# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 16:50:05 2022
#   Inital geometry file: a 99 line input string
#   Ligand name: 2-[(4~{Z})-2-(aminomethyl)-4-[(4-azidophenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC1=N\C(=C/c2ccc(cc2)N=[N+]=[N-])C(=O)N1CC(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
 LKE  LKE  '2-[(4~{Z})-2-(aminomethyl)-4-[(4-azidophenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic acid'  L-peptide  33  22  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LKE
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
 LKE  CA1  C  CH2    0  -0.413  24.5837   4.8405   0.8819
 LKE  N1   N  NH2    0  -0.795  25.6778   4.0440   0.3370
 LKE  C1   C  CR5    0   0.534  24.0615   4.2157   2.1325
 LKE  N2   N  N      0  -0.493  22.9660   3.5347   2.1896
 LKE  N3   N  NR5    0  -0.524  24.7598   4.2660   3.3184
 LKE  CA3  C  CH2    0  -0.482  25.8033   5.2038   3.6499
 LKE  C3   C  C      0   0.419  25.2596   6.6316   3.9174
 LKE  O3   O  O      0  -0.585  24.0504   6.8172   3.7026
 LKE  C2   C  CR5    0   0.529  24.0120   3.6144   4.2723
 LKE  O2   O  O      0  -0.443  24.2782   3.5163   5.4528
 LKE  CA2  C  CR5    0   0.097  22.8512   3.1025   3.5034
 LKE  CB2  C  C1     0  -0.390  21.8781   2.3614   4.0663
 LKE  CG2  C  CR6    0   0.146  20.6803   1.8063   3.4712
 LKE  CD2  C  CR16   0  -0.291  19.8167   1.0690   4.2927
 LKE  CE2  C  CR16   0  -0.295  18.6490   0.5203   3.8036
 LKE  CZ   C  CR6    0   0.252  18.3070   0.6948   2.4646
 LKE  CE1  C  CR16   0  -0.268  19.1555   1.4221   1.6268
 LKE  CD1  C  CR16   0  -0.304  20.3227   1.9666   2.1252
 LKE  NW   N  N      0  -0.391  17.1026   0.1083   2.0589
 LKE  NX   N  N      1   0.366  16.7520   0.2283   0.8928
 LKE  NY   N  N     -1  -0.177  16.3292   0.2713  -0.1436
 LKE  OXT  O  OC    -1  -0.598  26.1133   7.4430   4.3128
 LKE  H1   H  HCH2   0   0.237  24.8375   5.8892   1.0773
 LKE  H2   H  HCH2   0   0.265  23.7646   4.8400   0.1640
 LKE  H3   H  HNH2   0   0.363  25.8652   4.3600  -0.6058
 LKE  H4   H  HNH2   0   0.353  26.5296   4.2165   0.8556
 LKE  H6   H  HCH2   0   0.270  26.3257   4.8307   4.5310
 LKE  H7   H  HCH2   0   0.267  26.5456   5.2348   2.8499
 LKE  H8   H  H      0   0.265  22.0084   2.1538   5.1239
 LKE  H9   H  HCR6   0   0.265  20.0673   0.9270   5.3369
 LKE  H10  H  HCR6   0   0.272  17.9926  -0.0434   4.4530
 LKE  H11  H  HCR6   0   0.272  18.9144   1.5717   0.5813
 LKE  H12  H  HCR6   0   0.276  20.9665   2.5279   1.4634

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
 LKE  NY   NX   double    1.120  0.020  1.120
 LKE  N1   CA1  single    1.459  0.020  1.459
 LKE  CA1  C1   single    1.492  0.020  1.492
 LKE  NX   NW   double    1.224  0.020  1.224
 LKE  CE1  CD1  aromatic  1.381  0.020  1.381
 LKE  CE1  CZ   aromatic  1.397  0.020  1.397
 LKE  NW   CZ   single    1.400  0.020  1.400
 LKE  C1   N2   double    1.291  0.020  1.291
 LKE  C1   N3   single    1.377  0.020  1.377
 LKE  N2   CA2  single    1.388  0.020  1.388
 LKE  CD1  CG2  aromatic  1.402  0.020  1.402
 LKE  CZ   CE2  aromatic  1.393  0.020  1.393
 LKE  N3   CA3  single    1.442  0.020  1.442
 LKE  N3   C2   single    1.376  0.020  1.376
 LKE  O3   C3   deloc     1.242  0.020  1.242
 LKE  CA2  C2   single    1.484  0.020  1.484
 LKE  CA2  CB2  double    1.346  0.020  1.346
 LKE  CG2  CB2  single    1.448  0.020  1.448
 LKE  CG2  CD2  aromatic  1.401  0.020  1.401
 LKE  CA3  C3   single    1.551  0.020  1.551
 LKE  CE2  CD2  aromatic  1.380  0.020  1.380
 LKE  C2   O2   double    1.214  0.020  1.214
 LKE  C3   OXT  deloc     1.242  0.020  1.242
 LKE  CA1  H1   single    0.970  0.020  1.090
 LKE  CA1  H2   single    0.970  0.020  1.090
 LKE  N1   H3   single    0.890  0.020  1.040
 LKE  N1   H4   single    0.890  0.020  1.040
 LKE  CA3  H6   single    0.970  0.020  1.090
 LKE  CA3  H7   single    0.970  0.020  1.090
 LKE  CB2  H8   single    0.930  0.020  1.080
 LKE  CD2  H9   single    0.930  0.020  1.080
 LKE  CE2  H10  single    0.930  0.020  1.080
 LKE  CE1  H11  single    0.930  0.020  1.080
 LKE  CD1  H12  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
 LKE  H2   CA1  H1   106.97  3.000
 LKE  H2   CA1  C1   106.80  3.000
 LKE  H1   CA1  C1   109.39  3.000
 LKE  H2   CA1  N1   108.52  3.000
 LKE  H1   CA1  N1   114.53  3.000
 LKE  C1   CA1  N1   110.29  3.000
 LKE  H4   N1   H3   105.56  3.000
 LKE  H4   N1   CA1  110.29  3.000
 LKE  H3   N1   CA1  108.44  3.000
 LKE  N3   C1   N2   114.29  3.000
 LKE  N3   C1   CA1  121.93  3.000
 LKE  N2   C1   CA1  123.69  3.000
 LKE  CA2  N2   C1   106.04  3.000
 LKE  C2   N3   CA3  122.82  3.000
 LKE  C2   N3   C1   107.70  3.000
 LKE  CA3  N3   C1   126.07  3.000
 LKE  H7   CA3  H6   106.03  3.000
 LKE  H7   CA3  C3   109.79  3.000
 LKE  H6   CA3  C3   110.10  3.000
 LKE  H7   CA3  N3   110.01  3.000
 LKE  H6   CA3  N3   108.06  3.000
 LKE  C3   CA3  N3   112.63  3.000
 LKE  OXT  C3   O3   128.78  3.000
 LKE  OXT  C3   CA3  114.54  3.000
 LKE  O3   C3   CA3  116.68  3.000
 LKE  CA2  C2   O2   130.36  3.000
 LKE  O2   C2   N3   126.38  3.000
 LKE  CA2  C2   N3   103.26  3.000
 LKE  CB2  CA2  C2   122.60  3.000
 LKE  CB2  CA2  N2   128.82  3.000
 LKE  C2   CA2  N2   108.57  3.000
 LKE  H8   CB2  CG2  115.23  3.000
 LKE  H8   CB2  CA2  115.20  3.000
 LKE  CG2  CB2  CA2  129.57  3.000
 LKE  CD1  CG2  CD2  117.76  3.000
 LKE  CD2  CG2  CB2  118.07  3.000
 LKE  CD1  CG2  CB2  124.17  3.000
 LKE  H9   CD2  CE2  119.03  3.000
 LKE  H9   CD2  CG2  119.44  3.000
 LKE  CE2  CD2  CG2  121.53  3.000
 LKE  H10  CE2  CZ   119.56  3.000
 LKE  H10  CE2  CD2  120.53  3.000
 LKE  CZ   CE2  CD2  119.91  3.000
 LKE  NW   CZ   CE1  124.54  3.000
 LKE  NW   CZ   CE2  115.94  3.000
 LKE  CE1  CZ   CE2  119.52  3.000
 LKE  H11  CE1  CD1  118.81  3.000
 LKE  H11  CE1  CZ   121.04  3.000
 LKE  CD1  CE1  CZ   120.15  3.000
 LKE  H12  CD1  CE1  119.16  3.000
 LKE  H12  CD1  CG2  119.71  3.000
 LKE  CE1  CD1  CG2  121.13  3.000
 LKE  NX   NW   CZ   118.80  3.000
 LKE  NY   NX   NW   173.57  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
 LKE  CONST_01  CZ   CE1  CD1  CG2     0.00   0.0  0
 LKE  CONST_02  CZ   CE2  CD2  CG2     0.00   0.0  0
 LKE  CONST_03  CE1  CD1  CG2  CD2     0.00   0.0  0
 LKE  CONST_04  CE1  CZ   CE2  CD2     0.00   0.0  0
 LKE  CONST_05  CD1  CE1  CZ   CE2     0.00   0.0  0
 LKE  CONST_06  CD1  CG2  CD2  CE2     0.00   0.0  0
 LKE  CONST_07  C2   CA2  N2   C1      0.00   0.0  0
 LKE  CONST_08  CA2  C2   N3   C1      0.00   0.0  0
 LKE  CONST_09  C2   N3   C1   N2      0.00   0.0  0
 LKE  CONST_10  N3   C2   CA2  N2      0.00   0.0  0
 LKE  CONST_11  CA2  N2   C1   N3      0.00   0.0  0
 LKE  CONST_12  CE1  CD1  CG2  CB2   180.00   0.0  0
 LKE  CONST_13  CE2  CD2  CG2  CB2   180.00   0.0  0
 LKE  CONST_14  NW   CZ   CE2  CD2   180.00   0.0  0
 LKE  CONST_15  NW   CZ   CE1  CD1   180.00   0.0  0
 LKE  CONST_16  CA2  N2   C1   CA1   180.00   0.0  0
 LKE  CONST_17  C2   N3   C1   CA1   180.00   0.0  0
 LKE  CONST_18  O2   C2   N3   C1    180.00   0.0  0
 LKE  CONST_21  H11  CE1  CD1  CG2   180.00   0.0  0
 LKE  CONST_22  H10  CE2  CD2  CG2   180.00   0.0  0
 LKE  CONST_23  H12  CD1  CG2  CD2   180.00   0.0  0
 LKE  CONST_24  H9   CD2  CE2  CZ    180.00   0.0  0
 LKE  CONST_25  NX   NW   CZ   CE2   180.00   0.0  0
 LKE  CONST_26  NX   NW   CZ   CE1     0.00   0.0  0
 LKE  Var_01    CG2  CB2  CA2  N2     -0.05   0.0  2
 LKE  Var_02    CD1  CG2  CB2  CA2    -0.09  30.0  1
 LKE  Var_03    N2   C1   CA1  N1   -102.77  30.0  3
 LKE  Var_04    C3   CA3  N3   C1     72.68  30.0  3
 LKE  Var_05    O3   C3   CA3  N3     -6.16  30.0  3
 LKE  Var_06    H3   N1   CA1  C1    166.92  30.0  3

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
 LKE  plan-1  CA1  0.020
 LKE  plan-1  C1   0.020
 LKE  plan-1  N2   0.020
 LKE  plan-1  N3   0.020
 LKE  plan-1  CA3  0.020
 LKE  plan-1  C2   0.020
 LKE  plan-1  O2   0.020
 LKE  plan-1  CA2  0.020
 LKE  plan-1  CB2  0.020
 LKE  plan-1  CG2  0.020
 LKE  plan-1  H8   0.020
 LKE  plan-2  CA3  0.020
 LKE  plan-2  C3   0.020
 LKE  plan-2  O3   0.020
 LKE  plan-2  OXT  0.020
 LKE  plan-3  CB2  0.020
 LKE  plan-3  CG2  0.020
 LKE  plan-3  CD2  0.020
 LKE  plan-3  CE2  0.020
 LKE  plan-3  CZ   0.020
 LKE  plan-3  CE1  0.020
 LKE  plan-3  CD1  0.020
 LKE  plan-3  NW   0.020
 LKE  plan-3  NX   0.020
 LKE  plan-3  NY   0.020
 LKE  plan-3  H9   0.020
 LKE  plan-3  H10  0.020
 LKE  plan-3  H11  0.020
 LKE  plan-3  H12  0.020

