# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 08:23:03 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: {(4Z)-2-[(1R)-1-amino-2-sulfanylethyl]-4-[(2,3-difluoro-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)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
 KY4  KY4  '{(4Z)-2-[(1R)-1-amino-2-sulfanylethyl]-4-[(2,3-difluoro-4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid'  L-peptide  37  24  .  2022-03-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KY4
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
 KY4  N     N  NH2   0  -0.770  -2.0475  -2.5182  -1.5115
 KY4  SG1   S  S2    0  -0.225  -4.3930  -3.1480   0.6952
 KY4  CB1   C  CH2   0  -0.587  -3.1283  -1.8470   0.6674
 KY4  CA1   C  CH1   0  -0.202  -2.6876  -1.4657  -0.7594
 KY4  C1    C  CR5   0   0.576  -1.7468  -0.3050  -0.6389
 KY4  N2    N  N     0  -0.481  -0.4736  -0.4415  -0.5145
 KY4  N3    N  NR5   0  -0.568  -2.1720   1.0070  -0.5803
 KY4  C2    C  CR5   0   0.543  -1.0635   1.8076  -0.3784
 KY4  O2    O  O     0  -0.436  -1.0774   3.0146  -0.2724
 KY4  CA2   C  CR5   0   0.101   0.0485   0.8332  -0.3503
 KY4  CA3   C  CH2   0  -0.463  -3.4979   1.5391  -0.6641
 KY4  CB2   C  C1    0  -0.358   1.3331   1.2053  -0.1872
 KY4  CG2   C  CR6   0  -0.083   2.5134   0.3732  -0.1492
 KY4  CD1   C  CR6   0   0.410   3.7622   0.9712   0.0446
 KY4  CD2   C  CR16  0  -0.293   2.5103  -1.0217  -0.2995
 KY4  CE1   C  CR6   0   0.344   4.9290   0.2424   0.0869
 KY4  CE2   C  CR16  0  -0.367   3.6739  -1.7613  -0.2574
 KY4  CZ    C  CR6   0   0.223   4.9079  -1.1410  -0.0639
 KY4  OH    O  OH1   0  -0.603   6.0761  -1.7811  -0.0122
 KY4  C     C  C     0   0.553  -4.0424   1.9001   0.7024
 KY4  O     O  O     0  -0.427  -3.4857   1.6544   1.7392
 KY4  F1    F  F     0  -0.302   6.0939   0.8683   0.2759
 KY4  F2    F  F     0  -0.294   3.8558   2.2930   0.1968
 KY4  HN1   H  HNH2  0   0.353  -1.2368  -2.8617  -1.0111
 KY4  HN2   H  HNH2  0   0.355  -2.6872  -3.2959  -1.6140
 KY4  HG1   H  HSH1  0   0.228  -3.5861  -4.1930   0.4818
 KY4  HB11  H  HCH2  0   0.285  -3.5735  -0.9977   1.1860
 KY4  HB12  H  HCH2  0   0.293  -2.2652  -2.1643   1.2543
 KY4  HA1   H  HCH1  0   0.278  -3.5771  -1.1556  -1.3146
 KY4  HA31  H  HCH2  0   0.326  -3.4989   2.4257  -1.3011
 KY4  HA32  H  HCH2  0   0.327  -4.1660   0.8229  -1.1439
 KY4  HB2   H  H     0   0.279   1.4832   2.2721  -0.0709
 KY4  HD2   H  HCR6  0   0.295   1.5705  -1.5301  -0.4550
 KY4  HE2   H  HCR6  0   0.294   3.6309  -2.8369  -0.3754
 KY4  H1    H  HOH1  0   0.489   5.9479  -2.7312  -0.1212
 KY4  OXT   O  OH1   0  -0.582  -5.2093   2.5087   0.5939
 KY4  HXT   H  HOH1  0   0.491  -5.5665   2.7204   1.4700

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
 KY4  O    C     double    1.231  0.020  1.231
 KY4  SG1  CB1   single    1.815  0.020  1.815
 KY4  N    CA1   single    1.443  0.020  1.443
 KY4  C    CA3   single    1.515  0.020  1.515
 KY4  CA3  N3    single    1.431  0.020  1.431
 KY4  CA1  CB1   single    1.541  0.020  1.541
 KY4  CA1  C1    single    1.499  0.020  1.499
 KY4  N3   C1    single    1.380  0.020  1.380
 KY4  N3   C2    single    1.382  0.020  1.382
 KY4  C1   N2    double    1.287  0.020  1.287
 KY4  C2   O2    double    1.212  0.020  1.212
 KY4  C2   CA2   single    1.479  0.020  1.479
 KY4  N2   CA2   single    1.387  0.020  1.387
 KY4  CA2  CB2   double    1.347  0.020  1.347
 KY4  CB2  CG2   single    1.445  0.020  1.445
 KY4  CD2  CG2   aromatic  1.403  0.020  1.403
 KY4  CD2  CE2   aromatic  1.379  0.020  1.379
 KY4  CG2  CD1   aromatic  1.398  0.020  1.398
 KY4  CE2  CZ    aromatic  1.395  0.020  1.395
 KY4  CD1  F2    single    1.334  0.020  1.334
 KY4  CD1  CE1   aromatic  1.376  0.020  1.376
 KY4  CZ   CE1   aromatic  1.392  0.020  1.392
 KY4  CZ   OH    single    1.333  0.020  1.333
 KY4  CE1  F1    single    1.336  0.020  1.336
 KY4  N    HN1   single    0.890  0.020  1.040
 KY4  N    HN2   single    0.890  0.020  1.040
 KY4  SG1  HG1   single    1.200  0.020  1.300
 KY4  CB1  HB11  single    0.970  0.020  1.090
 KY4  CB1  HB12  single    0.970  0.020  1.090
 KY4  CA1  HA1   single    0.970  0.020  1.090
 KY4  CA3  HA31  single    0.970  0.020  1.090
 KY4  CA3  HA32  single    0.970  0.020  1.090
 KY4  CB2  HB2   single    0.930  0.020  1.080
 KY4  CD2  HD2   single    0.930  0.020  1.080
 KY4  CE2  HE2   single    0.930  0.020  1.080
 KY4  OH   H1    single    0.850  0.020  0.980
 KY4  C    OXT   single    1.321  0.020  1.321
 KY4  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
 KY4  HN2   N    HN1   107.18  3.000
 KY4  HN2   N    CA1   109.44  3.000
 KY4  HN1   N    CA1   110.17  3.000
 KY4  HG1   SG1  CB1    97.89  3.000
 KY4  HB12  CB1  HB11  107.08  3.000
 KY4  HB12  CB1  CA1   110.11  3.000
 KY4  HB11  CB1  CA1   111.37  3.000
 KY4  HB12  CB1  SG1   109.56  3.000
 KY4  HB11  CB1  SG1   105.47  3.000
 KY4  CA1   CB1  SG1   113.01  3.000
 KY4  HA1   CA1  C1    109.38  3.000
 KY4  HA1   CA1  CB1   107.92  3.000
 KY4  C1    CA1  CB1   107.26  3.000
 KY4  HA1   CA1  N     107.64  3.000
 KY4  C1    CA1  N     109.16  3.000
 KY4  CB1   CA1  N     115.39  3.000
 KY4  N3    C1   N2    113.68  3.000
 KY4  N2    C1   CA1   123.14  3.000
 KY4  N3    C1   CA1   123.10  3.000
 KY4  CA2   N2   C1    106.64  3.000
 KY4  CA3   N3   C2    122.43  3.000
 KY4  C2    N3   C1    108.04  3.000
 KY4  CA3   N3   C1    129.51  3.000
 KY4  CA2   C2   O2    131.56  3.000
 KY4  CA2   C2   N3    102.96  3.000
 KY4  O2    C2   N3    125.48  3.000
 KY4  CB2   CA2  C2    122.50  3.000
 KY4  CB2   CA2  N2    128.82  3.000
 KY4  C2    CA2  N2    108.68  3.000
 KY4  HA32  CA3  HA31  106.02  3.000
 KY4  HA32  CA3  C     109.47  3.000
 KY4  HA31  CA3  C     109.42  3.000
 KY4  HA32  CA3  N3    110.44  3.000
 KY4  HA31  CA3  N3    109.69  3.000
 KY4  C     CA3  N3    111.64  3.000
 KY4  HB2   CB2  CG2   116.81  3.000
 KY4  HB2   CB2  CA2   114.65  3.000
 KY4  CG2   CB2  CA2   128.54  3.000
 KY4  CD2   CG2  CD1   116.24  3.000
 KY4  CD1   CG2  CB2   119.15  3.000
 KY4  CD2   CG2  CB2   124.61  3.000
 KY4  F2    CD1  CE1   117.50  3.000
 KY4  CE1   CD1  CG2   122.35  3.000
 KY4  F2    CD1  CG2   120.16  3.000
 KY4  HD2   CD2  CE2   119.08  3.000
 KY4  HD2   CD2  CG2   119.05  3.000
 KY4  CE2   CD2  CG2   121.87  3.000
 KY4  F1    CE1  CZ    119.62  3.000
 KY4  F1    CE1  CD1   119.71  3.000
 KY4  CZ    CE1  CD1   120.67  3.000
 KY4  HE2   CE2  CZ    119.47  3.000
 KY4  HE2   CE2  CD2   119.72  3.000
 KY4  CZ    CE2  CD2   120.81  3.000
 KY4  OH    CZ   CE2   124.56  3.000
 KY4  OH    CZ   CE1   117.37  3.000
 KY4  CE2   CZ   CE1   118.07  3.000
 KY4  H1    OH   CZ    110.61  3.000
 KY4  OXT   C    O     125.05  3.000
 KY4  OXT   C    CA3   110.69  3.000
 KY4  O     C    CA3   124.26  3.000
 KY4  HXT   OXT  C     110.61  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
 KY4  CONST_01  CZ   CE2  CD2  CG2    0.00   0.0  0
 KY4  CONST_02  CZ   CE1  CD1  CG2    0.00   0.0  0
 KY4  CONST_03  CE2  CD2  CG2  CD1    0.00   0.0  0
 KY4  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 KY4  CONST_05  CE1  CD1  CG2  CD2    0.00   0.0  0
 KY4  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 KY4  CONST_07  CA2  C2   N3   C1     0.00   0.0  0
 KY4  CONST_08  C2   CA2  N2   C1     0.00   0.0  0
 KY4  CONST_09  C2   N3   C1   N2     0.00   0.0  0
 KY4  CONST_10  N3   C2   CA2  N2     0.00   0.0  0
 KY4  CONST_11  CA2  N2   C1   N3     0.00   0.0  0
 KY4  CONST_12  CE2  CD2  CG2  CB2  180.00   0.0  0
 KY4  CONST_13  CE1  CD1  CG2  CB2  180.00   0.0  0
 KY4  CONST_14  F1   CE1  CD1  CG2  180.00   0.0  0
 KY4  CONST_15  OH   CZ   CE1  CD1  180.00   0.0  0
 KY4  CONST_16  F2   CD1  CG2  CD2  180.00   0.0  0
 KY4  CONST_17  OH   CZ   CE2  CD2  180.00   0.0  0
 KY4  CONST_18  F1   CE1  CZ   CE2  180.00   0.0  0
 KY4  CONST_19  F2   CD1  CE1  CZ   180.00   0.0  0
 KY4  CONST_20  C2   N3   C1   CA1  180.00   0.0  0
 KY4  CONST_21  CA2  N2   C1   CA1  180.00   0.0  0
 KY4  CONST_22  O2   C2   N3   C1   180.00   0.0  0
 KY4  CONST_23  CA3  N3   C1   N2   180.00   0.0  0
 KY4  CONST_24  CA3  N3   C2   CA2  180.00   0.0  0
 KY4  CONST_25  HE2  CE2  CD2  CG2  180.00   0.0  0
 KY4  CONST_26  HD2  CD2  CG2  CD1  180.00   0.0  0
 KY4  CONST_27  CA3  N3   C1   CA1    0.00   0.0  0
 KY4  CONST_28  CA3  N3   C2   O2     0.00   0.0  0
 KY4  CONST_29  HXT  OXT  C    CA3  180.00   0.0  0
 KY4  Var_01    CG2  CB2  CA2  N2     0.48  30.0  2
 KY4  Var_02    CD2  CG2  CB2  CA2    0.84  30.0  2
 KY4  Var_03    C    CA3  N3   C1   101.34  30.0  1
 KY4  Var_04    O    C    CA3  N3    -6.62  30.0  1

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
 KY4  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
 KY4  plan-1  CA1  0.020
 KY4  plan-1  C1   0.020
 KY4  plan-1  N2   0.020
 KY4  plan-1  N3   0.020
 KY4  plan-1  C2   0.020
 KY4  plan-1  O2   0.020
 KY4  plan-1  CA2  0.020
 KY4  plan-1  CA3  0.020
 KY4  plan-1  CB2  0.020
 KY4  plan-2  CB2  0.020
 KY4  plan-2  CG2  0.020
 KY4  plan-2  CD1  0.020
 KY4  plan-2  CD2  0.020
 KY4  plan-2  CE1  0.020
 KY4  plan-2  CE2  0.020
 KY4  plan-2  CZ   0.020
 KY4  plan-2  OH   0.020
 KY4  plan-2  F1   0.020
 KY4  plan-2  F2   0.020
 KY4  plan-2  HD2  0.020
 KY4  plan-2  HE2  0.020
 KY4  plan-3  CA3  0.020
 KY4  plan-3  C    0.020
 KY4  plan-3  O    0.020
 KY4  plan-3  OXT  0.020
 KY4  plan-3  HXT  0.020

