# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 00:47:21 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: (3S)-3-amino-3-{(4Z)-1-(carboxymethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-2-yl}propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC(O)=O)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
 DYG  DYG  '(3S)-3-amino-3-{(4Z)-1-(carboxymethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-2-yl}propanoic acid'  L-peptide  39  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 PERFECT
;

data_comp_DYG
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
 DYG  N     N  NH2   0  -0.767   1.1862   2.3377  -1.5543
 DYG  OD2   O  OH1   0  -0.588   3.4699   3.7180   1.1253
 DYG  OD1   O  O     0  -0.443   4.3129   2.7507  -0.6983
 DYG  CG1   C  C     0   0.558   3.5038   2.7740   0.1948
 DYG  CB1   C  CH2   0  -0.574   2.4506   1.7201   0.4152
 DYG  CA1   C  CH1   0  -0.225   1.8648   1.2366  -0.9130
 DYG  C1    C  CR5   0   0.544   0.9756   0.0522  -0.6423
 DYG  N2    N  N     0  -0.478  -0.2916   0.1512  -0.4488
 DYG  N3    N  NR5   0  -0.564   1.4485  -1.2418  -0.5408
 DYG  C2    C  CR5   0   0.540   0.3840  -2.0661  -0.2269
 DYG  O2    O  O     0  -0.445   0.4519  -3.2659  -0.0566
 DYG  CA2   C  CR5   0   0.090  -0.7555  -1.1306  -0.1802
 DYG  CA3   C  CH2   0  -0.463   2.7829  -1.7343  -0.6956
 DYG  CB2   C  C1    0  -0.380  -2.0178  -1.5236   0.0875
 DYG  CG2   C  CR6   0   0.133  -3.2292  -0.7428   0.1702
 DYG  CD1   C  CR16  0  -0.283  -4.4267  -1.4141   0.4591
 DYG  CD2   C  CR16  0  -0.296  -3.2900   0.6462  -0.0186
 DYG  CE1   C  CR16  0  -0.331  -5.6297  -0.7465   0.5575
 DYG  CE2   C  CR16  0  -0.361  -4.4880   1.3245   0.0785
 DYG  CZ    C  CR6   0   0.365  -5.6687   0.6351   0.3668
 DYG  OH    O  OH1   0  -0.617  -6.8554   1.2475   0.4715
 DYG  C     C  C     0   0.552   3.4400  -2.0038   0.6420
 DYG  O     O  O     0  -0.428   2.9704  -1.6870   1.7025
 DYG  OXT   O  OH1   0  -0.582   4.5981  -2.6179   0.4800
 DYG  HXT   H  HOH1  0   0.490   5.0275  -2.7654   1.3367
 DYG  HD2   H  HOH1  0   0.481   4.1865   4.3552   0.9807
 DYG  HB11  H  HCH2  0   0.298   2.9189   0.9006   0.9683
 DYG  HB12  H  HCH2  0   0.285   1.6501   2.0995   1.0528
 DYG  HA1   H  HCH1  0   0.283   2.6858   0.9238  -1.5636
 DYG  HN1   H  HNH2  0   0.360   0.8869   2.0674  -2.4827
 DYG  HN2   H  HNH2  0   0.353   0.3418   2.5663  -1.0426
 DYG  HB2   H  H     0   0.270  -2.1411  -2.5872   0.2681
 DYG  H1    H  HCR6  0   0.280  -2.3882   1.1978  -0.2436
 DYG  HE2   H  HCR6  0   0.278  -4.5095   2.3982  -0.0692
 DYG  HOH   H  HOH1  0   0.480  -6.7648   2.1965   0.3252
 DYG  HE1   H  HCR6  0   0.271  -6.5408  -1.2860   0.7824
 DYG  HD1   H  HCR6  0   0.264  -4.4093  -2.4871   0.6077
 DYG  HA31  H  HCH2  0   0.324   2.7708  -2.6522  -1.2868
 DYG  HA32  H  HCH2  0   0.326   3.3885  -1.0232  -1.2593

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
 DYG  N    CA1   single    1.444  0.020  1.444
 DYG  N    HN1   single    0.890  0.020  1.040
 DYG  N    HN2   single    0.890  0.020  1.040
 DYG  OD2  HD2   single    0.850  0.020  0.980
 DYG  OD2  CG1   single    1.326  0.020  1.326
 DYG  OD1  CG1   double    1.205  0.020  1.205
 DYG  CG1  CB1   single    1.506  0.020  1.506
 DYG  CB1  HB11  single    0.970  0.020  1.090
 DYG  CB1  HB12  single    0.970  0.020  1.090
 DYG  CB1  CA1   single    1.530  0.020  1.530
 DYG  CA1  HA1   single    0.970  0.020  1.090
 DYG  CA1  C1    single    1.506  0.020  1.506
 DYG  C1   N2    double    1.286  0.020  1.286
 DYG  C1   N3    single    1.381  0.020  1.381
 DYG  N2   CA2   single    1.389  0.020  1.389
 DYG  N3   C2    single    1.383  0.020  1.383
 DYG  N3   CA3   single    1.431  0.020  1.431
 DYG  C2   CA2   single    1.475  0.020  1.475
 DYG  C2   O2    double    1.214  0.020  1.214
 DYG  CA2  CB2   double    1.349  0.020  1.349
 DYG  CA3  HA31  single    0.970  0.020  1.090
 DYG  CA3  HA32  single    0.970  0.020  1.090
 DYG  CA3  C     single    1.515  0.020  1.515
 DYG  CB2  HB2   single    0.930  0.020  1.080
 DYG  CB2  CG2   single    1.444  0.020  1.444
 DYG  CG2  CD2   aromatic  1.403  0.020  1.403
 DYG  CG2  CD1   aromatic  1.403  0.020  1.403
 DYG  CD1  CE1   aromatic  1.379  0.020  1.379
 DYG  CD1  HD1   single    0.930  0.020  1.080
 DYG  CD2  H1    single    0.930  0.020  1.080
 DYG  CD2  CE2   aromatic  1.380  0.020  1.380
 DYG  CE1  CZ    aromatic  1.395  0.020  1.395
 DYG  CE1  HE1   single    0.930  0.020  1.080
 DYG  CE2  HE2   single    0.930  0.020  1.080
 DYG  CE2  CZ    aromatic  1.397  0.020  1.397
 DYG  CZ   OH    single    1.340  0.020  1.340
 DYG  OH   HOH   single    0.850  0.020  0.980
 DYG  C    O     double    1.202  0.020  1.202
 DYG  C    OXT   single    1.321  0.020  1.321
 DYG  OXT  HXT   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
 DYG  HN2   N    HN1   106.08  3.000
 DYG  HN2   N    CA1   109.84  3.000
 DYG  HN1   N    CA1   110.05  3.000
 DYG  HD2   OD2  CG1   110.14  3.000
 DYG  CB1   CG1  OD1   124.35  3.000
 DYG  CB1   CG1  OD2   112.19  3.000
 DYG  OD1   CG1  OD2   123.43  3.000
 DYG  HB12  CB1  HB11  106.20  3.000
 DYG  HB12  CB1  CA1   109.64  3.000
 DYG  HB11  CB1  CA1   111.48  3.000
 DYG  CA1   CB1  CG1   111.21  3.000
 DYG  HB12  CB1  CG1   110.80  3.000
 DYG  HB11  CB1  CG1   107.38  3.000
 DYG  HA1   CA1  C1    108.99  3.000
 DYG  C1    CA1  CB1   108.58  3.000
 DYG  HA1   CA1  CB1   108.63  3.000
 DYG  C1    CA1  N     113.72  3.000
 DYG  HA1   CA1  N     107.87  3.000
 DYG  CB1   CA1  N     108.94  3.000
 DYG  N3    C1   N2    113.49  3.000
 DYG  N3    C1   CA1   123.22  3.000
 DYG  N2    C1   CA1   123.27  3.000
 DYG  CA2   N2   C1    106.68  3.000
 DYG  CA3   N3   C2    122.51  3.000
 DYG  CA3   N3   C1    129.33  3.000
 DYG  C2    N3   C1    108.15  3.000
 DYG  CA2   C2   O2    131.74  3.000
 DYG  O2    C2   N3    125.32  3.000
 DYG  CA2   C2   N3    102.94  3.000
 DYG  CB2   CA2  C2    122.99  3.000
 DYG  CB2   CA2  N2    128.29  3.000
 DYG  C2    CA2  N2    108.73  3.000
 DYG  HA32  CA3  HA31  105.92  3.000
 DYG  HA32  CA3  C     109.36  3.000
 DYG  HA31  CA3  C     109.48  3.000
 DYG  C     CA3  N3    111.74  3.000
 DYG  HA32  CA3  N3    110.44  3.000
 DYG  HA31  CA3  N3    109.74  3.000
 DYG  HB2   CB2  CG2   115.15  3.000
 DYG  CG2   CB2  CA2   129.72  3.000
 DYG  HB2   CB2  CA2   115.13  3.000
 DYG  CD2   CG2  CD1   117.67  3.000
 DYG  CD1   CG2  CB2   117.99  3.000
 DYG  CD2   CG2  CB2   124.34  3.000
 DYG  HD1   CD1  CE1   118.92  3.000
 DYG  HD1   CD1  CG2   119.24  3.000
 DYG  CE1   CD1  CG2   121.84  3.000
 DYG  H1    CD2  CE2   119.22  3.000
 DYG  CE2   CD2  CG2   120.98  3.000
 DYG  H1    CD2  CG2   119.80  3.000
 DYG  HE1   CE1  CZ    119.89  3.000
 DYG  HE1   CE1  CD1   120.51  3.000
 DYG  CZ    CE1  CD1   119.60  3.000
 DYG  HE2   CE2  CZ    120.01  3.000
 DYG  CZ    CE2  CD2   120.37  3.000
 DYG  HE2   CE2  CD2   119.63  3.000
 DYG  OH    CZ   CE2   122.63  3.000
 DYG  OH    CZ   CE1   117.83  3.000
 DYG  CE2   CZ   CE1   119.55  3.000
 DYG  HOH   OH   CZ    110.78  3.000
 DYG  OXT   C    O     124.97  3.000
 DYG  OXT   C    CA3   110.78  3.000
 DYG  O     C    CA3   124.24  3.000
 DYG  HXT   OXT  C     110.53  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
 DYG  CONST_01  CZ   CE2  CD2  CG2    0.00   0.0  0
 DYG  CONST_02  CZ   CE1  CD1  CG2    0.00   0.0  0
 DYG  CONST_03  CE2  CD2  CG2  CD1    0.00   0.0  0
 DYG  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 DYG  CONST_05  CE1  CD1  CG2  CD2    0.00   0.0  0
 DYG  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 DYG  CONST_07  C2   CA2  N2   C1     0.00   0.0  0
 DYG  CONST_08  CA2  C2   N3   C1     0.00   0.0  0
 DYG  CONST_09  C2   N3   C1   N2     0.00   0.0  0
 DYG  CONST_10  N3   C2   CA2  N2     0.00   0.0  0
 DYG  CONST_11  CA2  N2   C1   N3     0.00   0.0  0
 DYG  CONST_12  CE2  CD2  CG2  CB2  180.00   0.0  0
 DYG  CONST_13  CE1  CD1  CG2  CB2  180.00   0.0  0
 DYG  CONST_14  OH   CZ   CE1  CD1  180.00   0.0  0
 DYG  CONST_15  OH   CZ   CE2  CD2  180.00   0.0  0
 DYG  CONST_16  CA2  N2   C1   CA1  180.00   0.0  0
 DYG  CONST_17  C2   N3   C1   CA1  180.00   0.0  0
 DYG  CONST_18  O2   C2   N3   C1   180.00   0.0  0
 DYG  CONST_19  CA3  N3   C1   N2   180.00   0.0  0
 DYG  CONST_20  CA3  N3   C2   CA2  180.00   0.0  0
 DYG  CONST_21  HE2  CE2  CD2  CG2  180.00   0.0  0
 DYG  CONST_22  HE1  CE1  CD1  CG2  180.00   0.0  0
 DYG  CONST_23  H1   CD2  CG2  CD1  180.00   0.0  0
 DYG  CONST_24  HD1  CD1  CG2  CD2  180.00   0.0  0
 DYG  CONST_25  CA3  N3   C1   CA1    0.00   0.0  0
 DYG  CONST_26  CA3  N3   C2   O2     0.00   0.0  0
 DYG  CONST_27  HD2  OD2  CG1  OD1    0.00   0.0  0
 DYG  CONST_28  HXT  OXT  C    CA3  180.00   0.0  0
 DYG  Var_01    CG2  CB2  CA2  N2     0.04  30.0  2
 DYG  Var_02    CD2  CG2  CB2  CA2   -0.49  30.0  2
 DYG  Var_03    C    CA3  N3   C1   101.67  30.0  3
 DYG  Var_04    O    C    CA3  N3    -8.82  30.0  3
 DYG  Var_05    CA1  CB1  CG1  OD2  142.82  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
 DYG  chir_01  CA1  N  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
 DYG  plan-1  CA1  0.020
 DYG  plan-1  C1   0.020
 DYG  plan-1  N2   0.020
 DYG  plan-1  N3   0.020
 DYG  plan-1  C2   0.020
 DYG  plan-1  O2   0.020
 DYG  plan-1  CA2  0.020
 DYG  plan-1  CA3  0.020
 DYG  plan-1  CB2  0.020
 DYG  plan-2  CB2  0.020
 DYG  plan-2  CG2  0.020
 DYG  plan-2  CD1  0.020
 DYG  plan-2  CD2  0.020
 DYG  plan-2  CE1  0.020
 DYG  plan-2  CE2  0.020
 DYG  plan-2  CZ   0.020
 DYG  plan-2  OH   0.020
 DYG  plan-2  H1   0.020
 DYG  plan-2  HE2  0.020
 DYG  plan-2  HE1  0.020
 DYG  plan-2  HD1  0.020
 DYG  plan-3  OD2  0.020
 DYG  plan-3  OD1  0.020
 DYG  plan-3  CG1  0.020
 DYG  plan-3  CB1  0.020
 DYG  plan-3  HD2  0.020
 DYG  plan-4  CA3  0.020
 DYG  plan-4  C    0.020
 DYG  plan-4  O    0.020
 DYG  plan-4  OXT  0.020
 DYG  plan-4  HXT  0.020

