# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 13:30:59 2022
#   Inital geometry file: a 83 line input string
#   Ligand name: N~6~-[(2E)-but-2-enoyl]-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C\C=C\C(=O)NCCCC[C@H](N)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
 KCR  KCR  N~6~-[(2E)-but-2-enoyl]-L-lysine  L-peptide  32  15  .  2019-03-22  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_KCR
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
 KCR  N    N  NH2    0  -0.785  -5.5302  -23.1791  -0.6348
 KCR  CA   C  CH1    0  -0.217  -6.8578  -22.7549  -0.2142
 KCR  CB   C  CH2    0  -0.429  -7.7281  -22.4665  -1.4433
 KCR  CG   C  CH2    0  -0.406  -7.1654  -21.4294  -2.4116
 KCR  CD   C  CH2    0  -0.446  -7.0323  -20.0391  -1.8048
 KCR  CE   C  CH2    0  -0.284  -6.4711  -19.0002  -2.7678
 KCR  NZ   N  NH1    0  -0.645  -7.3335  -18.7684  -3.9049
 KCR  CH   C  C      0   0.540  -6.9759  -18.9373  -5.1915
 KCR  OH   O  O      0  -0.500  -5.8524  -19.2846  -5.5391
 KCR  CX   C  C1     0  -0.387  -8.0637  -18.6614  -6.1630
 KCR  CY   C  C1     0  -0.163  -7.8655  -18.7501  -7.4767
 KCR  CH3  C  CH3    0  -0.710  -8.8972  -18.4856  -8.5150
 KCR  C    C  C      0   0.385  -7.6119  -23.7425   0.7141
 KCR  O    O  O      0  -0.603  -7.1764  -24.9088   0.7876
 KCR  O1   O  OC    -1  -0.619  -8.6164  -23.2819   1.2975
 KCR  H1   H  HNH2   0   0.330  -4.9469  -23.2805   0.1873
 KCR  H2   H  HNH2   0   0.320  -5.6089  -24.1212  -1.0023
 KCR  H4   H  HCH1   0   0.207  -6.7406  -21.8181   0.3416
 KCR  H5   H  HCH2   0   0.212  -8.7138  -22.1404  -1.1013
 KCR  H6   H  HCH2   0   0.210  -7.8890  -23.4053  -1.9865
 KCR  H7   H  HCH2   0   0.213  -7.8244  -21.3791  -3.2838
 KCR  H8   H  HCH2   0   0.208  -6.1911  -21.7576  -2.7824
 KCR  H9   H  HCH2   0   0.230  -6.3690  -20.0660  -0.9364
 KCR  H10  H  HCH2   0   0.215  -8.0059  -19.7038  -1.4301
 KCR  H11  H  HCH2   0   0.240  -5.5004  -19.3220  -3.1421
 KCR  H12  H  HCH2   0   0.243  -6.3137  -18.0565  -2.2382
 KCR  H13  H  HNH1   0   0.395  -8.2792  -18.4819  -3.7060
 KCR  H14  H  H      0   0.256  -9.0377  -18.3746  -5.7772
 KCR  H15  H  H      0   0.252  -6.8821  -19.0379  -7.8361
 KCR  H16  H  HCH3   0   0.248  -9.0446  -19.3667  -9.1430
 KCR  H17  H  HCH3   0   0.242  -9.8559  -18.2018  -8.0836
 KCR  H18  H  HCH3   0   0.247  -8.5695  -17.6862  -9.1832

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
 KCR  CH3  CY   single  1.487  0.020  1.487
 KCR  CY   CX   double  1.332  0.020  1.332
 KCR  CX   CH   single  1.484  0.020  1.484
 KCR  OH   CH   double  1.226  0.020  1.226
 KCR  CH   NZ   single  1.346  0.020  1.346
 KCR  NZ   CE   single  1.446  0.020  1.446
 KCR  CE   CD   single  1.524  0.020  1.524
 KCR  CG   CD   single  1.523  0.020  1.523
 KCR  CG   CB   single  1.526  0.020  1.526
 KCR  CB   CA   single  1.530  0.020  1.530
 KCR  N    CA   single  1.458  0.019  1.458
 KCR  CA   C    single  1.525  0.021  1.525
 KCR  O    C    deloc   1.231  0.020  1.231
 KCR  C    O1   deloc   1.250  0.020  1.250
 KCR  N    H1   single  0.890  0.020  1.040
 KCR  N    H2   single  0.890  0.020  1.040
 KCR  CA   H4   single  0.970  0.020  1.090
 KCR  CB   H5   single  0.970  0.020  1.090
 KCR  CB   H6   single  0.970  0.020  1.090
 KCR  CG   H7   single  0.970  0.020  1.090
 KCR  CG   H8   single  0.970  0.020  1.090
 KCR  CD   H9   single  0.970  0.020  1.090
 KCR  CD   H10  single  0.970  0.020  1.090
 KCR  CE   H11  single  0.970  0.020  1.090
 KCR  CE   H12  single  0.970  0.020  1.090
 KCR  NZ   H13  single  0.860  0.020  1.020
 KCR  CX   H14  single  0.930  0.020  1.080
 KCR  CY   H15  single  0.930  0.020  1.080
 KCR  CH3  H16  single  0.970  0.020  1.090
 KCR  CH3  H17  single  0.970  0.020  1.090
 KCR  CH3  H18  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
 KCR  H2   N    H1   104.23  3.000
 KCR  H2   N    CA   107.74  3.000
 KCR  H1   N    CA   108.65  3.000
 KCR  H4   CA   C    107.03  3.000
 KCR  H4   CA   CB   107.85  3.000
 KCR  C    CA   CB   110.10  1.900
 KCR  H4   CA   N    107.35  3.000
 KCR  C    CA   N    111.00  2.800
 KCR  CB   CA   N    110.50  1.700
 KCR  H6   CB   H5   106.14  3.000
 KCR  H6   CB   CG   108.76  3.000
 KCR  H5   CB   CG   109.16  3.000
 KCR  H6   CB   CA   108.62  3.000
 KCR  H5   CB   CA   108.49  3.000
 KCR  CG   CB   CA   115.28  3.000
 KCR  H8   CG   H7   106.27  3.000
 KCR  H8   CG   CD   109.36  3.000
 KCR  H7   CG   CD   109.17  3.000
 KCR  H8   CG   CB   109.87  3.000
 KCR  H7   CG   CB   108.35  3.000
 KCR  CD   CG   CB   113.56  3.000
 KCR  H10  CD   H9   105.97  3.000
 KCR  H10  CD   CE   109.56  3.000
 KCR  H9   CD   CE   107.18  3.000
 KCR  H10  CD   CG   109.75  3.000
 KCR  H9   CD   CG   110.31  3.000
 KCR  CE   CD   CG   113.76  3.000
 KCR  H12  CE   H11  107.05  3.000
 KCR  H12  CE   NZ   109.17  3.000
 KCR  H11  CE   NZ   107.98  3.000
 KCR  H12  CE   CD   109.59  3.000
 KCR  H11  CE   CD   110.12  3.000
 KCR  NZ   CE   CD   112.75  3.000
 KCR  H13  NZ   CH   118.26  3.000
 KCR  H13  NZ   CE   116.74  3.000
 KCR  CH   NZ   CE   124.97  3.000
 KCR  CX   CH   OH   122.59  3.000
 KCR  OH   CH   NZ   123.36  3.000
 KCR  CX   CH   NZ   114.06  3.000
 KCR  H14  CX   CY   120.10  3.000
 KCR  H14  CX   CH   118.28  3.000
 KCR  CY   CX   CH   121.62  3.000
 KCR  H15  CY   CH3  116.37  3.000
 KCR  H15  CY   CX   118.62  3.000
 KCR  CH3  CY   CX   125.00  3.000
 KCR  H18  CH3  H17  108.41  3.000
 KCR  H18  CH3  H16  106.21  3.000
 KCR  H17  CH3  H16  108.62  3.000
 KCR  H18  CH3  CY   110.43  3.000
 KCR  H17  CH3  CY   112.36  3.000
 KCR  H16  CH3  CY   110.59  3.000
 KCR  O1   C    O    126.72  3.000
 KCR  O1   C    CA   115.82  3.000
 KCR  O    C    CA   120.80  1.700

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
 KCR  CONST_01  CX   CH   NZ  CE   180.00   0.0  0
 KCR  CONST_02  OH   CH   NZ  CE     0.00   0.0  0
 KCR  CONST_03  H13  NZ   CH  OH   180.00   0.0  0
 KCR  Var_01    CH3  CY   CX  CH  -179.74   0.0  2
 KCR  Var_02    CD   CG   CB  CA   -63.64  30.0  1
 KCR  Var_03    CE   CD   CG  CB  -179.99  30.0  3
 KCR  Var_04    NZ   CE   CD  CG    63.63  30.0  2
 KCR  Var_05    CH   NZ   CE  CD  -121.49  30.0  1
 KCR  Var_06    CY   CX   CH  NZ   178.35  30.0  2
 KCR  Var_07    H16  CH3  CY  CX  -121.39  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
 KCR  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
 KCR  plan-1  CE   0.020
 KCR  plan-1  NZ   0.020
 KCR  plan-1  CH   0.020
 KCR  plan-1  OH   0.020
 KCR  plan-1  CX   0.020
 KCR  plan-1  H13  0.020
 KCR  plan-2  CA   0.020
 KCR  plan-2  C    0.020
 KCR  plan-2  O    0.020
 KCR  plan-2  O1   0.020
 KCR  plan-3  CH   0.020
 KCR  plan-3  CX   0.020
 KCR  plan-3  CY   0.020
 KCR  plan-3  CH3  0.020
 KCR  plan-3  H14  0.020
 KCR  plan-3  H15  0.020

