# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 02:48:21 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: N~2~-[2-(5-chloro-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-fluoropyrimidin-4-yl]-N-(2,2,2-trifluoroethyl)-L-alaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](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
 4HZ  4HZ  N~2~-[2-(5-chloro-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-fluoropyrimidin-4-yl]-N-(2,2,2-trifluoroethyl)-L-alaninamide  ligand  41  28  .  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_4HZ
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
 4HZ  C1   C   CH1   0  -0.202  -2.4049  -0.5535  -0.6891
 4HZ  N2   N   N     0  -0.461   2.3504  -1.6582   0.4657
 4HZ  C3   C   CH2   0  -0.482  -6.0311   0.3961  -0.1898
 4HZ  C4   C   CT    0   0.978  -6.4069   0.7083   1.2428
 4HZ  C5   C   CR6   0   0.443  -0.3618  -1.6955   0.0211
 4HZ  C6   C   CR6   0   0.352   0.3116  -2.8448   0.4861
 4HZ  C8   C   CR6   0   0.327   1.6567  -0.6177   0.0292
 4HZ  C9   C   CR5   0  -0.102   2.3861   0.6106  -0.2390
 4HZ  C10  C   CR15  0   0.001   1.8417   1.7776  -0.7191
 4HZ  C15  C   CR16  0  -0.062   6.2075   2.1360  -0.0836
 4HZ  F3   F   F     0  -0.304  -0.3852  -3.9696   0.7148
 4HZ  C7   C   CR16  0  -0.179   1.6543  -2.7794   0.6935
 4HZ  N3   N   N     0  -0.491   0.3427  -0.5937  -0.1973
 4HZ  N1   N   NH1   0  -0.683  -1.6834  -1.6965  -0.1899
 4HZ  C2   C   C     0   0.565  -3.8768  -0.7508  -0.3445
 4HZ  N    N   NH1   0  -0.646  -4.6082   0.3780  -0.3732
 4HZ  F2   F   F     0  -0.310  -5.9579   1.9121   1.6248
 4HZ  F1   F   F     0  -0.307  -7.7369   0.7128   1.3965
 4HZ  F    F   F     0  -0.301  -5.9071  -0.1811   2.1077
 4HZ  O    O   O     0  -0.471  -4.3435  -1.8523  -0.1132
 4HZ  C    C   CH3   0  -0.655  -2.2460  -0.3735  -2.2016
 4HZ  C12  C   CR56  0   0.008   3.7870   0.8620  -0.0787
 4HZ  C13  C   CR16  0  -0.211   4.8975   0.1415   0.3521
 4HZ  C14  C   CR6   0  -0.114   6.1085   0.8065   0.3417
 4HZ  CL   CL  CL    0  -0.126   7.5476  -0.0060   0.8609
 4HZ  N5   N   N     0  -0.416   5.1636   2.8346  -0.4949
 4HZ  C11  C   CR56  0   0.485   4.0069   2.1980  -0.4823
 4HZ  N4   N   NR15  0  -0.661   2.8053   2.7196  -0.8625
 4HZ  H1   H   HCH1  0   0.285  -2.0357   0.3440  -0.1861
 4HZ  H2   H   HCH2  0   0.296  -6.4604  -0.5660  -0.4672
 4HZ  H3   H   HCH2  0   0.310  -6.4715   1.1548  -0.8374
 4HZ  H4   H   HCR5  0   0.302   0.8158   1.9928  -0.9692
 4HZ  H5   H   HCR6  0   0.279   7.1693   2.6352  -0.0865
 4HZ  H6   H   HCR6  0   0.286   2.1983  -3.6468   1.0519
 4HZ  H7   H   HNH1  0   0.404  -2.2098  -2.5464  -0.0564
 4HZ  H8   H   HNH1  0   0.421  -4.1504   1.2542  -0.5692
 4HZ  H9   H   HCH3  0   0.238  -2.6123  -1.2497  -2.7365
 4HZ  H10  H   HCH3  0   0.241  -2.7946   0.4999  -2.5527
 4HZ  H11  H   HCH3  0   0.257  -1.1955  -0.2287  -2.4468
 4HZ  H12  H   HCR6  0   0.283   4.8124  -0.8860   0.6755
 4HZ  H13  H   HNR5  0   0.421   2.6578   3.6559  -1.2048

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
 4HZ  F1   C4   single    1.339  0.020  1.339
 4HZ  C4   F2   single    1.340  0.020  1.340
 4HZ  C4   F    single    1.338  0.020  1.338
 4HZ  C4   C3   single    1.514  0.020  1.514
 4HZ  C15  N5   aromatic  1.322  0.020  1.322
 4HZ  C15  C14  aromatic  1.399  0.020  1.399
 4HZ  N5   C11  aromatic  1.320  0.020  1.320
 4HZ  CL   C14  single    1.732  0.020  1.732
 4HZ  C3   N    single    1.435  0.020  1.435
 4HZ  C14  C13  aromatic  1.382  0.020  1.382
 4HZ  C11  N4   aromatic  1.364  0.020  1.364
 4HZ  C11  C12  aromatic  1.413  0.020  1.413
 4HZ  N4   C10  aromatic  1.355  0.020  1.355
 4HZ  C13  C12  aromatic  1.392  0.020  1.392
 4HZ  C12  C9   aromatic  1.432  0.020  1.432
 4HZ  C10  C9   aromatic  1.374  0.020  1.374
 4HZ  N    C2   single    1.345  0.020  1.345
 4HZ  O    C2   double    1.218  0.020  1.218
 4HZ  C9   C8   single    1.453  0.020  1.453
 4HZ  C2   C1   single    1.524  0.020  1.524
 4HZ  C8   N3   aromatic  1.334  0.020  1.334
 4HZ  C8   N2   aromatic  1.325  0.020  1.325
 4HZ  N3   C5   aromatic  1.326  0.020  1.326
 4HZ  N2   C7   aromatic  1.339  0.020  1.339
 4HZ  C1   N1   single    1.441  0.020  1.441
 4HZ  C1   C    single    1.531  0.020  1.531
 4HZ  C5   N1   single    1.338  0.020  1.338
 4HZ  C5   C6   aromatic  1.411  0.020  1.411
 4HZ  C7   C6   aromatic  1.360  0.020  1.360
 4HZ  C6   F3   single    1.343  0.020  1.343
 4HZ  C1   H1   single    0.970  0.020  1.090
 4HZ  C3   H2   single    0.970  0.020  1.090
 4HZ  C3   H3   single    0.970  0.020  1.090
 4HZ  C10  H4   single    0.930  0.020  1.080
 4HZ  C15  H5   single    0.930  0.020  1.080
 4HZ  C7   H6   single    0.930  0.020  1.080
 4HZ  N1   H7   single    0.860  0.020  1.020
 4HZ  N    H8   single    0.860  0.020  1.020
 4HZ  C    H9   single    0.970  0.020  1.090
 4HZ  C    H10  single    0.970  0.020  1.090
 4HZ  C    H11  single    0.970  0.020  1.090
 4HZ  C13  H12  single    0.930  0.020  1.080
 4HZ  N4   H13  single    0.860  0.020  1.020

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
 4HZ  H1   C1   C    108.84  3.000
 4HZ  H1   C1   C2   109.17  3.000
 4HZ  C    C1   C2   109.79  3.000
 4HZ  H1   C1   N1   108.83  3.000
 4HZ  C    C1   N1   112.55  3.000
 4HZ  C2   C1   N1   107.61  3.000
 4HZ  C7   N2   C8   116.20  3.000
 4HZ  H3   C3   H2   107.70  3.000
 4HZ  H3   C3   N    109.47  3.000
 4HZ  H2   C3   N    110.31  3.000
 4HZ  H3   C3   C4   108.56  3.000
 4HZ  H2   C3   C4   108.98  3.000
 4HZ  N    C3   C4   111.71  3.000
 4HZ  F    C4   F1   107.41  3.000
 4HZ  F    C4   F2   106.72  3.000
 4HZ  F1   C4   F2   107.28  3.000
 4HZ  F    C4   C3   112.46  3.000
 4HZ  F2   C4   C3   111.83  3.000
 4HZ  F1   C4   C3   110.85  3.000
 4HZ  N1   C5   N3   119.96  3.000
 4HZ  N1   C5   C6   121.51  3.000
 4HZ  N3   C5   C6   118.53  3.000
 4HZ  C7   C6   F3   121.78  3.000
 4HZ  F3   C6   C5   119.39  3.000
 4HZ  C7   C6   C5   118.83  3.000
 4HZ  N3   C8   C9   116.61  3.000
 4HZ  N3   C8   N2   125.88  3.000
 4HZ  C9   C8   N2   117.51  3.000
 4HZ  C12  C9   C10  106.11  3.000
 4HZ  C10  C9   C8   125.68  3.000
 4HZ  C12  C9   C8   128.20  3.000
 4HZ  H4   C10  N4   120.90  3.000
 4HZ  H4   C10  C9   128.89  3.000
 4HZ  N4   C10  C9   110.22  3.000
 4HZ  H5   C15  N5   117.18  3.000
 4HZ  H5   C15  C14  120.08  3.000
 4HZ  N5   C15  C14  122.74  3.000
 4HZ  H6   C7   C6   120.46  3.000
 4HZ  H6   C7   N2   117.71  3.000
 4HZ  C6   C7   N2   121.83  3.000
 4HZ  C8   N3   C5   118.73  3.000
 4HZ  H7   N1   C5   119.68  3.000
 4HZ  H7   N1   C1   116.94  3.000
 4HZ  C5   N1   C1   123.26  3.000
 4HZ  O    C2   N    123.66  3.000
 4HZ  O    C2   C1   121.99  3.000
 4HZ  N    C2   C1   114.30  3.000
 4HZ  H8   N    C2   119.12  3.000
 4HZ  H8   N    C3   117.67  3.000
 4HZ  C2   N    C3   123.16  3.000
 4HZ  H11  C    H10  107.87  3.000
 4HZ  H11  C    H9   108.71  3.000
 4HZ  H10  C    H9   108.48  3.000
 4HZ  H11  C    C1   109.77  3.000
 4HZ  H10  C    C1   111.11  3.000
 4HZ  H9   C    C1   110.81  3.000
 4HZ  C11  C12  C13  116.98  3.000
 4HZ  C13  C12  C9   136.39  3.000
 4HZ  C11  C12  C9   106.63  3.000
 4HZ  H12  C13  C14  121.94  3.000
 4HZ  H12  C13  C12  121.46  3.000
 4HZ  C14  C13  C12  116.60  3.000
 4HZ  CL   C14  C13  120.01  3.000
 4HZ  C13  C14  C15  121.44  3.000
 4HZ  CL   C14  C15  118.55  3.000
 4HZ  C11  N5   C15  115.73  3.000
 4HZ  N4   C11  N5   125.78  3.000
 4HZ  N4   C11  C12  107.70  3.000
 4HZ  N5   C11  C12  126.51  3.000
 4HZ  H13  N4   C11  125.38  3.000
 4HZ  H13  N4   C10  125.28  3.000
 4HZ  C11  N4   C10  109.34  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
 4HZ  CONST_01  C12  C9   C8   N2      0.00   0.0  0
 4HZ  CONST_02  C10  C9   C8   N2    180.00   0.0  0
 4HZ  CONST_03  C5   N3   C8   N2      0.00   0.0  0
 4HZ  CONST_04  C5   C6   C7   N2      0.00   0.0  0
 4HZ  CONST_05  C9   C8   N3   C5    180.00   0.0  0
 4HZ  CONST_06  C8   N3   C5   C6      0.00   0.0  0
 4HZ  CONST_07  C8   N2   C7   C6      0.00   0.0  0
 4HZ  CONST_08  C11  C12  C9   C8    180.00   0.0  0
 4HZ  CONST_09  C13  C12  C9   C8      0.00   0.0  0
 4HZ  CONST_10  N4   C10  C9   C8    180.00   0.0  0
 4HZ  CONST_11  N5   C11  C12  C9    180.00   0.0  0
 4HZ  CONST_12  N4   C11  C12  C9      0.00   0.0  0
 4HZ  CONST_13  C14  C13  C12  C9    180.00   0.0  0
 4HZ  CONST_14  C11  N4   C10  C9      0.00   0.0  0
 4HZ  CONST_15  C7   N2   C8   C9    180.00   0.0  0
 4HZ  CONST_16  N5   C11  N4   C10   180.00   0.0  0
 4HZ  CONST_17  C12  C11  N4   C10     0.00   0.0  0
 4HZ  CONST_18  C11  C12  C9   C10     0.00   0.0  0
 4HZ  CONST_19  C13  C12  C9   C10   180.00   0.0  0
 4HZ  CONST_20  N3   C8   C9   C10     0.00   0.0  0
 4HZ  CONST_21  N4   C11  N5   C15   180.00   0.0  0
 4HZ  CONST_22  C12  C11  N5   C15     0.00   0.0  0
 4HZ  CONST_23  C12  C13  C14  C15     0.00   0.0  0
 4HZ  CONST_24  N3   C8   N2   C7      0.00   0.0  0
 4HZ  CONST_25  N3   C5   C6   C7      0.00   0.0  0
 4HZ  CONST_26  C12  C9   C8   N3    180.00   0.0  0
 4HZ  CONST_27  N4   C10  C9   C12     0.00   0.0  0
 4HZ  CONST_28  N5   C15  C14  C13     0.00   0.0  0
 4HZ  CONST_29  N5   C11  C12  C13     0.00   0.0  0
 4HZ  CONST_30  N4   C11  C12  C13   180.00   0.0  0
 4HZ  CONST_31  C11  N5   C15  C14     0.00   0.0  0
 4HZ  CONST_32  C11  C12  C13  C14     0.00   0.0  0
 4HZ  CONST_33  F3   C6   C7   N2    180.00   0.0  0
 4HZ  CONST_34  N1   C5   N3   C8    180.00   0.0  0
 4HZ  CONST_35  N3   C5   C6   F3    180.00   0.0  0
 4HZ  CONST_36  N1   C5   C6   C7    180.00   0.0  0
 4HZ  CONST_37  CL   C14  C13  C12   180.00   0.0  0
 4HZ  CONST_38  N5   C15  C14  CL    180.00   0.0  0
 4HZ  CONST_39  H6   C7   C6   C5    180.00   0.0  0
 4HZ  CONST_40  H4   C10  C9   C8      0.00   0.0  0
 4HZ  CONST_41  H12  C13  C12  C9      0.00   0.0  0
 4HZ  CONST_42  H13  N4   C10  C9    180.00   0.0  0
 4HZ  CONST_43  H5   C15  C14  C13   180.00   0.0  0
 4HZ  CONST_44  N3   C5   N1   C1      0.00   0.0  0
 4HZ  CONST_45  C6   C5   N1   C1    180.00   0.0  0
 4HZ  CONST_46  H7   N1   C5   C6      0.00   0.0  0
 4HZ  CONST_47  C3   N    C2   C1    180.00   0.0  0
 4HZ  CONST_48  O    C2   N    C3      0.00   0.0  0
 4HZ  CONST_49  H8   N    C2   C1      0.00   0.0  0
 4HZ  Var_01    C2   N    C3   C4     96.32  30.0  3
 4HZ  Var_02    F1   C4   C3   N    -179.62  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
 4HZ  chir_01  C1  C2  N1  C  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
 4HZ  plan-1  N2   0.020
 4HZ  plan-1  C5   0.020
 4HZ  plan-1  C6   0.020
 4HZ  plan-1  C8   0.020
 4HZ  plan-1  C9   0.020
 4HZ  plan-1  F3   0.020
 4HZ  plan-1  C7   0.020
 4HZ  plan-1  N3   0.020
 4HZ  plan-1  N1   0.020
 4HZ  plan-1  H6   0.020
 4HZ  plan-2  C8   0.020
 4HZ  plan-2  C9   0.020
 4HZ  plan-2  C10  0.020
 4HZ  plan-2  C15  0.020
 4HZ  plan-2  C12  0.020
 4HZ  plan-2  C13  0.020
 4HZ  plan-2  C14  0.020
 4HZ  plan-2  CL   0.020
 4HZ  plan-2  N5   0.020
 4HZ  plan-2  C11  0.020
 4HZ  plan-2  N4   0.020
 4HZ  plan-2  H4   0.020
 4HZ  plan-2  H5   0.020
 4HZ  plan-2  H12  0.020
 4HZ  plan-2  H13  0.020
 4HZ  plan-3  C1   0.020
 4HZ  plan-3  C3   0.020
 4HZ  plan-3  C2   0.020
 4HZ  plan-3  N    0.020
 4HZ  plan-3  O    0.020
 4HZ  plan-3  H8   0.020
 4HZ  plan-4  C1   0.020
 4HZ  plan-4  C5   0.020
 4HZ  plan-4  N1   0.020
 4HZ  plan-4  H7   0.020

