# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 15:19:53 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  30  15  .  2022-03-18  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.834   1.5640   0.8006   1.0437
 DFO  CA    C  CH1   0  -0.210   0.3499  -0.0056   0.9813
 DFO  CB    C  CH2   0  -0.405  -0.5749   0.3224   2.1554
 DFO  CG    C  CH1   0  -0.260   0.0302   0.0997   3.5470
 DFO  CD1   C  CH3   0  -0.647  -1.0280   0.3962   4.6056
 DFO  CD2   C  CH3   0  -0.660   0.5865  -1.3084   3.7265
 DFO  CH    C  CT    0   0.415  -0.3401   0.3486  -0.3891
 DFO  OH1   O  OH1   0  -0.651  -1.7247   0.2344  -0.3759
 DFO  OH2   O  OH1   0  -0.673  -0.0553   1.6527  -0.7097
 DFO  CM    C  CT    0   0.681   0.1967  -0.5514  -1.5353
 DFO  F1    F  F     0  -0.333   1.5462  -0.6312  -1.4778
 DFO  F2    F  F     0  -0.337  -0.2735  -1.8194  -1.3939
 DFO  C     C  C     0   0.436  -0.1660  -0.0245  -2.9284
 DFO  O     O  O     0  -0.410   0.6117   0.5856  -3.6065
 DFO  OXT   O  OH1   0  -0.572  -1.4036  -0.3270  -3.2512
 DFO  H     H  HNH2  0   0.376   2.3659   0.3124   0.6705
 DFO  H2    H  HNH2  0   0.380   1.7946   1.0676   1.9899
 DFO  HA    H  HCH1  0   0.259   0.5679  -1.0786   1.0103
 DFO  HB2   H  HCH2  0   0.225  -1.4686  -0.3035   2.0890
 DFO  HB3   H  HCH2  0   0.237  -0.9136   1.3603   2.0803
 DFO  HG    H  HCH1  0   0.219   0.8459   0.8140   3.7080
 DFO  HD11  H  HCH3  0   0.229  -0.6099   0.3191   5.6104
 DFO  HD12  H  HCH3  0   0.226  -1.4379   1.4014   4.4918
 DFO  HD13  H  HCH3  0   0.216  -1.8576  -0.3118   4.5365
 DFO  HD21  H  HCH3  0   0.217  -0.1880  -2.0588   3.5488
 DFO  HD22  H  HCH3  0   0.229   1.4158  -1.5171   3.0496
 DFO  HD23  H  HCH3  0   0.233   0.9551  -1.4501   4.7436
 DFO  HH1   H  HOH1  0   0.459  -1.9932  -0.6323  -0.0515
 DFO  HH2   H  HOH1  0   0.459   0.7291   1.8580  -0.1415
 DFO  HXT   H  HOH1  0   0.495  -1.6198   0.0221  -4.1304

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  1.575  0.020  1.575
 DFO  CA   HA    single  0.970  0.020  0.970
 DFO  CB   CG    single  1.534  0.020  1.534
 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  1.525  0.020  1.525
 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  1.389  0.020  1.389
 DFO  CH   OH2   single  1.373  0.020  1.373
 DFO  CH   CM    single  1.553  0.020  1.553
 DFO  OH1  HH1   single  0.850  0.020  0.980
 DFO  OH2  HH2   single  0.850  0.020  0.980
 DFO  CM   F1    single  1.353  0.020  1.353
 DFO  CM   F2    single  1.360  0.020  1.360
 DFO  CM   C     single  1.533  0.020  1.533
 DFO  C    O     double  1.231  0.020  1.231
 DFO  C    OXT   single  1.314  0.020  1.314
 DFO  OXT  HXT   single  0.850  0.020  0.980

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     107.01  3.000
 DFO  H2    N    CA    112.10  3.000
 DFO  H     N    CA    114.00  3.000
 DFO  HA    CA   CH    109.30  3.000
 DFO  HA    CA   CB    109.00  3.000
 DFO  CH    CA   CB    110.78  3.000
 DFO  HA    CA   N     110.00  3.000
 DFO  CH    CA   N     106.11  3.000
 DFO  CB    CA   N     110.40  1.500
 DFO  HB3   CB   HB2   106.61  3.000
 DFO  HB3   CB   CG    108.79  3.000
 DFO  HB2   CB   CG    107.13  3.000
 DFO  HB3   CB   CA    109.74  3.000
 DFO  HB2   CB   CA    108.95  3.000
 DFO  CG    CB   CA    115.26  3.000
 DFO  HG    CG   CD2   108.24  3.000
 DFO  HG    CG   CD1   106.71  3.000
 DFO  CD2   CG   CD1   110.54  3.000
 DFO  HG    CG   CB    109.40  3.000
 DFO  CD2   CG   CB    112.64  3.000
 DFO  CD1   CG   CB    109.12  3.000
 DFO  HD13  CD1  HD12  107.76  3.000
 DFO  HD13  CD1  HD11  107.66  3.000
 DFO  HD12  CD1  HD11  107.76  3.000
 DFO  HD13  CD1  CG    110.89  3.000
 DFO  HD12  CD1  CG    111.53  3.000
 DFO  HD11  CD1  CG    111.06  3.000
 DFO  HD23  CD2  HD22  107.27  3.000
 DFO  HD23  CD2  HD21  107.56  3.000
 DFO  HD22  CD2  HD21  107.85  3.000
 DFO  HD23  CD2  CG    110.67  3.000
 DFO  HD22  CD2  CG    112.40  3.000
 DFO  HD21  CD2  CG    110.88  3.000
 DFO  CM    CH   OH2   107.85  3.000
 DFO  CM    CH   OH1   107.69  3.000
 DFO  OH2   CH   OH1   106.68  3.000
 DFO  CM    CH   CA    111.13  3.000
 DFO  OH2   CH   CA    109.03  3.000
 DFO  OH1   CH   CA    114.20  3.000
 DFO  HH1   OH1  CH    110.78  3.000
 DFO  HH2   OH2  CH    103.14  3.000
 DFO  C     CM   F2    109.47  3.000
 DFO  C     CM   F1    107.15  3.000
 DFO  F2    CM   F1    106.58  3.000
 DFO  C     CM   CH    112.94  3.000
 DFO  F2    CM   CH    110.13  3.000
 DFO  F1    CM   CH    110.34  3.000
 DFO  OXT   C    O     126.10  3.000
 DFO  OXT   C    CM    111.52  3.000
 DFO  O     C    CM    122.38  3.000
 DFO  HXT   OXT  C     110.46  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  CONST_01  HXT   OXT  C   CM   180.00   0.0  0
 DFO  Var_01    CD1   CG   CB  CA  -177.01  30.0  3
 DFO  Var_02    F1    CM   CH  CA   -45.54  30.0  3
 DFO  Var_03    O     C    CM  CH   100.23  30.0  3
 DFO  Var_04    HD11  CD1  CG  CB  -175.80  30.0  3
 DFO  Var_05    HD21  CD2  CG  CB   -57.40  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
 DFO  plan-1  HXT  0.020

