# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 20 05:16:37 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: {(4E)-4-(4-hydroxybenzylidene)-2-[(1E)-3-methylbutanimidoyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CC(=N)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
 NRP  NRP  '{(4E)-4-(4-hydroxybenzylidene)-2-[(1E)-3-methylbutanimidoyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid'  L-peptide  43  24  .  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_NRP
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
 NRP  C     C  C     0   0.527  -2.0938  -3.3806  -0.5858
 NRP  N     N  N     0  -0.508  -3.9161  -1.1637  -0.4262
 NRP  O     O  O     0  -0.653  -1.6808  -3.1385  -1.6886
 NRP  C1    C  CR5   0   0.493  -1.7781  -0.2041  -0.2165
 NRP  C2    C  CR5   0   0.513   0.1985  -1.0758   0.3720
 NRP  N2    N  N     0  -0.516  -0.9591   0.7555  -0.4622
 NRP  O2    O  O     0  -0.392   1.0286  -1.8753   0.7622
 NRP  N3    N  NR5   0  -0.508  -1.1568  -1.3250   0.3060
 NRP  OXT   O  OH1   0  -0.426  -2.8771  -4.4037  -0.2844
 NRP  CZ    C  CR6   0   0.348   5.5877   1.0677   0.2390
 NRP  CA2   C  CR5   0   0.219   0.3144   0.3091  -0.1235
 NRP  CA3   C  CH2   0  -0.451  -1.7285  -2.5936   0.6504
 NRP  CB2   C  C1    0  -0.335   1.3746   1.1381  -0.3039
 NRP  CD1   C  CR16  0  -0.194   3.4729  -0.0619   0.4728
 NRP  CD2   C  CR16  0  -0.293   3.5649   2.1471  -0.4625
 NRP  CD3   C  CH3   0  -0.609  -4.3074   3.5750  -0.0329
 NRP  CD4   C  CH3   0  -0.647  -4.7421   1.6237   1.4868
 NRP  CE1   C  CR16  0  -0.361   4.8409  -0.0466   0.6322
 NRP  CE2   C  CR16  0  -0.306   4.9348   2.1716  -0.3108
 NRP  CG1   C  CH1   0  -0.229  -3.8284   2.1968   0.4102
 NRP  CG2   C  CR6   0   0.031   2.7929   1.0356  -0.0833
 NRP  HN    H  H     0   0.367  -4.8912  -0.9724  -0.6425
 NRP  HXT   H  HOH1  0   0.530  -3.0650  -4.9264  -1.0783
 NRP  HOH   H  HOH1  0   0.483   7.3282   1.8326   0.0938
 NRP  HA3   H  HCH2  0   0.314  -2.5897  -2.4762   1.3033
 NRP  HA3A  H  HCH2  0   0.308  -0.9760  -3.1581   1.2071
 NRP  HB1   H  HCH2  0   0.253  -3.0968   1.7297  -1.5643
 NRP  HB1A  H  HCH2  0   0.232  -4.7364   1.1649  -1.2560
 NRP  HB2   H  H     0   0.276   1.0711   2.0973  -0.7134
 NRP  HD1   H  HCR6  0   0.274   2.9242  -0.9366   0.7843
 NRP  HD2   H  HCR6  0   0.243   3.0751   3.0136  -0.8891
 NRP  HD3   H  HCH3  0   0.239  -5.3168   3.5252  -0.4480
 NRP  HD3A  H  HCH3  0   0.201  -4.3284   4.2693   0.8078
 NRP  HD3B  H  HCH3  0   0.223  -3.6539   3.9975  -0.7979
 NRP  HD4   H  HCH3  0   0.225  -5.7481   1.4545   1.0947
 NRP  HD4A  H  HCH3  0   0.152  -4.3760   0.6729   1.8773
 NRP  HD4B  H  HCH3  0   0.276  -4.8267   2.3108   2.3298
 NRP  HE1   H  HCR6  0   0.265   5.3455  -0.9023   1.0622
 NRP  HE2   H  HCR6  0   0.255   5.4970   3.0450  -0.6196
 NRP  HG1   H  HCH1  0   0.195  -2.8226   2.3056   0.8269
 NRP  CA1   C  C     0   0.139  -3.2244  -0.1020  -0.4875
 NRP  OH    O  OH1   0  -0.671   6.9125   1.0229   0.4126
 NRP  CB1   C  CH2   0  -0.482  -3.7412   1.2694  -0.8127

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
 NRP  C    OXT   single    1.323  0.020  1.323
 NRP  N    CA1   double    1.269  0.020  1.269
 NRP  N    HN    single    0.890  0.020  1.040
 NRP  O    C     double    1.202  0.020  1.202
 NRP  C1   CA1   single    1.475  0.020  1.475
 NRP  C1   N2    double    1.285  0.020  1.285
 NRP  C2   CA2   single    1.475  0.020  1.475
 NRP  O2   C2    double    1.217  0.020  1.217
 NRP  N3   C1    single    1.384  0.020  1.384
 NRP  N3   C2    single    1.380  0.020  1.380
 NRP  OXT  HXT   single    0.850  0.020  0.980
 NRP  OH   CZ    single    1.337  0.020  1.337
 NRP  OH   HOH   single    0.850  0.020  0.980
 NRP  CZ   CE2   aromatic  1.395  0.020  1.395
 NRP  CA1  CB1   single    1.501  0.020  1.501
 NRP  CA2  N2    single    1.391  0.020  1.391
 NRP  CA2  CB2   double    1.358  0.020  1.358
 NRP  CA3  C     single    1.510  0.020  1.510
 NRP  CA3  N3    single    1.433  0.020  1.433
 NRP  CA3  HA3   single    0.970  0.020  1.090
 NRP  CA3  HA3A  single    0.970  0.020  1.090
 NRP  CB1  CG1   single    1.537  0.020  1.537
 NRP  CB1  HB1   single    0.970  0.020  1.090
 NRP  CB1  HB1A  single    0.970  0.020  1.090
 NRP  CB2  HB2   single    0.930  0.020  1.080
 NRP  CD1  CG2   aromatic  1.406  0.020  1.406
 NRP  CD1  HD1   single    0.930  0.020  1.080
 NRP  CD2  HD2   single    0.930  0.020  1.080
 NRP  CD3  HD3   single    0.970  0.020  1.090
 NRP  CD3  HD3A  single    0.970  0.020  1.090
 NRP  CD3  HD3B  single    0.970  0.020  1.090
 NRP  CD4  HD4   single    0.970  0.020  1.090
 NRP  CD4  HD4A  single    0.970  0.020  1.090
 NRP  CD4  HD4B  single    0.970  0.020  1.090
 NRP  CE1  CZ    aromatic  1.398  0.020  1.398
 NRP  CE1  CD1   aromatic  1.377  0.020  1.377
 NRP  CE1  HE1   single    0.930  0.020  1.080
 NRP  CE2  CD2   aromatic  1.378  0.020  1.378
 NRP  CE2  HE2   single    0.930  0.020  1.080
 NRP  CG1  CD3   single    1.525  0.020  1.525
 NRP  CG1  CD4   single    1.524  0.020  1.524
 NRP  CG1  HG1   single    0.970  0.020  1.090
 NRP  CG2  CB2   single    1.439  0.020  1.439
 NRP  CG2  CD2   aromatic  1.405  0.020  1.405

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
 NRP  CA3   C    OXT   111.08  3.000
 NRP  CA3   C    O     124.25  3.000
 NRP  OXT   C    O     124.61  3.000
 NRP  HN    N    CA1   110.80  3.000
 NRP  CA1   C1   N3    124.44  3.000
 NRP  N3    C1   N2    113.00  3.000
 NRP  CA1   C1   N2    122.55  3.000
 NRP  CA2   C2   N3    103.34  3.000
 NRP  N3    C2   O2    124.52  3.000
 NRP  CA2   C2   O2    132.14  3.000
 NRP  CA2   N2   C1    107.29  3.000
 NRP  CA3   N3   C2    122.70  3.000
 NRP  CA3   N3   C1    128.94  3.000
 NRP  C2    N3   C1    108.22  3.000
 NRP  HXT   OXT  C     110.20  3.000
 NRP  CE2   CZ   CE1   119.44  3.000
 NRP  CE1   CZ   OH    117.79  3.000
 NRP  CE2   CZ   OH    122.77  3.000
 NRP  CB2   CA2  N2    119.11  3.000
 NRP  CB2   CA2  C2    132.76  3.000
 NRP  N2    CA2  C2    108.12  3.000
 NRP  HA3A  CA3  HA3   107.17  3.000
 NRP  HA3A  CA3  N3    107.75  3.000
 NRP  HA3   CA3  N3    111.39  3.000
 NRP  HA3A  CA3  C     108.32  3.000
 NRP  HA3   CA3  C     110.87  3.000
 NRP  N3    CA3  C     111.16  3.000
 NRP  HB2   CB2  CG2   113.33  3.000
 NRP  CG2   CB2  CA2   134.89  3.000
 NRP  HB2   CB2  CA2   111.77  3.000
 NRP  HD1   CD1  CG2   120.09  3.000
 NRP  HD1   CD1  CE1   118.74  3.000
 NRP  CG2   CD1  CE1   121.16  3.000
 NRP  HD2   CD2  CG2   119.38  3.000
 NRP  CG2   CD2  CE2   122.02  3.000
 NRP  HD2   CD2  CE2   118.59  3.000
 NRP  HD3B  CD3  HD3A  107.79  3.000
 NRP  HD3B  CD3  HD3   107.73  3.000
 NRP  HD3A  CD3  HD3   107.70  3.000
 NRP  HD3B  CD3  CG1   111.44  3.000
 NRP  HD3A  CD3  CG1   110.94  3.000
 NRP  HD3   CD3  CG1   111.06  3.000
 NRP  HD4B  CD4  HD4A  107.36  3.000
 NRP  HD4B  CD4  HD4   107.66  3.000
 NRP  HD4A  CD4  HD4   107.60  3.000
 NRP  HD4B  CD4  CG1   110.82  3.000
 NRP  HD4A  CD4  CG1   112.30  3.000
 NRP  HD4   CD4  CG1   110.89  3.000
 NRP  HE1   CE1  CD1   120.01  3.000
 NRP  HE1   CE1  CZ    119.53  3.000
 NRP  CD1   CE1  CZ    120.46  3.000
 NRP  HE2   CE2  CD2   119.90  3.000
 NRP  HE2   CE2  CZ    120.48  3.000
 NRP  CD2   CE2  CZ    119.62  3.000
 NRP  HG1   CG1  CD4   108.63  3.000
 NRP  HG1   CG1  CD3   108.03  3.000
 NRP  CD4   CG1  CD3   110.91  3.000
 NRP  HG1   CG1  CB1   108.10  3.000
 NRP  CD4   CG1  CB1   111.66  3.000
 NRP  CD3   CG1  CB1   109.38  3.000
 NRP  CD2   CG2  CD1   117.29  3.000
 NRP  CD2   CG2  CB2   116.35  3.000
 NRP  CD1   CG2  CB2   126.36  3.000
 NRP  CB1   CA1  C1    116.14  3.000
 NRP  CB1   CA1  N     125.97  3.000
 NRP  C1    CA1  N     117.89  3.000
 NRP  HOH   OH   CZ    110.86  3.000
 NRP  HB1A  CB1  HB1   107.34  3.000
 NRP  HB1A  CB1  CG1   109.16  3.000
 NRP  HB1   CB1  CG1   109.07  3.000
 NRP  HB1A  CB1  CA1   108.27  3.000
 NRP  HB1   CB1  CA1   109.34  3.000
 NRP  CG1   CB1  CA1   113.48  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
 NRP  CONST_01  CG2  CD2  CE2  CZ     0.00   0.0  0
 NRP  CONST_02  CG2  CD1  CE1  CZ     0.00   0.0  0
 NRP  CONST_03  CE2  CD2  CG2  CD1    0.00   0.0  0
 NRP  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 NRP  CONST_05  CE1  CZ   CE2  CD2    0.00   0.0  0
 NRP  CONST_06  CE1  CD1  CG2  CD2    0.00   0.0  0
 NRP  CONST_07  C2   CA2  N2   C1     0.00   0.0  0
 NRP  CONST_08  CA2  C2   N3   C1     0.00   0.0  0
 NRP  CONST_09  N2   C1   N3   C2     0.00   0.0  0
 NRP  CONST_10  N3   C2   CA2  N2     0.00   0.0  0
 NRP  CONST_11  CA2  N2   C1   N3     0.00   0.0  0
 NRP  CONST_12  CD2  CE2  CZ   OH   180.00   0.0  0
 NRP  CONST_13  CD1  CE1  CZ   OH   180.00   0.0  0
 NRP  CONST_14  CE1  CD1  CG2  CB2  180.00   0.0  0
 NRP  CONST_15  CE2  CD2  CG2  CB2  180.00   0.0  0
 NRP  CONST_16  O2   C2   N3   C1   180.00   0.0  0
 NRP  CONST_17  CA1  C1   N3   C2   180.00   0.0  0
 NRP  CONST_18  CA3  N3   C1   N2   180.00   0.0  0
 NRP  CONST_19  CA2  N2   C1   CA1  180.00   0.0  0
 NRP  CONST_20  CA3  N3   C2   CA2  180.00   0.0  0
 NRP  CONST_21  HD2  CD2  CE2  CZ   180.00   0.0  0
 NRP  CONST_22  HD1  CD1  CE1  CZ   180.00   0.0  0
 NRP  CONST_23  HE2  CE2  CZ   CE1  180.00   0.0  0
 NRP  CONST_24  HE1  CE1  CZ   CE2  180.00   0.0  0
 NRP  CONST_25  CA3  N3   C2   O2     0.00   0.0  0
 NRP  CONST_26  CA3  N3   C1   CA1    0.00   0.0  0
 NRP  CONST_27  HN   N    CA1  C1   180.00   0.0  0
 NRP  CONST_28  HXT  OXT  C    O      0.00   0.0  0
 NRP  Var_01    CG2  CB2  CA2  C2    -0.87  30.0  2
 NRP  Var_02    CD1  CG2  CB2  CA2   -2.38  30.0  2
 NRP  Var_03    C1   N3   CA3  C     72.15  30.0  3
 NRP  Var_04    N2   C1   CA1  N    168.40  30.0  1
 NRP  Var_05    N3   CA3  C    O     16.59  30.0  1
 NRP  Var_06    CG1  CB1  CA1  C1   -74.20  30.0  3
 NRP  Var_07    CD3  CG1  CB1  CA1  177.71  30.0  3
 NRP  Var_08    HD3  CD3  CG1  CB1   63.23  30.0  3
 NRP  Var_09    HD4  CD4  CG1  CB1  -58.15  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
 NRP  plan-1  C1   0.020
 NRP  plan-1  C2   0.020
 NRP  plan-1  N2   0.020
 NRP  plan-1  O2   0.020
 NRP  plan-1  N3   0.020
 NRP  plan-1  CA2  0.020
 NRP  plan-1  CA3  0.020
 NRP  plan-1  CB2  0.020
 NRP  plan-1  CA1  0.020
 NRP  plan-2  CZ   0.020
 NRP  plan-2  CB2  0.020
 NRP  plan-2  CD1  0.020
 NRP  plan-2  CD2  0.020
 NRP  plan-2  CE1  0.020
 NRP  plan-2  CE2  0.020
 NRP  plan-2  CG2  0.020
 NRP  plan-2  HD1  0.020
 NRP  plan-2  HD2  0.020
 NRP  plan-2  HE1  0.020
 NRP  plan-2  HE2  0.020
 NRP  plan-2  OH   0.020
 NRP  plan-3  C    0.020
 NRP  plan-3  O    0.020
 NRP  plan-3  OXT  0.020
 NRP  plan-3  CA3  0.020
 NRP  plan-3  HXT  0.020
 NRP  plan-4  N    0.020
 NRP  plan-4  C1   0.020
 NRP  plan-4  HN   0.020
 NRP  plan-4  CA1  0.020
 NRP  plan-4  CB1  0.020

