# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 20:28:25 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: {(4Z)-2-[(1R)-1-amino-2-sulfanylethyl]-4-[(3-bromo-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(Br)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
 KZ4  KZ4  '{(4Z)-2-[(1R)-1-amino-2-sulfanylethyl]-4-[(3-bromo-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_KZ4
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
 KZ4  N     N   NH2   0  -0.758  -1.2520   2.4587   1.4060
 KZ4  SG1   S   S2    0  -0.225  -3.3758   3.9392  -0.0125
 KZ4  CB1   C   CH2   0  -0.554  -2.8818   2.2224  -0.3727
 KZ4  CA1   C   CH1   0  -0.206  -2.3000   1.6088   0.9012
 KZ4  C1    C   CR5   0   0.545  -1.8505   0.2009   0.6082
 KZ4  N2    N   N     0  -0.483  -0.6216  -0.1221   0.4100
 KZ4  N3    N   NR5   0  -0.565  -2.7212  -0.8671   0.5207
 KZ4  C2    C   CR5   0   0.546  -1.9878  -1.9977   0.2139
 KZ4  O2    O   O     0  -0.441  -2.4449  -3.1100   0.0579
 KZ4  CA2   C   CR5   0   0.097  -0.6032  -1.4873   0.1556
 KZ4  CA3   C   CH2   0  -0.465  -4.1454  -0.8968   0.6645
 KZ4  CB2   C   C1    0  -0.380   0.4633  -2.2716  -0.0953
 KZ4  CG2   C   CR6   0   0.133   1.8632  -1.9151  -0.1622
 KZ4  CD1   C   CR16  0  -0.279   2.3413  -0.6110   0.0294
 KZ4  CD2   C   CR16  0  -0.280   2.7955  -2.9253  -0.4260
 KZ4  CE1   C   CR6   0  -0.188   3.6926  -0.3476  -0.0405
 KZ4  CE2   C   CR16  0  -0.375   4.1476  -2.6583  -0.4939
 KZ4  CZ    C   CR6   0   0.410   4.6223  -1.3621  -0.2991
 KZ4  OH    O   OH1   0  -0.595   5.9155  -1.0438  -0.3467
 KZ4  C     C   C     0   0.549  -4.8330  -1.0580  -0.6760
 KZ4  O     O   O     0  -0.426  -4.2800  -0.9422  -1.7368
 KZ4  BR    BR  BR    0  -0.023   4.3164   1.4104   0.2167
 KZ4  HN1   H   HNH2  0   0.362  -0.9163   2.1104   2.2948
 KZ4  HN2   H   HNH2  0   0.353  -0.4586   2.4489   0.7759
 KZ4  HG1   H   HSH1  0   0.216  -4.3164   4.0270  -0.9601
 KZ4  HB11  H   HCH2  0   0.281  -3.7526   1.6710  -0.7204
 KZ4  HB12  H   HCH2  0   0.281  -2.1353   2.2045  -1.1686
 KZ4  HA1   H   HCH1  0   0.283  -3.0903   1.5715   1.6573
 KZ4  HA31  H   HCH2  0   0.324  -4.4370  -1.7100   1.3314
 KZ4  HA32  H   HCH2  0   0.329  -4.5006   0.0214   1.1355
 KZ4  HB2   H   H     0   0.274   0.2424  -3.3205  -0.2665
 KZ4  HD1   H   HCR6  0   0.297   1.6422   0.1881   0.2322
 KZ4  HD2   H   HCR6  0   0.274   2.4543  -3.9410  -0.5809
 KZ4  HE2   H   HCR6  0   0.290   4.8474  -3.4605  -0.6965
 KZ4  H1    H   HOH1  0   0.489   6.4528  -1.8240  -0.5303
 KZ4  OXT   O   OH1   0  -0.583  -6.1176  -1.3206  -0.5154
 KZ4  HXT   H   HOH1  0   0.490  -6.5581  -1.3995  -1.3754

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
 KZ4  OH   CZ    single    1.333  0.020  1.333
 KZ4  BR   CE1   single    1.883  0.020  1.883
 KZ4  CZ   CE2   aromatic  1.394  0.020  1.394
 KZ4  CZ   CE1   aromatic  1.400  0.020  1.400
 KZ4  CE2  CD2   aromatic  1.380  0.020  1.380
 KZ4  CE1  CD1   aromatic  1.379  0.020  1.379
 KZ4  N    CA1   single    1.441  0.020  1.441
 KZ4  SG1  CB1   single    1.822  0.020  1.822
 KZ4  CD2  CG2   aromatic  1.400  0.020  1.400
 KZ4  CD1  CG2   aromatic  1.402  0.020  1.402
 KZ4  CB1  CA1   single    1.529  0.020  1.529
 KZ4  CG2  CB2   single    1.446  0.020  1.446
 KZ4  CA1  C1    single    1.507  0.020  1.507
 KZ4  N2   C1    double    1.286  0.020  1.286
 KZ4  N2   CA2   single    1.389  0.020  1.389
 KZ4  C1   N3    single    1.381  0.020  1.381
 KZ4  CA2  CB2   double    1.347  0.020  1.347
 KZ4  CA2  C2    single    1.477  0.020  1.477
 KZ4  N3   C2    single    1.382  0.020  1.382
 KZ4  N3   CA3   single    1.432  0.020  1.432
 KZ4  C2   O2    double    1.213  0.020  1.213
 KZ4  CA3  C     single    1.515  0.020  1.515
 KZ4  C    O     double    1.202  0.020  1.202
 KZ4  N    HN1   single    0.890  0.020  1.040
 KZ4  N    HN2   single    0.890  0.020  1.040
 KZ4  SG1  HG1   single    1.200  0.020  1.300
 KZ4  CB1  HB11  single    0.970  0.020  1.090
 KZ4  CB1  HB12  single    0.970  0.020  1.090
 KZ4  CA1  HA1   single    0.970  0.020  1.090
 KZ4  CA3  HA31  single    0.970  0.020  1.090
 KZ4  CA3  HA32  single    0.970  0.020  1.090
 KZ4  CB2  HB2   single    0.930  0.020  1.080
 KZ4  CD1  HD1   single    0.930  0.020  1.080
 KZ4  CD2  HD2   single    0.930  0.020  1.080
 KZ4  CE2  HE2   single    0.930  0.020  1.080
 KZ4  OH   H1    single    0.850  0.020  0.980
 KZ4  C    OXT   single    1.321  0.020  1.321
 KZ4  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
 KZ4  HN2   N    HN1   106.45  3.000
 KZ4  HN2   N    CA1   110.24  3.000
 KZ4  HN1   N    CA1   110.25  3.000
 KZ4  HG1   SG1  CB1    96.46  3.000
 KZ4  HB12  CB1  HB11  107.82  3.000
 KZ4  HB12  CB1  CA1   109.92  3.000
 KZ4  HB11  CB1  CA1   111.56  3.000
 KZ4  HB12  CB1  SG1   110.18  3.000
 KZ4  HB11  CB1  SG1   108.89  3.000
 KZ4  CA1   CB1  SG1   108.46  3.000
 KZ4  HA1   CA1  C1    108.54  3.000
 KZ4  HA1   CA1  CB1   108.33  3.000
 KZ4  C1    CA1  CB1   109.06  3.000
 KZ4  HA1   CA1  N     107.65  3.000
 KZ4  C1    CA1  N     113.73  3.000
 KZ4  CB1   CA1  N     109.39  3.000
 KZ4  N3    C1   N2    113.49  3.000
 KZ4  N3    C1   CA1   123.16  3.000
 KZ4  N2    C1   CA1   123.35  3.000
 KZ4  CA2   N2   C1    106.73  3.000
 KZ4  CA3   N3   C2    122.22  3.000
 KZ4  CA3   N3   C1    129.56  3.000
 KZ4  C2    N3   C1    108.19  3.000
 KZ4  CA2   C2   O2    131.71  3.000
 KZ4  O2    C2   N3    125.37  3.000
 KZ4  CA2   C2   N3    102.91  3.000
 KZ4  CB2   CA2  C2    123.25  3.000
 KZ4  C2    CA2  N2    108.67  3.000
 KZ4  CB2   CA2  N2    128.08  3.000
 KZ4  HA32  CA3  HA31  106.04  3.000
 KZ4  HA32  CA3  C     108.88  3.000
 KZ4  HA31  CA3  C     109.89  3.000
 KZ4  HA32  CA3  N3    110.47  3.000
 KZ4  HA31  CA3  N3    110.03  3.000
 KZ4  C     CA3  N3    111.39  3.000
 KZ4  HB2   CB2  CG2   115.33  3.000
 KZ4  HB2   CB2  CA2   115.52  3.000
 KZ4  CG2   CB2  CA2   129.15  3.000
 KZ4  CD2   CG2  CD1   118.02  3.000
 KZ4  CD1   CG2  CB2   123.58  3.000
 KZ4  CD2   CG2  CB2   118.40  3.000
 KZ4  HD1   CD1  CE1   120.15  3.000
 KZ4  HD1   CD1  CG2   119.51  3.000
 KZ4  CE1   CD1  CG2   120.34  3.000
 KZ4  HD2   CD2  CE2   118.90  3.000
 KZ4  HD2   CD2  CG2   119.61  3.000
 KZ4  CE2   CD2  CG2   121.49  3.000
 KZ4  BR    CE1  CZ    118.80  3.000
 KZ4  CZ    CE1  CD1   121.45  3.000
 KZ4  BR    CE1  CD1   119.75  3.000
 KZ4  HE2   CE2  CZ    119.64  3.000
 KZ4  HE2   CE2  CD2   119.92  3.000
 KZ4  CZ    CE2  CD2   120.44  3.000
 KZ4  OH    CZ   CE2   123.20  3.000
 KZ4  CE2   CZ   CE1   118.26  3.000
 KZ4  OH    CZ   CE1   118.54  3.000
 KZ4  H1    OH   CZ    110.74  3.000
 KZ4  OXT   C    O     125.02  3.000
 KZ4  OXT   C    CA3   110.78  3.000
 KZ4  O     C    CA3   124.19  3.000
 KZ4  HXT   OXT  C     110.50  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
 KZ4  CONST_01  CZ   CE2  CD2  CG2    0.00   0.0  0
 KZ4  CONST_02  CZ   CE1  CD1  CG2    0.00   0.0  0
 KZ4  CONST_03  CE2  CZ   CE1  CD1    0.00   0.0  0
 KZ4  CONST_04  CE2  CD2  CG2  CD1    0.00   0.0  0
 KZ4  CONST_05  CE1  CZ   CE2  CD2    0.00   0.0  0
 KZ4  CONST_06  CE1  CD1  CG2  CD2    0.00   0.0  0
 KZ4  CONST_07  C2   CA2  N2   C1     0.00   0.0  0
 KZ4  CONST_08  CA2  C2   N3   C1     0.00   0.0  0
 KZ4  CONST_09  C2   N3   C1   N2     0.00   0.0  0
 KZ4  CONST_10  N3   C2   CA2  N2     0.00   0.0  0
 KZ4  CONST_11  CA2  N2   C1   N3     0.00   0.0  0
 KZ4  CONST_12  CE2  CD2  CG2  CB2  180.00   0.0  0
 KZ4  CONST_13  CE1  CD1  CG2  CB2  180.00   0.0  0
 KZ4  CONST_14  BR   CE1  CD1  CG2  180.00   0.0  0
 KZ4  CONST_15  OH   CZ   CE1  CD1  180.00   0.0  0
 KZ4  CONST_16  OH   CZ   CE2  CD2  180.00   0.0  0
 KZ4  CONST_17  BR   CE1  CZ   CE2  180.00   0.0  0
 KZ4  CONST_18  CA2  N2   C1   CA1  180.00   0.0  0
 KZ4  CONST_19  C2   N3   C1   CA1  180.00   0.0  0
 KZ4  CONST_20  O2   C2   N3   C1   180.00   0.0  0
 KZ4  CONST_21  CA3  N3   C1   N2   180.00   0.0  0
 KZ4  CONST_22  CA3  N3   C2   CA2  180.00   0.0  0
 KZ4  CONST_23  HE2  CE2  CD2  CG2  180.00   0.0  0
 KZ4  CONST_24  HD2  CD2  CG2  CD1  180.00   0.0  0
 KZ4  CONST_25  HD1  CD1  CG2  CD2  180.00   0.0  0
 KZ4  CONST_26  CA3  N3   C1   CA1    0.00   0.0  0
 KZ4  CONST_27  CA3  N3   C2   O2     0.00   0.0  0
 KZ4  CONST_28  HXT  OXT  C    CA3  180.00   0.0  0
 KZ4  Var_01    CG2  CB2  CA2  N2     0.30  30.0  2
 KZ4  Var_02    CD2  CG2  CB2  CA2  179.23  30.0  2
 KZ4  Var_03    C    CA3  N3   C1   105.53  30.0  3
 KZ4  Var_04    O    C    CA3  N3   -12.06  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
 KZ4  chir_01  CA1  N  CB1  C1  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
 KZ4  plan-1  CA1  0.020
 KZ4  plan-1  C1   0.020
 KZ4  plan-1  N2   0.020
 KZ4  plan-1  N3   0.020
 KZ4  plan-1  C2   0.020
 KZ4  plan-1  O2   0.020
 KZ4  plan-1  CA2  0.020
 KZ4  plan-1  CA3  0.020
 KZ4  plan-1  CB2  0.020
 KZ4  plan-2  CB2  0.020
 KZ4  plan-2  CG2  0.020
 KZ4  plan-2  CD1  0.020
 KZ4  plan-2  CD2  0.020
 KZ4  plan-2  CE1  0.020
 KZ4  plan-2  CE2  0.020
 KZ4  plan-2  CZ   0.020
 KZ4  plan-2  OH   0.020
 KZ4  plan-2  BR   0.020
 KZ4  plan-2  HD1  0.020
 KZ4  plan-2  HD2  0.020
 KZ4  plan-2  HE2  0.020
 KZ4  plan-3  CA3  0.020
 KZ4  plan-3  C    0.020
 KZ4  plan-3  O    0.020
 KZ4  plan-3  OXT  0.020
 KZ4  plan-3  HXT  0.020

