# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 16:07:28 2022
#   Inital geometry file: a 68 line input string
#   Ligand name: 4-(trifluoromethyl)-D-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
 TDF  TDF  4-(trifluoromethyl)-D-phenylalanine  D-peptide  25  16  .  2016-04-26  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT (side chain)
;

data_comp_TDF
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
 TDF  C    C  C      0   0.409  27.5977  -43.4115  -2.6728
 TDF  N    N  NH2    0  -0.794  30.0158  -43.5972  -2.3419
 TDF  O    O  O      0  -0.600  26.7329  -42.6073  -2.2808
 TDF  CA   C  CH1    0  -0.178  28.7291  -43.7756  -1.6863
 TDF  CB   C  CH2    0  -0.528  28.5267  -45.2155  -1.1686
 TDF  CG   C  CR6    0   0.143  27.2161  -45.4230  -0.4721
 TDF  CZ   C  CR6    0  -0.216  24.7653  -45.7805   0.8358
 TDF  C13  C  CT     0   1.047  23.4831  -45.9743   1.5762
 TDF  F19  F  F      0  -0.317  23.6544  -46.6986   2.6940
 TDF  F20  F  F      0  -0.316  22.9529  -44.8047   1.9676
 TDF  F21  F  F      0  -0.303  22.5539  -46.6027   0.8502
 TDF  CD1  C  CR16   0  -0.294  26.1735  -46.1137  -1.0808
 TDF  CD2  C  CR16   0  -0.299  27.0027  -44.9032   0.8056
 TDF  CE1  C  CR16   0  -0.269  24.9574  -46.2983  -0.4369
 TDF  CE2  C  CR16   0  -0.252  25.7953  -45.0764   1.4561
 TDF  OXT  O  OC    -1  -0.609  27.6502  -43.9831  -3.7825
 TDF  HN   H  HNH2   0   0.333  30.7544  -43.9826  -1.7646
 TDF  HNA  H  HNH2   0   0.327  30.0097  -44.1404  -3.1972
 TDF  HA   H  HCH1   0   0.202  28.6843  -43.0988  -0.8273
 TDF  HB   H  HCH2   0   0.233  28.6129  -45.9036  -2.0128
 TDF  HBA  H  HCH2   0   0.240  29.3435  -45.4487  -0.4784
 TDF  HD1  H  HCR6   0   0.253  26.3131  -46.5220  -2.0741
 TDF  HD2  H  HCR6   0   0.255  27.7982  -44.3598   1.3016
 TDF  HE1  H  HCR6   0   0.264  24.1742  -46.8480  -0.9411
 TDF  HE2  H  HCR6   0   0.268  25.6641  -44.6635   2.4488

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
 TDF  C    O    deloc     1.231  0.020  1.231
 TDF  C    CA   single    1.525  0.021  1.525
 TDF  C    OXT  deloc     1.249  0.020  1.249
 TDF  N    CA   single    1.458  0.019  1.458
 TDF  N    HN   single    0.890  0.020  1.040
 TDF  N    HNA  single    0.890  0.020  1.040
 TDF  CA   CB   single    1.521  0.033  1.521
 TDF  CA   HA   single    0.970  0.020  0.970
 TDF  CB   CG   single    1.499  0.020  1.499
 TDF  CB   HB   single    0.970  0.020  1.090
 TDF  CB   HBA  single    0.970  0.020  1.090
 TDF  CG   CD1  aromatic  1.391  0.020  1.391
 TDF  CG   CD2  aromatic  1.396  0.020  1.396
 TDF  CZ   C13  single    1.493  0.020  1.493
 TDF  CZ   CE1  aromatic  1.387  0.020  1.387
 TDF  CZ   CE2  aromatic  1.393  0.020  1.393
 TDF  C13  F19  single    1.343  0.020  1.343
 TDF  C13  F20  single    1.342  0.020  1.342
 TDF  C13  F21  single    1.336  0.020  1.336
 TDF  CD1  CE1  aromatic  1.388  0.020  1.388
 TDF  CD1  HD1  single    0.930  0.020  1.080
 TDF  CD2  CE2  aromatic  1.382  0.020  1.382
 TDF  CD2  HD2  single    0.930  0.020  1.080
 TDF  CE1  HE1  single    0.930  0.020  1.080
 TDF  CE2  HE2  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
 TDF  OXT  C    CA   120.80  1.700
 TDF  OXT  C    O    127.21  3.000
 TDF  CA   C    O    120.80  1.700
 TDF  HNA  N    HN   106.34  3.000
 TDF  HNA  N    CA   108.01  3.000
 TDF  HN   N    CA   109.94  3.000
 TDF  HA   CA   CB   109.00  3.000
 TDF  HA   CA   N    110.00  3.000
 TDF  CB   CA   N    110.40  1.500
 TDF  HA   CA   C    110.00  3.000
 TDF  CB   CA   C    110.50  1.500
 TDF  N    CA   C    111.00  2.800
 TDF  HBA  CB   HB   107.10  3.000
 TDF  HBA  CB   CG   109.27  3.000
 TDF  HB   CB   CG   109.93  3.000
 TDF  HBA  CB   CA   108.20  3.000
 TDF  HB   CB   CA   108.55  3.000
 TDF  CG   CB   CA   113.57  3.000
 TDF  CD2  CG   CD1  118.10  3.000
 TDF  CD2  CG   CB   120.50  3.000
 TDF  CD1  CG   CB   121.39  3.000
 TDF  CE2  CZ   CE1  119.64  3.000
 TDF  CE2  CZ   C13  118.66  3.000
 TDF  CE1  CZ   C13  121.69  3.000
 TDF  F21  C13  F20  107.07  3.000
 TDF  F21  C13  F19  106.69  3.000
 TDF  F20  C13  F19  106.12  3.000
 TDF  F21  C13  CZ   112.88  3.000
 TDF  F20  C13  CZ   111.75  3.000
 TDF  F19  C13  CZ   111.91  3.000
 TDF  HD1  CD1  CE1  119.22  3.000
 TDF  HD1  CD1  CG   119.47  3.000
 TDF  CE1  CD1  CG   121.31  3.000
 TDF  HD2  CD2  CE2  119.25  3.000
 TDF  HD2  CD2  CG   119.58  3.000
 TDF  CE2  CD2  CG   121.17  3.000
 TDF  HE1  CE1  CD1  119.05  3.000
 TDF  HE1  CE1  CZ   121.14  3.000
 TDF  CD1  CE1  CZ   119.81  3.000
 TDF  HE2  CE2  CD2  119.29  3.000
 TDF  HE2  CE2  CZ   120.74  3.000
 TDF  CD2  CE2  CZ   119.97  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
 TDF  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 TDF  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 TDF  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 TDF  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 TDF  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 TDF  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 TDF  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 TDF  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 TDF  CONST_09  CD1  CE1  CZ   C13  180.00   0.0  0
 TDF  CONST_10  CD2  CE2  CZ   C13  180.00   0.0  0
 TDF  CONST_11  HE1  CE1  CD1  CG   180.00   0.0  0
 TDF  CONST_12  HE2  CE2  CD2  CG   180.00   0.0  0
 TDF  CONST_13  HD1  CD1  CE1  CZ   180.00   0.0  0
 TDF  CONST_14  HD2  CD2  CE2  CZ   180.00   0.0  0
 TDF  Var_01    CD1  CG   CB   CA   105.31  30.0  2
 TDF  Var_02    CE1  CZ   C13  F19  116.20  30.0  2

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
 TDF  chir_01  CA  C  N  CB  positiv

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
 TDF  plan-1  CB   0.020
 TDF  plan-1  CG   0.020
 TDF  plan-1  CZ   0.020
 TDF  plan-1  C13  0.020
 TDF  plan-1  CD1  0.020
 TDF  plan-1  CD2  0.020
 TDF  plan-1  CE1  0.020
 TDF  plan-1  CE2  0.020
 TDF  plan-1  HD1  0.020
 TDF  plan-1  HD2  0.020
 TDF  plan-1  HE1  0.020
 TDF  plan-1  HE2  0.020
 TDF  plan-2  C    0.020
 TDF  plan-2  O    0.020
 TDF  plan-2  CA   0.020
 TDF  plan-2  OXT  0.020

