# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 18:38:52 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: {(4Z)-2-[(1R)-1-amino-2-sulfanylethyl]-4-[(3-chloro-4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CS)C1=N\C(=C/c2ccc(O)c(Cl)c2)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
 KZ7  KZ7  '{(4Z)-2-[(1R)-1-amino-2-sulfanylethyl]-4-[(3-chloro-4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid'  L-peptide  37  23  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KZ7
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
 KZ7  N     N   NH2   0  -0.758  -2.1378   2.6067   1.5223
 KZ7  CB1   C   CH2   0  -0.552  -3.3461   1.9338  -0.4677
 KZ7  CA1   C   CH1   0  -0.207  -2.7780   1.4869   0.8791
 KZ7  C1    C   CR5   0   0.542  -1.8600   0.3144   0.6468
 KZ7  N2    N   N     0  -0.478  -0.5865   0.4335   0.5113
 KZ7  N3    N   NR5   0  -0.565  -2.3081  -0.9872   0.5354
 KZ7  C2    C   CR5   0   0.544  -1.2178  -1.7974   0.2813
 KZ7  O2    O   O     0  -0.440  -1.2561  -2.9984   0.1198
 KZ7  CA2   C   CR5   0   0.097  -0.0904  -0.8421   0.2785
 KZ7  CA3   C   CH2   0  -0.462  -3.6431  -1.4963   0.6132
 KZ7  CB2   C   C1    0  -0.384   1.1876  -1.2195   0.0804
 KZ7  CG2   C   CR6   0   0.134   2.3875  -0.4136   0.0505
 KZ7  CD1   C   CR16  0  -0.255   3.6040  -1.0736  -0.1488
 KZ7  CD2   C   CR16  0  -0.290   2.4134   0.9811   0.2072
 KZ7  CE1   C   CR6   0  -0.161   4.7908  -0.3721  -0.1903
 KZ7  CE2   C   CR16  0  -0.320   3.6020   1.6763   0.1611
 KZ7  CZ    C   CR6   0   0.424   4.8167   1.0165  -0.0391
 KZ7  OH    O   OH1   0  -0.598   5.9329   1.7442  -0.0766
 KZ7  C     C   C     0   0.551  -4.2047  -1.8006  -0.7603
 KZ7  O     O   O     0  -0.426  -3.6614  -1.5105  -1.7923
 KZ7  CL    CL  CL    0  -0.106   6.2860  -1.2146  -0.4346
 KZ7  HN1   H   HNH2  0   0.362  -1.8449   2.3528   2.4570
 KZ7  HN2   H   HNH2  0   0.354  -1.2965   2.8622   1.0185
 KZ7  HG1   H   HSH1  0   0.216  -5.2272   3.1598  -1.2477
 KZ7  HB11  H   HCH2  0   0.284  -3.9186   1.1400  -0.9438
 KZ7  HB12  H   HCH2  0   0.279  -2.5292   2.2022  -1.1396
 KZ7  HA1   H   HCH1  0   0.280  -3.6107   1.1696   1.5136
 KZ7  HA31  H   HCH2  0   0.324  -3.6585  -2.4012   1.2236
 KZ7  HA32  H   HCH2  0   0.327  -4.2937  -0.7811   1.1182
 KZ7  HB1   H   H     0   0.274   1.3375  -2.2827  -0.0793
 KZ7  HD1   H   HCR6  0   0.287   3.6199  -2.1492  -0.2697
 KZ7  HD2   H   HCR6  0   0.283   1.4922   1.5220   0.3672
 KZ7  HE2   H   HCR6  0   0.283   3.6085   2.7521   0.2802
 KZ7  H1    H   HOH1  0   0.475   6.7139   1.1903  -0.2099
 KZ7  OXT   O   OH1   0  -0.583  -5.3718  -2.4117  -0.6630
 KZ7  HXT   H   HOH1  0   0.490  -5.7406  -2.5823  -1.5431
 KZ7  SG1   S   S2    0  -0.226  -4.4318   3.3711  -0.1932

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
 KZ7  CL   CE1   single    1.734  0.020  1.734
 KZ7  OH   CZ    single    1.333  0.020  1.333
 KZ7  CE1  CZ    aromatic  1.397  0.020  1.397
 KZ7  CE1  CD1   aromatic  1.379  0.020  1.379
 KZ7  CZ   CE2   aromatic  1.397  0.020  1.397
 KZ7  CD1  CG2   aromatic  1.398  0.020  1.398
 KZ7  CE2  CD2   aromatic  1.378  0.020  1.378
 KZ7  CG2  CD2   aromatic  1.404  0.020  1.404
 KZ7  CG2  CB2   single    1.446  0.020  1.446
 KZ7  CB2  CA2   double    1.347  0.020  1.347
 KZ7  CA2  N2    single    1.388  0.020  1.388
 KZ7  CA2  C2    single    1.478  0.020  1.478
 KZ7  O2   C2    double    1.212  0.020  1.212
 KZ7  N2   C1    double    1.286  0.020  1.286
 KZ7  C2   N3    single    1.382  0.020  1.382
 KZ7  C1   N3    single    1.381  0.020  1.381
 KZ7  C1   CA1   single    1.507  0.020  1.507
 KZ7  N3   CA3   single    1.431  0.020  1.431
 KZ7  CB1  CA1   single    1.529  0.020  1.529
 KZ7  CB1  SG1   single    1.822  0.020  1.822
 KZ7  CA1  N     single    1.441  0.020  1.441
 KZ7  CA3  C     single    1.515  0.020  1.515
 KZ7  C    O     double    1.202  0.020  1.202
 KZ7  N    HN1   single    0.890  0.020  1.040
 KZ7  N    HN2   single    0.890  0.020  1.040
 KZ7  SG1  HG1   single    1.200  0.020  1.300
 KZ7  CB1  HB11  single    0.970  0.020  1.090
 KZ7  CB1  HB12  single    0.970  0.020  1.090
 KZ7  CA1  HA1   single    0.970  0.020  1.090
 KZ7  CA3  HA31  single    0.970  0.020  1.090
 KZ7  CA3  HA32  single    0.970  0.020  1.090
 KZ7  CB2  HB1   single    0.930  0.020  1.080
 KZ7  CD1  HD1   single    0.930  0.020  1.080
 KZ7  CD2  HD2   single    0.930  0.020  1.080
 KZ7  CE2  HE2   single    0.930  0.020  1.080
 KZ7  OH   H1    single    0.850  0.020  0.980
 KZ7  C    OXT   single    1.321  0.020  1.321
 KZ7  OXT  HXT   single    0.850  0.020  0.980

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
 KZ7  HN2   N    HN1   106.39  3.000
 KZ7  HN2   N    CA1   110.05  3.000
 KZ7  HN1   N    CA1   110.23  3.000
 KZ7  HB12  CB1  HB11  107.69  3.000
 KZ7  HB12  CB1  CA1   109.65  3.000
 KZ7  HB11  CB1  CA1   111.57  3.000
 KZ7  HB12  CB1  SG1   110.16  3.000
 KZ7  HB11  CB1  SG1   109.14  3.000
 KZ7  CA1   CB1  SG1   108.62  3.000
 KZ7  HA1   CA1  C1    109.11  3.000
 KZ7  HA1   CA1  CB1   108.24  3.000
 KZ7  C1    CA1  CB1   108.54  3.000
 KZ7  HA1   CA1  N     107.74  3.000
 KZ7  CB1   CA1  N     109.34  3.000
 KZ7  C1    CA1  N     113.74  3.000
 KZ7  N3    C1   N2    113.58  3.000
 KZ7  N3    C1   CA1   123.23  3.000
 KZ7  N2    C1   CA1   123.18  3.000
 KZ7  CA2   N2   C1    106.65  3.000
 KZ7  CA3   N3   C2    122.51  3.000
 KZ7  CA3   N3   C1    129.32  3.000
 KZ7  C2    N3   C1    108.14  3.000
 KZ7  CA2   C2   O2    131.62  3.000
 KZ7  O2    C2   N3    125.47  3.000
 KZ7  CA2   C2   N3    102.90  3.000
 KZ7  CB2   CA2  C2    122.88  3.000
 KZ7  C2    CA2  N2    108.72  3.000
 KZ7  CB2   CA2  N2    128.39  3.000
 KZ7  HA32  CA3  HA31  106.03  3.000
 KZ7  HA32  CA3  C     109.30  3.000
 KZ7  HA31  CA3  C     109.59  3.000
 KZ7  HA32  CA3  N3    110.38  3.000
 KZ7  HA31  CA3  N3    109.78  3.000
 KZ7  C     CA3  N3    111.60  3.000
 KZ7  HB1   CB2  CG2   115.36  3.000
 KZ7  HB1   CB2  CA2   115.28  3.000
 KZ7  CG2   CB2  CA2   129.36  3.000
 KZ7  CD2   CG2  CD1   117.95  3.000
 KZ7  CD2   CG2  CB2   124.53  3.000
 KZ7  CD1   CG2  CB2   117.51  3.000
 KZ7  HD1   CD1  CE1   119.30  3.000
 KZ7  HD1   CD1  CG2   119.84  3.000
 KZ7  CE1   CD1  CG2   120.86  3.000
 KZ7  HD2   CD2  CE2   119.21  3.000
 KZ7  HD2   CD2  CG2   119.89  3.000
 KZ7  CE2   CD2  CG2   120.90  3.000
 KZ7  CL    CE1  CZ    118.84  3.000
 KZ7  CZ    CE1  CD1   121.21  3.000
 KZ7  CL    CE1  CD1   119.95  3.000
 KZ7  HE2   CE2  CZ    118.69  3.000
 KZ7  HE2   CE2  CD2   120.20  3.000
 KZ7  CZ    CE2  CD2   121.11  3.000
 KZ7  OH    CZ   CE2   118.32  3.000
 KZ7  CE2   CZ   CE1   117.96  3.000
 KZ7  OH    CZ   CE1   123.72  3.000
 KZ7  H1    OH   CZ    111.56  3.000
 KZ7  OXT   C    O     125.05  3.000
 KZ7  OXT   C    CA3   110.72  3.000
 KZ7  O     C    CA3   124.23  3.000
 KZ7  HXT   OXT  C     110.53  3.000
 KZ7  HG1   SG1  CB1    96.37  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
 KZ7  CONST_01  CZ   CE1  CD1  CG2    0.00   0.0  0
 KZ7  CONST_02  CZ   CE2  CD2  CG2    0.00   0.0  0
 KZ7  CONST_03  CE2  CZ   CE1  CD1    0.00   0.0  0
 KZ7  CONST_04  CE2  CD2  CG2  CD1    0.00   0.0  0
 KZ7  CONST_05  CE1  CZ   CE2  CD2    0.00   0.0  0
 KZ7  CONST_06  CE1  CD1  CG2  CD2    0.00   0.0  0
 KZ7  CONST_07  C2   CA2  N2   C1     0.00   0.0  0
 KZ7  CONST_08  CA2  C2   N3   C1     0.00   0.0  0
 KZ7  CONST_09  N3   C2   CA2  N2     0.00   0.0  0
 KZ7  CONST_10  C2   N3   C1   N2     0.00   0.0  0
 KZ7  CONST_11  CA2  N2   C1   N3     0.00   0.0  0
 KZ7  CONST_12  CE1  CD1  CG2  CB2  180.00   0.0  0
 KZ7  CONST_13  CE2  CD2  CG2  CB2  180.00   0.0  0
 KZ7  CONST_14  CL   CE1  CD1  CG2  180.00   0.0  0
 KZ7  CONST_15  OH   CZ   CE1  CD1  180.00   0.0  0
 KZ7  CONST_16  OH   CZ   CE2  CD2  180.00   0.0  0
 KZ7  CONST_17  CL   CE1  CZ   CE2  180.00   0.0  0
 KZ7  CONST_18  CA2  N2   C1   CA1  180.00   0.0  0
 KZ7  CONST_19  C2   N3   C1   CA1  180.00   0.0  0
 KZ7  CONST_20  O2   C2   N3   C1   180.00   0.0  0
 KZ7  CONST_21  CA3  N3   C1   N2   180.00   0.0  0
 KZ7  CONST_22  CA3  N3   C2   CA2  180.00   0.0  0
 KZ7  CONST_23  HE2  CE2  CD2  CG2  180.00   0.0  0
 KZ7  CONST_24  HD2  CD2  CG2  CD1  180.00   0.0  0
 KZ7  CONST_25  HD1  CD1  CG2  CD2  180.00   0.0  0
 KZ7  CONST_26  CA3  N3   C1   CA1    0.00   0.0  0
 KZ7  CONST_27  CA3  N3   C2   O2     0.00   0.0  0
 KZ7  CONST_28  HXT  OXT  C    CA3  180.00   0.0  0
 KZ7  Var_01    CG2  CB2  CA2  N2    -0.21  30.0  2
 KZ7  Var_02    CD1  CG2  CB2  CA2  178.65  30.0  2
 KZ7  Var_03    C    CA3  N3   C1   101.99  30.0  3
 KZ7  Var_04    O    C    CA3  N3    -7.92  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
 KZ7  chir_01  CA1  C1  CB1  N  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
 KZ7  plan-1  CA1  0.020
 KZ7  plan-1  C1   0.020
 KZ7  plan-1  N2   0.020
 KZ7  plan-1  N3   0.020
 KZ7  plan-1  C2   0.020
 KZ7  plan-1  O2   0.020
 KZ7  plan-1  CA2  0.020
 KZ7  plan-1  CA3  0.020
 KZ7  plan-1  CB2  0.020
 KZ7  plan-2  CB2  0.020
 KZ7  plan-2  CG2  0.020
 KZ7  plan-2  CD1  0.020
 KZ7  plan-2  CD2  0.020
 KZ7  plan-2  CE1  0.020
 KZ7  plan-2  CE2  0.020
 KZ7  plan-2  CZ   0.020
 KZ7  plan-2  OH   0.020
 KZ7  plan-2  CL   0.020
 KZ7  plan-2  HD1  0.020
 KZ7  plan-2  HD2  0.020
 KZ7  plan-2  HE2  0.020
 KZ7  plan-3  CA3  0.020
 KZ7  plan-3  C    0.020
 KZ7  plan-3  O    0.020
 KZ7  plan-3  OXT  0.020
 KZ7  plan-3  HXT  0.020

