# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 05:05:27 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: {(4Z)-2-[(1S)-1-amino-2-sulfanylethyl]-4-[(4-hydroxy-3-nitrophenyl)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(c2)[N+]([O-])=O)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
 KY7  KY7  '{(4Z)-2-[(1S)-1-amino-2-sulfanylethyl]-4-[(4-hydroxy-3-nitrophenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid'  L-peptide  39  25  .  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_KY7
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
 KY7  N     N  NH2    0  -0.772   2.5615  -2.2569  -1.2113
 KY7  CB1   C  CH2    0  -0.590   3.4063  -2.0176   1.1591
 KY7  CA1   C  CH1    0  -0.193   3.0933  -1.3705  -0.2065
 KY7  C1    C  CR5    0   0.569   2.1202  -0.2602   0.0443
 KY7  N2    N  N      0  -0.480   0.8478  -0.3892  -0.0836
 KY7  N3    N  NR5    0  -0.565   2.5097   0.9671   0.5430
 KY7  C2    C  CR5    0   0.546   1.3744   1.7408   0.7057
 KY7  O2    O  O      0  -0.432   1.3468   2.8934   1.0763
 KY7  CA2   C  CR5    0   0.103   0.2864   0.8154   0.3172
 KY7  CA3   C  CH2    0  -0.473   3.8401   1.4863   0.6431
 KY7  CB2   C  C1     0  -0.385  -1.0157   1.1505   0.3737
 KY7  CG2   C  CR6    0   0.157  -2.1738   0.3512   0.0335
 KY7  CD1   C  CR16   0  -0.364  -3.4284   0.9160   0.1998
 KY7  CD2   C  CR16   0  -0.277  -2.1079  -0.9695  -0.4588
 KY7  CE1   C  CR6    0   0.191  -4.5850   0.2044  -0.1055
 KY7  CE2   C  CR16   0  -0.324  -3.2433  -1.6739  -0.7630
 KY7  CZ    C  CR6    0   0.370  -4.5180  -1.1150  -0.5963
 KY7  OH    O  OH1    0  -0.590  -5.5558  -1.8657  -0.9117
 KY7  C     C  C      0   0.552   4.3510   1.9511  -0.7055
 KY7  O     O  O      0  -0.424   3.7348   1.8349  -1.7310
 KY7  NA    N  N      1   0.366  -5.8525   0.8510   0.0958
 KY7  OA    O  O     -1  -0.424  -6.8679   0.2203  -0.1663
 KY7  HN1   H  HNH2   0   0.354   3.2261  -3.0008  -1.3827
 KY7  HN2   H  HNH2   0   0.353   1.7066  -2.6910  -0.8850
 KY7  HG1   H  HSH1   0   0.229   3.7601  -4.3332   0.6556
 KY7  HB11  H  HCH2   0   0.297   2.4928  -2.3855   1.6272
 KY7  HB12  H  HCH2   0   0.289   3.8534  -1.2945   1.8430
 KY7  HA1   H  HCH1   0   0.275   4.0261  -0.9518  -0.5947
 KY7  HA31  H  HCH2   0   0.332   3.8418   2.3226   1.3441
 KY7  HA32  H  HCH2   0   0.323   4.5235   0.7435   1.0599
 KY7  HB2   H  H      0   0.278  -1.2275   2.1548   0.7258
 KY7  HD1   H  HCR6   0   0.305  -3.5116   1.9275   0.5733
 KY7  HD2   H  HCR6   0   0.296  -1.1450  -1.4381  -0.6028
 KY7  HE1   H  HCR6   0   0.293  -3.1734  -2.6853  -1.1410
 KY7  H1    H  HOH1   0   0.487  -6.3752  -1.3594  -0.7531
 KY7  OXT   O  OH1    0  -0.582   5.5541   2.4833  -0.5966
 KY7  HXT   H  HOH1   0   0.491   5.8849   2.7612  -1.4647
 KY7  SG1   S  S2     0  -0.224   4.6089  -3.3733   1.0383
 KY7  OB    O  O      0  -0.360  -5.8790   1.9799   0.5123

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
 KY7  C    O     double    1.231  0.020  1.231
 KY7  C    CA3   single    1.515  0.020  1.515
 KY7  O2   C2    double    1.211  0.020  1.211
 KY7  C2   N3    single    1.383  0.020  1.383
 KY7  C2   CA2   single    1.480  0.020  1.480
 KY7  CA3  N3    single    1.432  0.020  1.432
 KY7  N3   C1    single    1.381  0.020  1.381
 KY7  CB2  CA2   double    1.346  0.020  1.346
 KY7  CB2  CG2   single    1.448  0.020  1.448
 KY7  CA2  N2    single    1.388  0.020  1.388
 KY7  C1   N2    double    1.285  0.020  1.285
 KY7  C1   CA1   single    1.498  0.020  1.498
 KY7  CG2  CD1   aromatic  1.386  0.020  1.386
 KY7  CG2  CD2   aromatic  1.411  0.020  1.411
 KY7  CD1  CE1   aromatic  1.392  0.020  1.392
 KY7  CB1  CA1   single    1.543  0.020  1.543
 KY7  CB1  SG1   single    1.816  0.020  1.816
 KY7  OA   NA    single    1.224  0.020  1.224
 KY7  CD2  CE2   aromatic  1.370  0.020  1.370
 KY7  NA   CE1   single    1.437  0.020  1.437
 KY7  NA   OB    double    1.204  0.020  1.204
 KY7  CA1  N     single    1.442  0.020  1.442
 KY7  CE1  CZ    aromatic  1.409  0.020  1.409
 KY7  CE2  CZ    aromatic  1.402  0.020  1.402
 KY7  CZ   OH    single    1.319  0.020  1.319
 KY7  N    HN1   single    0.890  0.020  1.040
 KY7  N    HN2   single    0.890  0.020  1.040
 KY7  SG1  HG1   single    1.200  0.020  1.300
 KY7  CB1  HB11  single    0.970  0.020  1.090
 KY7  CB1  HB12  single    0.970  0.020  1.090
 KY7  CA1  HA1   single    0.970  0.020  1.090
 KY7  CA3  HA31  single    0.970  0.020  1.090
 KY7  CA3  HA32  single    0.970  0.020  1.090
 KY7  CB2  HB2   single    0.930  0.020  1.080
 KY7  CD1  HD1   single    0.930  0.020  1.080
 KY7  CD2  HD2   single    0.930  0.020  1.080
 KY7  CE2  HE1   single    0.930  0.020  1.080
 KY7  OH   H1    single    0.850  0.020  0.980
 KY7  C    OXT   single    1.320  0.020  1.320
 KY7  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
 KY7  HN2   N    HN1   107.09  3.000
 KY7  HN2   N    CA1   110.51  3.000
 KY7  HN1   N    CA1   109.13  3.000
 KY7  HB12  CB1  HB11  107.33  3.000
 KY7  HB12  CB1  CA1   111.10  3.000
 KY7  HB11  CB1  CA1   110.57  3.000
 KY7  HB12  CB1  SG1   105.37  3.000
 KY7  HB11  CB1  SG1   109.36  3.000
 KY7  CA1   CB1  SG1   112.86  3.000
 KY7  HA1   CA1  C1    109.25  3.000
 KY7  HA1   CA1  CB1   107.55  3.000
 KY7  C1    CA1  CB1   107.13  3.000
 KY7  HA1   CA1  N     107.62  3.000
 KY7  CB1   CA1  N     115.71  3.000
 KY7  C1    CA1  N     109.44  3.000
 KY7  N3    C1   N2    113.85  3.000
 KY7  N2    C1   CA1   123.52  3.000
 KY7  N3    C1   CA1   122.42  3.000
 KY7  CA2   N2   C1    106.54  3.000
 KY7  CA3   N3   C2    123.48  3.000
 KY7  CA3   N3   C1    127.57  3.000
 KY7  C2    N3   C1    107.94  3.000
 KY7  CA2   C2   O2    131.19  3.000
 KY7  CA2   C2   N3    102.87  3.000
 KY7  O2    C2   N3    125.94  3.000
 KY7  CB2   CA2  C2    122.99  3.000
 KY7  CB2   CA2  N2    128.29  3.000
 KY7  C2    CA2  N2    108.72  3.000
 KY7  HA32  CA3  HA31  105.97  3.000
 KY7  HA32  CA3  C     109.72  3.000
 KY7  HA31  CA3  C     109.64  3.000
 KY7  HA32  CA3  N3    111.20  3.000
 KY7  HA31  CA3  N3    108.92  3.000
 KY7  C     CA3  N3    111.24  3.000
 KY7  HB2   CB2  CG2   115.53  3.000
 KY7  HB2   CB2  CA2   115.66  3.000
 KY7  CG2   CB2  CA2   128.80  3.000
 KY7  CD2   CG2  CD1   117.75  3.000
 KY7  CD2   CG2  CB2   124.15  3.000
 KY7  CD1   CG2  CB2   118.10  3.000
 KY7  HD1   CD1  CE1   119.34  3.000
 KY7  HD1   CD1  CG2   119.49  3.000
 KY7  CE1   CD1  CG2   121.17  3.000
 KY7  HD2   CD2  CE2   119.07  3.000
 KY7  HD2   CD2  CG2   119.61  3.000
 KY7  CE2   CD2  CG2   121.32  3.000
 KY7  NA    CE1  CZ    120.79  3.000
 KY7  CZ    CE1  CD1   121.03  3.000
 KY7  NA    CE1  CD1   118.18  3.000
 KY7  HE1   CE2  CZ    118.23  3.000
 KY7  HE1   CE2  CD2   120.30  3.000
 KY7  CZ    CE2  CD2   121.47  3.000
 KY7  OH    CZ   CE2   117.39  3.000
 KY7  OH    CZ   CE1   125.36  3.000
 KY7  CE2   CZ   CE1   117.25  3.000
 KY7  H1    OH   CZ    109.04  3.000
 KY7  OXT   C    O     125.21  3.000
 KY7  OXT   C    CA3   110.95  3.000
 KY7  O     C    CA3   123.84  3.000
 KY7  OA    NA   OB    122.64  3.000
 KY7  OB    NA   CE1   119.33  3.000
 KY7  OA    NA   CE1   118.03  3.000
 KY7  HXT   OXT  C     110.65  3.000
 KY7  HG1   SG1  CB1    97.73  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
 KY7  CONST_01  CZ   CE1  CD1  CG2    0.00   0.0  0
 KY7  CONST_02  CZ   CE2  CD2  CG2    0.00   0.0  0
 KY7  CONST_03  CE2  CD2  CG2  CD1    0.00   0.0  0
 KY7  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 KY7  CONST_05  CE1  CD1  CG2  CD2    0.00   0.0  0
 KY7  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 KY7  CONST_07  CA2  C2   N3   C1     0.00   0.0  0
 KY7  CONST_08  C2   CA2  N2   C1     0.00   0.0  0
 KY7  CONST_09  N3   C2   CA2  N2     0.00   0.0  0
 KY7  CONST_10  C2   N3   C1   N2     0.00   0.0  0
 KY7  CONST_11  CA2  N2   C1   N3     0.00   0.0  0
 KY7  CONST_12  CE1  CD1  CG2  CB2  180.00   0.0  0
 KY7  CONST_13  CE2  CD2  CG2  CB2  180.00   0.0  0
 KY7  CONST_14  NA   CE1  CD1  CG2  180.00   0.0  0
 KY7  CONST_15  OH   CZ   CE1  CD1  180.00   0.0  0
 KY7  CONST_16  OH   CZ   CE2  CD2  180.00   0.0  0
 KY7  CONST_17  NA   CE1  CZ   CE2  180.00   0.0  0
 KY7  CONST_18  C2   N3   C1   CA1  180.00   0.0  0
 KY7  CONST_19  CA2  N2   C1   CA1  180.00   0.0  0
 KY7  CONST_20  O2   C2   N3   C1   180.00   0.0  0
 KY7  CONST_21  CA3  N3   C1   N2   180.00   0.0  0
 KY7  CONST_22  CA3  N3   C2   CA2  180.00   0.0  0
 KY7  CONST_23  HE1  CE2  CD2  CG2  180.00   0.0  0
 KY7  CONST_24  HD2  CD2  CG2  CD1  180.00   0.0  0
 KY7  CONST_25  HD1  CD1  CG2  CD2  180.00   0.0  0
 KY7  CONST_26  OA   NA   CE1  CD1  180.00   0.0  0
 KY7  CONST_27  OB   NA   CE1  CD1    0.00   0.0  0
 KY7  CONST_28  OA   NA   CE1  CZ     0.00   0.0  0
 KY7  CONST_29  OB   NA   CE1  CZ   180.00   0.0  0
 KY7  CONST_30  CA3  N3   C1   CA1    0.00   0.0  0
 KY7  CONST_31  CA3  N3   C2   O2     0.00   0.0  0
 KY7  CONST_32  HXT  OXT  C    CA3  180.00   0.0  0
 KY7  Var_01    CG2  CB2  CA2  N2    -0.04  30.0  2
 KY7  Var_02    CD1  CG2  CB2  CA2  178.87  30.0  2
 KY7  Var_03    C    CA3  N3   C1    76.33  30.0  2
 KY7  Var_04    O    C    CA3  N3    -3.31  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
 KY7  chir_01  CA1  C1  CB1  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
 KY7  plan-1  CA1  0.020
 KY7  plan-1  C1   0.020
 KY7  plan-1  N2   0.020
 KY7  plan-1  N3   0.020
 KY7  plan-1  C2   0.020
 KY7  plan-1  O2   0.020
 KY7  plan-1  CA2  0.020
 KY7  plan-1  CA3  0.020
 KY7  plan-1  CB2  0.020
 KY7  plan-2  CB2  0.020
 KY7  plan-2  CG2  0.020
 KY7  plan-2  CD1  0.020
 KY7  plan-2  CD2  0.020
 KY7  plan-2  CE1  0.020
 KY7  plan-2  CE2  0.020
 KY7  plan-2  CZ   0.020
 KY7  plan-2  OH   0.020
 KY7  plan-2  NA   0.020
 KY7  plan-2  HD1  0.020
 KY7  plan-2  HD2  0.020
 KY7  plan-2  HE1  0.020
 KY7  plan-3  CE1  0.020
 KY7  plan-3  NA   0.020
 KY7  plan-3  OA   0.020
 KY7  plan-3  OB   0.020
 KY7  plan-4  CA3  0.020
 KY7  plan-4  C    0.020
 KY7  plan-4  O    0.020
 KY7  plan-4  OXT  0.020
 KY7  plan-4  HXT  0.020

