# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 00:37:33 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: {(4Z)-2-[(1E)-ethanimidoyl]-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: CC(=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
 XYG  XYG  '{(4Z)-2-[(1E)-ethanimidoyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid'  L-peptide  33  21  .  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_XYG
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
 XYG  N     N  N      0  -0.554  -6.0204  -1.7125   1.5617
 XYG  CB1   C  CH3    0  -0.728  -6.3821   0.3288   0.2106
 XYG  CA1   C  C      0   0.133  -5.5994  -0.8129   0.7764
 XYG  C1    C  CR5    0   0.546  -4.1675  -0.8428   0.4061
 XYG  N2    N  N      0  -0.488  -3.4789   0.2387   0.2649
 XYG  CD2   C  CR16   0  -0.283   0.2810   2.5843  -0.5684
 XYG  CE2   C  CR16   0  -0.376   0.4882   3.9498  -0.5990
 XYG  CZ    C  CR6    0   0.359  -0.5616   4.8145  -0.2923
 XYG  CE1   C  CR16   0  -0.314  -1.8122   4.2876   0.0423
 XYG  CD1   C  CR16   0  -0.299  -2.0087   2.9234   0.0654
 XYG  CG2   C  CR6    0   0.133  -0.9651   2.0343  -0.2409
 XYG  CA2   C  CR5    0   0.088  -2.1839  -0.1692  -0.0162
 XYG  C2    C  CR5    0   0.521  -2.1519  -1.6482  -0.0552
 XYG  O2    O  O      0  -0.457  -1.2377  -2.4069  -0.3144
 XYG  N3    N  NR5    0  -0.540  -3.4432  -2.0054   0.2661
 XYG  CA3   C  CH2    0  -0.454  -4.0006  -3.3173   0.0423
 XYG  C     C  C      0   0.422  -5.0458  -3.3250  -1.0961
 XYG  O     O  O      0  -0.585  -5.2220  -2.2598  -1.7129
 XYG  OXT   O  OC    -1  -0.606  -5.6044  -4.4200  -1.2800
 XYG  HA31  H  HCH2   0   0.264  -4.4450  -3.7025   0.9581
 XYG  HA32  H  HCH2   0   0.266  -3.1744  -3.9804  -0.2196
 XYG  HN2   H  H      0   0.346  -7.0064  -1.5745   1.7701
 XYG  HB11  H  HCH3   0   0.261  -5.9677   1.2814   0.5402
 XYG  HB12  H  HCH3   0   0.261  -6.3311   0.3107  -0.8780
 XYG  HB13  H  HCH3   0   0.252  -7.4255   0.2758   0.5169
 XYG  HB2   H  H      0   0.266  -0.1846   0.0472  -0.4588
 XYG  HD2   H  HCR6   0   0.265   1.1063   1.9248  -0.8086
 XYG  HE2   H  HCR6   0   0.278   1.4633   4.3431  -0.8620
 XYG  HOH   H  HOH1   0   0.480   0.4656   6.4015  -0.5540
 XYG  HE1   H  HCR6   0   0.270  -2.6270   4.9589   0.2831
 XYG  HD1   H  HCR6   0   0.277  -2.9830   2.5353   0.3253
 XYG  CB2   C  C1     0  -0.386  -1.0960   0.5959  -0.2402
 XYG  OH    O  OH1    0  -0.618  -0.4299   6.1483  -0.3014

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
 XYG  N    CA1   double    1.266  0.020  1.266
 XYG  N    HN2   single    0.890  0.020  1.040
 XYG  CB1  CA1   single    1.495  0.020  1.495
 XYG  CB1  HB11  single    0.970  0.020  1.090
 XYG  CB1  HB12  single    0.970  0.020  1.090
 XYG  CB1  HB13  single    0.970  0.020  1.090
 XYG  CA1  C1    single    1.479  0.020  1.479
 XYG  C1   N2    double    1.290  0.020  1.290
 XYG  C1   N3    single    1.377  0.020  1.377
 XYG  N2   CA2   single    1.387  0.020  1.387
 XYG  OH   CZ    single    1.340  0.020  1.340
 XYG  OH   HOH   single    0.850  0.020  0.980
 XYG  CD2  CG2   aromatic  1.401  0.020  1.401
 XYG  CD2  CE2   aromatic  1.382  0.020  1.382
 XYG  CD2  HD2   single    0.930  0.020  1.080
 XYG  CE2  CZ    aromatic  1.394  0.020  1.394
 XYG  CE2  HE2   single    0.930  0.020  1.080
 XYG  CZ   CE1   aromatic  1.398  0.020  1.398
 XYG  CE1  CD1   aromatic  1.378  0.020  1.378
 XYG  CE1  HE1   single    0.930  0.020  1.080
 XYG  CD1  CG2   aromatic  1.405  0.020  1.405
 XYG  CD1  HD1   single    0.930  0.020  1.080
 XYG  CG2  CB2   single    1.444  0.020  1.444
 XYG  CB2  CA2   double    1.349  0.020  1.349
 XYG  CB2  HB2   single    0.930  0.020  1.080
 XYG  CA2  C2    single    1.480  0.020  1.480
 XYG  C2   N3    single    1.378  0.020  1.378
 XYG  C2   O2    double    1.216  0.020  1.216
 XYG  N3   CA3   single    1.443  0.020  1.443
 XYG  CA3  C     single    1.545  0.020  1.545
 XYG  CA3  HA31  single    0.970  0.020  1.090
 XYG  CA3  HA32  single    0.970  0.020  1.090
 XYG  C    OXT   deloc     1.243  0.020  1.243
 XYG  C    O     deloc     1.243  0.020  1.243

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
 XYG  HN2   N    CA1   110.67  3.000
 XYG  HB13  CB1  HB12  108.96  3.000
 XYG  HB13  CB1  HB11  108.77  3.000
 XYG  HB12  CB1  HB11  107.39  3.000
 XYG  HB13  CB1  CA1   110.97  3.000
 XYG  HB12  CB1  CA1   109.92  3.000
 XYG  HB11  CB1  CA1   110.73  3.000
 XYG  C1    CA1  CB1   115.30  3.000
 XYG  C1    CA1  N     117.56  3.000
 XYG  CB1   CA1  N     127.09  3.000
 XYG  N3    C1   N2    114.58  3.000
 XYG  N3    C1   CA1   123.48  3.000
 XYG  N2    C1   CA1   121.82  3.000
 XYG  CA2   N2   C1    105.91  3.000
 XYG  HD2   CD2  CG2   119.37  3.000
 XYG  HD2   CD2  CE2   118.85  3.000
 XYG  CG2   CD2  CE2   121.78  3.000
 XYG  HE2   CE2  CZ    120.38  3.000
 XYG  HE2   CE2  CD2   119.93  3.000
 XYG  CZ    CE2  CD2   119.69  3.000
 XYG  CE1   CZ   CE2   119.51  3.000
 XYG  CE1   CZ   OH    117.70  3.000
 XYG  CE2   CZ   OH    122.80  3.000
 XYG  HE1   CE1  CD1   120.17  3.000
 XYG  HE1   CE1  CZ    119.52  3.000
 XYG  CD1   CE1  CZ    120.31  3.000
 XYG  HD1   CD1  CG2   119.67  3.000
 XYG  HD1   CD1  CE1   119.21  3.000
 XYG  CG2   CD1  CE1   121.11  3.000
 XYG  CB2   CG2  CD1   124.25  3.000
 XYG  CB2   CG2  CD2   118.14  3.000
 XYG  CD1   CG2  CD2   117.61  3.000
 XYG  C2    CA2  CB2   123.04  3.000
 XYG  C2    CA2  N2    108.63  3.000
 XYG  CB2   CA2  N2    128.32  3.000
 XYG  N3    C2   O2    126.34  3.000
 XYG  O2    C2   CA2   130.19  3.000
 XYG  N3    C2   CA2   103.46  3.000
 XYG  CA3   N3   C2    124.17  3.000
 XYG  CA3   N3   C1    125.47  3.000
 XYG  C2    N3   C1    107.33  3.000
 XYG  HA32  CA3  HA31  107.22  3.000
 XYG  HA32  CA3  C     109.40  3.000
 XYG  HA31  CA3  C     109.99  3.000
 XYG  HA32  CA3  N3    107.29  3.000
 XYG  HA31  CA3  N3    110.43  3.000
 XYG  C     CA3  N3    112.34  3.000
 XYG  OXT   C    O     128.14  3.000
 XYG  O     C    CA3   117.19  3.000
 XYG  OXT   C    CA3   114.67  3.000
 XYG  HB2   CB2  CA2   115.07  3.000
 XYG  HB2   CB2  CG2   115.28  3.000
 XYG  CA2   CB2  CG2   129.65  3.000
 XYG  HOH   OH   CZ    110.76  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
 XYG  CONST_01  CE1   CD1  CG2  CD2     0.00   0.0  0
 XYG  CONST_02  CE1   CZ   CE2  CD2     0.00   0.0  0
 XYG  CONST_03  CD1   CG2  CD2  CE2     0.00   0.0  0
 XYG  CONST_04  CD1   CE1  CZ   CE2     0.00   0.0  0
 XYG  CONST_05  CG2   CD2  CE2  CZ      0.00   0.0  0
 XYG  CONST_06  CG2   CD1  CE1  CZ      0.00   0.0  0
 XYG  CONST_07  C2    CA2  N2   C1      0.00   0.0  0
 XYG  CONST_08  CA2   C2   N3   C1      0.00   0.0  0
 XYG  CONST_09  C2    N3   C1   N2      0.00   0.0  0
 XYG  CONST_10  N3    C2   CA2  N2      0.00   0.0  0
 XYG  CONST_11  N3    C1   N2   CA2     0.00   0.0  0
 XYG  CONST_12  CD2   CE2  CZ   OH    180.00   0.0  0
 XYG  CONST_13  CD1   CE1  CZ   OH    180.00   0.0  0
 XYG  CONST_14  CB2   CG2  CD2  CE2   180.00   0.0  0
 XYG  CONST_15  CB2   CG2  CD1  CE1   180.00   0.0  0
 XYG  CONST_16  CA2   N2   C1   CA1   180.00   0.0  0
 XYG  CONST_17  C2    N3   C1   CA1   180.00   0.0  0
 XYG  CONST_18  O2    C2   N3   C1    180.00   0.0  0
 XYG  CONST_21  HD1   CD1  CG2  CD2   180.00   0.0  0
 XYG  CONST_22  HE1   CE1  CZ   CE2   180.00   0.0  0
 XYG  CONST_23  HD2   CD2  CE2  CZ    180.00   0.0  0
 XYG  CONST_24  HE2   CE2  CZ   CE1   180.00   0.0  0
 XYG  CONST_27  HN2   N    CA1  C1    180.00   0.0  0
 XYG  Var_01    CG2   CB2  CA2  N2      0.57  30.0  2
 XYG  Var_02    CA2   CB2  CG2  CD2  -177.07  30.0  2
 XYG  Var_03    N2    C1   CA1  N    -142.44  30.0  2
 XYG  Var_04    C     CA3  N3   C1     48.70  30.0  3
 XYG  Var_05    OXT   C    CA3  N3   -176.48  30.0  3
 XYG  Var_06    HB11  CB1  CA1  C1    -59.76  30.0  3

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
 XYG  plan-1  CA1  0.020
 XYG  plan-1  C1   0.020
 XYG  plan-1  N2   0.020
 XYG  plan-1  CA2  0.020
 XYG  plan-1  C2   0.020
 XYG  plan-1  O2   0.020
 XYG  plan-1  N3   0.020
 XYG  plan-1  CA3  0.020
 XYG  plan-1  CB2  0.020
 XYG  plan-2  CD2  0.020
 XYG  plan-2  CE2  0.020
 XYG  plan-2  CZ   0.020
 XYG  plan-2  CE1  0.020
 XYG  plan-2  CD1  0.020
 XYG  plan-2  CG2  0.020
 XYG  plan-2  HD2  0.020
 XYG  plan-2  HE2  0.020
 XYG  plan-2  HE1  0.020
 XYG  plan-2  HD1  0.020
 XYG  plan-2  CB2  0.020
 XYG  plan-2  OH   0.020
 XYG  plan-3  CA3  0.020
 XYG  plan-3  C    0.020
 XYG  plan-3  O    0.020
 XYG  plan-3  OXT  0.020
 XYG  plan-4  N    0.020
 XYG  plan-4  CB1  0.020
 XYG  plan-4  CA1  0.020
 XYG  plan-4  C1   0.020
 XYG  plan-4  HN2  0.020

