23  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_467
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
 467  F3   F   F     0  -0.302   1.3929   2.8200   0.4144
 467  C7   C   CR6   0   0.355   0.3640   1.9665   0.2918
 467  C8   C   CR16  0  -0.175  -0.9190   2.4083   0.1809
 467  N2   N   N     0  -0.455  -1.9459   1.5607   0.0581
 467  C9   C   CR6   0   0.331  -1.6434   0.2713   0.0522
 467  N3   N   N     0  -0.485  -0.4162  -0.2420   0.1572
 467  C6   C   CR6   0   0.449   0.6129   0.5788   0.2760
 467  N1   N   NH1   0  -0.714   1.8810   0.1178   0.3646
 467  C1   C   CT    0  -0.025   2.2687  -1.2855   0.5267
 467  C2   C   CH3   0  -0.658   1.7891  -2.1511  -0.6482
 467  C3   C   C     0   0.567   3.8076  -1.3305   0.4776
 467  N    N   NH1   0  -0.650   4.3744  -0.5294  -0.4511
 467  C4   C   CH2   0  -0.481   5.7881  -0.4984  -0.6966
 467  C5   C   CT    0   0.978   6.4515   0.6307   0.0617
 467  F2   F   F     0  -0.310   5.9518   1.8249  -0.2855
 467  F1   F   F     0  -0.302   6.2898   0.5172   1.3852
 467  F    F   F     0  -0.307   7.7678   0.6646  -0.1790
 467  O    O   O     0  -0.456   4.4499  -2.0747   1.1916
 467  C    C   CH3   0  -0.642   1.7762  -1.8512   1.8552
 467  C10  C   CR5   0  -0.104  -2.7381  -0.6763  -0.0672
 467  C13  C   CR56  0   0.009  -4.1385  -0.4014  -0.1905
 467  C14  C   CR16  0  -0.210  -4.9423   0.7339  -0.2456
 467  C15  C   CR6   0  -0.114  -6.3021   0.5235  -0.3702
 467  CL   CL  CL    0  -0.125  -7.3840   1.8740  -0.4473
 467  C16  C   CR16  0  -0.061  -6.8383  -0.7675  -0.4364
 467  N5   N   N     0  -0.415  -6.0899  -1.8554  -0.3850
 467  C12  C   CR56  0   0.486  -4.7909  -1.6522  -0.2661
 467  N4   N   NR15  0  -0.661  -3.8361  -2.6235  -0.1921
 467  C11  C   CR15  0   0.002  -2.6164  -2.0457  -0.0724
 467  H1   H   HCR6  0   0.289  -1.1381   3.4707   0.1890
 467  H2   H   HNH1  0   0.397   2.5401   0.7911   0.7260
 467  H3   H   HCH3  0   0.241   2.0679  -1.7163  -1.6084
 467  H4   H   HCH3  0   0.246   2.2414  -3.1408  -0.5793
 467  H5   H   HCH3  0   0.271   0.7098  -2.2694  -0.6261
 467  H6   H   HNH1  0   0.416   3.7795  -0.0071  -1.0751
 467  H7   H   HCH2  0   0.294   6.2484  -1.4421  -0.4049
 467  H8   H   HCH2  0   0.310   5.9682  -0.3557  -1.7623
 467  H9   H   HCH3  0   0.249   0.6896  -1.8016   1.8922
 467  H10  H   HCH3  0   0.239   2.0678  -2.8935   1.9701
 467  H11  H   HCH3  0   0.238   2.1769  -1.2891   2.6989
 467  H12  H   HCR6  0   0.283  -4.5226   1.7280  -0.1914
 467  H13  H   HCR6  0   0.279  -7.9086  -0.9062  -0.5331
 467  H14  H   HNR5  0   0.422  -4.0110  -3.6159  -0.2140
 467  H15  H   HCR5  0   0.304  -1.7269  -2.6490   0.0057

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
 467  F    C5   single    1.339  0.020  1.339
 467  F2   C5   single    1.340  0.020  1.340
 467  C5   F1   single    1.338  0.020  1.338
 467  C5   C4   single    1.513  0.020  1.513
 467  N4   C11  aromatic  1.355  0.020  1.355
 467  N4   C12  aromatic  1.364  0.020  1.364
 467  C11  C10  aromatic  1.375  0.020  1.375
 467  C12  N5   aromatic  1.320  0.020  1.320
 467  C12  C13  aromatic  1.413  0.020  1.413
 467  N5   C16  aromatic  1.322  0.020  1.322
 467  C4   N    single    1.435  0.020  1.435
 467  N2   C9   aromatic  1.324  0.020  1.324
 467  N2   C8   aromatic  1.337  0.020  1.337
 467  C10  C13  aromatic  1.433  0.020  1.433
 467  C10  C9   single    1.453  0.020  1.453
 467  C13  C14  aromatic  1.392  0.020  1.392
 467  C16  C15  aromatic  1.399  0.020  1.399
 467  C9   N3   aromatic  1.334  0.020  1.334
 467  C8   C7   aromatic  1.361  0.020  1.361
 467  C15  C14  aromatic  1.382  0.020  1.382
 467  C15  CL   single    1.732  0.020  1.732
 467  N    C3   single    1.351  0.020  1.351
 467  N3   C6   aromatic  1.322  0.020  1.322
 467  C7   C6   aromatic  1.410  0.020  1.410
 467  C7   F3   single    1.342  0.020  1.342
 467  C6   N1   single    1.352  0.020  1.352
 467  O    C3   double    1.215  0.020  1.215
 467  C3   C1   single    1.540  0.020  1.540
 467  N1   C1   single    1.465  0.020  1.465
 467  C1   C2   single    1.536  0.020  1.536
 467  C1   C    single    1.526  0.020  1.526
 467  C8   H1   single    0.930  0.020  1.080
 467  N1   H2   single    0.890  0.020  1.040
 467  C2   H3   single    0.970  0.020  1.090
 467  C2   H4   single    0.970  0.020  1.090
 467  C2   H5   single    0.970  0.020  1.090
 467  N    H6   single    0.860  0.020  1.020
 467  C4   H7   single    0.970  0.020  1.090
 467  C4   H8   single    0.970  0.020  1.090
 467  C    H9   single    0.970  0.020  1.090
 467  C    H10  single    0.970  0.020  1.090
 467  C    H11  single    0.970  0.020  1.090
 467  C14  H12  single    0.930  0.020  1.080
 467  C16  H13  single    0.930  0.020  1.080
 467  N4   H14  single    0.860  0.020  1.020
 467  C11  H15  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
 467  C6   C7   C8   119.00  3.000
 467  C6   C7   F3   119.43  3.000
 467  C8   C7   F3   121.56  3.000
 467  H1   C8   N2   117.80  3.000
 467  H1   C8   C7   120.50  3.000
 467  N2   C8   C7   121.70  3.000
 467  C9   N2   C8   116.24  3.000
 467  C10  C9   N3   116.65  3.000
 467  N3   C9   N2   125.75  3.000
 467  C10  C9   N2   117.60  3.000
 467  C6   N3   C9   118.96  3.000
 467  N1   C6   N3   121.63  3.000
 467  N1   C6   C7   120.03  3.000
 467  N3   C6   C7   118.34  3.000
 467  H2   N1   C1   115.25  3.000
 467  H2   N1   C6   114.11  3.000
 467  C1   N1   C6   125.59  3.000
 467  C    C1   C3   109.84  3.000
 467  C    C1   C2   110.87  3.000
 467  C3   C1   C2   105.73  3.000
 467  C    C1   N1   111.48  3.000
 467  C2   C1   N1   111.87  3.000
 467  C3   C1   N1   106.79  3.000
 467  H5   C2   H4   108.18  3.000
 467  H5   C2   H3   108.40  3.000
 467  H4   C2   H3   108.15  3.000
 467  H5   C2   C1   110.86  3.000
 467  H4   C2   C1   109.49  3.000
 467  H3   C2   C1   111.65  3.000
 467  O    C3   N    123.05  3.000
 467  O    C3   C1   121.83  3.000
 467  N    C3   C1   115.07  3.000
 467  H6   N    C4   117.66  3.000
 467  H6   N    C3   119.02  3.000
 467  C4   N    C3   122.93  3.000
 467  H8   C4   H7   107.77  3.000
 467  H8   C4   C5   108.65  3.000
 467  H7   C4   C5   109.08  3.000
 467  H8   C4   N    109.44  3.000
 467  H7   C4   N    110.58  3.000
 467  C5   C4   N    111.24  3.000
 467  F    C5   F1   107.39  3.000
 467  F1   C5   F2   106.66  3.000
 467  F    C5   F2   107.31  3.000
 467  F1   C5   C4   112.30  3.000
 467  F2   C5   C4   111.81  3.000
 467  F    C5   C4   111.10  3.000
 467  H11  C    H10  108.28  3.000
 467  H11  C    H9   108.49  3.000
 467  H10  C    H9   107.91  3.000
 467  H11  C    C1   111.35  3.000
 467  H10  C    C1   111.13  3.000
 467  H9   C    C1   109.57  3.000
 467  C11  C10  C13  106.10  3.000
 467  C13  C10  C9   128.21  3.000
 467  C11  C10  C9   125.69  3.000
 467  C12  C13  C14  116.96  3.000
 467  C14  C13  C10  136.42  3.000
 467  C12  C13  C10  106.62  3.000
 467  H12  C14  C15  121.80  3.000
 467  H12  C14  C13  121.61  3.000
 467  C15  C14  C13  116.59  3.000
 467  C16  C15  CL   118.54  3.000
 467  CL   C15  C14  120.00  3.000
 467  C16  C15  C14  121.46  3.000
 467  H13  C16  N5   117.23  3.000
 467  H13  C16  C15  120.05  3.000
 467  N5   C16  C15  122.72  3.000
 467  C12  N5   C16  115.72  3.000
 467  N4   C12  N5   125.74  3.000
 467  N5   C12  C13  126.55  3.000
 467  N4   C12  C13  107.72  3.000
 467  H14  N4   C11  125.32  3.000
 467  H14  N4   C12  125.34  3.000
 467  C11  N4   C12  109.34  3.000
 467  H15  C11  N4   120.71  3.000
 467  H15  C11  C10  129.08  3.000
 467  N4   C11  C10  110.21  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
 467  CONST_01  C9   N2   C8   C7      0.00   0.0  0
 467  CONST_02  C9   N3   C6   C7      0.00   0.0  0
 467  CONST_03  C10  C9   N2   C8    180.00   0.0  0
 467  CONST_04  N3   C9   N2   C8      0.00   0.0  0
 467  CONST_05  N3   C6   C7   C8      0.00   0.0  0
 467  CONST_06  C11  C10  C9   N2    180.00   0.0  0
 467  CONST_07  C13  C10  C9   N2      0.00   0.0  0
 467  CONST_08  C6   N3   C9   N2      0.00   0.0  0
 467  CONST_09  C6   C7   C8   N2      0.00   0.0  0
 467  CONST_10  N4   C11  C10  C9    180.00   0.0  0
 467  CONST_11  C12  C13  C10  C9    180.00   0.0  0
 467  CONST_12  C14  C13  C10  C9      0.00   0.0  0
 467  CONST_13  C11  C10  C9   N3      0.00   0.0  0
 467  CONST_14  C13  C10  C9   N3    180.00   0.0  0
 467  CONST_15  C10  C9   N3   C6    180.00   0.0  0
 467  CONST_16  C12  N4   C11  C10     0.00   0.0  0
 467  CONST_17  N4   C12  C13  C10     0.00   0.0  0
 467  CONST_18  N5   C12  C13  C10   180.00   0.0  0
 467  CONST_19  C15  C14  C13  C10   180.00   0.0  0
 467  CONST_20  C11  N4   C12  C13     0.00   0.0  0
 467  CONST_21  C16  N5   C12  C13     0.00   0.0  0
 467  CONST_22  N4   C11  C10  C13     0.00   0.0  0
 467  CONST_23  C16  C15  C14  C13     0.00   0.0  0
 467  CONST_24  N4   C12  C13  C14   180.00   0.0  0
 467  CONST_25  N5   C12  C13  C14     0.00   0.0  0
 467  CONST_26  C11  C10  C13  C14   180.00   0.0  0
 467  CONST_27  N5   C16  C15  C14     0.00   0.0  0
 467  CONST_28  C12  N5   C16  C15     0.00   0.0  0
 467  CONST_29  C12  C13  C14  C15     0.00   0.0  0
 467  CONST_30  N4   C12  N5   C16   180.00   0.0  0
 467  CONST_31  C11  N4   C12  N5    180.00   0.0  0
 467  CONST_32  C11  C10  C13  C12     0.00   0.0  0
 467  CONST_33  N2   C8   C7   F3    180.00   0.0  0
 467  CONST_34  N3   C6   C7   F3    180.00   0.0  0
 467  CONST_35  N1   C6   C7   C8    180.00   0.0  0
 467  CONST_36  N1   C6   N3   C9    180.00   0.0  0
 467  CONST_37  CL   C15  C14  C13   180.00   0.0  0
 467  CONST_38  N5   C16  C15  CL    180.00   0.0  0
 467  CONST_39  H1   C8   N2   C9    180.00   0.0  0
 467  CONST_40  H15  C11  C10  C9      0.00   0.0  0
 467  CONST_41  H14  N4   C11  C10   180.00   0.0  0
 467  CONST_42  H12  C14  C13  C10     0.00   0.0  0
 467  CONST_43  H13  C16  C15  C14   180.00   0.0  0
 467  CONST_44  C1   N1   C6   C7    180.00   0.0  0
 467  CONST_45  C1   N1   C6   N3      0.00   0.0  0
 467  CONST_47  C4   N    C3   C1    180.00   0.0  0
 467  CONST_48  O    C3   N    C4      0.00   0.0  0
 467  CONST_49  H6   N    C3   C1      0.00   0.0  0
 467  Var_01    C3   C1   N1   C6    176.08  30.0  3
 467  Var_02    N    C3   C1   N1    -40.91  30.0  3
 467  Var_03    C5   C4   N    C3    -96.23  30.0  1
 467  Var_04    F    C5   C4   N    -179.43  30.0  3
 467  Var_05    H3   C2   C1   N1     50.45  30.0  3
 467  Var_06    H9   C    C1   N1     60.87  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
 467  plan-1  F3   0.020
 467  plan-1  C7   0.020
 467  plan-1  C8   0.020
 467  plan-1  N2   0.020
 467  plan-1  C9   0.020
 467  plan-1  N3   0.020
 467  plan-1  C6   0.020
 467  plan-1  N1   0.020
 467  plan-1  C10  0.020
 467  plan-1  H1   0.020
 467  plan-2  C9   0.020
 467  plan-2  C10  0.020
 467  plan-2  C13  0.020
 467  plan-2  C14  0.020
 467  plan-2  C15  0.020
 467  plan-2  CL   0.020
 467  plan-2  C16  0.020
 467  plan-2  N5   0.020
 467  plan-2  C12  0.020
 467  plan-2  N4   0.020
 467  plan-2  C11  0.020
 467  plan-2  H12  0.020
 467  plan-2  H13  0.020
 467  plan-2  H14  0.020
 467  plan-2  H15  0.020
 467  plan-3  C1   0.020
 467  plan-3  C3   0.020
 467  plan-3  N    0.020
 467  plan-3  C4   0.020
 467  plan-3  O    0.020
 467  plan-3  H6   0.020
 467  plan-4  C6   0.020
 467  plan-4  N1   0.020
 467  plan-4  C1   0.020
 467  plan-4  H2   0.020

