# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 13:32:19 2022
#   Inital geometry file: a 54 line input string
#   Ligand name: (4S)-5-fluoro-L-leucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CF)C[C@H](N)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
 LEF  LEF  '(4S)-5-fluoro-L-leucine  '  L-peptide  21  10  .  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_LEF
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
 LEF  CD1   C  CH2    0   0.018  25.8514  26.1767  17.3429
 LEF  CD2   C  CH3    0  -0.675  24.2885  25.2395  18.9905
 LEF  CG    C  CH1    0  -0.317  25.6512  25.9091  18.8210
 LEF  CB    C  CH2    0  -0.382  26.7864  25.0623  19.4019
 LEF  N     N  NH2    0  -0.816  26.7688  26.1577  21.5937
 LEF  CA    C  CH1    0  -0.232  26.7189  24.8683  20.9164
 LEF  C     C  C      0   0.417  27.8426  23.9296  21.4330
 LEF  O     O  O      0  -0.602  28.3727  24.2311  22.5220
 LEF  F1    F  F      0  -0.385  27.0188  26.9054  17.1062
 LEF  OXT   O  OC    -1  -0.604  28.0914  22.9233  20.7408
 LEF  HD12  H  HCH2   0   0.191  25.9250  25.2381  16.7858
 LEF  HD13  H  HCH2   0   0.205  25.0182  26.7561  16.9379
 LEF  HD21  H  HCH3   0   0.219  24.2707  24.2602  18.5067
 LEF  HD22  H  HCH3   0   0.240  24.0435  25.0903  20.0414
 LEF  HD23  H  HCH3   0   0.230  23.4898  25.8422  18.5546
 LEF  HG    H  HCH1   0   0.225  25.6237  26.8789  19.3301
 LEF  HB3   H  HCH2   0   0.208  27.7471  25.5268  19.1595
 LEF  HB2   H  HCH2   0   0.202  26.7746  24.0849  18.9128
 LEF  HA    H  HCH1   0   0.198  25.7847  24.3270  21.1458
 LEF  H     H  HNH2   0   0.329  25.8389  26.5466  21.6766
 LEF  H2    H  HNH2   0   0.332  27.1034  25.9952  22.5348

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
 LEF  CD1  CG    single  1.515  0.020  1.515
 LEF  CD1  F1    single  1.396  0.020  1.396
 LEF  CD1  HD12  single  0.970  0.020  1.090
 LEF  CD1  HD13  single  0.970  0.020  1.090
 LEF  CD2  CG    single  1.528  0.020  1.528
 LEF  CD2  HD21  single  0.970  0.020  1.090
 LEF  CD2  HD22  single  0.970  0.020  1.090
 LEF  CD2  HD23  single  0.970  0.020  1.090
 LEF  CG   CB    single  1.531  0.020  1.531
 LEF  CG   HG    single  0.970  0.020  1.090
 LEF  CB   CA    single  1.530  0.020  1.530
 LEF  CB   HB3   single  0.970  0.020  1.090
 LEF  CB   HB2   single  0.970  0.020  1.090
 LEF  N    CA    single  1.458  0.019  1.458
 LEF  N    H     single  0.860  0.020  0.860
 LEF  N    H2    single  0.890  0.020  1.040
 LEF  CA   C     single  1.525  0.021  1.525
 LEF  CA   HA    single  0.970  0.020  0.970
 LEF  C    O     deloc   1.231  0.020  1.231
 LEF  C    OXT   deloc   1.246  0.020  1.246

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
 LEF  HD13  CD1  HD12  108.51  3.000
 LEF  HD13  CD1  F1    107.34  3.000
 LEF  HD12  CD1  F1    107.77  3.000
 LEF  HD13  CD1  CG    110.76  3.000
 LEF  HD12  CD1  CG    110.74  3.000
 LEF  F1    CD1  CG    111.58  3.000
 LEF  HD23  CD2  HD22  107.24  3.000
 LEF  HD23  CD2  HD21  107.83  3.000
 LEF  HD22  CD2  HD21  107.50  3.000
 LEF  HD23  CD2  CG    111.50  3.000
 LEF  HD22  CD2  CG    111.58  3.000
 LEF  HD21  CD2  CG    111.00  3.000
 LEF  HG    CG   CB    109.39  3.000
 LEF  HG    CG   CD2   108.30  3.000
 LEF  CB    CG   CD2   112.14  3.000
 LEF  HG    CG   CD1   107.48  3.000
 LEF  CB    CG   CD1   111.71  3.000
 LEF  CD2   CG   CD1   107.66  3.000
 LEF  HB2   CB   HB3   106.85  3.000
 LEF  HB2   CB   CA    109.24  3.000
 LEF  HB3   CB   CA    108.19  3.000
 LEF  HB2   CB   CG    108.47  3.000
 LEF  HB3   CB   CG    109.39  3.000
 LEF  CA    CB   CG    114.43  3.000
 LEF  H2    N    H     106.83  3.000
 LEF  H2    N    CA    107.54  3.000
 LEF  H     N    CA    114.00  3.000
 LEF  HA    CA   C     109.00  3.000
 LEF  HA    CA   N     110.00  3.000
 LEF  C     CA   N     111.00  2.800
 LEF  HA    CA   CB    109.00  3.000
 LEF  C     CA   CB    110.10  1.900
 LEF  N     CA   CB    110.50  1.700
 LEF  OXT   C    O     126.50  3.000
 LEF  OXT   C    CA    116.61  3.000
 LEF  O     C    CA    120.80  1.700

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
 LEF  chir_01  CG  CD1  CD2  CB  negativ
 LEF  chir_02  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
 LEF  plan-1  CA   0.020
 LEF  plan-1  C    0.020
 LEF  plan-1  O    0.020
 LEF  plan-1  OXT  0.020

