# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 17:04:03 2022
#   Inital geometry file: a 83 line input string
#   Ligand name: (E)-N~6~-(4-oxobutylidene)-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCN=CCCC=O)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
 LGY  LGY  (E)-N~6~-(4-oxobutylidene)-L-lysine  L-peptide  32  15  .  2012-08-28  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_LGY
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
 LGY  OXT  O  OC    -1  -0.602  33.4524  -18.0770  4.2891
 LGY  C    C  C      0   0.412  34.3274  -17.1881  4.3240
 LGY  N    N  NH2    0  -0.816  33.2071  -16.4838  6.4196
 LGY  O    O  O      0  -0.606  35.3075  -17.0815  3.5611
 LGY  N1   N  N      0  -0.328  37.8402  -12.4275  8.9819
 LGY  C3   C  CH2    0  -0.538  39.6090  -10.7886  9.1477
 LGY  C4   C  CH2    0  -0.556  40.5394  -10.4579  7.9747
 LGY  C5   C  C1     0   0.176  40.0856   -9.2539  7.2059
 LGY  O6   O  O      0  -0.368  40.0052   -9.1823  6.0057
 LGY  CA   C  CH1    0  -0.220  34.1519  -16.0720  5.3889
 LGY  CB   C  CH2    0  -0.387  35.4793  -15.6562  6.0163
 LGY  CD   C  CH2    0  -0.424  36.6925  -14.0158  7.5225
 LGY  CE   C  CH2    0  -0.293  36.5528  -12.8215  8.4587
 LGY  CG   C  CH2    0  -0.424  35.3489  -14.4853  6.9818
 LGY  C11  C  C1     0  -0.003  38.2764  -11.2831  8.6841
 LGY  HN   H  HNH2   0   0.329  32.7305  -15.6773  6.7998
 LGY  HNA  H  HNH2   0   0.331  32.5037  -17.0624  5.9796
 LGY  H3   H  HCH2   0   0.264  40.0729  -11.5410  9.7849
 LGY  H3A  H  HCH2   0   0.258  39.4659   -9.8891  9.7559
 LGY  H4   H  HCH2   0   0.286  41.5251  -10.2070  8.3832
 LGY  H4A  H  HCH2   0   0.263  40.6665  -11.3115  7.3072
 LGY  H5   H  H      0   0.184  39.8315   -8.3846  7.8424
 LGY  HA   H  HCH1   0   0.188  33.7795  -15.1961  4.8261
 LGY  HB   H  HCH2   0   0.195  35.9147  -16.5135  6.5425
 LGY  HBA  H  HCH2   0   0.202  36.1780  -15.3877  5.2216
 LGY  HD   H  HCH2   0   0.213  37.3476  -13.7413  6.6896
 LGY  HDA  H  HCH2   0   0.216  37.1886  -14.8349  8.0518
 LGY  HE   H  HCH2   0   0.225  35.9152  -13.1054  9.3017
 LGY  HEA  H  HCH2   0   0.197  36.0461  -11.9996  7.9318
 LGY  HG   H  HCH2   0   0.204  34.8528  -13.6510  6.4718
 LGY  HGA  H  HCH2   0   0.209  34.7005  -14.7616  7.8193
 LGY  H11  H  H      0   0.215  37.6942  -10.5896  8.0607

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
 LGY  OXT  C    deloc   1.248  0.020  1.248
 LGY  C    O    deloc   1.231  0.020  1.231
 LGY  C    CA   single  1.525  0.021  1.525
 LGY  N    CA   single  1.458  0.019  1.458
 LGY  N1   CE   single  1.444  0.020  1.444
 LGY  N1   C11  double  1.260  0.020  1.260
 LGY  C3   C4   single  1.533  0.020  1.533
 LGY  C3   C11  single  1.495  0.020  1.495
 LGY  C4   C5   single  1.499  0.020  1.499
 LGY  C5   O6   double  1.205  0.020  1.205
 LGY  CA   CB   single  1.530  0.020  1.530
 LGY  CB   CG   single  1.523  0.020  1.523
 LGY  CD   CE   single  1.524  0.020  1.524
 LGY  CD   CG   single  1.522  0.020  1.522
 LGY  N    HN   single  0.890  0.020  1.040
 LGY  N    HNA  single  0.890  0.020  1.040
 LGY  C3   H3   single  0.970  0.020  1.090
 LGY  C3   H3A  single  0.970  0.020  1.090
 LGY  C4   H4   single  0.970  0.020  1.090
 LGY  C4   H4A  single  0.970  0.020  1.090
 LGY  C5   H5   single  0.930  0.020  1.080
 LGY  CA   HA   single  0.970  0.020  0.970
 LGY  CB   HB   single  0.970  0.020  1.090
 LGY  CB   HBA  single  0.970  0.020  1.090
 LGY  CD   HD   single  0.970  0.020  1.090
 LGY  CD   HDA  single  0.970  0.020  1.090
 LGY  CE   HE   single  0.970  0.020  1.090
 LGY  CE   HEA  single  0.970  0.020  1.090
 LGY  CG   HG   single  0.970  0.020  1.090
 LGY  CG   HGA  single  0.970  0.020  1.090
 LGY  C11  H11  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
 LGY  CA   C    O    120.80  1.700
 LGY  CA   C    OXT  116.88  3.000
 LGY  O    C    OXT  126.52  3.000
 LGY  HNA  N    HN   106.98  3.000
 LGY  HNA  N    CA   107.74  3.000
 LGY  HN   N    CA   110.25  3.000
 LGY  C11  N1   CE   118.07  3.000
 LGY  H3A  C3   H3   107.34  3.000
 LGY  H3A  C3   C11  109.11  3.000
 LGY  H3   C3   C11  109.41  3.000
 LGY  H3A  C3   C4   109.09  3.000
 LGY  H3   C3   C4   109.75  3.000
 LGY  C11  C3   C4   112.02  3.000
 LGY  H4A  C4   H4   107.60  3.000
 LGY  H4A  C4   C5   110.48  3.000
 LGY  H4   C4   C5   106.23  3.000
 LGY  H4A  C4   C3   111.72  3.000
 LGY  H4   C4   C3   108.05  3.000
 LGY  C5   C4   C3   112.45  3.000
 LGY  H5   C5   O6   120.71  3.000
 LGY  H5   C5   C4   113.92  3.000
 LGY  O6   C5   C4   125.37  3.000
 LGY  HA   CA   CB   109.00  3.000
 LGY  HA   CA   N    110.00  3.000
 LGY  CB   CA   N    110.50  1.700
 LGY  HA   CA   C    109.00  3.000
 LGY  CB   CA   C    110.10  1.900
 LGY  N    CA   C    111.00  2.800
 LGY  HBA  CB   HB   106.72  3.000
 LGY  HBA  CB   CG   109.10  3.000
 LGY  HB   CB   CG   109.32  3.000
 LGY  HBA  CB   CA   108.93  3.000
 LGY  HB   CB   CA   109.26  3.000
 LGY  CG   CB   CA   113.30  3.000
 LGY  HDA  CD   HD   106.53  3.000
 LGY  HDA  CD   CG   109.94  3.000
 LGY  HD   CD   CG   109.58  3.000
 LGY  HDA  CD   CE   109.34  3.000
 LGY  HD   CD   CE   109.01  3.000
 LGY  CG   CD   CE   112.27  3.000
 LGY  HEA  CE   HE   107.12  3.000
 LGY  HEA  CE   CD   109.49  3.000
 LGY  HE   CE   CD   108.86  3.000
 LGY  HEA  CE   N1   112.35  3.000
 LGY  HE   CE   N1   108.12  3.000
 LGY  CD   CE   N1   110.77  3.000
 LGY  HGA  CG   HG   106.25  3.000
 LGY  HGA  CG   CD   109.20  3.000
 LGY  HG   CG   CD   109.26  3.000
 LGY  HGA  CG   CB   109.98  3.000
 LGY  HG   CG   CB   109.20  3.000
 LGY  CD   CG   CB   112.75  3.000
 LGY  H11  C11  C3   116.05  3.000
 LGY  H11  C11  N1   121.57  3.000
 LGY  C3   C11  N1   122.38  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
 LGY  Var_01  CG   CD   CE   N1   178.36  30.0  1
 LGY  Var_02  C4   C3   C11  N1   119.52  30.0  1
 LGY  Var_03  O6   C5   C4   C3  -132.92  30.0  3
 LGY  Var_04  C11  C3   C4   C5    69.04  30.0  1
 LGY  Var_05  CE   CD   CG   CB   178.51  30.0  2
 LGY  Var_06  H11  C11  N1   CE     1.13   0.0  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
 LGY  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
 LGY  plan-1  OXT  0.020
 LGY  plan-1  C    0.020
 LGY  plan-1  O    0.020
 LGY  plan-1  CA   0.020
 LGY  plan-2  N1   0.020
 LGY  plan-2  C3   0.020
 LGY  plan-2  CE   0.020
 LGY  plan-2  C11  0.020
 LGY  plan-2  H11  0.020
 LGY  plan-3  C4   0.020
 LGY  plan-3  C5   0.020
 LGY  plan-3  O6   0.020
 LGY  plan-3  H5   0.020

