# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 03:37:15 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: (3R,4S)-4-amino-2,2-difluoro-3-hydroxy-6-methylheptanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N)[C@@H](O)C(F)(F)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
 DFI  DFI  '(3R,4S)-4-amino-2,2-difluoro-3-hydroxy-6-methylheptanoic acid'  L-peptide  28  14  .  2022-03-18  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DFI
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
 DFI  N     N  NH2    0  -0.827  -0.4267   1.7103   1.0361
 DFI  CA    C  CH1    0  -0.148   0.0106   0.3183   0.9780
 DFI  CB    C  CH2    0  -0.416  -0.5562  -0.4726   2.1558
 DFI  CG    C  CH1    0  -0.249  -0.0767  -0.0452   3.5464
 DFI  CD1   C  CH3    0  -0.649  -0.7295  -0.9320   4.6027
 DFI  CD2   C  CH3    0  -0.661   1.4430  -0.0888   3.6708
 DFI  CH    C  CH1    0  -0.056  -0.5189  -0.2811  -0.3504
 DFI  OH    O  OH1    0  -0.685  -1.7786   0.2595  -0.6355
 DFI  CM    C  CT     0   0.633   0.4113  -0.0527  -1.5348
 DFI  F1    F  F      0  -0.359   0.7627   1.2661  -1.6151
 DFI  F2    F  F      0  -0.372   1.5907  -0.7241  -1.2975
 DFI  C     C  C      0   0.322  -0.1695  -0.5490  -2.8814
 DFI  O     O  O      0  -0.584  -0.2644   0.2776  -3.7973
 DFI  OXT   O  OC    -1  -0.602  -0.4702  -1.7541  -2.8785
 DFI  H     H  HNH2   0   0.364   0.2629   2.3364   0.6448
 DFI  H2    H  HNH2   0   0.367  -0.5927   2.0093   1.9863
 DFI  HA    H  HCH1   0   0.240   1.1018   0.2275   1.0013
 DFI  HB2   H  HCH2   0   0.226  -0.2898  -1.5249   2.0136
 DFI  HB3   H  HCH2   0   0.228  -1.6504  -0.4254   2.1221
 DFI  HG    H  HCH1   0   0.214  -0.4036   0.9826   3.7444
 DFI  HD11  H  HCH3   0   0.227  -0.4317  -0.6343   5.6092
 DFI  HD12  H  HCH3   0   0.225  -1.8184  -0.8804   4.5475
 DFI  HD13  H  HCH3   0   0.214  -0.4411  -1.9775   4.4679
 DFI  HD21  H  HCH3   0   0.215   1.8260  -1.0850   3.4345
 DFI  HD22  H  HCH3   0   0.229   1.9339   0.6214   3.0041
 DFI  HD23  H  HCH3   0   0.229   1.7563   0.1537   4.6875
 DFI  HC    H  HCH1   0   0.235  -0.6096  -1.3663  -0.2404
 DFI  HH    H  HOH1   0   0.441  -1.7532   1.1215  -0.1683

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
 DFI  N    CA    single  1.458  0.019  1.458
 DFI  N    H     single  0.860  0.020  0.860
 DFI  N    H2    single  0.890  0.020  1.040
 DFI  CA   CB    single  1.521  0.033  1.521
 DFI  CA   CH    single  1.551  0.020  1.551
 DFI  CA   HA    single  0.970  0.020  0.970
 DFI  CB   CG    single  1.532  0.020  1.532
 DFI  CB   HB2   single  0.970  0.020  1.090
 DFI  CB   HB3   single  0.970  0.020  1.090
 DFI  CG   CD1   single  1.526  0.020  1.526
 DFI  CG   CD2   single  1.525  0.020  1.525
 DFI  CG   HG    single  0.970  0.020  1.090
 DFI  CD1  HD11  single  0.970  0.020  1.090
 DFI  CD1  HD12  single  0.970  0.020  1.090
 DFI  CD1  HD13  single  0.970  0.020  1.090
 DFI  CD2  HD21  single  0.970  0.020  1.090
 DFI  CD2  HD22  single  0.970  0.020  1.090
 DFI  CD2  HD23  single  0.970  0.020  1.090
 DFI  CH   OH    single  1.400  0.020  1.400
 DFI  CH   CM    single  1.523  0.020  1.523
 DFI  CH   HC    single  0.970  0.020  1.090
 DFI  OH   HH    single  0.850  0.020  0.980
 DFI  CM   F1    single  1.367  0.020  1.367
 DFI  CM   F2    single  1.378  0.020  1.378
 DFI  CM   C     single  1.548  0.020  1.548
 DFI  C    O     deloc   1.231  0.020  1.231
 DFI  C    OXT   deloc   1.242  0.020  1.242

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
 DFI  H2    N    H     107.04  3.000
 DFI  H2    N    CA    111.65  3.000
 DFI  H     N    CA    114.00  3.000
 DFI  HA    CA   CH    109.05  3.000
 DFI  HA    CA   CB    109.00  3.000
 DFI  CH    CA   CB    109.49  3.000
 DFI  HA    CA   N     110.00  3.000
 DFI  CH    CA   N     107.47  3.000
 DFI  CB    CA   N     110.40  1.500
 DFI  HB3   CB   HB2   106.29  3.000
 DFI  HB3   CB   CG    109.18  3.000
 DFI  HB2   CB   CG    108.06  3.000
 DFI  HB3   CB   CA    108.94  3.000
 DFI  HB2   CB   CA    107.89  3.000
 DFI  CG    CB   CA    116.06  3.000
 DFI  HG    CG   CD2   108.00  3.000
 DFI  HG    CG   CD1   106.98  3.000
 DFI  CD2   CG   CD1   110.68  3.000
 DFI  HG    CG   CB    109.40  3.000
 DFI  CD2   CG   CB    112.21  3.000
 DFI  CD1   CG   CB    109.41  3.000
 DFI  HD13  CD1  HD12  107.59  3.000
 DFI  HD13  CD1  HD11  107.62  3.000
 DFI  HD12  CD1  HD11  107.82  3.000
 DFI  HD13  CD1  CG    110.96  3.000
 DFI  HD12  CD1  CG    111.37  3.000
 DFI  HD11  CD1  CG    111.30  3.000
 DFI  HD23  CD2  HD22  107.20  3.000
 DFI  HD23  CD2  HD21  107.65  3.000
 DFI  HD22  CD2  HD21  107.67  3.000
 DFI  HD23  CD2  CG    110.84  3.000
 DFI  HD22  CD2  CG    112.33  3.000
 DFI  HD21  CD2  CG    110.94  3.000
 DFI  HC    CH   CM    106.11  3.000
 DFI  HC    CH   OH    109.19  3.000
 DFI  CM    CH   OH    109.46  3.000
 DFI  HC    CH   CA    108.99  3.000
 DFI  CM    CH   CA    113.55  3.000
 DFI  OH    CH   CA    109.42  3.000
 DFI  HH    OH   CH    102.65  3.000
 DFI  C     CM   F2    108.34  3.000
 DFI  C     CM   F1    110.76  3.000
 DFI  F2    CM   F1    105.08  3.000
 DFI  C     CM   CH    113.52  3.000
 DFI  F2    CM   CH    108.41  3.000
 DFI  F1    CM   CH    110.32  3.000
 DFI  OXT   C    O     129.14  3.000
 DFI  OXT   C    CM    113.57  3.000
 DFI  O     C    CM    117.29  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
 DFI  Var_01  CD1   CG   CB  CA  -179.84  30.0  3
 DFI  Var_02  O     C    CM  CH   123.18  30.0  3
 DFI  Var_03  HD11  CD1  CG  CB  -178.30  30.0  3
 DFI  Var_04  HD21  CD2  CG  CB   -56.61  30.0  3

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
 DFI  chir_01  CA  N   CB  CH  negativ
 DFI  chir_02  CH  OH  CA  CM  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
 DFI  plan-1  CM   0.020
 DFI  plan-1  C    0.020
 DFI  plan-1  O    0.020
 DFI  plan-1  OXT  0.020

