# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 22:49:50 2021
#   Inital geometry file: a 114 line input string
#   Ligand name: {(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-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: C[C@@H](O)[C@H](N)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
 QCA  QCA  '{(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-[(4-hydroxy-3-nitrophenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid'  L-peptide  42  26  .  2022-08-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QCA
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
 QCA  N1   N  NH2    0  -0.799  8.7580   6.0921   2.1396
 QCA  CA1  C  CH1    0  -0.230  7.5533   6.2269   2.9484
 QCA  CB1  C  CH1    0   0.059  7.8960   6.5916   4.4047
 QCA  CG1  C  CH3    0  -0.696  8.6996   5.4917   5.0727
 QCA  OG1  O  OH1    0  -0.681  8.6242   7.7893   4.5049
 QCA  C1   C  CR5    0   0.610  6.6724   7.2727   2.3353
 QCA  N2   N  N      0  -0.547  6.5288   8.4730   2.7826
 QCA  N3   N  NR5    0  -0.572  5.9465   7.0252   1.1899
 QCA  C2   C  CR5    0   0.548  5.2322   8.1679   0.8741
 QCA  O2   O  O      0  -0.428  4.4588   8.2836  -0.0498
 QCA  CA2  C  CR5    0   0.125  5.6402   9.1176   1.9306
 QCA  CA3  C  CH2    0  -0.471  5.7274   5.7647   0.5407
 QCA  C3   C  C      0   0.557  4.5360   4.9896   1.0674
 QCA  O3   O  O      0  -0.434  4.1379   3.9870   0.5363
 QCA  CB2  C  C1     0  -0.379  5.1631  10.3733   2.0069
 QCA  CG2  C  CR6    0   0.164  5.4127  11.3937   3.0015
 QCA  CD1  C  CR16   0  -0.380  6.1624  11.1884   4.1508
 QCA  CD2  C  CR16   0  -0.267  4.8433  12.6672   2.8106
 QCA  CE1  C  CR6    0   0.213  6.3396  12.2106   5.0740
 QCA  CE2  C  CR16   0  -0.340  5.0163  13.6822   3.7163
 QCA  CZ   C  CR6    0   0.376  5.7686  13.4867   4.8809
 QCA  OH   O  OH1    0  -0.590  5.8839  14.5083   5.7078
 QCA  N4   N  N      1   0.367  7.1241  11.9245   6.2475
 QCA  O4   O  O     -1  -0.357  7.6178  10.8346   6.3737
 QCA  O5   O  O      0  -0.422  7.2582  12.8118   7.0781
 QCA  H1   H  HNH2   0   0.367  9.2345   5.2367   2.3956
 QCA  H2   H  HNH2   0   0.360  8.5402   5.9947   1.1560
 QCA  H4   H  HCH1   0   0.253  6.9568   5.3014   2.9973
 QCA  H5   H  HCH1   0   0.206  6.9354   6.6716   4.9343
 QCA  H6   H  HCH3   0   0.246  8.8810   5.7397   6.1187
 QCA  H7   H  HCH3   0   0.232  8.1561   4.5469   5.0473
 QCA  H8   H  HCH3   0   0.229  9.6685   5.3428   4.5936
 QCA  H9   H  HOH1   0   0.457  8.0925   8.4690   4.0695
 QCA  H10  H  HCH2   0   0.320  6.6075   5.1265   0.6321
 QCA  H11  H  HCH2   0   0.332  5.5842   5.9293  -0.5277
 QCA  H13  H  H      0   0.281  4.4845  10.6593   1.2097
 QCA  H14  H  HCR6   0   0.307  6.6054  10.2229   4.3380
 QCA  H15  H  HCR6   0   0.284  4.2496  12.8548   1.9248
 QCA  H16  H  HCR6   0   0.295  4.5679  14.6524   3.5484
 QCA  H17  H  HOH1   0   0.488  6.4156  14.2383   6.4801
 QCA  OXT  O  OH1    0  -0.578  4.0204   5.5245   2.1583
 QCA  HXT  H  HOH1   0   0.493  3.2713   4.9947   2.4730

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
 QCA  O3   C3   double    1.202  0.020  1.202
 QCA  O2   C2   double    1.210  0.020  1.210
 QCA  CA3  C3   single    1.516  0.020  1.516
 QCA  CA3  N3   single    1.435  0.020  1.435
 QCA  C2   N3   single    1.384  0.020  1.384
 QCA  C2   CA2  single    1.478  0.020  1.478
 QCA  N3   C1   single    1.378  0.020  1.378
 QCA  CA2  CB2  double    1.345  0.020  1.345
 QCA  CA2  N2   single    1.390  0.020  1.390
 QCA  N1   CA1  single    1.457  0.020  1.457
 QCA  CB2  CG2  single    1.447  0.020  1.447
 QCA  C1   N2   double    1.289  0.020  1.289
 QCA  C1   CA1  single    1.499  0.020  1.499
 QCA  CD2  CG2  aromatic  1.408  0.020  1.408
 QCA  CD2  CE2  aromatic  1.371  0.020  1.371
 QCA  CA1  CB1  single    1.540  0.020  1.540
 QCA  CG2  CD1  aromatic  1.388  0.020  1.388
 QCA  CE2  CZ   aromatic  1.400  0.020  1.400
 QCA  CD1  CE1  aromatic  1.389  0.020  1.389
 QCA  CB1  OG1  single    1.405  0.020  1.405
 QCA  CB1  CG1  single    1.517  0.020  1.517
 QCA  CZ   CE1  aromatic  1.411  0.020  1.411
 QCA  CZ   OH   single    1.319  0.020  1.319
 QCA  CE1  N4   single    1.440  0.020  1.440
 QCA  N4   O4   single    1.203  0.020  1.203
 QCA  N4   O5   double    1.223  0.020  1.223
 QCA  N1   H1   single    0.890  0.020  1.040
 QCA  N1   H2   single    0.890  0.020  1.040
 QCA  CA1  H4   single    0.970  0.020  1.090
 QCA  CB1  H5   single    0.970  0.020  1.090
 QCA  CG1  H6   single    0.970  0.020  1.090
 QCA  CG1  H7   single    0.970  0.020  1.090
 QCA  CG1  H8   single    0.970  0.020  1.090
 QCA  OG1  H9   single    0.850  0.020  0.980
 QCA  CA3  H10  single    0.970  0.020  1.090
 QCA  CA3  H11  single    0.970  0.020  1.090
 QCA  CB2  H13  single    0.930  0.020  1.080
 QCA  CD1  H14  single    0.930  0.020  1.080
 QCA  CD2  H15  single    0.930  0.020  1.080
 QCA  CE2  H16  single    0.930  0.020  1.080
 QCA  OH   H17  single    0.850  0.020  0.980
 QCA  C3   OXT  single    1.320  0.020  1.320
 QCA  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
 QCA  H2   N1   H1   105.42  3.000
 QCA  H2   N1   CA1  111.74  3.000
 QCA  H1   N1   CA1  109.09  3.000
 QCA  H4   CA1  C1   106.62  3.000
 QCA  H4   CA1  CB1  106.10  3.000
 QCA  C1   CA1  CB1  110.64  3.000
 QCA  H4   CA1  N1   113.22  3.000
 QCA  CB1  CA1  N1   111.27  3.000
 QCA  C1   CA1  N1   108.87  3.000
 QCA  H5   CB1  OG1  110.87  3.000
 QCA  H5   CB1  CG1  107.66  3.000
 QCA  OG1  CB1  CG1  108.18  3.000
 QCA  H5   CB1  CA1  106.15  3.000
 QCA  CG1  CB1  CA1  111.26  3.000
 QCA  OG1  CB1  CA1  112.62  3.000
 QCA  H8   CG1  H7   108.31  3.000
 QCA  H8   CG1  H6   107.73  3.000
 QCA  H7   CG1  H6   107.60  3.000
 QCA  H8   CG1  CB1  112.08  3.000
 QCA  H7   CG1  CB1  110.73  3.000
 QCA  H6   CG1  CB1  110.23  3.000
 QCA  H9   OG1  CB1  106.39  3.000
 QCA  N3   C1   N2   113.39  3.000
 QCA  N2   C1   CA1  124.99  3.000
 QCA  N3   C1   CA1  121.61  3.000
 QCA  CA2  N2   C1   106.88  3.000
 QCA  CA3  N3   C2   122.91  3.000
 QCA  C2   N3   C1   108.24  3.000
 QCA  CA3  N3   C1   127.90  3.000
 QCA  CA2  C2   O2   131.34  3.000
 QCA  CA2  C2   N3   103.00  3.000
 QCA  O2   C2   N3   125.65  3.000
 QCA  CB2  CA2  C2   122.84  3.000
 QCA  CB2  CA2  N2   128.67  3.000
 QCA  C2   CA2  N2   108.47  3.000
 QCA  H11  CA3  H10  106.05  3.000
 QCA  H11  CA3  C3   108.33  3.000
 QCA  H10  CA3  C3   107.81  3.000
 QCA  H11  CA3  N3   109.32  3.000
 QCA  H10  CA3  N3   110.66  3.000
 QCA  C3   CA3  N3   114.33  3.000
 QCA  OXT  C3   O3   125.00  3.000
 QCA  OXT  C3   CA3  112.77  3.000
 QCA  O3   C3   CA3  122.21  3.000
 QCA  H13  CB2  CG2  115.28  3.000
 QCA  H13  CB2  CA2  115.21  3.000
 QCA  CG2  CB2  CA2  129.51  3.000
 QCA  CD2  CG2  CD1  117.69  3.000
 QCA  CD1  CG2  CB2  123.94  3.000
 QCA  CD2  CG2  CB2  118.36  3.000
 QCA  H14  CD1  CE1  119.41  3.000
 QCA  H14  CD1  CG2  119.88  3.000
 QCA  CE1  CD1  CG2  120.71  3.000
 QCA  H15  CD2  CE2  118.77  3.000
 QCA  H15  CD2  CG2  119.29  3.000
 QCA  CE2  CD2  CG2  121.93  3.000
 QCA  N4   CE1  CZ   120.76  3.000
 QCA  N4   CE1  CD1  117.71  3.000
 QCA  CZ   CE1  CD1  121.53  3.000
 QCA  H16  CE2  CZ   118.49  3.000
 QCA  H16  CE2  CD2  120.59  3.000
 QCA  CZ   CE2  CD2  120.92  3.000
 QCA  OH   CZ   CE2  117.40  3.000
 QCA  OH   CZ   CE1  125.38  3.000
 QCA  CE2  CZ   CE1  117.22  3.000
 QCA  H17  OH   CZ   109.24  3.000
 QCA  O5   N4   O4   122.75  3.000
 QCA  O5   N4   CE1  117.98  3.000
 QCA  O4   N4   CE1  119.27  3.000
 QCA  HXT  OXT  C3   110.40  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
 QCA  CONST_01  CZ   CE2  CD2  CG2    0.00   0.0  0
 QCA  CONST_02  CZ   CE1  CD1  CG2    0.00   0.0  0
 QCA  CONST_03  CE2  CD2  CG2  CD1    0.00   0.0  0
 QCA  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 QCA  CONST_05  CE1  CD1  CG2  CD2    0.00   0.0  0
 QCA  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 QCA  CONST_07  CA2  C2   N3   C1     0.00   0.0  0
 QCA  CONST_08  C2   CA2  N2   C1     0.00   0.0  0
 QCA  CONST_09  N3   C2   CA2  N2     0.00   0.0  0
 QCA  CONST_10  C2   N3   C1   N2     0.00   0.0  0
 QCA  CONST_11  CA2  N2   C1   N3     0.00   0.0  0
 QCA  CONST_12  CE2  CD2  CG2  CB2  180.00   0.0  0
 QCA  CONST_13  CE1  CD1  CG2  CB2  180.00   0.0  0
 QCA  CONST_14  N4   CE1  CD1  CG2  180.00   0.0  0
 QCA  CONST_15  OH   CZ   CE1  CD1  180.00   0.0  0
 QCA  CONST_16  OH   CZ   CE2  CD2  180.00   0.0  0
 QCA  CONST_17  N4   CE1  CZ   CE2  180.00   0.0  0
 QCA  CONST_18  C2   N3   C1   CA1  180.00   0.0  0
 QCA  CONST_19  CA2  N2   C1   CA1  180.00   0.0  0
 QCA  CONST_20  O2   C2   N3   C1   180.00   0.0  0
 QCA  CONST_21  CA3  N3   C1   N2   180.00   0.0  0
 QCA  CONST_22  CA3  N3   C2   CA2  180.00   0.0  0
 QCA  CONST_23  H16  CE2  CD2  CG2  180.00   0.0  0
 QCA  CONST_24  H15  CD2  CG2  CD1  180.00   0.0  0
 QCA  CONST_25  H14  CD1  CG2  CD2  180.00   0.0  0
 QCA  CONST_26  O4   N4   CE1  CD1    0.00   0.0  0
 QCA  CONST_27  O5   N4   CE1  CD1  180.00   0.0  0
 QCA  CONST_28  O4   N4   CE1  CZ   180.00   0.0  0
 QCA  CONST_29  O5   N4   CE1  CZ     0.00   0.0  0
 QCA  CONST_30  CA3  N3   C1   CA1    0.00   0.0  0
 QCA  CONST_31  CA3  N3   C2   O2     0.00   0.0  0
 QCA  CONST_32  HXT  OXT  C3   CA3  180.00   0.0  0
 QCA  Var_01    CG2  CB2  CA2  N2    -1.43   0.0  2
 QCA  Var_02    CD2  CG2  CB2  CA2  176.47  30.0  2
 QCA  Var_03    C3   CA3  N3   C1    87.12  30.0  1
 QCA  Var_04    O3   C3   CA3  N3   171.99  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
 QCA  chir_01  CA1  N1   C1   CB1  positiv
 QCA  chir_02  CB1  OG1  CA1  CG1  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
 QCA  plan-1  CA1  0.020
 QCA  plan-1  C1   0.020
 QCA  plan-1  N2   0.020
 QCA  plan-1  N3   0.020
 QCA  plan-1  C2   0.020
 QCA  plan-1  O2   0.020
 QCA  plan-1  CA2  0.020
 QCA  plan-1  CA3  0.020
 QCA  plan-1  CB2  0.020
 QCA  plan-1  CG2  0.020
 QCA  plan-1  H13  0.020
 QCA  plan-2  CB2  0.020
 QCA  plan-2  CG2  0.020
 QCA  plan-2  CD1  0.020
 QCA  plan-2  CD2  0.020
 QCA  plan-2  CE1  0.020
 QCA  plan-2  CE2  0.020
 QCA  plan-2  CZ   0.020
 QCA  plan-2  OH   0.020
 QCA  plan-2  N4   0.020
 QCA  plan-2  H14  0.020
 QCA  plan-2  H15  0.020
 QCA  plan-2  H16  0.020
 QCA  plan-3  CE1  0.020
 QCA  plan-3  N4   0.020
 QCA  plan-3  O4   0.020
 QCA  plan-3  O5   0.020
 QCA  plan-4  CA3  0.020
 QCA  plan-4  C3   0.020
 QCA  plan-4  O3   0.020
 QCA  plan-4  OXT  0.020
 QCA  plan-4  HXT  0.020

