# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 00:42:58 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: 1-[(2-chloroquinolin-3-yl)methyl]-6-fluoro-5-methyl-3-(2-oxo-1,2-dihydropyridin-3-yl)-1H-indole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc2c(cc1F)n(Cc3cc4ccccc4nc3Cl)c(C(O)=O)c2C5=CC=CNC5=O
#
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
 2F3  2F3  '1-[(2-chloroquinolin-3-yl)methyl]-6-fluoro-5-methyl-3-(2-oxo-1,2-dihydropyridin-3-yl)-1H-indole-2-carboxylic acid'  ligand  50  33  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2F3
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
 2F3  C1   C   CR66  0   0.202  -4.4392  -1.4204   0.1109
 2F3  C2   C   CR66  0   0.111  -3.2535  -1.3259  -0.6521
 2F3  C3   C   CR16  0  -0.312  -3.1919  -1.9484  -1.9170
 2F3  C7   C   CR6   0   0.073  -2.2732  -0.0310   1.1359
 2F3  C8   C   CR16  0  -0.222  -2.1716  -0.6068  -0.0991
 2F3  C9   C   CR6   0   0.090  -3.5230  -0.1915   1.7881
 2F3  C10  C   CR6   0  -0.245   3.0506  -1.0911  -0.2826
 2F3  C11  C   CR16  0  -0.398   2.4622   1.9336  -1.2542
 2F3  C12  C   CR6   0  -0.105   2.0149   3.2073  -1.5344
 2F3  C13  C   CR56  0   0.085   1.7409   1.1091  -0.3812
 2F3  C14  C   CR56  0   0.359   0.5758   1.5960   0.2358
 2F3  C15  C   CR5   0   0.163   0.9121  -0.4808   0.9691
 2F3  C16  C   CR5   0   0.079   1.9348  -0.2232   0.0881
 2F3  C19  C   C     0   0.497   0.6908  -1.7727   1.6325
 2F3  C20  C   CH2   0  -0.374  -1.1578   0.7468   1.7835
 2F3  C21  C   CR6   0   0.517   3.8913  -1.6300   0.7701
 2F3  C22  C   CR16  0   0.048   5.2204  -2.6617  -0.9846
 2F3  C24  C   CR16  0  -0.172   3.3454  -1.3445  -1.5921
 2F3  C4   C   CR16  0  -0.250  -4.2735  -2.6381  -2.3955
 2F3  C5   C   CR16  0  -0.258  -5.4552  -2.7310  -1.6317
 2F3  C6   C   CR16  0  -0.287  -5.5419  -2.1347  -0.4017
 2F3  N1   N   N     0  -0.414  -4.5392  -0.8340   1.3288
 2F3  N2   N   NR5   0  -0.602   0.0943   0.6332   1.0755
 2F3  C17  C   CR6   0   0.530   0.8240   3.6282  -0.9134
 2F3  C18  C   CR16  0  -0.477   0.0867   2.8764  -0.0362
 2F3  O1   O   OH1   0  -0.594  -0.0323  -1.6881   2.7400
 2F3  N3   N   NR16  0  -0.655   4.9377  -2.4024   0.3119
 2F3  C23  C   CR16  0  -0.385   4.4468  -2.1450  -1.9705
 2F3  O2   O   O     0  -0.491   3.7403  -1.4384   1.9721
 2F3  O3   O   O     0  -0.426   1.1321  -2.8090   1.2010
 2F3  F1   F   F     0  -0.313   0.3870   4.8657  -1.2053
 2F3  H1   H   HCR6  0   0.267  -2.2815  -1.8773  -2.4991
 2F3  H2   H   HCR6  0   0.280  -1.2598  -0.5249  -0.6796
 2F3  H4   H   HCR6  0   0.257   3.3770   1.5779  -1.7129
 2F3  H5   H   HCH2  0   0.307  -1.4229   1.8040   1.8197
 2F3  H6   H   HCH2  0   0.303  -1.0260   0.4419   2.8189
 2F3  H7   H   HCR6  0   0.312   6.0821  -3.2871  -1.1647
 2F3  H8   H   HCR6  0   0.275   2.7083  -0.9325  -2.3658
 2F3  H9   H   HCR6  0   0.268  -4.2248  -3.1181  -3.3637
 2F3  H10  H   HCR6  0   0.269  -6.3001  -3.2810  -2.0244
 2F3  H11  H   HCR6  0   0.269  -6.4444  -2.1982   0.1921
 2F3  H12  H   HCR6  0   0.291  -0.8171   3.2762   0.4042
 2F3  H13  H   HOH1  0   0.493  -0.1770  -2.5724   3.1103
 2F3  H14  H   HNR6  0   0.423   5.5454  -2.7916   1.0202
 2F3  H15  H   HCR6  0   0.277   4.6674  -2.3477  -3.0068
 2F3  H16  H   HCH3  0   0.249   2.1605   4.3746  -3.3441
 2F3  H17  H   HCH3  0   0.248   3.0156   5.0673  -1.9752
 2F3  H18  H   HCH3  0   0.249   3.6747   3.6611  -2.8013
 2F3  CL1  CL  CL    0  -0.095  -3.7264   0.5515   3.3483
 2F3  C25  C   CH3   0  -0.715   2.7520   4.1272  -2.4613

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
 2F3  C4   C5   aromatic  1.410  0.020  1.410
 2F3  C4   C3   aromatic  1.369  0.020  1.369
 2F3  C5   C6   aromatic  1.370  0.020  1.370
 2F3  C3   C2   aromatic  1.411  0.020  1.411
 2F3  C6   C1   aromatic  1.410  0.020  1.410
 2F3  C2   C1   aromatic  1.413  0.020  1.413
 2F3  C2   C8   aromatic  1.412  0.020  1.412
 2F3  C1   N1   aromatic  1.355  0.020  1.355
 2F3  C8   C7   aromatic  1.366  0.020  1.366
 2F3  O3   C19  double    1.206  0.020  1.206
 2F3  N1   C9   aromatic  1.287  0.020  1.287
 2F3  C7   C9   aromatic  1.419  0.020  1.419
 2F3  C7   C20  single    1.506  0.020  1.506
 2F3  O1   C19  single    1.325  0.020  1.325
 2F3  C19  C15  single    1.469  0.020  1.469
 2F3  C20  N2   single    1.443  0.020  1.443
 2F3  O2   C21  double    1.227  0.020  1.227
 2F3  C15  N2   aromatic  1.386  0.020  1.386
 2F3  C15  C16  aromatic  1.374  0.020  1.374
 2F3  N2   C14  aromatic  1.365  0.020  1.365
 2F3  C21  N3   single    1.379  0.020  1.379
 2F3  C21  C10  single    1.451  0.020  1.451
 2F3  N3   C22  single    1.352  0.020  1.352
 2F3  C16  C10  single    1.461  0.020  1.461
 2F3  C16  C13  aromatic  1.426  0.020  1.426
 2F3  C10  C24  double    1.366  0.020  1.366
 2F3  C14  C18  aromatic  1.397  0.020  1.397
 2F3  C14  C13  aromatic  1.405  0.020  1.405
 2F3  C22  C23  double    1.356  0.020  1.356
 2F3  C18  C17  aromatic  1.371  0.020  1.371
 2F3  C13  C11  aromatic  1.401  0.020  1.401
 2F3  C24  C23  single    1.413  0.020  1.413
 2F3  C17  F1   single    1.344  0.020  1.344
 2F3  C17  C12  aromatic  1.407  0.020  1.407
 2F3  C11  C12  aromatic  1.379  0.020  1.379
 2F3  C12  C25  single    1.500  0.020  1.500
 2F3  C3   H1   single    0.930  0.020  1.080
 2F3  C8   H2   single    0.930  0.020  1.080
 2F3  C11  H4   single    0.930  0.020  1.080
 2F3  C20  H5   single    0.970  0.020  1.090
 2F3  C20  H6   single    0.970  0.020  1.090
 2F3  C22  H7   single    0.930  0.020  1.080
 2F3  C24  H8   single    0.930  0.020  1.080
 2F3  C4   H9   single    0.930  0.020  1.080
 2F3  C5   H10  single    0.930  0.020  1.080
 2F3  C6   H11  single    0.930  0.020  1.080
 2F3  C18  H12  single    0.930  0.020  1.080
 2F3  O1   H13  single    0.850  0.020  0.980
 2F3  N3   H14  single    0.860  0.020  1.020
 2F3  C23  H15  single    0.930  0.020  1.080
 2F3  C25  H16  single    0.970  0.020  1.090
 2F3  C25  H17  single    0.970  0.020  1.090
 2F3  C25  H18  single    0.970  0.020  1.090
 2F3  C9   CL1  single    1.740  0.020  1.740

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
 2F3  N1   C1   C6   119.21  3.000
 2F3  N1   C1   C2   121.20  3.000
 2F3  C6   C1   C2   119.59  3.000
 2F3  C8   C2   C3   122.84  3.000
 2F3  C8   C2   C1   117.75  3.000
 2F3  C3   C2   C1   119.41  3.000
 2F3  H1   C3   C4   120.62  3.000
 2F3  H1   C3   C2   119.31  3.000
 2F3  C4   C3   C2   120.07  3.000
 2F3  C20  C7   C9   120.87  3.000
 2F3  C20  C7   C8   123.45  3.000
 2F3  C9   C7   C8   115.68  3.000
 2F3  H2   C8   C7   120.98  3.000
 2F3  H2   C8   C2   118.25  3.000
 2F3  C7   C8   C2   120.77  3.000
 2F3  CL1  C9   N1   116.16  3.000
 2F3  CL1  C9   C7   117.83  3.000
 2F3  N1   C9   C7   126.01  3.000
 2F3  C24  C10  C21  120.10  3.000
 2F3  C24  C10  C16  121.21  3.000
 2F3  C21  C10  C16  118.62  3.000
 2F3  H4   C11  C13  120.36  3.000
 2F3  H4   C11  C12  119.42  3.000
 2F3  C13  C11  C12  120.22  3.000
 2F3  C25  C12  C17  120.34  3.000
 2F3  C25  C12  C11  122.20  3.000
 2F3  C17  C12  C11  117.46  3.000
 2F3  C16  C13  C14  106.98  3.000
 2F3  C14  C13  C11  119.77  3.000
 2F3  C16  C13  C11  133.24  3.000
 2F3  C18  C14  N2   129.98  3.000
 2F3  C18  C14  C13  121.48  3.000
 2F3  N2   C14  C13  108.55  3.000
 2F3  N2   C15  C19  125.68  3.000
 2F3  N2   C15  C16  109.73  3.000
 2F3  C19  C15  C16  124.51  3.000
 2F3  C15  C16  C13  106.56  3.000
 2F3  C13  C16  C10  125.12  3.000
 2F3  C15  C16  C10  128.28  3.000
 2F3  O3   C19  O1   123.60  3.000
 2F3  O1   C19  C15  113.79  3.000
 2F3  O3   C19  C15  122.61  3.000
 2F3  H6   C20  H5   105.65  3.000
 2F3  H6   C20  N2   109.88  3.000
 2F3  H5   C20  N2   107.67  3.000
 2F3  H6   C20  C7   110.75  3.000
 2F3  H5   C20  C7   109.56  3.000
 2F3  N2   C20  C7   113.02  3.000
 2F3  O2   C21  N3   120.44  3.000
 2F3  N3   C21  C10  114.00  3.000
 2F3  O2   C21  C10  125.57  3.000
 2F3  H7   C22  C23  123.70  3.000
 2F3  H7   C22  N3   115.97  3.000
 2F3  C23  C22  N3   120.33  3.000
 2F3  H8   C24  C23  118.84  3.000
 2F3  H8   C24  C10  119.14  3.000
 2F3  C23  C24  C10  122.01  3.000
 2F3  H9   C4   C5   119.55  3.000
 2F3  H9   C4   C3   120.05  3.000
 2F3  C5   C4   C3   120.39  3.000
 2F3  H10  C5   C6   119.85  3.000
 2F3  H10  C5   C4   119.43  3.000
 2F3  C6   C5   C4   120.71  3.000
 2F3  H11  C6   C5   121.33  3.000
 2F3  H11  C6   C1   118.84  3.000
 2F3  C5   C6   C1   119.83  3.000
 2F3  C9   N1   C1   118.58  3.000
 2F3  C20  N2   C15  127.80  3.000
 2F3  C15  N2   C14  108.15  3.000
 2F3  C20  N2   C14  123.53  3.000
 2F3  F1   C17  C18  117.97  3.000
 2F3  F1   C17  C12  117.03  3.000
 2F3  C18  C17  C12  125.00  3.000
 2F3  H12  C18  C17  120.47  3.000
 2F3  H12  C18  C14  123.49  3.000
 2F3  C17  C18  C14  116.04  3.000
 2F3  H13  O1   C19  110.02  3.000
 2F3  H14  N3   C22  118.18  3.000
 2F3  H14  N3   C21  116.03  3.000
 2F3  C22  N3   C21  125.79  3.000
 2F3  H15  C23  C24  121.54  3.000
 2F3  H15  C23  C22  120.69  3.000
 2F3  C24  C23  C22  117.77  3.000
 2F3  H18  C25  H17  107.67  3.000
 2F3  H18  C25  H16  107.69  3.000
 2F3  H17  C25  H16  107.24  3.000
 2F3  H18  C25  C12  110.31  3.000
 2F3  H17  C25  C12  111.84  3.000
 2F3  H16  C25  C12  111.89  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
 2F3  CONST_01  C4   C5   C6   C1     0.00   0.0  0
 2F3  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 2F3  CONST_03  C7   C8   C2   C1     0.00   0.0  0
 2F3  CONST_04  C7   C9   N1   C1     0.00   0.0  0
 2F3  CONST_05  C5   C4   C3   C2     0.00   0.0  0
 2F3  CONST_06  C5   C6   C1   C2     0.00   0.0  0
 2F3  CONST_07  C9   N1   C1   C2     0.00   0.0  0
 2F3  CONST_08  C9   C7   C8   C2     0.00   0.0  0
 2F3  CONST_09  C6   C5   C4   C3     0.00   0.0  0
 2F3  CONST_10  C6   C1   C2   C3     0.00   0.0  0
 2F3  CONST_11  N1   C1   C2   C3   180.00   0.0  0
 2F3  CONST_12  C7   C8   C2   C3   180.00   0.0  0
 2F3  CONST_13  C4   C3   C2   C8   180.00   0.0  0
 2F3  CONST_14  C6   C1   C2   C8   180.00   0.0  0
 2F3  CONST_15  N1   C1   C2   C8     0.00   0.0  0
 2F3  CONST_16  N1   C9   C7   C8     0.00   0.0  0
 2F3  CONST_17  C6   C1   N1   C9   180.00   0.0  0
 2F3  CONST_18  C15  C16  C13  C11  180.00   0.0  0
 2F3  CONST_19  N2   C14  C13  C11  180.00   0.0  0
 2F3  CONST_20  C18  C14  C13  C11    0.00   0.0  0
 2F3  CONST_21  C18  C17  C12  C11    0.00   0.0  0
 2F3  CONST_22  C14  C18  C17  C12    0.00   0.0  0
 2F3  CONST_23  C16  C13  C11  C12  180.00   0.0  0
 2F3  CONST_24  C14  C13  C11  C12    0.00   0.0  0
 2F3  CONST_25  N2   C15  C16  C13    0.00   0.0  0
 2F3  CONST_26  C15  N2   C14  C13    0.00   0.0  0
 2F3  CONST_27  C17  C18  C14  C13    0.00   0.0  0
 2F3  CONST_28  C17  C12  C11  C13    0.00   0.0  0
 2F3  CONST_29  C16  C15  N2   C14    0.00   0.0  0
 2F3  CONST_30  C15  C16  C13  C14    0.00   0.0  0
 2F3  CONST_31  C18  C14  N2   C15  180.00   0.0  0
 2F3  CONST_32  N2   C14  C13  C16    0.00   0.0  0
 2F3  CONST_33  C18  C14  C13  C16  180.00   0.0  0
 2F3  CONST_34  N1   C1   C6   C5   180.00   0.0  0
 2F3  CONST_35  C17  C18  C14  N2   180.00   0.0  0
 2F3  CONST_36  N2   C15  C16  C10  180.00   0.0  0
 2F3  CONST_37  C14  C13  C16  C10  180.00   0.0  0
 2F3  CONST_38  C11  C13  C16  C10    0.00   0.0  0
 2F3  CONST_39  C22  N3   C21  C10    0.00   0.0  0
 2F3  CONST_40  CL1  C9   N1   C1   180.00   0.0  0
 2F3  CONST_41  C20  C7   C8   C2   180.00   0.0  0
 2F3  CONST_42  CL1  C9   C7   C8   180.00   0.0  0
 2F3  CONST_43  C19  C15  C16  C10    0.00   0.0  0
 2F3  CONST_44  F1   C17  C12  C11  180.00   0.0  0
 2F3  CONST_45  C19  C15  C16  C13  180.00   0.0  0
 2F3  CONST_46  C20  N2   C14  C13  180.00   0.0  0
 2F3  CONST_47  C25  C12  C11  C13  180.00   0.0  0
 2F3  CONST_48  C19  C15  N2   C14  180.00   0.0  0
 2F3  CONST_49  F1   C17  C18  C14  180.00   0.0  0
 2F3  CONST_50  C20  N2   C15  C16  180.00   0.0  0
 2F3  CONST_51  N1   C9   C7   C20  180.00   0.0  0
 2F3  CONST_52  C18  C14  N2   C20    0.00   0.0  0
 2F3  CONST_53  C25  C12  C17  C18  180.00   0.0  0
 2F3  CONST_54  O2   C21  N3   C22  180.00   0.0  0
 2F3  CONST_55  H10  C5   C6   C1   180.00   0.0  0
 2F3  CONST_56  H1   C3   C2   C1   180.00   0.0  0
 2F3  CONST_57  H2   C8   C2   C1   180.00   0.0  0
 2F3  CONST_58  H9   C4   C3   C2   180.00   0.0  0
 2F3  CONST_59  H11  C6   C1   C2   180.00   0.0  0
 2F3  CONST_60  H12  C18  C17  C12  180.00   0.0  0
 2F3  CONST_61  H4   C11  C13  C14  180.00   0.0  0
 2F3  CONST_62  H14  N3   C21  C10  180.00   0.0  0
 2F3  CONST_63  H13  O1   C19  C15  180.00   0.0  0
 2F3  Var_01    C21  C10  C16  C13  122.81  30.0  2
 2F3  Var_02    C15  N2   C20  C7   -69.83  30.0  2
 2F3  Var_03    N2   C20  C7   C8    -9.82  30.0  2
 2F3  Var_04    O3   C19  C15  C16  -21.50  30.0  2
 2F3  Var_05    H16  C25  C12  C11  116.56  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
 2F3  plan-1  C10  0.020
 2F3  plan-1  C16  0.020
 2F3  plan-1  C21  0.020
 2F3  plan-1  C22  0.020
 2F3  plan-1  C24  0.020
 2F3  plan-1  N3   0.020
 2F3  plan-1  C23  0.020
 2F3  plan-1  O2   0.020
 2F3  plan-1  H7   0.020
 2F3  plan-1  H8   0.020
 2F3  plan-1  H14  0.020
 2F3  plan-1  H15  0.020
 2F3  plan-2  C10  0.020
 2F3  plan-2  C11  0.020
 2F3  plan-2  C12  0.020
 2F3  plan-2  C13  0.020
 2F3  plan-2  C14  0.020
 2F3  plan-2  C15  0.020
 2F3  plan-2  C16  0.020
 2F3  plan-2  C19  0.020
 2F3  plan-2  C20  0.020
 2F3  plan-2  N2   0.020
 2F3  plan-2  C17  0.020
 2F3  plan-2  C18  0.020
 2F3  plan-2  F1   0.020
 2F3  plan-2  H4   0.020
 2F3  plan-2  H12  0.020
 2F3  plan-2  C25  0.020
 2F3  plan-3  C1   0.020
 2F3  plan-3  C2   0.020
 2F3  plan-3  C3   0.020
 2F3  plan-3  C7   0.020
 2F3  plan-3  C8   0.020
 2F3  plan-3  C9   0.020
 2F3  plan-3  C20  0.020
 2F3  plan-3  C4   0.020
 2F3  plan-3  C5   0.020
 2F3  plan-3  C6   0.020
 2F3  plan-3  N1   0.020
 2F3  plan-3  H1   0.020
 2F3  plan-3  H2   0.020
 2F3  plan-3  H9   0.020
 2F3  plan-3  H10  0.020
 2F3  plan-3  H11  0.020
 2F3  plan-3  CL1  0.020
 2F3  plan-4  C15  0.020
 2F3  plan-4  C19  0.020
 2F3  plan-4  O1   0.020
 2F3  plan-4  O3   0.020
 2F3  plan-4  H13  0.020

