# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 16:45:17 2022
#   Inital geometry file: a 99 line input string
#   Ligand name: (2S)-2-{(4Z)-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N1C(=NC(=C\c2ccc(O)cc2)/C1=O)CN)C(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
 JBY  JBY  "(2S)-2-{(4Z)-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}propanoic acid"  L-peptide  35  21  .  2022-09-15  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_JBY
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
 JBY  C1   C  CR5    0   0.530   1.1867  -1.3221  -0.2554
 JBY  C2   C  CR5    0   0.544   1.2427   0.8789  -0.5451
 JBY  N2   N  N      0  -0.496  -0.0576  -1.0112  -0.1256
 JBY  N3   N  NR5    0  -0.545   2.0125  -0.2619  -0.5567
 JBY  O2   O  O      0  -0.460   1.6312   2.0200  -0.6999
 JBY  C    C  C      0   0.430   3.9643   0.3250   0.8317
 JBY  CA3  C  CH1    0  -0.259   3.4641  -0.2621  -0.5184
 JBY  CB3  C  CH3    0  -0.652   4.0795   0.3786  -1.7543
 JBY  CA1  C  CH2    0  -0.389   1.7242  -2.6977  -0.0616
 JBY  N    N  NH2    0  -0.789   0.6588  -3.6629   0.0864
 JBY  CA2  C  CR5    0   0.086  -0.1262   0.3633  -0.3082
 JBY  CB2  C  C1     0  -0.392  -1.2140   1.1571  -0.2798
 JBY  CG2  C  CR6    0   0.132  -2.6010   0.8075  -0.0599
 JBY  CD2  C  CR16   0  -0.302  -3.0608  -0.5017   0.1439
 JBY  CE2  C  CR16   0  -0.361  -4.4005  -0.7611   0.3579
 JBY  CZ   C  CR6    0   0.358  -5.3275   0.2828   0.3772
 JBY  O3   O  OH1    0  -0.622  -6.6378   0.0833   0.5881
 JBY  CE1  C  CR16   0  -0.331  -4.8916   1.5913   0.1710
 JBY  CD1  C  CR16   0  -0.288  -3.5507   1.8389  -0.0436
 JBY  H4   H  HCH1   0   0.275   3.7717  -1.3120  -0.5219
 JBY  H5   H  HCH3   0   0.224   3.6688  -0.0638  -2.6624
 JBY  H6   H  HCH3   0   0.232   3.9129   1.4527  -1.7914
 JBY  H7   H  HCH3   0   0.234   5.1532   0.2057  -1.7559
 JBY  H8   H  HCH2   0   0.263   2.3309  -2.9663  -0.9319
 JBY  H9   H  HCH2   0   0.242   2.4241  -2.6528   0.7875
 JBY  H1   H  HNH2   0   0.358   1.0696  -4.5726   0.2477
 JBY  H2   H  HNH2   0   0.348   0.1154  -3.4465   0.9118
 JBY  H13  H  H      0   0.260  -1.0204   2.2133  -0.4413
 JBY  H14  H  HCR6   0   0.280  -2.3567  -1.3217   0.1349
 JBY  H16  H  HCR6   0   0.275  -4.7296  -1.7822   0.5146
 JBY  H17  H  HCR6   0   0.268  -5.6056   2.4048   0.1822
 JBY  H18  H  HCR6   0   0.260  -3.2264   2.8604  -0.2017
 JBY  H3   H  HOH1   0   0.478  -6.8208  -0.8529   0.7279
 JBY  O    O  O      0  -0.593   3.1484   0.3252   1.7684
 JBY  OXT  O  OC    -1  -0.598   5.1524   0.6909   0.8527

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
 JBY  O    C    deloc     1.231  0.020  1.231
 JBY  CB3  CA3  single    1.522  0.020  1.522
 JBY  C    CA3  single    1.555  0.020  1.555
 JBY  N    CA1  single    1.445  0.020  1.445
 JBY  CA3  N3   single    1.452  0.020  1.452
 JBY  CA1  C1   single    1.490  0.020  1.490
 JBY  N3   C1   single    1.377  0.020  1.377
 JBY  N3   C2   single    1.376  0.020  1.376
 JBY  C1   N2   double    1.289  0.020  1.289
 JBY  C2   O2   double    1.215  0.020  1.215
 JBY  C2   CA2  single    1.482  0.020  1.482
 JBY  N2   CA2  single    1.388  0.020  1.388
 JBY  CA2  CB2  double    1.347  0.020  1.347
 JBY  CB2  CG2  single    1.447  0.020  1.447
 JBY  CD1  CG2  aromatic  1.402  0.020  1.402
 JBY  CD1  CE1  aromatic  1.380  0.020  1.380
 JBY  CG2  CD2  aromatic  1.403  0.020  1.403
 JBY  CE1  CZ   aromatic  1.395  0.020  1.395
 JBY  CD2  CE2  aromatic  1.381  0.020  1.381
 JBY  CZ   CE2  aromatic  1.396  0.020  1.396
 JBY  CZ   O3   single    1.342  0.020  1.342
 JBY  CA3  H4   single    0.970  0.020  1.090
 JBY  CB3  H5   single    0.970  0.020  1.090
 JBY  CB3  H6   single    0.970  0.020  1.090
 JBY  CB3  H7   single    0.970  0.020  1.090
 JBY  CA1  H8   single    0.970  0.020  1.090
 JBY  CA1  H9   single    0.970  0.020  1.090
 JBY  N    H1   single    0.890  0.020  1.040
 JBY  N    H2   single    0.890  0.020  1.040
 JBY  CB2  H13  single    0.930  0.020  1.080
 JBY  CD2  H14  single    0.930  0.020  1.080
 JBY  CE2  H16  single    0.930  0.020  1.080
 JBY  CE1  H17  single    0.930  0.020  1.080
 JBY  CD1  H18  single    0.930  0.020  1.080
 JBY  C    OXT  deloc     1.243  0.020  1.243
 JBY  O3   H3   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
 JBY  CA1  C1   N3   121.54  3.000
 JBY  N3   C1   N2   114.53  3.000
 JBY  CA1  C1   N2   123.91  3.000
 JBY  CA2  C2   O2   129.97  3.000
 JBY  CA2  C2   N3   103.28  3.000
 JBY  O2   C2   N3   126.76  3.000
 JBY  CA2  N2   C1   105.85  3.000
 JBY  CA3  N3   C2   123.99  3.000
 JBY  C2   N3   C1   107.51  3.000
 JBY  CA3  N3   C1   126.41  3.000
 JBY  OXT  C    CA3  115.67  3.000
 JBY  OXT  C    O    127.94  3.000
 JBY  CA3  C    O    116.33  3.000
 JBY  H4   CA3  CB3  106.72  3.000
 JBY  H4   CA3  C    105.94  3.000
 JBY  CB3  CA3  C    114.59  3.000
 JBY  H4   CA3  N3   106.32  3.000
 JBY  C    CA3  N3   110.15  3.000
 JBY  CB3  CA3  N3   112.50  3.000
 JBY  H7   CB3  H6   107.95  3.000
 JBY  H7   CB3  H5   107.83  3.000
 JBY  H6   CB3  H5   108.34  3.000
 JBY  H7   CB3  CA3  109.48  3.000
 JBY  H6   CB3  CA3  112.42  3.000
 JBY  H5   CB3  CA3  110.68  3.000
 JBY  H9   CA1  H8   105.71  3.000
 JBY  H9   CA1  N    114.63  3.000
 JBY  H8   CA1  N    109.04  3.000
 JBY  H9   CA1  C1   106.98  3.000
 JBY  H8   CA1  C1   108.86  3.000
 JBY  N    CA1  C1   111.35  3.000
 JBY  H2   N    H1   106.29  3.000
 JBY  H2   N    CA1  109.68  3.000
 JBY  H1   N    CA1  108.53  3.000
 JBY  CB2  CA2  N2   128.36  3.000
 JBY  CB2  CA2  C2   122.98  3.000
 JBY  N2   CA2  C2   108.66  3.000
 JBY  H13  CB2  CG2  115.37  3.000
 JBY  H13  CB2  CA2  115.22  3.000
 JBY  CG2  CB2  CA2  129.41  3.000
 JBY  CD1  CG2  CD2  117.58  3.000
 JBY  CD2  CG2  CB2  124.18  3.000
 JBY  CD1  CG2  CB2  118.25  3.000
 JBY  H14  CD2  CE2  119.38  3.000
 JBY  H14  CD2  CG2  119.57  3.000
 JBY  CE2  CD2  CG2  121.05  3.000
 JBY  H16  CE2  CZ   120.04  3.000
 JBY  H16  CE2  CD2  119.58  3.000
 JBY  CZ   CE2  CD2  120.38  3.000
 JBY  CE1  CZ   O3   117.90  3.000
 JBY  O3   CZ   CE2  122.64  3.000
 JBY  CE1  CZ   CE2  119.47  3.000
 JBY  H3   O3   CZ   110.63  3.000
 JBY  H17  CE1  CD1  120.50  3.000
 JBY  H17  CE1  CZ   119.83  3.000
 JBY  CD1  CE1  CZ   119.66  3.000
 JBY  H18  CD1  CE1  118.85  3.000
 JBY  H18  CD1  CG2  119.28  3.000
 JBY  CE1  CD1  CG2  121.86  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
 JBY  CONST_01  CZ   CE1  CD1  CG2     0.00   0.0  0
 JBY  CONST_02  CZ   CE2  CD2  CG2     0.00   0.0  0
 JBY  CONST_03  CE1  CD1  CG2  CD2     0.00   0.0  0
 JBY  CONST_04  CE1  CZ   CE2  CD2     0.00   0.0  0
 JBY  CONST_05  CD1  CG2  CD2  CE2     0.00   0.0  0
 JBY  CONST_06  CD1  CE1  CZ   CE2     0.00   0.0  0
 JBY  CONST_07  CA2  C2   N3   C1      0.00   0.0  0
 JBY  CONST_08  C2   CA2  N2   C1      0.00   0.0  0
 JBY  CONST_09  N2   C1   N3   C2      0.00   0.0  0
 JBY  CONST_10  N3   C2   CA2  N2      0.00   0.0  0
 JBY  CONST_11  CA2  N2   C1   N3      0.00   0.0  0
 JBY  CONST_12  CE1  CD1  CG2  CB2   180.00   0.0  0
 JBY  CONST_13  CE2  CD2  CG2  CB2   180.00   0.0  0
 JBY  CONST_14  O3   CZ   CE2  CD2   180.00   0.0  0
 JBY  CONST_15  CD1  CE1  CZ   O3    180.00   0.0  0
 JBY  CONST_16  O2   C2   N3   C1    180.00   0.0  0
 JBY  CONST_17  CA1  C1   N3   C2    180.00   0.0  0
 JBY  CONST_18  CA3  N3   C1   N2    180.00   0.0  0
 JBY  CONST_19  CA2  C2   N3   CA3   180.00   0.0  0
 JBY  CONST_20  CA2  N2   C1   CA1   180.00   0.0  0
 JBY  CONST_21  H17  CE1  CD1  CG2   180.00   0.0  0
 JBY  CONST_22  H16  CE2  CD2  CG2   180.00   0.0  0
 JBY  CONST_23  H18  CD1  CG2  CD2   180.00   0.0  0
 JBY  CONST_24  H17  CE1  CZ   CE2   180.00   0.0  0
 JBY  CONST_25  H18  CD1  CE1  CZ    180.00   0.0  0
 JBY  CONST_26  H14  CD2  CE2  CZ    180.00   0.0  0
 JBY  CONST_27  H16  CE2  CZ   CE1   180.00   0.0  0
 JBY  CONST_28  H14  CD2  CG2  CD1   180.00   0.0  0
 JBY  CONST_29  CA3  N3   C2   O2      0.00   0.0  0
 JBY  CONST_30  CA1  C1   N3   CA3     0.00   0.0  0
 JBY  Var_01    CG2  CB2  CA2  C2   -179.86   0.0  2
 JBY  Var_02    CG2  CB2  CA2  N2     -0.29   0.0  2
 JBY  Var_03    CD1  CG2  CB2  CA2   178.30  30.0  2
 JBY  Var_04    CD2  CG2  CB2  CA2    -1.46  30.0  2
 JBY  Var_05    N    CA1  C1   N2      8.73  30.0  2
 JBY  Var_06    N    CA1  C1   N3   -173.14  30.0  2
 JBY  Var_07    H13  CB2  CA2  C2     -0.15   0.0  2
 JBY  Var_08    H13  CB2  CA2  N2    179.41   0.0  2
 JBY  Var_09    H8   CA1  C1   N2    128.97  30.0  2
 JBY  Var_10    H9   CA1  C1   N2   -117.23  30.0  2
 JBY  Var_11    H8   CA1  C1   N3    -52.90  30.0  2
 JBY  Var_12    H9   CA1  C1   N3     60.90  30.0  2
 JBY  Var_13    H13  CB2  CG2  CD2   178.84  30.0  2
 JBY  Var_14    H13  CB2  CG2  CD1    -1.40  30.0  2
 JBY  Var_15    H1   N    CA1  C1   -178.01  30.0  3
 JBY  Var_16    H2   N    CA1  C1    -62.29  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
 JBY  chir_01  CA3  CB3  C  N3  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
 JBY  plan-1  C1   0.020
 JBY  plan-1  C2   0.020
 JBY  plan-1  N2   0.020
 JBY  plan-1  N3   0.020
 JBY  plan-1  O2   0.020
 JBY  plan-1  CA3  0.020
 JBY  plan-1  CA1  0.020
 JBY  plan-1  CA2  0.020
 JBY  plan-1  CB2  0.020
 JBY  plan-1  CG2  0.020
 JBY  plan-1  H13  0.020
 JBY  plan-2  CB2  0.020
 JBY  plan-2  CG2  0.020
 JBY  plan-2  CD2  0.020
 JBY  plan-2  CE2  0.020
 JBY  plan-2  CZ   0.020
 JBY  plan-2  O3   0.020
 JBY  plan-2  CE1  0.020
 JBY  plan-2  CD1  0.020
 JBY  plan-2  H14  0.020
 JBY  plan-2  H16  0.020
 JBY  plan-2  H17  0.020
 JBY  plan-2  H18  0.020
 JBY  plan-3  C    0.020
 JBY  plan-3  CA3  0.020
 JBY  plan-3  O    0.020
 JBY  plan-3  OXT  0.020

