# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 01:42:25 2022
#   Inital geometry file: a 91 line input string
#   Ligand name: N~6~-(4-bromobenzoyl)-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCNC(=O)c1ccc(Br)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
 2KP  2KP  N~6~-(4-bromobenzoyl)-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_2KP
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
 2KP  N    N   NH2    0  -0.818  11.8067  19.5970  23.3213
 2KP  CA   C   CH1    0  -0.213  10.8911  18.6408  22.7075
 2KP  C    C   C      0   0.406   9.4129  18.9994  23.0124
 2KP  O    O   O      0  -0.600   9.1917  20.0896  23.5776
 2KP  CB   C   CH2    0  -0.395  11.2246  17.2189  23.1619
 2KP  CG   C   CH2    0  -0.430  12.6229  16.7778  22.7503
 2KP  CD   C   CH2    0  -0.444  13.0396  15.4156  23.2972
 2KP  CE   C   CH2    0  -0.298  13.2515  15.3740  24.8099
 2KP  NZ   N   NH1    0  -0.628  14.2760  16.2997  25.2468
 2KP  C02  C   C      0   0.511  14.0372  17.4274  25.9347
 2KP  O03  O   O      0  -0.478  12.9372  17.7601  26.3533
 2KP  C04  C   CR6    0  -0.029  15.2308  18.2996  26.1696
 2KP  C05  C   CR16   0  -0.265  15.0458  19.6792  26.1699
 2KP  C06  C   CR16   0  -0.215  16.1099  20.5367  26.3959
 2KP  C07  C   CR6    0  -0.112  17.3657  20.0018  26.6479
 2KP  BR   BR  BR     0  -0.036  18.8180  21.1613  26.9721
 2KP  C09  C   CR16   0  -0.213  17.5707  18.6307  26.6691
 2KP  C10  C   CR16   0  -0.280  16.4985  17.7854  26.4235
 2KP  OXT  O   OC    -1  -0.608   8.5605  18.1712  22.6359
 2KP  H1   H   HNH2   0   0.330  12.6022  19.7583  22.7196
 2KP  H2   H   HNH2   0   0.333  11.3175  20.4780  23.4124
 2KP  H4   H   HCH1   0   0.189  10.9730  18.6579  21.6067
 2KP  H5   H   HCH2   0   0.201  11.1198  17.1762  24.2501
 2KP  H6   H   HCH2   0   0.202  10.4928  16.5233  22.7459
 2KP  H7   H   HCH2   0   0.216  12.6723  16.7442  21.6570
 2KP  H8   H   HCH2   0   0.211  13.3590  17.5264  23.0574
 2KP  H9   H   HCH2   0   0.224  12.2874  14.6623  23.0438
 2KP  H10  H   HCH2   0   0.227  13.9648  15.0967  22.8076
 2KP  H11  H   HCH2   0   0.248  12.3339  15.6116  25.3435
 2KP  H12  H   HCH2   0   0.251  13.5417  14.3642  25.1083
 2KP  H13  H   HNH1   0   0.402  15.1953  16.1664  24.8549
 2KP  H14  H   HCR6   0   0.268  14.0657  20.0941  25.9732
 2KP  H15  H   HCR6   0   0.283  15.9533  21.6068  26.3764
 2KP  H16  H   HCR6   0   0.285  18.5468  18.2137  26.8775
 2KP  H17  H   HCR6   0   0.274  16.6663  16.7162  26.4585

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
 2KP  CA   N    single    1.458  0.019  1.458
 2KP  CA   C    single    1.525  0.021  1.525
 2KP  CA   CB   single    1.530  0.020  1.530
 2KP  C    O    deloc     1.231  0.020  1.231
 2KP  CG   CB   single    1.523  0.020  1.523
 2KP  CG   CD   single    1.526  0.020  1.526
 2KP  CD   CE   single    1.528  0.020  1.528
 2KP  CE   NZ   single    1.448  0.020  1.448
 2KP  NZ   C02  single    1.342  0.020  1.342
 2KP  C02  O03  double    1.223  0.020  1.223
 2KP  C02  C04  single    1.497  0.020  1.497
 2KP  C10  C04  aromatic  1.391  0.020  1.391
 2KP  C10  C09  aromatic  1.387  0.020  1.387
 2KP  C04  C05  aromatic  1.392  0.020  1.392
 2KP  C09  C07  aromatic  1.387  0.020  1.387
 2KP  C05  C06  aromatic  1.385  0.020  1.385
 2KP  C07  C06  aromatic  1.388  0.020  1.388
 2KP  C07  BR   single    1.886  0.020  1.886
 2KP  C    OXT  deloc     1.247  0.020  1.247
 2KP  N    H1   single    0.890  0.020  1.040
 2KP  N    H2   single    0.890  0.020  1.040
 2KP  CA   H4   single    0.970  0.020  1.090
 2KP  CB   H5   single    0.970  0.020  1.090
 2KP  CB   H6   single    0.970  0.020  1.090
 2KP  CG   H7   single    0.970  0.020  1.090
 2KP  CG   H8   single    0.970  0.020  1.090
 2KP  CD   H9   single    0.970  0.020  1.090
 2KP  CD   H10  single    0.970  0.020  1.090
 2KP  CE   H11  single    0.970  0.020  1.090
 2KP  CE   H12  single    0.970  0.020  1.090
 2KP  NZ   H13  single    0.860  0.020  1.020
 2KP  C05  H14  single    0.930  0.020  1.080
 2KP  C06  H15  single    0.930  0.020  1.080
 2KP  C09  H16  single    0.930  0.020  1.080
 2KP  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
 2KP  H2   N    H1   107.18  3.000
 2KP  H2   N    CA   107.76  3.000
 2KP  H1   N    CA   110.37  3.000
 2KP  H4   CA   CB   107.13  3.000
 2KP  H4   CA   C    105.25  3.000
 2KP  CB   CA   C    110.10  1.900
 2KP  H4   CA   N    111.27  3.000
 2KP  CB   CA   N    110.50  1.700
 2KP  C    CA   N    111.00  2.800
 2KP  OXT  C    O    126.59  3.000
 2KP  OXT  C    CA   116.01  3.000
 2KP  O    C    CA   120.80  1.700
 2KP  H6   CB   H5   106.85  3.000
 2KP  H6   CB   CG   109.13  3.000
 2KP  H5   CB   CG   110.21  3.000
 2KP  H6   CB   CA   109.44  3.000
 2KP  H5   CB   CA   108.12  3.000
 2KP  CG   CB   CA   112.90  3.000
 2KP  H8   CG   H7   105.72  3.000
 2KP  H8   CG   CD   109.06  3.000
 2KP  H7   CG   CD   108.55  3.000
 2KP  H8   CG   CB   110.11  3.000
 2KP  H7   CG   CB   108.68  3.000
 2KP  CD   CG   CB   114.36  3.000
 2KP  H10  CD   H9   106.08  3.000
 2KP  H10  CD   CE   108.52  3.000
 2KP  H9   CD   CE   107.81  3.000
 2KP  H10  CD   CG   109.31  3.000
 2KP  H9   CD   CG   110.11  3.000
 2KP  CE   CD   CG   114.64  3.000
 2KP  H12  CE   H11  106.99  3.000
 2KP  H12  CE   NZ   108.70  3.000
 2KP  H11  CE   NZ   108.01  3.000
 2KP  H12  CE   CD   109.42  3.000
 2KP  H11  CE   CD   111.26  3.000
 2KP  NZ   CE   CD   112.29  3.000
 2KP  H13  NZ   C02  118.19  3.000
 2KP  H13  NZ   CE   116.32  3.000
 2KP  C02  NZ   CE   124.45  3.000
 2KP  C04  C02  O03  120.33  3.000
 2KP  C04  C02  NZ   115.34  3.000
 2KP  O03  C02  NZ   124.33  3.000
 2KP  C10  C04  C05  119.16  3.000
 2KP  C05  C04  C02  118.14  3.000
 2KP  C10  C04  C02  122.67  3.000
 2KP  H14  C05  C06  119.21  3.000
 2KP  H14  C05  C04  120.02  3.000
 2KP  C06  C05  C04  120.76  3.000
 2KP  H15  C06  C07  121.03  3.000
 2KP  H15  C06  C05  119.88  3.000
 2KP  C07  C06  C05  119.09  3.000
 2KP  C09  C07  BR   119.43  3.000
 2KP  BR   C07  C06  119.40  3.000
 2KP  C09  C07  C06  121.17  3.000
 2KP  H16  C09  C10  119.78  3.000
 2KP  H16  C09  C07  121.17  3.000
 2KP  C10  C09  C07  119.05  3.000
 2KP  H17  C10  C09  118.43  3.000
 2KP  H17  C10  C04  120.80  3.000
 2KP  C09  C10  C04  120.76  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
 2KP  CONST_01  C07  C09  C10  C04    0.00   0.0  0
 2KP  CONST_02  C07  C06  C05  C04    0.00   0.0  0
 2KP  CONST_03  C09  C10  C04  C05    0.00   0.0  0
 2KP  CONST_04  C09  C07  C06  C05    0.00   0.0  0
 2KP  CONST_05  C10  C04  C05  C06    0.00   0.0  0
 2KP  CONST_06  C10  C09  C07  C06    0.00   0.0  0
 2KP  CONST_07  C09  C10  C04  C02  180.00   0.0  0
 2KP  CONST_08  C06  C05  C04  C02  180.00   0.0  0
 2KP  CONST_09  BR   C07  C06  C05  180.00   0.0  0
 2KP  CONST_10  C10  C09  C07  BR   180.00   0.0  0
 2KP  CONST_11  H16  C09  C10  C04  180.00   0.0  0
 2KP  CONST_12  H15  C06  C05  C04  180.00   0.0  0
 2KP  CONST_13  H17  C10  C04  C05  180.00   0.0  0
 2KP  CONST_14  H14  C05  C06  C07  180.00   0.0  0
 2KP  CONST_15  C04  C02  NZ   CE   180.00   0.0  0
 2KP  CONST_16  H13  NZ   C02  C04    0.00   0.0  0
 2KP  CONST_17  O03  C02  NZ   CE     0.00   0.0  0
 2KP  Var_01    C10  C04  C02  NZ   -36.68  30.0  2
 2KP  Var_02    CD   CG   CB   CA   174.58  30.0  1
 2KP  Var_03    CE   CD   CG   CB   -68.44  30.0  3
 2KP  Var_04    NZ   CE   CD   CG   -59.44  30.0  3
 2KP  Var_05    C02  NZ   CE   CD   108.75  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
 2KP  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
 2KP  plan-1  C02  0.020
 2KP  plan-1  C04  0.020
 2KP  plan-1  C05  0.020
 2KP  plan-1  C06  0.020
 2KP  plan-1  C07  0.020
 2KP  plan-1  BR   0.020
 2KP  plan-1  C09  0.020
 2KP  plan-1  C10  0.020
 2KP  plan-1  H14  0.020
 2KP  plan-1  H15  0.020
 2KP  plan-1  H16  0.020
 2KP  plan-1  H17  0.020
 2KP  plan-2  CE   0.020
 2KP  plan-2  NZ   0.020
 2KP  plan-2  C02  0.020
 2KP  plan-2  O03  0.020
 2KP  plan-2  C04  0.020
 2KP  plan-2  H13  0.020
 2KP  plan-3  CA   0.020
 2KP  plan-3  C    0.020
 2KP  plan-3  O    0.020
 2KP  plan-3  OXT  0.020

