# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 13:51:11 2022
#   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-imidazol-2-yl]propanoic acid"  L-peptide  37  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 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  -0.773   1.1510   2.3387  -1.5964
 DYG  OD2   O  OC    -1  -0.617   3.6942   3.6111   0.9755
 DYG  OD1   O  O      0  -0.610   4.3980   2.4352  -0.7813
 DYG  CG1   C  C      0   0.416   3.6120   2.6746   0.1562
 DYG  CB1   C  CH2    0  -0.574   2.4508   1.6838   0.3554
 DYG  CA1   C  CH1    0  -0.216   1.8301   1.2266  -0.9642
 DYG  C1    C  CR5    0   0.538   0.9328   0.0496  -0.7077
 DYG  N2    N  N      0  -0.497  -0.3391   0.1578  -0.5086
 DYG  N3    N  NR5    0  -0.540   1.3986  -1.2455  -0.6389
 DYG  C2    C  CR5    0   0.530   0.3388  -2.0638  -0.3300
 DYG  O2    O  O      0  -0.460   0.3835  -3.2702  -0.1843
 DYG  CA2   C  CR5    0   0.090  -0.8043  -1.1246  -0.2578
 DYG  CA3   C  CH2    0  -0.471   2.7584  -1.7174  -0.6866
 DYG  CB2   C  C1     0  -0.396  -2.0621  -1.5212   0.0182
 DYG  CG2   C  CR6    0   0.133  -3.2706  -0.7332   0.1298
 DYG  CD1   C  CR16   0  -0.289  -4.4669  -1.3948   0.4422
 DYG  CD2   C  CR16   0  -0.302  -3.3263   0.6563  -0.0524
 DYG  CE1   C  CR16   0  -0.331  -5.6628  -0.7175   0.5704
 DYG  CE2   C  CR16   0  -0.361  -4.5177   1.3441   0.0729
 DYG  CZ    C  CR6    0   0.358  -5.6964   0.6644   0.3857
 DYG  OH    O  OH1    0  -0.622  -6.8776   1.2872   0.5195
 DYG  C     C  C      0   0.421   3.3672  -2.0063   0.7059
 DYG  O     O  O      0  -0.589   2.7005  -1.6798   1.7002
 DYG  OXT   O  OC    -1  -0.610   4.4928  -2.5353   0.6714
 DYG  HB11  H  HCH2   0   0.253   2.8291   0.8180   0.9091
 DYG  HB12  H  HCH2   0   0.217   1.6690   2.1227   0.9818
 DYG  HA1   H  HCH1   0   0.256   2.6454   0.9164  -1.6223
 DYG  HN1   H  HNH2   0   0.346   0.8024   2.0567  -2.5044
 DYG  HN2   H  HNH2   0   0.342   0.3304   2.5832  -1.0540
 DYG  HB2   H  H      0   0.261  -2.1871  -2.5868   0.1849
 DYG  H1    H  HCR6   0   0.278  -2.4245   1.2002  -0.2952
 DYG  HE2   H  HCR6   0   0.275  -4.5330   2.4185  -0.0716
 DYG  HOH   H  HOH1   0   0.478  -6.7802   2.2353   0.3735
 DYG  HE1   H  HCR6   0   0.268  -6.5728  -1.2512   0.8141
 DYG  HD1   H  HCR6   0   0.260  -4.4555  -2.4685   0.5871
 DYG  HA31  H  HCH2   0   0.266   2.7935  -2.6210  -1.2977
 DYG  HA32  H  HCH2   0   0.271   3.3719  -0.9778  -1.2023

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    1.448  0.020  1.448
 DYG  N    HN1   single    0.890  0.020  1.040
 DYG  N    HN2   single    0.890  0.020  1.040
 DYG  OD2  CG1   deloc     1.247  0.020  1.247
 DYG  OD1  CG1   deloc     1.247  0.020  1.247
 DYG  CG1  CB1   single    1.539  0.020  1.539
 DYG  CB1  HB11  single    0.970  0.020  1.090
 DYG  CB1  HB12  single    0.970  0.020  1.090
 DYG  CB1  CA1   single    1.528  0.020  1.528
 DYG  CA1  HA1   single    0.970  0.020  1.090
 DYG  CA1  C1    single    1.502  0.020  1.502
 DYG  C1   N2    double    1.292  0.020  1.292
 DYG  C1   N3    single    1.378  0.020  1.378
 DYG  N2   CA2   single    1.387  0.020  1.387
 DYG  N3   C2    single    1.374  0.020  1.374
 DYG  N3   CA3   single    1.440  0.020  1.440
 DYG  C2   CA2   single    1.481  0.020  1.481
 DYG  C2   O2    double    1.216  0.020  1.216
 DYG  CA2  CB2   double    1.347  0.020  1.347
 DYG  CA3  HA31  single    0.970  0.020  1.090
 DYG  CA3  HA32  single    0.970  0.020  1.090
 DYG  CA3  C     single    1.547  0.020  1.547
 DYG  CB2  HB2   single    0.930  0.020  1.080
 DYG  CB2  CG2   single    1.447  0.020  1.447
 DYG  CG2  CD2   aromatic  1.402  0.020  1.402
 DYG  CG2  CD1   aromatic  1.402  0.020  1.402
 DYG  CD1  CE1   aromatic  1.380  0.020  1.380
 DYG  CD1  HD1   single    0.930  0.020  1.080
 DYG  CD2  H1    single    0.930  0.020  1.080
 DYG  CD2  CE2   aromatic  1.381  0.020  1.381
 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  1.396  0.020  1.396
 DYG  CZ   OH    single    1.342  0.020  1.342
 DYG  OH   HOH   single    0.850  0.020  0.980
 DYG  C    O     deloc     1.241  0.020  1.241
 DYG  C    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
 DYG  HN2   N    HN1   105.56  3.000
 DYG  HN2   N    CA1   109.34  3.000
 DYG  HN1   N    CA1   109.81  3.000
 DYG  CB1   CG1  OD1   116.70  3.000
 DYG  CB1   CG1  OD2   116.62  3.000
 DYG  OD1   CG1  OD2   126.64  3.000
 DYG  HB12  CB1  HB11  105.94  3.000
 DYG  HB12  CB1  CA1   108.92  3.000
 DYG  HB11  CB1  CA1   109.90  3.000
 DYG  CA1   CB1  CG1   112.78  3.000
 DYG  HB12  CB1  CG1   110.79  3.000
 DYG  HB11  CB1  CG1   108.28  3.000
 DYG  HA1   CA1  C1    109.03  3.000
 DYG  C1    CA1  CB1   109.24  3.000
 DYG  HA1   CA1  CB1   107.57  3.000
 DYG  C1    CA1  N     113.34  3.000
 DYG  HA1   CA1  N     107.75  3.000
 DYG  CB1   CA1  N     109.74  3.000
 DYG  N3    C1   N2    113.81  3.000
 DYG  N3    C1   CA1   122.89  3.000
 DYG  N2    C1   CA1   123.28  3.000
 DYG  CA2   N2   C1    106.30  3.000
 DYG  CA3   N3   C2    122.72  3.000
 DYG  CA3   N3   C1    128.72  3.000
 DYG  C2    N3   C1    108.07  3.000
 DYG  CA2   C2   O2    130.66  3.000
 DYG  O2    C2   N3    126.11  3.000
 DYG  CA2   C2   N3    103.21  3.000
 DYG  CB2   CA2  C2    122.94  3.000
 DYG  CB2   CA2  N2    128.48  3.000
 DYG  C2    CA2  N2    108.58  3.000
 DYG  HA32  CA3  HA31  106.18  3.000
 DYG  HA32  CA3  C     109.32  3.000
 DYG  HA31  CA3  C     109.68  3.000
 DYG  C     CA3  N3    113.76  3.000
 DYG  HA32  CA3  N3    108.94  3.000
 DYG  HA31  CA3  N3    108.67  3.000
 DYG  HB2   CB2  CG2   115.25  3.000
 DYG  CG2   CB2  CA2   129.43  3.000
 DYG  HB2   CB2  CA2   115.32  3.000
 DYG  CD2   CG2  CD1   117.55  3.000
 DYG  CD1   CG2  CB2   118.21  3.000
 DYG  CD2   CG2  CB2   124.24  3.000
 DYG  HD1   CD1  CE1   118.87  3.000
 DYG  HD1   CD1  CG2   119.24  3.000
 DYG  CE1   CD1  CG2   121.89  3.000
 DYG  H1    CD2  CE2   119.30  3.000
 DYG  CE2   CD2  CG2   121.05  3.000
 DYG  H1    CD2  CG2   119.65  3.000
 DYG  HE1   CE1  CZ    119.87  3.000
 DYG  HE1   CE1  CD1   120.48  3.000
 DYG  CZ    CE1  CD1   119.66  3.000
 DYG  HE2   CE2  CZ    120.02  3.000
 DYG  CZ    CE2  CD2   120.40  3.000
 DYG  HE2   CE2  CD2   119.57  3.000
 DYG  OH    CZ   CE2   122.65  3.000
 DYG  OH    CZ   CE1   117.90  3.000
 DYG  CE2   CZ   CE1   119.45  3.000
 DYG  HOH   OH   CZ    110.63  3.000
 DYG  OXT   C    O     128.32  3.000
 DYG  OXT   C    CA3   114.24  3.000
 DYG  O     C    CA3   117.44  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  HE2   CE2  CZ   CE1   180.00   0.0  0
 DYG  CONST_26  HE1   CE1  CZ   CE2   180.00   0.0  0
 DYG  CONST_27  HD1   CD1  CE1  CZ    180.00   0.0  0
 DYG  CONST_28  H1    CD2  CE2  CZ    180.00   0.0  0
 DYG  CONST_29  CA3   N3   C1   CA1     0.00   0.0  0
 DYG  CONST_30  CA3   N3   C2   O2      0.00   0.0  0
 DYG  Var_01    CG2   CB2  CA2  N2      0.04   0.0  2
 DYG  Var_02    CG2   CB2  CA2  C2    179.65   0.0  2
 DYG  Var_03    CD2   CG2  CB2  CA2     0.45  30.0  2
 DYG  Var_04    CD1   CG2  CB2  CA2  -179.43  30.0  2
 DYG  Var_05    C     CA3  N3   C1     98.16  30.0  3
 DYG  Var_06    C     CA3  N3   C2    -72.79  30.0  3
 DYG  Var_07    HB2   CB2  CA2  N2   -179.72   0.0  2
 DYG  Var_08    HB2   CB2  CA2  C2     -0.10   0.0  2
 DYG  Var_09    HA31  CA3  N3   C1   -139.35  30.0  3
 DYG  Var_10    HA32  CA3  N3   C1    -24.07  30.0  3
 DYG  Var_11    HA31  CA3  N3   C2     49.70  30.0  3
 DYG  Var_12    HA32  CA3  N3   C2    164.98  30.0  3
 DYG  Var_13    HB2   CB2  CG2  CD1     0.32  30.0  2
 DYG  Var_14    HB2   CB2  CG2  CD2  -179.79  30.0  2
 DYG  Var_15    O     C    CA3  N3     -7.30  30.0  3
 DYG  Var_16    OXT   C    CA3  N3    173.41  30.0  3
 DYG  Var_17    CA1   CB1  CG1  OD2   141.52  30.0  3
 DYG  Var_18    CA1   CB1  CG1  OD1   -40.68  30.0  3
 DYG  Var_19    HB11  CB1  CG1  OD2   -96.64  30.0  3
 DYG  Var_20    HB12  CB1  CG1  OD2    19.13  30.0  3
 DYG  Var_21    HB11  CB1  CG1  OD1    81.16  30.0  3
 DYG  Var_22    HB12  CB1  CG1  OD1  -163.07  30.0  3
 DYG  Var_23    HA31  CA3  C    O    -129.24  30.0  2
 DYG  Var_24    HA32  CA3  C    O     114.72  30.0  2
 DYG  Var_25    HA31  CA3  C    OXT    51.47  30.0  2
 DYG  Var_26    HA32  CA3  C    OXT   -64.58  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
 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-1  CG2  0.020
 DYG  plan-1  HB2  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-4  CA3  0.020
 DYG  plan-4  C    0.020
 DYG  plan-4  O    0.020
 DYG  plan-4  OXT  0.020

