# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 02:05:52 2022
#   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  "{4-[(4-hydroxyphenyl)methylidene]-2-[(1E)-3-methylbutanimidoyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid"  L-peptide  42  24  .  2022-09-22  2022-09-22
;
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   0.421  -2.0379  -3.4369  -0.7203
 NRP  N     N  N      0  -0.543  -4.0647  -1.1178  -0.1771
 NRP  O     O  O      0  -0.597  -1.5982  -2.9216  -1.7604
 NRP  C1    C  CR5    0   0.534  -1.8557  -0.2603  -0.1428
 NRP  C2    C  CR5    0   0.520   0.1197  -1.1227   0.4172
 NRP  N2    N  N      0  -0.476  -1.0428   0.7023  -0.4143
 NRP  O2    O  O      0  -0.461   0.9670  -1.9188   0.7851
 NRP  N3    N  NR5    0  -0.543  -1.2320  -1.3684   0.3957
 NRP  OXT   O  OC    -1  -0.621  -2.6490  -4.5146  -0.5948
 NRP  CZ    C  CR6    0   0.365   5.5076   1.0514   0.2651
 NRP  CA2   C  CR5    0   0.118   0.2344   0.2617  -0.0881
 NRP  CA3   C  CH2    0  -0.453  -1.7726  -2.6893   0.6029
 NRP  CB2   C  C1     0  -0.373   1.2894   1.0940  -0.2750
 NRP  CD1   C  CR16   0  -0.321   3.4019  -0.1007   0.4773
 NRP  CD2   C  CR16   0  -0.285   3.4742   2.1231  -0.4195
 NRP  CD3   C  CH3    0  -0.654  -4.2429   3.6278  -0.1580
 NRP  CD4   C  CH3    0  -0.660  -4.6890   1.8149   1.5182
 NRP  CE1   C  CR16   0  -0.314   4.7707  -0.0759   0.6375
 NRP  CE2   C  CR16   0  -0.377   4.8446   2.1577  -0.2664
 NRP  CG1   C  CH1    0  -0.240  -3.7934   2.2708   0.3719
 NRP  CG2   C  CR6    0   0.105   2.7117   0.9998  -0.0585
 NRP  HN    H  H      0   0.347  -5.0321  -0.8687  -0.3710
 NRP  HOH   H  HOH1   0   0.481   7.2415   1.8337   0.1293
 NRP  HA3   H  HCH2   0   0.263  -2.6809  -2.6331   1.1956
 NRP  HA3A  H  HCH2   0   0.260  -1.0383  -3.2475   1.1865
 NRP  HB1   H  HCH2   0   0.254  -3.1397   1.6317  -1.5816
 NRP  HB1A  H  HCH2   0   0.246  -4.7867   1.1576  -1.1875
 NRP  HB2   H  H      0   0.272   0.9809   2.0530  -0.6818
 NRP  HD1   H  HCR6   0   0.294   2.8591  -0.9852   0.7714
 NRP  HD2   H  HCR6   0   0.269   2.9775   2.9923  -0.8327
 NRP  HD3   H  HCH3   0   0.216  -5.2657   3.5808  -0.5399
 NRP  HD3A  H  HCH3   0   0.230  -4.2175   4.3829   0.6288
 NRP  HD3B  H  HCH3   0   0.227  -3.6010   3.9724  -0.9705
 NRP  HD4   H  HCH3   0   0.216  -5.7142   1.6562   1.1740
 NRP  HD4A  H  HCH3   0   0.229  -4.3447   0.8830   1.9691
 NRP  HD4B  H  HCH3   0   0.231  -4.7196   2.5663   2.3087
 NRP  HE1   H  HCR6   0   0.271   5.2826  -0.9353   1.0515
 NRP  HE2   H  HCR6   0   0.280   5.3986   3.0415  -0.5605
 NRP  HG1   H  HCH1   0   0.234  -2.7716   2.3746   0.7476
 NRP  OH    O  OH1    0  -0.614   6.8340   1.0161   0.4387
 NRP  CB1   C  CH2    0  -0.496  -3.7755   1.2522  -0.7794
 NRP  CA1   C  C      0   0.145  -3.3090  -0.1165  -0.3651

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   deloc     1.245  0.020  1.245
 NRP  N    CA1   double    1.268  0.020  1.268
 NRP  N    HN    single    0.890  0.020  1.040
 NRP  O    C     deloc     1.241  0.020  1.241
 NRP  C1   CA1   single    1.477  0.020  1.477
 NRP  C1   N2    double    1.289  0.020  1.289
 NRP  C2   CA2   single    1.478  0.020  1.478
 NRP  O2   C2    double    1.219  0.020  1.219
 NRP  N3   C1    single    1.381  0.020  1.381
 NRP  N3   C2    single    1.374  0.020  1.374
 NRP  OH   CZ    single    1.338  0.020  1.338
 NRP  OH   HOH   single    0.850  0.020  0.980
 NRP  CZ   CE2   aromatic  1.395  0.020  1.395
 NRP  CA1  CB1   single    1.504  0.020  1.504
 NRP  CA2  N2    single    1.390  0.020  1.390
 NRP  CA2  CB2   double    1.357  0.020  1.357
 NRP  CA3  C     single    1.543  0.020  1.543
 NRP  CA3  N3    single    1.442  0.020  1.442
 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  1.405  0.020  1.405
 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  1.397  0.020  1.397
 NRP  CE1  CD1   aromatic  1.378  0.020  1.378
 NRP  CE1  HE1   single    0.930  0.020  1.080
 NRP  CE2  CD2   aromatic  1.379  0.020  1.379
 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    1.442  0.020  1.442
 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   114.67  3.000
 NRP  CA3   C    O     117.17  3.000
 NRP  OXT   C    O     128.13  3.000
 NRP  HN    N    CA1   110.18  3.000
 NRP  CA1   C1   N3    125.53  3.000
 NRP  N3    C1   N2    113.37  3.000
 NRP  CA1   C1   N2    121.07  3.000
 NRP  CA2   C2   N3    103.79  3.000
 NRP  N3    C2   O2    124.86  3.000
 NRP  CA2   C2   O2    131.35  3.000
 NRP  CA2   N2   C1    107.06  3.000
 NRP  CA3   N3   C2    122.02  3.000
 NRP  CA3   N3   C1    128.44  3.000
 NRP  C2    N3   C1    107.88  3.000
 NRP  CE2   CZ   CE1   119.39  3.000
 NRP  CE1   CZ   OH    117.84  3.000
 NRP  CE2   CZ   OH    122.78  3.000
 NRP  CB2   CA2  N2    119.20  3.000
 NRP  CB2   CA2  C2    132.99  3.000
 NRP  N2    CA2  C2    107.81  3.000
 NRP  HA3A  CA3  HA3   107.29  3.000
 NRP  HA3A  CA3  N3    107.04  3.000
 NRP  HA3   CA3  N3    110.16  3.000
 NRP  HA3A  CA3  C     109.05  3.000
 NRP  HA3   CA3  C     110.45  3.000
 NRP  N3    CA3  C     112.65  3.000
 NRP  HB2   CB2  CG2   113.21  3.000
 NRP  CG2   CB2  CA2   134.94  3.000
 NRP  HB2   CB2  CA2   111.85  3.000
 NRP  HD1   CD1  CG2   119.93  3.000
 NRP  HD1   CD1  CE1   118.87  3.000
 NRP  CG2   CD1  CE1   121.20  3.000
 NRP  HD2   CD2  CG2   119.39  3.000
 NRP  CG2   CD2  CE2   122.06  3.000
 NRP  HD2   CD2  CE2   118.55  3.000
 NRP  HD3B  CD3  HD3A  107.74  3.000
 NRP  HD3B  CD3  HD3   107.69  3.000
 NRP  HD3A  CD3  HD3   107.67  3.000
 NRP  HD3B  CD3  CG1   111.50  3.000
 NRP  HD3A  CD3  CG1   111.01  3.000
 NRP  HD3   CD3  CG1   111.05  3.000
 NRP  HD4B  CD4  HD4A  107.32  3.000
 NRP  HD4B  CD4  HD4   107.56  3.000
 NRP  HD4A  CD4  HD4   107.58  3.000
 NRP  HD4B  CD4  CG1   110.82  3.000
 NRP  HD4A  CD4  CG1   112.38  3.000
 NRP  HD4   CD4  CG1   110.96  3.000
 NRP  HE1   CE1  CD1   119.98  3.000
 NRP  HE1   CE1  CZ    119.54  3.000
 NRP  CD1   CE1  CZ    120.48  3.000
 NRP  HE2   CE2  CD2   119.88  3.000
 NRP  HE2   CE2  CZ    120.47  3.000
 NRP  CD2   CE2  CZ    119.64  3.000
 NRP  HG1   CG1  CD4   108.60  3.000
 NRP  HG1   CG1  CD3   108.08  3.000
 NRP  CD4   CG1  CD3   110.75  3.000
 NRP  HG1   CG1  CB1   108.01  3.000
 NRP  CD4   CG1  CB1   111.83  3.000
 NRP  CD3   CG1  CB1   109.44  3.000
 NRP  CD2   CG2  CD1   117.23  3.000
 NRP  CD2   CG2  CB2   116.40  3.000
 NRP  CD1   CG2  CB2   126.37  3.000
 NRP  HOH   OH   CZ    110.78  3.000
 NRP  HB1A  CB1  HB1   107.10  3.000
 NRP  HB1A  CB1  CG1   109.01  3.000
 NRP  HB1   CB1  CG1   109.07  3.000
 NRP  HB1A  CB1  CA1   108.09  3.000
 NRP  HB1   CB1  CA1   109.76  3.000
 NRP  CG1   CB1  CA1   113.60  3.000
 NRP  CB1   CA1  C1    115.79  3.000
 NRP  CB1   CA1  N     125.05  3.000
 NRP  C1    CA1  N     119.14  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  HD2   CD2  CG2  CD1   180.00   0.0  0
 NRP  CONST_24  HD1   CD1  CG2  CD2   180.00   0.0  0
 NRP  CONST_25  HE2   CE2  CZ   CE1   180.00   0.0  0
 NRP  CONST_26  HE1   CE1  CZ   CE2   180.00   0.0  0
 NRP  CONST_27  HE1   CE1  CD1  CG2   180.00   0.0  0
 NRP  CONST_28  HE2   CE2  CD2  CG2   180.00   0.0  0
 NRP  CONST_29  CA3   N3   C2   O2      0.00   0.0  0
 NRP  CONST_30  CA3   N3   C1   CA1     0.00   0.0  0
 NRP  CONST_31  HN    N    CA1  C1    180.00   0.0  0
 NRP  CONST_32  HN    N    CA1  CB1     0.00   0.0  0
 NRP  Var_01    CG2   CB2  CA2  C2     -0.65   0.0  2
 NRP  Var_02    CG2   CB2  CA2  N2    179.77   0.0  2
 NRP  Var_03    CD1   CG2  CB2  CA2    -1.15  30.0  2
 NRP  Var_04    CD2   CG2  CB2  CA2   178.95  30.0  2
 NRP  Var_05    C1    N3   CA3  C      68.70  30.0  3
 NRP  Var_06    C2    N3   CA3  C     -94.77  30.0  3
 NRP  Var_07    N2    C1   CA1  N     174.96  30.0  2
 NRP  Var_08    N3    C1   CA1  N      -7.21  30.0  2
 NRP  Var_09    CB1   CA1  C1   N2     -6.27  30.0  2
 NRP  Var_10    CB1   CA1  C1   N3    171.56  30.0  2
 NRP  Var_11    HB2   CB2  CA2  C2    179.43   0.0  2
 NRP  Var_12    HB2   CB2  CA2  N2     -0.15   0.0  2
 NRP  Var_13    HA3   CA3  N3   C1    -55.10  30.0  2
 NRP  Var_14    HA3A  CA3  N3   C1   -171.45  30.0  2
 NRP  Var_15    HA3   CA3  N3   C2    141.43  30.0  2
 NRP  Var_16    HA3A  CA3  N3   C2     25.08  30.0  2
 NRP  Var_17    HB2   CB2  CG2  CD1   178.77  30.0  2
 NRP  Var_18    HB2   CB2  CG2  CD2    -1.13  30.0  2
 NRP  Var_19    N3    CA3  C    O       9.74  30.0  2
 NRP  Var_20    CG1   CB1  CA1  C1    -75.19  30.0  3
 NRP  Var_21    OXT   C    CA3  N3   -171.94  30.0  3
 NRP  Var_22    HB1   CB1  CA1  C1     47.21  30.0  3
 NRP  Var_23    HB1A  CB1  CA1  C1    163.70  30.0  3
 NRP  Var_24    CG1   CB1  CA1  N     103.50  30.0  3
 NRP  Var_25    CD3   CG1  CB1  CA1   178.50  30.0  3
 NRP  Var_26    CD4   CG1  CB1  CA1   -58.39  30.0  3
 NRP  Var_27    HB1   CB1  CA1  N    -134.10  30.0  3
 NRP  Var_28    HB1A  CB1  CA1  N     -17.61  30.0  3
 NRP  Var_29    HA3   CA3  C    O     133.39  30.0  2
 NRP  Var_30    HA3A  CA3  C    O    -108.94  30.0  2
 NRP  Var_31    HA3   CA3  C    OXT   -48.30  30.0  2
 NRP  Var_32    HA3A  CA3  C    OXT    69.37  30.0  2
 NRP  Var_33    HG1   CG1  CB1  CA1    61.06  30.0  3
 NRP  Var_34    HD3   CD3  CG1  CB1    63.05  30.0  3
 NRP  Var_35    HD3A  CD3  CG1  CB1  -177.19  30.0  3
 NRP  Var_36    HD3B  CD3  CG1  CB1   -57.05  30.0  3
 NRP  Var_37    HD4   CD4  CG1  CB1   -58.41  30.0  3
 NRP  Var_38    HD4A  CD4  CG1  CB1    62.10  30.0  3
 NRP  Var_39    HD4B  CD4  CG1  CB1  -177.84  30.0  3
 NRP  Var_40    HB1   CB1  CG1  CD3    55.72  30.0  2
 NRP  Var_41    HB1A  CB1  CG1  CD3   -60.91  30.0  2
 NRP  Var_42    HD4   CD4  CG1  CD3    63.95  30.0  3
 NRP  Var_43    HD4A  CD4  CG1  CD3  -175.54  30.0  3
 NRP  Var_44    HD4B  CD4  CG1  CD3   -55.48  30.0  3
 NRP  Var_45    HB1   CB1  CG1  CD4   178.83  30.0  2
 NRP  Var_46    HB1A  CB1  CG1  CD4    62.20  30.0  2
 NRP  Var_47    HD3   CD3  CG1  CD4   -60.69  30.0  3
 NRP  Var_48    HD3A  CD3  CG1  CD4    59.07  30.0  3
 NRP  Var_49    HD3B  CD3  CG1  CD4   179.21  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  CG2  0.020
 NRP  plan-1  HB2  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-4  N    0.020
 NRP  plan-4  C1   0.020
 NRP  plan-4  HN   0.020
 NRP  plan-4  CB1  0.020
 NRP  plan-4  CA1  0.020

