# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 15:13:28 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: (2R)-2-amino-7-oxo-7-{[(2R,3S)-4,4,4-trifluoro-3-hydroxybutan-2-yl]amino}heptanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC(=O)CCCC[C@@H](N)C(O)=O)[C@H](O)C(F)(F)F
#
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
 TFR  TFR  '(2R)-2-amino-7-oxo-7-{[(2R,3S)-4,4,4-trifluoro-3-hydroxybutan-2-yl]amino}heptanoic acid'  D-peptide  38  20  .  2022-07-22  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_TFR
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
 TFR  N     N  NH1    0  -0.636  -1.8911   0.6708   0.2797
 TFR  O     O  O      0  -0.764   7.2048   0.2485  -0.5644
 TFR  C1    C  C      0   0.557  -1.1195  -0.2486  -0.3408
 TFR  O1    O  O      0  -0.535  -1.3757  -0.6903  -1.4504
 TFR  CA    C  CH1    0  -0.155  -3.0355   1.3172  -0.3294
 TFR  CB    C  CH3    0  -0.664  -2.9445   2.8252  -0.1311
 TFR  CC    C  CH1    0  -0.141  -4.3618   0.7862   0.2413
 TFR  CD    C  CT     0   0.996  -4.6963  -0.6404  -0.1840
 TFR  FE    F  F      0  -0.315  -5.9217  -0.9875   0.2337
 TFR  FF    F  F      0  -0.298  -4.6841  -0.7767  -1.5152
 TFR  FG    F  F      0  -0.303  -3.8523  -1.5503   0.3200
 TFR  CA1   C  CH2    0  -0.554   0.1181  -0.6650   0.4186
 TFR  CB1   C  CH2    0  -0.412   1.3679   0.0075  -0.1536
 TFR  OB1   O  OH1    0  -0.617  -4.4373   0.8918   1.6330
 TFR  CD1   C  CH2    0  -0.408   3.8836   0.2459   0.0127
 TFR  CE1   C  CH1    0  -0.228   5.1912  -0.2404   0.6436
 TFR  CG1   C  CH2    0  -0.410   2.6431  -0.4700   0.5288
 TFR  CZ1   C  C      0   0.420   6.3455   0.7011   0.2181
 TFR  NZ1   N  NH2    0  -0.736   5.3934  -1.6501   0.3452
 TFR  HN    H  HNH1   0   0.380  -1.5503   1.0570   1.1466
 TFR  HA    H  HCH1   0   0.261  -3.0061   1.1102  -1.3993
 TFR  HB    H  HCH3   0   0.251  -2.9495   3.0960   0.9254
 TFR  HBA   H  HCH3   0   0.242  -2.0258   3.2061  -0.5754
 TFR  HBB   H  HCH3   0   0.245  -3.7844   3.3278  -0.6102
 TFR  HC    H  HCH1   0   0.265  -5.1630   1.4106  -0.1667
 TFR  HA1   H  HCH2   0   0.232   0.0306  -0.4324   1.4825
 TFR  HA1A  H  HCH2   0   0.264   0.2156  -1.7497   0.3344
 TFR  HB1   H  HCH2   0   0.215   1.4317  -0.1934  -1.2266
 TFR  HB1A  H  HCH2   0   0.217   1.2767   1.0930  -0.0456
 TFR  HOB1  H  HOH1   0   0.433  -3.6807   0.4434   2.0298
 TFR  HD1   H  HCH2   0   0.247   3.7851   1.3184   0.1971
 TFR  HD1A  H  HCH2   0   0.176   3.9467   0.1276  -1.0768
 TFR  HE1   H  HCH1   0   0.233   5.0812  -0.1476   1.7312
 TFR  HG1   H  HCH2   0   0.211   2.5602  -0.3118   1.6100
 TFR  HG1A  H  HCH2   0   0.238   2.7528  -1.5476   0.3848
 TFR  HNZ1  H  HNH2   0   0.283   5.6604  -1.7252  -0.6303
 TFR  HNZA  H  HNH2   0   0.324   6.2084  -1.9757   0.8512
 TFR  OH1   O  OC    -1  -0.510   6.3058   1.8598   0.6843

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
 TFR  C1   N     single  1.351  0.020  1.351
 TFR  CA   N     single  1.458  0.019  1.458
 TFR  N    HN    single  0.860  0.020  1.020
 TFR  O    CZ1   deloc   1.247  0.020  1.247
 TFR  O1   C1    double  1.221  0.020  1.221
 TFR  C1   CA1   single  1.511  0.020  1.511
 TFR  CC   CA    single  1.538  0.020  1.538
 TFR  CA   CB    single  1.521  0.033  1.521
 TFR  CA   HA    single  0.970  0.020  0.970
 TFR  CB   HB    single  0.970  0.020  1.090
 TFR  CB   HBA   single  0.970  0.020  1.090
 TFR  CB   HBB   single  0.970  0.020  1.090
 TFR  CD   CC    single  1.526  0.020  1.526
 TFR  CC   OB1   single  1.398  0.020  1.398
 TFR  CC   HC    single  0.970  0.020  1.090
 TFR  FF   CD    single  1.338  0.020  1.338
 TFR  FE   CD    single  1.340  0.020  1.340
 TFR  CD   FG    single  1.340  0.020  1.340
 TFR  CA1  CB1   single  1.530  0.020  1.530
 TFR  CA1  HA1   single  0.970  0.020  1.090
 TFR  CA1  HA1A  single  0.970  0.020  1.090
 TFR  CB1  CG1   single  1.523  0.020  1.523
 TFR  CB1  HB1   single  0.970  0.020  1.090
 TFR  CB1  HB1A  single  0.970  0.020  1.090
 TFR  OB1  HOB1  single  0.850  0.020  0.980
 TFR  CG1  CD1   single  1.522  0.020  1.522
 TFR  CD1  CE1   single  1.531  0.020  1.531
 TFR  CD1  HD1   single  0.970  0.020  1.090
 TFR  CD1  HD1A  single  0.970  0.020  1.090
 TFR  CE1  CZ1   single  1.549  0.020  1.549
 TFR  CE1  NZ1   single  1.455  0.020  1.455
 TFR  CE1  HE1   single  0.970  0.020  1.090
 TFR  CG1  HG1   single  0.970  0.020  1.090
 TFR  CG1  HG1A  single  0.970  0.020  1.090
 TFR  CZ1  OH1   deloc   1.250  0.020  1.250
 TFR  NZ1  HNZ1  single  0.890  0.020  1.040
 TFR  NZ1  HNZA  single  0.890  0.020  1.040

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
 TFR  HN    N    CA    117.23  3.000
 TFR  HN    N    C1    117.55  3.000
 TFR  CA    N    C1    124.17  3.000
 TFR  CA1   C1   O1    121.93  3.000
 TFR  CA1   C1   N     115.12  3.000
 TFR  O1    C1   N     122.92  3.000
 TFR  HA    CA   CC    108.77  3.000
 TFR  HA    CA   CB    109.00  3.000
 TFR  CC    CA   CB    110.17  3.000
 TFR  HA    CA   N     110.00  3.000
 TFR  CB    CA   N     110.40  1.500
 TFR  CC    CA   N     111.78  3.000
 TFR  HBB   CB   HBA   108.03  3.000
 TFR  HBB   CB   HB    107.93  3.000
 TFR  HBA   CB   HB    108.19  3.000
 TFR  HBB   CB   CA    110.68  3.000
 TFR  HBA   CB   CA    110.08  3.000
 TFR  HB    CB   CA    111.81  3.000
 TFR  HC    CC   OB1   106.76  3.000
 TFR  HC    CC   CD    105.60  3.000
 TFR  OB1   CC   CD    109.65  3.000
 TFR  HC    CC   CA    107.21  3.000
 TFR  OB1   CC   CA    112.95  3.000
 TFR  CD    CC   CA    114.10  3.000
 TFR  FG    CD   FF    107.42  3.000
 TFR  FG    CD   FE    106.43  3.000
 TFR  FF    CD   FE    106.98  3.000
 TFR  FG    CD   CC    113.09  3.000
 TFR  FE    CD   CC    110.84  3.000
 TFR  FF    CD   CC    111.75  3.000
 TFR  HA1A  CA1  HA1   107.08  3.000
 TFR  HA1A  CA1  CB1   109.55  3.000
 TFR  HA1   CA1  CB1   109.64  3.000
 TFR  HA1A  CA1  C1    107.94  3.000
 TFR  HA1   CA1  C1    111.42  3.000
 TFR  CB1   CA1  C1    111.10  3.000
 TFR  HB1A  CB1  HB1   106.49  3.000
 TFR  HB1A  CB1  CG1   109.66  3.000
 TFR  HB1   CB1  CG1   109.46  3.000
 TFR  HB1A  CB1  CA1   109.32  3.000
 TFR  HB1   CB1  CA1   109.50  3.000
 TFR  CG1   CB1  CA1   112.24  3.000
 TFR  HOB1  OB1  CC    109.39  3.000
 TFR  HD1A  CD1  HD1   106.17  3.000
 TFR  HD1A  CD1  CG1   109.43  3.000
 TFR  HD1   CD1  CG1   109.32  3.000
 TFR  HD1A  CD1  CE1   109.01  3.000
 TFR  HD1   CD1  CE1   108.62  3.000
 TFR  CG1   CD1  CE1   114.01  3.000
 TFR  HE1   CE1  NZ1   107.41  3.000
 TFR  HE1   CE1  CZ1   107.20  3.000
 TFR  NZ1   CE1  CZ1   115.40  3.000
 TFR  HE1   CE1  CD1   107.22  3.000
 TFR  NZ1   CE1  CD1   109.99  3.000
 TFR  CZ1   CE1  CD1   109.28  3.000
 TFR  HG1A  CG1  HG1   106.26  3.000
 TFR  HG1A  CG1  CD1   109.71  3.000
 TFR  HG1   CG1  CD1   109.16  3.000
 TFR  HG1A  CG1  CB1   109.52  3.000
 TFR  HG1   CG1  CB1   109.47  3.000
 TFR  CD1   CG1  CB1   112.51  3.000
 TFR  OH1   CZ1  CE1   115.94  3.000
 TFR  OH1   CZ1  O     126.33  3.000
 TFR  CE1   CZ1  O     117.72  3.000
 TFR  HNZA  NZ1  HNZ1  104.17  3.000
 TFR  HNZA  NZ1  CE1   108.70  3.000
 TFR  HNZ1  NZ1  CE1   107.79  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
 TFR  CONST_01  CA   N    C1   O1      0.00   0.0  0
 TFR  CONST_02  CA1  C1   N    CA    180.00   0.0  0
 TFR  CONST_03  HN   N    C1   O1    180.00   0.0  0
 TFR  Var_01    CB1  CA1  C1   N    -102.74  30.0  3
 TFR  Var_02    CG1  CB1  CA1  C1   -175.93  30.0  3
 TFR  Var_03    CD1  CG1  CB1  CA1  -177.12  30.0  3
 TFR  Var_04    CE1  CD1  CG1  CB1  -178.12  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
 TFR  chir_01  CA   N    CC   CB   negativ
 TFR  chir_02  CC   OB1  CA   CD   negativ
 TFR  chir_03  CE1  CD1  CZ1  NZ1  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
 TFR  plan-1  N    0.020
 TFR  plan-1  C1   0.020
 TFR  plan-1  O1   0.020
 TFR  plan-1  CA   0.020
 TFR  plan-1  CA1  0.020
 TFR  plan-1  HN   0.020
 TFR  plan-2  O    0.020
 TFR  plan-2  CE1  0.020
 TFR  plan-2  CZ1  0.020
 TFR  plan-2  OH1  0.020

