# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 28 23:17:36 2022
#   Inital geometry file: a 68 line input string
#   Ligand name: 4-(trifluoromethyl)-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(cc1)C(F)(F)F)C(O)=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
 55I  55I  "4-(trifluoromethyl)-L-phenylalanine"  L-peptide  25  16  .  2022-09-15  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_55I
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
 55I  C    C  C      0   0.394  14.8183  -0.2665  2.9902
 55I  N    N  NH2    0  -0.792  13.5736  -1.5463  1.2031
 55I  O    O  O      0  -0.604  14.6883  -0.0822  4.2153
 55I  CA   C  CH1    0  -0.189  14.3651  -1.6352  2.4261
 55I  CB   C  CH2    0  -0.506  15.5973  -2.5072  2.1327
 55I  CG   C  CR6    0   0.138  16.4559  -2.7284  3.3411
 55I  CZ   C  CR6    0  -0.218  17.9966  -3.0921  5.6502
 55I  C13  C  CT     0   1.046  18.7796  -3.2192  6.9153
 55I  F19  F  F      0  -0.317  18.3660  -2.3354  7.8399
 55I  F20  F  F      0  -0.310  20.0861  -2.9900  6.7292
 55I  F21  F  F      0  -0.307  18.6726  -4.4317  7.4711
 55I  CD1  C  CR16   0  -0.299  16.1107  -3.6894  4.2885
 55I  CD2  C  CR16   0  -0.286  17.5974  -1.9639  3.5668
 55I  CE1  C  CR16   0  -0.261  16.8661  -3.8726  5.4349
 55I  CE2  C  CR16   0  -0.260  18.3626  -2.1376  4.7084
 55I  OXT  O  OC    -1  -0.611  15.2970   0.5321  2.1557
 55I  H4   H  HCH1   0   0.207  13.7604  -2.1485  3.1803
 55I  H5   H  HCH2   0   0.241  15.2507  -3.4672  1.7426
 55I  H6   H  HCH2   0   0.234  16.1846  -2.0313  1.3425
 55I  H7   H  HCR6   0   0.254  15.2346  -4.3071  4.1302
 55I  H8   H  HCR6   0   0.253  17.8889  -1.2138  2.8422
 55I  H9   H  HCR6   0   0.265  16.5655  -4.6264  6.1507
 55I  H10  H  HCR6   0   0.266  19.2408  -1.5212  4.8517
 55I  H    H  HNH2   0   0.337  12.6898  -1.0997  1.4192
 55I  HN   H  HNH2   0   0.325  14.0469  -0.8983  0.5821

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
 55I  N    CA   single    1.458  0.019  1.458
 55I  CB   CA   single    1.530  0.020  1.530
 55I  CB   CG   single    1.499  0.020  1.499
 55I  CA   C    single    1.525  0.021  1.525
 55I  C    O    deloc     1.231  0.020  1.231
 55I  CG   CD2  aromatic  1.392  0.020  1.392
 55I  CG   CD1  aromatic  1.393  0.020  1.393
 55I  CD2  CE2  aromatic  1.385  0.020  1.385
 55I  CD1  CE1  aromatic  1.385  0.020  1.385
 55I  CE2  CZ   aromatic  1.390  0.020  1.390
 55I  CE1  CZ   aromatic  1.391  0.020  1.391
 55I  CZ   C13  single    1.493  0.020  1.493
 55I  F20  C13  single    1.339  0.020  1.339
 55I  C13  F21  single    1.338  0.020  1.338
 55I  C13  F19  single    1.344  0.020  1.344
 55I  C    OXT  deloc     1.250  0.020  1.250
 55I  N    H    single    0.860  0.020  0.860
 55I  N    HN   single    0.890  0.020  1.040
 55I  CA   H4   single    0.970  0.020  1.090
 55I  CB   H5   single    0.970  0.020  1.090
 55I  CB   H6   single    0.970  0.020  1.090
 55I  CD1  H7   single    0.930  0.020  1.080
 55I  CD2  H8   single    0.930  0.020  1.080
 55I  CE1  H9   single    0.930  0.020  1.080
 55I  CE2  H10  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
 55I  OXT  C    CA   115.69  3.000
 55I  OXT  C    O    127.01  3.000
 55I  CA   C    O    120.80  1.700
 55I  HN   N    H    104.82  3.000
 55I  HN   N    CA   107.38  3.000
 55I  H    N    CA   114.00  3.000
 55I  H4   CA   CB   107.95  3.000
 55I  H4   CA   N    107.84  3.000
 55I  CB   CA   N    110.50  1.700
 55I  H4   CA   C    108.98  3.000
 55I  CB   CA   C    110.10  1.900
 55I  N    CA   C    111.00  2.800
 55I  H6   CB   H5   107.15  3.000
 55I  H6   CB   CG   109.83  3.000
 55I  H5   CB   CG   109.87  3.000
 55I  H6   CB   CA   108.74  3.000
 55I  H5   CB   CA   108.19  3.000
 55I  CG   CB   CA   112.88  3.000
 55I  CD2  CG   CD1  118.14  3.000
 55I  CD1  CG   CB   120.55  3.000
 55I  CD2  CG   CB   121.29  3.000
 55I  CE2  CZ   CE1  119.65  3.000
 55I  CE1  CZ   C13  120.65  3.000
 55I  CE2  CZ   C13  119.63  3.000
 55I  F21  C13  F20  106.90  3.000
 55I  F21  C13  F19  106.58  3.000
 55I  F20  C13  F19  106.45  3.000
 55I  F19  C13  CZ   111.44  3.000
 55I  F21  C13  CZ   112.77  3.000
 55I  F20  C13  CZ   112.29  3.000
 55I  H7   CD1  CE1  119.11  3.000
 55I  H7   CD1  CG   119.62  3.000
 55I  CE1  CD1  CG   121.27  3.000
 55I  H8   CD2  CE2  119.31  3.000
 55I  H8   CD2  CG   119.51  3.000
 55I  CE2  CD2  CG   121.18  3.000
 55I  H9   CE1  CD1  119.22  3.000
 55I  H9   CE1  CZ   120.96  3.000
 55I  CD1  CE1  CZ   119.82  3.000
 55I  H10  CE2  CD2  119.07  3.000
 55I  H10  CE2  CZ   120.99  3.000
 55I  CD2  CE2  CZ   119.93  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
 55I  CONST_01  CZ   CE2  CD2  CG      0.00   0.0  0
 55I  CONST_02  CZ   CE1  CD1  CG      0.00   0.0  0
 55I  CONST_03  CE2  CD2  CG   CD1     0.00   0.0  0
 55I  CONST_04  CE2  CZ   CE1  CD1     0.00   0.0  0
 55I  CONST_05  CE1  CD1  CG   CD2     0.00   0.0  0
 55I  CONST_06  CE1  CZ   CE2  CD2     0.00   0.0  0
 55I  CONST_07  CE2  CD2  CG   CB    180.00   0.0  0
 55I  CONST_08  CE1  CD1  CG   CB    180.00   0.0  0
 55I  CONST_09  CD2  CE2  CZ   C13   180.00   0.0  0
 55I  CONST_10  CD1  CE1  CZ   C13   180.00   0.0  0
 55I  CONST_11  H10  CE2  CD2  CG    180.00   0.0  0
 55I  CONST_12  H9   CE1  CD1  CG    180.00   0.0  0
 55I  CONST_13  H8   CD2  CE2  CZ    180.00   0.0  0
 55I  CONST_14  H7   CD1  CE1  CZ    180.00   0.0  0
 55I  CONST_15  H8   CD2  CG   CD1   180.00   0.0  0
 55I  CONST_16  H7   CD1  CG   CD2   180.00   0.0  0
 55I  CONST_17  H10  CE2  CZ   CE1   180.00   0.0  0
 55I  CONST_18  H9   CE1  CZ   CE2   180.00   0.0  0
 55I  Var_01    CD2  CG   CB   CA    -98.23  30.0  2
 55I  Var_02    CD1  CG   CB   CA     80.23  30.0  2
 55I  Var_03    CE2  CZ   C13  F19    83.96  30.0  3
 55I  Var_04    CE1  CZ   C13  F19   -92.80  30.0  3
 55I  Var_05    CE2  CZ   C13  F20   -35.36  30.0  3
 55I  Var_06    CE1  CZ   C13  F20   147.88  30.0  3
 55I  Var_07    CE2  CZ   C13  F21  -156.21  30.0  3
 55I  Var_08    CE1  CZ   C13  F21    27.03  30.0  3
 55I  Var_09    H5   CB   CG   CD1   -40.62  30.0  3
 55I  Var_10    H6   CB   CG   CD1  -158.24  30.0  3
 55I  Var_11    H5   CB   CG   CD2   140.92  30.0  3
 55I  Var_12    H6   CB   CG   CD2    23.30  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 55I  chir_01  CA  N  CB  C  negativ

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
 55I  plan-1  CB   0.020
 55I  plan-1  CG   0.020
 55I  plan-1  CZ   0.020
 55I  plan-1  C13  0.020
 55I  plan-1  CD1  0.020
 55I  plan-1  CD2  0.020
 55I  plan-1  CE1  0.020
 55I  plan-1  CE2  0.020
 55I  plan-1  H7   0.020
 55I  plan-1  H8   0.020
 55I  plan-1  H9   0.020
 55I  plan-1  H10  0.020
 55I  plan-2  C    0.020
 55I  plan-2  O    0.020
 55I  plan-2  CA   0.020
 55I  plan-2  OXT  0.020

