# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 01:21:22 2022
#   Inital geometry file: a 91 line input string
#   Ligand name: N~6~-(4-fluorobenzoyl)-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCNC(=O)c1ccc(F)cc1)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
 2KK  2KK  N~6~-(4-fluorobenzoyl)-L-lysine  L-peptide  35  19  .  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_2KK
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
 2KK  N    N  NH2    0  -0.786  11.9164  19.2935  22.6816
 2KK  CA   C  CH1    0  -0.205  10.9217  18.2918  22.3208
 2KK  C    C  C      0   0.378   9.4399  18.7167  22.5083
 2KK  O    O  O      0  -0.603   9.2161  19.7709  23.1352
 2KK  CB   C  CH2    0  -0.427  11.1811  17.0041  23.1057
 2KK  CG   C  CH2    0  -0.417  12.5491  16.3810  22.8545
 2KK  CD   C  CH2    0  -0.440  12.7871  15.0899  23.6309
 2KK  CE   C  CH2    0  -0.301  12.8388  15.2580  25.1477
 2KK  NZ   N  NH1    0  -0.637  13.9097  16.1355  25.5696
 2KK  O01  O  O      0  -0.485  12.6418  17.7904  26.4523
 2KK  C02  C  C      0   0.527  13.7359  17.3408  26.1342
 2KK  C04  C  CR6    0  -0.042  14.9830  18.1305  26.3888
 2KK  C05  C  CR16   0  -0.275  16.1385  17.9934  25.6221
 2KK  C06  C  CR16   0  -0.395  17.2636  18.7599  25.8841
 2KK  C07  C  CR6    0   0.531  17.2180  19.6660  26.9257
 2KK  F08  F  F      0  -0.308  18.3040  20.4033  27.1916
 2KK  C09  C  CR16   0  -0.399  16.0851  19.8391  27.6988
 2KK  C10  C  CR16   0  -0.250  14.9670  19.0726  27.4158
 2KK  OXT  O  OC    -1  -0.618   8.5881  17.9443  22.0189
 2KK  H1   H  HNH2   0   0.330  11.7070  20.1516  22.1857
 2KK  H2   H  HNH2   0   0.319  11.7827  19.5310  23.6585
 2KK  H4   H  HCH1   0   0.199  11.0591  18.0629  21.2559
 2KK  H5   H  HCH2   0   0.208  11.0575  17.2210  24.1729
 2KK  H6   H  HCH2   0   0.213  10.4074  16.2760  22.8512
 2KK  H7   H  HCH2   0   0.215  12.6448  16.1645  21.7855
 2KK  H8   H  HCH2   0   0.213  13.3390  17.1003  23.0820
 2KK  H9   H  HCH2   0   0.222  11.9977  14.3670  23.4031
 2KK  H10  H  HCH2   0   0.226  13.7228  14.6306  23.2972
 2KK  H11  H  HCH2   0   0.248  11.9018  15.6572  25.5304
 2KK  H12  H  HCH2   0   0.249  12.9821  14.2820  25.6167
 2KK  H13  H  HNH1   0   0.402  14.8469  15.8040  25.4072
 2KK  H14  H  HCR6   0   0.269  16.1771  17.3050  24.7875
 2KK  H15  H  HCR6   0   0.285  18.1568  18.6570  25.2823
 2KK  H16  H  HCR6   0   0.284  16.0752  20.5595  28.5062
 2KK  H17  H  HCR6   0   0.269  14.0735  19.2048  28.0105

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
 2KK  CA   N    single    1.458  0.019  1.458
 2KK  CA   C    single    1.525  0.021  1.525
 2KK  CA   CB   single    1.530  0.020  1.530
 2KK  C    O    deloc     1.231  0.020  1.231
 2KK  CG   CB   single    1.524  0.020  1.524
 2KK  CG   CD   single    1.525  0.020  1.525
 2KK  CD   CE   single    1.527  0.020  1.527
 2KK  CE   NZ   single    1.447  0.020  1.447
 2KK  NZ   C02  single    1.342  0.020  1.342
 2KK  C05  C06  aromatic  1.386  0.020  1.386
 2KK  C05  C04  aromatic  1.394  0.020  1.394
 2KK  C02  O01  double    1.225  0.020  1.225
 2KK  C02  C04  single    1.498  0.020  1.498
 2KK  C06  C07  aromatic  1.381  0.020  1.381
 2KK  C04  C10  aromatic  1.394  0.020  1.394
 2KK  C07  F08  single    1.339  0.020  1.339
 2KK  C07  C09  aromatic  1.382  0.020  1.382
 2KK  C10  C09  aromatic  1.385  0.020  1.385
 2KK  C    OXT  deloc     1.250  0.020  1.250
 2KK  N    H1   single    0.890  0.020  1.040
 2KK  N    H2   single    0.890  0.020  1.040
 2KK  CA   H4   single    0.970  0.020  1.090
 2KK  CB   H5   single    0.970  0.020  1.090
 2KK  CB   H6   single    0.970  0.020  1.090
 2KK  CG   H7   single    0.970  0.020  1.090
 2KK  CG   H8   single    0.970  0.020  1.090
 2KK  CD   H9   single    0.970  0.020  1.090
 2KK  CD   H10  single    0.970  0.020  1.090
 2KK  CE   H11  single    0.970  0.020  1.090
 2KK  CE   H12  single    0.970  0.020  1.090
 2KK  NZ   H13  single    0.860  0.020  1.020
 2KK  C05  H14  single    0.930  0.020  1.080
 2KK  C06  H15  single    0.930  0.020  1.080
 2KK  C09  H16  single    0.930  0.020  1.080
 2KK  C10  H17  single    0.930  0.020  1.080

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
 2KK  H2   N    H1   104.24  3.000
 2KK  H2   N    CA   108.02  3.000
 2KK  H1   N    CA   108.67  3.000
 2KK  H4   CA   CB   107.51  3.000
 2KK  H4   CA   C    107.07  3.000
 2KK  CB   CA   C    110.10  1.900
 2KK  H4   CA   N    107.34  3.000
 2KK  CB   CA   N    110.50  1.700
 2KK  C    CA   N    111.00  2.800
 2KK  OXT  C    O    126.67  3.000
 2KK  OXT  C    CA   115.72  3.000
 2KK  O    C    CA   120.80  1.700
 2KK  H6   CB   H5   106.19  3.000
 2KK  H6   CB   CG   108.96  3.000
 2KK  H5   CB   CG   110.04  3.000
 2KK  H6   CB   CA   108.74  3.000
 2KK  H5   CB   CA   108.29  3.000
 2KK  CG   CB   CA   114.31  3.000
 2KK  H8   CG   H7   105.69  3.000
 2KK  H8   CG   CD   109.78  3.000
 2KK  H7   CG   CD   108.42  3.000
 2KK  H8   CG   CB   110.22  3.000
 2KK  H7   CG   CB   108.68  3.000
 2KK  CD   CG   CB   113.72  3.000
 2KK  H10  CD   H9   106.02  3.000
 2KK  H10  CD   CE   108.67  3.000
 2KK  H9   CD   CE   107.69  3.000
 2KK  H10  CD   CG   109.48  3.000
 2KK  H9   CD   CG   109.92  3.000
 2KK  CE   CD   CG   114.69  3.000
 2KK  H12  CE   H11  106.84  3.000
 2KK  H12  CE   NZ   108.63  3.000
 2KK  H11  CE   NZ   108.20  3.000
 2KK  H12  CE   CD   109.42  3.000
 2KK  H11  CE   CD   111.14  3.000
 2KK  NZ   CE   CD   112.42  3.000
 2KK  H13  NZ   C02  118.94  3.000
 2KK  H13  NZ   CE   116.22  3.000
 2KK  C02  NZ   CE   124.83  3.000
 2KK  C04  C02  O01  120.39  3.000
 2KK  C04  C02  NZ   115.92  3.000
 2KK  O01  C02  NZ   123.68  3.000
 2KK  C10  C04  C05  118.78  3.000
 2KK  C10  C04  C02  118.17  3.000
 2KK  C05  C04  C02  123.02  3.000
 2KK  H14  C05  C06  117.93  3.000
 2KK  H14  C05  C04  121.09  3.000
 2KK  C06  C05  C04  120.97  3.000
 2KK  H15  C06  C07  120.61  3.000
 2KK  H15  C06  C05  120.81  3.000
 2KK  C07  C06  C05  118.58  3.000
 2KK  C09  C07  F08  118.98  3.000
 2KK  C09  C07  C06  122.07  3.000
 2KK  F08  C07  C06  118.95  3.000
 2KK  H16  C09  C10  120.91  3.000
 2KK  H16  C09  C07  120.54  3.000
 2KK  C10  C09  C07  118.56  3.000
 2KK  H17  C10  C09  119.14  3.000
 2KK  H17  C10  C04  119.82  3.000
 2KK  C09  C10  C04  121.03  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
 2KK  CONST_01  C07  C06  C05  C04     0.00   0.0  0
 2KK  CONST_02  C07  C09  C10  C04     0.00   0.0  0
 2KK  CONST_03  C09  C07  C06  C05     0.00   0.0  0
 2KK  CONST_04  C09  C10  C04  C05     0.00   0.0  0
 2KK  CONST_05  C10  C04  C05  C06     0.00   0.0  0
 2KK  CONST_06  C10  C09  C07  C06     0.00   0.0  0
 2KK  CONST_07  C06  C05  C04  C02   180.00   0.0  0
 2KK  CONST_08  C09  C10  C04  C02   180.00   0.0  0
 2KK  CONST_09  F08  C07  C06  C05   180.00   0.0  0
 2KK  CONST_10  C10  C09  C07  F08   180.00   0.0  0
 2KK  CONST_11  H15  C06  C05  C04   180.00   0.0  0
 2KK  CONST_12  H16  C09  C10  C04   180.00   0.0  0
 2KK  CONST_13  H17  C10  C04  C05   180.00   0.0  0
 2KK  CONST_14  H14  C05  C06  C07   180.00   0.0  0
 2KK  CONST_15  C04  C02  NZ   CE    180.00   0.0  0
 2KK  CONST_16  H13  NZ   C02  C04     0.00   0.0  0
 2KK  CONST_17  O01  C02  NZ   CE      0.00   0.0  0
 2KK  Var_01    C05  C04  C02  NZ     28.09  30.0  2
 2KK  Var_02    CD   CG   CB   CA   -179.33  30.0  1
 2KK  Var_03    CE   CD   CG   CB    -65.39  30.0  3
 2KK  Var_04    NZ   CE   CD   CG    -60.89  30.0  3
 2KK  Var_05    C02  NZ   CE   CD    112.83  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
 2KK  chir_01  CA  N  C  CB  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
 2KK  plan-1  C02  0.020
 2KK  plan-1  C04  0.020
 2KK  plan-1  C05  0.020
 2KK  plan-1  C06  0.020
 2KK  plan-1  C07  0.020
 2KK  plan-1  F08  0.020
 2KK  plan-1  C09  0.020
 2KK  plan-1  C10  0.020
 2KK  plan-1  H14  0.020
 2KK  plan-1  H15  0.020
 2KK  plan-1  H16  0.020
 2KK  plan-1  H17  0.020
 2KK  plan-2  CE   0.020
 2KK  plan-2  NZ   0.020
 2KK  plan-2  O01  0.020
 2KK  plan-2  C02  0.020
 2KK  plan-2  C04  0.020
 2KK  plan-2  H13  0.020
 2KK  plan-3  CA   0.020
 2KK  plan-3  C    0.020
 2KK  plan-3  O    0.020
 2KK  plan-3  OXT  0.020

