# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 18:22:44 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 1-[(2-aminopyridin-4-yl)methyl]-3-(2-oxo-1,2-dihydropyridin-3-yl)-5-(trifluoromethyl)-1H-indole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cc(Cn2c3ccc(cc3c(C4=CC=CNC4=O)c2C(O)=O)C(F)(F)F)ccn1
#
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
 053  053  '1-[(2-aminopyridin-4-yl)methyl]-3-(2-oxo-1,2-dihydropyridin-3-yl)-5-(trifluoromethyl)-1H-indole-2-carboxylic acid'  ligand  46  31  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_053
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
 053  C1    C  CR6   0  -0.247  -1.1597   2.1391  -0.5722
 053  C2    C  CR16  0  -0.177  -1.8679   2.0677  -1.7392
 053  C3    C  CR16  0  -0.385  -2.5425   3.1867  -2.2757
 053  C4    C  CR16  0   0.049  -2.4695   4.3560  -1.5933
 053  N5    N  NR16  0  -0.655  -1.7743   4.4286  -0.4366
 053  C6    C  CR6   0   0.518  -1.0914   3.3903   0.1598
 053  C7    C  CR6   0   0.178   3.2882  -0.9571   0.3333
 053  C8    C  CR16  0  -0.439   4.6221  -0.8448   0.6615
 053  C9    C  CR6   0   0.463   5.5848  -0.8973  -0.3613
 053  N10   N  N     0  -0.462   5.2478  -1.0397  -1.6419
 053  C11   C  CR16  0  -0.054   3.9571  -1.1371  -1.9398
 053  C12   C  CR16  0  -0.389   2.9366  -1.1065  -1.0099
 053  C13   C  CR6   0  -0.209  -2.7007  -2.0939   0.3509
 053  C14   C  CR16  0  -0.295  -1.7239  -2.9162   0.9429
 053  C15   C  CR16  0  -0.294  -0.4542  -2.4486   1.1969
 053  C16   C  CR16  0  -0.406  -2.4144  -0.7879   0.0058
 053  C17   C  CR56  0   0.092  -1.1297  -0.3000   0.2415
 053  C18   C  CR56  0   0.371  -0.1643  -1.1280   0.8490
 053  N19   N  NR5   0  -0.595   0.9825  -0.4047   1.0017
 053  C20   C  CR5   0   0.208   0.7716   0.8540   0.4764
 053  C21   C  CR5   0   0.065  -0.5092   0.9632  -0.0007
 053  O23   O  O     0  -0.422   1.8513   2.6946  -0.5158
 053  C24   C  CH2   0  -0.371   2.2517  -0.9591   1.4262
 053  C25   C  CT    0   1.050  -4.0865  -2.6086   0.1338
 053  O26   O  OH1   0  -0.587   2.6302   1.9024   1.4245
 053  F27   F  F     0  -0.306  -4.1459  -3.9451   0.1344
 053  F28   F  F     0  -0.318  -4.9344  -2.1872   1.0876
 053  F29   F  F     0  -0.313  -4.6019  -2.1959  -1.0332
 053  O30   O  O     0  -0.490  -0.5014   3.5632   1.2217
 053  N31   N  NH2   0  -0.835   6.9104  -0.7515  -0.0804
 053  H2    H  HCR6  0   0.278  -1.9043   1.1289  -2.2794
 053  H3    H  HCR6  0   0.278  -3.0949   3.1217  -3.2001
 053  H4    H  HCR6  0   0.313  -2.9452   5.2698  -1.9171
 053  HN5   H  HNR6  0   0.425  -1.7415   5.3167   0.0462
 053  H8    H  HCR6  0   0.265   4.9312  -0.7086   1.6911
 053  H11   H  HCR6  0   0.258   3.7217  -1.2500  -2.9927
 053  H12   H  HCR6  0   0.258   1.9079  -1.2036  -1.3296
 053  H14   H  HCR6  0   0.273  -1.9582  -3.9364   1.2126
 053  H15   H  HCR6  0   0.281   0.2764  -3.0980   1.6597
 053  H16   H  HCR6  0   0.270  -3.1624  -0.1460  -0.4429
 053  H24   H  HCH2  0   0.304   2.0707  -1.9887   1.7339
 053  H24A  H  HCH2  0   0.294   2.6169  -0.4359   2.3081
 053  HO26  H  HOH1  0   0.493   3.3118   2.5823   1.3082
 053  HN31  H  HNH2  0   0.391   7.2165  -0.9483   0.8576
 053  HN3A  H  HNH2  0   0.383   7.5518  -1.0526  -0.7958
 053  C22   C  C     0   0.493   1.7973   1.9096   0.3962

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
 053  C1   C2    double    1.367  0.020  1.367
 053  C6   C1    single    1.451  0.020  1.451
 053  C21  C1    single    1.460  0.020  1.460
 053  C2   C3    single    1.413  0.020  1.413
 053  C2   H2    single    0.930  0.020  1.080
 053  C3   C4    double    1.356  0.020  1.356
 053  C3   H3    single    0.930  0.020  1.080
 053  N5   C4    single    1.352  0.020  1.352
 053  C4   H4    single    0.930  0.020  1.080
 053  C6   N5    single    1.378  0.020  1.378
 053  N5   HN5   single    0.860  0.020  1.020
 053  O30  C6    double    1.227  0.020  1.227
 053  C12  C7    aromatic  1.396  0.020  1.396
 053  C7   C24   single    1.506  0.020  1.506
 053  C7   C8    aromatic  1.378  0.020  1.378
 053  C9   C8    aromatic  1.406  0.020  1.406
 053  C8   H8    single    0.930  0.020  1.080
 053  N10  C9    aromatic  1.332  0.020  1.332
 053  C9   N31   single    1.363  0.020  1.363
 053  C11  N10   aromatic  1.328  0.020  1.328
 053  C11  C12   aromatic  1.381  0.020  1.381
 053  C11  H11   single    0.930  0.020  1.080
 053  C12  H12   single    0.930  0.020  1.080
 053  C14  C13   aromatic  1.407  0.020  1.407
 053  C16  C13   aromatic  1.381  0.020  1.381
 053  C13  C25   single    1.494  0.020  1.494
 053  C15  C14   aromatic  1.377  0.020  1.377
 053  C14  H14   single    0.930  0.020  1.080
 053  C18  C15   aromatic  1.396  0.020  1.396
 053  C15  H15   single    0.930  0.020  1.080
 053  C17  C16   aromatic  1.394  0.020  1.394
 053  C16  H16   single    0.930  0.020  1.080
 053  C21  C17   aromatic  1.428  0.020  1.428
 053  C18  C17   aromatic  1.409  0.020  1.409
 053  N19  C18   aromatic  1.364  0.020  1.364
 053  C24  N19   single    1.449  0.020  1.449
 053  C20  N19   aromatic  1.380  0.020  1.380
 053  C22  C20   single    1.474  0.020  1.474
 053  C20  C21   aromatic  1.371  0.020  1.371
 053  O23  C22   double    1.205  0.020  1.205
 053  C22  O26   single    1.323  0.020  1.323
 053  C24  H24   single    0.970  0.020  1.090
 053  C24  H24A  single    0.970  0.020  1.090
 053  C25  F27   single    1.338  0.020  1.338
 053  C25  F28   single    1.344  0.020  1.344
 053  C25  F29   single    1.341  0.020  1.341
 053  O26  HO26  single    0.850  0.020  0.980
 053  N31  HN31  single    0.890  0.020  1.040
 053  N31  HN3A  single    0.890  0.020  1.040

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
 053  C21   C1   C6    118.42  3.000
 053  C21   C1   C2    121.52  3.000
 053  C6    C1   C2    120.00  3.000
 053  H2    C2   C3    118.74  3.000
 053  H2    C2   C1    119.23  3.000
 053  C3    C2   C1    122.03  3.000
 053  H3    C3   C4    120.71  3.000
 053  H3    C3   C2    121.49  3.000
 053  C4    C3   C2    117.80  3.000
 053  H4    C4   N5    115.96  3.000
 053  H4    C4   C3    123.72  3.000
 053  N5    C4   C3    120.31  3.000
 053  HN5   N5   C6    116.03  3.000
 053  HN5   N5   C4    118.19  3.000
 053  C6    N5   C4    125.78  3.000
 053  O30   C6   N5    120.43  3.000
 053  O30   C6   C1    125.49  3.000
 053  N5    C6   C1    114.08  3.000
 053  C24   C7   C12   121.64  3.000
 053  C24   C7   C8    119.56  3.000
 053  C12   C7   C8    118.78  3.000
 053  H8    C8   C9    120.05  3.000
 053  H8    C8   C7    120.83  3.000
 053  C9    C8   C7    119.12  3.000
 053  N31   C9   N10   117.11  3.000
 053  N31   C9   C8    120.81  3.000
 053  N10   C9   C8    122.03  3.000
 053  C11   N10  C9    117.99  3.000
 053  H11   C11  C12   119.71  3.000
 053  H11   C11  N10   115.86  3.000
 053  C12   C11  N10   124.43  3.000
 053  H12   C12  C11   120.12  3.000
 053  H12   C12  C7    122.23  3.000
 053  C11   C12  C7    117.65  3.000
 053  C25   C13  C16   118.80  3.000
 053  C25   C13  C14   120.24  3.000
 053  C16   C13  C14   120.92  3.000
 053  H14   C14  C15   118.32  3.000
 053  H14   C14  C13   120.40  3.000
 053  C15   C14  C13   121.28  3.000
 053  H15   C15  C18   122.30  3.000
 053  H15   C15  C14   119.87  3.000
 053  C18   C15  C14   117.83  3.000
 053  H16   C16  C17   119.94  3.000
 053  H16   C16  C13   121.39  3.000
 053  C17   C16  C13   118.67  3.000
 053  C21   C17  C18   107.17  3.000
 053  C18   C17  C16   119.90  3.000
 053  C21   C17  C16   132.93  3.000
 053  N19   C18  C17   108.21  3.000
 053  N19   C18  C15   130.39  3.000
 053  C17   C18  C15   121.39  3.000
 053  C24   N19  C20   126.47  3.000
 053  C20   N19  C18   108.20  3.000
 053  C24   N19  C18   124.50  3.000
 053  C22   C20  C21   125.03  3.000
 053  C21   C20  N19   110.35  3.000
 053  C22   C20  N19   124.58  3.000
 053  C20   C21  C17   106.04  3.000
 053  C20   C21  C1    128.06  3.000
 053  C17   C21  C1    125.81  3.000
 053  H24A  C24  H24   106.32  3.000
 053  H24A  C24  N19   110.33  3.000
 053  H24   C24  N19   107.38  3.000
 053  H24A  C24  C7    110.88  3.000
 053  H24   C24  C7    108.69  3.000
 053  N19   C24  C7    112.94  3.000
 053  F29   C25  F28   106.18  3.000
 053  F29   C25  F27   106.90  3.000
 053  F28   C25  F27   106.55  3.000
 053  F29   C25  C13   112.15  3.000
 053  F28   C25  C13   111.97  3.000
 053  F27   C25  C13   112.66  3.000
 053  HO26  O26  C22   110.21  3.000
 053  HN3A  N31  HN31  114.21  3.000
 053  HN3A  N31  C9    116.18  3.000
 053  HN31  N31  C9    117.85  3.000
 053  O26   C22  O23   124.31  3.000
 053  O26   C22  C20   113.07  3.000
 053  O23   C22  C20   122.62  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
 053  CONST_01  N10   C11  C12  C7     0.00   0.0  0
 053  CONST_02  N10   C9   C8   C7     0.00   0.0  0
 053  CONST_03  C11   C12  C7   C8     0.00   0.0  0
 053  CONST_04  C11   N10  C9   C8     0.00   0.0  0
 053  CONST_05  C12   C7   C8   C9     0.00   0.0  0
 053  CONST_06  C12   C11  N10  C9     0.00   0.0  0
 053  CONST_07  C18   C15  C14  C13    0.00   0.0  0
 053  CONST_08  C21   C17  C16  C13  180.00   0.0  0
 053  CONST_09  C18   C17  C16  C13    0.00   0.0  0
 053  CONST_10  C17   C16  C13  C14    0.00   0.0  0
 053  CONST_11  C17   C18  C15  C14    0.00   0.0  0
 053  CONST_12  N19   C18  C15  C14  180.00   0.0  0
 053  CONST_13  C16   C13  C14  C15    0.00   0.0  0
 053  CONST_14  C16   C17  C18  C15    0.00   0.0  0
 053  CONST_15  C21   C17  C18  C15  180.00   0.0  0
 053  CONST_16  C20   N19  C18  C15  180.00   0.0  0
 053  CONST_17  C20   C21  C17  C16  180.00   0.0  0
 053  CONST_18  N19   C18  C17  C16  180.00   0.0  0
 053  CONST_19  N19   C20  C21  C17    0.00   0.0  0
 053  CONST_20  C20   N19  C18  C17    0.00   0.0  0
 053  CONST_21  C20   C21  C17  C18    0.00   0.0  0
 053  CONST_22  C21   C20  N19  C18    0.00   0.0  0
 053  CONST_23  C21   C17  C18  N19    0.00   0.0  0
 053  CONST_24  C16   C17  C21  C1     0.00   0.0  0
 053  CONST_25  C18   C17  C21  C1   180.00   0.0  0
 053  CONST_26  N19   C20  C21  C1   180.00   0.0  0
 053  CONST_27  C4    N5   C6   C1     0.00   0.0  0
 053  CONST_28  C22   C20  C21  C1     0.00   0.0  0
 053  CONST_29  N31   C9   C8   C7   180.00   0.0  0
 053  CONST_30  C24   C7   C8   C9   180.00   0.0  0
 053  CONST_31  N31   C9   N10  C11  180.00   0.0  0
 053  CONST_32  C24   C7   C12  C11  180.00   0.0  0
 053  CONST_33  C25   C13  C14  C15  180.00   0.0  0
 053  CONST_34  C24   N19  C18  C15    0.00   0.0  0
 053  CONST_35  C25   C13  C16  C17  180.00   0.0  0
 053  CONST_36  C22   C20  C21  C17  180.00   0.0  0
 053  CONST_37  C24   N19  C18  C17  180.00   0.0  0
 053  CONST_38  C22   C20  N19  C18  180.00   0.0  0
 053  CONST_39  C24   N19  C20  C21  180.00   0.0  0
 053  CONST_40  O30   C6   N5   C4   180.00   0.0  0
 053  CONST_41  H11   C11  C12  C7   180.00   0.0  0
 053  CONST_42  H12   C12  C7   C8   180.00   0.0  0
 053  CONST_43  H8    C8   C9   N10  180.00   0.0  0
 053  CONST_44  H15   C15  C14  C13  180.00   0.0  0
 053  CONST_45  H16   C16  C13  C14  180.00   0.0  0
 053  CONST_46  H14   C14  C13  C16  180.00   0.0  0
 053  CONST_47  HN5   N5   C6   C1   180.00   0.0  0
 053  CONST_50  HO26  O26  C22  C20  180.00   0.0  0
 053  Var_01    C17   C21  C1   C2   -51.28  30.0  2
 053  Var_02    C18   N19  C24  C7   111.41  30.0  2
 053  Var_03    N19   C24  C7   C8   150.08  30.0  2
 053  Var_04    F27   C25  C13  C14  -20.44  30.0  2
 053  Var_05    O23   C22  C20  N19  145.25  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
 053  plan-1  C1    0.020
 053  plan-1  C2    0.020
 053  plan-1  C3    0.020
 053  plan-1  C4    0.020
 053  plan-1  N5    0.020
 053  plan-1  C6    0.020
 053  plan-1  C21   0.020
 053  plan-1  O30   0.020
 053  plan-1  H2    0.020
 053  plan-1  H3    0.020
 053  plan-1  H4    0.020
 053  plan-1  HN5   0.020
 053  plan-2  C7    0.020
 053  plan-2  C8    0.020
 053  plan-2  C9    0.020
 053  plan-2  N10   0.020
 053  plan-2  C11   0.020
 053  plan-2  C12   0.020
 053  plan-2  C24   0.020
 053  plan-2  N31   0.020
 053  plan-2  H8    0.020
 053  plan-2  H11   0.020
 053  plan-2  H12   0.020
 053  plan-3  C1    0.020
 053  plan-3  C13   0.020
 053  plan-3  C14   0.020
 053  plan-3  C15   0.020
 053  plan-3  C16   0.020
 053  plan-3  C17   0.020
 053  plan-3  C18   0.020
 053  plan-3  N19   0.020
 053  plan-3  C20   0.020
 053  plan-3  C21   0.020
 053  plan-3  C24   0.020
 053  plan-3  C25   0.020
 053  plan-3  H14   0.020
 053  plan-3  H15   0.020
 053  plan-3  H16   0.020
 053  plan-3  C22   0.020
 053  plan-4  C9    0.020
 053  plan-4  N31   0.020
 053  plan-4  HN31  0.020
 053  plan-4  HN3A  0.020
 053  plan-5  C20   0.020
 053  plan-5  O23   0.020
 053  plan-5  O26   0.020
 053  plan-5  HO26  0.020
 053  plan-5  C22   0.020

