# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 08:58:30 2021
#   Inital geometry file: a 119 line input string
#   Ligand name: (4Z)-4-amino-4-{1-(carboxymethyl)-5-oxo-4-[(4-oxocyclohexa-2,5-dien-1-ylidene)methyl]-1,5-dihydro-2H-imidazol-2-ylidene}butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(/CCC(O)=O)=C1/N=C(C=C2C=CC(=O)C=C2)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
 BJO  BJO  '(4Z)-4-amino-4-{1-(carboxymethyl)-5-oxo-4-[(4-oxocyclohexa-2,5-dien-1-ylidene)methyl]-1,5-dihydro-2H-imidazol-2-ylidene}butanoic acid'  L-peptide  40  25  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_BJO
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
 BJO  OE1  O  O     0  -0.438  42.2607  -10.0885  155.9210
 BJO  CD3  C  C     0   0.562  42.2697  -10.9107  156.8017
 BJO  OE2  O  OH1   0  -0.591  43.1357  -11.9135  156.8614
 BJO  CG1  C  CH2   0  -0.588  41.3163  -10.9337  157.9662
 BJO  CB1  C  CH2   0  -0.532  40.2897   -9.8062  157.8831
 BJO  CA1  C  C     0   0.322  39.3319   -9.8974  159.0289
 BJO  N    N  NH2   0  -0.752  38.2149  -10.5509  158.8227
 BJO  C1   C  C     0   0.491  39.6986   -9.3385  160.2665
 BJO  N2   N  N     0  -0.419  40.7155   -8.5026  160.3505
 BJO  CA2  C  C     0   0.071  40.8293   -8.1016  161.6223
 BJO  C2   C  C     0   0.515  39.8208   -8.7780  162.4370
 BJO  O2   O  O     0  -0.481  39.5861   -8.7753  163.6373
 BJO  N3   N  NT    0  -0.569  39.1136   -9.5240  161.5121
 BJO  CA3  C  CH2   0  -0.494  38.1605  -10.5167  161.9173
 BJO  C    C  C     0   0.541  38.6050  -11.9515  161.7134
 BJO  O    O  O     0  -0.429  37.8370  -12.8751  161.7777
 BJO  CB2  C  C1    0  -0.355  41.8479   -7.1643  161.9292
 BJO  CG2  C  C     0   0.088  42.2258   -6.4877  163.0649
 BJO  CD1  C  C1    0  -0.241  43.3507   -5.5932  162.9516
 BJO  CE1  C  C1    0  -0.405  43.8032   -4.8618  163.9912
 BJO  CZ   C  C     0   0.373  43.1715   -4.9317  165.3010
 BJO  OH   O  O     0  -0.483  43.5673   -4.2657  166.2600
 BJO  CE2  C  C1    0  -0.383  42.0372   -5.8413  165.4036
 BJO  CD2  C  C1    0  -0.286  41.5964   -6.5704  164.3561
 BJO  OXT  O  OH1   0  -0.574  39.9006  -12.0588  161.4873
 BJO  H1   H  HOH1  0   0.483  43.7372  -11.8800  156.1023
 BJO  H11  H  HCH2  0   0.301  40.8262  -11.9106  157.9940
 BJO  H12  H  HCH2  0   0.303  41.8992  -10.8603  158.8878
 BJO  H10  H  HCH2  0   0.300  40.7901   -8.8408  157.9072
 BJO  H9   H  HCH2  0   0.292  39.7310   -9.8679  156.9488
 BJO  H    H  HNH2  0   0.441  37.4593  -10.6025  159.4862
 BJO  H2   H  HNH2  0   0.446  38.0149  -10.9416  157.9141
 BJO  H31  H  HCH2  0   0.340  37.9925  -10.3830  162.9892
 BJO  H32  H  HCH2  0   0.315  37.1807  -10.3670  161.4608
 BJO  H13  H  H     0   0.277  42.4408   -6.9374  161.0475
 BJO  H15  H  H     0   0.263  43.8429   -5.5150  161.9885
 BJO  H16  H  H     0   0.256  44.6523   -4.1998  163.8708
 BJO  H18  H  H     0   0.255  41.5436   -5.9194  166.3651
 BJO  H19  H  H     0   0.294  40.7521   -7.2325  164.4801
 BJO  HXT  H  HOH1  0   0.493  40.1479  -12.9900  161.3756

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
 BJO  OE1  CD3  double  1.205  0.020  1.205
 BJO  OE2  CD3  single  1.326  0.020  1.326
 BJO  CD3  CG1  single  1.505  0.020  1.505
 BJO  CG1  CB1  single  1.527  0.020  1.527
 BJO  CB1  CA1  single  1.496  0.020  1.496
 BJO  N    CA1  single  1.310  0.020  1.310
 BJO  CA1  C1   double  1.407  0.020  1.407
 BJO  C1   N2   single  1.319  0.020  1.319
 BJO  C1   N3   single  1.389  0.020  1.389
 BJO  N2   CA2  double  1.338  0.020  1.338
 BJO  N3   CA3  single  1.435  0.020  1.435
 BJO  N3   C2   single  1.383  0.020  1.383
 BJO  CA2  CB2  single  1.418  0.020  1.418
 BJO  CA2  C2   single  1.462  0.020  1.462
 BJO  CA3  C    single  1.516  0.020  1.516
 BJO  C    O    double  1.203  0.020  1.203
 BJO  CB2  CG2  double  1.375  0.020  1.375
 BJO  C2   O2   double  1.223  0.020  1.223
 BJO  CD1  CG2  single  1.442  0.020  1.442
 BJO  CD1  CE1  double  1.349  0.020  1.349
 BJO  CG2  CD2  single  1.439  0.020  1.439
 BJO  CE1  CZ   single  1.456  0.020  1.456
 BJO  CD2  CE2  double  1.350  0.020  1.350
 BJO  CZ   CE2  single  1.458  0.020  1.458
 BJO  CZ   OH   double  1.233  0.020  1.233
 BJO  C    OXT  single  1.320  0.020  1.320
 BJO  OE2  H1   single  0.850  0.020  0.980
 BJO  CG1  H11  single  0.970  0.020  1.090
 BJO  CG1  H12  single  0.970  0.020  1.090
 BJO  CB1  H10  single  0.970  0.020  1.090
 BJO  CB1  H9   single  0.970  0.020  1.090
 BJO  N    H    single  0.860  0.020  1.020
 BJO  N    H2   single  0.860  0.020  1.020
 BJO  CA3  H31  single  0.970  0.020  1.090
 BJO  CA3  H32  single  0.970  0.020  1.090
 BJO  CB2  H13  single  0.930  0.020  1.080
 BJO  CD1  H15  single  0.930  0.020  1.080
 BJO  CE1  H16  single  0.930  0.020  1.080
 BJO  CE2  H18  single  0.930  0.020  1.080
 BJO  CD2  H19  single  0.930  0.020  1.080
 BJO  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
 BJO  CG1  CD3  OE2  111.55  3.000
 BJO  CG1  CD3  OE1  124.83  3.000
 BJO  OE2  CD3  OE1  123.62  3.000
 BJO  H1   OE2  CD3  110.11  3.000
 BJO  H12  CG1  H11  106.11  3.000
 BJO  H12  CG1  CB1  110.78  3.000
 BJO  H11  CG1  CB1  111.08  3.000
 BJO  H12  CG1  CD3  108.27  3.000
 BJO  H11  CG1  CD3  108.50  3.000
 BJO  CB1  CG1  CD3  111.87  3.000
 BJO  H9   CB1  H10  107.76  3.000
 BJO  H9   CB1  CA1  108.95  3.000
 BJO  H10  CB1  CA1  109.37  3.000
 BJO  H9   CB1  CG1  110.44  3.000
 BJO  H10  CB1  CG1  110.17  3.000
 BJO  CA1  CB1  CG1  110.10  3.000
 BJO  C1   CA1  N    123.97  3.000
 BJO  C1   CA1  CB1  118.86  3.000
 BJO  N    CA1  CB1  117.10  3.000
 BJO  H2   N    H    115.14  3.000
 BJO  H2   N    CA1  120.24  3.000
 BJO  H    N    CA1  124.16  3.000
 BJO  N3   C1   N2   110.63  3.000
 BJO  N3   C1   CA1  128.78  3.000
 BJO  N2   C1   CA1  120.59  3.000
 BJO  CA2  N2   C1   108.42  3.000
 BJO  CB2  CA2  C2   132.90  3.000
 BJO  C2   CA2  N2   109.40  3.000
 BJO  CB2  CA2  N2   117.70  3.000
 BJO  N3   C2   O2   124.02  3.000
 BJO  O2   C2   CA2  132.70  3.000
 BJO  N3   C2   CA2  103.27  3.000
 BJO  CA3  N3   C2   121.61  3.000
 BJO  C2   N3   C1   108.21  3.000
 BJO  CA3  N3   C1   128.73  3.000
 BJO  H32  CA3  H31  104.79  3.000
 BJO  H32  CA3  C    109.69  3.000
 BJO  H31  CA3  C    107.02  3.000
 BJO  H32  CA3  N3   112.55  3.000
 BJO  H31  CA3  N3   107.12  3.000
 BJO  C    CA3  N3   114.97  3.000
 BJO  OXT  C    O    125.00  3.000
 BJO  OXT  C    CA3  112.82  3.000
 BJO  O    C    CA3  122.17  3.000
 BJO  H13  CB2  CG2  114.68  3.000
 BJO  H13  CB2  CA2  110.76  3.000
 BJO  CG2  CB2  CA2  134.55  3.000
 BJO  CD2  CG2  CD1  116.58  3.000
 BJO  CD2  CG2  CB2  126.36  3.000
 BJO  CD1  CG2  CB2  117.06  3.000
 BJO  H15  CD1  CE1  119.54  3.000
 BJO  H15  CD1  CG2  117.95  3.000
 BJO  CE1  CD1  CG2  122.52  3.000
 BJO  H16  CE1  CZ   117.99  3.000
 BJO  H16  CE1  CD1  120.56  3.000
 BJO  CZ   CE1  CD1  121.44  3.000
 BJO  CE2  CZ   OH   122.16  3.000
 BJO  OH   CZ   CE1  122.31  3.000
 BJO  CE2  CZ   CE1  115.53  3.000
 BJO  H18  CE2  CD2  120.05  3.000
 BJO  H18  CE2  CZ   117.51  3.000
 BJO  CD2  CE2  CZ   122.44  3.000
 BJO  H19  CD2  CE2  119.81  3.000
 BJO  H19  CD2  CG2  118.70  3.000
 BJO  CE2  CD2  CG2  121.49  3.000
 BJO  HXT  OXT  C    110.37  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
 BJO  CONST_01  C2   CA2  N2   C1      0.00   0.0  0
 BJO  CONST_02  CA2  C2   N3   C1      0.00   0.0  0
 BJO  CONST_03  C2   N3   C1   N2      0.00   0.0  0
 BJO  CONST_04  N3   C2   CA2  N2      0.00   0.0  0
 BJO  CONST_05  N3   C1   N2   CA2     0.00   0.0  0
 BJO  CONST_06  CA2  N2   C1   CA1   180.00   0.0  0
 BJO  CONST_07  C2   N3   C1   CA1   180.00   0.0  0
 BJO  CONST_08  O2   C2   N3   C1    180.00   0.0  0
 BJO  CONST_09  CA3  N3   C1   N2    180.00   0.0  0
 BJO  CONST_10  CA3  N3   C2   CA2   180.00   0.0  0
 BJO  CONST_11  CA3  N3   C1   CA1     0.00   0.0  0
 BJO  CONST_12  CA3  N3   C2   O2      0.00   0.0  0
 BJO  CONST_13  H1   OE2  CD3  OE1     0.00   0.0  0
 BJO  CONST_14  HXT  OXT  C    CA3   180.00   0.0  0
 BJO  Var_01    CD1  CG2  CB2  CA2  -179.84   0.0  2
 BJO  Var_02    CG2  CB2  CA2  N2    176.30  30.0  2
 BJO  Var_03    N2   C1   CA1  CB1    14.79   0.0  2
 BJO  Var_04    C    CA3  N3   C1     57.31  30.0  3
 BJO  Var_05    C1   CA1  CB1  CG1    83.32  30.0  3
 BJO  Var_06    O    C    CA3  N3   -166.38  30.0  3
 BJO  Var_07    H    N    CA1  C1      9.10  30.0  2
 BJO  Var_08    CB1  CG1  CD3  OE1     1.86  30.0  3
 BJO  Var_09    CA1  CB1  CG1  CD3   177.84  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
 BJO  plan-1  CB1  0.020
 BJO  plan-1  CA1  0.020
 BJO  plan-1  N    0.020
 BJO  plan-1  C1   0.020
 BJO  plan-1  N2   0.020
 BJO  plan-1  CA2  0.020
 BJO  plan-1  C2   0.020
 BJO  plan-1  O2   0.020
 BJO  plan-1  N3   0.020
 BJO  plan-1  CA3  0.020
 BJO  plan-1  CB2  0.020
 BJO  plan-2  CA2  0.020
 BJO  plan-2  CB2  0.020
 BJO  plan-2  CG2  0.020
 BJO  plan-2  CD1  0.020
 BJO  plan-2  CE1  0.020
 BJO  plan-2  CZ   0.020
 BJO  plan-2  OH   0.020
 BJO  plan-2  CE2  0.020
 BJO  plan-2  CD2  0.020
 BJO  plan-2  H13  0.020
 BJO  plan-2  H15  0.020
 BJO  plan-2  H16  0.020
 BJO  plan-2  H18  0.020
 BJO  plan-2  H19  0.020
 BJO  plan-3  OE1  0.020
 BJO  plan-3  CD3  0.020
 BJO  plan-3  OE2  0.020
 BJO  plan-3  CG1  0.020
 BJO  plan-3  H1   0.020
 BJO  plan-4  CA3  0.020
 BJO  plan-4  C    0.020
 BJO  plan-4  O    0.020
 BJO  plan-4  OXT  0.020
 BJO  plan-4  HXT  0.020

