# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jun  6 16:44:43 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  39  25  .  2022-07-25  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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   0.586   1.8220   0.5797  -0.0110
 MJ1  C2   C  CR5    0   0.528   1.2661  -1.4165   0.7927
 MJ1  C3   C  C      0   0.421   4.1350  -1.5159  -0.8276
 MJ1  CB1  C  CH1    0   0.046   3.1476   2.4579   0.9096
 MJ1  CB2  C  C1     0  -0.377  -1.1703  -1.0808   0.4501
 MJ1  CG1  C  CH3    0  -0.707   4.0745   3.6238   0.6071
 MJ1  OG1  O  OH1    0  -0.664   1.9780   2.8674   1.5815
 MJ1  CG2  C  CR6    0  -0.085  -2.3962  -0.4095   0.0736
 MJ1  CD1  C  CR16   0  -0.302  -2.4609   0.8871  -0.4626
 MJ1  CD2  C  CR6    0   0.410  -3.6158  -1.0649   0.2457
 MJ1  CE1  C  CR16   0  -0.341  -3.6590   1.4799  -0.8011
 MJ1  CE2  C  CR6    0   0.304  -4.8176  -0.4792  -0.0884
 MJ1  CZ   C  CR6    0   0.250  -4.8658   0.8046  -0.6186
 MJ1  OH   O  OH1    0  -0.613  -6.0108   1.4066  -0.9531
 MJ1  CA1  C  CH1    0  -0.241   2.6983   1.7361  -0.3809
 MJ1  CA2  C  CR5    0   0.103   0.0924  -0.6257   0.3481
 MJ1  CA3  C  CH2    0  -0.491   3.6921  -1.0064   0.5644
 MJ1  F1   F  F      0  -0.310  -5.9597  -1.1568   0.1000
 MJ1  F2   F  F      0  -0.296  -3.6513  -2.3013   0.7467
 MJ1  N1   N  NH2    0  -0.784   2.0086   2.5577  -1.3502
 MJ1  N2   N  N      0  -0.486   0.5406   0.5877  -0.1467
 MJ1  N3   N  NR5    0  -0.543   2.3221  -0.5585   0.5868
 MJ1  O2   O  O      0  -0.449   1.3320  -2.5463   1.2327
 MJ1  O3   O  O      0  -0.587   3.3096  -1.4192  -1.7498
 MJ1  H2   H  HCH1   0   0.209   3.7099   1.7392   1.5225
 MJ1  H3   H  H      0   0.271  -1.2652  -2.0743   0.8724
 MJ1  H4   H  HCH3   0   0.245   4.4375   4.0724   1.5334
 MJ1  H5   H  HCH3   0   0.234   4.9470   3.2939   0.0415
 MJ1  H6   H  HCH3   0   0.228   3.5696   4.4036   0.0361
 MJ1  H7   H  HOH1   0   0.455   2.2370   3.3520   2.3715
 MJ1  H9   H  HCR6   0   0.295  -1.5398   1.4309  -0.6124
 MJ1  H10  H  HCR6   0   0.285  -3.6754   2.4799  -1.2143
 MJ1  H11  H  HCH1   0   0.277   3.6034   1.3460  -0.8570
 MJ1  H12  H  HCH2   0   0.277   3.7975  -1.8026   1.3018
 MJ1  H13  H  HCH2   0   0.270   4.3541  -0.2039   0.8922
 MJ1  H14  H  HNH2   0   0.348   1.1976   2.9881  -0.9250
 MJ1  H15  H  HNH2   0   0.359   2.6141   3.3084  -1.6553
 MJ1  O1   O  OC    -1  -0.608   5.2931  -1.9666  -0.8689
 MJ1  H1   H  HOH1   0   0.484  -6.7737   0.8352  -0.8014

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   deloc     1.241  0.020  1.241
 MJ1  C3   CA3  single    1.547  0.020  1.547
 MJ1  CA3  N3   single    1.442  0.020  1.442
 MJ1  N3   C2   single    1.376  0.020  1.376
 MJ1  N3   C1   single    1.379  0.020  1.379
 MJ1  N1   CA1  single    1.446  0.020  1.446
 MJ1  O2   C2   double    1.214  0.020  1.214
 MJ1  CA1  C1   single    1.497  0.020  1.497
 MJ1  CA1  CB1  single    1.545  0.020  1.545
 MJ1  C2   CA2  single    1.483  0.020  1.483
 MJ1  C1   N2   double    1.289  0.020  1.289
 MJ1  CG1  CB1  single    1.520  0.020  1.520
 MJ1  CB1  OG1  single    1.410  0.020  1.410
 MJ1  CA2  N2   single    1.385  0.020  1.385
 MJ1  CA2  CB2  double    1.346  0.020  1.346
 MJ1  CB2  CG2  single    1.448  0.020  1.448
 MJ1  CG2  CD2  aromatic  1.395  0.020  1.395
 MJ1  CG2  CD1  aromatic  1.405  0.020  1.405
 MJ1  F2   CD2  single    1.335  0.020  1.335
 MJ1  CD2  CE2  aromatic  1.378  0.020  1.378
 MJ1  CD1  CE1  aromatic  1.379  0.020  1.379
 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    1.336  0.020  1.336
 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   deloc     1.243  0.020  1.243
 MJ1  OH   H1   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   114.29  3.000
 MJ1  N2   C1   CA1  123.45  3.000
 MJ1  N3   C1   CA1  122.15  3.000
 MJ1  O2   C2   N3   126.34  3.000
 MJ1  O2   C2   CA2  130.36  3.000
 MJ1  N3   C2   CA2  103.29  3.000
 MJ1  O1   C3   O3   128.53  3.000
 MJ1  O1   C3   CA3  114.58  3.000
 MJ1  O3   C3   CA3  116.90  3.000
 MJ1  H2   CB1  CA1  107.99  3.000
 MJ1  H2   CB1  OG1  110.40  3.000
 MJ1  CA1  CB1  OG1  107.01  3.000
 MJ1  H2   CB1  CG1  107.49  3.000
 MJ1  OG1  CB1  CG1  112.21  3.000
 MJ1  CA1  CB1  CG1  111.68  3.000
 MJ1  H3   CB2  CA2  114.94  3.000
 MJ1  H3   CB2  CG2  116.90  3.000
 MJ1  CA2  CB2  CG2  128.16  3.000
 MJ1  H6   CG1  H5   108.37  3.000
 MJ1  H6   CG1  H4   107.73  3.000
 MJ1  H5   CG1  H4   107.37  3.000
 MJ1  H6   CG1  CB1  111.74  3.000
 MJ1  H5   CG1  CB1  111.04  3.000
 MJ1  H4   CG1  CB1  110.44  3.000
 MJ1  H7   OG1  CB1  108.32  3.000
 MJ1  CD2  CG2  CD1  116.14  3.000
 MJ1  CD1  CG2  CB2  124.50  3.000
 MJ1  CD2  CG2  CB2  119.36  3.000
 MJ1  H9   CD1  CE1  119.37  3.000
 MJ1  H9   CD1  CG2  118.59  3.000
 MJ1  CE1  CD1  CG2  122.04  3.000
 MJ1  F2   CD2  CE2  117.49  3.000
 MJ1  CE2  CD2  CG2  122.19  3.000
 MJ1  F2   CD2  CG2  120.32  3.000
 MJ1  H10  CE1  CZ   118.96  3.000
 MJ1  H10  CE1  CD1  120.27  3.000
 MJ1  CZ   CE1  CD1  120.76  3.000
 MJ1  F1   CE2  CZ   119.39  3.000
 MJ1  CZ   CE2  CD2  121.02  3.000
 MJ1  F1   CE2  CD2  119.59  3.000
 MJ1  OH   CZ   CE2  122.77  3.000
 MJ1  OH   CZ   CE1  119.38  3.000
 MJ1  CE2  CZ   CE1  117.85  3.000
 MJ1  H1   OH   CZ   111.80  3.000
 MJ1  H11  CA1  N1   107.78  3.000
 MJ1  H11  CA1  CB1  106.81  3.000
 MJ1  N1   CA1  CB1  115.67  3.000
 MJ1  H11  CA1  C1   108.43  3.000
 MJ1  CB1  CA1  C1   108.94  3.000
 MJ1  N1   CA1  C1   108.99  3.000
 MJ1  N2   CA2  CB2  128.82  3.000
 MJ1  CB2  CA2  C2   122.63  3.000
 MJ1  N2   CA2  C2   108.55  3.000
 MJ1  H13  CA3  H12  105.98  3.000
 MJ1  H13  CA3  N3   110.10  3.000
 MJ1  H12  CA3  N3   107.95  3.000
 MJ1  H13  CA3  C3   109.81  3.000
 MJ1  H12  CA3  C3   109.90  3.000
 MJ1  N3   CA3  C3   112.86  3.000
 MJ1  H15  N1   H14  106.91  3.000
 MJ1  H15  N1   CA1  109.78  3.000
 MJ1  H14  N1   CA1  110.02  3.000
 MJ1  CA2  N2   C1   106.19  3.000
 MJ1  CA3  N3   C2   122.54  3.000
 MJ1  C2   N3   C1   107.52  3.000
 MJ1  CA3  N3   C1   126.45  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_25  H10  CE1  CD1  CG2  180.00   0.0  0
 MJ1  CONST_26  H9   CD1  CG2  CD2  180.00   0.0  0
 MJ1  Var_01    CG2  CB2  CA2  C2   179.13  30.0  2
 MJ1  Var_02    CA2  CB2  CG2  CD1   -1.02  30.0  2
 MJ1  Var_03    C3   CA3  N3   C1   -70.68  30.0  1
 MJ1  Var_04    O3   C3   CA3  N3     3.50  30.0  2

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

