# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 15:19:31 2022
#   Inital geometry file: a 64 line input string
#   Ligand name: 3,5-difluoro-L-tyrosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1cc(F)c(O)c(F)c1)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
 F2Y  F2Y  '3,5-difluoro-L-tyrosine  '  L-peptide  23  15  .  2016-04-22  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_F2Y
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
 F2Y  OXT  O  OC    -1  -0.614  23.6164  38.2345   -5.5750
 F2Y  C    C  C      0   0.382  23.7131  37.6275   -6.6616
 F2Y  O    O  O      0  -0.596  23.9604  36.4171   -6.8235
 F2Y  CA   C  CH1    0  -0.208  23.4850  38.4899   -7.9361
 F2Y  N    N  NH2    0  -0.778  23.7566  37.8314   -9.2020
 F2Y  CB   C  CH2    0  -0.518  22.0470  39.0331   -7.9274
 F2Y  CG   C  CR6    0   0.169  21.7935  40.0639   -8.9878
 F2Y  CD1  C  CR16   0  -0.483  21.2873  39.7154  -10.2370
 F2Y  CE1  C  CR6    0   0.483  21.0895  40.6834  -11.1980
 F2Y  F1   F  F      0  -0.314  20.6038  40.3390  -12.4007
 F2Y  CD2  C  CR16   0  -0.481  22.0902  41.4015   -8.7449
 F2Y  CE2  C  CR6    0   0.473  21.8811  42.3435   -9.7296
 F2Y  F2   F  F      0  -0.321  22.1639  43.6372   -9.4858
 F2Y  CZ   C  CR6    0   0.051  21.3774  42.0263  -10.9846
 F2Y  OH   O  OH1    0  -0.618  21.1552  42.9105  -11.9732
 F2Y  H2   H  HCH1   0   0.219  24.1564  39.3542   -7.8652
 F2Y  H3   H  HNH2   0   0.334  24.7398  37.5916   -9.2386
 F2Y  H4   H  HNH2   0   0.322  23.2794  36.9367   -9.1982
 F2Y  H6   H  HCH2   0   0.246  21.8485  39.4678   -6.9474
 F2Y  H7   H  HCH2   0   0.236  21.3507  38.1971   -8.0503
 F2Y  H8   H  HCR6   0   0.268  21.0401  38.6865  -10.4648
 F2Y  H9   H  HCR6   0   0.272  22.4833  41.7166   -7.7856
 F2Y  H10  H  HOH1   0   0.477  21.3761  43.8056  -11.6907

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
 F2Y  F1   CE1  single    1.342  0.020  1.342
 F2Y  OH   CZ   single    1.345  0.020  1.345
 F2Y  CE1  CZ   aromatic  1.390  0.020  1.390
 F2Y  CE1  CD1  aromatic  1.378  0.020  1.378
 F2Y  CZ   CE2  aromatic  1.389  0.020  1.389
 F2Y  CD1  CG   aromatic  1.392  0.020  1.392
 F2Y  CE2  F2   single    1.346  0.020  1.346
 F2Y  CE2  CD2  aromatic  1.379  0.020  1.379
 F2Y  N    CA   single    1.458  0.019  1.458
 F2Y  CG   CD2  aromatic  1.392  0.020  1.392
 F2Y  CG   CB   single    1.500  0.020  1.500
 F2Y  CB   CA   single    1.521  0.033  1.521
 F2Y  CA   C    single    1.525  0.021  1.525
 F2Y  O    C    deloc     1.231  0.020  1.231
 F2Y  C    OXT  deloc     1.248  0.020  1.248
 F2Y  CA   H2   single    0.970  0.020  1.090
 F2Y  N    H3   single    0.890  0.020  1.040
 F2Y  N    H4   single    0.890  0.020  1.040
 F2Y  CB   H6   single    0.970  0.020  1.090
 F2Y  CB   H7   single    0.970  0.020  1.090
 F2Y  CD1  H8   single    0.930  0.020  1.080
 F2Y  CD2  H9   single    0.930  0.020  1.080
 F2Y  OH   H10  single    0.850  0.020  0.980

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
 F2Y  CA   C    O    120.80  1.700
 F2Y  O    C    OXT  126.93  3.000
 F2Y  CA   C    OXT  120.80  1.700
 F2Y  H2   CA   CB   107.08  3.000
 F2Y  H2   CA   N    107.41  3.000
 F2Y  CB   CA   N    110.40  1.500
 F2Y  H2   CA   C    107.11  3.000
 F2Y  CB   CA   C    110.50  1.500
 F2Y  N    CA   C    111.00  2.800
 F2Y  H4   N    H3   104.36  3.000
 F2Y  H4   N    CA   107.98  3.000
 F2Y  H3   N    CA   108.69  3.000
 F2Y  H7   CB   H6   106.83  3.000
 F2Y  H7   CB   CG   109.74  3.000
 F2Y  H6   CB   CG   109.31  3.000
 F2Y  H7   CB   CA   108.93  3.000
 F2Y  H6   CB   CA   108.44  3.000
 F2Y  CG   CB   CA   113.38  3.000
 F2Y  CD2  CG   CD1  118.34  3.000
 F2Y  CD2  CG   CB   120.06  3.000
 F2Y  CD1  CG   CB   121.58  3.000
 F2Y  H8   CD1  CE1  119.22  3.000
 F2Y  H8   CD1  CG   120.65  3.000
 F2Y  CE1  CD1  CG   120.13  3.000
 F2Y  CZ   CE1  F1   117.42  3.000
 F2Y  CZ   CE1  CD1  122.81  3.000
 F2Y  F1   CE1  CD1  119.77  3.000
 F2Y  H9   CD2  CE2  119.25  3.000
 F2Y  H9   CD2  CG   120.76  3.000
 F2Y  CE2  CD2  CG   119.99  3.000
 F2Y  CZ   CE2  F2   117.33  3.000
 F2Y  F2   CE2  CD2  119.69  3.000
 F2Y  CZ   CE2  CD2  122.97  3.000
 F2Y  OH   CZ   CE2  125.03  3.000
 F2Y  CE2  CZ   CE1  115.75  3.000
 F2Y  OH   CZ   CE1  119.22  3.000
 F2Y  H10  OH   CZ   110.92  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
 F2Y  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 F2Y  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 F2Y  CONST_03  CE2  CZ   CE1  CD1    0.00   0.0  0
 F2Y  CONST_04  CE2  CD2  CG   CD1    0.00   0.0  0
 F2Y  CONST_05  CD2  CE2  CZ   CE1    0.00   0.0  0
 F2Y  CONST_06  CD2  CG   CD1  CE1    0.00   0.0  0
 F2Y  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 F2Y  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 F2Y  CONST_09  F1   CE1  CD1  CG   180.00   0.0  0
 F2Y  CONST_10  F2   CE2  CD2  CG   180.00   0.0  0
 F2Y  CONST_11  OH   CZ   CE1  CD1  180.00   0.0  0
 F2Y  CONST_12  F2   CE2  CZ   CE1  180.00   0.0  0
 F2Y  CONST_13  CE2  CZ   CE1  F1   180.00   0.0  0
 F2Y  CONST_14  OH   CZ   CE2  CD2  180.00   0.0  0
 F2Y  CONST_15  H9   CD2  CG   CD1  180.00   0.0  0
 F2Y  CONST_16  H8   CD1  CG   CD2  180.00   0.0  0
 F2Y  Var_01    CD1  CG   CB   CA    92.84  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
 F2Y  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
 F2Y  plan-1  CB   0.020
 F2Y  plan-1  CG   0.020
 F2Y  plan-1  CD1  0.020
 F2Y  plan-1  CE1  0.020
 F2Y  plan-1  F1   0.020
 F2Y  plan-1  CD2  0.020
 F2Y  plan-1  CE2  0.020
 F2Y  plan-1  F2   0.020
 F2Y  plan-1  CZ   0.020
 F2Y  plan-1  OH   0.020
 F2Y  plan-1  H8   0.020
 F2Y  plan-1  H9   0.020
 F2Y  plan-2  OXT  0.020
 F2Y  plan-2  C    0.020
 F2Y  plan-2  O    0.020
 F2Y  plan-2  CA   0.020

