# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 11:41:52 2022
#   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-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID"  L-peptide  46  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 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  -0.784  -1.9527   0.6032   1.5361
 CR7  CA1   C  CH1    0  -0.239  -0.6342   0.9430   2.0567
 CR7  CB1   C  CH2    0  -0.411  -0.2662   0.2959   3.3919
 CR7  CG1   C  CH2    0  -0.430  -1.2530   0.6461   4.4982
 CR7  C1    C  CR5    0   0.599   0.3661   0.6198   0.9881
 CR7  N2    N  N      0  -0.493   1.2504  -0.3150   1.0691
 CR7  N3    N  NR5    0  -0.534   0.3652   1.2880  -0.2180
 CR7  C2    C  CR5    0   0.521   1.3944   0.7919  -0.9776
 CR7  O2    O  O      0  -0.463   1.7323   1.1820  -2.0799
 CR7  CA2   C  CR5    0   0.091   1.9415  -0.2967  -0.1354
 CR7  CA3   C  CH2    0  -0.480  -0.3560   2.4958  -0.5226
 CR7  C3    C  C      0   0.416   0.2676   3.7578   0.1156
 CR7  O3    O  O      0  -0.593   1.2668   3.5952   0.8350
 CR7  CB2   C  C1     0  -0.395   2.9320  -1.1133  -0.5435
 CR7  CG2   C  CR6    0   0.133   3.5449  -2.2317   0.1400
 CR7  CD1   C  CR16   0  -0.286   4.5502  -2.9426  -0.5267
 CR7  CD2   C  CR16   0  -0.303   3.1916  -2.6603   1.4299
 CR7  CE1   C  CR16   0  -0.377   5.1784  -4.0298   0.0506
 CR7  CE2   C  CR16   0  -0.315   3.8128  -3.7435   2.0162
 CR7  CZ    C  CR6    0   0.357   4.8115  -4.4404   1.3309
 CR7  OH    O  OH1    0  -0.620   5.3781  -5.4890   1.9470
 CR7  CD    C  CH2    0  -0.425  -0.8527   0.0674   5.8496
 CR7  CE    C  CH2    0  -0.270  -1.8557   0.3955   6.9449
 CR7  NZ    N  NH2    0  -0.801  -1.4441  -0.1725   8.2214
 CR7  O1    O  OC    -1  -0.612  -0.3175   4.8207  -0.1610
 CR7  HN11  H  HNH2   0   0.362  -2.6702   1.0369   2.1015
 CR7  HN12  H  HNH2   0   0.349  -2.0989  -0.3978   1.5987
 CR7  HA1   H  HCH1   0   0.265  -0.6129   2.0295   2.1914
 CR7  HB11  H  HCH2   0   0.222  -0.2138  -0.7900   3.2685
 CR7  HB12  H  HCH2   0   0.222   0.7376   0.6196   3.6818
 CR7  HG11  H  HCH2   0   0.214  -1.3372   1.7354   4.5825
 CR7  HG12  H  HCH2   0   0.210  -2.2505   0.2806   4.2357
 CR7  HA31  H  HCH2   0   0.275  -1.3900   2.3777  -0.1967
 CR7  HA32  H  HCH2   0   0.266  -0.3798   2.6093  -1.6076
 CR7  HB2   H  H      0   0.262   3.3193  -0.9088  -1.5372
 CR7  HD1   H  HCR6   0   0.263   4.8442  -2.6387  -1.5241
 CR7  HD2   H  HCR6   0   0.279   2.4196  -2.1350   1.9743
 CR7  HE1   H  HCR6   0   0.276   5.9506  -4.5592  -0.4952
 CR7  HE2   H  HCR6   0   0.268   3.5286  -4.0604   3.0119
 CR7  HOH   H  HOH1   0   0.479   6.0417  -5.8990   1.3801
 CR7  HD1A  H  HCH2   0   0.211  -0.7558  -1.0208   5.7626
 CR7  HD2A  H  HCH2   0   0.213   0.1328   0.4441   6.1400
 CR7  HE1A  H  HCH2   0   0.186  -2.8543   0.0667   6.6211
 CR7  HE2A  H  HCH2   0   0.210  -1.9157   1.4816   7.0592
 CR7  HNZ1  H  HNH2   0   0.336  -1.4856  -1.1830   8.1633
 CR7  HNZ2  H  HNH2   0   0.345  -2.1146   0.0828   8.9354

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    1.529  0.020  1.529
 CR7  CA1  C1    single    1.499  0.020  1.499
 CR7  CA1  HA1   single    0.970  0.020  1.090
 CR7  CB1  CG1   single    1.523  0.020  1.523
 CR7  CB1  HB11  single    0.970  0.020  1.090
 CR7  CB1  HB12  single    0.970  0.020  1.090
 CR7  CG1  CD    single    1.524  0.020  1.524
 CR7  CG1  HG11  single    0.970  0.020  1.090
 CR7  CG1  HG12  single    0.970  0.020  1.090
 CR7  C1   N2    double    1.289  0.020  1.289
 CR7  C1   N3    single    1.379  0.020  1.379
 CR7  N2   CA2   single    1.389  0.020  1.389
 CR7  N3   C2    single    1.372  0.020  1.372
 CR7  N3   CA3   single    1.439  0.020  1.439
 CR7  C2   O2    double    1.217  0.020  1.217
 CR7  C2   CA2   single    1.481  0.020  1.481
 CR7  CA2  CB2   double    1.347  0.020  1.347
 CR7  CA3  C3    single    1.546  0.020  1.546
 CR7  CA3  HA31  single    0.970  0.020  1.090
 CR7  CA3  HA32  single    0.970  0.020  1.090
 CR7  C3   O3    deloc     1.242  0.020  1.242
 CR7  C3   O1    deloc     1.244  0.020  1.244
 CR7  CB2  CG2   single    1.447  0.020  1.447
 CR7  CB2  HB2   single    0.930  0.020  1.080
 CR7  CG2  CD1   aromatic  1.400  0.020  1.400
 CR7  CG2  CD2   aromatic  1.404  0.020  1.404
 CR7  CD1  CE1   aromatic  1.382  0.020  1.382
 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  1.394  0.020  1.394
 CR7  CE1  HE1   single    0.930  0.020  1.080
 CR7  CE2  CZ    aromatic  1.397  0.020  1.397
 CR7  CE2  HE2   single    0.930  0.020  1.080
 CR7  CZ   OH    single    1.342  0.020  1.342
 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    1.457  0.020  1.457
 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

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  106.66  3.000
 CR7  HN12  N1   CA1   109.79  3.000
 CR7  HN11  N1   CA1   110.00  3.000
 CR7  HA1   CA1  C1    106.77  3.000
 CR7  HA1   CA1  CB1   107.93  3.000
 CR7  C1    CA1  CB1   111.76  3.000
 CR7  HA1   CA1  N1    107.03  3.000
 CR7  C1    CA1  N1    107.38  3.000
 CR7  CB1   CA1  N1    115.54  3.000
 CR7  HB12  CB1  HB11  106.24  3.000
 CR7  HB12  CB1  CG1   109.51  3.000
 CR7  HB11  CB1  CG1   109.94  3.000
 CR7  HB12  CB1  CA1   109.10  3.000
 CR7  HB11  CB1  CA1   109.46  3.000
 CR7  CG1   CB1  CA1   112.40  3.000
 CR7  HG12  CG1  HG11  106.29  3.000
 CR7  HG12  CG1  CD    108.99  3.000
 CR7  HG11  CG1  CD    109.24  3.000
 CR7  HG12  CG1  CB1   109.85  3.000
 CR7  HG11  CG1  CB1   109.52  3.000
 CR7  CD    CG1  CB1   112.74  3.000
 CR7  N3    C1   N2    114.00  3.000
 CR7  N3    C1   CA1   121.24  3.000
 CR7  N2    C1   CA1   124.70  3.000
 CR7  CA2   N2   C1    106.10  3.000
 CR7  CA3   N3   C2    124.20  3.000
 CR7  CA3   N3   C1    126.31  3.000
 CR7  C2    N3   C1    107.98  3.000
 CR7  CA2   C2   O2    130.39  3.000
 CR7  CA2   C2   N3    103.18  3.000
 CR7  O2    C2   N3    126.43  3.000
 CR7  CB2   CA2  C2    123.02  3.000
 CR7  CB2   CA2  N2    128.37  3.000
 CR7  C2    CA2  N2    108.60  3.000
 CR7  HA32  CA3  HA31  106.72  3.000
 CR7  HA32  CA3  C3    109.54  3.000
 CR7  HA31  CA3  C3    110.34  3.000
 CR7  HA32  CA3  N3    107.98  3.000
 CR7  HA31  CA3  N3    108.72  3.000
 CR7  C3    CA3  N3    113.30  3.000
 CR7  O1    C3   O3    128.23  3.000
 CR7  O1    C3   CA3   114.58  3.000
 CR7  O3    C3   CA3   117.19  3.000
 CR7  HB2   CB2  CG2   115.26  3.000
 CR7  HB2   CB2  CA2   115.17  3.000
 CR7  CG2   CB2  CA2   129.56  3.000
 CR7  CD2   CG2  CD1   117.58  3.000
 CR7  CD2   CG2  CB2   124.28  3.000
 CR7  CD1   CG2  CB2   118.14  3.000
 CR7  HD1   CD1  CE1   118.81  3.000
 CR7  HD1   CD1  CG2   119.39  3.000
 CR7  CE1   CD1  CG2   121.79  3.000
 CR7  HD2   CD2  CE2   119.29  3.000
 CR7  HD2   CD2  CG2   119.60  3.000
 CR7  CE2   CD2  CG2   121.11  3.000
 CR7  HE1   CE1  CZ    120.42  3.000
 CR7  HE1   CE1  CD1   119.85  3.000
 CR7  CZ    CE1  CD1   119.73  3.000
 CR7  HE2   CE2  CZ    119.51  3.000
 CR7  HE2   CE2  CD2   120.16  3.000
 CR7  CZ    CE2  CD2   120.33  3.000
 CR7  OH    CZ   CE2   117.80  3.000
 CR7  OH    CZ   CE1   122.74  3.000
 CR7  CE2   CZ   CE1   119.46  3.000
 CR7  HOH   OH   CZ    110.67  3.000
 CR7  HD2A  CD   HD1A  106.45  3.000
 CR7  HD2A  CD   CE    109.18  3.000
 CR7  HD1A  CD   CE    109.25  3.000
 CR7  HD2A  CD   CG1   109.95  3.000
 CR7  HD1A  CD   CG1   109.26  3.000
 CR7  CE    CD   CG1   112.55  3.000
 CR7  HE2A  CE   HE1A  106.13  3.000
 CR7  HE2A  CE   NZ    108.12  3.000
 CR7  HE1A  CE   NZ    113.45  3.000
 CR7  HE2A  CE   CD    109.01  3.000
 CR7  HE1A  CE   CD    108.80  3.000
 CR7  NZ    CE   CD    111.14  3.000
 CR7  HNZ2  NZ   HNZ1  105.36  3.000
 CR7  HNZ2  NZ   CE    109.43  3.000
 CR7  HNZ1  NZ   CE    109.10  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  HE2   CE2  CZ   CE1   180.00   0.0  0
 CR7  CONST_26  HE1   CE1  CZ   CE2   180.00   0.0  0
 CR7  CONST_27  HD1   CD1  CE1  CZ    180.00   0.0  0
 CR7  CONST_28  HD2   CD2  CE2  CZ    180.00   0.0  0
 CR7  CONST_29  CA3   N3   C1   CA1     0.00   0.0  0
 CR7  CONST_30  CA3   N3   C2   O2      0.00   0.0  0
 CR7  Var_01    CG2   CB2  CA2  N2      0.45   0.0  2
 CR7  Var_02    CG2   CB2  CA2  C2   -178.24   0.0  2
 CR7  Var_03    CD1   CG2  CB2  CA2   178.65  30.0  2
 CR7  Var_04    CD2   CG2  CB2  CA2    -0.89  30.0  2
 CR7  Var_05    C3    CA3  N3   C1     74.32  30.0  3
 CR7  Var_06    C3    CA3  N3   C2    -89.92  30.0  3
 CR7  Var_07    HB2   CB2  CA2  N2    179.65   0.0  2
 CR7  Var_08    HB2   CB2  CA2  C2      0.95   0.0  2
 CR7  Var_09    HA31  CA3  N3   C1    -48.74  30.0  3
 CR7  Var_10    HA32  CA3  N3   C1   -164.16  30.0  3
 CR7  Var_11    HA31  CA3  N3   C2    147.03  30.0  3
 CR7  Var_12    HA32  CA3  N3   C2     31.60  30.0  3
 CR7  Var_13    HB2   CB2  CG2  CD1    -0.55  30.0  2
 CR7  Var_14    HB2   CB2  CG2  CD2   179.91  30.0  2
 CR7  Var_15    O3    C3   CA3  N3     -2.19  30.0  3
 CR7  Var_16    O1    C3   CA3  N3    178.23  30.0  3
 CR7  Var_17    CD    CG1  CB1  CA1  -176.89  30.0  3
 CR7  Var_18    CE    CD   CG1  CB1  -178.82  30.0  3
 CR7  Var_19    NZ    CE   CD   CG1   179.96  30.0  3
 CR7  Var_20    HG11  CG1  CB1  CA1   -55.03  30.0  3
 CR7  Var_21    HG12  CG1  CB1  CA1    61.35  30.0  3
 CR7  Var_22    HD1A  CD   CG1  CB1   -57.26  30.0  3
 CR7  Var_23    HD2A  CD   CG1  CB1    59.23  30.0  3
 CR7  Var_24    HE1A  CE   CD   CG1    54.34  30.0  3
 CR7  Var_25    HE2A  CE   CD   CG1   -60.97  30.0  3
 CR7  Var_26    HA31  CA3  C3   O3    119.97  30.0  2
 CR7  Var_27    HA32  CA3  C3   O3   -122.83  30.0  2
 CR7  Var_28    HB11  CB1  CG1  CD     60.92  30.0  2
 CR7  Var_29    HB12  CB1  CG1  CD    -55.46  30.0  2
 CR7  Var_30    HNZ1  NZ   CE   CD    -66.79  30.0  3
 CR7  Var_31    HNZ2  NZ   CE   CD    178.42  30.0  3
 CR7  Var_32    HG11  CG1  CD   CE     59.17  30.0  1
 CR7  Var_33    HG12  CG1  CD   CE    -56.57  30.0  1
 CR7  Var_34    HD1A  CD   CE   NZ     58.40  30.0  2
 CR7  Var_35    HD2A  CD   CE   NZ    -57.65  30.0  2
 CR7  Var_36    HA31  CA3  C3   O1    -59.60  30.0  2
 CR7  Var_37    HA32  CA3  C3   O1     57.60  30.0  2

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-1  CG2  0.020
 CR7  plan-1  HB2  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

