# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 20:10:00 2022
#   Inital geometry file: a 112 line input string
#   Ligand name: {(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-[(4-nitrophenyl)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(cc2)[N+]([O-])=O)/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
 GMO  GMO  "{(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-[(4-nitrophenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid"  L-peptide  40  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 OK
;

data_comp_GMO
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
 GMO  N    N  NH2    0  -0.797  -1.4942   2.7102   1.1465
 GMO  CA   C  CH1    0  -0.232  -2.3593   1.8931   0.3223
 GMO  C    C  C      0   0.423  -4.3685  -0.9441   0.9518
 GMO  O    O  O      0  -0.586  -3.5004  -0.9222   1.8394
 GMO  CB1  C  CH1    0   0.033  -2.7321   2.6629  -0.9694
 GMO  CG1  C  CH3    0  -0.689  -3.6440   3.8375  -0.6573
 GMO  OG1  O  OH1    0  -0.662  -1.5668   3.0610  -1.6515
 GMO  CG2  C  CR6    0   0.179   2.2217  -1.2027  -0.2843
 GMO  CD1  C  CR16   0  -0.313   2.5488   0.0405   0.2756
 GMO  CD2  C  CR16   0  -0.299   3.2592  -2.1009  -0.5660
 GMO  CE1  C  CR16   0  -0.245   3.8625   0.3689   0.5439
 GMO  CE2  C  CR16   0  -0.259   4.5775  -1.7835  -0.3064
 GMO  CZ   C  CR6    0   0.245   4.8660  -0.5455   0.2498
 GMO  C1   C  CR5    0   0.561  -1.7391   0.5799  -0.0464
 GMO  C2   C  CR5    0   0.537  -1.6085  -1.5016  -0.8083
 GMO  CA2  C  CR5    0   0.132  -0.2796  -0.9328  -0.4434
 GMO  N2   N  N      0  -0.504  -0.4699   0.3513   0.0305
 GMO  N3   N  NR5    0  -0.536  -2.4714  -0.4545  -0.5819
 GMO  NO   N  N      1   0.329   6.2481  -0.1976   0.5294
 GMO  O2   O  O      0  -0.431  -1.9019  -2.6078  -1.2035
 GMO  O40  O  O      0  -0.380   7.1062  -0.9986   0.2398
 GMO  ON1  O  O     -1  -0.379   6.4730   0.8763   1.0375
 GMO  H1   H  HNH2   0   0.363  -1.6131   2.4653   2.1199
 GMO  H2   H  HNH2   0   0.359  -0.5255   2.5106   0.9271
 GMO  H4   H  HCH1   0   0.277  -3.2837   1.6949   0.8704
 GMO  H8   H  HCH1   0   0.240  -3.2570   1.9871  -1.6521
 GMO  H9   H  H      0   0.272   0.7640  -2.6242  -0.9900
 GMO  H11  H  HCH3   0   0.230  -3.1672   4.5275   0.0402
 GMO  H12  H  HCH3   0   0.240  -3.8898   4.3811  -1.5700
 GMO  H13  H  HCH3   0   0.229  -4.5787   3.4991  -0.2085
 GMO  H14  H  HOH1   0   0.443  -1.1130   3.7067  -1.0972
 GMO  H15  H  HCR6   0   0.293   1.7693   0.7527   0.5015
 GMO  H16  H  HCR6   0   0.277   3.0264  -3.0653  -0.9988
 GMO  H17  H  HCR6   0   0.298   4.0952   1.3306   0.9772
 GMO  H18  H  HCR6   0   0.299   5.3579  -2.4941  -0.5355
 GMO  H20  H  HCH2   0   0.280  -4.1944  -1.4163  -1.1680
 GMO  H21  H  HCH2   0   0.271  -4.4030   0.2840  -0.8458
 GMO  O1   O  OC    -1  -0.604  -5.5827  -1.1846   1.0599
 GMO  CA3  C  CH2    0  -0.489  -3.9010  -0.6168  -0.4874
 GMO  CB2  C  C1     0  -0.404   0.8658  -1.6215  -0.5887

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
 GMO  O    C    deloc     1.242  0.020  1.242
 GMO  C    CA3  single    1.548  0.020  1.548
 GMO  CA3  N3   single    1.442  0.020  1.442
 GMO  N3   C2   single    1.376  0.020  1.376
 GMO  N3   C1   single    1.376  0.020  1.376
 GMO  O2   C2   double    1.211  0.020  1.211
 GMO  CA   N    single    1.448  0.020  1.448
 GMO  CA   C1   single    1.498  0.020  1.498
 GMO  CA   CB1  single    1.549  0.020  1.549
 GMO  CG1  CB1  single    1.519  0.020  1.519
 GMO  C2   CA2  single    1.491  0.020  1.491
 GMO  C1   N2   double    1.292  0.020  1.292
 GMO  CB1  OG1  single    1.408  0.020  1.408
 GMO  CA2  N2   single    1.382  0.020  1.382
 GMO  CA2  CB2  double    1.344  0.020  1.344
 GMO  CB2  CG2  single    1.451  0.020  1.451
 GMO  CG2  CD1  aromatic  1.402  0.020  1.402
 GMO  CG2  CD2  aromatic  1.401  0.020  1.401
 GMO  CD1  CE1  aromatic  1.380  0.020  1.380
 GMO  CD2  CE2  aromatic  1.381  0.020  1.381
 GMO  CE1  CZ   aromatic  1.389  0.020  1.389
 GMO  CE2  CZ   aromatic  1.388  0.020  1.388
 GMO  CZ   NO   single    1.452  0.020  1.452
 GMO  NO   ON1  single    1.209  0.020  1.209
 GMO  NO   O40  double    1.209  0.020  1.209
 GMO  N    H1   single    0.890  0.020  1.040
 GMO  N    H2   single    0.890  0.020  1.040
 GMO  CA   H4   single    0.970  0.020  1.090
 GMO  CB1  H8   single    0.970  0.020  1.090
 GMO  CB2  H9   single    0.930  0.020  1.080
 GMO  CG1  H11  single    0.970  0.020  1.090
 GMO  CG1  H12  single    0.970  0.020  1.090
 GMO  CG1  H13  single    0.970  0.020  1.090
 GMO  OG1  H14  single    0.850  0.020  0.980
 GMO  CD1  H15  single    0.930  0.020  1.080
 GMO  CD2  H16  single    0.930  0.020  1.080
 GMO  CE1  H17  single    0.930  0.020  1.080
 GMO  CE2  H18  single    0.930  0.020  1.080
 GMO  CA3  H20  single    0.970  0.020  1.090
 GMO  CA3  H21  single    0.970  0.020  1.090
 GMO  C    O1   deloc     1.242  0.020  1.242

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
 GMO  H2   N    H1   105.86  3.000
 GMO  H2   N    CA   109.69  3.000
 GMO  H1   N    CA   109.95  3.000
 GMO  H4   CA   C1   108.34  3.000
 GMO  H4   CA   CB1  107.74  3.000
 GMO  C1   CA   CB1  109.27  3.000
 GMO  H4   CA   N    108.80  3.000
 GMO  CB1  CA   N    109.76  3.000
 GMO  C1   CA   N    112.79  3.000
 GMO  O1   C    CA3  114.64  3.000
 GMO  O1   C    O    128.64  3.000
 GMO  CA3  C    O    116.72  3.000
 GMO  H8   CB1  OG1  105.62  3.000
 GMO  H8   CB1  CG1  108.52  3.000
 GMO  OG1  CB1  CG1  112.19  3.000
 GMO  H8   CB1  CA   109.19  3.000
 GMO  OG1  CB1  CA   110.20  3.000
 GMO  CG1  CB1  CA   110.93  3.000
 GMO  H13  CG1  H12  107.81  3.000
 GMO  H13  CG1  H11  107.93  3.000
 GMO  H12  CG1  H11  108.57  3.000
 GMO  H13  CG1  CB1  111.04  3.000
 GMO  H12  CG1  CB1  110.41  3.000
 GMO  H11  CG1  CB1  110.98  3.000
 GMO  H14  OG1  CB1  107.48  3.000
 GMO  CD2  CG2  CD1  118.43  3.000
 GMO  CD2  CG2  CB2  117.69  3.000
 GMO  CD1  CG2  CB2  123.88  3.000
 GMO  H15  CD1  CE1  119.31  3.000
 GMO  H15  CD1  CG2  119.99  3.000
 GMO  CE1  CD1  CG2  120.70  3.000
 GMO  H16  CD2  CE2  119.04  3.000
 GMO  H16  CD2  CG2  119.50  3.000
 GMO  CE2  CD2  CG2  121.46  3.000
 GMO  H17  CE1  CZ   121.03  3.000
 GMO  H17  CE1  CD1  119.65  3.000
 GMO  CZ   CE1  CD1  119.32  3.000
 GMO  H18  CE2  CZ   121.46  3.000
 GMO  H18  CE2  CD2  119.92  3.000
 GMO  CZ   CE2  CD2  118.62  3.000
 GMO  NO   CZ   CE2  119.26  3.000
 GMO  NO   CZ   CE1  119.28  3.000
 GMO  CE2  CZ   CE1  121.47  3.000
 GMO  N3   C1   N2   114.40  3.000
 GMO  N2   C1   CA   123.17  3.000
 GMO  N3   C1   CA   122.30  3.000
 GMO  O2   C2   N3   126.66  3.000
 GMO  O2   C2   CA2  130.13  3.000
 GMO  N3   C2   CA2  103.21  3.000
 GMO  N2   CA2  C2   108.40  3.000
 GMO  N2   CA2  CB2  129.08  3.000
 GMO  C2   CA2  CB2  122.52  3.000
 GMO  CA2  N2   C1   106.22  3.000
 GMO  CA3  N3   C2   123.17  3.000
 GMO  C2   N3   C1   107.60  3.000
 GMO  CA3  N3   C1   125.93  3.000
 GMO  ON1  NO   O40  123.85  3.000
 GMO  O40  NO   CZ   118.08  3.000
 GMO  ON1  NO   CZ   118.07  3.000
 GMO  H21  CA3  H20  106.04  3.000
 GMO  H21  CA3  N3   109.97  3.000
 GMO  H20  CA3  N3   107.97  3.000
 GMO  H21  CA3  C    109.92  3.000
 GMO  H20  CA3  C    110.12  3.000
 GMO  N3   CA3  C    112.59  3.000
 GMO  H9   CB2  CA2  115.69  3.000
 GMO  H9   CB2  CG2  115.59  3.000
 GMO  CA2  CB2  CG2  128.72  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
 GMO  CONST_01  CZ   CE1  CD1  CG2     0.00   0.0  0
 GMO  CONST_02  CZ   CE2  CD2  CG2     0.00   0.0  0
 GMO  CONST_03  CE2  CD2  CG2  CD1     0.00   0.0  0
 GMO  CONST_04  CE2  CZ   CE1  CD1     0.00   0.0  0
 GMO  CONST_05  CE1  CD1  CG2  CD2     0.00   0.0  0
 GMO  CONST_06  CE1  CZ   CE2  CD2     0.00   0.0  0
 GMO  CONST_07  CA2  C2   N3   C1      0.00   0.0  0
 GMO  CONST_08  C2   CA2  N2   C1      0.00   0.0  0
 GMO  CONST_09  N2   C1   N3   C2      0.00   0.0  0
 GMO  CONST_10  N3   C1   N2   CA2     0.00   0.0  0
 GMO  CONST_11  N3   C2   CA2  N2      0.00   0.0  0
 GMO  CONST_12  CE1  CD1  CG2  CB2   180.00   0.0  0
 GMO  CONST_13  CE2  CD2  CG2  CB2   180.00   0.0  0
 GMO  CONST_14  NO   CZ   CE1  CD1   180.00   0.0  0
 GMO  CONST_15  NO   CZ   CE2  CD2   180.00   0.0  0
 GMO  CONST_16  C2   N3   C1   CA    180.00   0.0  0
 GMO  CONST_17  CA2  N2   C1   CA    180.00   0.0  0
 GMO  CONST_18  O2   C2   N3   C1    180.00   0.0  0
 GMO  CONST_21  H17  CE1  CD1  CG2   180.00   0.0  0
 GMO  CONST_22  H18  CE2  CD2  CG2   180.00   0.0  0
 GMO  CONST_23  H16  CD2  CG2  CD1   180.00   0.0  0
 GMO  CONST_24  H15  CD1  CG2  CD2   180.00   0.0  0
 GMO  CONST_25  H18  CE2  CZ   CE1   180.00   0.0  0
 GMO  CONST_26  H17  CE1  CZ   CE2   180.00   0.0  0
 GMO  CONST_27  H15  CD1  CE1  CZ    180.00   0.0  0
 GMO  CONST_28  H16  CD2  CE2  CZ    180.00   0.0  0
 GMO  CONST_29  ON1  NO   CZ   CE1     0.00   0.0  0
 GMO  CONST_30  O40  NO   CZ   CE1   180.00   0.0  0
 GMO  CONST_31  ON1  NO   CZ   CE2   180.00   0.0  0
 GMO  CONST_32  O40  NO   CZ   CE2     0.00   0.0  0
 GMO  Var_01    C2   CA2  CB2  CG2   179.77   0.0  2
 GMO  Var_02    N2   CA2  CB2  CG2     0.07   0.0  2
 GMO  Var_03    CA2  CB2  CG2  CD1     2.09  30.0  1
 GMO  Var_04    CA2  CB2  CG2  CD2  -178.10  30.0  1
 GMO  Var_05    C2   N3   CA3  C      87.87  30.0  3
 GMO  Var_06    C1   N3   CA3  C     -69.03  30.0  3
 GMO  Var_07    H9   CB2  CA2  C2     -0.03   0.0  2
 GMO  Var_08    H9   CB2  CA2  N2   -179.72   0.0  2
 GMO  Var_09    H9   CB2  CG2  CD1  -178.11  30.0  1
 GMO  Var_10    H9   CB2  CG2  CD2     1.69  30.0  1
 GMO  Var_11    H20  CA3  N3   C1    169.20  30.0  2
 GMO  Var_12    H21  CA3  N3   C1     53.92  30.0  2
 GMO  Var_13    H20  CA3  N3   C2    -33.90  30.0  2
 GMO  Var_14    H21  CA3  N3   C2   -149.18  30.0  2
 GMO  Var_15    N3   CA3  C    O       5.43  30.0  3
 GMO  Var_16    O1   C    CA3  N3   -175.18  30.0  3
 GMO  Var_17    H20  CA3  C    O     125.98  30.0  3
 GMO  Var_18    H21  CA3  C    O    -117.55  30.0  3
 GMO  Var_19    O1   C    CA3  H20   -54.63  30.0  3
 GMO  Var_20    O1   C    CA3  H21    61.85  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
 GMO  chir_01  CA   N    C1  CB1  positiv
 GMO  chir_02  CB1  OG1  CA  CG1  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
 GMO  plan-1  CA   0.020
 GMO  plan-1  CG2  0.020
 GMO  plan-1  C1   0.020
 GMO  plan-1  C2   0.020
 GMO  plan-1  CA2  0.020
 GMO  plan-1  N2   0.020
 GMO  plan-1  N3   0.020
 GMO  plan-1  O2   0.020
 GMO  plan-1  H9   0.020
 GMO  plan-1  CA3  0.020
 GMO  plan-1  CB2  0.020
 GMO  plan-2  CG2  0.020
 GMO  plan-2  CD1  0.020
 GMO  plan-2  CD2  0.020
 GMO  plan-2  CE1  0.020
 GMO  plan-2  CE2  0.020
 GMO  plan-2  CZ   0.020
 GMO  plan-2  NO   0.020
 GMO  plan-2  H15  0.020
 GMO  plan-2  H16  0.020
 GMO  plan-2  H17  0.020
 GMO  plan-2  H18  0.020
 GMO  plan-2  CB2  0.020
 GMO  plan-3  CZ   0.020
 GMO  plan-3  NO   0.020
 GMO  plan-3  O40  0.020
 GMO  plan-3  ON1  0.020
 GMO  plan-4  C    0.020
 GMO  plan-4  O    0.020
 GMO  plan-4  O1   0.020
 GMO  plan-4  CA3  0.020

