# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 10:02:48 2021
#   Inital geometry file: a 115 line input string
#   Ligand name: {(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-[(4-hydroxy-3-methoxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(ccc1O)\C=C2/N=C([C@@H](N)[C@@H](C)O)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
 QCD  QCD  '{(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-[(4-hydroxy-3-methoxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid'  L-peptide  44  25  .  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_QCD
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
 QCD  N1   N  NH2   0  -0.799  8.4890   6.8533   2.2926
 QCD  CA1  C  CH1   0  -0.223  7.2081   6.9465   2.9832
 QCD  CB1  C  CH1   0   0.059  7.4025   7.2948   4.4625
 QCD  CG1  C  CH3   0  -0.701  7.9723   6.1079   5.2314
 QCD  OG1  O  OH1   0  -0.659  8.2414   8.4206   4.5627
 QCD  C1   C  CR5   0   0.576  6.3410   7.9473   2.2803
 QCD  N2   N  N     0  -0.466  6.0516   9.1234   2.7024
 QCD  N3   N  NR5   0  -0.574  5.7582   7.6490   1.0562
 QCD  C2   C  CR5   0   0.540  4.9838   8.7270   0.6728
 QCD  O2   O  O     0  -0.447  4.2958   8.7762  -0.3269
 QCD  CA2  C  CR5   0   0.090  5.2081   9.6964   1.7591
 QCD  CA3  C  CH2   0  -0.461  5.6993   6.3907   0.3715
 QCD  C3   C  C     0   0.551  4.4027   5.6351   0.5815
 QCD  O3   O  O     0  -0.435  4.0474   4.7445  -0.1449
 QCD  CB2  C  C1    0  -0.382  4.6467  10.9226   1.8005
 QCD  CG2  C  CR6   0   0.153  4.7777  11.9452   2.8114
 QCD  CD1  C  CR16  0  -0.477  5.6114  11.8099   3.9386
 QCD  CD2  C  CR16  0  -0.316  4.0352  13.1181   2.6635
 QCD  CE1  C  CR6   0   0.347  5.6810  12.8152   4.8775
 QCD  CE2  C  CR16  0  -0.338  4.1028  14.1296   3.6078
 QCD  CZ   C  CR6   0   0.297  4.9184  13.9915   4.7196
 QCD  OH   O  OH1   0  -0.616  4.9680  14.9773   5.6249
 QCD  C4   C  CH3   0  -0.437  7.2277  11.6400   6.2396
 QCD  O4   O  O2    0  -0.489  6.4406  12.7885   5.9919
 QCD  H1   H  HNH2  0   0.361  9.0090   6.0651   2.6578
 QCD  H2   H  HNH2  0   0.359  8.3640   6.6564   1.3077
 QCD  H4   H  HCH1  0   0.247  6.6466   5.9972   2.9800
 QCD  H5   H  HCH1  0   0.213  6.4059   7.5111   4.8696
 QCD  H6   H  HCH3  0   0.243  8.0850   6.3609   6.2872
 QCD  H7   H  HCH3  0   0.230  7.3056   5.2466   5.1753
 QCD  H8   H  HCH3  0   0.227  8.9538   5.8081   4.8599
 QCD  H9   H  HOH1  0   0.448  8.2884   8.6657   5.4912
 QCD  H10  H  HCH2  0   0.317  6.5103   5.7417   0.7054
 QCD  H11  H  HCH2  0   0.322  5.8467   6.5370  -0.6983
 QCD  H13  H  H     0   0.268  4.0001  11.1709   0.9645
 QCD  H14  H  HCR6  0   0.318  6.1913  10.9035   4.0492
 QCD  H15  H  HCR6  0   0.261  3.3908  13.2423   1.8023
 QCD  H16  H  HCR6  0   0.273  3.5199  15.0340   3.4883
 QCD  H17  H  HOH1  0   0.478  5.5674  14.7439   6.3455
 QCD  H18  H  HCH3  0   0.267  7.7430  11.8141   7.1803
 QCD  H19  H  HCH3  0   0.229  6.6119  10.7421   6.3320
 QCD  H20  H  HCH3  0   0.232  7.9674  11.4824   5.4509
 QCD  OXT  O  OH1   0  -0.578  3.7495   6.0381   1.6563
 QCD  HXT  H  HOH1  0   0.491  2.9401   5.5173   1.7734

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
 QCD  O3   C3   double    1.203  0.020  1.203
 QCD  O2   C2   double    1.215  0.020  1.215
 QCD  CA3  C3   single    1.515  0.020  1.515
 QCD  CA3  N3   single    1.434  0.020  1.434
 QCD  C2   N3   single    1.382  0.020  1.382
 QCD  C2   CA2  single    1.473  0.020  1.473
 QCD  N3   C1   single    1.388  0.020  1.388
 QCD  CA2  CB2  double    1.349  0.020  1.349
 QCD  CA2  N2   single    1.389  0.020  1.389
 QCD  CB2  CG2  single    1.444  0.020  1.444
 QCD  N1   CA1  single    1.458  0.020  1.458
 QCD  C1   N2   double    1.283  0.020  1.283
 QCD  C1   CA1  single    1.499  0.020  1.499
 QCD  CD2  CG2  aromatic  1.396  0.020  1.396
 QCD  CD2  CE2  aromatic  1.385  0.020  1.385
 QCD  CA1  CB1  single    1.532  0.020  1.532
 QCD  CG2  CD1  aromatic  1.408  0.020  1.408
 QCD  CE2  CZ   aromatic  1.386  0.020  1.386
 QCD  CD1  CE1  aromatic  1.377  0.020  1.377
 QCD  CB1  OG1  single    1.408  0.020  1.408
 QCD  CB1  CG1  single    1.525  0.020  1.525
 QCD  CZ   CE1  aromatic  1.411  0.020  1.411
 QCD  CZ   OH   single    1.339  0.020  1.339
 QCD  CE1  O4   single    1.349  0.020  1.349
 QCD  O4   C4   single    1.414  0.020  1.414
 QCD  N1   H1   single    0.890  0.020  1.040
 QCD  N1   H2   single    0.890  0.020  1.040
 QCD  CA1  H4   single    0.970  0.020  1.090
 QCD  CB1  H5   single    0.970  0.020  1.090
 QCD  CG1  H6   single    0.970  0.020  1.090
 QCD  CG1  H7   single    0.970  0.020  1.090
 QCD  CG1  H8   single    0.970  0.020  1.090
 QCD  OG1  H9   single    0.850  0.020  0.980
 QCD  CA3  H10  single    0.970  0.020  1.090
 QCD  CA3  H11  single    0.970  0.020  1.090
 QCD  CB2  H13  single    0.930  0.020  1.080
 QCD  CD1  H14  single    0.930  0.020  1.080
 QCD  CD2  H15  single    0.930  0.020  1.080
 QCD  CE2  H16  single    0.930  0.020  1.080
 QCD  OH   H17  single    0.850  0.020  0.980
 QCD  C4   H18  single    0.970  0.020  1.090
 QCD  C4   H19  single    0.970  0.020  1.090
 QCD  C4   H20  single    0.970  0.020  1.090
 QCD  C3   OXT  single    1.321  0.020  1.321
 QCD  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
 QCD  H2   N1   H1   105.25  3.000
 QCD  H2   N1   CA1  111.40  3.000
 QCD  H1   N1   CA1  109.28  3.000
 QCD  H4   CA1  C1   106.18  3.000
 QCD  H4   CA1  CB1  105.25  3.000
 QCD  C1   CA1  CB1  111.98  3.000
 QCD  H4   CA1  N1   113.01  3.000
 QCD  CB1  CA1  N1   111.12  3.000
 QCD  C1   CA1  N1   109.19  3.000
 QCD  H5   CB1  OG1  110.92  3.000
 QCD  H5   CB1  CG1  107.79  3.000
 QCD  OG1  CB1  CG1  111.34  3.000
 QCD  H5   CB1  CA1  106.72  3.000
 QCD  CG1  CB1  CA1  110.94  3.000
 QCD  OG1  CB1  CA1  109.04  3.000
 QCD  H8   CG1  H7   108.38  3.000
 QCD  H8   CG1  H6   107.46  3.000
 QCD  H7   CG1  H6   107.21  3.000
 QCD  H8   CG1  CB1  112.23  3.000
 QCD  H7   CG1  CB1  111.12  3.000
 QCD  H6   CG1  CB1  110.24  3.000
 QCD  H9   OG1  CB1  107.56  3.000
 QCD  N3   C1   N2   113.11  3.000
 QCD  N2   C1   CA1  126.03  3.000
 QCD  N3   C1   CA1  120.86  3.000
 QCD  CA2  N2   C1   106.96  3.000
 QCD  CA3  N3   C2   121.96  3.000
 QCD  C2   N3   C1   108.20  3.000
 QCD  CA3  N3   C1   128.82  3.000
 QCD  CA2  C2   O2   131.81  3.000
 QCD  CA2  C2   N3   102.91  3.000
 QCD  O2   C2   N3   125.27  3.000
 QCD  CB2  CA2  C2   123.86  3.000
 QCD  CB2  CA2  N2   127.35  3.000
 QCD  C2   CA2  N2   108.77  3.000
 QCD  H11  CA3  H10  106.25  3.000
 QCD  H11  CA3  C3   108.59  3.000
 QCD  H10  CA3  C3   107.28  3.000
 QCD  H11  CA3  N3   110.21  3.000
 QCD  H10  CA3  N3   110.20  3.000
 QCD  C3   CA3  N3   113.99  3.000
 QCD  OXT  C3   O3   124.84  3.000
 QCD  OXT  C3   CA3  112.57  3.000
 QCD  O3   C3   CA3  122.56  3.000
 QCD  H13  CB2  CG2  115.55  3.000
 QCD  H13  CB2  CA2  115.60  3.000
 QCD  CG2  CB2  CA2  128.85  3.000
 QCD  CD2  CG2  CD1  118.70  3.000
 QCD  CD1  CG2  CB2  123.10  3.000
 QCD  CD2  CG2  CB2  118.20  3.000
 QCD  H14  CD1  CE1  120.99  3.000
 QCD  H14  CD1  CG2  118.66  3.000
 QCD  CE1  CD1  CG2  120.36  3.000
 QCD  H15  CD2  CE2  119.17  3.000
 QCD  H15  CD2  CG2  119.81  3.000
 QCD  CE2  CD2  CG2  121.01  3.000
 QCD  O4   CE1  CZ   114.42  3.000
 QCD  O4   CE1  CD1  125.25  3.000
 QCD  CZ   CE1  CD1  120.33  3.000
 QCD  H16  CE2  CZ   119.25  3.000
 QCD  H16  CE2  CD2  120.56  3.000
 QCD  CZ   CE2  CD2  120.18  3.000
 QCD  OH   CZ   CE2  119.39  3.000
 QCD  OH   CZ   CE1  121.20  3.000
 QCD  CE2  CZ   CE1  119.41  3.000
 QCD  H17  OH   CZ   110.45  3.000
 QCD  H20  C4   H19  108.91  3.000
 QCD  H20  C4   H18  109.08  3.000
 QCD  H19  C4   H18  109.01  3.000
 QCD  H20  C4   O4   111.56  3.000
 QCD  H19  C4   O4   111.63  3.000
 QCD  H18  C4   O4   106.59  3.000
 QCD  C4   O4   CE1  118.30  3.000
 QCD  HXT  OXT  C3   110.32  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
 QCD  CONST_01  CZ   CE2  CD2  CG2     0.00   0.0  0
 QCD  CONST_02  CZ   CE1  CD1  CG2     0.00   0.0  0
 QCD  CONST_03  CE2  CD2  CG2  CD1     0.00   0.0  0
 QCD  CONST_04  CE2  CZ   CE1  CD1     0.00   0.0  0
 QCD  CONST_05  CE1  CD1  CG2  CD2     0.00   0.0  0
 QCD  CONST_06  CE1  CZ   CE2  CD2     0.00   0.0  0
 QCD  CONST_07  CA2  C2   N3   C1      0.00   0.0  0
 QCD  CONST_08  C2   CA2  N2   C1      0.00   0.0  0
 QCD  CONST_09  N3   C2   CA2  N2      0.00   0.0  0
 QCD  CONST_10  C2   N3   C1   N2      0.00   0.0  0
 QCD  CONST_11  CA2  N2   C1   N3      0.00   0.0  0
 QCD  CONST_12  CE2  CD2  CG2  CB2   180.00   0.0  0
 QCD  CONST_13  CE1  CD1  CG2  CB2   180.00   0.0  0
 QCD  CONST_14  O4   CE1  CD1  CG2   180.00   0.0  0
 QCD  CONST_15  OH   CZ   CE1  CD1   180.00   0.0  0
 QCD  CONST_16  OH   CZ   CE2  CD2   180.00   0.0  0
 QCD  CONST_17  O4   CE1  CZ   CE2   180.00   0.0  0
 QCD  CONST_18  C2   N3   C1   CA1   180.00   0.0  0
 QCD  CONST_19  CA2  N2   C1   CA1   180.00   0.0  0
 QCD  CONST_20  O2   C2   N3   C1    180.00   0.0  0
 QCD  CONST_21  CA3  N3   C1   N2    180.00   0.0  0
 QCD  CONST_22  CA3  N3   C2   CA2   180.00   0.0  0
 QCD  CONST_23  H16  CE2  CD2  CG2   180.00   0.0  0
 QCD  CONST_24  H15  CD2  CG2  CD1   180.00   0.0  0
 QCD  CONST_25  H14  CD1  CG2  CD2   180.00   0.0  0
 QCD  CONST_26  CA3  N3   C1   CA1     0.00   0.0  0
 QCD  CONST_27  CA3  N3   C2   O2      0.00   0.0  0
 QCD  CONST_28  HXT  OXT  C3   CA3   180.00   0.0  0
 QCD  Var_01    CG2  CB2  CA2  N2      0.39   0.0  2
 QCD  Var_02    CD2  CG2  CB2  CA2  -176.68  30.0  2
 QCD  Var_03    C3   CA3  N3   C1     97.21  30.0  1
 QCD  Var_04    O3   C3   CA3  N3    161.79  30.0  3
 QCD  Var_05    H18  C4   O4   CE1  -179.19  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
 QCD  chir_01  CA1  N1   C1   CB1  positiv
 QCD  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
 QCD  plan-1  CA1  0.020
 QCD  plan-1  C1   0.020
 QCD  plan-1  N2   0.020
 QCD  plan-1  N3   0.020
 QCD  plan-1  C2   0.020
 QCD  plan-1  O2   0.020
 QCD  plan-1  CA2  0.020
 QCD  plan-1  CA3  0.020
 QCD  plan-1  CB2  0.020
 QCD  plan-1  CG2  0.020
 QCD  plan-1  H13  0.020
 QCD  plan-2  CB2  0.020
 QCD  plan-2  CG2  0.020
 QCD  plan-2  CD1  0.020
 QCD  plan-2  CD2  0.020
 QCD  plan-2  CE1  0.020
 QCD  plan-2  CE2  0.020
 QCD  plan-2  CZ   0.020
 QCD  plan-2  OH   0.020
 QCD  plan-2  O4   0.020
 QCD  plan-2  H14  0.020
 QCD  plan-2  H15  0.020
 QCD  plan-2  H16  0.020
 QCD  plan-3  CA3  0.020
 QCD  plan-3  C3   0.020
 QCD  plan-3  O3   0.020
 QCD  plan-3  OXT  0.020
 QCD  plan-3  HXT  0.020

