# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 22:48:55 2022
#   Inital geometry file: a 112 line input string
#   Ligand name: {(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-[(4-cyanophenyl)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)C#N)/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
 M3V  M3V  '{(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-[(4-cyanophenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid'  L-peptide  39  24  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_M3V
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
 M3V  N     N  NH2    0  -0.798  75.0718  -1.8292  12.5991
 M3V  CA    C  CH1    0  -0.221  73.6626  -2.2021  12.4975
 M3V  C     C  C      0   0.422  71.8156  -0.7759   9.8401
 M3V  O     O  O      0  -0.595  71.8903  -0.7090   8.6022
 M3V  CB1   C  CH1    0   0.045  73.3417  -3.4404  13.3430
 M3V  CG1   C  CH3    0  -0.697  73.8286  -4.7129  12.6571
 M3V  OG1   O  OH1    0  -0.659  73.9159  -3.2971  14.6216
 M3V  CG2   C  CR6    0   0.173  70.7589   0.6150  16.3345
 M3V  CD1   C  CR16   0  -0.305  71.2314  -0.5935  16.8676
 M3V  CD2   C  CR16   0  -0.292  70.0163   1.4667  17.1631
 M3V  CE1   C  CR16   0  -0.214  70.9660  -0.9336  18.1785
 M3V  CE2   C  CR16   0  -0.230  69.7455   1.1343  18.4754
 M3V  CZ    C  CR6    0  -0.006  70.2213  -0.0726  18.9870
 M3V  C1    C  CR5    0   0.590  72.8428  -1.0072  12.8916
 M3V  C2    C  CR5    0   0.531  71.8769   0.9813  12.6373
 M3V  CA2   C  CR5    0   0.128  71.6671   0.4027  13.9926
 M3V  CN    C  CSP    0   0.054  69.9486  -0.4273  20.3412
 M3V  N2    N  N      0  -0.486  72.2829  -0.8339  14.0411
 M3V  N3    N  NR5    0  -0.542  72.6867   0.0540  12.0229
 M3V  N40   N  NS     0  -0.246  69.7285  -0.7149  21.4353
 M3V  O2    O  O      0  -0.429  71.4563   2.0089  12.1531
 M3V  H     H  HNH2   0   0.358  75.6462  -2.6243  12.3463
 M3V  H2    H  HNH2   0   0.356  75.2934  -1.1160  11.9155
 M3V  HA    H  HCH1   0   0.254  73.3599  -2.4637  11.4745
 M3V  H8    H  HCH1   0   0.211  72.2467  -3.5000  13.4082
 M3V  H9    H  H      0   0.272  70.5958   2.0164  14.7052
 M3V  HG21  H  HCH3   0   0.240  73.5525  -5.5891  13.2470
 M3V  HG22  H  HCH3   0   0.230  73.3742  -4.8268  11.6723
 M3V  HG23  H  HCH3   0   0.226  74.9132  -4.7284  12.5355
 M3V  HG1   H  HOH1   0   0.448  73.6446  -4.0538  15.1500
 M3V  H14   H  HCR6   0   0.284  71.8114  -1.2645  16.2512
 M3V  H15   H  HCR6   0   0.274  69.6463   2.4048  16.7690
 M3V  H16   H  HCR6   0   0.281  71.3366  -1.8674  18.5794
 M3V  H17   H  HCR6   0   0.282  69.1703   1.8038  19.1003
 M3V  H18   H  HCH2   0   0.269  73.8880  -0.3771  10.3731
 M3V  H19   H  HCH2   0   0.274  72.9165   1.0644  10.2442
 M3V  OXT   O  OC    -1  -0.585  71.0080  -1.4088  10.5402
 M3V  CA3   C  CH2    0  -0.489  72.9012   0.0329  10.5960
 M3V  CB2   C  C1     0  -0.407  71.0009   1.0448  14.9683

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
 M3V  O    C     deloc     1.242  0.020  1.242
 M3V  C    CA3   single    1.550  0.020  1.550
 M3V  CA3  N3    single    1.443  0.020  1.443
 M3V  N3   C2    single    1.376  0.020  1.376
 M3V  N3   C1    single    1.380  0.020  1.380
 M3V  O2   C2    double    1.211  0.020  1.211
 M3V  CA   N     single    1.461  0.020  1.461
 M3V  CA   C1    single    1.502  0.020  1.502
 M3V  CA   CB1   single    1.533  0.020  1.533
 M3V  C2   CA2   single    1.488  0.020  1.488
 M3V  CG1  CB1   single    1.525  0.020  1.525
 M3V  C1   N2    double    1.290  0.020  1.290
 M3V  CB1  OG1   single    1.409  0.020  1.409
 M3V  CA2  N2    single    1.382  0.020  1.382
 M3V  CA2  CB2   double    1.345  0.020  1.345
 M3V  CB2  CG2   single    1.452  0.020  1.452
 M3V  CG2  CD1   aromatic  1.403  0.020  1.403
 M3V  CG2  CD2   aromatic  1.401  0.020  1.401
 M3V  CD1  CE1   aromatic  1.380  0.020  1.380
 M3V  CD2  CE2   aromatic  1.380  0.020  1.380
 M3V  CE1  CZ    aromatic  1.396  0.020  1.396
 M3V  CE2  CZ    aromatic  1.395  0.020  1.395
 M3V  CZ   CN    single    1.426  0.020  1.426
 M3V  CN   N40   triple    1.152  0.020  1.152
 M3V  N    H     single    0.860  0.020  1.020
 M3V  N    H2    single    0.890  0.020  1.040
 M3V  CA   HA    single    0.970  0.020  1.090
 M3V  CB1  H8    single    0.970  0.020  1.090
 M3V  CB2  H9    single    0.930  0.020  1.080
 M3V  CG1  HG21  single    0.970  0.020  1.090
 M3V  CG1  HG22  single    0.970  0.020  1.090
 M3V  CG1  HG23  single    0.970  0.020  1.090
 M3V  OG1  HG1   single    0.850  0.020  0.980
 M3V  CD1  H14   single    0.930  0.020  1.080
 M3V  CD2  H15   single    0.930  0.020  1.080
 M3V  CE1  H16   single    0.930  0.020  1.080
 M3V  CE2  H17   single    0.930  0.020  1.080
 M3V  CA3  H18   single    0.970  0.020  1.090
 M3V  CA3  H19   single    0.970  0.020  1.090
 M3V  C    OXT   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
 M3V  H2    N    H     105.09  3.000
 M3V  H2    N    CA    110.11  3.000
 M3V  H     N    CA    109.23  3.000
 M3V  HA    CA   C1    106.47  3.000
 M3V  HA    CA   CB1   105.27  3.000
 M3V  C1    CA   CB1   112.56  3.000
 M3V  HA    CA   N     113.03  3.000
 M3V  CB1   CA   N     111.69  3.000
 M3V  C1    CA   N     107.77  3.000
 M3V  OXT   C    CA3   116.50  3.000
 M3V  OXT   C    O     128.92  3.000
 M3V  CA3   C    O     114.57  3.000
 M3V  H8    CB1  OG1   110.97  3.000
 M3V  H8    CB1  CG1   107.44  3.000
 M3V  OG1   CB1  CG1   111.27  3.000
 M3V  H8    CB1  CA    106.57  3.000
 M3V  OG1   CB1  CA    109.45  3.000
 M3V  CG1   CB1  CA    111.04  3.000
 M3V  HG23  CG1  HG22  108.18  3.000
 M3V  HG23  CG1  HG21  107.47  3.000
 M3V  HG22  CG1  HG21  107.38  3.000
 M3V  HG23  CG1  CB1   112.28  3.000
 M3V  HG22  CG1  CB1   111.11  3.000
 M3V  HG21  CG1  CB1   110.23  3.000
 M3V  HG1   OG1  CB1   107.66  3.000
 M3V  CD2   CG2  CD1   118.51  3.000
 M3V  CD2   CG2  CB2   117.69  3.000
 M3V  CD1   CG2  CB2   123.79  3.000
 M3V  H14   CD1  CE1   119.49  3.000
 M3V  H14   CD1  CG2   119.95  3.000
 M3V  CE1   CD1  CG2   120.56  3.000
 M3V  H15   CD2  CE2   119.18  3.000
 M3V  H15   CD2  CG2   119.50  3.000
 M3V  CE2   CD2  CG2   121.32  3.000
 M3V  H16   CE1  CZ    120.03  3.000
 M3V  H16   CE1  CD1   119.93  3.000
 M3V  CZ    CE1  CD1   120.04  3.000
 M3V  H17   CE2  CZ    120.34  3.000
 M3V  H17   CE2  CD2   120.30  3.000
 M3V  CZ    CE2  CD2   119.35  3.000
 M3V  CN    CZ   CE2   119.90  3.000
 M3V  CN    CZ   CE1   119.90  3.000
 M3V  CE2   CZ   CE1   120.21  3.000
 M3V  N3    C1   N2    114.10  3.000
 M3V  N2    C1   CA    125.28  3.000
 M3V  N3    C1   CA    120.55  3.000
 M3V  O2    C2   N3    126.69  3.000
 M3V  O2    C2   CA2   130.15  3.000
 M3V  N3    C2   CA2   103.16  3.000
 M3V  N2    CA2  C2    108.47  3.000
 M3V  N2    CA2  CB2   128.49  3.000
 M3V  C2    CA2  CB2   123.02  3.000
 M3V  N40   CN   CZ    180.00  3.000
 M3V  CA2   N2   C1    106.39  3.000
 M3V  CA3   N3   C2    122.60  3.000
 M3V  C2    N3   C1    107.67  3.000
 M3V  CA3   N3   C1    126.47  3.000
 M3V  H19   CA3  H18   106.07  3.000
 M3V  H19   CA3  N3    107.91  3.000
 M3V  H18   CA3  N3    109.98  3.000
 M3V  H19   CA3  C     110.25  3.000
 M3V  H18   CA3  C     109.72  3.000
 M3V  N3    CA3  C     112.68  3.000
 M3V  H9    CB2  CA2   115.89  3.000
 M3V  H9    CB2  CG2   115.52  3.000
 M3V  CA2   CB2  CG2   128.59  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
 M3V  CONST_01  CZ   CE1  CD1  CG2     0.00   0.0  0
 M3V  CONST_02  CZ   CE2  CD2  CG2     0.00   0.0  0
 M3V  CONST_03  CE2  CD2  CG2  CD1     0.00   0.0  0
 M3V  CONST_04  CE2  CZ   CE1  CD1     0.00   0.0  0
 M3V  CONST_05  CE1  CD1  CG2  CD2     0.00   0.0  0
 M3V  CONST_06  CE1  CZ   CE2  CD2     0.00   0.0  0
 M3V  CONST_07  CA2  C2   N3   C1      0.00   0.0  0
 M3V  CONST_08  C2   CA2  N2   C1      0.00   0.0  0
 M3V  CONST_09  N2   C1   N3   C2      0.00   0.0  0
 M3V  CONST_10  N3   C1   N2   CA2     0.00   0.0  0
 M3V  CONST_11  N3   C2   CA2  N2      0.00   0.0  0
 M3V  CONST_12  CE1  CD1  CG2  CB2   180.00   0.0  0
 M3V  CONST_13  CE2  CD2  CG2  CB2   180.00   0.0  0
 M3V  CONST_14  CN   CZ   CE1  CD1   180.00   0.0  0
 M3V  CONST_15  CN   CZ   CE2  CD2   180.00   0.0  0
 M3V  CONST_16  C2   N3   C1   CA    180.00   0.0  0
 M3V  CONST_17  CA2  N2   C1   CA    180.00   0.0  0
 M3V  CONST_18  O2   C2   N3   C1    180.00   0.0  0
 M3V  CONST_19  CA3  N3   C2   CA2   180.00   0.0  0
 M3V  CONST_21  H16  CE1  CD1  CG2   180.00   0.0  0
 M3V  CONST_22  H17  CE2  CD2  CG2   180.00   0.0  0
 M3V  CONST_23  H15  CD2  CG2  CD1   180.00   0.0  0
 M3V  CONST_24  H14  CD1  CG2  CD2   180.00   0.0  0
 M3V  CONST_26  O2   C2   N3   CA3     0.00   0.0  0
 M3V  Var_01    C2   CA2  CB2  CG2  -178.09   0.0  2
 M3V  Var_02    CA2  CB2  CG2  CD1     1.07  30.0  2
 M3V  Var_03    C2   N3   CA3  C     -86.27  30.0  3
 M3V  Var_04    N3   CA3  C    O     173.29  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
 M3V  chir_01  CA   N    C1  CB1  positiv
 M3V  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
 M3V  plan-1  CA   0.020
 M3V  plan-1  CG2  0.020
 M3V  plan-1  C1   0.020
 M3V  plan-1  C2   0.020
 M3V  plan-1  CA2  0.020
 M3V  plan-1  N2   0.020
 M3V  plan-1  N3   0.020
 M3V  plan-1  O2   0.020
 M3V  plan-1  H9   0.020
 M3V  plan-1  CA3  0.020
 M3V  plan-1  CB2  0.020
 M3V  plan-2  CG2  0.020
 M3V  plan-2  CD1  0.020
 M3V  plan-2  CD2  0.020
 M3V  plan-2  CE1  0.020
 M3V  plan-2  CE2  0.020
 M3V  plan-2  CZ   0.020
 M3V  plan-2  CN   0.020
 M3V  plan-2  N40  0.020
 M3V  plan-2  H14  0.020
 M3V  plan-2  H15  0.020
 M3V  plan-2  H16  0.020
 M3V  plan-2  H17  0.020
 M3V  plan-2  CB2  0.020
 M3V  plan-3  C    0.020
 M3V  plan-3  O    0.020
 M3V  plan-3  OXT  0.020
 M3V  plan-3  CA3  0.020

