# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 11:44:14 2022
#   Inital geometry file: a 114 line input string
#   Ligand name: (4Z)-4-[(4E)-1-(carboxymethyl)-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-2-yl]-4-iminobutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCC(=N)C1=N\C(=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
 CRU  CRU  "4-[(4Z)-1-(CARBOXYMETHYL)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-2-YL]-4-IMINOBUTANOIC ACID"  L-peptide  38  25  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT (side chain)
;

data_comp_CRU
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
 CRU  OE1   O  O      0  -0.606   5.7822   0.0520  -1.7448
 CRU  CD3   C  C      0   0.417   5.8612   1.1397  -1.1409
 CRU  OE2   O  OC    -1  -0.631   6.8125   1.9474  -1.1910
 CRU  CG1   C  CH2    0  -0.579   4.6916   1.5467  -0.2263
 CRU  CB1   C  CH2    0  -0.516   3.4911   0.6191  -0.2862
 CRU  CA1   C  C      0   0.212   2.3702   1.0103   0.6345
 CRU  N     N  N      0  -0.571   2.5616   1.8166   1.5925
 CRU  C1    C  CR5    0   0.480   0.9936   0.5235   0.3405
 CRU  N2    N  N      0  -0.482  -0.0254   1.2633   0.6071
 CRU  CA2   C  CR5    0   0.108  -1.1544   0.5728   0.1759
 CRU  C2    C  CR5    0   0.524  -0.7070  -0.7144  -0.3970
 CRU  O2    O  O      0  -0.455  -1.3301  -1.6542  -0.8574
 CRU  N3    N  NR5    0  -0.547   0.6664  -0.6567  -0.2946
 CRU  CA3   C  CH2    0  -0.485   1.5076  -1.8166  -0.4653
 CRU  C     C  C      0   0.419   2.1176  -2.3222   0.8622
 CRU  O     O  O      0  -0.579   1.8470  -1.6793   1.8897
 CRU  CB2   C  C1     0  -0.368  -2.3778   1.1390   0.3186
 CRU  CG2   C  C      0   0.102  -3.7288   0.7456  -0.0021
 CRU  CD1   C  C1     0  -0.286  -4.7360   1.6843   0.2860
 CRU  CE1   C  C1     0  -0.332  -6.0662   1.4349   0.0279
 CRU  CZ    C  C      0   0.367  -6.4408   0.2134  -0.5340
 CRU  OH    O  OH1    0  -0.616  -7.7423   0.0046  -0.7686
 CRU  CE2   C  C1     0  -0.361  -5.4603  -0.7365  -0.8260
 CRU  CD2   C  C1     0  -0.320  -4.1301  -0.4751  -0.5657
 CRU  OXT   O  OC    -1  -0.605   2.8302  -3.3342   0.7491
 CRU  HG11  H  HCH2   0   0.232   5.0650   1.6087   0.7996
 CRU  HG12  H  HCH2   0   0.225   4.3881   2.5671  -0.4789
 CRU  HB11  H  HCH2   0   0.244   3.1071   0.5695  -1.3091
 CRU  HB12  H  HCH2   0   0.260   3.8106  -0.3983  -0.0479
 CRU  HN1   H  H      0   0.338   1.6925   1.9846   2.0960
 CRU  HA31  H  HCH2   0   0.280   0.8883  -2.6008  -0.9014
 CRU  HA32  H  HCH2   0   0.270   2.2963  -1.6188  -1.1923
 CRU  HB1   H  H      0   0.271  -2.3185   2.1205   0.7807
 CRU  HD1   H  H      0   0.266  -4.4603   2.6354   0.7253
 CRU  HE1   H  H      0   0.271  -6.8197   2.1769   0.2595
 CRU  HH    H  HOH1   0   0.480  -7.8841  -0.8693  -1.1512
 CRU  HE2   H  H      0   0.278  -5.7425  -1.6892  -1.2593
 CRU  HD2   H  H      0   0.296  -3.3954  -1.2296  -0.7995

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
 CRU  OE1  CD3   deloc     1.247  0.020  1.247
 CRU  CD3  OE2   deloc     1.249  0.020  1.249
 CRU  CD3  CG1   single    1.539  0.020  1.539
 CRU  CG1  CB1   single    1.518  0.020  1.518
 CRU  CG1  HG11  single    0.970  0.020  1.090
 CRU  CG1  HG12  single    0.970  0.020  1.090
 CRU  CB1  CA1   single    1.502  0.020  1.502
 CRU  CB1  HB11  single    0.970  0.020  1.090
 CRU  CB1  HB12  single    0.970  0.020  1.090
 CRU  CA1  N     double    1.267  0.020  1.267
 CRU  CA1  C1    single    1.489  0.020  1.489
 CRU  N    HN1   single    0.890  0.020  1.040
 CRU  C1   N2    double    1.287  0.020  1.287
 CRU  C1   N3    single    1.380  0.020  1.380
 CRU  N2   CA2   single    1.392  0.020  1.392
 CRU  CA2  C2    single    1.478  0.020  1.478
 CRU  CA2  CB2   double    1.356  0.020  1.356
 CRU  C2   O2    double    1.218  0.020  1.218
 CRU  C2   N3    single    1.378  0.020  1.378
 CRU  N3   CA3   single    1.443  0.020  1.443
 CRU  CA3  C     single    1.546  0.020  1.546
 CRU  CA3  HA31  single    0.970  0.020  1.090
 CRU  CA3  HA32  single    0.970  0.020  1.090
 CRU  C    O     deloc     1.242  0.020  1.242
 CRU  C    OXT   deloc     1.243  0.020  1.243
 CRU  CB2  CG2   single    1.443  0.020  1.443
 CRU  CB2  HB1   single    0.930  0.020  1.080
 CRU  CG2  CD1   aromatic  1.407  0.020  1.407
 CRU  CG2  CD2   aromatic  1.403  0.020  1.403
 CRU  CD1  CE1   aromatic  1.378  0.020  1.378
 CRU  CD1  HD1   single    0.930  0.020  1.080
 CRU  CE1  CZ    aromatic  1.396  0.020  1.396
 CRU  CE1  HE1   single    0.930  0.020  1.080
 CRU  CZ   OH    single    1.339  0.020  1.339
 CRU  CZ   CE2   aromatic  1.396  0.020  1.396
 CRU  OH   HH    single    0.850  0.020  0.980
 CRU  CE2  CD2   aromatic  1.380  0.020  1.380
 CRU  CE2  HE2   single    0.930  0.020  1.080
 CRU  CD2  HD2   single    0.930  0.020  1.080

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
 CRU  CG1   CD3  OE2   115.56  3.000
 CRU  CG1   CD3  OE1   118.06  3.000
 CRU  OE2   CD3  OE1   126.38  3.000
 CRU  HG12  CG1  HG11  104.98  3.000
 CRU  HG12  CG1  CB1   109.96  3.000
 CRU  HG11  CG1  CB1   109.97  3.000
 CRU  HG12  CG1  CD3   108.67  3.000
 CRU  HG11  CG1  CD3   108.24  3.000
 CRU  CB1   CG1  CD3   114.57  3.000
 CRU  HB12  CB1  HB11  105.33  3.000
 CRU  HB12  CB1  CA1   109.08  3.000
 CRU  HB11  CB1  CA1   108.84  3.000
 CRU  HB12  CB1  CG1   109.21  3.000
 CRU  HB11  CB1  CG1   110.01  3.000
 CRU  CA1   CB1  CG1   114.00  3.000
 CRU  C1    CA1  N     119.80  3.000
 CRU  C1    CA1  CB1   118.91  3.000
 CRU  N     CA1  CB1   121.10  3.000
 CRU  HN1   N    CA1   110.49  3.000
 CRU  N3    C1   N2    113.53  3.000
 CRU  N3    C1   CA1   126.14  3.000
 CRU  N2    C1   CA1   120.19  3.000
 CRU  CA2   N2   C1    107.03  3.000
 CRU  CB2   CA2  C2    132.66  3.000
 CRU  CB2   CA2  N2    119.49  3.000
 CRU  C2    CA2  N2    107.85  3.000
 CRU  N3    C2   O2    124.76  3.000
 CRU  N3    C2   CA2   103.67  3.000
 CRU  O2    C2   CA2   131.57  3.000
 CRU  CA3   N3   C2    122.58  3.000
 CRU  CA3   N3   C1    127.14  3.000
 CRU  C2    N3   C1    107.84  3.000
 CRU  HA32  CA3  HA31  105.94  3.000
 CRU  HA32  CA3  C     110.27  3.000
 CRU  HA31  CA3  C     109.41  3.000
 CRU  HA32  CA3  N3    110.77  3.000
 CRU  HA31  CA3  N3    107.12  3.000
 CRU  C     CA3  N3    113.04  3.000
 CRU  OXT   C    O     128.44  3.000
 CRU  OXT   C    CA3   114.48  3.000
 CRU  O     C    CA3   117.07  3.000
 CRU  HB1   CB2  CG2   113.07  3.000
 CRU  HB1   CB2  CA2   111.89  3.000
 CRU  CG2   CB2  CA2   135.04  3.000
 CRU  CD2   CG2  CD1   117.26  3.000
 CRU  CD2   CG2  CB2   126.45  3.000
 CRU  CD1   CG2  CB2   116.29  3.000
 CRU  HD1   CD1  CE1   118.72  3.000
 CRU  HD1   CD1  CG2   119.13  3.000
 CRU  CE1   CD1  CG2   122.15  3.000
 CRU  HE1   CE1  CZ    119.95  3.000
 CRU  HE1   CE1  CD1   120.52  3.000
 CRU  CZ    CE1  CD1   119.53  3.000
 CRU  CE2   CZ   OH    122.68  3.000
 CRU  CE2   CZ   CE1   119.42  3.000
 CRU  OH    CZ   CE1   117.90  3.000
 CRU  HH    OH   CZ    110.72  3.000
 CRU  HE2   CE2  CD2   119.52  3.000
 CRU  HE2   CE2  CZ    119.92  3.000
 CRU  CD2   CE2  CZ    120.56  3.000
 CRU  HD2   CD2  CE2   118.88  3.000
 CRU  HD2   CD2  CG2   120.05  3.000
 CRU  CE2   CD2  CG2   121.07  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
 CRU  CONST_01  CZ    CE1  CD1  CG2     0.00   0.0  0
 CRU  CONST_02  CZ    CE2  CD2  CG2     0.00   0.0  0
 CRU  CONST_03  CE2   CD2  CG2  CD1     0.00   0.0  0
 CRU  CONST_04  CE2   CZ   CE1  CD1     0.00   0.0  0
 CRU  CONST_05  CD2   CG2  CD1  CE1     0.00   0.0  0
 CRU  CONST_06  CD2   CE2  CZ   CE1     0.00   0.0  0
 CRU  CONST_07  C2    CA2  N2   C1      0.00   0.0  0
 CRU  CONST_08  CA2   C2   N3   C1      0.00   0.0  0
 CRU  CONST_09  C2    N3   C1   N2      0.00   0.0  0
 CRU  CONST_10  N3    C2   CA2  N2      0.00   0.0  0
 CRU  CONST_11  N3    C1   N2   CA2     0.00   0.0  0
 CRU  CONST_12  CE1   CD1  CG2  CB2   180.00   0.0  0
 CRU  CONST_13  CE2   CD2  CG2  CB2   180.00   0.0  0
 CRU  CONST_14  OH    CZ   CE1  CD1   180.00   0.0  0
 CRU  CONST_15  CD2   CE2  CZ   OH    180.00   0.0  0
 CRU  CONST_16  CA2   N2   C1   CA1   180.00   0.0  0
 CRU  CONST_17  C2    N3   C1   CA1   180.00   0.0  0
 CRU  CONST_18  O2    C2   N3   C1    180.00   0.0  0
 CRU  CONST_19  CA3   N3   C1   N2    180.00   0.0  0
 CRU  CONST_20  CA3   N3   C2   CA2   180.00   0.0  0
 CRU  CONST_21  HE1   CE1  CD1  CG2   180.00   0.0  0
 CRU  CONST_22  HE2   CE2  CD2  CG2   180.00   0.0  0
 CRU  CONST_23  HD2   CD2  CG2  CD1   180.00   0.0  0
 CRU  CONST_24  HE2   CE2  CZ   CE1   180.00   0.0  0
 CRU  CONST_25  HD1   CD1  CE1  CZ    180.00   0.0  0
 CRU  CONST_26  HD2   CD2  CE2  CZ    180.00   0.0  0
 CRU  CONST_27  HE1   CE1  CZ   CE2   180.00   0.0  0
 CRU  CONST_28  HD1   CD1  CG2  CD2   180.00   0.0  0
 CRU  CONST_30  CA3   N3   C2   O2      0.00   0.0  0
 CRU  Var_01    CG2   CB2  CA2  N2    179.71   0.0  2
 CRU  Var_02    CG2   CB2  CA2  C2      0.63   0.0  2
 CRU  Var_03    CD1   CG2  CB2  CA2  -177.90  30.0  2
 CRU  Var_04    CD2   CG2  CB2  CA2     2.30  30.0  2
 CRU  Var_05    N2    C1   CA1  CB1  -145.57  30.0  2
 CRU  Var_06    N3    C1   CA1  CB1    29.88  30.0  2
 CRU  Var_07    N2    C1   CA1  N      29.49  30.0  2
 CRU  Var_08    N3    C1   CA1  N    -155.06  30.0  2
 CRU  Var_09    C     CA3  N3   C1     52.62  30.0  3
 CRU  Var_10    C     CA3  N3   C2   -107.44  30.0  3
 CRU  Var_11    HB1   CB2  CA2  N2     -0.04   0.0  2
 CRU  Var_12    HB1   CB2  CA2  C2   -179.11   0.0  2
 CRU  Var_13    HA31  CA3  N3   C1    173.20  30.0  3
 CRU  Var_14    HA32  CA3  N3   C1    -71.71  30.0  3
 CRU  Var_15    HA31  CA3  N3   C2     13.14  30.0  3
 CRU  Var_16    HA32  CA3  N3   C2    128.23  30.0  3
 CRU  Var_17    HB1   CB2  CG2  CD1     1.85  30.0  2
 CRU  Var_18    HB1   CB2  CG2  CD2  -177.96  30.0  2
 CRU  Var_19    C1    CA1  CB1  CG1   158.03  30.0  3
 CRU  Var_20    O     C    CA3  N3     -1.39  30.0  3
 CRU  Var_21    OXT   C    CA3  N3    178.89  30.0  3
 CRU  Var_22    HN1   N    CA1  C1      3.70   0.0  2
 CRU  Var_23    HB11  CB1  CA1  C1     34.82  30.0  1
 CRU  Var_24    HB12  CB1  CA1  C1    -79.61  30.0  1
 CRU  Var_25    CB1   CG1  CD3  OE1    -6.26  30.0  3
 CRU  Var_26    CA1   CB1  CG1  CD3   178.66  30.0  3
 CRU  Var_27    CB1   CG1  CD3  OE2   174.29  30.0  3
 CRU  Var_28    N     CA1  CB1  CG1   -16.97  30.0  3
 CRU  Var_29    HN1   N    CA1  CB1   178.65   0.0  2
 CRU  Var_30    HG11  CG1  CD3  OE1   116.84  30.0  3
 CRU  Var_31    HG12  CG1  CD3  OE1  -129.67  30.0  3
 CRU  Var_32    HB11  CB1  CG1  CD3   -58.76  30.0  3
 CRU  Var_33    HB12  CB1  CG1  CD3    56.38  30.0  3
 CRU  Var_34    HG11  CG1  CD3  OE2   -62.61  30.0  3
 CRU  Var_35    HG12  CG1  CD3  OE2    50.88  30.0  3
 CRU  Var_36    HG11  CG1  CB1  CA1    56.50  30.0  2
 CRU  Var_37    HG12  CG1  CB1  CA1   -58.62  30.0  2
 CRU  Var_38    HB11  CB1  CA1  N    -140.18  30.0  1
 CRU  Var_39    HB12  CB1  CA1  N     105.39  30.0  1
 CRU  Var_40    HA31  CA3  C    O    -120.66  30.0  2
 CRU  Var_41    HA32  CA3  C    O     123.21  30.0  2
 CRU  Var_42    HA31  CA3  C    OXT    59.62  30.0  2
 CRU  Var_43    HA32  CA3  C    OXT   -56.51  30.0  2

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
 CRU  plan-1  CA1  0.020
 CRU  plan-1  C1   0.020
 CRU  plan-1  N2   0.020
 CRU  plan-1  CA2  0.020
 CRU  plan-1  C2   0.020
 CRU  plan-1  O2   0.020
 CRU  plan-1  N3   0.020
 CRU  plan-1  CA3  0.020
 CRU  plan-1  CB2  0.020
 CRU  plan-1  CG2  0.020
 CRU  plan-1  HB1  0.020
 CRU  plan-2  CB2  0.020
 CRU  plan-2  CG2  0.020
 CRU  plan-2  CD1  0.020
 CRU  plan-2  CE1  0.020
 CRU  plan-2  CZ   0.020
 CRU  plan-2  OH   0.020
 CRU  plan-2  CE2  0.020
 CRU  plan-2  CD2  0.020
 CRU  plan-2  HD1  0.020
 CRU  plan-2  HE1  0.020
 CRU  plan-2  HE2  0.020
 CRU  plan-2  HD2  0.020
 CRU  plan-3  OE1  0.020
 CRU  plan-3  CD3  0.020
 CRU  plan-3  OE2  0.020
 CRU  plan-3  CG1  0.020
 CRU  plan-4  CA3  0.020
 CRU  plan-4  C    0.020
 CRU  plan-4  O    0.020
 CRU  plan-4  OXT  0.020
 CRU  plan-5  CB1  0.020
 CRU  plan-5  CA1  0.020
 CRU  plan-5  N    0.020
 CRU  plan-5  C1   0.020
 CRU  plan-5  HN1  0.020

