# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 15:39:28 2021
#   Inital geometry file: a 107 line input string
#   Ligand name: {(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-5-oxo-4-[(2,3,5-trifluoro-4-hydroxyphenyl)methylidene]-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/c2cc(F)c(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
 QC4  QC4  '{(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-5-oxo-4-[(2,3,5-trifluoro-4-hydroxyphenyl)methylidene]-4,5-dihydro-1H-imidazol-1-yl}acetic acid'  L-peptide  40  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_QC4
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
 QC4  N1   N  NH2   0  -0.794  8.7254   8.1988   1.7809
 QC4  CA1  C  CH1   0  -0.227  7.5346   8.2595   2.6202
 QC4  CB1  C  CH1   0   0.050  7.8912   8.5822   4.0749
 QC4  CG1  C  CH3   0  -0.696  8.5172   7.3761   4.7668
 QC4  OG1  O  OH1   0  -0.659  8.7549   9.6928   4.0989
 QC4  C1   C  CR5   0   0.593  6.5956   9.2742   2.0393
 QC4  N2   N  N     0  -0.470  6.3984  10.4628   2.4842
 QC4  N3   N  NR5   0  -0.574  5.8479   8.9789   0.9090
 QC4  C2   C  CR5   0   0.547  5.0581  10.0741   0.6171
 QC4  O2   O  O     0  -0.432  4.2441  10.1434  -0.2775
 QC4  CA2  C  CR5   0   0.115  5.4580  11.0512   1.6532
 QC4  CA3  C  CH2   0  -0.473  5.6620   7.7053   0.2766
 QC4  C3   C  C     0   0.556  4.5338   6.8754   0.8569
 QC4  O3   O  O     0  -0.435  4.1691   5.8462   0.3525
 QC4  CB2  C  C1    0  -0.365  4.9474  12.2939   1.7304
 QC4  CG2  C  CR6   0  -0.081  5.2610  13.3200   2.6998
 QC4  CD1  C  CR16  0  -0.496  6.2205  13.1723   3.7146
 QC4  CD2  C  CR6   0   0.402  4.5835  14.5377   2.6428
 QC4  CE1  C  CR6   0   0.516  6.4549  14.1943   4.5949
 QC4  CE2  C  CR6   0   0.348  4.8318  15.5565   3.5385
 QC4  CZ   C  CR6   0   0.083  5.7778  15.4137   4.5452
 QC4  OH   O  OH1   0  -0.597  5.9766  16.4305   5.3807
 QC4  F1   F  F     0  -0.297  4.1563  16.7015   3.4431
 QC4  F2   F  F     0  -0.293  3.6590  14.7508   1.7060
 QC4  F3   F  F     0  -0.315  7.3750  14.0492   5.5622
 QC4  O1   O  OH1   0  -0.578  4.0293   7.3972   1.9595
 QC4  H1   H  HNH2  0   0.361  9.3590   7.5014   2.1513
 QC4  H2   H  HNH2  0   0.358  8.4936   7.8782   0.8493
 QC4  H4   H  HCH1  0   0.248  6.9832   7.3059   2.6574
 QC4  H5   H  HCH1  0   0.219  6.9466   8.8083   4.5857
 QC4  H6   H  HCH3  0   0.244  8.7414   7.6144   5.8076
 QC4  H7   H  HCH3  0   0.230  7.8361   6.5244   4.7669
 QC4  H8   H  HCH3  0   0.224  9.4508   7.0680   4.2931
 QC4  H9   H  HOH1  0   0.450  8.7908  10.0152   5.0041
 QC4  H10  H  HCH2  0   0.321  6.5738   7.1084   0.3258
 QC4  H11  H  HCH2  0   0.330  5.4610   7.8557  -0.7847
 QC4  H12  H  H     0   0.282  4.2142  12.5409   0.9722
 QC4  H14  H  HCR6  0   0.321  6.7779  12.2484   3.7987
 QC4  H15  H  HOH1  0   0.492  3.3190   6.8345   2.3052
 QC4  H3   H  HOH1  0   0.490  6.6455  16.2188   6.0442

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
 QC4  O3   C3   double    1.203  0.020  1.203
 QC4  O2   C2   double    1.211  0.020  1.211
 QC4  CA3  C3   single    1.516  0.020  1.516
 QC4  CA3  N3   single    1.434  0.020  1.434
 QC4  C2   N3   single    1.381  0.020  1.381
 QC4  C2   CA2  single    1.479  0.020  1.479
 QC4  N3   C1   single    1.387  0.020  1.387
 QC4  F2   CD2  single    1.333  0.020  1.333
 QC4  N1   CA1  single    1.458  0.020  1.458
 QC4  CA2  CB2  double    1.346  0.020  1.346
 QC4  CA2  N2   single    1.386  0.020  1.386
 QC4  CB2  CG2  single    1.446  0.020  1.446
 QC4  C1   N2   double    1.284  0.020  1.284
 QC4  C1   CA1  single    1.500  0.020  1.500
 QC4  CD2  CG2  aromatic  1.395  0.020  1.395
 QC4  CD2  CE2  aromatic  1.379  0.020  1.379
 QC4  CA1  CB1  single    1.532  0.020  1.532
 QC4  CG2  CD1  aromatic  1.404  0.020  1.404
 QC4  F1   CE2  single    1.333  0.020  1.333
 QC4  CE2  CZ   aromatic  1.389  0.020  1.389
 QC4  CD1  CE1  aromatic  1.369  0.020  1.369
 QC4  CB1  OG1  single    1.407  0.020  1.407
 QC4  CB1  CG1  single    1.525  0.020  1.525
 QC4  CZ   CE1  aromatic  1.396  0.020  1.396
 QC4  CZ   OH   single    1.331  0.020  1.331
 QC4  CE1  F3   single    1.343  0.020  1.343
 QC4  C3   O1   single    1.320  0.020  1.320
 QC4  N1   H1   single    0.890  0.020  1.040
 QC4  N1   H2   single    0.890  0.020  1.040
 QC4  CA1  H4   single    0.970  0.020  1.090
 QC4  CB1  H5   single    0.970  0.020  1.090
 QC4  CG1  H6   single    0.970  0.020  1.090
 QC4  CG1  H7   single    0.970  0.020  1.090
 QC4  CG1  H8   single    0.970  0.020  1.090
 QC4  OG1  H9   single    0.850  0.020  0.980
 QC4  CA3  H10  single    0.970  0.020  1.090
 QC4  CA3  H11  single    0.970  0.020  1.090
 QC4  CB2  H12  single    0.930  0.020  1.080
 QC4  CD1  H14  single    0.930  0.020  1.080
 QC4  O1   H15  single    0.850  0.020  0.980
 QC4  OH   H3   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
 QC4  H2   N1   H1   105.18  3.000
 QC4  H2   N1   CA1  110.85  3.000
 QC4  H1   N1   CA1  109.22  3.000
 QC4  H4   CA1  C1   106.57  3.000
 QC4  H4   CA1  CB1  105.46  3.000
 QC4  C1   CA1  CB1  111.78  3.000
 QC4  H4   CA1  N1   113.08  3.000
 QC4  CB1  CA1  N1   111.42  3.000
 QC4  C1   CA1  N1   108.45  3.000
 QC4  H5   CB1  OG1  110.96  3.000
 QC4  H5   CB1  CG1  107.76  3.000
 QC4  OG1  CB1  CG1  111.38  3.000
 QC4  H5   CB1  CA1  106.56  3.000
 QC4  CG1  CB1  CA1  111.09  3.000
 QC4  OG1  CB1  CA1  108.99  3.000
 QC4  H8   CG1  H7   108.29  3.000
 QC4  H8   CG1  H6   107.45  3.000
 QC4  H7   CG1  H6   107.39  3.000
 QC4  H8   CG1  CB1  112.18  3.000
 QC4  H7   CG1  CB1  111.19  3.000
 QC4  H6   CG1  CB1  110.15  3.000
 QC4  H9   OG1  CB1  107.68  3.000
 QC4  N3   C1   N2   113.37  3.000
 QC4  N2   C1   CA1  126.02  3.000
 QC4  N3   C1   CA1  120.61  3.000
 QC4  CA2  N2   C1   106.81  3.000
 QC4  CA3  N3   C2   122.47  3.000
 QC4  C2   N3   C1   108.15  3.000
 QC4  CA3  N3   C1   128.19  3.000
 QC4  CA2  C2   O2   131.38  3.000
 QC4  CA2  C2   N3   102.77  3.000
 QC4  O2   C2   N3   125.84  3.000
 QC4  CB2  CA2  C2   123.20  3.000
 QC4  CB2  CA2  N2   127.96  3.000
 QC4  C2   CA2  N2   108.84  3.000
 QC4  H11  CA3  H10  105.87  3.000
 QC4  H11  CA3  C3   108.11  3.000
 QC4  H10  CA3  C3   107.78  3.000
 QC4  H11  CA3  N3   109.30  3.000
 QC4  H10  CA3  N3   110.96  3.000
 QC4  C3   CA3  N3   114.45  3.000
 QC4  O1   C3   O3   124.94  3.000
 QC4  O1   C3   CA3  112.81  3.000
 QC4  O3   C3   CA3  122.25  3.000
 QC4  H12  CB2  CG2  117.01  3.000
 QC4  H12  CB2  CA2  115.30  3.000
 QC4  CG2  CB2  CA2  127.69  3.000
 QC4  CD2  CG2  CD1  116.95  3.000
 QC4  CD1  CG2  CB2  123.91  3.000
 QC4  CD2  CG2  CB2  119.13  3.000
 QC4  H14  CD1  CE1  119.94  3.000
 QC4  H14  CD1  CG2  119.86  3.000
 QC4  CE1  CD1  CG2  120.21  3.000
 QC4  F2   CD2  CE2  117.59  3.000
 QC4  CE2  CD2  CG2  122.07  3.000
 QC4  F2   CD2  CG2  120.34  3.000
 QC4  F3   CE1  CZ   116.90  3.000
 QC4  F3   CE1  CD1  119.99  3.000
 QC4  CZ   CE1  CD1  123.11  3.000
 QC4  F1   CE2  CZ   119.04  3.000
 QC4  CZ   CE2  CD2  121.16  3.000
 QC4  F1   CE2  CD2  119.80  3.000
 QC4  OH   CZ   CE2  118.57  3.000
 QC4  OH   CZ   CE1  124.94  3.000
 QC4  CE2  CZ   CE1  116.49  3.000
 QC4  H3   OH   CZ   111.55  3.000
 QC4  H15  O1   C3   110.38  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
 QC4  CONST_01  CZ   CE2  CD2  CG2     0.00   0.0  0
 QC4  CONST_02  CZ   CE1  CD1  CG2     0.00   0.0  0
 QC4  CONST_03  CE2  CD2  CG2  CD1     0.00   0.0  0
 QC4  CONST_04  CE2  CZ   CE1  CD1     0.00   0.0  0
 QC4  CONST_05  CE1  CD1  CG2  CD2     0.00   0.0  0
 QC4  CONST_06  CE1  CZ   CE2  CD2     0.00   0.0  0
 QC4  CONST_07  CA2  C2   N3   C1      0.00   0.0  0
 QC4  CONST_08  C2   CA2  N2   C1      0.00   0.0  0
 QC4  CONST_09  N3   C2   CA2  N2      0.00   0.0  0
 QC4  CONST_10  C2   N3   C1   N2      0.00   0.0  0
 QC4  CONST_11  CA2  N2   C1   N3      0.00   0.0  0
 QC4  CONST_12  CE2  CD2  CG2  CB2   180.00   0.0  0
 QC4  CONST_13  CE1  CD1  CG2  CB2   180.00   0.0  0
 QC4  CONST_14  F1   CE2  CD2  CG2   180.00   0.0  0
 QC4  CONST_15  F3   CE1  CD1  CG2   180.00   0.0  0
 QC4  CONST_16  F2   CD2  CG2  CD1   180.00   0.0  0
 QC4  CONST_17  OH   CZ   CE1  CD1   180.00   0.0  0
 QC4  CONST_18  OH   CZ   CE2  CD2   180.00   0.0  0
 QC4  CONST_19  F1   CE2  CZ   CE1   180.00   0.0  0
 QC4  CONST_20  F3   CE1  CZ   CE2   180.00   0.0  0
 QC4  CONST_21  F2   CD2  CE2  CZ    180.00   0.0  0
 QC4  CONST_22  C2   N3   C1   CA1   180.00   0.0  0
 QC4  CONST_23  CA2  N2   C1   CA1   180.00   0.0  0
 QC4  CONST_24  O2   C2   N3   C1    180.00   0.0  0
 QC4  CONST_25  CA3  N3   C1   N2    180.00   0.0  0
 QC4  CONST_26  CA3  N3   C2   CA2   180.00   0.0  0
 QC4  CONST_27  H14  CD1  CG2  CD2   180.00   0.0  0
 QC4  CONST_28  CA3  N3   C1   CA1     0.00   0.0  0
 QC4  CONST_29  CA3  N3   C2   O2      0.00   0.0  0
 QC4  CONST_30  H15  O1   C3   CA3   180.00   0.0  0
 QC4  Var_01    CG2  CB2  CA2  N2      0.22   0.0  2
 QC4  Var_02    CD2  CG2  CB2  CA2  -177.61  30.0  2
 QC4  Var_03    C3   CA3  N3   C1     85.99  30.0  3
 QC4  Var_04    O3   C3   CA3  N3    172.50  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
 QC4  chir_01  CA1  N1   C1   CB1  positiv
 QC4  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
 QC4  plan-1  CA1  0.020
 QC4  plan-1  C1   0.020
 QC4  plan-1  N2   0.020
 QC4  plan-1  N3   0.020
 QC4  plan-1  C2   0.020
 QC4  plan-1  O2   0.020
 QC4  plan-1  CA2  0.020
 QC4  plan-1  CA3  0.020
 QC4  plan-1  CB2  0.020
 QC4  plan-1  CG2  0.020
 QC4  plan-1  H12  0.020
 QC4  plan-2  CB2  0.020
 QC4  plan-2  CG2  0.020
 QC4  plan-2  CD1  0.020
 QC4  plan-2  CD2  0.020
 QC4  plan-2  CE1  0.020
 QC4  plan-2  CE2  0.020
 QC4  plan-2  CZ   0.020
 QC4  plan-2  OH   0.020
 QC4  plan-2  F1   0.020
 QC4  plan-2  F2   0.020
 QC4  plan-2  F3   0.020
 QC4  plan-2  H14  0.020
 QC4  plan-3  CA3  0.020
 QC4  plan-3  C3   0.020
 QC4  plan-3  O3   0.020
 QC4  plan-3  O1   0.020
 QC4  plan-3  H15  0.020

