# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 20:47:19 2022
#   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  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_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  -0.761  -2.1099   2.5539   1.4821
 KZ7  CB1   C   CH2    0  -0.558  -3.2358   1.8534  -0.5467
 KZ7  CA1   C   CH1    0  -0.205  -2.7310   1.4260   0.8296
 KZ7  C1    C   CR5    0   0.541  -1.8150   0.2433   0.6514
 KZ7  N2    N   N      0  -0.489  -0.5414   0.3687   0.4854
 KZ7  N3    N   NR5    0  -0.541  -2.2603  -1.0574   0.6362
 KZ7  C2    C   CR5    0   0.534  -1.1784  -1.8708   0.3876
 KZ7  O2    O   O      0  -0.451  -1.2015  -3.0803   0.2827
 KZ7  CA2   C   CR5    0   0.096  -0.0470  -0.9159   0.3170
 KZ7  CA3   C   CH2    0  -0.476  -3.6139  -1.5479   0.6768
 KZ7  CB2   C   C1     0  -0.395   1.2284  -1.3068   0.1328
 KZ7  CG2   C   CR6    0   0.133   2.4311  -0.5043   0.0648
 KZ7  CD1   C   CR16   0  -0.256   3.6495  -1.1714  -0.1101
 KZ7  CD2   C   CR16   0  -0.294   2.4577   0.8932   0.1677
 KZ7  CE1   C   CR6    0  -0.134   4.8378  -0.4754  -0.1796
 KZ7  CE2   C   CR16   0  -0.363   3.6494   1.5855   0.0953
 KZ7  CZ    C   CR6    0   0.416   4.8613   0.9170  -0.0800
 KZ7  OH    O   OH1    0  -0.599   6.0398   1.5379  -0.1576
 KZ7  C     C   C      0   0.423  -4.2335  -1.7819  -0.7204
 KZ7  O     O   O      0  -0.587  -3.5714  -1.4143  -1.7040
 KZ7  CL    CL  CL     0  -0.104   6.3290  -1.3230  -0.3939
 KZ7  HN1   H   HNH2   0   0.359  -1.8428   2.3062   2.4263
 KZ7  HN2   H   HNH2   0   0.351  -1.2528   2.7989   1.0001
 KZ7  HG1   H   HSH1   0   0.214  -5.1221   3.0206  -1.4140
 KZ7  HB11  H   HCH2   0   0.295  -3.7574   1.0391  -1.0444
 KZ7  HB12  H   HCH2   0   0.271  -2.3882   2.1374  -1.1731
 KZ7  HA1   H   HCH1   0   0.274  -3.5919   1.1228   1.4310
 KZ7  HA31  H   HCH2   0   0.271  -3.6216  -2.4808   1.2424
 KZ7  HA32  H   HCH2   0   0.273  -4.2324  -0.8492   1.2415
 KZ7  HB1   H   H      0   0.268   1.3753  -2.3768   0.0246
 KZ7  HD1   H   HCR6   0   0.281   3.6640  -2.2511  -0.1896
 KZ7  HD2   H   HCR6   0   0.284   1.5372   1.4410   0.3075
 KZ7  HE2   H   HCR6   0   0.287   3.6457   2.6664   0.1749
 KZ7  H1    H   HOH1   0   0.487   5.9254   2.4930  -0.0830
 KZ7  OXT   O   OC    -1  -0.607  -5.3577  -2.3132  -0.7000
 KZ7  SG1   S   S2     0  -0.237  -4.3614   3.2728  -0.3430

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    1.729  0.020  1.729
 KZ7  OH   CZ    single    1.334  0.020  1.334
 KZ7  CE1  CZ    aromatic  1.396  0.020  1.396
 KZ7  CE1  CD1   aromatic  1.379  0.020  1.379
 KZ7  CZ   CE2   aromatic  1.395  0.020  1.395
 KZ7  CD1  CG2   aromatic  1.400  0.020  1.400
 KZ7  CE2  CD2   aromatic  1.380  0.020  1.380
 KZ7  CG2  CD2   aromatic  1.402  0.020  1.402
 KZ7  CG2  CB2   single    1.447  0.020  1.447
 KZ7  CB2  CA2   double    1.347  0.020  1.347
 KZ7  CA2  N2    single    1.387  0.020  1.387
 KZ7  CA2  C2    single    1.482  0.020  1.482
 KZ7  O2   C2    double    1.214  0.020  1.214
 KZ7  N2   C1    double    1.290  0.020  1.290
 KZ7  C2   N3    single    1.376  0.020  1.376
 KZ7  C1   N3    single    1.375  0.020  1.375
 KZ7  C1   CA1   single    1.507  0.020  1.507
 KZ7  N3   CA3   single    1.440  0.020  1.440
 KZ7  CB1  CA1   single    1.527  0.020  1.527
 KZ7  CB1  SG1   single    1.823  0.020  1.823
 KZ7  CA1  N     single    1.444  0.020  1.444
 KZ7  CA3  C     single    1.546  0.020  1.546
 KZ7  C    O     deloc     1.241  0.020  1.241
 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   deloc     1.244  0.020  1.244

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   106.24  3.000
 KZ7  HN2   N    CA1   109.74  3.000
 KZ7  HN1   N    CA1   110.12  3.000
 KZ7  HB12  CB1  HB11  107.73  3.000
 KZ7  HB12  CB1  CA1   109.47  3.000
 KZ7  HB11  CB1  CA1   111.19  3.000
 KZ7  HB12  CB1  SG1   109.94  3.000
 KZ7  HB11  CB1  SG1   109.75  3.000
 KZ7  CA1   CB1  SG1   108.74  3.000
 KZ7  HA1   CA1  C1    109.04  3.000
 KZ7  HA1   CA1  CB1   108.25  3.000
 KZ7  C1    CA1  CB1   108.31  3.000
 KZ7  HA1   CA1  N     107.87  3.000
 KZ7  CB1   CA1  N     109.32  3.000
 KZ7  C1    CA1  N     113.91  3.000
 KZ7  N3    C1   N2    114.22  3.000
 KZ7  N3    C1   CA1   123.17  3.000
 KZ7  N2    C1   CA1   122.61  3.000
 KZ7  CA2   N2   C1    106.11  3.000
 KZ7  CA3   N3   C2    122.86  3.000
 KZ7  CA3   N3   C1    128.78  3.000
 KZ7  C2    N3   C1    107.85  3.000
 KZ7  CA2   C2   O2    130.70  3.000
 KZ7  O2    C2   N3    126.12  3.000
 KZ7  CA2   C2   N3    103.18  3.000
 KZ7  CB2   CA2  C2    122.86  3.000
 KZ7  C2    CA2  N2    108.59  3.000
 KZ7  CB2   CA2  N2    128.55  3.000
 KZ7  HA32  CA3  HA31  105.98  3.000
 KZ7  HA32  CA3  C     109.73  3.000
 KZ7  HA31  CA3  C     109.65  3.000
 KZ7  HA32  CA3  N3    109.23  3.000
 KZ7  HA31  CA3  N3    108.21  3.000
 KZ7  C     CA3  N3    113.75  3.000
 KZ7  HB1   CB2  CG2   115.43  3.000
 KZ7  HB1   CB2  CA2   115.34  3.000
 KZ7  CG2   CB2  CA2   129.24  3.000
 KZ7  CD2   CG2  CD1   117.89  3.000
 KZ7  CD2   CG2  CB2   124.41  3.000
 KZ7  CD1   CG2  CB2   117.70  3.000
 KZ7  HD1   CD1  CE1   119.21  3.000
 KZ7  HD1   CD1  CG2   119.74  3.000
 KZ7  CE1   CD1  CG2   121.05  3.000
 KZ7  HD2   CD2  CE2   119.22  3.000
 KZ7  HD2   CD2  CG2   119.93  3.000
 KZ7  CE2   CD2  CG2   120.85  3.000
 KZ7  CL    CE1  CZ    118.90  3.000
 KZ7  CZ    CE1  CD1   120.95  3.000
 KZ7  CL    CE1  CD1   120.15  3.000
 KZ7  HE2   CE2  CZ    119.34  3.000
 KZ7  HE2   CE2  CD2   119.57  3.000
 KZ7  CZ    CE2  CD2   121.09  3.000
 KZ7  OH    CZ   CE2   123.48  3.000
 KZ7  CE2   CZ   CE1   118.18  3.000
 KZ7  OH    CZ   CE1   118.34  3.000
 KZ7  H1    OH   CZ    110.57  3.000
 KZ7  OXT   C    O     128.44  3.000
 KZ7  OXT   C    CA3   114.34  3.000
 KZ7  O     C    CA3   117.22  3.000
 KZ7  HG1   SG1  CB1    96.59  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  CG2   CB2  CA2  N2       0.00   0.0  0
 KZ7  CONST_22  CA3   N3   C1   N2     180.00   0.0  0
 KZ7  CONST_23  CG2   CB2  CA2  C2     180.00   0.0  0
 KZ7  CONST_24  CA3   N3   C2   CA2    180.00   0.0  0
 KZ7  CONST_25  HE2   CE2  CD2  CG2    180.00   0.0  0
 KZ7  CONST_26  HD2   CD2  CG2  CD1    180.00   0.0  0
 KZ7  CONST_27  HD1   CD1  CG2  CD2    180.00   0.0  0
 KZ7  CONST_28  HE2   CE2  CZ   CE1    180.00   0.0  0
 KZ7  CONST_29  HD1   CD1  CE1  CZ     180.00   0.0  0
 KZ7  CONST_30  HD2   CD2  CE2  CZ     180.00   0.0  0
 KZ7  CONST_31  CA3   N3   C1   CA1      0.00   0.0  0
 KZ7  CONST_32  CA3   N3   C2   O2       0.00   0.0  0
 KZ7  CONST_33  HB1   CB2  CA2  N2     180.00   0.0  0
 KZ7  CONST_34  HB1   CB2  CA2  C2       0.00   0.0  0
 KZ7  Var_01    CD1   CG2  CB2  CA2    178.74  30.0  2
 KZ7  Var_02    CD2   CG2  CB2  CA2     -0.98  30.0  2
 KZ7  Var_03    C     CA3  N3   C1      92.47  30.0  3
 KZ7  Var_04    C     CA3  N3   C2     -78.28  30.0  3
 KZ7  Var_05    HA31  CA3  N3   C1    -145.43  30.0  3
 KZ7  Var_06    HA32  CA3  N3   C1     -30.48  30.0  3
 KZ7  Var_07    HA31  CA3  N3   C2      43.82  30.0  3
 KZ7  Var_08    HA32  CA3  N3   C2     158.76  30.0  3
 KZ7  Var_09    HB1   CB2  CG2  CD1     -0.95  30.0  2
 KZ7  Var_10    HB1   CB2  CG2  CD2    179.33  30.0  2
 KZ7  Var_11    O     C    CA3  N3      -6.56  30.0  3
 KZ7  Var_12    OXT   C    CA3  N3     174.11  30.0  3
 KZ7  Var_13    HA31  CA3  C    O     -127.86  30.0  2
 KZ7  Var_14    HA32  CA3  C    O      116.12  30.0  2
 KZ7  Var_15    OXT   C    CA3  HA31    52.80  30.0  3
 KZ7  Var_16    OXT   C    CA3  HA32   -63.21  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-1  CG2  0.020
 KZ7  plan-1  HB1  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

