# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 16 22:29:50 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: {(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-[(2,3-difluoro-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: C[C@@H](O)[C@H](N)C1=NC(=C\c2ccc(O)c(F)c2F)/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
 MJ1  MJ1  '{(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-[(2,3-difluoro-4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid'  L-peptide  40  25  .  2022-07-25  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MJ1
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
 MJ1  C1   C  CR5   0   0.584   1.8133   0.5984  -0.0474
 MJ1  C2   C  CR5   0   0.539   1.2661  -1.4198   0.7483
 MJ1  C3   C  C     0   0.552   4.1236  -1.5475  -0.7862
 MJ1  CB1  C  CH1   0   0.047   3.1395   2.4780   0.8724
 MJ1  CB2  C  C1    0  -0.365  -1.1703  -1.0797   0.4394
 MJ1  CG1  C  CH3   0  -0.707   4.0530   3.6526   0.5651
 MJ1  OG1  O  OH1   0  -0.662   1.9724   2.8703   1.5562
 MJ1  CG2  C  CR6   0  -0.086  -2.3999  -0.4122   0.0755
 MJ1  CD1  C  CR16  0  -0.298  -2.4742   0.8823  -0.4653
 MJ1  CD2  C  CR6   0   0.414  -3.6149  -1.0740   0.2605
 MJ1  CE1  C  CR16  0  -0.341  -3.6773   1.4672  -0.7970
 MJ1  CE2  C  CR6   0   0.305  -4.8216  -0.4958  -0.0668
 MJ1  CZ   C  CR6   0   0.254  -4.8793   0.7858  -0.6025
 MJ1  OH   O  OH1   0  -0.611  -6.0284   1.3795  -0.9317
 MJ1  CA1  C  CH1   0  -0.242   2.6834   1.7599  -0.4187
 MJ1  CA2  C  CR5   0   0.102   0.0919  -0.6220   0.3328
 MJ1  CA3  C  CH2   0  -0.476   3.6881  -0.9900   0.5532
 MJ1  F1   F  F     0  -0.309  -5.9588  -1.1772   0.1324
 MJ1  F2   F  F     0  -0.294  -3.6395  -2.3077   0.7665
 MJ1  N1   N  NH2   0  -0.781   1.9813   2.5795  -1.3793
 MJ1  N2   N  N     0  -0.473   0.5329   0.5991  -0.1540
 MJ1  N3   N  NR5   0  -0.566   2.3232  -0.5597   0.5154
 MJ1  O2   O  O     0  -0.437   1.3515  -2.5484   1.1816
 MJ1  O3   O  O     0  -0.425   3.4243  -1.5650  -1.7637
 MJ1  H2   H  HCH1  0   0.210   3.7145   1.7614   1.4766
 MJ1  H3   H  H     0   0.277  -1.2590  -2.0774   0.8529
 MJ1  H4   H  HCH3  0   0.247   4.4209   4.1006   1.4896
 MJ1  H5   H  HCH3  0   0.236   4.9229   3.3318  -0.0095
 MJ1  H6   H  HCH3  0   0.230   3.5358   4.4296   0.0016
 MJ1  H7   H  HOH1  0   0.456   2.2315   3.3648   2.3401
 MJ1  H9   H  HCR6  0   0.295  -1.5577   1.4308  -0.6247
 MJ1  H10  H  HCR6  0   0.287  -3.7024   2.4651  -1.2147
 MJ1  H11  H  HCH1  0   0.277   3.5896   1.3809  -0.9041
 MJ1  H12  H  HCH2  0   0.330   3.7985  -1.7569   1.3218
 MJ1  H13  H  HCH2  0   0.323   4.3534  -0.1764   0.8449
 MJ1  H14  H  HNH2  0   0.351   1.1781   3.0147  -0.9441
 MJ1  H15  H  HNH2  0   0.362   2.5849   3.3254  -1.6990
 MJ1  O1   O  OH1   0  -0.583   5.3643  -1.9963  -0.7308
 MJ1  H1   H  HOH1  0   0.485  -6.7884   0.8064  -0.7710
 MJ1  H8   H  HOH1  0   0.490   5.6437  -2.3365  -1.5946

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
 MJ1  O3   C3   double    1.202  0.020  1.202
 MJ1  C3   CA3  single    1.515  0.020  1.515
 MJ1  CA3  N3   single    1.432  0.020  1.432
 MJ1  N3   C2   single    1.383  0.020  1.383
 MJ1  N3   C1   single    1.385  0.020  1.385
 MJ1  N1   CA1  single    1.445  0.020  1.445
 MJ1  O2   C2   double    1.212  0.020  1.212
 MJ1  CA1  C1   single    1.498  0.020  1.498
 MJ1  CA1  CB1  single    1.546  0.020  1.546
 MJ1  C2   CA2  single    1.479  0.020  1.479
 MJ1  C1   N2   double    1.285  0.020  1.285
 MJ1  CG1  CB1  single    1.519  0.020  1.519
 MJ1  CB1  OG1  single    1.408  0.020  1.408
 MJ1  CA2  N2   single    1.387  0.020  1.387
 MJ1  CA2  CB2  double    1.347  0.020  1.347
 MJ1  CB2  CG2  single    1.446  0.020  1.446
 MJ1  CG2  CD2  aromatic  1.396  0.020  1.396
 MJ1  CG2  CD1  aromatic  1.405  0.020  1.405
 MJ1  F2   CD2  single    1.334  0.020  1.334
 MJ1  CD2  CE2  aromatic  1.377  0.020  1.377
 MJ1  CD1  CE1  aromatic  1.378  0.020  1.378
 MJ1  CE2  F1   single    1.341  0.020  1.341
 MJ1  CE2  CZ   aromatic  1.390  0.020  1.390
 MJ1  CE1  CZ   aromatic  1.395  0.020  1.395
 MJ1  CZ   OH   single    1.335  0.020  1.335
 MJ1  CB1  H2   single    0.970  0.020  1.090
 MJ1  CB2  H3   single    0.930  0.020  1.080
 MJ1  CG1  H4   single    0.970  0.020  1.090
 MJ1  CG1  H5   single    0.970  0.020  1.090
 MJ1  CG1  H6   single    0.970  0.020  1.090
 MJ1  OG1  H7   single    0.850  0.020  0.980
 MJ1  CD1  H9   single    0.930  0.020  1.080
 MJ1  CE1  H10  single    0.930  0.020  1.080
 MJ1  CA1  H11  single    0.970  0.020  1.090
 MJ1  CA3  H12  single    0.970  0.020  1.090
 MJ1  CA3  H13  single    0.970  0.020  1.090
 MJ1  N1   H14  single    0.890  0.020  1.040
 MJ1  N1   H15  single    0.890  0.020  1.040
 MJ1  C3   O1   single    1.321  0.020  1.321
 MJ1  OH   H1   single    0.850  0.020  0.980
 MJ1  O1   H8   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
 MJ1  N3   C1   N2   113.65  3.000
 MJ1  N2   C1   CA1  123.91  3.000
 MJ1  N3   C1   CA1  122.36  3.000
 MJ1  O2   C2   N3   125.85  3.000
 MJ1  O2   C2   CA2  131.20  3.000
 MJ1  N3   C2   CA2  102.95  3.000
 MJ1  O1   C3   O3   125.15  3.000
 MJ1  O1   C3   CA3  110.98  3.000
 MJ1  O3   C3   CA3  123.86  3.000
 MJ1  H2   CB1  CA1  108.09  3.000
 MJ1  H2   CB1  OG1  110.37  3.000
 MJ1  CA1  CB1  OG1  106.88  3.000
 MJ1  H2   CB1  CG1  107.49  3.000
 MJ1  OG1  CB1  CG1  112.40  3.000
 MJ1  CA1  CB1  CG1  111.56  3.000
 MJ1  H3   CB2  CA2  114.82  3.000
 MJ1  H3   CB2  CG2  116.84  3.000
 MJ1  CA2  CB2  CG2  128.34  3.000
 MJ1  H6   CG1  H5   108.40  3.000
 MJ1  H6   CG1  H4   107.78  3.000
 MJ1  H5   CG1  H4   107.35  3.000
 MJ1  H6   CG1  CB1  111.72  3.000
 MJ1  H5   CG1  CB1  111.01  3.000
 MJ1  H4   CG1  CB1  110.41  3.000
 MJ1  H7   OG1  CB1  108.39  3.000
 MJ1  CD2  CG2  CD1  116.22  3.000
 MJ1  CD1  CG2  CB2  124.56  3.000
 MJ1  CD2  CG2  CB2  119.22  3.000
 MJ1  H9   CD1  CE1  119.33  3.000
 MJ1  H9   CD1  CG2  118.68  3.000
 MJ1  CE1  CD1  CG2  121.99  3.000
 MJ1  F2   CD2  CE2  117.53  3.000
 MJ1  CE2  CD2  CG2  122.14  3.000
 MJ1  F2   CD2  CG2  120.33  3.000
 MJ1  H10  CE1  CZ   118.96  3.000
 MJ1  H10  CE1  CD1  120.30  3.000
 MJ1  CZ   CE1  CD1  120.74  3.000
 MJ1  F1   CE2  CZ   119.38  3.000
 MJ1  CZ   CE2  CD2  120.99  3.000
 MJ1  F1   CE2  CD2  119.63  3.000
 MJ1  OH   CZ   CE2  122.75  3.000
 MJ1  OH   CZ   CE1  119.34  3.000
 MJ1  CE2  CZ   CE1  117.91  3.000
 MJ1  H1   OH   CZ   111.88  3.000
 MJ1  H11  CA1  N1   107.68  3.000
 MJ1  H11  CA1  CB1  106.65  3.000
 MJ1  N1   CA1  CB1  115.79  3.000
 MJ1  H11  CA1  C1   108.79  3.000
 MJ1  CB1  CA1  C1   108.93  3.000
 MJ1  N1   CA1  C1   108.81  3.000
 MJ1  N2   CA2  CB2  128.69  3.000
 MJ1  CB2  CA2  C2   122.58  3.000
 MJ1  N2   CA2  C2   108.73  3.000
 MJ1  H13  CA3  H12  105.91  3.000
 MJ1  H13  CA3  N3   111.37  3.000
 MJ1  H12  CA3  N3   109.05  3.000
 MJ1  H13  CA3  C3   109.61  3.000
 MJ1  H12  CA3  C3   109.57  3.000
 MJ1  N3   CA3  C3   111.18  3.000
 MJ1  H15  N1   H14  107.00  3.000
 MJ1  H15  N1   CA1  109.79  3.000
 MJ1  H14  N1   CA1  110.11  3.000
 MJ1  CA2  N2   C1   106.70  3.000
 MJ1  CA3  N3   C2   122.51  3.000
 MJ1  C2   N3   C1   107.89  3.000
 MJ1  CA3  N3   C1   127.82  3.000
 MJ1  H8   O1   C3   110.65  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
 MJ1  CONST_01  CZ   CE2  CD2  CG2    0.00   0.0  0
 MJ1  CONST_02  CZ   CE1  CD1  CG2    0.00   0.0  0
 MJ1  CONST_03  CE2  CD2  CG2  CD1    0.00   0.0  0
 MJ1  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 MJ1  CONST_05  CE1  CD1  CG2  CD2    0.00   0.0  0
 MJ1  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 MJ1  CONST_07  CA2  C2   N3   C1     0.00   0.0  0
 MJ1  CONST_08  C2   CA2  N2   C1     0.00   0.0  0
 MJ1  CONST_09  N2   C1   N3   C2     0.00   0.0  0
 MJ1  CONST_10  N3   C1   N2   CA2    0.00   0.0  0
 MJ1  CONST_11  N3   C2   CA2  N2     0.00   0.0  0
 MJ1  CONST_12  CE2  CD2  CG2  CB2  180.00   0.0  0
 MJ1  CONST_13  CE1  CD1  CG2  CB2  180.00   0.0  0
 MJ1  CONST_14  F1   CE2  CD2  CG2  180.00   0.0  0
 MJ1  CONST_15  F2   CD2  CG2  CD1  180.00   0.0  0
 MJ1  CONST_16  OH   CZ   CE1  CD1  180.00   0.0  0
 MJ1  CONST_17  OH   CZ   CE2  CD2  180.00   0.0  0
 MJ1  CONST_18  F1   CE2  CZ   CE1  180.00   0.0  0
 MJ1  CONST_19  F2   CD2  CE2  CZ   180.00   0.0  0
 MJ1  CONST_20  O2   C2   N3   C1   180.00   0.0  0
 MJ1  CONST_21  CA1  C1   N3   C2   180.00   0.0  0
 MJ1  CONST_22  CA2  N2   C1   CA1  180.00   0.0  0
 MJ1  CONST_23  CA3  N3   C2   CA2  180.00   0.0  0
 MJ1  CONST_24  N2   C1   N3   CA3  180.00   0.0  0
 MJ1  CONST_25  H10  CE1  CD1  CG2  180.00   0.0  0
 MJ1  CONST_26  H9   CD1  CG2  CD2  180.00   0.0  0
 MJ1  CONST_28  O2   C2   N3   CA3    0.00   0.0  0
 MJ1  CONST_29  H8   O1   C3   CA3  180.00   0.0  0
 MJ1  Var_01    CG2  CB2  CA2  C2   179.98  30.0  2
 MJ1  Var_02    CA2  CB2  CG2  CD1   -0.37  30.0  2
 MJ1  Var_03    C3   CA3  N3   C1   -76.87  30.0  2
 MJ1  Var_04    O3   C3   CA3  N3     3.14  30.0  1

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
 MJ1  chir_01  CB1  CA1  CG1  OG1  negativ
 MJ1  chir_02  CA1  N1   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
 MJ1  plan-1  C1   0.020
 MJ1  plan-1  C2   0.020
 MJ1  plan-1  CB2  0.020
 MJ1  plan-1  CA1  0.020
 MJ1  plan-1  CA2  0.020
 MJ1  plan-1  CA3  0.020
 MJ1  plan-1  N2   0.020
 MJ1  plan-1  N3   0.020
 MJ1  plan-1  O2   0.020
 MJ1  plan-2  CB2  0.020
 MJ1  plan-2  CG2  0.020
 MJ1  plan-2  CD1  0.020
 MJ1  plan-2  CD2  0.020
 MJ1  plan-2  CE1  0.020
 MJ1  plan-2  CE2  0.020
 MJ1  plan-2  CZ   0.020
 MJ1  plan-2  OH   0.020
 MJ1  plan-2  F1   0.020
 MJ1  plan-2  F2   0.020
 MJ1  plan-2  H9   0.020
 MJ1  plan-2  H10  0.020
 MJ1  plan-3  C3   0.020
 MJ1  plan-3  CA3  0.020
 MJ1  plan-3  O3   0.020
 MJ1  plan-3  O1   0.020
 MJ1  plan-3  H8   0.020

