# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 17:00:37 2022
#   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  38  25  .  2022-09-22  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_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  -0.594  42.5303   -9.9644  156.1579
 BJO  CD3  C  C      0   0.423  42.4115  -11.0190  156.8088
 BJO  OE2  O  OC    -1  -0.609  43.0646  -12.0704  156.6697
 BJO  CG1  C  CH2    0  -0.588  41.3553  -11.0459  157.9393
 BJO  CB1  C  CH2    0  -0.520  40.3915   -9.8554  157.9130
 BJO  CA1  C  C      0   0.330  39.4210   -9.9540  159.0407
 BJO  N    N  NH2    0  -0.741  38.3159  -10.6156  158.8251
 BJO  C1   C  C      0   0.492  39.7551   -9.3699  160.2913
 BJO  N2   N  N      0  -0.435  40.7410   -8.5061  160.3677
 BJO  CA2  C  C      0   0.062  40.8138   -8.0758  161.6450
 BJO  C2   C  C      0   0.491  39.7932   -8.7557  162.4391
 BJO  O2   O  O      0  -0.491  39.5173   -8.7180  163.6341
 BJO  N3   N  NT     0  -0.540  39.1355   -9.5401  161.5156
 BJO  CA3  C  CH2    0  -0.516  38.2090  -10.5754  161.8976
 BJO  C    C  C      0   0.407  38.7195  -12.0160  161.6153
 BJO  O    O  O      0  -0.592  37.8437  -12.8922  161.7074
 BJO  CB2  C  C1     0  -0.356  41.7939   -7.1145  161.9588
 BJO  CG2  C  CR6    0   0.076  42.1582   -6.4299  163.1037
 BJO  CD1  C  CR16   0  -0.245  43.2469   -5.4981  162.9944
 BJO  CE1  C  CR16   0  -0.411  43.6860   -4.7631  164.0416
 BJO  CZ   C  CR6    0   0.363  43.0757   -4.8703  165.3567
 BJO  OH   O  O      0  -0.491  43.4595   -4.2036  166.3235
 BJO  CE2  C  CR16   0  -0.389  41.9776   -5.8204  165.4532
 BJO  CD2  C  CR16   0  -0.293  41.5490   -6.5504  164.3970
 BJO  OXT  O  OC    -1  -0.578  39.9263  -12.1442  161.3566
 BJO  H11  H  HCH2   0   0.236  40.7962  -11.9836  157.8853
 BJO  H12  H  HCH2   0   0.245  41.8813  -11.0688  158.8989
 BJO  H10  H  HCH2   0   0.272  40.9497   -8.9273  157.9915
 BJO  H9   H  HCH2   0   0.264  39.8417   -9.8375  156.9705
 BJO  H    H  HNH2   0   0.443  37.5912  -10.7502  159.5125
 BJO  H2   H  HNH2   0   0.440  38.1352  -11.0153  157.9155
 BJO  H31  H  HCH2   0   0.285  38.0575  -10.4757  162.9741
 BJO  H32  H  HCH2   0   0.258  37.2224  -10.4030  161.4581
 BJO  H13  H  H      0   0.268  42.3846   -6.8646  161.0811
 BJO  H15  H  HCR6   0   0.256  43.7276   -5.3875  162.0283
 BJO  H16  H  HCR6   0   0.244  44.5102   -4.0707  163.9173
 BJO  H18  H  HCR6   0   0.243  41.4967   -5.9329  166.4180
 BJO  H19  H  HCR6   0   0.291  40.7299   -7.2441  164.5208

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  deloc   1.245  0.020  1.245
 BJO  OE2  CD3  deloc   1.245  0.020  1.245
 BJO  CD3  CG1  single  1.547  0.020  1.547
 BJO  CG1  CB1  single  1.532  0.020  1.532
 BJO  CB1  CA1  single  1.491  0.020  1.491
 BJO  N    CA1  single  1.306  0.020  1.306
 BJO  CA1  C1   double  1.420  0.020  1.420
 BJO  C1   N2   single  1.313  0.020  1.313
 BJO  C1   N3   single  1.383  0.020  1.383
 BJO  N2   CA2  double  1.350  0.020  1.350
 BJO  N3   CA3  single  1.441  0.020  1.441
 BJO  N3   C2   single  1.379  0.020  1.379
 BJO  CA2  CB2  single  1.408  0.020  1.408
 BJO  CA2  C2   single  1.461  0.020  1.461
 BJO  CA3  C    single  1.554  0.020  1.554
 BJO  C    O    deloc   1.242  0.020  1.242
 BJO  CB2  CG2  double  1.383  0.020  1.383
 BJO  C2   O2   double  1.227  0.020  1.227
 BJO  CD1  CG2  single  1.437  0.020  1.437
 BJO  CD1  CE1  double  1.353  0.020  1.353
 BJO  CG2  CD2  single  1.435  0.020  1.435
 BJO  CE1  CZ   single  1.454  0.020  1.454
 BJO  CD2  CE2  double  1.354  0.020  1.354
 BJO  CZ   CE2  single  1.455  0.020  1.455
 BJO  CZ   OH   double  1.236  0.020  1.236
 BJO  C    OXT  deloc   1.241  0.020  1.241
 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

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  115.14  3.000
 BJO  CG1  CD3  OE1  117.50  3.000
 BJO  OE2  CD3  OE1  127.35  3.000
 BJO  H12  CG1  H11  105.73  3.000
 BJO  H12  CG1  CB1  109.49  3.000
 BJO  H11  CG1  CB1  110.12  3.000
 BJO  H12  CG1  CD3  108.23  3.000
 BJO  H11  CG1  CD3  109.14  3.000
 BJO  CB1  CG1  CD3  113.79  3.000
 BJO  H9   CB1  H10  107.90  3.000
 BJO  H9   CB1  CA1  109.05  3.000
 BJO  H10  CB1  CA1  109.66  3.000
 BJO  H9   CB1  CG1  110.15  3.000
 BJO  H10  CB1  CG1  109.85  3.000
 BJO  CA1  CB1  CG1  110.19  3.000
 BJO  C1   CA1  N    123.56  3.000
 BJO  C1   CA1  CB1  119.06  3.000
 BJO  N    CA1  CB1  117.35  3.000
 BJO  H2   N    H    115.64  3.000
 BJO  H2   N    CA1  120.04  3.000
 BJO  H    N    CA1  124.30  3.000
 BJO  N3   C1   N2   111.47  3.000
 BJO  N3   C1   CA1  128.59  3.000
 BJO  N2   C1   CA1  119.89  3.000
 BJO  CA2  N2   C1   107.77  3.000
 BJO  CB2  CA2  C2   133.06  3.000
 BJO  C2   CA2  N2   109.17  3.000
 BJO  CB2  CA2  N2   117.77  3.000
 BJO  N3   C2   O2   124.24  3.000
 BJO  O2   C2   CA2  132.23  3.000
 BJO  N3   C2   CA2  103.53  3.000
 BJO  CA3  N3   C2   122.54  3.000
 BJO  C2   N3   C1   108.02  3.000
 BJO  CA3  N3   C1   127.68  3.000
 BJO  H32  CA3  H31  104.88  3.000
 BJO  H32  CA3  C    111.68  3.000
 BJO  H31  CA3  C    108.02  3.000
 BJO  H32  CA3  N3   111.11  3.000
 BJO  H31  CA3  N3   106.56  3.000
 BJO  C    CA3  N3   113.99  3.000
 BJO  OXT  C    O    128.92  3.000
 BJO  OXT  C    CA3  116.94  3.000
 BJO  O    C    CA3  114.13  3.000
 BJO  H13  CB2  CG2  114.30  3.000
 BJO  H13  CB2  CA2  110.81  3.000
 BJO  CG2  CB2  CA2  134.89  3.000
 BJO  CD2  CG2  CD1  116.40  3.000
 BJO  CD2  CG2  CB2  126.37  3.000
 BJO  CD1  CG2  CB2  117.23  3.000
 BJO  H15  CD1  CE1  119.36  3.000
 BJO  H15  CD1  CG2  118.00  3.000
 BJO  CE1  CD1  CG2  122.63  3.000
 BJO  H16  CE1  CZ   118.05  3.000
 BJO  H16  CE1  CD1  120.35  3.000
 BJO  CZ   CE1  CD1  121.60  3.000
 BJO  CE2  CZ   OH   122.33  3.000
 BJO  OH   CZ   CE1  122.53  3.000
 BJO  CE2  CZ   CE1  115.14  3.000
 BJO  H18  CE2  CD2  119.87  3.000
 BJO  H18  CE2  CZ   117.49  3.000
 BJO  CD2  CE2  CZ   122.64  3.000
 BJO  H19  CD2  CE2  119.80  3.000
 BJO  H19  CD2  CG2  118.63  3.000
 BJO  CE2  CD2  CG2  121.58  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_12  CA3  N3   C2   O2      0.00   0.0  0
 BJO  Var_01    CD1  CG2  CB2  CA2  -179.68   0.0  2
 BJO  Var_02    CG2  CB2  CA2  N2    178.58  30.0  2
 BJO  Var_03    N2   C1   CA1  CB1    15.48   0.0  2
 BJO  Var_04    C    CA3  N3   C1     52.26  30.0  3
 BJO  Var_05    C1   CA1  CB1  CG1    89.22  30.0  3
 BJO  Var_06    O    C    CA3  N3   -167.35  30.0  3
 BJO  Var_07    H    N    CA1  C1      1.79  30.0  2
 BJO  Var_08    CB1  CG1  CD3  OE1    12.12  30.0  3
 BJO  Var_09    CA1  CB1  CG1  CD3  -179.40  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-4  CA3  0.020
 BJO  plan-4  C    0.020
 BJO  plan-4  O    0.020
 BJO  plan-4  OXT  0.020

