# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 23:40:10 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 1-[3-(trifluoromethyl)phenyl]indole-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cc2ccccc2n1c3cccc(c3)C(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
 AYN  AYN  1-[3-(trifluoromethyl)phenyl]indole-2-carboxamide  ligand  33  22  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AYN
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
 AYN  C1   C  CR16  0  -0.268   4.6880   1.8451   0.7408
 AYN  C2   C  CR16  0  -0.339   4.6044   0.4697   0.7796
 AYN  C3   C  CR56  0   0.081   3.4080  -0.1430   0.3865
 AYN  C8   C  CR5   0   0.228   1.6807  -1.4802  -0.1353
 AYN  C9   C  CR15  0  -0.416   2.9665  -1.4956   0.3263
 AYN  C10  C  C     0   0.459   0.8183  -2.6281  -0.4984
 AYN  C13  C  CR6   0   0.325  -0.0025   0.2712  -0.7261
 AYN  C14  C  CR16  0  -0.285  -1.0616   0.0375   0.1346
 AYN  C15  C  CR6   0  -0.190  -2.3296   0.4973  -0.1993
 AYN  C16  C  CR16  0  -0.285  -2.5327   1.2075  -1.3746
 AYN  C19  C  CT    0   1.055  -3.4551   0.2087   0.7445
 AYN  C4   C  CR56  0   0.344   2.3331   0.6554  -0.0530
 AYN  C5   C  CR16  0  -0.296   2.4069   2.0483  -0.0774
 AYN  C6   C  CR16  0  -0.273   3.5962   2.6249   0.3198
 AYN  N7   N  NR5   0  -0.677   1.2930  -0.1785  -0.3828
 AYN  O11  O  O     0  -0.467  -0.0004  -2.5496  -1.4022
 AYN  N12  N  NH2   0  -0.805   1.0396  -3.7393   0.2175
 AYN  C17  C  CR16  0  -0.243  -1.4586   1.4526  -2.2188
 AYN  C18  C  CR16  0  -0.274  -0.1950   0.9815  -1.9036
 AYN  F20  F  F     0  -0.313  -3.2004   0.6801   1.9737
 AYN  F21  F  F     0  -0.300  -4.6118   0.7453   0.3502
 AYN  F22  F  F     0  -0.313  -3.6584  -1.1100   0.8791
 AYN  H1   H  HCR6  0   0.254   5.6025   2.3365   1.0450
 AYN  H2   H  HCR6  0   0.254   5.4436  -0.1266   1.1147
 AYN  H3   H  HCR5  0   0.272   3.5493  -2.3753   0.5515
 AYN  H4   H  HCR6  0   0.287  -0.8856  -0.5005   1.0582
 AYN  H5   H  HCR6  0   0.277  -3.5127   1.5742  -1.6451
 AYN  H6   H  HCR6  0   0.267   1.5707   2.6580  -0.3946
 AYN  H7   H  HCR6  0   0.258   3.6901   3.7029   0.3085
 AYN  H8   H  HNH2  0   0.416   1.6344  -3.7471   1.0282
 AYN  H9   H  HNH2  0   0.409   0.5339  -4.5835   0.0038
 AYN  H10  H  HCR6  0   0.276  -1.6130   2.0061  -3.1347
 AYN  H11  H  HCR6  0   0.285   0.6373   1.1560  -2.5731

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
 AYN  F20  C19  single    1.341  0.020  1.341
 AYN  C6   C5   aromatic  1.380  0.020  1.380
 AYN  C6   C1   aromatic  1.406  0.020  1.406
 AYN  F22  C19  single    1.341  0.020  1.341
 AYN  C5   C4   aromatic  1.395  0.020  1.395
 AYN  C1   C2   aromatic  1.378  0.020  1.378
 AYN  C19  C15  single    1.497  0.020  1.497
 AYN  C19  F21  single    1.335  0.020  1.335
 AYN  C15  C16  aromatic  1.388  0.020  1.388
 AYN  C15  C14  aromatic  1.389  0.020  1.389
 AYN  C16  C17  aromatic  1.388  0.020  1.388
 AYN  C14  C13  aromatic  1.385  0.020  1.385
 AYN  C4   C3   aromatic  1.409  0.020  1.409
 AYN  C4   N7   aromatic  1.373  0.020  1.373
 AYN  C17  C18  aromatic  1.385  0.020  1.385
 AYN  C2   C3   aromatic  1.401  0.020  1.401
 AYN  C13  C18  aromatic  1.389  0.020  1.389
 AYN  C13  N7   single    1.414  0.020  1.414
 AYN  C3   C9   aromatic  1.424  0.020  1.424
 AYN  N7   C8   aromatic  1.381  0.020  1.381
 AYN  C9   C8   aromatic  1.366  0.020  1.366
 AYN  C8   C10  single    1.481  0.020  1.481
 AYN  C10  N12  single    1.340  0.020  1.340
 AYN  C10  O11  double    1.222  0.020  1.222
 AYN  C1   H1   single    0.930  0.020  1.080
 AYN  C2   H2   single    0.930  0.020  1.080
 AYN  C9   H3   single    0.930  0.020  1.080
 AYN  C14  H4   single    0.930  0.020  1.080
 AYN  C16  H5   single    0.930  0.020  1.080
 AYN  C5   H6   single    0.930  0.020  1.080
 AYN  C6   H7   single    0.930  0.020  1.080
 AYN  N12  H8   single    0.860  0.020  1.020
 AYN  N12  H9   single    0.860  0.020  1.020
 AYN  C17  H10  single    0.930  0.020  1.080
 AYN  C18  H11  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
 AYN  H1   C1   C6   119.24  3.000
 AYN  H1   C1   C2   119.78  3.000
 AYN  C6   C1   C2   120.98  3.000
 AYN  H2   C2   C3   120.54  3.000
 AYN  H2   C2   C1   120.75  3.000
 AYN  C3   C2   C1   118.71  3.000
 AYN  C4   C3   C9   106.77  3.000
 AYN  C9   C3   C2   133.81  3.000
 AYN  C4   C3   C2   119.42  3.000
 AYN  N7   C8   C10  121.55  3.000
 AYN  C10  C8   C9   128.47  3.000
 AYN  N7   C8   C9   109.60  3.000
 AYN  H3   C9   C8   126.02  3.000
 AYN  H3   C9   C3   126.73  3.000
 AYN  C8   C9   C3   107.18  3.000
 AYN  N12  C10  O11  123.99  3.000
 AYN  O11  C10  C8   121.44  3.000
 AYN  N12  C10  C8   114.55  3.000
 AYN  C18  C13  N7   119.72  3.000
 AYN  N7   C13  C14  119.76  3.000
 AYN  C18  C13  C14  120.49  3.000
 AYN  H4   C14  C15  121.17  3.000
 AYN  H4   C14  C13  119.31  3.000
 AYN  C15  C14  C13  119.52  3.000
 AYN  C19  C15  C16  121.50  3.000
 AYN  C16  C15  C14  120.42  3.000
 AYN  C19  C15  C14  118.08  3.000
 AYN  H5   C16  C17  119.31  3.000
 AYN  H5   C16  C15  121.21  3.000
 AYN  C17  C16  C15  119.48  3.000
 AYN  F22  C19  F21  107.08  3.000
 AYN  F21  C19  F20  107.10  3.000
 AYN  F22  C19  F20  106.41  3.000
 AYN  F21  C19  C15  112.82  3.000
 AYN  F22  C19  C15  111.52  3.000
 AYN  F20  C19  C15  111.55  3.000
 AYN  N7   C4   C5   129.95  3.000
 AYN  N7   C4   C3   107.97  3.000
 AYN  C5   C4   C3   122.06  3.000
 AYN  H6   C5   C6   120.98  3.000
 AYN  H6   C5   C4   121.78  3.000
 AYN  C6   C5   C4   117.24  3.000
 AYN  H7   C6   C5   119.20  3.000
 AYN  H7   C6   C1   119.23  3.000
 AYN  C5   C6   C1   121.57  3.000
 AYN  C4   N7   C13  124.00  3.000
 AYN  C13  N7   C8   126.93  3.000
 AYN  C4   N7   C8   108.47  3.000
 AYN  H9   N12  H8   117.49  3.000
 AYN  H9   N12  C10  119.92  3.000
 AYN  H8   N12  C10  122.33  3.000
 AYN  H10  C17  C18  119.82  3.000
 AYN  H10  C17  C16  119.68  3.000
 AYN  C18  C17  C16  120.50  3.000
 AYN  H11  C18  C17  120.40  3.000
 AYN  H11  C18  C13  120.03  3.000
 AYN  C17  C18  C13  119.57  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
 AYN  CONST_01  C4   C5   C6   C1     0.00   0.0  0
 AYN  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 AYN  CONST_03  C9   C3   C2   C1   180.00   0.0  0
 AYN  CONST_04  C5   C6   C1   C2     0.00   0.0  0
 AYN  CONST_05  C5   C4   C3   C2     0.00   0.0  0
 AYN  CONST_06  N7   C4   C3   C2   180.00   0.0  0
 AYN  CONST_07  C8   C9   C3   C2   180.00   0.0  0
 AYN  CONST_08  C6   C5   C4   C3     0.00   0.0  0
 AYN  CONST_09  C13  N7   C4   C3   180.00   0.0  0
 AYN  CONST_10  C8   N7   C4   C3     0.00   0.0  0
 AYN  CONST_11  C6   C1   C2   C3     0.00   0.0  0
 AYN  CONST_12  N7   C8   C9   C3     0.00   0.0  0
 AYN  CONST_13  C5   C4   N7   C8   180.00   0.0  0
 AYN  CONST_16  C4   C3   C9   C8     0.00   0.0  0
 AYN  CONST_17  C5   C4   C3   C9   180.00   0.0  0
 AYN  CONST_18  N7   C4   C3   C9     0.00   0.0  0
 AYN  CONST_19  C4   N7   C8   C9     0.00   0.0  0
 AYN  CONST_20  C13  N7   C8   C9   180.00   0.0  0
 AYN  CONST_21  C16  C15  C14  C13    0.00   0.0  0
 AYN  CONST_22  C16  C17  C18  C13    0.00   0.0  0
 AYN  CONST_23  C5   C4   N7   C13    0.00   0.0  0
 AYN  CONST_24  C17  C16  C15  C14    0.00   0.0  0
 AYN  CONST_25  C17  C18  C13  C14    0.00   0.0  0
 AYN  CONST_27  C18  C17  C16  C15    0.00   0.0  0
 AYN  CONST_28  C18  C13  C14  C15    0.00   0.0  0
 AYN  CONST_29  N7   C13  C14  C15  180.00   0.0  0
 AYN  CONST_31  N7   C4   C5   C6   180.00   0.0  0
 AYN  CONST_32  C17  C18  C13  N7   180.00   0.0  0
 AYN  CONST_33  C10  C8   C9   C3   180.00   0.0  0
 AYN  CONST_34  C4   N7   C8   C10  180.00   0.0  0
 AYN  CONST_35  C13  N7   C8   C10    0.00   0.0  0
 AYN  CONST_36  C19  C15  C14  C13  180.00   0.0  0
 AYN  CONST_37  C17  C16  C15  C19  180.00   0.0  0
 AYN  CONST_38  H6   C5   C6   C1   180.00   0.0  0
 AYN  CONST_39  H7   C6   C1   C2   180.00   0.0  0
 AYN  CONST_40  H3   C9   C3   C2     0.00   0.0  0
 AYN  CONST_41  H1   C1   C2   C3   180.00   0.0  0
 AYN  CONST_42  H2   C2   C3   C9     0.00   0.0  0
 AYN  CONST_43  H10  C17  C18  C13  180.00   0.0  0
 AYN  CONST_44  H5   C16  C15  C14  180.00   0.0  0
 AYN  CONST_45  H11  C18  C13  C14  180.00   0.0  0
 AYN  CONST_46  H4   C14  C15  C16  180.00   0.0  0
 AYN  CONST_47  H8   N12  C10  C8     0.00   0.0  0
 AYN  CONST_48  H9   N12  C10  C8   180.00   0.0  0
 AYN  Var_01    N12  C10  C8   C9    32.03  30.0  2
 AYN  Var_02    F20  C19  C15  C14   56.72  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
 AYN  plan-1  C13  0.020
 AYN  plan-1  C14  0.020
 AYN  plan-1  C15  0.020
 AYN  plan-1  C16  0.020
 AYN  plan-1  C19  0.020
 AYN  plan-1  N7   0.020
 AYN  plan-1  C17  0.020
 AYN  plan-1  C18  0.020
 AYN  plan-1  H4   0.020
 AYN  plan-1  H5   0.020
 AYN  plan-1  H10  0.020
 AYN  plan-1  H11  0.020
 AYN  plan-2  C1   0.020
 AYN  plan-2  C2   0.020
 AYN  plan-2  C3   0.020
 AYN  plan-2  C8   0.020
 AYN  plan-2  C9   0.020
 AYN  plan-2  C10  0.020
 AYN  plan-2  C13  0.020
 AYN  plan-2  C4   0.020
 AYN  plan-2  C5   0.020
 AYN  plan-2  C6   0.020
 AYN  plan-2  N7   0.020
 AYN  plan-2  H1   0.020
 AYN  plan-2  H2   0.020
 AYN  plan-2  H3   0.020
 AYN  plan-2  H6   0.020
 AYN  plan-2  H7   0.020
 AYN  plan-3  C8   0.020
 AYN  plan-3  C10  0.020
 AYN  plan-3  O11  0.020
 AYN  plan-3  N12  0.020
 AYN  plan-3  H8   0.020
 AYN  plan-3  H9   0.020

