# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:01:28 2022
#   Inital geometry file: a 57 line input string
#   Ligand name: 3-(2-fluoro-1H-imidazol-3-ium-4-yl)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1c[nH]c(F)[nH+]1)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
 2HF  2HF  3-(2-fluoro-1H-imidazol-3-ium-4-yl)-L-alanine  L-peptide  20  12  .  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_2HF
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
 2HF  C     C  C      0   0.423  -52.7232  11.2709  -0.5896
 2HF  N     N  NH2    0  -0.811  -54.1598  10.9655   1.4149
 2HF  O     O  O      0  -0.597  -51.9725  12.0364  -1.2220
 2HF  F1    F  F      0  -0.211  -56.3248  16.0181   2.8009
 2HF  CA    C  CH1    0  -0.224  -53.6518  11.9373   0.4656
 2HF  CB    C  CH2    0  -0.503  -52.9107  13.0572   1.2080
 2HF  CG    C  CR5    0   0.337  -53.7863  13.7711   2.1669
 2HF  ND1   N  NR15   1  -0.636  -54.7375  14.6972   1.7609
 2HF  CD2   C  CR15   0  -0.123  -53.9146  13.6771   3.5102
 2HF  CE1   C  CR5    0   0.846  -55.3864  15.1324   2.8191
 2HF  NE2   N  NR15   0  -0.593  -54.9221  14.5424   3.8952
 2HF  OXT   O  OC    -1  -0.590  -52.8421  10.0402  -0.7364
 2HF  H     H  HNH2   0   0.336  -55.0862  11.2211   1.7284
 2HF  H2    H  HNH2   0   0.340  -54.2409  10.0788   0.9342
 2HF  HA    H  HCH1   0   0.216  -54.4585  12.4093  -0.1207
 2HF  HB    H  HCH2   0   0.257  -52.0778  12.6296   1.7681
 2HF  HBA   H  HCH2   0   0.264  -52.4950  13.7681   0.4935
 2HF  HND1  H  HNR5   0   0.468  -54.9087  15.0001   0.8085
 2HF  HD2   H  HCR5   0   0.329  -53.3796  13.0776   4.2247
 2HF  HE2   H  HNR5   0   0.471  -55.2506  14.7009   4.8404

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
 2HF  C    O     deloc     1.231  0.020  1.231
 2HF  C    CA    single    1.525  0.021  1.525
 2HF  C    OXT   deloc     1.245  0.020  1.245
 2HF  N    CA    single    1.458  0.019  1.458
 2HF  N    H     single    0.860  0.020  0.860
 2HF  N    H2    single    0.890  0.020  1.040
 2HF  F1   CE1   single    1.290  0.020  1.290
 2HF  CA   CB    single    1.530  0.020  1.530
 2HF  CA   HA    single    0.970  0.020  0.970
 2HF  CB   CG    single    1.482  0.020  1.482
 2HF  CB   HB    single    0.970  0.020  1.090
 2HF  CB   HBA   single    0.970  0.020  1.090
 2HF  CG   ND1   aromatic  1.388  0.020  1.388
 2HF  CG   CD2   aromatic  1.353  0.020  1.353
 2HF  ND1  CE1   aromatic  1.315  0.020  1.315
 2HF  ND1  HND1  single    0.860  0.020  1.020
 2HF  CD2  NE2   aromatic  1.383  0.020  1.383
 2HF  CD2  HD2   single    0.930  0.020  1.080
 2HF  CE1  NE2   aromatic  1.312  0.020  1.312
 2HF  NE2  HE2   single    0.860  0.020  1.020

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
 2HF  OXT   C    CA   116.51  3.000
 2HF  OXT   C    O    127.27  3.000
 2HF  CA    C    O    120.80  1.700
 2HF  H2    N    H    107.19  3.000
 2HF  H2    N    CA   107.71  3.000
 2HF  H     N    CA   114.00  3.000
 2HF  HA    CA   CB   109.00  3.000
 2HF  HA    CA   N    110.00  3.000
 2HF  CB    CA   N    110.50  1.700
 2HF  HA    CA   C    109.00  3.000
 2HF  CB    CA   C    110.10  1.900
 2HF  N     CA   C    111.00  2.800
 2HF  HBA   CB   HB   107.51  3.000
 2HF  HBA   CB   CG   109.58  3.000
 2HF  HB    CB   CG   107.92  3.000
 2HF  HBA   CB   CA   110.06  3.000
 2HF  HB    CB   CA   109.33  3.000
 2HF  CG    CB   CA   112.29  3.000
 2HF  CD2   CG   ND1  105.77  3.000
 2HF  CD2   CG   CB   131.69  3.000
 2HF  ND1   CG   CB   122.48  3.000
 2HF  HND1  ND1  CE1  125.00  3.000
 2HF  HND1  ND1  CG   126.13  3.000
 2HF  CE1   ND1  CG   108.87  3.000
 2HF  HD2   CD2  NE2  121.76  3.000
 2HF  HD2   CD2  CG   130.66  3.000
 2HF  NE2   CD2  CG   107.58  3.000
 2HF  NE2   CE1  ND1  109.66  3.000
 2HF  NE2   CE1  F1   125.27  3.000
 2HF  ND1   CE1  F1   125.06  3.000
 2HF  HE2   NE2  CE1  125.46  3.000
 2HF  HE2   NE2  CD2  126.43  3.000
 2HF  CE1   NE2  CD2  108.11  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
 2HF  CONST_01  NE2   CE1  ND1  CG     0.00   0.0  0
 2HF  CONST_02  CE1   NE2  CD2  CG     0.00   0.0  0
 2HF  CONST_03  NE2   CD2  CG   ND1    0.00   0.0  0
 2HF  CONST_04  CD2   NE2  CE1  ND1    0.00   0.0  0
 2HF  CONST_05  CE1   ND1  CG   CD2    0.00   0.0  0
 2HF  CONST_06  CG    ND1  CE1  F1   180.00   0.0  0
 2HF  CONST_07  CD2   NE2  CE1  F1   180.00   0.0  0
 2HF  CONST_08  CE1   ND1  CG   CB   180.00   0.0  0
 2HF  CONST_09  NE2   CD2  CG   CB   180.00   0.0  0
 2HF  CONST_10  HE2   NE2  CD2  CG   180.00   0.0  0
 2HF  CONST_11  HD2   CD2  CG   ND1  180.00   0.0  0
 2HF  CONST_12  HND1  ND1  CG   CD2  180.00   0.0  0
 2HF  Var_01    ND1   CG   CB   CA   -75.97  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
 2HF  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
 2HF  plan-1  F1    0.020
 2HF  plan-1  CB    0.020
 2HF  plan-1  CG    0.020
 2HF  plan-1  ND1   0.020
 2HF  plan-1  CD2   0.020
 2HF  plan-1  CE1   0.020
 2HF  plan-1  NE2   0.020
 2HF  plan-1  HND1  0.020
 2HF  plan-1  HD2   0.020
 2HF  plan-1  HE2   0.020
 2HF  plan-2  C     0.020
 2HF  plan-2  O     0.020
 2HF  plan-2  CA    0.020
 2HF  plan-2  OXT   0.020

