# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 20:00:00 2022
#   Inital geometry file: a 93 line input string
#   Ligand name: N~6~-[(1Z)-4-amino-3-oxopenta-1,4-dien-1-yl]-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCN\C=C/C(=O)C(N)=C)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
 3ZL  3ZL  N~6~-[(1Z)-4-amino-3-oxopenta-1,4-dien-1-yl]-L-lysine  L-peptide  35  17  .  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_3ZL
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
 3ZL  C1   C  C1     0   0.049  -43.6614  -48.0899  -55.1275
 3ZL  C2   C  C1     0  -0.495  -43.3314  -48.5926  -53.8964
 3ZL  C3   C  C      0   0.321  -42.3277  -49.5699  -53.5670
 3ZL  C4   C  C      0   0.253  -41.9454  -49.7197  -52.1146
 3ZL  C5   C  C2     0  -0.649  -42.1968  -48.7591  -51.2104
 3ZL  N14  N  NH2    0  -0.835  -41.2366  -50.8678  -51.8403
 3ZL  N    N  NH2    0  -0.815  -41.3640  -50.3366  -61.4268
 3ZL  CA   C  CH1    0  -0.219  -41.7586  -48.9379  -61.5482
 3ZL  CB   C  CH2    0  -0.388  -41.2129  -48.1287  -60.3732
 3ZL  CG   C  CH2    0  -0.421  -41.7107  -48.6176  -59.0197
 3ZL  CD   C  CH2    0  -0.474  -41.1501  -47.8016  -57.8598
 3ZL  CE   C  CH2    0  -0.266  -41.5867  -48.3031  -56.4925
 3ZL  NZ   N  NH1    0  -0.581  -43.0029  -48.0704  -56.2855
 3ZL  C    C  C      0   0.410  -41.3049  -48.3471  -62.9095
 3ZL  O    O  O      0  -0.601  -40.9055  -49.1516  -63.7758
 3ZL  O13  O  O      0  -0.453  -41.8190  -50.3442  -54.3748
 3ZL  O1   O  OC    -1  -0.607  -41.4080  -47.1108  -63.0353
 3ZL  H1   H  H      0   0.278  -44.6100  -47.5666  -55.1848
 3ZL  H2   H  H      0   0.253  -43.9990  -48.2895  -53.1028
 3ZL  H4   H  H      0   0.238  -41.8986  -48.8677  -50.1750
 3ZL  H5   H  H      0   0.239  -42.6695  -47.8308  -51.4895
 3ZL  H6   H  HNH2   0   0.372  -41.1864  -51.1309  -50.8695
 3ZL  H7   H  HNH2   0   0.370  -41.4172  -51.6496  -52.4485
 3ZL  H11  H  HCH1   0   0.189  -42.8576  -48.8248  -61.5318
 3ZL  H12  H  HCH2   0   0.196  -40.1176  -48.1694  -60.3906
 3ZL  H13  H  HCH2   0   0.204  -41.4914  -47.0809  -60.5002
 3ZL  H14  H  HCH2   0   0.209  -42.8066  -48.5902  -59.0137
 3ZL  H15  H  HCH2   0   0.213  -41.4295  -49.6649  -58.8748
 3ZL  H16  H  HCH2   0   0.239  -40.0582  -47.8438  -57.8904
 3ZL  H17  H  HCH2   0   0.225  -41.4175  -46.7456  -57.9729
 3ZL  H18  H  HCH2   0   0.245  -41.3547  -49.3637  -56.3962
 3ZL  H19  H  HCH2   0   0.235  -41.0303  -47.7863  -55.7037
 3ZL  H20  H  HNH1   0   0.405  -43.4830  -47.6001  -57.0360
 3ZL  H8   H  HNH2   0   0.329  -42.0315  -50.8385  -60.8567
 3ZL  H9   H  HNH2   0   0.332  -41.4006  -50.7471  -62.3505

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
 3ZL  O    C    deloc   1.231  0.020  1.231
 3ZL  C    CA   single  1.525  0.021  1.525
 3ZL  N    CA   single  1.458  0.019  1.458
 3ZL  CA   CB   single  1.521  0.033  1.521
 3ZL  CB   CG   single  1.523  0.020  1.523
 3ZL  CG   CD   single  1.525  0.020  1.525
 3ZL  CD   CE   single  1.520  0.020  1.520
 3ZL  CE   NZ   single  1.450  0.020  1.450
 3ZL  NZ   C1   single  1.332  0.020  1.332
 3ZL  C1   C2   double  1.370  0.020  1.370
 3ZL  O13  C3   double  1.229  0.020  1.229
 3ZL  C2   C3   single  1.439  0.020  1.439
 3ZL  C3   C4   single  1.509  0.020  1.509
 3ZL  C4   N14  single  1.377  0.020  1.377
 3ZL  C4   C5   double  1.343  0.020  1.343
 3ZL  C    O1   deloc   1.247  0.020  1.247
 3ZL  C1   H1   single  0.930  0.020  1.080
 3ZL  C2   H2   single  0.930  0.020  1.080
 3ZL  C5   H4   single  0.930  0.020  1.080
 3ZL  C5   H5   single  0.930  0.020  1.080
 3ZL  N14  H6   single  0.890  0.020  1.040
 3ZL  N14  H7   single  0.890  0.020  1.040
 3ZL  N    H8   single  0.890  0.020  1.040
 3ZL  N    H9   single  0.890  0.020  1.040
 3ZL  CA   H11  single  0.970  0.020  1.090
 3ZL  CB   H12  single  0.970  0.020  1.090
 3ZL  CB   H13  single  0.970  0.020  1.090
 3ZL  CG   H14  single  0.970  0.020  1.090
 3ZL  CG   H15  single  0.970  0.020  1.090
 3ZL  CD   H16  single  0.970  0.020  1.090
 3ZL  CD   H17  single  0.970  0.020  1.090
 3ZL  CE   H18  single  0.970  0.020  1.090
 3ZL  CE   H19  single  0.970  0.020  1.090
 3ZL  NZ   H20  single  0.860  0.020  1.020

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
 3ZL  H1   C1   NZ   112.28  3.000
 3ZL  H1   C1   C2   115.79  3.000
 3ZL  NZ   C1   C2   131.86  3.000
 3ZL  H2   C2   C3   116.95  3.000
 3ZL  H2   C2   C1   114.10  3.000
 3ZL  C3   C2   C1   128.52  3.000
 3ZL  O13  C3   C4   117.71  3.000
 3ZL  C4   C3   C2   117.67  3.000
 3ZL  O13  C3   C2   124.47  3.000
 3ZL  N14  C4   C5   123.97  3.000
 3ZL  C5   C4   C3   121.97  3.000
 3ZL  N14  C4   C3   113.88  3.000
 3ZL  H5   C5   H4   117.03  3.000
 3ZL  H5   C5   C4   121.57  3.000
 3ZL  H4   C5   C4   121.36  3.000
 3ZL  H7   N14  H6   112.86  3.000
 3ZL  H7   N14  C4   115.78  3.000
 3ZL  H6   N14  C4   115.81  3.000
 3ZL  H9   N    H8   106.83  3.000
 3ZL  H9   N    CA   107.67  3.000
 3ZL  H8   N    CA   110.14  3.000
 3ZL  H11  CA   C    105.36  3.000
 3ZL  H11  CA   CB   106.84  3.000
 3ZL  C    CA   CB   110.50  1.500
 3ZL  H11  CA   N    111.48  3.000
 3ZL  CB   CA   N    110.40  1.500
 3ZL  C    CA   N    111.00  2.800
 3ZL  H13  CB   H12  106.78  3.000
 3ZL  H13  CB   CG   109.16  3.000
 3ZL  H12  CB   CG   109.19  3.000
 3ZL  H13  CB   CA   109.14  3.000
 3ZL  H12  CB   CA   108.97  3.000
 3ZL  CG   CB   CA   113.38  3.000
 3ZL  H15  CG   H14  106.27  3.000
 3ZL  H15  CG   CD   108.48  3.000
 3ZL  H14  CG   CD   110.48  3.000
 3ZL  H15  CG   CB   109.94  3.000
 3ZL  H14  CG   CB   108.88  3.000
 3ZL  CD   CG   CB   112.59  3.000
 3ZL  H17  CD   H16  106.15  3.000
 3ZL  H17  CD   CE   109.93  3.000
 3ZL  H16  CD   CE   107.42  3.000
 3ZL  H17  CD   CG   110.35  3.000
 3ZL  H16  CD   CG   108.98  3.000
 3ZL  CE   CD   CG   113.70  3.000
 3ZL  H19  CE   H18  106.71  3.000
 3ZL  H19  CE   NZ   108.53  3.000
 3ZL  H18  CE   NZ   110.58  3.000
 3ZL  H19  CE   CD   110.25  3.000
 3ZL  H18  CE   CD   109.83  3.000
 3ZL  NZ   CE   CD   110.84  3.000
 3ZL  H20  NZ   CE   115.72  3.000
 3ZL  H20  NZ   C1   114.76  3.000
 3ZL  CE   NZ   C1   127.19  3.000
 3ZL  O1   C    O    126.56  3.000
 3ZL  O1   C    CA   116.22  3.000
 3ZL  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
 3ZL  Var_01  NZ   C1   C2  C3   -18.85   0.0  2
 3ZL  Var_02  CD   CE   NZ  C1  -163.36  30.0  1
 3ZL  Var_03  O13  C3   C2  C1   -18.34  30.0  2
 3ZL  Var_04  CE   NZ   C1  C2   -16.38  30.0  1
 3ZL  Var_05  N14  C4   C3  C2   165.19  30.0  2
 3ZL  Var_06  CD   CG   CB  CA   179.74  30.0  3
 3ZL  Var_07  CE   CD   CG  CB  -177.68  30.0  3
 3ZL  Var_08  NZ   CE   CD  CG   -68.93  30.0  3
 3ZL  Var_09  H4   C5   C4  C3  -178.64   0.0  2
 3ZL  Var_10  H6   N14  C4  C3  -163.66  30.0  2

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
 3ZL  chir_01  CA  C  N  CB  negativ

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
 3ZL  plan-1  C2   0.020
 3ZL  plan-1  C3   0.020
 3ZL  plan-1  C4   0.020
 3ZL  plan-1  O13  0.020
 3ZL  plan-2  CA   0.020
 3ZL  plan-2  C    0.020
 3ZL  plan-2  O    0.020
 3ZL  plan-2  O1   0.020
 3ZL  plan-3  C1   0.020
 3ZL  plan-3  C2   0.020
 3ZL  plan-3  C3   0.020
 3ZL  plan-3  NZ   0.020
 3ZL  plan-3  H1   0.020
 3ZL  plan-3  H2   0.020
 3ZL  plan-4  C3   0.020
 3ZL  plan-4  C4   0.020
 3ZL  plan-4  C5   0.020
 3ZL  plan-4  N14  0.020
 3ZL  plan-4  H4   0.020
 3ZL  plan-4  H5   0.020

