# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 18:59:51 2022
#   Inital geometry file: a 71 line input string
#   Ligand name: N~6~-(trifluoroacetyl)-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCNC(=O)C(F)(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
 FAK  FAK  N~6~-(trifluoroacetyl)-L-lysine  L-peptide  28  16  .  2016-04-22  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_FAK
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
 FAK  N    N  NH2    0  -0.794  -17.9974  79.8390  83.2838
 FAK  CA   C  CH1    0  -0.191  -18.2276  81.2749  83.1367
 FAK  C    C  C      0   0.384  -18.2593  82.0500  84.4766
 FAK  O    O  O      0  -0.610  -18.8428  81.4808  85.4240
 FAK  CB   C  CH2    0  -0.414  -19.5478  81.4769  82.3884
 FAK  CG   C  CH2    0  -0.424  -19.8619  82.9204  82.0176
 FAK  CD   C  CH2    0  -0.474  -21.1628  83.0436  81.2366
 FAK  CE   C  CH2    0  -0.241  -21.4577  84.4859  80.8635
 FAK  NZ   N  NH1    0  -0.644  -22.7366  84.5870  80.1793
 FAK  CH   C  C      0   0.359  -23.2319  85.7565  79.7937
 FAK  OH   O  O      0  -0.462  -22.6941  86.8383  79.9283
 FAK  CT   C  CT     0   0.962  -24.6373  85.7154  79.1689
 FAK  FI1  F  F      0  -0.298  -24.7239  86.5899  78.1729
 FAK  FI2  F  F      0  -0.307  -25.5458  86.0531  80.0879
 FAK  FI3  F  F      0  -0.300  -24.9741  84.5143  78.6930
 FAK  OXT  O  OC    -1  -0.612  -17.7340  83.1821  84.4966
 FAK  H1   H  HNH2   0   0.331  -17.0658  79.6944  83.6567
 FAK  H2   H  HNH2   0   0.321  -18.6174  79.5121  84.0177
 FAK  H4   H  HCH1   0   0.194  -17.4216  81.6795  82.5150
 FAK  H6   H  HCH2   0   0.202  -20.3648  81.0718  82.9973
 FAK  H7   H  HCH2   0   0.212  -19.0380  83.3311  81.4246
 FAK  H8   H  HCH2   0   0.231  -21.9877  82.6470  81.8372
 FAK  H9   H  HCH2   0   0.245  -20.6658  84.8771  80.2197
 FAK  H10  H  HNH1   0   0.419  -23.2474  83.7340  80.0107
 FAK  H3   H  HCH2   0   0.211  -19.5194  80.8719  81.4765
 FAK  H5   H  HCH2   0   0.223  -19.9257  83.5368  82.9174
 FAK  H11  H  HCH2   0   0.232  -21.1137  82.4347  80.3283
 FAK  H12  H  HCH2   0   0.244  -21.4779  85.1084  81.7616

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
 FAK  FI1  CT   single  1.328  0.020  1.328
 FAK  FI3  CT   single  1.335  0.020  1.335
 FAK  CT   CH   single  1.539  0.020  1.539
 FAK  CT   FI2  single  1.336  0.020  1.336
 FAK  CH   OH   double  1.216  0.020  1.216
 FAK  CH   NZ   single  1.327  0.020  1.327
 FAK  NZ   CE   single  1.454  0.020  1.454
 FAK  CE   CD   single  1.519  0.020  1.519
 FAK  CD   CG   single  1.522  0.020  1.522
 FAK  CG   CB   single  1.523  0.020  1.523
 FAK  CB   CA   single  1.530  0.020  1.530
 FAK  CA   N    single  1.458  0.019  1.458
 FAK  CA   C    single  1.525  0.021  1.525
 FAK  C    OXT  deloc   1.248  0.020  1.248
 FAK  C    O    deloc   1.231  0.020  1.231
 FAK  N    H1   single  0.890  0.020  1.040
 FAK  N    H2   single  0.890  0.020  1.040
 FAK  CA   H4   single  0.970  0.020  1.090
 FAK  CB   H6   single  0.970  0.020  1.090
 FAK  CG   H7   single  0.970  0.020  1.090
 FAK  CD   H8   single  0.970  0.020  1.090
 FAK  CE   H9   single  0.970  0.020  1.090
 FAK  NZ   H10  single  0.860  0.020  1.020
 FAK  CB   H3   single  0.970  0.020  1.090
 FAK  CG   H5   single  0.970  0.020  1.090
 FAK  CD   H11  single  0.970  0.020  1.090
 FAK  CE   H12  single  0.970  0.020  1.090

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
 FAK  H2   N   H1   104.44  3.000
 FAK  H2   N   CA   107.03  3.000
 FAK  H1   N   CA   108.77  3.000
 FAK  H4   CA  CB   107.96  3.000
 FAK  H4   CA  C    108.75  3.000
 FAK  CB   CA  C    110.10  1.900
 FAK  H4   CA  N    107.70  3.000
 FAK  C    CA  N    111.00  2.800
 FAK  CB   CA  N    110.50  1.700
 FAK  OXT  C   O    126.69  3.000
 FAK  O    C   CA   120.80  1.700
 FAK  OXT  C   CA   117.34  3.000
 FAK  H3   CB  H6   106.13  3.000
 FAK  H3   CB  CG   109.05  3.000
 FAK  H6   CB  CG   109.37  3.000
 FAK  H3   CB  CA   108.17  3.000
 FAK  H6   CB  CA   108.80  3.000
 FAK  CG   CB  CA   114.95  3.000
 FAK  H5   CG  H7   106.16  3.000
 FAK  H5   CG  CD   109.08  3.000
 FAK  H7   CG  CD   109.56  3.000
 FAK  H5   CG  CB   110.26  3.000
 FAK  H7   CG  CB   109.40  3.000
 FAK  CD   CG  CB   112.20  3.000
 FAK  H11  CD  H8   106.72  3.000
 FAK  H11  CD  CE   109.46  3.000
 FAK  H8   CD  CE   109.43  3.000
 FAK  H11  CD  CG   110.02  3.000
 FAK  H8   CD  CG   109.45  3.000
 FAK  CE   CD  CG   111.64  3.000
 FAK  H12  CE  H9   107.07  3.000
 FAK  H12  CE  NZ   109.32  3.000
 FAK  H9   CE  NZ   109.59  3.000
 FAK  H12  CE  CD   110.04  3.000
 FAK  H9   CE  CD   110.12  3.000
 FAK  NZ   CE  CD   110.64  3.000
 FAK  H10  NZ  CH   120.51  3.000
 FAK  H10  NZ  CE   117.73  3.000
 FAK  CH   NZ  CE   121.75  3.000
 FAK  CT   CH  OH   118.22  3.000
 FAK  OH   CH  NZ   125.94  3.000
 FAK  CT   CH  NZ   115.81  3.000
 FAK  FI3  CT  FI2  107.52  3.000
 FAK  FI2  CT  FI1  107.77  3.000
 FAK  FI3  CT  FI1  107.97  3.000
 FAK  FI2  CT  CH   109.58  3.000
 FAK  FI3  CT  CH   113.53  3.000
 FAK  FI1  CT  CH   110.28  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
 FAK  CONST_01  CT   CH  NZ  CE   180.00   0.0  0
 FAK  CONST_02  OH   CH  NZ  CE     0.00   0.0  0
 FAK  CONST_03  H10  NZ  CH  OH   180.00   0.0  0
 FAK  Var_01    CD   CG  CB  CA   178.09  30.0  1
 FAK  Var_02    CE   CD  CG  CB  -179.52  30.0  1
 FAK  Var_03    NZ   CE  CD  CG  -177.08  30.0  1
 FAK  Var_04    CH   NZ  CE  CD   177.73  30.0  1
 FAK  Var_05    FI1  CT  CH  NZ  -142.66  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
 FAK  chir_01  CA  CB  N  C  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
 FAK  plan-1  CE   0.020
 FAK  plan-1  NZ   0.020
 FAK  plan-1  CH   0.020
 FAK  plan-1  OH   0.020
 FAK  plan-1  CT   0.020
 FAK  plan-1  H10  0.020
 FAK  plan-2  CA   0.020
 FAK  plan-2  C    0.020
 FAK  plan-2  O    0.020
 FAK  plan-2  OXT  0.020

