# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 21:00:01 2022
#   Inital geometry file: a 92 line input string
#   Ligand name: (E)-N~6~-(1-carboxy-3-oxobutylidene)-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)CC(=NCCCC[C@H](N)C(O)=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
 74P  74P  (E)-N~6~-(1-carboxy-3-oxobutylidene)-L-lysine  L-peptide  34  18  .  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_74P
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
 74P  C2   C  C      0   0.414  21.8361  10.6426  24.5745
 74P  O2   O  O      0  -0.579  23.2503  12.5896  21.0152
 74P  O4   O  O      0  -0.409  20.6816  10.8931  24.3064
 74P  N    N  NH2    0  -0.793  18.2047  19.3340  26.0241
 74P  CA   C  CH1    0  -0.191  19.1528  18.3125  26.4651
 74P  CB   C  CH2    0  -0.413  19.7471  17.6345  25.2271
 74P  CG   C  CH2    0  -0.424  20.6175  16.4168  25.5123
 74P  CD   C  CH2    0  -0.423  21.0661  15.7037  24.2440
 74P  CE   C  CH2    0  -0.311  21.9211  14.4816  24.5457
 74P  NZ   N  N      0  -0.352  22.3100  13.8056  23.3251
 74P  CX1  C  C      0   0.073  22.7174  12.6101  23.3438
 74P  C1   C  CH2    0  -0.650  22.8875  11.7297  24.5557
 74P  CX2  C  C      0   0.403  23.0378  11.8964  22.0194
 74P  O6   O  OC    -1  -0.580  23.0358  10.6498  22.1043
 74P  C    C  C      0   0.384  20.2869  18.8439  27.3748
 74P  O    O  O      0  -0.610  20.7463  19.9693  27.0846
 74P  C3   C  CH3    0  -0.773  22.2908   9.2862  25.0257
 74P  O1   O  OC    -1  -0.613  20.6716  18.0979  28.2991
 74P  H6   H  HCH1   0   0.193  18.5858  17.5561  27.0187
 74P  H7   H  HCH2   0   0.200  20.3255  18.3734  24.6597
 74P  H8   H  HCH2   0   0.208  18.9171  17.3352  24.5786
 74P  H9   H  HCH2   0   0.203  20.0595  15.7147  26.1418
 74P  H10  H  HCH2   0   0.213  21.4973  16.7067  26.0928
 74P  H11  H  HCH2   0   0.211  21.6297  16.3926  23.6072
 74P  H12  H  HCH2   0   0.209  20.1903  15.3936  23.6648
 74P  H13  H  HCH2   0   0.212  21.3702  13.8231  25.2275
 74P  H14  H  HCH2   0   0.227  22.8195  14.7995  25.0890
 74P  H15  H  HCH2   0   0.269  23.8860  11.2899  24.5584
 74P  H16  H  HCH2   0   0.285  22.7919  12.2866  25.4920
 74P  H18  H  HCH3   0   0.249  21.4680   8.5753  25.0643
 74P  H19  H  HCH3   0   0.261  23.0606   8.9169  24.3476
 74P  H20  H  HCH3   0   0.256  22.7494   9.3599  26.0143
 74P  H3   H  HNH2   0   0.331  17.7210  19.6998  26.8366
 74P  H4   H  HNH2   0   0.320  18.7471  20.1190  25.6789

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
 74P  O2   CX2  deloc   1.239  0.020  1.239
 74P  O6   CX2  deloc   1.249  0.020  1.249
 74P  CX2  CX1  single  1.538  0.020  1.538
 74P  O4   C2   double  1.211  0.020  1.211
 74P  CX1  NZ   double  1.263  0.020  1.263
 74P  CX1  C1   single  1.508  0.020  1.508
 74P  NZ   CE   single  1.448  0.020  1.448
 74P  C2   C1   single  1.512  0.020  1.512
 74P  C2   C3   single  1.500  0.020  1.500
 74P  CD   CE   single  1.522  0.020  1.522
 74P  CD   CG   single  1.523  0.020  1.523
 74P  CB   CG   single  1.524  0.020  1.524
 74P  CB   CA   single  1.530  0.020  1.530
 74P  N    CA   single  1.458  0.019  1.458
 74P  CA   C    single  1.525  0.021  1.525
 74P  O    C    deloc   1.231  0.020  1.231
 74P  C    O1   deloc   1.249  0.020  1.249
 74P  N    H3   single  0.890  0.020  1.040
 74P  N    H4   single  0.890  0.020  1.040
 74P  CA   H6   single  0.970  0.020  1.090
 74P  CB   H7   single  0.970  0.020  1.090
 74P  CB   H8   single  0.970  0.020  1.090
 74P  CG   H9   single  0.970  0.020  1.090
 74P  CG   H10  single  0.970  0.020  1.090
 74P  CD   H11  single  0.970  0.020  1.090
 74P  CD   H12  single  0.970  0.020  1.090
 74P  CE   H13  single  0.970  0.020  1.090
 74P  CE   H14  single  0.970  0.020  1.090
 74P  C1   H15  single  0.970  0.020  1.090
 74P  C1   H16  single  0.970  0.020  1.090
 74P  C3   H18  single  0.970  0.020  1.090
 74P  C3   H19  single  0.970  0.020  1.090
 74P  C3   H20  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
 74P  C3   C2   C1   116.29  3.000
 74P  C3   C2   O4   122.85  3.000
 74P  C1   C2   O4   120.74  3.000
 74P  H4   N    H3   104.39  3.000
 74P  H4   N    CA   107.26  3.000
 74P  H3   N    CA   108.66  3.000
 74P  H6   CA   C    108.62  3.000
 74P  H6   CA   CB   107.67  3.000
 74P  C    CA   CB   110.10  1.900
 74P  H6   CA   N    107.42  3.000
 74P  C    CA   N    111.00  2.800
 74P  CB   CA   N    110.50  1.700
 74P  H8   CB   H7   106.11  3.000
 74P  H8   CB   CG   108.99  3.000
 74P  H7   CB   CG   109.51  3.000
 74P  H8   CB   CA   107.80  3.000
 74P  H7   CB   CA   108.94  3.000
 74P  CG   CB   CA   115.10  3.000
 74P  H10  CG   H9   105.94  3.000
 74P  H10  CG   CD   109.24  3.000
 74P  H9   CG   CD   109.18  3.000
 74P  H10  CG   CB   110.31  3.000
 74P  H9   CG   CB   109.19  3.000
 74P  CD   CG   CB   112.75  3.000
 74P  H12  CD   H11  106.40  3.000
 74P  H12  CD   CE   109.08  3.000
 74P  H11  CD   CE   109.36  3.000
 74P  H12  CD   CG   109.73  3.000
 74P  H11  CD   CG   109.97  3.000
 74P  CE   CD   CG   112.12  3.000
 74P  H14  CE   H13  106.11  3.000
 74P  H14  CE   NZ   109.43  3.000
 74P  H13  CE   NZ   112.25  3.000
 74P  H14  CE   CD   109.01  3.000
 74P  H13  CE   CD   108.87  3.000
 74P  NZ   CE   CD   111.02  3.000
 74P  CX1  NZ   CE   121.06  3.000
 74P  CX2  CX1  C1   113.43  3.000
 74P  C1   CX1  NZ   126.94  3.000
 74P  CX2  CX1  NZ   119.58  3.000
 74P  H16  C1   H15  106.44  3.000
 74P  H16  C1   CX1  112.39  3.000
 74P  H15  C1   CX1  109.91  3.000
 74P  H16  C1   C2   107.14  3.000
 74P  H15  C1   C2   110.27  3.000
 74P  CX1  C1   C2   110.57  3.000
 74P  O6   CX2  CX1  113.84  3.000
 74P  CX1  CX2  O2   118.30  3.000
 74P  O6   CX2  O2   127.86  3.000
 74P  O1   C    O    126.63  3.000
 74P  O1   C    CA   117.11  3.000
 74P  O    C    CA   120.80  1.700
 74P  H20  C3   H19  106.82  3.000
 74P  H20  C3   H18  109.23  3.000
 74P  H19  C3   H18  109.55  3.000
 74P  H20  C3   C2   109.78  3.000
 74P  H19  C3   C2   109.47  3.000
 74P  H18  C3   C2   111.85  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
 74P  Var_01  CX2  CX1  NZ  CE   176.18   0.0  2
 74P  Var_02  CX1  C1   C2  O4   -43.29  30.0  3
 74P  Var_03  CD   CG   CB  CA   174.28  30.0  3
 74P  Var_04  CE   CD   CG  CB  -179.36  30.0  1
 74P  Var_05  NZ   CE   CD  CG   178.76  30.0  3
 74P  Var_06  H18  C3   C2  O4     0.79  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
 74P  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
 74P  plan-1  C2   0.020
 74P  plan-1  O4   0.020
 74P  plan-1  C1   0.020
 74P  plan-1  C3   0.020
 74P  plan-2  O2   0.020
 74P  plan-2  CX1  0.020
 74P  plan-2  CX2  0.020
 74P  plan-2  O6   0.020
 74P  plan-3  CA   0.020
 74P  plan-3  C    0.020
 74P  plan-3  O    0.020
 74P  plan-3  O1   0.020
 74P  plan-4  CE   0.020
 74P  plan-4  NZ   0.020
 74P  plan-4  CX1  0.020
 74P  plan-4  C1   0.020
 74P  plan-4  CX2  0.020

