# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 11:21:27 2021
#   Inital geometry file: a 54 line input string
#   Ligand name: 4-(trifluoromethyl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccc(cc1)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
 LR5  LR5  4-(trifluoromethyl)benzamide  ligand  19  13  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LR5
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
 LR5  C1  C  CR6   0  -0.031  14.4251  2.9437  19.7826
 LR5  C2  C  CR16  0  -0.265  13.4020  3.8655  19.5919
 LR5  C6  C  CR16  0  -0.256  12.9395  1.1788  19.0879
 LR5  C4  C  CR6   0  -0.193  11.9212  2.1088  18.8986
 LR5  C3  C  CR16  0  -0.268  12.1520  3.4520  19.1540
 LR5  N   N  NH2   0  -0.808  16.1660  4.5916  20.0347
 LR5  C   C  C     0   0.489  15.7799  3.3348  20.2911
 LR5  O   O  O     0  -0.475  16.4680  2.5344  20.9077
 LR5  C7  C  CR16  0  -0.254  14.1783  1.5948  19.5382
 LR5  F   F  F     0  -0.300   9.6572  2.5802  18.4250
 LR5  F1  F  F     0  -0.311  10.1313  0.6084  19.1435
 LR5  F2  F  F     0  -0.313  10.6693  1.1795  17.1438
 LR5  H1  H  HCR6  0   0.273  13.5491  4.9163  19.8039
 LR5  H2  H  HCR6  0   0.281  12.7756  0.1268  18.8938
 LR5  H3  H  HCR6  0   0.279  11.3738  4.1909  19.0256
 LR5  H4  H  HNH2  0   0.408  17.0736  4.9050  20.3395
 LR5  H5  H  HNH2  0   0.415  15.6667  5.1942  19.4041
 LR5  H6  H  HCR6  0   0.274  14.9611  0.8649  19.6921
 LR5  C5  C  CT    0   1.054  10.5919  1.6273  18.4055

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
 LR5  F2  C5  single    1.341  0.020  1.341
 LR5  C5  F   single    1.335  0.020  1.335
 LR5  C5  C4  single    1.497  0.020  1.497
 LR5  C5  F1  single    1.340  0.020  1.340
 LR5  C4  C3  aromatic  1.387  0.020  1.387
 LR5  C4  C6  aromatic  1.392  0.020  1.392
 LR5  C3  C2  aromatic  1.387  0.020  1.387
 LR5  C6  C7  aromatic  1.382  0.020  1.382
 LR5  C2  C1  aromatic  1.390  0.020  1.390
 LR5  C7  C1  aromatic  1.393  0.020  1.393
 LR5  C1  C   single    1.499  0.020  1.499
 LR5  C   N   single    1.340  0.020  1.340
 LR5  C   O   double    1.222  0.020  1.222
 LR5  C2  H1  single    0.930  0.020  1.080
 LR5  C6  H2  single    0.930  0.020  1.080
 LR5  C3  H3  single    0.930  0.020  1.080
 LR5  N   H4  single    0.860  0.020  1.020
 LR5  N   H5  single    0.860  0.020  1.020
 LR5  C7  H6  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
 LR5  C7  C1  C   118.18  3.000
 LR5  C   C1  C2  122.59  3.000
 LR5  C7  C1  C2  119.18  3.000
 LR5  H1  C2  C3  118.27  3.000
 LR5  H1  C2  C1  121.13  3.000
 LR5  C3  C2  C1  120.58  3.000
 LR5  H2  C6  C7  119.13  3.000
 LR5  H2  C6  C4  120.95  3.000
 LR5  C7  C6  C4  119.93  3.000
 LR5  C3  C4  C5  121.33  3.000
 LR5  C3  C4  C6  120.02  3.000
 LR5  C5  C4  C6  118.65  3.000
 LR5  H3  C3  C4  121.36  3.000
 LR5  H3  C3  C2  118.85  3.000
 LR5  C4  C3  C2  119.79  3.000
 LR5  H5  N   H4  116.80  3.000
 LR5  H5  N   C   122.65  3.000
 LR5  H4  N   C   119.58  3.000
 LR5  O   C   N   123.27  3.000
 LR5  O   C   C1  120.60  3.000
 LR5  N   C   C1  116.13  3.000
 LR5  H6  C7  C6  119.47  3.000
 LR5  H6  C7  C1  120.03  3.000
 LR5  C6  C7  C1  120.49  3.000
 LR5  F2  C5  F1  106.51  3.000
 LR5  F1  C5  F   107.10  3.000
 LR5  F2  C5  F   107.01  3.000
 LR5  F1  C5  C4  111.61  3.000
 LR5  F   C5  C4  112.79  3.000
 LR5  F2  C5  C4  111.47  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
 LR5  CONST_01  C4  C3  C2  C1    0.00   0.0  0
 LR5  CONST_02  C4  C6  C7  C1    0.00   0.0  0
 LR5  CONST_03  C6  C4  C3  C2    0.00   0.0  0
 LR5  CONST_04  C6  C7  C1  C2    0.00   0.0  0
 LR5  CONST_05  C7  C6  C4  C3    0.00   0.0  0
 LR5  CONST_06  C7  C1  C2  C3    0.00   0.0  0
 LR5  CONST_07  C5  C4  C3  C2  180.00   0.0  0
 LR5  CONST_08  C   C1  C7  C6  180.00   0.0  0
 LR5  CONST_09  C7  C6  C4  C5  180.00   0.0  0
 LR5  CONST_10  C   C1  C2  C3  180.00   0.0  0
 LR5  CONST_11  H3  C3  C2  C1  180.00   0.0  0
 LR5  CONST_12  H2  C6  C7  C1  180.00   0.0  0
 LR5  CONST_13  H6  C7  C1  C2  180.00   0.0  0
 LR5  CONST_14  H1  C2  C3  C4  180.00   0.0  0
 LR5  CONST_15  H4  N   C   C1  180.00   0.0  0
 LR5  CONST_16  H5  N   C   C1    0.00   0.0  0
 LR5  Var_01    N   C   C1  C2  -27.09  30.0  2
 LR5  Var_02    F2  C5  C4  C6  -67.48  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
 LR5  plan-1  C1  0.020
 LR5  plan-1  C2  0.020
 LR5  plan-1  C6  0.020
 LR5  plan-1  C4  0.020
 LR5  plan-1  C3  0.020
 LR5  plan-1  C   0.020
 LR5  plan-1  C7  0.020
 LR5  plan-1  H1  0.020
 LR5  plan-1  H2  0.020
 LR5  plan-1  H3  0.020
 LR5  plan-1  H6  0.020
 LR5  plan-1  C5  0.020
 LR5  plan-2  C1  0.020
 LR5  plan-2  N   0.020
 LR5  plan-2  C   0.020
 LR5  plan-2  O   0.020
 LR5  plan-2  H4  0.020
 LR5  plan-2  H5  0.020

