# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 07:38:08 2020
#   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  '(4Z)-4-[(4E)-1-(carboxymethyl)-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-2-yl]-4-iminobutanoic acid'  L-peptide  40  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 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  -0.442   6.0875  -0.6465  -0.5862
 CRU  CD3   C  C     0   0.557   6.0859   0.5010  -0.2157
 CRU  OE2   O  OH1   0  -0.596   7.1974   1.2025  -0.0203
 CRU  CG1   C  CH2   0  -0.571   4.8588   1.3150   0.0885
 CRU  CB1   C  CH2   0  -0.530   3.5805   0.5392  -0.1638
 CRU  CA1   C  C     0   0.204   2.3471   1.3139   0.1951
 CRU  N     N  N     0  -0.561   2.4528   2.4809   0.6728
 CRU  C1    C  CR5   0   0.503   0.9863   0.7255  -0.0050
 CRU  N2    N  N     0  -0.472  -0.0482   1.4327   0.2791
 CRU  CA2   C  CR5   0   0.120  -1.1765   0.6735   0.0066
 CRU  C2    C  CR5   0   0.536  -0.7300  -0.6374  -0.4860
 CRU  O2    O  O     0  -0.445  -1.3345  -1.6389  -0.8168
 CRU  N3    N  NR5   0  -0.587   0.6520  -0.5251  -0.5013
 CRU  CA3   C  CH2   0  -0.477   1.4616  -1.6684  -0.8066
 CRU  C     C  C     0   0.540   1.8022  -2.4533   0.4423
 CRU  O     O  O     0  -0.423   1.4729  -2.1271   1.5514
 CRU  CB2   C  C1    0  -0.352  -2.4074   1.2066   0.2262
 CRU  CG2   C  CR6   0   0.101  -3.7580   0.7443   0.0560
 CRU  CD1   C  CR16  0  -0.281  -4.7755   1.6473   0.4187
 CRU  CE1   C  CR16  0  -0.331  -6.1099   1.3343   0.2941
 CRU  CZ    C  CR6   0   0.374  -6.4788   0.0843  -0.2083
 CRU  OH    O  OH1   0  -0.611  -7.7832  -0.1822  -0.3186
 CRU  CE2   C  CR16  0  -0.361  -5.4880  -0.8314  -0.5722
 CRU  CD2   C  CR16  0  -0.313  -4.1541  -0.5081  -0.4417
 CRU  OXT   O  OH1   0  -0.581   2.5058  -3.5307   0.1443
 CRU  HE21  H  HOH1  0   0.480   7.9723   0.6532  -0.2114
 CRU  HG11  H  HCH2  0   0.290   4.9158   1.6496   1.1270
 CRU  HG12  H  HCH2  0   0.288   4.8857   2.2254  -0.5145
 CRU  HB11  H  HCH2  0   0.279   3.5300   0.2528  -1.2176
 CRU  HB12  H  HCH2  0   0.271   3.5994  -0.3893   0.4120
 CRU  HN1   H  H     0   0.354   1.5323   2.8743   0.8660
 CRU  HA31  H  HCH2  0   0.335   0.9033  -2.3129  -1.4881
 CRU  HA32  H  HCH2  0   0.325   2.3665  -1.3913  -1.3418
 CRU  HB1   H  H     0   0.280  -2.3449   2.2189   0.6151
 CRU  HD1   H  HCR6  0   0.270  -4.5029   2.6203   0.8086
 CRU  HE1   H  HCR6  0   0.275  -6.8719   2.0480   0.5799
 CRU  HH    H  HOH1  0   0.483  -7.9257  -1.0671  -0.6752
 CRU  HE2   H  HCR6  0   0.281  -5.7674  -1.8035  -0.9617
 CRU  HD2   H  HCR6  0   0.297  -3.4121  -1.2366  -0.7290
 CRU  HXT   H  HOH1  0   0.491   2.7245  -4.0280   0.9473

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   double    1.206  0.020  1.206
 CRU  CD3  OE2   single    1.329  0.020  1.329
 CRU  CD3  CG1   single    1.504  0.020  1.504
 CRU  OE2  HE21  single    0.850  0.020  0.980
 CRU  CG1  CB1   single    1.516  0.020  1.516
 CRU  CG1  HG11  single    0.970  0.020  1.090
 CRU  CG1  HG12  single    0.970  0.020  1.090
 CRU  CB1  CA1   single    1.500  0.020  1.500
 CRU  CB1  HB11  single    0.970  0.020  1.090
 CRU  CB1  HB12  single    0.970  0.020  1.090
 CRU  CA1  N     double    1.265  0.020  1.265
 CRU  CA1  C1    single    1.496  0.020  1.496
 CRU  N    HN1   single    0.890  0.020  1.040
 CRU  C1   N2    double    1.285  0.020  1.285
 CRU  C1   N3    single    1.386  0.020  1.386
 CRU  N2   CA2   single    1.387  0.020  1.387
 CRU  CA2  C2    single    1.470  0.020  1.470
 CRU  CA2  CB2   double    1.359  0.020  1.359
 CRU  C2   O2    double    1.216  0.020  1.216
 CRU  C2   N3    single    1.387  0.020  1.387
 CRU  N3   CA3   single    1.434  0.020  1.434
 CRU  CA3  C     single    1.514  0.020  1.514
 CRU  CA3  HA31  single    0.970  0.020  1.090
 CRU  CA3  HA32  single    0.970  0.020  1.090
 CRU  C    O     double    1.202  0.020  1.202
 CRU  C    OXT   single    1.321  0.020  1.321
 CRU  CB2  CG2   single    1.438  0.020  1.438
 CRU  CB2  HB1   single    0.930  0.020  1.080
 CRU  CG2  CD1   aromatic  1.408  0.020  1.408
 CRU  CG2  CD2   aromatic  1.405  0.020  1.405
 CRU  CD1  CE1   aromatic  1.376  0.020  1.376
 CRU  CD1  HD1   single    0.930  0.020  1.080
 CRU  CE1  CZ    aromatic  1.397  0.020  1.397
 CRU  CE1  HE1   single    0.930  0.020  1.080
 CRU  CZ   OH    single    1.336  0.020  1.336
 CRU  CZ   CE2   aromatic  1.397  0.020  1.397
 CRU  OH   HH    single    0.850  0.020  0.980
 CRU  CE2  CD2   aromatic  1.379  0.020  1.379
 CRU  CE2  HE2   single    0.930  0.020  1.080
 CRU  CD2  HD2   single    0.930  0.020  1.080
 CRU  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
 CRU  CG1   CD3  OE2   111.54  3.000
 CRU  CG1   CD3  OE1   125.34  3.000
 CRU  OE2   CD3  OE1   123.12  3.000
 CRU  HE21  OE2  CD3   109.93  3.000
 CRU  HG12  CG1  HG11  105.55  3.000
 CRU  HG12  CG1  CB1   110.81  3.000
 CRU  HG11  CG1  CB1   111.03  3.000
 CRU  HG12  CG1  CD3   108.63  3.000
 CRU  HG11  CG1  CD3   108.39  3.000
 CRU  CB1   CG1  CD3   112.17  3.000
 CRU  HB12  CB1  HB11  106.62  3.000
 CRU  HB12  CB1  CA1   109.09  3.000
 CRU  HB11  CB1  CA1   109.15  3.000
 CRU  HB12  CB1  CG1   109.42  3.000
 CRU  HB11  CB1  CG1   109.47  3.000
 CRU  CA1   CB1  CG1   112.90  3.000
 CRU  C1    CA1  N     119.28  3.000
 CRU  C1    CA1  CB1   120.85  3.000
 CRU  N     CA1  CB1   119.87  3.000
 CRU  HN1   N    CA1   110.61  3.000
 CRU  N3    C1   N2    112.42  3.000
 CRU  N3    C1   CA1   128.47  3.000
 CRU  N2    C1   CA1   119.10  3.000
 CRU  CA2   N2   C1    108.07  3.000
 CRU  CB2   CA2  C2    132.77  3.000
 CRU  CB2   CA2  N2    119.35  3.000
 CRU  C2    CA2  N2    107.87  3.000
 CRU  N3    C2   O2    124.01  3.000
 CRU  N3    C2   CA2   103.55  3.000
 CRU  O2    C2   CA2   132.44  3.000
 CRU  CA3   N3   C2    120.04  3.000
 CRU  CA3   N3   C1    131.25  3.000
 CRU  C2    N3   C1    108.03  3.000
 CRU  HA32  CA3  HA31  105.59  3.000
 CRU  HA32  CA3  C     110.55  3.000
 CRU  HA31  CA3  C     108.90  3.000
 CRU  HA32  CA3  N3    111.81  3.000
 CRU  HA31  CA3  N3    108.36  3.000
 CRU  C     CA3  N3    111.40  3.000
 CRU  OXT   C    O     125.13  3.000
 CRU  OXT   C    CA3   110.90  3.000
 CRU  O     C    CA3   123.98  3.000
 CRU  HB1   CB2  CG2   113.33  3.000
 CRU  HB1   CB2  CA2   111.79  3.000
 CRU  CG2   CB2  CA2   134.87  3.000
 CRU  CD2   CG2  CD1   117.35  3.000
 CRU  CD2   CG2  CB2   126.40  3.000
 CRU  CD1   CG2  CB2   116.25  3.000
 CRU  HD1   CD1  CE1   118.75  3.000
 CRU  HD1   CD1  CG2   119.15  3.000
 CRU  CE1   CD1  CG2   122.11  3.000
 CRU  HE1   CE1  CZ    119.94  3.000
 CRU  HE1   CE1  CD1   120.57  3.000
 CRU  CZ    CE1  CD1   119.49  3.000
 CRU  CE2   CZ   OH    122.69  3.000
 CRU  CE2   CZ   CE1   119.52  3.000
 CRU  OH    CZ   CE1   117.78  3.000
 CRU  HH    OH   CZ    110.96  3.000
 CRU  HE2   CE2  CD2   119.58  3.000
 CRU  HE2   CE2  CZ    119.90  3.000
 CRU  CD2   CE2  CZ    120.51  3.000
 CRU  HD2   CD2  CE2   118.81  3.000
 CRU  HD2   CD2  CG2   120.17  3.000
 CRU  CE2   CD2  CG2   121.02  3.000
 CRU  HXT   OXT  C     110.59  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  HD1   CD1  CE1  CZ    180.00   0.0  0
 CRU  CONST_25  CA3   N3   C1   CA1     0.00   0.0  0
 CRU  CONST_26  CA3   N3   C2   O2      0.00   0.0  0
 CRU  CONST_27  HE21  OE2  CD3  OE1     0.00   0.0  0
 CRU  CONST_28  HXT   OXT  C    CA3   180.00   0.0  0
 CRU  Var_01    CG2   CB2  CA2  N2    179.29  30.0  2
 CRU  Var_02    CD1   CG2  CB2  CA2  -179.98  30.0  2
 CRU  Var_03    N2    C1   CA1  CB1  -178.09  30.0  2
 CRU  Var_04    C     CA3  N3   C1     79.92  30.0  3
 CRU  Var_05    C1    CA1  CB1  CG1   178.95  30.0  3
 CRU  Var_06    O     C    CA3  N3     -2.49  30.0  3
 CRU  Var_07    CB1   CG1  CD3  OE1    -1.75  30.0  3
 CRU  Var_08    CA1   CB1  CG1  CD3   177.32  30.0  3

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-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-3  HE21  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-4  HXT   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

