# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:56:57 2022
#   Inital geometry file: a 74 line input string
#   Ligand name: N~6~-[(1Z)-ethanimidoyl]-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=N)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
 IEL  IEL  N~6~-[(1Z)-ethanimidoyl]-L-lysine  L-peptide  29  13  .  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_IEL
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
 IEL  O     O  O      0  -0.605  34.4066  16.2937  22.6159
 IEL  C     C  C      0   0.380  33.5573  17.1060  22.1955
 IEL  OXT   O  OC    -1  -0.617  33.4020  18.2868  22.5727
 IEL  CA    C  CH1    0  -0.205  32.5561  16.5920  21.1286
 IEL  N     N  NH2    0  -0.787  33.0049  15.4361  20.3625
 IEL  CB    C  CH2    0  -0.410  31.2251  16.2764  21.8184
 IEL  CG'   C  CH2    0  -0.411  30.0825  15.9546  20.8647
 IEL  CG    C  CH2    0  -0.413  28.7912  15.6222  21.6012
 IEL  CD    C  CH2    0  -0.313  27.5888  15.3868  20.6924
 IEL  NE    N  NH1    0  -0.616  27.7301  14.2695  19.7885
 IEL  CZ    C  C      0   0.387  28.1253  14.3310  18.4896
 IEL  NH1   N  N      0  -0.684  28.4133  15.3760  17.8062
 IEL  CH2   C  CH3    0  -0.733  28.1985  12.9849  17.8215
 IEL  HA    H  HCH1   0   0.197  32.3731  17.4060  20.4175
 IEL  HN    H  HNH2   0   0.331  33.8118  15.7062  19.8123
 IEL  HNA   H  HNH2   0   0.319  33.3690  14.7579  21.0230
 IEL  HB    H  HCH2   0   0.200  31.3743  15.4354  22.5078
 IEL  HBA   H  HCH2   0   0.211  30.9431  17.1310  22.4396
 IEL  HG'   H  HCH2   0   0.200  29.9143  16.8124  20.2034
 IEL  HG'A  H  HCH2   0   0.216  30.3679  15.1206  20.2214
 IEL  HG    H  HCH2   0   0.214  28.9457  14.7404  22.2319
 IEL  HGA   H  HCH2   0   0.214  28.5370  16.4398  22.2837
 IEL  HD    H  HCH2   0   0.250  26.7014  15.2131  21.3045
 IEL  HDA   H  HCH2   0   0.229  27.3782  16.2888  20.1130
 IEL  HNE   H  HNH1   0   0.388  27.6000  13.3540  20.1858
 IEL  HNH1  H  H      0   0.314  28.3486  16.2250  18.3600
 IEL  HH2   H  HCH3   0   0.248  28.4925  13.0974  16.7818
 IEL  HH2A  H  HCH3   0   0.249  28.9258  12.3424  18.3209
 IEL  HH2B  H  HCH3   0   0.248  27.2345  12.4752  17.8596

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
 IEL  O    C     deloc   1.231  0.020  1.231
 IEL  CA   C     single  1.525  0.021  1.525
 IEL  C    OXT   deloc   1.249  0.020  1.249
 IEL  N    CA    single  1.458  0.019  1.458
 IEL  CA   CB    single  1.530  0.020  1.530
 IEL  CA   HA    single  0.970  0.020  0.970
 IEL  N    HN    single  0.890  0.020  1.040
 IEL  N    HNA   single  0.890  0.020  1.040
 IEL  CG'  CB    single  1.523  0.020  1.523
 IEL  CB   HB    single  0.970  0.020  1.090
 IEL  CB   HBA   single  0.970  0.020  1.090
 IEL  CG'  CG    single  1.523  0.020  1.523
 IEL  CG'  HG'   single  0.970  0.020  1.090
 IEL  CG'  HG'A  single  0.970  0.020  1.090
 IEL  CD   CG    single  1.525  0.020  1.525
 IEL  CG   HG    single  0.970  0.020  1.090
 IEL  CG   HGA   single  0.970  0.020  1.090
 IEL  NE   CD    single  1.444  0.020  1.444
 IEL  CD   HD    single  0.970  0.020  1.090
 IEL  CD   HDA   single  0.970  0.020  1.090
 IEL  CZ   NE    single  1.359  0.020  1.359
 IEL  NE   HNE   single  0.860  0.020  1.020
 IEL  CH2  CZ    single  1.505  0.020  1.505
 IEL  NH1  CZ    double  1.281  0.020  1.281
 IEL  NH1  HNH1  single  0.890  0.020  1.040
 IEL  CH2  HH2   single  0.970  0.020  1.090
 IEL  CH2  HH2A  single  0.970  0.020  1.090
 IEL  CH2  HH2B  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
 IEL  CA    C    OXT   116.15  3.000
 IEL  OXT   C    O     126.73  3.000
 IEL  CA    C    O     120.80  1.700
 IEL  HA    CA   CB    109.00  3.000
 IEL  HA    CA   N     110.00  3.000
 IEL  CB    CA   N     110.50  1.700
 IEL  HA    CA   C     109.00  3.000
 IEL  CB    CA   C     110.10  1.900
 IEL  N     CA   C     111.00  2.800
 IEL  HNA   N    HN    104.24  3.000
 IEL  HNA   N    CA    107.37  3.000
 IEL  HN    N    CA    108.61  3.000
 IEL  HBA   CB   HB    106.08  3.000
 IEL  HBA   CB   CG'   109.11  3.000
 IEL  HB    CB   CG'   109.48  3.000
 IEL  HBA   CB   CA    108.59  3.000
 IEL  HB    CB   CA    108.82  3.000
 IEL  CG'   CB   CA    114.42  3.000
 IEL  HG'A  CG'  HG'   106.41  3.000
 IEL  HG'A  CG'  CG    109.87  3.000
 IEL  HG'   CG'  CG    109.42  3.000
 IEL  HG'A  CG'  CB    109.54  3.000
 IEL  HG'   CG'  CB    109.13  3.000
 IEL  CG    CG'  CB    112.30  3.000
 IEL  HGA   CG   HG    105.97  3.000
 IEL  HGA   CG   CD    107.67  3.000
 IEL  HG    CG   CD    109.27  3.000
 IEL  HGA   CG   CG'   109.58  3.000
 IEL  HG    CG   CG'   109.55  3.000
 IEL  CD    CG   CG'   114.44  3.000
 IEL  HDA   CD   HD    105.77  3.000
 IEL  HDA   CD   NE    109.01  3.000
 IEL  HD    CD   NE    107.90  3.000
 IEL  HDA   CD   CG    109.91  3.000
 IEL  HD    CD   CG    109.34  3.000
 IEL  NE    CD   CG    114.53  3.000
 IEL  HNE   NE   CZ    117.14  3.000
 IEL  HNE   NE   CD    116.36  3.000
 IEL  CZ    NE   CD    126.27  3.000
 IEL  CH2   CZ   NH1   118.81  3.000
 IEL  NH1   CZ   NE    127.74  3.000
 IEL  CH2   CZ   NE    113.45  3.000
 IEL  HNH1  NH1  CZ    112.12  3.000
 IEL  HH2B  CH2  HH2A  107.32  3.000
 IEL  HH2B  CH2  HH2   108.72  3.000
 IEL  HH2A  CH2  HH2   108.57  3.000
 IEL  HH2B  CH2  CZ    111.07  3.000
 IEL  HH2A  CH2  CZ    110.85  3.000
 IEL  HH2   CH2  CZ    110.21  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
 IEL  CONST_01  CH2   CZ   NE   CD   180.00   0.0  0
 IEL  CONST_02  NH1   CZ   NE   CD     0.00   0.0  0
 IEL  CONST_03  HNH1  NH1  CZ   NE     0.00   0.0  0
 IEL  CONST_04  HNE   NE   CZ   NH1  180.00   0.0  0
 IEL  Var_01    CG    CG'  CB   CA   178.88  30.0  1
 IEL  Var_02    CD    CG   CG'  CB   175.95  30.0  3
 IEL  Var_03    NE    CD   CG   CG'   62.02  30.0  1
 IEL  Var_04    CZ    NE   CD   CG   -96.86  30.0  1
 IEL  Var_05    HH2   CH2  CZ   NE   178.48  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
 IEL  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
 IEL  plan-1  CD    0.020
 IEL  plan-1  NE    0.020
 IEL  plan-1  CZ    0.020
 IEL  plan-1  NH1   0.020
 IEL  plan-1  CH2   0.020
 IEL  plan-1  HNE   0.020
 IEL  plan-1  HNH1  0.020
 IEL  plan-2  O     0.020
 IEL  plan-2  C     0.020
 IEL  plan-2  OXT   0.020
 IEL  plan-2  CA    0.020

