# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 13:07:05 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: 3,4-difluoro-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(F)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
 F2F  F2F  3,4-difluoro-L-phenylalanine  L-peptide  22  14  .  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_F2F
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
 F2F  O    O  O      0  -0.601  32.2449  -17.2546  -5.1133
 F2F  C    C  C      0   0.417  32.3368  -17.6661  -3.9411
 F2F  CA   C  CH1    0  -0.213  31.1157  -18.4471  -3.3820
 F2F  N    N  NH2    0  -0.808  31.1434  -18.4885  -1.9293
 F2F  CB   C  CH2    0  -0.490  29.7847  -17.8601  -3.8677
 F2F  CG   C  CR6    0   0.131  28.6173  -18.6948  -3.4281
 F2F  CD2  C  CR16   0  -0.455  28.2778  -19.8403  -4.1485
 F2F  CE2  C  CR6    0   0.409  27.2600  -20.6596  -3.7118
 F2F  F2   F  F      0  -0.310  26.9361  -21.7606  -4.4029
 F2F  CZ   C  CR6    0   0.371  26.5617  -20.3631  -2.5538
 F2F  F1   F  F      0  -0.310  25.5969  -21.1959  -2.1416
 F2F  CE1  C  CR16   0  -0.391  26.8669  -19.2261  -1.8369
 F2F  CD1  C  CR16   0  -0.305  27.8936  -18.3990  -2.2765
 F2F  OXT  O  OC    -1  -0.598  33.3240  -17.5598  -3.1865
 F2F  HA   H  HCH1   0   0.203  31.1969  -19.4566  -3.8244
 F2F  HN   H  HNH2   0   0.333  30.6497  -19.3043  -1.5921
 F2F  HNA  H  HNH2   0   0.335  32.1079  -18.5830  -1.6397
 F2F  HB   H  HCH2   0   0.229  29.6812  -16.8425  -3.4820
 F2F  HBA  H  HCH2   0   0.236  29.8027  -17.7967  -4.9556
 F2F  HD2  H  HCR6   0   0.277  28.8110  -20.1007  -5.0554
 F2F  HE1  H  HCR6   0   0.284  26.3116  -18.9919  -0.9378
 F2F  HD1  H  HCR6   0   0.257  28.1346  -17.5106  -1.7073

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
 F2F  O    C    deloc     1.231  0.020  1.231
 F2F  C    CA   single    1.525  0.021  1.525
 F2F  C    OXT  deloc     1.247  0.020  1.247
 F2F  CA   N    single    1.458  0.019  1.458
 F2F  CA   CB   single    1.530  0.020  1.530
 F2F  CA   HA   single    0.970  0.020  0.970
 F2F  N    HN   single    0.890  0.020  1.040
 F2F  N    HNA  single    0.890  0.020  1.040
 F2F  CB   CG   single    1.501  0.020  1.501
 F2F  CB   HB   single    0.970  0.020  1.090
 F2F  CB   HBA  single    0.970  0.020  1.090
 F2F  CG   CD2  aromatic  1.395  0.020  1.395
 F2F  CG   CD1  aromatic  1.392  0.020  1.392
 F2F  CD2  CE2  aromatic  1.378  0.020  1.378
 F2F  CD2  HD2  single    0.930  0.020  1.080
 F2F  CE2  F2   single    1.340  0.020  1.340
 F2F  CE2  CZ   aromatic  1.384  0.020  1.384
 F2F  CZ   F1   single    1.340  0.020  1.340
 F2F  CZ   CE1  aromatic  1.378  0.020  1.378
 F2F  CE1  CD1  aromatic  1.390  0.020  1.390
 F2F  CE1  HE1  single    0.930  0.020  1.080
 F2F  CD1  HD1  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
 F2F  OXT  C    CA   116.57  3.000
 F2F  OXT  C    O    126.84  3.000
 F2F  CA   C    O    120.80  1.700
 F2F  HA   CA   CB   109.00  3.000
 F2F  HA   CA   N    110.00  3.000
 F2F  CB   CA   N    110.50  1.700
 F2F  HA   CA   C    109.00  3.000
 F2F  CB   CA   C    110.10  1.900
 F2F  N    CA   C    111.00  2.800
 F2F  HNA  N    HN   107.14  3.000
 F2F  HNA  N    CA   107.88  3.000
 F2F  HN   N    CA   110.30  3.000
 F2F  HBA  CB   HB   107.44  3.000
 F2F  HBA  CB   CG   109.72  3.000
 F2F  HB   CB   CG   109.92  3.000
 F2F  HBA  CB   CA   108.91  3.000
 F2F  HB   CB   CA   109.07  3.000
 F2F  CG   CB   CA   111.67  3.000
 F2F  CD1  CG   CD2  118.37  3.000
 F2F  CD1  CG   CB   121.90  3.000
 F2F  CD2  CG   CB   119.65  3.000
 F2F  HD2  CD2  CE2  119.06  3.000
 F2F  HD2  CD2  CG   120.64  3.000
 F2F  CE2  CD2  CG   120.30  3.000
 F2F  CZ   CE2  F2   119.05  3.000
 F2F  CZ   CE2  CD2  120.69  3.000
 F2F  F2   CE2  CD2  120.26  3.000
 F2F  CE1  CZ   F1   120.81  3.000
 F2F  CE1  CZ   CE2  120.00  3.000
 F2F  F1   CZ   CE2  119.18  3.000
 F2F  HE1  CE1  CD1  120.86  3.000
 F2F  HE1  CE1  CZ   119.79  3.000
 F2F  CD1  CE1  CZ   119.34  3.000
 F2F  HD1  CD1  CE1  119.13  3.000
 F2F  HD1  CD1  CG   119.59  3.000
 F2F  CE1  CD1  CG   121.28  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
 F2F  CONST_01  CZ   CE2  CD2  CG     0.00   0.0  0
 F2F  CONST_02  CZ   CE1  CD1  CG     0.00   0.0  0
 F2F  CONST_03  CE1  CD1  CG   CD2    0.00   0.0  0
 F2F  CONST_04  CE1  CZ   CE2  CD2    0.00   0.0  0
 F2F  CONST_05  CD1  CG   CD2  CE2    0.00   0.0  0
 F2F  CONST_06  CD1  CE1  CZ   CE2    0.00   0.0  0
 F2F  CONST_07  CE2  CD2  CG   CB   180.00   0.0  0
 F2F  CONST_08  CE1  CD1  CG   CB   180.00   0.0  0
 F2F  CONST_09  F2   CE2  CD2  CG   180.00   0.0  0
 F2F  CONST_10  F1   CZ   CE2  CD2  180.00   0.0  0
 F2F  CONST_11  CE1  CZ   CE2  F2   180.00   0.0  0
 F2F  CONST_12  CD1  CE1  CZ   F1   180.00   0.0  0
 F2F  CONST_13  HE1  CE1  CD1  CG   180.00   0.0  0
 F2F  CONST_14  HD1  CD1  CG   CD2  180.00   0.0  0
 F2F  CONST_15  HD2  CD2  CE2  CZ   180.00   0.0  0
 F2F  Var_01    CD2  CG   CB   CA   -81.29  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
 F2F  chir_01  CA  C  N  CB  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
 F2F  plan-1  CB   0.020
 F2F  plan-1  CG   0.020
 F2F  plan-1  CD2  0.020
 F2F  plan-1  CE2  0.020
 F2F  plan-1  F2   0.020
 F2F  plan-1  CZ   0.020
 F2F  plan-1  F1   0.020
 F2F  plan-1  CE1  0.020
 F2F  plan-1  CD1  0.020
 F2F  plan-1  HD2  0.020
 F2F  plan-1  HE1  0.020
 F2F  plan-1  HD1  0.020
 F2F  plan-2  O    0.020
 F2F  plan-2  C    0.020
 F2F  plan-2  CA   0.020
 F2F  plan-2  OXT  0.020

