# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 20:49:11 2022
#   Inital geometry file: a 107 line input string
#   Ligand name: {(4Z)-2-[(1R)-1-amino-2-sulfanylethyl]-4-[(4-hydroxy-3-methylphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(ccc1O)\C=C2/N=C([C@@H](N)CS)N(CC(O)=O)C2=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
 KZY  KZY  "{(4Z)-2-[(1R)-1-amino-2-sulfanylethyl]-4-[(4-hydroxy-3-methylphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid"  L-peptide  39  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_KZY
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
 KZY  N     N  NH2    0  -0.772   1.4425   2.4078  -1.5155
 KZY  CB1   C  CH2    0  -0.593   2.5570   1.8799   0.6879
 KZY  CA1   C  CH1    0  -0.200   2.1864   1.4403  -0.7402
 KZY  C1    C  CR5    0   0.567   1.3850   0.1789  -0.6230
 KZY  N2    N  N      0  -0.489   0.1088   0.1812  -0.4358
 KZY  N3    N  NR5    0  -0.543   1.9479  -1.0749  -0.6557
 KZY  C2    C  CR5    0   0.531   0.9469  -1.9915  -0.4239
 KZY  O2    O  O      0  -0.457   1.0850  -3.1977  -0.3603
 KZY  CA2   C  CR5    0   0.080  -0.2641  -1.1500  -0.3094
 KZY  CA3   C  CH2    0  -0.477   3.3400  -1.4404  -0.7124
 KZY  CB2   C  C1     0  -0.390  -1.4960  -1.6658  -0.1238
 KZY  CG2   C  CR6    0   0.151  -2.7728  -0.9985  -0.0114
 KZY  CD1   C  CR16   0  -0.360  -2.9459   0.3925  -0.1008
 KZY  CD2   C  CR16   0  -0.305  -3.9110  -1.7849   0.1932
 KZY  CE1   C  CR6    0   0.039  -4.1876   0.9907   0.0090
 KZY  CE2   C  CR16   0  -0.373  -5.1632  -1.2125   0.3087
 KZY  CZ    C  CR6    0   0.325  -5.3075   0.1692   0.2185
 KZY  OH    O  OH1    0  -0.612  -6.5003   0.7752   0.3239
 KZY  C     C  C      0   0.424   3.9885  -1.6452   0.6759
 KZY  O     O  O      0  -0.587   3.3026  -1.3657   1.6726
 KZY  CF    C  CH3    0  -0.711  -4.3480   2.4782  -0.0919
 KZY  HN1   H  HNH2   0   0.349   0.5983   2.6714  -1.0216
 KZY  HN2   H  HNH2   0   0.350   1.9966   3.2483  -1.6209
 KZY  HG1   H  HSH1   0   0.221   2.7798   4.2573   0.4556
 KZY  HB11  H  HCH2   0   0.296   3.0700   1.0767   1.2174
 KZY  HB12  H  HCH2   0   0.283   1.6545   2.1176   1.2533
 KZY  HA1   H  HCH1   0   0.271   3.1146   1.2292  -1.2766
 KZY  HA31  H  HCH2   0   0.270   3.4273  -2.3581  -1.2957
 KZY  HA32  H  HCH2   0   0.273   3.8915  -0.6794  -1.2657
 KZY  HB2   H  H      0   0.263  -1.5333  -2.7487  -0.0505
 KZY  HD1   H  HCR6   0   0.267  -2.0794   1.0198  -0.2621
 KZY  HD2   H  HCR6   0   0.262  -3.8143  -2.8615   0.2625
 KZY  HE2   H  HCR6   0   0.274  -6.0324  -1.8404   0.4674
 KZY  H1    H  HOH1   0   0.479  -7.2012   0.1260   0.4560
 KZY  OXT   O  OC    -1  -0.607   5.1576  -2.0672   0.6381
 KZY  H2    H  HCH3   0   0.245  -5.0454   2.7577  -0.8832
 KZY  H3    H  HCH3   0   0.246  -4.7292   2.9082   0.8361
 KZY  H4    H  HCH3   0   0.245  -3.3925   2.9533  -0.3089
 KZY  SG1   S  S2     0  -0.235   3.6808   3.3066   0.7262

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
 KZY  SG1  CB1   single    1.817  0.020  1.817
 KZY  CB1  CA1   single    1.539  0.020  1.539
 KZY  CA1  C1    single    1.499  0.020  1.499
 KZY  C1   N2    double    1.290  0.020  1.290
 KZY  C1   N3    single    1.375  0.020  1.375
 KZY  N2   CA2   single    1.388  0.020  1.388
 KZY  N3   C2    single    1.377  0.020  1.377
 KZY  N3   CA3   single    1.440  0.020  1.440
 KZY  C2   O2    double    1.216  0.020  1.216
 KZY  C2   CA2   single    1.479  0.020  1.479
 KZY  CA2  CB2   double    1.348  0.020  1.348
 KZY  CA3  C     single    1.546  0.020  1.546
 KZY  CB2  CG2   single    1.445  0.020  1.445
 KZY  CG2  CD1   aromatic  1.405  0.020  1.405
 KZY  CG2  CD2   aromatic  1.398  0.020  1.398
 KZY  CD1  CE1   aromatic  1.383  0.020  1.383
 KZY  CD2  CE2   aromatic  1.382  0.020  1.382
 KZY  CE1  CZ    aromatic  1.405  0.020  1.405
 KZY  CE1  CF    single    1.500  0.020  1.500
 KZY  CE2  CZ    aromatic  1.392  0.020  1.392
 KZY  CZ   OH    single    1.342  0.020  1.342
 KZY  C    O     deloc     1.242  0.020  1.242
 KZY  CA1  N     single    1.446  0.020  1.446
 KZY  N    HN1   single    0.890  0.020  1.040
 KZY  N    HN2   single    0.890  0.020  1.040
 KZY  SG1  HG1   single    1.200  0.020  1.300
 KZY  CB1  HB11  single    0.970  0.020  1.090
 KZY  CB1  HB12  single    0.970  0.020  1.090
 KZY  CA1  HA1   single    0.970  0.020  1.090
 KZY  CA3  HA31  single    0.970  0.020  1.090
 KZY  CA3  HA32  single    0.970  0.020  1.090
 KZY  CB2  HB2   single    0.930  0.020  1.080
 KZY  CD1  HD1   single    0.930  0.020  1.080
 KZY  CD2  HD2   single    0.930  0.020  1.080
 KZY  CE2  HE2   single    0.930  0.020  1.080
 KZY  OH   H1    single    0.850  0.020  0.980
 KZY  C    OXT   deloc     1.244  0.020  1.244
 KZY  CF   H2    single    0.970  0.020  1.090
 KZY  CF   H3    single    0.970  0.020  1.090
 KZY  CF   H4    single    0.970  0.020  1.090

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
 KZY  HN2   N    HN1   106.91  3.000
 KZY  HN2   N    CA1   109.26  3.000
 KZY  HN1   N    CA1   109.97  3.000
 KZY  HB12  CB1  HB11  107.34  3.000
 KZY  HB12  CB1  CA1   110.11  3.000
 KZY  HB11  CB1  CA1   110.69  3.000
 KZY  HB12  CB1  SG1   109.25  3.000
 KZY  HB11  CB1  SG1   106.09  3.000
 KZY  CA1   CB1  SG1   113.13  3.000
 KZY  HA1   CA1  C1    109.27  3.000
 KZY  HA1   CA1  CB1   107.82  3.000
 KZY  C1    CA1  CB1   107.24  3.000
 KZY  HA1   CA1  N     107.65  3.000
 KZY  C1    CA1  N     109.26  3.000
 KZY  CB1   CA1  N     115.47  3.000
 KZY  N3    C1   N2    114.22  3.000
 KZY  N3    C1   CA1   123.14  3.000
 KZY  N2    C1   CA1   122.60  3.000
 KZY  CA2   N2   C1    106.10  3.000
 KZY  CA3   N3   C2    122.70  3.000
 KZY  CA3   N3   C1    128.91  3.000
 KZY  C2    N3   C1    107.79  3.000
 KZY  CA2   C2   O2    130.80  3.000
 KZY  CA2   C2   N3    103.27  3.000
 KZY  O2    C2   N3    125.93  3.000
 KZY  CB2   CA2  C2    122.76  3.000
 KZY  CB2   CA2  N2    128.66  3.000
 KZY  C2    CA2  N2    108.58  3.000
 KZY  HA32  CA3  HA31  105.98  3.000
 KZY  HA32  CA3  C     109.62  3.000
 KZY  HA31  CA3  C     109.59  3.000
 KZY  HA32  CA3  N3    109.36  3.000
 KZY  HA31  CA3  N3    108.17  3.000
 KZY  C     CA3  N3    113.81  3.000
 KZY  HB2   CB2  CG2   115.14  3.000
 KZY  HB2   CB2  CA2   114.97  3.000
 KZY  CG2   CB2  CA2   129.89  3.000
 KZY  CD2   CG2  CD1   117.77  3.000
 KZY  CD2   CG2  CB2   118.09  3.000
 KZY  CD1   CG2  CB2   124.14  3.000
 KZY  HD1   CD1  CE1   118.71  3.000
 KZY  HD1   CD1  CG2   119.01  3.000
 KZY  CE1   CD1  CG2   122.28  3.000
 KZY  HD2   CD2  CE2   119.17  3.000
 KZY  HD2   CD2  CG2   119.71  3.000
 KZY  CE2   CD2  CG2   121.12  3.000
 KZY  CF    CE1  CZ    120.32  3.000
 KZY  CF    CE1  CD1   121.33  3.000
 KZY  CZ    CE1  CD1   118.35  3.000
 KZY  HE2   CE2  CZ    120.08  3.000
 KZY  HE2   CE2  CD2   119.94  3.000
 KZY  CZ    CE2  CD2   119.98  3.000
 KZY  OH    CZ   CE2   122.35  3.000
 KZY  OH    CZ   CE1   117.15  3.000
 KZY  CE2   CZ   CE1   120.50  3.000
 KZY  H1    OH   CZ    110.66  3.000
 KZY  OXT   C    O     128.32  3.000
 KZY  OXT   C    CA3   114.34  3.000
 KZY  O     C    CA3   117.34  3.000
 KZY  H4    CF   H3    107.69  3.000
 KZY  H4    CF   H2    107.73  3.000
 KZY  H3    CF   H2    107.01  3.000
 KZY  H4    CF   CE1   110.63  3.000
 KZY  H3    CF   CE1   111.78  3.000
 KZY  H2    CF   CE1   111.80  3.000
 KZY  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
 KZY  CONST_01  CZ    CE1  CD1  CG2      0.00   0.0  0
 KZY  CONST_02  CZ    CE2  CD2  CG2      0.00   0.0  0
 KZY  CONST_03  CE2   CD2  CG2  CD1      0.00   0.0  0
 KZY  CONST_04  CE2   CZ   CE1  CD1      0.00   0.0  0
 KZY  CONST_05  CE1   CD1  CG2  CD2      0.00   0.0  0
 KZY  CONST_06  CE1   CZ   CE2  CD2      0.00   0.0  0
 KZY  CONST_07  C2    CA2  N2   C1       0.00   0.0  0
 KZY  CONST_08  CA2   C2   N3   C1       0.00   0.0  0
 KZY  CONST_09  C2    N3   C1   N2       0.00   0.0  0
 KZY  CONST_10  N3    C2   CA2  N2       0.00   0.0  0
 KZY  CONST_11  CA2   N2   C1   N3       0.00   0.0  0
 KZY  CONST_12  CE1   CD1  CG2  CB2    180.00   0.0  0
 KZY  CONST_13  CE2   CD2  CG2  CB2    180.00   0.0  0
 KZY  CONST_14  CF    CE1  CD1  CG2    180.00   0.0  0
 KZY  CONST_15  OH    CZ   CE1  CD1    180.00   0.0  0
 KZY  CONST_16  OH    CZ   CE2  CD2    180.00   0.0  0
 KZY  CONST_17  CF    CE1  CZ   CE2    180.00   0.0  0
 KZY  CONST_18  CA2   N2   C1   CA1    180.00   0.0  0
 KZY  CONST_19  C2    N3   C1   CA1    180.00   0.0  0
 KZY  CONST_20  O2    C2   N3   C1     180.00   0.0  0
 KZY  CONST_21  CA3   N3   C1   N2     180.00   0.0  0
 KZY  CONST_22  CA3   N3   C2   CA2    180.00   0.0  0
 KZY  CONST_23  HE2   CE2  CD2  CG2    180.00   0.0  0
 KZY  CONST_24  HD2   CD2  CG2  CD1    180.00   0.0  0
 KZY  CONST_25  HD1   CD1  CG2  CD2    180.00   0.0  0
 KZY  CONST_26  HE2   CE2  CZ   CE1    180.00   0.0  0
 KZY  CONST_27  HD1   CD1  CE1  CZ     180.00   0.0  0
 KZY  CONST_28  HD2   CD2  CE2  CZ     180.00   0.0  0
 KZY  CONST_29  CA3   N3   C1   CA1      0.00   0.0  0
 KZY  CONST_30  CA3   N3   C2   O2       0.00   0.0  0
 KZY  Var_01    CG2   CB2  CA2  N2       0.41   0.0  2
 KZY  Var_02    CG2   CB2  CA2  C2    -179.01   0.0  2
 KZY  Var_03    CD1   CG2  CB2  CA2      0.88  30.0  2
 KZY  Var_04    CD2   CG2  CB2  CA2   -179.42  30.0  2
 KZY  Var_05    C     CA3  N3   C1      91.42  30.0  3
 KZY  Var_06    C     CA3  N3   C2     -78.58  30.0  3
 KZY  Var_07    HB2   CB2  CA2  N2    -179.78   0.0  2
 KZY  Var_08    HB2   CB2  CA2  C2       0.80   0.0  2
 KZY  Var_09    HA31  CA3  N3   C1    -146.54  30.0  3
 KZY  Var_10    HA32  CA3  N3   C1     -31.55  30.0  3
 KZY  Var_11    HA31  CA3  N3   C2      43.47  30.0  3
 KZY  Var_12    HA32  CA3  N3   C2     158.45  30.0  3
 KZY  Var_13    HB2   CB2  CG2  CD1   -178.92  30.0  2
 KZY  Var_14    H2    CF   CE1  CD1    123.19  30.0  2
 KZY  Var_15    H3    CF   CE1  CD1   -116.88  30.0  2
 KZY  Var_16    H4    CF   CE1  CD1      3.12  30.0  2
 KZY  Var_17    HB2   CB2  CG2  CD2      0.77  30.0  2
 KZY  Var_18    H2    CF   CE1  CZ     -56.79  30.0  2
 KZY  Var_19    H3    CF   CE1  CZ      63.14  30.0  2
 KZY  Var_20    H4    CF   CE1  CZ    -176.85  30.0  2
 KZY  Var_21    O     C    CA3  N3      -6.18  30.0  3
 KZY  Var_22    OXT   C    CA3  N3     174.38  30.0  3
 KZY  Var_23    HA31  CA3  C    O     -127.44  30.0  2
 KZY  Var_24    HA32  CA3  C    O      116.65  30.0  2
 KZY  Var_25    OXT   C    CA3  HA31    53.12  30.0  3
 KZY  Var_26    OXT   C    CA3  HA32   -62.80  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
 KZY  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
 KZY  plan-1  CA1  0.020
 KZY  plan-1  C1   0.020
 KZY  plan-1  N2   0.020
 KZY  plan-1  N3   0.020
 KZY  plan-1  C2   0.020
 KZY  plan-1  O2   0.020
 KZY  plan-1  CA2  0.020
 KZY  plan-1  CA3  0.020
 KZY  plan-1  CB2  0.020
 KZY  plan-1  CG2  0.020
 KZY  plan-1  HB2  0.020
 KZY  plan-2  CB2  0.020
 KZY  plan-2  CG2  0.020
 KZY  plan-2  CD1  0.020
 KZY  plan-2  CD2  0.020
 KZY  plan-2  CE1  0.020
 KZY  plan-2  CE2  0.020
 KZY  plan-2  CZ   0.020
 KZY  plan-2  OH   0.020
 KZY  plan-2  CF   0.020
 KZY  plan-2  HD1  0.020
 KZY  plan-2  HD2  0.020
 KZY  plan-2  HE2  0.020
 KZY  plan-3  CA3  0.020
 KZY  plan-3  C    0.020
 KZY  plan-3  O    0.020
 KZY  plan-3  OXT  0.020

