# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 20:47:11 2022
#   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  36  23  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.713  -2.0516   2.0798   1.8661
 KZ4  SG1   S   S2     0  -0.250  -2.7022   3.9438  -0.3320
 KZ4  CB1   C   CH2    0  -0.549  -2.1613   2.2179  -0.5641
 KZ4  CA1   C   CH1    0  -0.217  -2.5479   1.4189   0.6720
 KZ4  C1    C   CR5    0   0.577  -2.0214   0.0151   0.5401
 KZ4  N2    N   N      0  -0.545  -0.7775  -0.2332   0.2978
 KZ4  N3    N   NR5    0  -0.598  -2.7841  -1.1052   0.7726
 KZ4  C2    C   CR5    0   0.546  -1.9769  -2.2077   0.5998
 KZ4  O2    O   O      0  -0.212  -2.3212  -3.3698   0.6608
 KZ4  CA2   C   CR5    0   0.122  -0.6473  -1.6126   0.3251
 KZ4  CA3   C   CH2    0  -0.429  -4.2218  -1.1564   0.8445
 KZ4  CB2   C   C1     0  -0.424   0.4639  -2.3503   0.1393
 KZ4  CG2   C   CR6    0  -0.034   1.8154  -1.9076  -0.1317
 KZ4  CD1   C   CR16   0  -0.214   2.1808  -0.5589  -0.2443
 KZ4  CD2   C   CR16   0  -0.284   2.8158  -2.8731  -0.2909
 KZ4  CE1   C   CR6    0  -0.241   3.4895  -0.2103  -0.5060
 KZ4  CE2   C   CR16   0  -0.357   4.1244  -2.5204  -0.5523
 KZ4  CZ    C   CR6    0   0.497   4.4861  -1.1791  -0.6664
 KZ4  OH    O   OH1    0  -0.663   5.7332  -0.7785  -0.9205
 KZ4  C     C   C      0   0.423  -4.9058  -0.7834  -0.4922
 KZ4  O     O   O      0  -0.637  -4.1640  -0.4354  -1.4261
 KZ4  BR    BR  BR     0  -0.025   3.9594   1.6083  -0.6546
 KZ4  HN1   H   HNH2   0   0.369  -2.4218   1.6375   2.6975
 KZ4  HN2   H   HNH2   0   0.350  -1.0429   1.9967   1.9157
 KZ4  HG1   H   HSH1   0   0.230  -2.8559   4.2313  -1.6296
 KZ4  HB11  H   HCH2   0   0.297  -2.6514   1.7953  -1.4385
 KZ4  HB12  H   HCH2   0   0.242  -1.0832   2.1813  -0.7205
 KZ4  HA1   H   HCH1   0   0.224  -3.6364   1.4052   0.7349
 KZ4  HA31  H   HCH2   0   0.252  -4.5010  -2.1705   1.1322
 KZ4  HA32  H   HCH2   0   0.275  -4.5807  -0.5040   1.6437
 KZ4  HB2   H   H      0   0.240   0.3296  -3.4255   0.2021
 KZ4  HD1   H   HCR6   0   0.327   1.4264   0.2066  -0.1263
 KZ4  HD2   H   HCR6   0   0.281   2.5634  -3.9227  -0.2075
 KZ4  HE2   H   HCR6   0   0.287   4.8787  -3.2896  -0.6693
 KZ4  H1    H   HOH1   0   0.462   6.3222  -1.5371  -1.0124
 KZ4  OXT   O   OC    -1  -0.611  -6.1455  -0.8681  -0.4812

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    1.334  0.020  1.334
 KZ4  BR   CE1   single    1.884  0.020  1.884
 KZ4  CZ   CE2   aromatic  1.394  0.020  1.394
 KZ4  CZ   CE1   aromatic  1.399  0.020  1.399
 KZ4  CE2  CD2   aromatic  1.380  0.020  1.380
 KZ4  CE1  CD1   aromatic  1.379  0.020  1.379
 KZ4  N    CA1   single    1.452  0.020  1.452
 KZ4  SG1  CB1   single    1.824  0.020  1.824
 KZ4  CD2  CG2   aromatic  1.399  0.020  1.399
 KZ4  CD1  CG2   aromatic  1.402  0.020  1.402
 KZ4  CB1  CA1   single    1.522  0.020  1.522
 KZ4  CG2  CB2   single    1.448  0.020  1.448
 KZ4  CA1  C1    single    1.505  0.020  1.505
 KZ4  N2   C1    double    1.291  0.020  1.291
 KZ4  N2   CA2   single    1.386  0.020  1.386
 KZ4  C1   N3    single    1.375  0.020  1.375
 KZ4  CA2  CB2   double    1.347  0.020  1.347
 KZ4  CA2  C2    single    1.482  0.020  1.482
 KZ4  N3   C2    single    1.377  0.020  1.377
 KZ4  N3   CA3   single    1.440  0.020  1.440
 KZ4  C2   O2    double    1.214  0.020  1.214
 KZ4  CA3  C     single    1.547  0.020  1.547
 KZ4  C    O     deloc     1.242  0.020  1.242
 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   deloc     1.243  0.020  1.243

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   106.75  3.000
 KZ4  HN2   N    CA1   110.07  3.000
 KZ4  HN1   N    CA1   110.58  3.000
 KZ4  HG1   SG1  CB1    96.55  3.000
 KZ4  HB12  CB1  HB11  108.50  3.000
 KZ4  HB12  CB1  CA1   110.50  3.000
 KZ4  HB11  CB1  CA1   109.54  3.000
 KZ4  HB12  CB1  SG1   110.08  3.000
 KZ4  HB11  CB1  SG1   109.65  3.000
 KZ4  CA1   CB1  SG1   108.55  3.000
 KZ4  HA1   CA1  C1    110.03  3.000
 KZ4  HA1   CA1  CB1   107.88  3.000
 KZ4  C1    CA1  CB1   109.24  3.000
 KZ4  HA1   CA1  N     107.43  3.000
 KZ4  C1    CA1  N     112.15  3.000
 KZ4  CB1   CA1  N     110.01  3.000
 KZ4  N3    C1   N2    114.16  3.000
 KZ4  N3    C1   CA1   123.44  3.000
 KZ4  N2    C1   CA1   122.19  3.000
 KZ4  CA2   N2   C1    106.16  3.000
 KZ4  CA3   N3   C2    124.25  3.000
 KZ4  CA3   N3   C1    126.23  3.000
 KZ4  C2    N3   C1    107.81  3.000
 KZ4  CA2   C2   O2    130.40  3.000
 KZ4  O2    C2   N3    126.44  3.000
 KZ4  CA2   C2   N3    103.16  3.000
 KZ4  CB2   CA2  C2    123.08  3.000
 KZ4  C2    CA2  N2    108.60  3.000
 KZ4  CB2   CA2  N2    128.33  3.000
 KZ4  HA32  CA3  HA31  106.15  3.000
 KZ4  HA32  CA3  C     110.05  3.000
 KZ4  HA31  CA3  C     109.81  3.000
 KZ4  HA32  CA3  N3    110.07  3.000
 KZ4  HA31  CA3  N3    107.57  3.000
 KZ4  C     CA3  N3    112.93  3.000
 KZ4  HB2   CB2  CG2   115.42  3.000
 KZ4  HB2   CB2  CA2   115.63  3.000
 KZ4  CG2   CB2  CA2   128.95  3.000
 KZ4  CD2   CG2  CD1   117.93  3.000
 KZ4  CD1   CG2  CB2   123.54  3.000
 KZ4  CD2   CG2  CB2   118.53  3.000
 KZ4  HD1   CD1  CE1   120.25  3.000
 KZ4  HD1   CD1  CG2   119.38  3.000
 KZ4  CE1   CD1  CG2   120.37  3.000
 KZ4  HD2   CD2  CE2   118.90  3.000
 KZ4  HD2   CD2  CG2   119.57  3.000
 KZ4  CE2   CD2  CG2   121.53  3.000
 KZ4  BR    CE1  CZ    118.79  3.000
 KZ4  CZ    CE1  CD1   121.50  3.000
 KZ4  BR    CE1  CD1   119.70  3.000
 KZ4  HE2   CE2  CZ    119.57  3.000
 KZ4  HE2   CE2  CD2   119.94  3.000
 KZ4  CZ    CE2  CD2   120.49  3.000
 KZ4  OH    CZ   CE2   123.17  3.000
 KZ4  CE2   CZ   CE1   118.17  3.000
 KZ4  OH    CZ   CE1   118.66  3.000
 KZ4  H1    OH   CZ    110.65  3.000
 KZ4  OXT   C    O     128.42  3.000
 KZ4  OXT   C    CA3   114.64  3.000
 KZ4  O     C    CA3   116.93  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  CG2   CB2  CA2  N2       0.00   0.0  0
 KZ4  CONST_23  CG2   CB2  CA2  C2     180.00   0.0  0
 KZ4  CONST_24  CA3   N3   C2   CA2    180.00   0.0  0
 KZ4  CONST_25  HE2   CE2  CD2  CG2    180.00   0.0  0
 KZ4  CONST_26  HD2   CD2  CG2  CD1    180.00   0.0  0
 KZ4  CONST_27  HD1   CD1  CG2  CD2    180.00   0.0  0
 KZ4  CONST_28  HE2   CE2  CZ   CE1    180.00   0.0  0
 KZ4  CONST_29  HD2   CD2  CE2  CZ     180.00   0.0  0
 KZ4  CONST_30  HD1   CD1  CE1  CZ     180.00   0.0  0
 KZ4  CONST_32  CA3   N3   C2   O2       0.00   0.0  0
 KZ4  CONST_33  HB2   CB2  CA2  N2     180.00   0.0  0
 KZ4  CONST_34  HB2   CB2  CA2  C2       0.00   0.0  0
 KZ4  Var_01    CD2   CG2  CB2  CA2   -179.90  30.0  3
 KZ4  Var_02    CD1   CG2  CB2  CA2      0.09  30.0  3
 KZ4  Var_03    C     CA3  N3   C1      63.84  30.0  3
 KZ4  Var_04    C     CA3  N3   C2     -99.41  30.0  3
 KZ4  Var_05    HA31  CA3  N3   C1    -174.83  30.0  3
 KZ4  Var_06    HA32  CA3  N3   C1     -59.59  30.0  3
 KZ4  Var_07    HA31  CA3  N3   C2      21.92  30.0  3
 KZ4  Var_08    HA32  CA3  N3   C2     137.15  30.0  3
 KZ4  Var_09    HB2   CB2  CG2  CD1   -179.84  30.0  2
 KZ4  Var_10    HB2   CB2  CG2  CD2      0.18  30.0  2
 KZ4  Var_11    O     C    CA3  N3      -3.07  30.0  3
 KZ4  Var_12    OXT   C    CA3  N3     177.31  30.0  3
 KZ4  Var_13    HA31  CA3  C    O     -123.11  30.0  2
 KZ4  Var_14    HA32  CA3  C    O      120.38  30.0  2
 KZ4  Var_15    OXT   C    CA3  HA31    57.26  30.0  3
 KZ4  Var_16    OXT   C    CA3  HA32   -59.25  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-1  CG2  0.020
 KZ4  plan-1  HB2  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

