# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 17:48:10 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: {(4Z)-2-[(1R)-1-amino-2-sulfanylethyl]-4-[(3-fluoro-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(F)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
 KZV  KZV  '{(4Z)-2-[(1R)-1-amino-2-sulfanylethyl]-4-[(3-fluoro-4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid'  L-peptide  37  23  .  2022-07-25  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KZV
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
 KZV  N     N  NH2   0  -0.758  -1.1679   2.5882   1.4881
 KZV  CB1   C  CH2   0  -0.551  -2.6266   2.0988  -0.3825
 KZV  CA1   C  CH1   0  -0.207  -2.0172   1.5731   0.9171
 KZV  C1    C  CR5   0   0.544  -1.3019   0.2781   0.6320
 KZV  N2    N  N     0  -0.482  -0.0316   0.2010   0.4452
 KZV  N3    N  NR5   0  -0.565  -1.9482  -0.9377   0.5323
 KZV  C2    C  CR5   0   0.546  -1.0061  -1.9033   0.2324
 KZV  O2    O  O     0  -0.441  -1.2373  -3.0826   0.0690
 KZV  CA2   C  CR5   0   0.095   0.2532  -1.1334   0.1867
 KZV  CA3   C  CH2   0  -0.463  -3.3428  -1.2405   0.6480
 KZV  CB2   C  C1    0  -0.382   1.4502  -1.6976  -0.0684
 KZV  CG2   C  CR6   0   0.151   2.7541  -1.0815  -0.1501
 KZV  CD1   C  CR16  0  -0.298   3.8570  -1.8994  -0.4149
 KZV  CD2   C  CR16  0  -0.484   2.9774   0.2954   0.0192
 KZV  CE1   C  CR16  0  -0.366   5.1360  -1.3807  -0.5108
 KZV  CE2   C  CR6   0   0.520   4.2489   0.7930  -0.0792
 KZV  CZ    C  CR6   0   0.212   5.3565  -0.0179  -0.3445
 KZV  OH    O  OH1   0  -0.606   6.5537   0.5699  -0.4220
 KZV  C     C  C     0   0.550  -3.9633  -1.5049  -0.7088
 KZV  O     O  O     0  -0.426  -3.4164  -1.2830  -1.7559
 KZV  F     F  F     0  -0.313   4.4624   2.1078   0.0811
 KZV  HN1   H  HNH2  0   0.362  -0.8458   2.3006   2.4032
 KZV  HN2   H  HNH2  0   0.354  -0.3387   2.7078   0.9185
 KZV  HG1   H  HSH1  0   0.215  -4.3682   3.6021  -1.0012
 KZV  HB11  H  HCH2  0   0.282  -3.3550   1.4047  -0.7968
 KZV  HB12  H  HCH2  0   0.280  -1.8417   2.2384  -1.1277
 KZV  HA1   H  HCH1  0   0.283  -2.8282   1.3815   1.6263
 KZV  HA31  H  HCH2  0   0.323  -3.4839  -2.1076   1.2956
 KZV  HA32  H  HCH2  0   0.329  -3.8737  -0.4157   1.1266
 KZV  HB2   H  H     0   0.274   1.4319  -2.7699  -0.2358
 KZV  HD1   H  HCR6  0   0.271   3.7136  -2.9643  -0.5469
 KZV  HD2   H  HCR6  0   0.297   2.1554   0.9674   0.2257
 KZV  HE1   H  HCR6  0   0.291   5.9726  -2.0377  -0.7159
 KZV  H1    H  HOH1  0   0.486   7.2416  -0.0854  -0.5898
 KZV  OXT   O  OH1   0  -0.583  -5.1842  -1.9922  -0.5794
 KZV  HXT   H  HOH1  0   0.490  -5.5870  -2.1359  -1.4494
 KZV  SG1   S  S2    0  -0.226  -3.4490   3.6866  -0.0325

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
 KZV  OH   CZ    single    1.336  0.020  1.336
 KZV  CE1  CZ    aromatic  1.391  0.020  1.391
 KZV  CE1  CD1   aromatic  1.384  0.020  1.384
 KZV  CZ   CE2   aromatic  1.398  0.020  1.398
 KZV  CD1  CG2   aromatic  1.398  0.020  1.398
 KZV  CE2  F     single    1.342  0.020  1.342
 KZV  CE2  CD2   aromatic  1.369  0.020  1.369
 KZV  CG2  CD2   aromatic  1.405  0.020  1.405
 KZV  CG2  CB2   single    1.444  0.020  1.444
 KZV  CB2  CA2   double    1.348  0.020  1.348
 KZV  CA2  N2    single    1.389  0.020  1.389
 KZV  CA2  C2    single    1.477  0.020  1.477
 KZV  O2   C2    double    1.213  0.020  1.213
 KZV  N2   C1    double    1.286  0.020  1.286
 KZV  C2   N3    single    1.382  0.020  1.382
 KZV  C1   N3    single    1.380  0.020  1.380
 KZV  C1   CA1   single    1.507  0.020  1.507
 KZV  N3   CA3   single    1.432  0.020  1.432
 KZV  CB1  CA1   single    1.529  0.020  1.529
 KZV  CB1  SG1   single    1.822  0.020  1.822
 KZV  CA1  N     single    1.442  0.020  1.442
 KZV  CA3  C     single    1.515  0.020  1.515
 KZV  C    O     double    1.202  0.020  1.202
 KZV  N    HN1   single    0.890  0.020  1.040
 KZV  N    HN2   single    0.890  0.020  1.040
 KZV  SG1  HG1   single    1.200  0.020  1.300
 KZV  CB1  HB11  single    0.970  0.020  1.090
 KZV  CB1  HB12  single    0.970  0.020  1.090
 KZV  CA1  HA1   single    0.970  0.020  1.090
 KZV  CA3  HA31  single    0.970  0.020  1.090
 KZV  CA3  HA32  single    0.970  0.020  1.090
 KZV  CB2  HB2   single    0.930  0.020  1.080
 KZV  CD1  HD1   single    0.930  0.020  1.080
 KZV  CD2  HD2   single    0.930  0.020  1.080
 KZV  CE1  HE1   single    0.930  0.020  1.080
 KZV  OH   H1    single    0.850  0.020  0.980
 KZV  C    OXT   single    1.321  0.020  1.321
 KZV  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
 KZV  HN2   N    HN1   106.35  3.000
 KZV  HN2   N    CA1   110.04  3.000
 KZV  HN1   N    CA1   110.22  3.000
 KZV  HB12  CB1  HB11  107.64  3.000
 KZV  HB12  CB1  CA1   109.75  3.000
 KZV  HB11  CB1  CA1   111.79  3.000
 KZV  HB12  CB1  SG1   110.14  3.000
 KZV  HB11  CB1  SG1   109.07  3.000
 KZV  CA1   CB1  SG1   108.45  3.000
 KZV  HA1   CA1  C1    108.91  3.000
 KZV  HA1   CA1  CB1   108.41  3.000
 KZV  C1    CA1  CB1   108.91  3.000
 KZV  HA1   CA1  N     107.65  3.000
 KZV  CB1   CA1  N     109.23  3.000
 KZV  C1    CA1  N     113.61  3.000
 KZV  N3    C1   N2    113.52  3.000
 KZV  N3    C1   CA1   123.26  3.000
 KZV  N2    C1   CA1   123.22  3.000
 KZV  CA2   N2   C1    106.69  3.000
 KZV  CA3   N3   C2    122.26  3.000
 KZV  CA3   N3   C1    129.52  3.000
 KZV  C2    N3   C1    108.18  3.000
 KZV  CA2   C2   O2    131.71  3.000
 KZV  O2    C2   N3    125.36  3.000
 KZV  CA2   C2   N3    102.93  3.000
 KZV  CB2   CA2  C2    123.03  3.000
 KZV  C2    CA2  N2    108.69  3.000
 KZV  CB2   CA2  N2    128.29  3.000
 KZV  HA32  CA3  HA31  106.10  3.000
 KZV  HA32  CA3  C     108.99  3.000
 KZV  HA31  CA3  C     109.86  3.000
 KZV  HA32  CA3  N3    110.45  3.000
 KZV  HA31  CA3  N3    109.99  3.000
 KZV  C     CA3  N3    111.31  3.000
 KZV  HB2   CB2  CG2   115.34  3.000
 KZV  HB2   CB2  CA2   115.32  3.000
 KZV  CG2   CB2  CA2   129.34  3.000
 KZV  CD2   CG2  CD1   118.08  3.000
 KZV  CD2   CG2  CB2   123.68  3.000
 KZV  CD1   CG2  CB2   118.24  3.000
 KZV  HD1   CD1  CE1   118.87  3.000
 KZV  HD1   CD1  CG2   119.60  3.000
 KZV  CE1   CD1  CG2   121.53  3.000
 KZV  HD2   CD2  CE2   119.58  3.000
 KZV  HD2   CD2  CG2   120.74  3.000
 KZV  CE2   CD2  CG2   119.68  3.000
 KZV  HE1   CE1  CZ    119.64  3.000
 KZV  HE1   CE1  CD1   119.98  3.000
 KZV  CZ    CE1  CD1   120.38  3.000
 KZV  F     CE2  CZ    117.71  3.000
 KZV  F     CE2  CD2   119.70  3.000
 KZV  CZ    CE2  CD2   122.59  3.000
 KZV  OH    CZ   CE2   117.76  3.000
 KZV  CE2   CZ   CE1   117.74  3.000
 KZV  OH    CZ   CE1   124.50  3.000
 KZV  H1    OH   CZ    110.50  3.000
 KZV  OXT   C    O     125.03  3.000
 KZV  OXT   C    CA3   110.80  3.000
 KZV  O     C    CA3   124.16  3.000
 KZV  HXT   OXT  C     110.54  3.000
 KZV  HG1   SG1  CB1    96.66  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
 KZV  CONST_01  CZ   CE1  CD1  CG2    0.00   0.0  0
 KZV  CONST_02  CZ   CE2  CD2  CG2    0.00   0.0  0
 KZV  CONST_03  CE2  CZ   CE1  CD1    0.00   0.0  0
 KZV  CONST_04  CE2  CD2  CG2  CD1    0.00   0.0  0
 KZV  CONST_05  CE1  CZ   CE2  CD2    0.00   0.0  0
 KZV  CONST_06  CE1  CD1  CG2  CD2    0.00   0.0  0
 KZV  CONST_07  C2   CA2  N2   C1     0.00   0.0  0
 KZV  CONST_08  CA2  C2   N3   C1     0.00   0.0  0
 KZV  CONST_09  N3   C2   CA2  N2     0.00   0.0  0
 KZV  CONST_10  C2   N3   C1   N2     0.00   0.0  0
 KZV  CONST_11  CA2  N2   C1   N3     0.00   0.0  0
 KZV  CONST_12  CE1  CD1  CG2  CB2  180.00   0.0  0
 KZV  CONST_13  CE2  CD2  CG2  CB2  180.00   0.0  0
 KZV  CONST_14  F    CE2  CD2  CG2  180.00   0.0  0
 KZV  CONST_15  OH   CZ   CE1  CD1  180.00   0.0  0
 KZV  CONST_16  OH   CZ   CE2  CD2  180.00   0.0  0
 KZV  CONST_17  F    CE2  CZ   CE1  180.00   0.0  0
 KZV  CONST_18  CA2  N2   C1   CA1  180.00   0.0  0
 KZV  CONST_19  C2   N3   C1   CA1  180.00   0.0  0
 KZV  CONST_20  O2   C2   N3   C1   180.00   0.0  0
 KZV  CONST_21  CA3  N3   C1   N2   180.00   0.0  0
 KZV  CONST_22  CA3  N3   C2   CA2  180.00   0.0  0
 KZV  CONST_23  HE1  CE1  CD1  CG2  180.00   0.0  0
 KZV  CONST_24  HD2  CD2  CG2  CD1  180.00   0.0  0
 KZV  CONST_25  HD1  CD1  CG2  CD2  180.00   0.0  0
 KZV  CONST_26  CA3  N3   C1   CA1    0.00   0.0  0
 KZV  CONST_27  CA3  N3   C2   O2     0.00   0.0  0
 KZV  CONST_28  HXT  OXT  C    CA3  180.00   0.0  0
 KZV  Var_01    CG2  CB2  CA2  N2    -0.34  30.0  2
 KZV  Var_02    CD1  CG2  CB2  CA2  179.19  30.0  2
 KZV  Var_03    C    CA3  N3   C1   104.41  30.0  3
 KZV  Var_04    O    C    CA3  N3   -11.00  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
 KZV  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
 KZV  plan-1  CA1  0.020
 KZV  plan-1  C1   0.020
 KZV  plan-1  N2   0.020
 KZV  plan-1  N3   0.020
 KZV  plan-1  C2   0.020
 KZV  plan-1  O2   0.020
 KZV  plan-1  CA2  0.020
 KZV  plan-1  CA3  0.020
 KZV  plan-1  CB2  0.020
 KZV  plan-2  CB2  0.020
 KZV  plan-2  CG2  0.020
 KZV  plan-2  CD1  0.020
 KZV  plan-2  CD2  0.020
 KZV  plan-2  CE1  0.020
 KZV  plan-2  CE2  0.020
 KZV  plan-2  CZ   0.020
 KZV  plan-2  OH   0.020
 KZV  plan-2  F    0.020
 KZV  plan-2  HD1  0.020
 KZV  plan-2  HD2  0.020
 KZV  plan-2  HE1  0.020
 KZV  plan-3  CA3  0.020
 KZV  plan-3  C    0.020
 KZV  plan-3  O    0.020
 KZV  plan-3  OXT  0.020
 KZV  plan-3  HXT  0.020

