# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 25 11:44:39 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: {(4E)-2-[(1S)-1,4-diamino-4-oxobutyl]-4-[(4-hydroxyphenyl)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](CCC(N)=O)C1=NC(=C/c2ccc(O)cc2)/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
 QYG  QYG  '{(4E)-2-[(1S)-1,4-diamino-4-oxobutyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid'  L-peptide  43  25  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_QYG
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
 QYG  C3   C  C     0   0.551   1.6264   2.7552   0.1765
 QYG  O    O  O     0  -0.426   1.3968   2.4483  -0.9624
 QYG  CA3  C  CH2   0  -0.463   1.3764   1.8601   1.3725
 QYG  N3   N  NR5   0  -0.552   0.6396   0.6875   1.0112
 QYG  C1   C  CR5   0   0.528   1.0750  -0.6205   0.8898
 QYG  CA1  C  CH1   0  -0.217   2.5066  -1.0303   1.1108
 QYG  CB1  C  CH2   0  -0.422   3.3419  -0.6635  -0.1235
 QYG  CG1  C  CH2   0  -0.582   4.8271  -0.8388   0.1359
 QYG  CD3  C  C     0   0.523   5.6924  -0.4896  -1.0576
 QYG  N    N  NH2   0  -0.766   2.6561  -2.4351   1.4137
 QYG  C2   C  CR5   0   0.539  -0.7043   0.7356   0.7110
 QYG  O2   O  O     0  -0.449  -1.3664   1.7556   0.7329
 QYG  CA2  C  CR5   0   0.110  -1.0339  -0.6746   0.4191
 QYG  N2   N  N     0  -0.477   0.1363  -1.4284   0.5583
 QYG  CB2  C  C1    0  -0.364  -2.1947  -1.2913   0.0935
 QYG  CG2  C  CR6   0   0.102  -3.5525  -0.8522  -0.1298
 QYG  CD2  C  CR16  0  -0.285  -4.4999  -1.8582  -0.3803
 QYG  CE2  C  CR16  0  -0.377  -5.8301  -1.5713  -0.6089
 QYG  CZ   C  CR6   0   0.363  -6.2609  -0.2451  -0.6014
 QYG  OH   O  OH1   0  -0.615  -7.5348   0.1050  -0.8189
 QYG  CE1  C  CR16  0  -0.314  -5.3364   0.7742  -0.3616
 QYG  CD1  C  CR16  0  -0.321  -4.0106   0.4757  -0.1284
 QYG  NE1  N  NH2   0  -0.806   7.0084  -0.6777  -0.8647
 QYG  OE1  O  O     0  -0.491   5.2329  -0.0681  -2.1090
 QYG  OXT  O  OH1   0  -0.585   2.1414   3.9114   0.5584
 QYG  H1   H  HCH2  0   0.325   2.3317   1.5838   1.8215
 QYG  H2   H  HCH2  0   0.322   0.8366   2.4208   2.1387
 QYG  H3   H  HCH1  0   0.265   2.8907  -0.4660   1.9687
 QYG  H4   H  HCH2  0   0.245   3.0189  -1.2925  -0.9576
 QYG  H5   H  HCH2  0   0.244   3.1377   0.3639  -0.4291
 QYG  H6   H  HCH2  0   0.268   5.1363  -0.2097   0.9776
 QYG  H7   H  HCH2  0   0.276   5.0352  -1.8659   0.4443
 QYG  H8   H  HNH2  0   0.355   2.1662  -2.6591   2.2706
 QYG  H9   H  HNH2  0   0.346   2.2152  -2.9879   0.6877
 QYG  H11  H  H     0   0.271  -2.0691  -2.3646  -0.0188
 QYG  H12  H  HCR6  0   0.268  -4.1840  -2.8943  -0.3933
 QYG  H13  H  HCR6  0   0.280  -6.5322  -2.3762  -0.7931
 QYG  H14  H  HOH1  0   0.481  -8.0825  -0.6738  -0.9723
 QYG  H15  H  HCR6  0   0.270  -5.6678   1.8051  -0.3602
 QYG  H16  H  HCR6  0   0.293  -3.3220   1.2857   0.0540
 QYG  H17  H  HNH2  0   0.404   7.3751  -1.0086   0.0106
 QYG  H18  H  HNH2  0   0.397   7.6703  -0.4437  -1.5861
 QYG  HXT  H  HOH1  0   0.489   2.3221   4.4723  -0.2113

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
 QYG  OE1  CD3  double    1.222  0.020  1.222
 QYG  CE1  CD1  aromatic  1.379  0.020  1.379
 QYG  CE1  CZ   aromatic  1.397  0.020  1.397
 QYG  CD1  CG2  aromatic  1.405  0.020  1.405
 QYG  CD3  NE1  single    1.343  0.020  1.343
 QYG  CD3  CG1  single    1.515  0.020  1.515
 QYG  CB2  CG2  single    1.444  0.020  1.444
 QYG  CB2  CA2  double    1.354  0.020  1.354
 QYG  OH   CZ   single    1.339  0.020  1.339
 QYG  CZ   CE2  aromatic  1.394  0.020  1.394
 QYG  CG2  CD2  aromatic  1.404  0.020  1.404
 QYG  CG1  CB1  single    1.518  0.020  1.518
 QYG  CB1  CA1  single    1.535  0.020  1.535
 QYG  N2   CA2  single    1.399  0.020  1.399
 QYG  N2   C1   double    1.282  0.020  1.282
 QYG  N    CA1  single    1.445  0.020  1.445
 QYG  CA2  C2   single    1.477  0.020  1.477
 QYG  CD2  CE2  aromatic  1.380  0.020  1.380
 QYG  CA1  C1   single    1.505  0.020  1.505
 QYG  C1   N3   single    1.384  0.020  1.384
 QYG  C2   N3   single    1.378  0.020  1.378
 QYG  C2   O2   double    1.216  0.020  1.216
 QYG  N3   CA3  single    1.431  0.020  1.431
 QYG  CA3  C3   single    1.515  0.020  1.515
 QYG  C3   O    double    1.202  0.020  1.202
 QYG  C3   OXT  single    1.322  0.020  1.322
 QYG  CA3  H1   single    0.970  0.020  1.090
 QYG  CA3  H2   single    0.970  0.020  1.090
 QYG  CA1  H3   single    0.970  0.020  1.090
 QYG  CB1  H4   single    0.970  0.020  1.090
 QYG  CB1  H5   single    0.970  0.020  1.090
 QYG  CG1  H6   single    0.970  0.020  1.090
 QYG  CG1  H7   single    0.970  0.020  1.090
 QYG  N    H8   single    0.890  0.020  1.040
 QYG  N    H9   single    0.890  0.020  1.040
 QYG  CB2  H11  single    0.930  0.020  1.080
 QYG  CD2  H12  single    0.930  0.020  1.080
 QYG  CE2  H13  single    0.930  0.020  1.080
 QYG  OH   H14  single    0.850  0.020  0.980
 QYG  CE1  H15  single    0.930  0.020  1.080
 QYG  CD1  H16  single    0.930  0.020  1.080
 QYG  NE1  H17  single    0.860  0.020  1.020
 QYG  NE1  H18  single    0.860  0.020  1.020
 QYG  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
 QYG  OXT  C3   CA3  110.67  3.000
 QYG  OXT  C3   O    124.86  3.000
 QYG  CA3  C3   O    124.46  3.000
 QYG  H2   CA3  H1   105.90  3.000
 QYG  H2   CA3  N3   110.08  3.000
 QYG  H1   CA3  N3   110.32  3.000
 QYG  H2   CA3  C3   109.40  3.000
 QYG  H1   CA3  C3   109.27  3.000
 QYG  N3   CA3  C3   111.70  3.000
 QYG  C2   N3   C1   108.71  3.000
 QYG  C2   N3   CA3  121.91  3.000
 QYG  C1   N3   CA3  129.38  3.000
 QYG  N2   C1   CA1  124.25  3.000
 QYG  CA1  C1   N3   122.93  3.000
 QYG  N2   C1   N3   112.82  3.000
 QYG  H3   CA1  N    107.47  3.000
 QYG  H3   CA1  CB1  108.40  3.000
 QYG  N    CA1  CB1  110.16  3.000
 QYG  H3   CA1  C1   107.94  3.000
 QYG  N    CA1  C1   113.20  3.000
 QYG  CB1  CA1  C1   109.54  3.000
 QYG  H5   CB1  H4   105.83  3.000
 QYG  H5   CB1  CG1  109.86  3.000
 QYG  H4   CB1  CG1  110.67  3.000
 QYG  H5   CB1  CA1  110.39  3.000
 QYG  H4   CB1  CA1  108.37  3.000
 QYG  CG1  CB1  CA1  111.56  3.000
 QYG  H7   CG1  H6   105.63  3.000
 QYG  H7   CG1  CD3  109.28  3.000
 QYG  H6   CG1  CD3  108.16  3.000
 QYG  H7   CG1  CB1  110.08  3.000
 QYG  H6   CG1  CB1  109.95  3.000
 QYG  CD3  CG1  CB1  113.43  3.000
 QYG  OE1  CD3  NE1  122.69  3.000
 QYG  NE1  CD3  CG1  114.47  3.000
 QYG  OE1  CD3  CG1  122.84  3.000
 QYG  H9   N    H8   105.97  3.000
 QYG  H9   N    CA1  109.58  3.000
 QYG  H8   N    CA1  110.03  3.000
 QYG  CA2  C2   O2   133.05  3.000
 QYG  O2   C2   N3   123.80  3.000
 QYG  CA2  C2   N3   103.14  3.000
 QYG  CB2  CA2  N2   119.71  3.000
 QYG  N2   CA2  C2   107.94  3.000
 QYG  CB2  CA2  C2   132.34  3.000
 QYG  CA2  N2   C1   107.38  3.000
 QYG  H11  CB2  CG2  113.14  3.000
 QYG  H11  CB2  CA2  112.07  3.000
 QYG  CG2  CB2  CA2  134.80  3.000
 QYG  CD1  CG2  CD2  117.22  3.000
 QYG  CD2  CG2  CB2  116.36  3.000
 QYG  CD1  CG2  CB2  126.42  3.000
 QYG  H12  CD2  CE2  118.55  3.000
 QYG  H12  CD2  CG2  119.38  3.000
 QYG  CE2  CD2  CG2  122.07  3.000
 QYG  H13  CE2  CZ   120.47  3.000
 QYG  H13  CE2  CD2  119.88  3.000
 QYG  CZ   CE2  CD2  119.65  3.000
 QYG  CE1  CZ   OH   117.83  3.000
 QYG  OH   CZ   CE2  122.80  3.000
 QYG  CE1  CZ   CE2  119.37  3.000
 QYG  H14  OH   CZ   110.80  3.000
 QYG  H15  CE1  CD1  120.01  3.000
 QYG  H15  CE1  CZ   119.49  3.000
 QYG  CD1  CE1  CZ   120.49  3.000
 QYG  H16  CD1  CE1  118.68  3.000
 QYG  H16  CD1  CG2  120.12  3.000
 QYG  CE1  CD1  CG2  121.20  3.000
 QYG  H18  NE1  H17  117.43  3.000
 QYG  H18  NE1  CD3  120.58  3.000
 QYG  H17  NE1  CD3  121.91  3.000
 QYG  HXT  OXT  C3   110.44  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
 QYG  CONST_01  CZ   CE1  CD1  CG2    0.00   0.0  0
 QYG  CONST_02  CZ   CE2  CD2  CG2    0.00   0.0  0
 QYG  CONST_03  CE1  CD1  CG2  CD2    0.00   0.0  0
 QYG  CONST_04  CE1  CZ   CE2  CD2    0.00   0.0  0
 QYG  CONST_05  CD1  CE1  CZ   CE2    0.00   0.0  0
 QYG  CONST_06  CD1  CG2  CD2  CE2    0.00   0.0  0
 QYG  CONST_07  CA2  N2   C1   N3     0.00   0.0  0
 QYG  CONST_08  N2   CA2  C2   N3     0.00   0.0  0
 QYG  CONST_09  C2   CA2  N2   C1     0.00   0.0  0
 QYG  CONST_10  CA2  C2   N3   C1     0.00   0.0  0
 QYG  CONST_11  N2   C1   N3   C2     0.00   0.0  0
 QYG  CONST_12  CE1  CD1  CG2  CB2  180.00   0.0  0
 QYG  CONST_13  CE2  CD2  CG2  CB2  180.00   0.0  0
 QYG  CONST_14  OH   CZ   CE2  CD2  180.00   0.0  0
 QYG  CONST_15  CD1  CE1  CZ   OH   180.00   0.0  0
 QYG  CONST_16  N2   C1   N3   CA3  180.00   0.0  0
 QYG  CONST_17  CA2  C2   N3   CA3  180.00   0.0  0
 QYG  CONST_18  O2   C2   N3   C1   180.00   0.0  0
 QYG  CONST_19  CA2  N2   C1   CA1  180.00   0.0  0
 QYG  CONST_20  C2   N3   C1   CA1  180.00   0.0  0
 QYG  CONST_21  H15  CE1  CD1  CG2  180.00   0.0  0
 QYG  CONST_22  H13  CE2  CD2  CG2  180.00   0.0  0
 QYG  CONST_23  H16  CD1  CG2  CD2  180.00   0.0  0
 QYG  CONST_24  H12  CD2  CE2  CZ   180.00   0.0  0
 QYG  CONST_25  CA1  C1   N3   CA3    0.00   0.0  0
 QYG  CONST_26  O2   C2   N3   CA3    0.00   0.0  0
 QYG  CONST_27  H17  NE1  CD3  CG1    0.00   0.0  0
 QYG  CONST_28  H18  NE1  CD3  CG1  180.00   0.0  0
 QYG  CONST_29  HXT  OXT  C3   O      0.00   0.0  0
 QYG  Var_01    CG2  CB2  CA2  C2     1.61  30.0  2
 QYG  Var_02    CD1  CG2  CB2  CA2    4.12  30.0  2
 QYG  Var_03    C1   N3   CA3  C3   106.39  30.0  2
 QYG  Var_04    N3   CA3  C3   O     -9.20  30.0  1
 QYG  Var_05    CD3  CG1  CB1  CA1  179.92  30.0  1
 QYG  Var_06    OE1  CD3  CG1  CB1    2.18  30.0  2

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
 QYG  chir_01  CA1  CB1  N  C1  positiv

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
 QYG  plan-1  CA3  0.020
 QYG  plan-1  N3   0.020
 QYG  plan-1  C1   0.020
 QYG  plan-1  CA1  0.020
 QYG  plan-1  C2   0.020
 QYG  plan-1  O2   0.020
 QYG  plan-1  CA2  0.020
 QYG  plan-1  N2   0.020
 QYG  plan-1  CB2  0.020
 QYG  plan-2  CB2  0.020
 QYG  plan-2  CG2  0.020
 QYG  plan-2  CD2  0.020
 QYG  plan-2  CE2  0.020
 QYG  plan-2  CZ   0.020
 QYG  plan-2  OH   0.020
 QYG  plan-2  CE1  0.020
 QYG  plan-2  CD1  0.020
 QYG  plan-2  H12  0.020
 QYG  plan-2  H13  0.020
 QYG  plan-2  H15  0.020
 QYG  plan-2  H16  0.020
 QYG  plan-3  CG1  0.020
 QYG  plan-3  CD3  0.020
 QYG  plan-3  NE1  0.020
 QYG  plan-3  OE1  0.020
 QYG  plan-3  H17  0.020
 QYG  plan-3  H18  0.020
 QYG  plan-4  C3   0.020
 QYG  plan-4  O    0.020
 QYG  plan-4  CA3  0.020
 QYG  plan-4  OXT  0.020
 QYG  plan-4  HXT  0.020

