# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 10:40:58 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: {(4Z)-2-[(1S)-1,5-diaminopentyl]-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: NCCCC[C@H](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
 CR7  CR7  '{(4Z)-2-[(1S)-1,5-diaminopentyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid'  L-peptide  47  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
;

data_comp_CR7
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
 CR7  N1    N  NH2   0  -0.773  -2.0763   0.3635   1.9090
 CR7  CA1   C  CH1   0  -0.233  -0.7208   0.8455   2.1458
 CR7  CB1   C  CH2   0  -0.396  -0.1797   0.3071   3.4666
 CR7  CG1   C  CH2   0  -0.423  -0.9402   0.8487   4.6688
 CR7  C1    C  CR5   0   0.574   0.1917   0.5007   1.0021
 CR7  N2    N  N     0  -0.478   1.0091  -0.4925   0.9872
 CR7  N3    N  NR5   0  -0.567   0.1474   1.1906  -0.1985
 CR7  C2    C  CR5   0   0.535   1.0603   0.6171  -1.0616
 CR7  O2    O  O     0  -0.447   1.3136   1.0007  -2.1853
 CR7  CA2   C  CR5   0   0.088   1.5996  -0.5061  -0.2704
 CR7  CA3   C  CH2   0  -0.472  -0.5302   2.4200  -0.4704
 CR7  C3    C  C     0   0.550   0.2516   3.6096   0.0478
 CR7  O3    O  O     0  -0.426   1.2905   3.5210   0.6458
 CR7  CB2   C  C1    0  -0.382   2.5308  -1.3574  -0.7465
 CR7  CG2   C  CR6   0   0.132   3.1720  -2.4767  -0.0966
 CR7  CD1   C  CR16  0  -0.298   2.9076  -2.8832   1.2198
 CR7  CD2   C  CR16  0  -0.284   4.1306  -3.2007  -0.8211
 CR7  CE1   C  CR16  0  -0.361   3.5733  -3.9547   1.7800
 CR7  CE2   C  CR16  0  -0.331   4.8019  -4.2731  -0.2709
 CR7  CZ    C  CR6   0   0.364   4.5286  -4.6577   1.0420
 CR7  OH    O  OH1   0  -0.618   5.2057  -5.6996   1.5436
 CR7  CD    C  CH2   0  -0.429  -0.4164   0.2991   5.9888
 CR7  CE    C  CH2   0  -0.272  -1.1311   0.8906   7.1935
 CR7  NZ    N  NH2   0  -0.801  -0.5958   0.3551   8.4373
 CR7  O1    O  OH1   0  -0.583  -0.3637   4.7422  -0.2419
 CR7  HN11  H  HNH2  0   0.359  -2.5240   0.8550   1.1463
 CR7  HN12  H  HNH2  0   0.351  -2.0596  -0.6171   1.6565
 CR7  HA1   H  HCH1  0   0.257  -0.7735   1.9362   2.2289
 CR7  HB11  H  HCH2  0   0.225  -0.2165  -0.7864   3.4562
 CR7  HB12  H  HCH2  0   0.229   0.8763   0.5745   3.5551
 CR7  HG11  H  HCH2  0   0.210  -0.8635   1.9421   4.6769
 CR7  HG12  H  HCH2  0   0.221  -2.0031   0.6179   4.5653
 CR7  HA31  H  HCH2  0   0.317  -1.5317   2.4226  -0.0380
 CR7  HA32  H  HCH2  0   0.328  -0.6680   2.5200  -1.5487
 CR7  HB2   H  H     0   0.268   2.8508  -1.1679  -1.7666
 CR7  HD1   H  HCR6  0   0.282   2.1752  -2.3511   1.8099
 CR7  HD2   H  HCR6  0   0.263   4.3537  -2.9112  -1.8408
 CR7  HE1   H  HCR6  0   0.278   3.3535  -4.2470   2.8005
 CR7  HE2   H  HCR6  0   0.271   5.5396  -4.8139  -0.8499
 CR7  HOH   H  HOH1  0   0.480   4.9482  -5.8669   2.4577
 CR7  HD1A  H  HCH2  0   0.211  -0.5287  -0.7912   5.9997
 CR7  HD2A  H  HCH2  0   0.212   0.6562   0.4989   6.0770
 CR7  HE1A  H  HCH2  0   0.186  -2.2137   0.7323   7.0777
 CR7  HE2A  H  HCH2  0   0.210  -0.9824   1.9742   7.1973
 CR7  HNZ1  H  HNH2  0   0.336  -0.8235  -0.6297   8.5021
 CR7  HNZ2  H  HNH2  0   0.345  -1.0618   0.7929   9.2215
 CR7  HO1   H  HOH1  0   0.490   0.1417   5.4990   0.0922

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
 CR7  N1   CA1   single    1.458  0.020  1.458
 CR7  N1   HN11  single    0.890  0.020  1.040
 CR7  N1   HN12  single    0.890  0.020  1.040
 CR7  CA1  CB1   single    1.526  0.020  1.526
 CR7  CA1  C1    single    1.503  0.020  1.503
 CR7  CA1  HA1   single    0.970  0.020  1.090
 CR7  CB1  CG1   single    1.522  0.020  1.522
 CR7  CB1  HB11  single    0.970  0.020  1.090
 CR7  CB1  HB12  single    0.970  0.020  1.090
 CR7  CG1  CD    single    1.523  0.020  1.523
 CR7  CG1  HG11  single    0.970  0.020  1.090
 CR7  CG1  HG12  single    0.970  0.020  1.090
 CR7  C1   N2    double    1.286  0.020  1.286
 CR7  C1   N3    single    1.385  0.020  1.385
 CR7  N2   CA2   single    1.389  0.020  1.389
 CR7  N3   C2    single    1.381  0.020  1.381
 CR7  N3   CA3   single    1.430  0.020  1.430
 CR7  C2   O2    double    1.214  0.020  1.214
 CR7  C2   CA2   single    1.476  0.020  1.476
 CR7  CA2  CB2   double    1.349  0.020  1.349
 CR7  CA3  C3    single    1.515  0.020  1.515
 CR7  CA3  HA31  single    0.970  0.020  1.090
 CR7  CA3  HA32  single    0.970  0.020  1.090
 CR7  C3   O3    double    1.202  0.020  1.202
 CR7  C3   O1    single    1.321  0.020  1.321
 CR7  CB2  CG2   single    1.444  0.020  1.444
 CR7  CB2  HB2   single    0.930  0.020  1.080
 CR7  CG2  CD1   aromatic  1.403  0.020  1.403
 CR7  CG2  CD2   aromatic  1.403  0.020  1.403
 CR7  CD1  CE1   aromatic  1.380  0.020  1.380
 CR7  CD1  HD1   single    0.930  0.020  1.080
 CR7  CD2  CE2   aromatic  1.380  0.020  1.380
 CR7  CD2  HD2   single    0.930  0.020  1.080
 CR7  CE1  CZ    aromatic  1.397  0.020  1.397
 CR7  CE1  HE1   single    0.930  0.020  1.080
 CR7  CE2  CZ    aromatic  1.395  0.020  1.395
 CR7  CE2  HE2   single    0.930  0.020  1.080
 CR7  CZ   OH    single    1.340  0.020  1.340
 CR7  OH   HOH   single    0.850  0.020  0.980
 CR7  CD   CE    single    1.521  0.020  1.521
 CR7  CD   HD1A  single    0.970  0.020  1.090
 CR7  CD   HD2A  single    0.970  0.020  1.090
 CR7  CE   NZ    single    1.456  0.020  1.456
 CR7  CE   HE1A  single    0.970  0.020  1.090
 CR7  CE   HE2A  single    0.970  0.020  1.090
 CR7  NZ   HNZ1  single    0.890  0.020  1.040
 CR7  NZ   HNZ2  single    0.890  0.020  1.040
 CR7  O1   HO1   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
 CR7  HN12  N1   HN11  106.84  3.000
 CR7  HN12  N1   CA1   110.20  3.000
 CR7  HN11  N1   CA1   111.92  3.000
 CR7  HA1   CA1  C1    108.38  3.000
 CR7  HA1   CA1  CB1   107.63  3.000
 CR7  C1    CA1  CB1   111.25  3.000
 CR7  HA1   CA1  N1    107.27  3.000
 CR7  C1    CA1  N1    111.41  3.000
 CR7  CB1   CA1  N1    110.72  3.000
 CR7  HB12  CB1  HB11  106.14  3.000
 CR7  HB12  CB1  CG1   109.37  3.000
 CR7  HB11  CB1  CG1   110.26  3.000
 CR7  HB12  CB1  CA1   109.05  3.000
 CR7  HB11  CB1  CA1   109.43  3.000
 CR7  CG1   CB1  CA1   112.39  3.000
 CR7  HG12  CG1  HG11  106.24  3.000
 CR7  HG12  CG1  CD    109.91  3.000
 CR7  HG11  CG1  CD    109.24  3.000
 CR7  HG12  CG1  CB1   109.63  3.000
 CR7  HG11  CG1  CB1   109.02  3.000
 CR7  CD    CG1  CB1   112.60  3.000
 CR7  N3    C1   N2    113.25  3.000
 CR7  N3    C1   CA1   121.72  3.000
 CR7  N2    C1   CA1   124.86  3.000
 CR7  CA2   N2   C1    106.74  3.000
 CR7  CA3   N3   C2    123.47  3.000
 CR7  CA3   N3   C1    127.45  3.000
 CR7  C2    N3   C1    108.28  3.000
 CR7  CA2   C2   O2    131.32  3.000
 CR7  CA2   C2   N3    102.86  3.000
 CR7  O2    C2   N3    125.82  3.000
 CR7  CB2   CA2  C2    122.92  3.000
 CR7  CB2   CA2  N2    128.26  3.000
 CR7  C2    CA2  N2    108.81  3.000
 CR7  HA32  CA3  HA31  105.98  3.000
 CR7  HA32  CA3  C3    109.34  3.000
 CR7  HA31  CA3  C3    109.65  3.000
 CR7  HA32  CA3  N3    109.05  3.000
 CR7  HA31  CA3  N3    111.21  3.000
 CR7  C3    CA3  N3    111.45  3.000
 CR7  O1    C3   O3    125.09  3.000
 CR7  O1    C3   CA3   110.97  3.000
 CR7  O3    C3   CA3   123.94  3.000
 CR7  HB2   CB2  CG2   115.29  3.000
 CR7  HB2   CB2  CA2   115.15  3.000
 CR7  CG2   CB2  CA2   129.56  3.000
 CR7  CD2   CG2  CD1   117.64  3.000
 CR7  CD2   CG2  CB2   118.09  3.000
 CR7  CD1   CG2  CB2   124.27  3.000
 CR7  HD1   CD1  CE1   119.18  3.000
 CR7  HD1   CD1  CG2   119.83  3.000
 CR7  CE1   CD1  CG2   120.99  3.000
 CR7  HD2   CD2  CE2   118.87  3.000
 CR7  HD2   CD2  CG2   119.28  3.000
 CR7  CE2   CD2  CG2   121.85  3.000
 CR7  HE1   CE1  CZ    120.02  3.000
 CR7  HE1   CE1  CD1   119.58  3.000
 CR7  CZ    CE1  CD1   120.40  3.000
 CR7  HE2   CE2  CZ    119.94  3.000
 CR7  HE2   CE2  CD2   120.45  3.000
 CR7  CZ    CE2  CD2   119.62  3.000
 CR7  OH    CZ   CE2   117.88  3.000
 CR7  OH    CZ   CE1   122.62  3.000
 CR7  CE2   CZ   CE1   119.50  3.000
 CR7  HOH   OH   CZ    110.78  3.000
 CR7  HD2A  CD   HD1A  106.33  3.000
 CR7  HD2A  CD   CE    109.01  3.000
 CR7  HD1A  CD   CE    109.32  3.000
 CR7  HD2A  CD   CG1   109.94  3.000
 CR7  HD1A  CD   CG1   109.41  3.000
 CR7  CE    CD   CG1   112.62  3.000
 CR7  HE2A  CE   HE1A  106.06  3.000
 CR7  HE2A  CE   NZ    108.14  3.000
 CR7  HE1A  CE   NZ    113.50  3.000
 CR7  HE2A  CE   CD    108.92  3.000
 CR7  HE1A  CE   CD    108.86  3.000
 CR7  NZ    CE   CD    111.16  3.000
 CR7  HNZ2  NZ   HNZ1  105.52  3.000
 CR7  HNZ2  NZ   CE    109.49  3.000
 CR7  HNZ1  NZ   CE    109.24  3.000
 CR7  HO1   O1   C3    110.55  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
 CR7  CONST_01  CZ    CE1  CD1  CG2     0.00   0.0  0
 CR7  CONST_02  CZ    CE2  CD2  CG2     0.00   0.0  0
 CR7  CONST_03  CE2   CD2  CG2  CD1     0.00   0.0  0
 CR7  CONST_04  CE2   CZ   CE1  CD1     0.00   0.0  0
 CR7  CONST_05  CE1   CD1  CG2  CD2     0.00   0.0  0
 CR7  CONST_06  CE1   CZ   CE2  CD2     0.00   0.0  0
 CR7  CONST_07  C2    CA2  N2   C1      0.00   0.0  0
 CR7  CONST_08  CA2   C2   N3   C1      0.00   0.0  0
 CR7  CONST_09  C2    N3   C1   N2      0.00   0.0  0
 CR7  CONST_10  N3    C2   CA2  N2      0.00   0.0  0
 CR7  CONST_11  CA2   N2   C1   N3      0.00   0.0  0
 CR7  CONST_12  CE1   CD1  CG2  CB2   180.00   0.0  0
 CR7  CONST_13  CE2   CD2  CG2  CB2   180.00   0.0  0
 CR7  CONST_14  OH    CZ   CE1  CD1   180.00   0.0  0
 CR7  CONST_15  OH    CZ   CE2  CD2   180.00   0.0  0
 CR7  CONST_16  CA2   N2   C1   CA1   180.00   0.0  0
 CR7  CONST_17  C2    N3   C1   CA1   180.00   0.0  0
 CR7  CONST_18  O2    C2   N3   C1    180.00   0.0  0
 CR7  CONST_19  CA3   N3   C1   N2    180.00   0.0  0
 CR7  CONST_20  CA3   N3   C2   CA2   180.00   0.0  0
 CR7  CONST_21  HE1   CE1  CD1  CG2   180.00   0.0  0
 CR7  CONST_22  HE2   CE2  CD2  CG2   180.00   0.0  0
 CR7  CONST_23  HD2   CD2  CG2  CD1   180.00   0.0  0
 CR7  CONST_24  HD1   CD1  CG2  CD2   180.00   0.0  0
 CR7  CONST_25  CA3   N3   C1   CA1     0.00   0.0  0
 CR7  CONST_26  CA3   N3   C2   O2      0.00   0.0  0
 CR7  CONST_27  HO1   O1   C3   CA3   180.00   0.0  0
 CR7  Var_01    CG2   CB2  CA2  N2     -0.16  30.0  2
 CR7  Var_02    CD1   CG2  CB2  CA2     0.12  30.0  2
 CR7  Var_03    C3    CA3  N3   C1     78.74  30.0  3
 CR7  Var_04    O3    C3   CA3  N3     -2.03  30.0  3
 CR7  Var_05    CD    CG1  CB1  CA1   179.20  30.0  3
 CR7  Var_06    CE    CD   CG1  CB1   177.24  30.0  3
 CR7  Var_07    NZ    CE   CD   CG1  -179.36  30.0  3
 CR7  Var_08    HNZ1  NZ   CE   CD    -67.23  30.0  3

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
 CR7  chir_01  CA1  N1  CB1  C1  negativ

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
 CR7  plan-1  CA1  0.020
 CR7  plan-1  C1   0.020
 CR7  plan-1  N2   0.020
 CR7  plan-1  N3   0.020
 CR7  plan-1  C2   0.020
 CR7  plan-1  O2   0.020
 CR7  plan-1  CA2  0.020
 CR7  plan-1  CA3  0.020
 CR7  plan-1  CB2  0.020
 CR7  plan-2  CB2  0.020
 CR7  plan-2  CG2  0.020
 CR7  plan-2  CD1  0.020
 CR7  plan-2  CD2  0.020
 CR7  plan-2  CE1  0.020
 CR7  plan-2  CE2  0.020
 CR7  plan-2  CZ   0.020
 CR7  plan-2  OH   0.020
 CR7  plan-2  HD1  0.020
 CR7  plan-2  HD2  0.020
 CR7  plan-2  HE1  0.020
 CR7  plan-2  HE2  0.020
 CR7  plan-3  CA3  0.020
 CR7  plan-3  C3   0.020
 CR7  plan-3  O3   0.020
 CR7  plan-3  O1   0.020
 CR7  plan-3  HO1  0.020

