# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 21:39:27 2022
#   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  39  26  .  2022-08-10  2022-08-10
;
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  -0.799  8.7776   8.4455   1.7348
 QC4  CA1  C  CH1    0  -0.217  7.5593   8.3327   2.5324
 QC4  CB1  C  CH1    0   0.049  7.8345   8.5216   4.0292
 QC4  CG1  C  CH3    0  -0.700  8.4975   7.2815   4.6203
 QC4  OG1  O  OH1    0  -0.657  8.6256   9.6692   4.2282
 QC4  C1   C  CR5    0   0.584  6.5707   9.3286   1.9974
 QC4  N2   N  N      0  -0.485  6.3950  10.5213   2.4551
 QC4  N3   N  NR5    0  -0.543  5.8133   9.0390   0.8803
 QC4  C2   C  CR5    0   0.526  5.0190  10.1314   0.6153
 QC4  O2   O  O      0  -0.436  4.1782  10.2199  -0.2546
 QC4  CA2  C  CR5    0   0.117  5.4440  11.1145   1.6440
 QC4  CA3  C  CH2    0  -0.488  5.5622   7.7276   0.3343
 QC4  C3   C  C      0   0.420  4.6604   6.8538   1.2461
 QC4  O3   O  O      0  -0.596  4.3562   5.7513   0.7616
 QC4  CB2  C  C1     0  -0.377  4.9508  12.3642   1.7152
 QC4  CG2  C  CR6    0  -0.076  5.2749  13.3900   2.6854
 QC4  CD1  C  CR16   0  -0.494  6.0848  13.1733   3.8111
 QC4  CD2  C  CR6    0   0.394  4.7478  14.6717   2.5291
 QC4  CE1  C  CR6    0   0.513  6.3247  14.1882   4.6994
 QC4  CE2  C  CR6    0   0.346  5.0075  15.6862   3.4277
 QC4  CZ   C  CR6    0   0.076  5.8057  15.4738   4.5441
 QC4  OH   O  OH1    0  -0.598  6.0208  16.4938   5.3744
 QC4  F1   F  F      0  -0.297  4.4848  16.8970   3.2313
 QC4  F2   F  F      0  -0.294  3.9718  14.9577   1.4825
 QC4  F3   F  F      0  -0.315  7.0878  13.9635   5.7815
 QC4  O1   O  OC    -1  -0.585  4.3502   7.3315   2.3504
 QC4  H1   H  HNH2   0   0.357  9.4643   7.7858   2.0800
 QC4  H2   H  HNH2   0   0.355  8.5918   8.1567   0.7816
 QC4  H4   H  HCH1   0   0.252  7.0904   7.3434   2.4560
 QC4  H5   H  HCH1   0   0.208  6.8534   8.6328   4.5119
 QC4  H6   H  HCH3   0   0.241  8.6409   7.4046   5.6954
 QC4  H7   H  HCH3   0   0.231  7.8753   6.3982   4.4733
 QC4  H8   H  HCH3   0   0.226  9.4768   7.0854   4.1798
 QC4  H9   H  HOH1   0   0.447  8.7533   9.7756   5.1757
 QC4  H10  H  HCH2   0   0.269  6.5071   7.2145   0.1438
 QC4  H11  H  HCH2   0   0.273  5.0900   7.8575  -0.6399
 QC4  H12  H  H      0   0.275  4.2254  12.6208   0.9524
 QC4  H14  H  HCR6   0   0.312  6.5282  12.2011   3.9772
 QC4  H3   H  HOH1   0   0.488  6.5898  16.2367   6.1112

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   deloc     1.242  0.020  1.242
 QC4  O2   C2   double    1.213  0.020  1.213
 QC4  CA3  C3   single    1.552  0.020  1.552
 QC4  CA3  N3   single    1.443  0.020  1.443
 QC4  C2   N3   single    1.376  0.020  1.376
 QC4  C2   CA2  single    1.485  0.020  1.485
 QC4  N3   C1   single    1.380  0.020  1.380
 QC4  F2   CD2  single    1.334  0.020  1.334
 QC4  N1   CA1  single    1.461  0.020  1.461
 QC4  CA2  CB2  double    1.345  0.020  1.345
 QC4  CA2  N2   single    1.384  0.020  1.384
 QC4  CB2  CG2  single    1.449  0.020  1.449
 QC4  C1   N2   double    1.290  0.020  1.290
 QC4  C1   CA1  single    1.502  0.020  1.502
 QC4  CD2  CG2  aromatic  1.395  0.020  1.395
 QC4  CD2  CE2  aromatic  1.380  0.020  1.380
 QC4  CA1  CB1  single    1.534  0.020  1.534
 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  1.370  0.020  1.370
 QC4  CB1  OG1  single    1.408  0.020  1.408
 QC4  CB1  CG1  single    1.525  0.020  1.525
 QC4  CZ   CE1  aromatic  1.395  0.020  1.395
 QC4  CZ   OH   single    1.333  0.020  1.333
 QC4  CE1  F3   single    1.343  0.020  1.343
 QC4  C3   O1   deloc     1.243  0.020  1.243
 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  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   105.04  3.000
 QC4  H2   N1   CA1  109.80  3.000
 QC4  H1   N1   CA1  109.21  3.000
 QC4  H4   CA1  C1   106.96  3.000
 QC4  H4   CA1  CB1  104.82  3.000
 QC4  C1   CA1  CB1  112.59  3.000
 QC4  H4   CA1  N1   112.82  3.000
 QC4  CB1  CA1  N1   111.95  3.000
 QC4  C1   CA1  N1   107.66  3.000
 QC4  H5   CB1  OG1  110.92  3.000
 QC4  H5   CB1  CG1  107.46  3.000
 QC4  OG1  CB1  CG1  111.33  3.000
 QC4  H5   CB1  CA1  106.31  3.000
 QC4  CG1  CB1  CA1  110.86  3.000
 QC4  OG1  CB1  CA1  109.82  3.000
 QC4  H8   CG1  H7   108.18  3.000
 QC4  H8   CG1  H6   107.45  3.000
 QC4  H7   CG1  H6   107.40  3.000
 QC4  H8   CG1  CB1  112.31  3.000
 QC4  H7   CG1  CB1  111.00  3.000
 QC4  H6   CG1  CB1  110.31  3.000
 QC4  H9   OG1  CB1  107.69  3.000
 QC4  N3   C1   N2   113.99  3.000
 QC4  N2   C1   CA1  125.21  3.000
 QC4  N3   C1   CA1  120.69  3.000
 QC4  CA2  N2   C1   106.38  3.000
 QC4  CA3  N3   C2   123.24  3.000
 QC4  C2   N3   C1   107.82  3.000
 QC4  CA3  N3   C1   126.34  3.000
 QC4  CA2  C2   O2   130.30  3.000
 QC4  CA2  C2   N3   103.11  3.000
 QC4  O2   C2   N3   126.58  3.000
 QC4  CB2  CA2  C2   123.14  3.000
 QC4  CB2  CA2  N2   128.26  3.000
 QC4  C2   CA2  N2   108.60  3.000
 QC4  H11  CA3  H10  105.95  3.000
 QC4  H11  CA3  C3   109.90  3.000
 QC4  H10  CA3  C3   109.92  3.000
 QC4  H11  CA3  N3   107.77  3.000
 QC4  H10  CA3  N3   110.04  3.000
 QC4  C3   CA3  N3   112.99  3.000
 QC4  O1   C3   O3   128.81  3.000
 QC4  O1   C3   CA3  116.80  3.000
 QC4  O3   C3   CA3  114.39  3.000
 QC4  H12  CB2  CG2  116.97  3.000
 QC4  H12  CB2  CA2  115.35  3.000
 QC4  CG2  CB2  CA2  127.68  3.000
 QC4  CD2  CG2  CD1  116.73  3.000
 QC4  CD1  CG2  CB2  123.84  3.000
 QC4  CD2  CG2  CB2  119.42  3.000
 QC4  H14  CD1  CE1  119.65  3.000
 QC4  H14  CD1  CG2  119.91  3.000
 QC4  CE1  CD1  CG2  120.44  3.000
 QC4  F2   CD2  CE2  117.57  3.000
 QC4  CE2  CD2  CG2  122.11  3.000
 QC4  F2   CD2  CG2  120.32  3.000
 QC4  F3   CE1  CZ   117.08  3.000
 QC4  F3   CE1  CD1  119.86  3.000
 QC4  CZ   CE1  CD1  123.05  3.000
 QC4  F1   CE2  CZ   118.86  3.000
 QC4  CZ   CE2  CD2  121.28  3.000
 QC4  F1   CE2  CD2  119.87  3.000
 QC4  OH   CZ   CE2  118.46  3.000
 QC4  OH   CZ   CE1  125.16  3.000
 QC4  CE2  CZ   CE1  116.38  3.000
 QC4  H3   OH   CZ   111.50  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_26  CA3  N3   C2   CA2  180.00   0.0  0
 QC4  CONST_27  H14  CD1  CG2  CD2  180.00   0.0  0
 QC4  CONST_29  CA3  N3   C2   O2     0.00   0.0  0
 QC4  Var_01    CG2  CB2  CA2  N2    -1.61   0.0  2
 QC4  Var_02    CD2  CG2  CB2  CA2  174.35  30.0  2
 QC4  Var_03    C3   CA3  N3   C1    68.65  30.0  2
 QC4  Var_04    O3   C3   CA3  N3   175.56  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

