# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 22:29:31 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: {(4Z)-2-[(1R)-1-amino-2-sulfanylethyl]-5-oxo-4-[(2,3,5-trifluoro-4-hydroxyphenyl)methylidene]-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/c2cc(F)c(O)c(F)c2F)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
 KZ1  KZ1  '{(4Z)-2-[(1R)-1-amino-2-sulfanylethyl]-5-oxo-4-[(2,3,5-trifluoro-4-hydroxyphenyl)methylidene]-4,5-dihydro-1H-imidazol-1-yl}acetic acid'  L-peptide  37  25  .  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_KZ1
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
 KZ1  N     N  NH2   0  -0.771   2.1034   2.5179  -1.3935
 KZ1  CB1   C  CH2   0  -0.588   3.2521   1.8095   0.7392
 KZ1  CA1   C  CH1   0  -0.202   2.7911   1.4625  -0.6899
 KZ1  C1    C  CR5   0   0.583   1.8914   0.2683  -0.5885
 KZ1  N2    N  N     0  -0.486   0.6172   0.3575  -0.4305
 KZ1  N3    N  NR5   0  -0.569   2.3615  -1.0292  -0.5861
 KZ1  C2    C  CR5   0   0.548   1.2857  -1.8739  -0.3896
 KZ1  O2    O  O     0  -0.431   1.3400  -3.0821  -0.3293
 KZ1  CA2   C  CR5   0   0.108   0.1420  -0.9385  -0.2998
 KZ1  CA3   C  CH2   0  -0.463   3.7023  -1.5127  -0.7205
 KZ1  CB2   C  C1    0  -0.361  -1.1243  -1.3577  -0.1173
 KZ1  CG2   C  CR6   0  -0.074  -2.3251  -0.5585  -0.0216
 KZ1  CD1   C  CR6   0   0.405  -3.5468  -1.1898   0.2010
 KZ1  CD2   C  CR16  0  -0.495  -2.3467   0.8407  -0.1466
 KZ1  CE1   C  CR6   0   0.331  -4.7264  -0.4801   0.2958
 KZ1  CE2   C  CR6   0   0.522  -3.5250   1.5304  -0.0516
 KZ1  CZ    C  CR6   0   0.094  -4.7522   0.9018   0.1716
 KZ1  OH    O  OH1   0  -0.598  -5.8549   1.6426   0.2533
 KZ1  C     C  C     0   0.554   4.2848  -1.9166   0.6183
 KZ1  O     O  O     0  -0.427   3.7466  -1.7229   1.6755
 KZ1  F1    F  F     0  -0.303  -5.8747  -1.1296   0.5134
 KZ1  F2    F  F     0  -0.292  -3.6115  -2.5146   0.3318
 KZ1  F3    F  F     0  -0.306  -3.5342   2.8623  -0.1749
 KZ1  HN1   H  HNH2  0   0.353   1.3006   2.8305  -0.8609
 KZ1  HN2   H  HNH2  0   0.356   2.7215   3.3130  -1.4943
 KZ1  HG1   H  HSH1  0   0.227   3.6388   4.1737   0.6402
 KZ1  HB11  H  HCH2  0   0.287   3.7316   0.9562   1.2194
 KZ1  HB12  H  HCH2  0   0.294   2.3945   2.0846   1.3546
 KZ1  HA1   H  HCH1  0   0.279   3.6764   1.1976  -1.2741
 KZ1  HA31  H  HCH2  0   0.326   3.7201  -2.3673  -1.3995
 KZ1  HB32  H  HCH2  0   0.327   4.3370  -0.7518  -1.1758
 KZ1  HB2   H  H     0   0.282  -1.2438  -2.4310  -0.0332
 KZ1  HD2   H  HCR6  0   0.314  -1.4261   1.3791  -0.3228
 KZ1  H1    H  HOH1  0   0.491  -6.6406   1.0992   0.3941
 KZ1  OXT   O  OH1   0  -0.582   5.4612  -2.4949   0.4607
 KZ1  HXT   H  HOH1  0   0.491   5.8436  -2.7281   1.3205
 KZ1  SG1   S  S2    0  -0.224   4.4811   3.1444   0.7801

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
 KZ1  SG1  CB1   single    1.815  0.020  1.815
 KZ1  CB1  CA1   single    1.541  0.020  1.541
 KZ1  CA1  C1    single    1.499  0.020  1.499
 KZ1  C1   N2    double    1.287  0.020  1.287
 KZ1  C1   N3    single    1.380  0.020  1.380
 KZ1  N2   CA2   single    1.387  0.020  1.387
 KZ1  N3   C2    single    1.382  0.020  1.382
 KZ1  N3   CA3   single    1.432  0.020  1.432
 KZ1  C2   O2    double    1.211  0.020  1.211
 KZ1  C2   CA2   single    1.480  0.020  1.480
 KZ1  CA2  CB2   double    1.346  0.020  1.346
 KZ1  CA3  C     single    1.515  0.020  1.515
 KZ1  CB2  CG2   single    1.446  0.020  1.446
 KZ1  CG2  CD1   aromatic  1.393  0.020  1.393
 KZ1  CG2  CD2   aromatic  1.405  0.020  1.405
 KZ1  CD1  CE1   aromatic  1.380  0.020  1.380
 KZ1  CD1  F2    single    1.333  0.020  1.333
 KZ1  CD2  CE2   aromatic  1.369  0.020  1.369
 KZ1  CE1  CZ    aromatic  1.388  0.020  1.388
 KZ1  CE1  F1    single    1.337  0.020  1.337
 KZ1  CE2  CZ    aromatic  1.397  0.020  1.397
 KZ1  CE2  F3    single    1.338  0.020  1.338
 KZ1  CZ   OH    single    1.331  0.020  1.331
 KZ1  C    O     double    1.202  0.020  1.202
 KZ1  CA1  N     single    1.443  0.020  1.443
 KZ1  N    HN1   single    0.890  0.020  1.040
 KZ1  N    HN2   single    0.890  0.020  1.040
 KZ1  SG1  HG1   single    1.200  0.020  1.300
 KZ1  CB1  HB11  single    0.970  0.020  1.090
 KZ1  CB1  HB12  single    0.970  0.020  1.090
 KZ1  CA1  HA1   single    0.970  0.020  1.090
 KZ1  CA3  HA31  single    0.970  0.020  1.090
 KZ1  CA3  HB32  single    0.970  0.020  1.090
 KZ1  CB2  HB2   single    0.930  0.020  1.080
 KZ1  CD2  HD2   single    0.930  0.020  1.080
 KZ1  OH   H1    single    0.850  0.020  0.980
 KZ1  C    OXT   single    1.320  0.020  1.320
 KZ1  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
 KZ1  HN2   N    HN1   107.10  3.000
 KZ1  HN2   N    CA1   109.40  3.000
 KZ1  HN1   N    CA1   110.30  3.000
 KZ1  HB12  CB1  HB11  107.13  3.000
 KZ1  HB12  CB1  CA1   110.17  3.000
 KZ1  HB11  CB1  CA1   111.33  3.000
 KZ1  HB12  CB1  SG1   109.52  3.000
 KZ1  HB11  CB1  SG1   105.54  3.000
 KZ1  CA1   CB1  SG1   112.90  3.000
 KZ1  HA1   CA1  C1    109.22  3.000
 KZ1  HA1   CA1  CB1   107.93  3.000
 KZ1  C1    CA1  CB1   107.23  3.000
 KZ1  HA1   CA1  N     107.61  3.000
 KZ1  C1    CA1  N     109.25  3.000
 KZ1  CB1   CA1  N     115.47  3.000
 KZ1  N3    C1   N2    113.71  3.000
 KZ1  N3    C1   CA1   123.02  3.000
 KZ1  N2    C1   CA1   123.19  3.000
 KZ1  CA2   N2   C1    106.63  3.000
 KZ1  CA3   N3   C2    122.41  3.000
 KZ1  CA3   N3   C1    129.52  3.000
 KZ1  C2    N3   C1    108.05  3.000
 KZ1  CA2   C2   O2    131.47  3.000
 KZ1  CA2   C2   N3    102.93  3.000
 KZ1  O2    C2   N3    125.60  3.000
 KZ1  CB2   CA2  C2    122.56  3.000
 KZ1  CB2   CA2  N2    128.77  3.000
 KZ1  C2    CA2  N2    108.67  3.000
 KZ1  HB32  CA3  HA31  106.09  3.000
 KZ1  HB32  CA3  C     109.34  3.000
 KZ1  HA31  CA3  C     109.55  3.000
 KZ1  HB32  CA3  N3    110.40  3.000
 KZ1  HA31  CA3  N3    109.76  3.000
 KZ1  C     CA3  N3    111.54  3.000
 KZ1  HB2   CB2  CG2   116.81  3.000
 KZ1  HB2   CB2  CA2   115.01  3.000
 KZ1  CG2   CB2  CA2   128.18  3.000
 KZ1  CD2   CG2  CD1   116.87  3.000
 KZ1  CD2   CG2  CB2   123.88  3.000
 KZ1  CD1   CG2  CB2   119.25  3.000
 KZ1  F2    CD1  CE1   117.58  3.000
 KZ1  F2    CD1  CG2   120.58  3.000
 KZ1  CE1   CD1  CG2   121.85  3.000
 KZ1  HD2   CD2  CE2   119.57  3.000
 KZ1  HD2   CD2  CG2   119.83  3.000
 KZ1  CE2   CD2  CG2   120.60  3.000
 KZ1  F1    CE1  CZ    118.84  3.000
 KZ1  F1    CE1  CD1   119.70  3.000
 KZ1  CZ    CE1  CD1   121.46  3.000
 KZ1  F3    CE2  CZ    117.18  3.000
 KZ1  F3    CE2  CD2   120.09  3.000
 KZ1  CZ    CE2  CD2   122.73  3.000
 KZ1  OH    CZ   CE2   119.16  3.000
 KZ1  OH    CZ   CE1   124.35  3.000
 KZ1  CE2   CZ   CE1   116.49  3.000
 KZ1  H1    OH   CZ    111.71  3.000
 KZ1  OXT   C    O     125.06  3.000
 KZ1  OXT   C    CA3   110.73  3.000
 KZ1  O     C    CA3   124.21  3.000
 KZ1  HXT   OXT  C     110.55  3.000
 KZ1  HG1   SG1  CB1    97.89  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
 KZ1  CONST_01  CZ   CE1  CD1  CG2     0.00   0.0  0
 KZ1  CONST_02  CZ   CE2  CD2  CG2     0.00   0.0  0
 KZ1  CONST_03  CE2  CD2  CG2  CD1     0.00   0.0  0
 KZ1  CONST_04  CE2  CZ   CE1  CD1     0.00   0.0  0
 KZ1  CONST_05  CE1  CD1  CG2  CD2     0.00   0.0  0
 KZ1  CONST_06  CE1  CZ   CE2  CD2     0.00   0.0  0
 KZ1  CONST_07  C2   CA2  N2   C1      0.00   0.0  0
 KZ1  CONST_08  CA2  C2   N3   C1      0.00   0.0  0
 KZ1  CONST_09  C2   N3   C1   N2      0.00   0.0  0
 KZ1  CONST_10  N3   C2   CA2  N2      0.00   0.0  0
 KZ1  CONST_11  CA2  N2   C1   N3      0.00   0.0  0
 KZ1  CONST_12  CE1  CD1  CG2  CB2   180.00   0.0  0
 KZ1  CONST_13  CE2  CD2  CG2  CB2   180.00   0.0  0
 KZ1  CONST_14  F1   CE1  CD1  CG2   180.00   0.0  0
 KZ1  CONST_15  F3   CE2  CD2  CG2   180.00   0.0  0
 KZ1  CONST_16  OH   CZ   CE1  CD1   180.00   0.0  0
 KZ1  CONST_17  F2   CD1  CG2  CD2   180.00   0.0  0
 KZ1  CONST_18  OH   CZ   CE2  CD2   180.00   0.0  0
 KZ1  CONST_19  F3   CE2  CZ   CE1   180.00   0.0  0
 KZ1  CONST_20  F1   CE1  CZ   CE2   180.00   0.0  0
 KZ1  CONST_21  F2   CD1  CE1  CZ    180.00   0.0  0
 KZ1  CONST_22  CA2  N2   C1   CA1   180.00   0.0  0
 KZ1  CONST_23  C2   N3   C1   CA1   180.00   0.0  0
 KZ1  CONST_24  O2   C2   N3   C1    180.00   0.0  0
 KZ1  CONST_25  CA3  N3   C1   N2    180.00   0.0  0
 KZ1  CONST_26  CA3  N3   C2   CA2   180.00   0.0  0
 KZ1  CONST_27  HD2  CD2  CG2  CD1   180.00   0.0  0
 KZ1  CONST_28  CA3  N3   C1   CA1     0.00   0.0  0
 KZ1  CONST_29  CA3  N3   C2   O2      0.00   0.0  0
 KZ1  CONST_30  HXT  OXT  C    CA3   180.00   0.0  0
 KZ1  Var_01    CG2  CB2  CA2  N2      0.60  30.0  2
 KZ1  Var_02    CD1  CG2  CB2  CA2  -178.51  30.0  2
 KZ1  Var_03    C    CA3  N3   C1    102.03  30.0  3
 KZ1  Var_04    O    C    CA3  N3     -7.45  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
 KZ1  chir_01  CA1  CB1  C1  N  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
 KZ1  plan-1  CA1  0.020
 KZ1  plan-1  C1   0.020
 KZ1  plan-1  N2   0.020
 KZ1  plan-1  N3   0.020
 KZ1  plan-1  C2   0.020
 KZ1  plan-1  O2   0.020
 KZ1  plan-1  CA2  0.020
 KZ1  plan-1  CA3  0.020
 KZ1  plan-1  CB2  0.020
 KZ1  plan-2  CB2  0.020
 KZ1  plan-2  CG2  0.020
 KZ1  plan-2  CD1  0.020
 KZ1  plan-2  CD2  0.020
 KZ1  plan-2  CE1  0.020
 KZ1  plan-2  CE2  0.020
 KZ1  plan-2  CZ   0.020
 KZ1  plan-2  OH   0.020
 KZ1  plan-2  F1   0.020
 KZ1  plan-2  F2   0.020
 KZ1  plan-2  F3   0.020
 KZ1  plan-2  HD2  0.020
 KZ1  plan-3  CA3  0.020
 KZ1  plan-3  C    0.020
 KZ1  plan-3  O    0.020
 KZ1  plan-3  OXT  0.020
 KZ1  plan-3  HXT  0.020

