# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 07:22:26 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: [(4Z)-2-[(1S)-1-aminoethyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](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
 AYG  AYG  '[(4Z)-2-[(1S)-1-aminoethyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid'  L-peptide  35  21  .  2022-07-24  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AYG
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
 AYG  CA1   C  CH1    0  -0.125   2.0006  -2.2485   0.5523
 AYG  CA2   C  CR5    0  -0.024  -0.1079   0.6488   0.2218
 AYG  CA3   C  CH2    0  -0.468   3.4821   0.4482   0.7736
 AYG  CB1   C  CH3    0  -0.665   2.5935  -2.6106  -0.8108
 AYG  CB2   C  C1     0  -0.295  -1.2596   1.3264   0.0520
 AYG  CG2   C  CR6    0   0.105  -2.6067   0.8201  -0.0982
 AYG  CD1   C  CR16   0  -0.360  -3.6445   1.7390  -0.3082
 AYG  CD2   C  CR16   0  -0.300  -2.9489  -0.5376  -0.0169
 AYG  CE1   C  CR16   0  -0.342  -4.9604   1.3387  -0.4260
 AYG  CE2   C  CR16   0  -0.323  -4.2623  -0.9491  -0.1274
 AYG  CZ    C  CR6    0   0.351  -5.2807  -0.0146  -0.3258
 AYG  OH    O  OH1    0  -0.660  -6.5740  -0.3612  -0.4122
 AYG  C1    C  CR5    0   0.565   1.3443  -0.9045   0.4720
 AYG  N1    N  NH2    0  -0.792   1.0225  -3.2501   0.9317
 AYG  C2    C  CR5    0   0.526   1.1971   1.3169   0.4287
 AYG  N2    N  N      0  -0.519   0.0838  -0.7250   0.2610
 AYG  O2    O  O      0  -0.347   1.4838   2.4950   0.4817
 AYG  C3    C  C      0   0.391   4.2304   0.7712  -0.5424
 AYG  N3    N  NR5    0  -0.544   2.0623   0.2636   0.6133
 AYG  O3    O  O      0  -0.492   3.5622   0.7977  -1.5900
 AYG  OXT   O  OC    -1  -0.742   5.4498   0.9692  -0.3943
 AYG  HA1   H  HCH1   0   0.288   2.8277  -2.1727   1.2720
 AYG  HA31  H  HCH2   0   0.307   3.9120  -0.4383   1.2413
 AYG  HA32  H  HCH2   0   0.306   3.6405   1.2669   1.4785
 AYG  HB11  H  HCH3   0   0.174   1.7889  -2.7551  -1.5316
 AYG  HB12  H  HCH3   0   0.235   3.2516  -1.8316  -1.1909
 AYG  HB13  H  HCH3   0   0.281   3.1646  -3.5370  -0.7384
 AYG  HB2   H  H      0   0.271  -1.1632   2.4080   0.0385
 AYG  HD1   H  HCR6   0   0.231  -3.4123   2.7951  -0.3775
 AYG  HD2   H  HCR6   0   0.332  -2.1738  -1.2755   0.1366
 AYG  HE1   H  HCR6   0   0.270  -5.7441   2.0686  -0.5843
 AYG  HE2   H  HCR6   0   0.232  -4.5003  -2.0045  -0.0508
 AYG  HOH   H  HOH1   0   0.471  -6.6756  -1.3173  -0.3483
 AYG  HN11  H  HNH2   0   0.333   1.4965  -4.1416   1.0130
 AYG  H2    H  HNH2   0   0.332   0.6521  -3.0447   1.8509

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
 AYG  CA1  CB1   single    1.530  0.020  1.530
 AYG  CA1  C1    single    1.498  0.020  1.498
 AYG  CA1  N1    single    1.450  0.020  1.450
 AYG  CA1  HA1   single    0.970  0.020  1.090
 AYG  CA2  CB2   double    1.347  0.020  1.347
 AYG  CA2  C2    single    1.481  0.020  1.481
 AYG  CA2  N2    single    1.388  0.020  1.388
 AYG  CA3  C3    single    1.548  0.020  1.548
 AYG  CA3  N3    single    1.441  0.020  1.441
 AYG  CA3  HA31  single    0.970  0.020  1.090
 AYG  CA3  HA32  single    0.970  0.020  1.090
 AYG  CB1  HB11  single    0.970  0.020  1.090
 AYG  CB1  HB12  single    0.970  0.020  1.090
 AYG  CB1  HB13  single    0.970  0.020  1.090
 AYG  CB2  CG2   single    1.447  0.020  1.447
 AYG  CB2  HB2   single    0.930  0.020  1.080
 AYG  CG2  CD1   aromatic  1.402  0.020  1.402
 AYG  CG2  CD2   aromatic  1.403  0.020  1.403
 AYG  CD1  CE1   aromatic  1.381  0.020  1.381
 AYG  CD1  HD1   single    0.930  0.020  1.080
 AYG  CD2  CE2   aromatic  1.381  0.020  1.381
 AYG  CD2  HD2   single    0.930  0.020  1.080
 AYG  CE1  CZ    aromatic  1.394  0.020  1.394
 AYG  CE1  HE1   single    0.930  0.020  1.080
 AYG  CE2  CZ    aromatic  1.396  0.020  1.396
 AYG  CE2  HE2   single    0.930  0.020  1.080
 AYG  CZ   OH    single    1.342  0.020  1.342
 AYG  OH   HOH   single    0.850  0.020  0.980
 AYG  C1   N2    double    1.291  0.020  1.291
 AYG  C1   N3    single    1.378  0.020  1.378
 AYG  N1   HN11  single    0.890  0.020  1.040
 AYG  N1   H2    single    0.890  0.020  1.040
 AYG  C2   O2    double    1.214  0.020  1.214
 AYG  C2   N3    single    1.375  0.020  1.375
 AYG  C3   O3    deloc     1.243  0.020  1.243
 AYG  C3   OXT   deloc     1.244  0.020  1.244

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
 AYG  HA1   CA1  N1    112.56  3.000
 AYG  HA1   CA1  C1    107.64  3.000
 AYG  N1    CA1  C1    109.77  3.000
 AYG  HA1   CA1  CB1   107.95  3.000
 AYG  N1    CA1  CB1   109.33  3.000
 AYG  C1    CA1  CB1   109.54  3.000
 AYG  N2    CA2  C2    108.73  3.000
 AYG  N2    CA2  CB2   128.30  3.000
 AYG  C2    CA2  CB2   122.97  3.000
 AYG  HA32  CA3  HA31  105.99  3.000
 AYG  HA32  CA3  N3    108.11  3.000
 AYG  HA31  CA3  N3    109.39  3.000
 AYG  HA32  CA3  C3    108.80  3.000
 AYG  HA31  CA3  C3    110.10  3.000
 AYG  N3    CA3  C3    114.11  3.000
 AYG  HB13  CB1  HB12  108.33  3.000
 AYG  HB13  CB1  HB11  108.53  3.000
 AYG  HB12  CB1  HB11  108.08  3.000
 AYG  HB13  CB1  CA1   110.17  3.000
 AYG  HB12  CB1  CA1   112.09  3.000
 AYG  HB11  CB1  CA1   109.54  3.000
 AYG  HB2   CB2  CG2   115.46  3.000
 AYG  HB2   CB2  CA2   115.26  3.000
 AYG  CG2   CB2  CA2   129.28  3.000
 AYG  CD2   CG2  CD1   117.55  3.000
 AYG  CD2   CG2  CB2   124.05  3.000
 AYG  CD1   CG2  CB2   118.38  3.000
 AYG  HD1   CD1  CE1   118.78  3.000
 AYG  HD1   CD1  CG2   119.33  3.000
 AYG  CE1   CD1  CG2   121.89  3.000
 AYG  HD2   CD2  CE2   119.33  3.000
 AYG  HD2   CD2  CG2   119.61  3.000
 AYG  CE2   CD2  CG2   121.06  3.000
 AYG  HE1   CE1  CZ    119.91  3.000
 AYG  HE1   CE1  CD1   120.46  3.000
 AYG  CZ    CE1  CD1   119.62  3.000
 AYG  HE2   CE2  CZ    120.08  3.000
 AYG  HE2   CE2  CD2   119.55  3.000
 AYG  CZ    CE2  CD2   120.38  3.000
 AYG  OH    CZ   CE2   122.64  3.000
 AYG  OH    CZ   CE1   117.87  3.000
 AYG  CE2   CZ   CE1   119.49  3.000
 AYG  HOH   OH   CZ    110.71  3.000
 AYG  N3    C1   N2    114.06  3.000
 AYG  N3    C1   CA1   121.78  3.000
 AYG  N2    C1   CA1   124.16  3.000
 AYG  H2    N1   HN11  106.08  3.000
 AYG  H2    N1   CA1   110.14  3.000
 AYG  HN11  N1   CA1   108.25  3.000
 AYG  N3    C2   O2    126.08  3.000
 AYG  N3    C2   CA2   103.16  3.000
 AYG  O2    C2   CA2   130.72  3.000
 AYG  C1    N2   CA2   106.09  3.000
 AYG  OXT   C3   O3    128.60  3.000
 AYG  OXT   C3   CA3   113.94  3.000
 AYG  O3    C3   CA3   117.46  3.000
 AYG  C2    N3   C1    107.91  3.000
 AYG  C2    N3   CA3   122.46  3.000
 AYG  C1    N3   CA3   129.30  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
 AYG  CONST_01  CZ   CE1  CD1  CG2     0.00   0.0  0
 AYG  CONST_02  CZ   CE2  CD2  CG2     0.00   0.0  0
 AYG  CONST_03  CE2  CD2  CG2  CD1     0.00   0.0  0
 AYG  CONST_04  CE2  CZ   CE1  CD1     0.00   0.0  0
 AYG  CONST_05  CE1  CD1  CG2  CD2     0.00   0.0  0
 AYG  CONST_06  CE1  CZ   CE2  CD2     0.00   0.0  0
 AYG  CONST_07  C1   N3   C2   CA2     0.00   0.0  0
 AYG  CONST_08  N3   C1   N2   CA2     0.00   0.0  0
 AYG  CONST_09  C2   CA2  N2   C1      0.00   0.0  0
 AYG  CONST_10  N2   C1   N3   C2      0.00   0.0  0
 AYG  CONST_11  N3   C2   CA2  N2      0.00   0.0  0
 AYG  CONST_12  CE1  CD1  CG2  CB2   180.00   0.0  0
 AYG  CONST_13  CE2  CD2  CG2  CB2   180.00   0.0  0
 AYG  CONST_14  OH   CZ   CE1  CD1   180.00   0.0  0
 AYG  CONST_15  OH   CZ   CE2  CD2   180.00   0.0  0
 AYG  CONST_16  CA2  N2   C1   CA1   180.00   0.0  0
 AYG  CONST_17  C2   N3   C1   CA1   180.00   0.0  0
 AYG  CONST_18  CA3  N3   C2   CA2   180.00   0.0  0
 AYG  CONST_19  N2   C1   N3   CA3   180.00   0.0  0
 AYG  CONST_20  O2   C2   N3   C1    180.00   0.0  0
 AYG  CONST_21  HE1  CE1  CD1  CG2   180.00   0.0  0
 AYG  CONST_22  HE2  CE2  CD2  CG2   180.00   0.0  0
 AYG  CONST_23  HD2  CD2  CG2  CD1   180.00   0.0  0
 AYG  CONST_24  HD1  CD1  CG2  CD2   180.00   0.0  0
 AYG  CONST_25  CA3  N3   C1   CA1     0.00   0.0  0
 AYG  CONST_26  O2   C2   N3   CA3     0.00   0.0  0
 AYG  Var_01    CD1  CG2  CB2  CA2  -177.91  30.0  2
 AYG  Var_02    C2   CA2  CB2  CG2  -176.89  30.0  2
 AYG  Var_03    C3   CA3  N3   C1     96.73  30.0  2
 AYG  Var_04    O3   C3   CA3  N3     -2.20  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
 AYG  chir_01  CA1  CB1  C1  N1  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
 AYG  plan-1  CA1  0.020
 AYG  plan-1  CA2  0.020
 AYG  plan-1  CA3  0.020
 AYG  plan-1  CB2  0.020
 AYG  plan-1  C1   0.020
 AYG  plan-1  C2   0.020
 AYG  plan-1  N2   0.020
 AYG  plan-1  O2   0.020
 AYG  plan-1  N3   0.020
 AYG  plan-2  CB2  0.020
 AYG  plan-2  CG2  0.020
 AYG  plan-2  CD1  0.020
 AYG  plan-2  CD2  0.020
 AYG  plan-2  CE1  0.020
 AYG  plan-2  CE2  0.020
 AYG  plan-2  CZ   0.020
 AYG  plan-2  OH   0.020
 AYG  plan-2  HD1  0.020
 AYG  plan-2  HD2  0.020
 AYG  plan-2  HE1  0.020
 AYG  plan-2  HE2  0.020
 AYG  plan-3  CA3  0.020
 AYG  plan-3  C3   0.020
 AYG  plan-3  O3   0.020
 AYG  plan-3  OXT  0.020

