# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 01:03:37 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: 2,3,4,5,6-pentafluoro-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1c(F)c(F)c(F)c(F)c1F)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
 PF5  PF5  2,3,4,5,6-pentafluoro-L-phenylalanine  L-peptide  22  17  .  2012-08-28  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_PF5
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
 PF5  N    N  NH2    0  -0.782   3.4328  -4.2372  -2.0606
 PF5  CA   C  CH1    0  -0.214   3.5071  -3.1731  -3.0449
 PF5  CB   C  CH2    0  -0.496   2.8087  -1.9099  -2.5068
 PF5  CG   C  CR6    0  -0.275   1.4001  -2.2066  -2.0922
 PF5  CD1  C  CR6    0   0.417   1.0739  -2.5421  -0.7880
 PF5  FD1  F  F      0  -0.293   2.0056  -2.5099   0.1638
 PF5  CD2  C  CR6    0   0.414   0.3677  -2.2452  -3.0162
 PF5  FD2  F  F      0  -0.295   0.6083  -1.9361  -4.2917
 PF5  CE1  C  CR6    0   0.266  -0.2063  -2.9077  -0.4185
 PF5  FE1  F  F      0  -0.294  -0.4819  -3.2338   0.8416
 PF5  CE2  C  CR6    0   0.271  -0.9220  -2.6104  -2.6770
 PF5  FE2  F  F      0  -0.293  -1.8795  -2.6455  -3.6001
 PF5  CZ   C  CR6    0   0.267  -1.2083  -2.9484  -1.3688
 PF5  FZ   F  F      0  -0.290  -2.4362  -3.3152  -1.0214
 PF5  C    C  C      0   0.389   4.9352  -2.7914  -3.5286
 PF5  O    O  O      0  -0.609   4.9832  -1.9279  -4.4275
 PF5  OXT  O  OC    -1  -0.591   5.8955  -3.3647  -2.9815
 PF5  H    H  HNH2   0   0.339   3.6568  -5.1152  -2.5120
 PF5  H2   H  HNH2   0   0.326   4.1797  -4.0982  -1.3895
 PF5  HA   H  HCH1   0   0.230   2.9443  -3.5019  -3.9255
 PF5  HB2  H  HCH2   0   0.254   3.3699  -1.5155  -1.6576
 PF5  HB3  H  HCH2   0   0.261   2.8210  -1.1345  -3.2706

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
 PF5  N    CA   single    1.458  0.019  1.458
 PF5  N    H    single    0.860  0.020  0.860
 PF5  N    H2   single    0.890  0.020  1.040
 PF5  CA   C    single    1.525  0.021  1.525
 PF5  CA   CB   single    1.530  0.020  1.530
 PF5  CA   HA   single    0.970  0.020  0.970
 PF5  CB   CG   single    1.498  0.020  1.498
 PF5  CB   HB2  single    0.970  0.020  1.090
 PF5  CB   HB3  single    0.970  0.020  1.090
 PF5  CG   CD2  aromatic  1.386  0.020  1.386
 PF5  CG   CD1  aromatic  1.386  0.020  1.386
 PF5  CD1  CE1  aromatic  1.382  0.020  1.382
 PF5  CD1  FD1  single    1.332  0.020  1.332
 PF5  CD2  FD2  single    1.334  0.020  1.334
 PF5  CD2  CE2  aromatic  1.383  0.020  1.383
 PF5  CE1  CZ   aromatic  1.382  0.020  1.382
 PF5  CE1  FE1  single    1.330  0.020  1.330
 PF5  CE2  FE2  single    1.331  0.020  1.331
 PF5  CE2  CZ   aromatic  1.381  0.020  1.381
 PF5  CZ   FZ   single    1.328  0.020  1.328
 PF5  C    O    deloc     1.231  0.020  1.231
 PF5  C    OXT  deloc     1.245  0.020  1.245

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
 PF5  H2   N    H    104.55  3.000
 PF5  H2   N    CA   108.10  3.000
 PF5  H    N    CA   114.00  3.000
 PF5  HA   CA   C    109.00  3.000
 PF5  HA   CA   CB   109.00  3.000
 PF5  C    CA   CB   110.10  1.900
 PF5  HA   CA   N    110.00  3.000
 PF5  CB   CA   N    110.50  1.700
 PF5  C    CA   N    111.00  2.800
 PF5  HB3  CB   HB2  106.42  3.000
 PF5  HB3  CB   CG   110.24  3.000
 PF5  HB2  CB   CG   109.85  3.000
 PF5  HB3  CB   CA   109.51  3.000
 PF5  HB2  CB   CA   109.57  3.000
 PF5  CG   CB   CA   111.13  3.000
 PF5  CD2  CG   CD1  116.45  3.000
 PF5  CD1  CG   CB   121.99  3.000
 PF5  CD2  CG   CB   121.42  3.000
 PF5  CE1  CD1  FD1  117.59  3.000
 PF5  FD1  CD1  CG   120.13  3.000
 PF5  CE1  CD1  CG   122.27  3.000
 PF5  CE2  CD2  FD2  117.64  3.000
 PF5  CE2  CD2  CG   122.58  3.000
 PF5  FD2  CD2  CG   119.77  3.000
 PF5  CZ   CE1  FE1  119.61  3.000
 PF5  FE1  CE1  CD1  120.67  3.000
 PF5  CZ   CE1  CD1  119.72  3.000
 PF5  CZ   CE2  FE2  120.10  3.000
 PF5  CZ   CE2  CD2  119.37  3.000
 PF5  FE2  CE2  CD2  120.53  3.000
 PF5  FZ   CZ   CE2  120.47  3.000
 PF5  FZ   CZ   CE1  119.92  3.000
 PF5  CE2  CZ   CE1  119.60  3.000
 PF5  OXT  C    O    127.28  3.000
 PF5  OXT  C    CA   117.29  3.000
 PF5  O    C    CA   120.80  1.700

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
 PF5  CONST_01  CZ   CE2  CD2  CG     0.00   0.0  0
 PF5  CONST_02  CZ   CE1  CD1  CG     0.00   0.0  0
 PF5  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 PF5  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 PF5  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 PF5  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 PF5  CONST_07  CE2  CD2  CG   CB   180.00   0.0  0
 PF5  CONST_08  CE1  CD1  CG   CB   180.00   0.0  0
 PF5  CONST_09  FE2  CE2  CD2  CG   180.00   0.0  0
 PF5  CONST_10  FE1  CE1  CD1  CG   180.00   0.0  0
 PF5  CONST_11  FD2  CD2  CG   CD1  180.00   0.0  0
 PF5  CONST_12  FZ   CZ   CE1  CD1  180.00   0.0  0
 PF5  CONST_13  CD2  CG   CD1  FD1  180.00   0.0  0
 PF5  CONST_14  CZ   CE1  CD1  FD1  180.00   0.0  0
 PF5  CONST_15  FZ   CZ   CE2  CD2  180.00   0.0  0
 PF5  CONST_16  CZ   CE2  CD2  FD2  180.00   0.0  0
 PF5  CONST_17  FE2  CE2  CZ   CE1  180.00   0.0  0
 PF5  CONST_18  CE2  CZ   CE1  FE1  180.00   0.0  0
 PF5  Var_01    CD2  CG   CB   CA   -82.35  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
 PF5  chir_01  CA  N  C  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
 PF5  plan-1  CB   0.020
 PF5  plan-1  CG   0.020
 PF5  plan-1  CD1  0.020
 PF5  plan-1  FD1  0.020
 PF5  plan-1  CD2  0.020
 PF5  plan-1  FD2  0.020
 PF5  plan-1  CE1  0.020
 PF5  plan-1  FE1  0.020
 PF5  plan-1  CE2  0.020
 PF5  plan-1  FE2  0.020
 PF5  plan-1  CZ   0.020
 PF5  plan-1  FZ   0.020
 PF5  plan-2  CA   0.020
 PF5  plan-2  C    0.020
 PF5  plan-2  O    0.020
 PF5  plan-2  OXT  0.020

