# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 07:35:31 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: N-{3-[3-(trifluoromethyl)phenyl]prop-2-yn-1-yl}acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)NCC#Cc1cccc(c1)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
 J5M  J5M  N-{3-[3-(trifluoromethyl)phenyl]prop-2-yn-1-yl}acetamide  ligand  27  17  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_J5M
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
 J5M  C    C  CH3   0  -0.774   6.3592   0.1169   1.4416
 J5M  O    O  O     0  -0.507   6.1855  -0.8257  -0.7550
 J5M  C1   C  C     0   0.535   5.6236  -0.2906   0.1915
 J5M  C2   C  CH2   0  -0.438   3.4747  -0.3891  -0.9500
 J5M  C3   C  CSP   0   0.008   2.0985   0.0296  -0.7296
 J5M  C4   C  CSP   0   0.206   0.9609   0.3793  -0.5492
 J5M  C5   C  CR6   0  -0.101  -0.3860   0.7963  -0.3359
 J5M  C6   C  CR16  0  -0.277  -0.7089   2.1563  -0.3052
 J5M  F1   F  F     0  -0.301  -4.9871  -0.2860   0.2851
 J5M  F2   F  F     0  -0.314  -3.5672  -1.4483   1.4085
 J5M  F    F  F     0  -0.312  -3.7260  -1.7124  -0.7168
 J5M  C9   C  CR6   0  -0.187  -2.7036   0.2600   0.0485
 J5M  C10  C  CR16  0  -0.314  -1.3927  -0.1504  -0.1571
 J5M  C7   C  CR16  0  -0.233  -2.0167   2.5544  -0.0961
 J5M  C8   C  CR16  0  -0.278  -3.0204   1.6114   0.0827
 J5M  N    N  NH1   0  -0.637   4.3053  -0.0334   0.1827
 J5M  H1   H  HCH3  0   0.267   7.2026   0.7529   1.1747
 J5M  H2   H  HCH3  0   0.251   5.7379   0.6481   2.1598
 J5M  H3   H  HCH3  0   0.269   6.7633  -0.7715   1.9272
 J5M  H4   H  HCH2  0   0.280   3.5008  -1.4688  -1.1239
 J5M  H5   H  HCH2  0   0.280   3.8537   0.0823  -1.8613
 J5M  H6   H  HCR6  0   0.273   0.0695   2.8942  -0.4448
 J5M  H7   H  HCR6  0   0.282  -1.1354  -1.2016  -0.1846
 J5M  H8   H  HCR6  0   0.277  -2.2611   3.6075  -0.0715
 J5M  H9   H  HCR6  0   0.279  -4.0357   1.9445   0.2463
 J5M  H10  H  HNH1  0   0.411   3.8705   0.3901   0.9853
 J5M  C11  C  CT    0   1.055  -3.7514  -0.7898   0.2548

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
 J5M  C    C1   single    1.507  0.020  1.507
 J5M  O    C1   double    1.224  0.020  1.224
 J5M  C1   N    single    1.343  0.020  1.343
 J5M  N    C2   single    1.449  0.020  1.449
 J5M  C2   C3   single    1.455  0.020  1.455
 J5M  C3   C4   triple    1.204  0.020  1.204
 J5M  C4   C5   single    1.426  0.020  1.426
 J5M  C10  C5   aromatic  1.393  0.020  1.393
 J5M  C10  C9   aromatic  1.389  0.020  1.389
 J5M  C5   C6   aromatic  1.398  0.020  1.398
 J5M  F    C11  single    1.340  0.020  1.340
 J5M  F2   C11  single    1.341  0.020  1.341
 J5M  C11  C9   single    1.497  0.020  1.497
 J5M  C11  F1   single    1.335  0.020  1.335
 J5M  C9   C8   aromatic  1.388  0.020  1.388
 J5M  C6   C7   aromatic  1.383  0.020  1.383
 J5M  C8   C7   aromatic  1.389  0.020  1.389
 J5M  C    H1   single    0.970  0.020  1.090
 J5M  C    H2   single    0.970  0.020  1.090
 J5M  C    H3   single    0.970  0.020  1.090
 J5M  C2   H4   single    0.970  0.020  1.090
 J5M  C2   H5   single    0.970  0.020  1.090
 J5M  C6   H6   single    0.930  0.020  1.080
 J5M  C10  H7   single    0.930  0.020  1.080
 J5M  C7   H8   single    0.930  0.020  1.080
 J5M  C8   H9   single    0.930  0.020  1.080
 J5M  N    H10  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
 J5M  H3   C    H2   108.39  3.000
 J5M  H3   C    H1   107.33  3.000
 J5M  H2   C    H1   108.59  3.000
 J5M  H3   C    C1   109.28  3.000
 J5M  H2   C    C1   113.63  3.000
 J5M  H1   C    C1   109.42  3.000
 J5M  N    C1   O    121.95  3.000
 J5M  N    C1   C    115.65  3.000
 J5M  O    C1   C    122.40  3.000
 J5M  H5   C2   H4   106.54  3.000
 J5M  H5   C2   N    110.30  3.000
 J5M  H4   C2   N    110.66  3.000
 J5M  H5   C2   C3   109.26  3.000
 J5M  H4   C2   C3   109.31  3.000
 J5M  N    C2   C3   110.67  3.000
 J5M  C4   C3   C2   180.00  3.000
 J5M  C5   C4   C3   180.00  3.000
 J5M  C10  C5   C6   119.42  3.000
 J5M  C6   C5   C4   120.39  3.000
 J5M  C10  C5   C4   120.19  3.000
 J5M  H6   C6   C7   120.24  3.000
 J5M  H6   C6   C5   119.64  3.000
 J5M  C7   C6   C5   120.11  3.000
 J5M  C8   C9   C10  120.44  3.000
 J5M  C8   C9   C11  121.28  3.000
 J5M  C10  C9   C11  118.27  3.000
 J5M  H7   C10  C9   121.00  3.000
 J5M  H7   C10  C5   119.00  3.000
 J5M  C9   C10  C5   120.00  3.000
 J5M  H8   C7   C8   119.67  3.000
 J5M  H8   C7   C6   119.83  3.000
 J5M  C8   C7   C6   120.49  3.000
 J5M  H9   C8   C7   119.28  3.000
 J5M  H9   C8   C9   121.19  3.000
 J5M  C7   C8   C9   119.53  3.000
 J5M  H10  N    C2   118.63  3.000
 J5M  H10  N    C1   119.96  3.000
 J5M  C2   N    C1   121.38  3.000
 J5M  C9   C11  F    111.68  3.000
 J5M  C9   C11  F2   111.51  3.000
 J5M  F    C11  F2   106.44  3.000
 J5M  C9   C11  F1   112.73  3.000
 J5M  F2   C11  F1   107.03  3.000
 J5M  F    C11  F1   107.09  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
 J5M  CONST_01  C8   C9   C10  C5      0.00   0.0  0
 J5M  CONST_02  C8   C7   C6   C5      0.00   0.0  0
 J5M  CONST_03  C9   C10  C5   C6      0.00   0.0  0
 J5M  CONST_04  C9   C8   C7   C6      0.00   0.0  0
 J5M  CONST_05  C7   C6   C5   C10     0.00   0.0  0
 J5M  CONST_06  C7   C8   C9   C10     0.00   0.0  0
 J5M  CONST_07  C9   C10  C5   C4    180.00   0.0  0
 J5M  CONST_08  C7   C6   C5   C4    180.00   0.0  0
 J5M  CONST_09  C11  C9   C10  C5    180.00   0.0  0
 J5M  CONST_10  C7   C8   C9   C11   180.00   0.0  0
 J5M  CONST_11  H8   C7   C6   C5    180.00   0.0  0
 J5M  CONST_12  H7   C10  C5   C6    180.00   0.0  0
 J5M  CONST_13  H9   C8   C7   C6    180.00   0.0  0
 J5M  CONST_14  H6   C6   C5   C10   180.00   0.0  0
 J5M  CONST_15  C2   N    C1   C     180.00   0.0  0
 J5M  CONST_16  C2   N    C1   O       0.00   0.0  0
 J5M  CONST_17  H10  N    C1   C       0.00   0.0  0
 J5M  Var_01    C10  C9   C11  F1   -172.64  30.0  2
 J5M  Var_02    C3   C2   N    C1   -178.31  30.0  3
 J5M  Var_03    N    C2   C3   C4     95.70  30.0  2
 J5M  Var_04    H1   C    C1   O      54.02  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
 J5M  plan-1  C3   0.020
 J5M  plan-1  C4   0.020
 J5M  plan-1  C5   0.020
 J5M  plan-1  C6   0.020
 J5M  plan-1  C9   0.020
 J5M  plan-1  C10  0.020
 J5M  plan-1  C7   0.020
 J5M  plan-1  C8   0.020
 J5M  plan-1  H6   0.020
 J5M  plan-1  H7   0.020
 J5M  plan-1  H8   0.020
 J5M  plan-1  H9   0.020
 J5M  plan-1  C11  0.020
 J5M  plan-2  C    0.020
 J5M  plan-2  O    0.020
 J5M  plan-2  C1   0.020
 J5M  plan-2  C2   0.020
 J5M  plan-2  N    0.020
 J5M  plan-2  H10  0.020

