# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 02:31:04 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: (4S)-4-amino-2,2-difluoro-3,3-dihydroxy-6-methylheptanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N)C(O)(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
 DFO  DFO  '(4S)-4-amino-2,2-difluoro-3,3-dihydroxy-6-methylheptanoic acid'  L-peptide  29  15  .  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_DFO
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
 DFO  N     N  NH2    0  -0.801   1.7350   0.4951   1.0361
 DFO  CA    C  CH1    0  -0.182   0.3699  -0.0097   1.0113
 DFO  CB    C  CH2    0  -0.406  -0.4707   0.4442   2.2104
 DFO  CG    C  CH1    0  -0.236   0.0550  -0.0347   3.5661
 DFO  CD1   C  CH3    0  -0.650  -0.7990   0.5550   4.6845
 DFO  CD2   C  CH3    0  -0.663   0.0886  -1.5572   3.6669
 DFO  CH    C  CT     0   0.404  -0.2865   0.3942  -0.3320
 DFO  OH1   O  OH1    0  -0.662  -1.6253   0.0052  -0.3747
 DFO  OH2   O  OH1    0  -0.665  -0.3484   1.7764  -0.4684
 DFO  CM    C  CT     0   0.630   0.4325  -0.2163  -1.5769
 DFO  F1    F  F      0  -0.358   1.5419   0.5208  -1.8922
 DFO  F2    F  F      0  -0.354   0.8972  -1.4611  -1.2654
 DFO  C     C  C      0   0.316  -0.4957  -0.2952  -2.8188
 DFO  O     O  O      0  -0.595  -0.6203   0.7679  -3.4428
 DFO  OXT   O  OC    -1  -0.590  -1.0105  -1.3998  -3.0401
 DFO  H     H  HNH2   0   0.354   2.2852  -0.0284   1.7035
 DFO  H2    H  HNH2   0   0.342   1.7419   1.4529   1.3684
 DFO  HA    H  HCH1   0   0.241   0.4300  -1.1008   1.0305
 DFO  HB2   H  HCH2   0   0.213  -1.5020   0.0946   2.1076
 DFO  HB3   H  HCH2   0   0.220  -0.5180   1.5386   2.2136
 DFO  HG    H  HCH1   0   0.206   1.0772   0.3373   3.7016
 DFO  HD11  H  HCH3   0   0.224  -0.4407   0.2411   5.6664
 DFO  HD12  H  HCH3   0   0.223  -0.7894   1.6463   4.6592
 DFO  HD13  H  HCH3   0   0.212  -1.8394   0.2325   4.5935
 DFO  HD21  H  HCH3   0   0.214  -0.8973  -1.9846   3.4661
 DFO  HD22  H  HCH3   0   0.227   0.7912  -2.0065   2.9632
 DFO  HD23  H  HCH3   0   0.228   0.3902  -1.8745   4.6665
 DFO  HH1   H  HOH1   0   0.456  -1.6993  -0.9342  -0.1733
 DFO  HH2   H  HOH1   0   0.455   0.5316   2.1160  -0.6613

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
 DFO  N    CA    single  1.458  0.019  1.458
 DFO  N    H     single  0.860  0.020  0.860
 DFO  N    H2    single  0.890  0.020  1.040
 DFO  CA   CB    single  1.521  0.033  1.521
 DFO  CA   CH    single  1.549  0.020  1.549
 DFO  CA   HA    single  0.970  0.020  0.970
 DFO  CB   CG    single  1.531  0.020  1.531
 DFO  CB   HB2   single  0.970  0.020  1.090
 DFO  CB   HB3   single  0.970  0.020  1.090
 DFO  CG   CD1   single  1.526  0.020  1.526
 DFO  CG   CD2   single  1.526  0.020  1.526
 DFO  CG   HG    single  0.970  0.020  1.090
 DFO  CD1  HD11  single  0.970  0.020  1.090
 DFO  CD1  HD12  single  0.970  0.020  1.090
 DFO  CD1  HD13  single  0.970  0.020  1.090
 DFO  CD2  HD21  single  0.970  0.020  1.090
 DFO  CD2  HD22  single  0.970  0.020  1.090
 DFO  CD2  HD23  single  0.970  0.020  1.090
 DFO  CH   OH1   single  1.395  0.020  1.395
 DFO  CH   OH2   single  1.390  0.020  1.390
 DFO  CH   CM    single  1.562  0.020  1.562
 DFO  OH1  HH1   single  0.850  0.020  0.980
 DFO  OH2  HH2   single  0.850  0.020  0.980
 DFO  CM   F1    single  1.369  0.020  1.369
 DFO  CM   F2    single  1.365  0.020  1.365
 DFO  CM   C     single  1.552  0.020  1.552
 DFO  C    O     deloc   1.231  0.020  1.231
 DFO  C    OXT   deloc   1.239  0.020  1.239

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
 DFO  H2    N    H     105.62  3.000
 DFO  H2    N    CA    109.85  3.000
 DFO  H     N    CA    114.00  3.000
 DFO  HA    CA   CH    107.39  3.000
 DFO  HA    CA   CB    109.00  3.000
 DFO  CH    CA   CB    111.64  3.000
 DFO  HA    CA   N     110.00  3.000
 DFO  CH    CA   N     108.77  3.000
 DFO  CB    CA   N     110.40  1.500
 DFO  HB3   CB   HB2   106.20  3.000
 DFO  HB3   CB   CG    108.95  3.000
 DFO  HB2   CB   CG    107.88  3.000
 DFO  HB3   CB   CA    108.77  3.000
 DFO  HB2   CB   CA    110.42  3.000
 DFO  CG    CB   CA    114.31  3.000
 DFO  HG    CG   CD2   108.05  3.000
 DFO  HG    CG   CD1   107.47  3.000
 DFO  CD2   CG   CD1   110.46  3.000
 DFO  HG    CG   CB    108.88  3.000
 DFO  CD2   CG   CB    112.21  3.000
 DFO  CD1   CG   CB    109.63  3.000
 DFO  HD13  CD1  HD12  107.54  3.000
 DFO  HD13  CD1  HD11  107.61  3.000
 DFO  HD12  CD1  HD11  107.79  3.000
 DFO  HD13  CD1  CG    110.96  3.000
 DFO  HD12  CD1  CG    111.37  3.000
 DFO  HD11  CD1  CG    111.38  3.000
 DFO  HD23  CD2  HD22  107.04  3.000
 DFO  HD23  CD2  HD21  107.69  3.000
 DFO  HD22  CD2  HD21  107.54  3.000
 DFO  HD23  CD2  CG    110.89  3.000
 DFO  HD22  CD2  CG    112.48  3.000
 DFO  HD21  CD2  CG    110.98  3.000
 DFO  CM    CH   OH2   109.32  3.000
 DFO  CM    CH   OH1   107.97  3.000
 DFO  OH2   CH   OH1   103.38  3.000
 DFO  CM    CH   CA    113.22  3.000
 DFO  OH2   CH   CA    111.30  3.000
 DFO  OH1   CH   CA    111.14  3.000
 DFO  HH1   OH1  CH    109.83  3.000
 DFO  HH2   OH2  CH    109.24  3.000
 DFO  C     CM   F2    109.87  3.000
 DFO  C     CM   F1    109.13  3.000
 DFO  F2    CM   F1    105.53  3.000
 DFO  C     CM   CH    112.47  3.000
 DFO  F2    CM   CH    109.35  3.000
 DFO  F1    CM   CH    110.25  3.000
 DFO  OXT   C    O     129.31  3.000
 DFO  OXT   C    CM    115.89  3.000
 DFO  O     C    CM    114.80  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
 DFO  Var_01  CD1   CG   CB  CA   176.06  30.0  3
 DFO  Var_02  F1    CM   CH  CA   -80.67  30.0  3
 DFO  Var_03  O     C    CM  CH    80.35  30.0  3
 DFO  Var_04  HD11  CD1  CG  CB  -179.30  30.0  3
 DFO  Var_05  HD21  CD2  CG  CB   -55.84  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
 DFO  chir_01  CA  N  CB  CH  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
 DFO  plan-1  CM   0.020
 DFO  plan-1  C    0.020
 DFO  plan-1  O    0.020
 DFO  plan-1  OXT  0.020

