# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 17:46:41 2021
#   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  40  24  .  2022-08-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  75.0329  -1.8974  12.4223
 M3V  CA    C  CH1   0  -0.223  73.6155  -2.2322  12.4965
 M3V  C     C  C     0   0.556  71.7628  -0.3480   9.7088
 M3V  O     O  O     0  -0.434  71.7450  -0.1497   8.5228
 M3V  CB1   C  CH1   0   0.053  73.3715  -3.3856  13.4750
 M3V  CG1   C  CH3   0  -0.694  73.8510  -4.7129  12.8980
 M3V  OG1   O  OH1   0  -0.662  74.0162  -3.0966  14.6923
 M3V  CG2   C  CR6   0   0.171  70.7587   0.6463  16.2983
 M3V  CD1   C  CR16  0  -0.308  71.2818  -0.5337  16.8484
 M3V  CD2   C  CR16  0  -0.290  69.9478   1.4603  17.0994
 M3V  CE1   C  CR16  0  -0.213  70.9955  -0.8836  18.1524
 M3V  CE2   C  CR16  0  -0.230  69.6542   1.1159  18.4039
 M3V  CZ    C  CR6   0  -0.004  70.1799  -0.0618  18.9328
 M3V  C1    C  CR5   0   0.590  72.8474  -1.0055  12.8894
 M3V  C2    C  CR5   0   0.552  71.8821   0.9960  12.6046
 M3V  CA2   C  CR5   0   0.125  71.6919   0.4449  13.9683
 M3V  CN    C  CSP   0   0.059  69.8867  -0.4283  20.2798
 M3V  N2    N  N     0  -0.466  72.3132  -0.7907  14.0377
 M3V  N3    N  NR5   0  -0.575  72.6549   0.0318  11.9889
 M3V  N40   N  NS    0  -0.247  69.6513  -0.7267  21.3677
 M3V  O2    O  O     0  -0.425  71.4785   2.0150  12.0917
 M3V  H     H  HNH2  0   0.363  75.5423  -2.6851  12.0405
 M3V  H2    H  HNH2  0   0.360  75.1971  -1.1381  11.7736
 M3V  HA    H  HCH1  0   0.252  73.1966  -2.5647  11.5319
 M3V  H8    H  HCH1  0   0.220  72.2853  -3.4554  13.6133
 M3V  H9    H  H     0   0.279  70.5890   2.0449  14.6656
 M3V  HG21  H  HCH3  0   0.242  73.6318  -5.5238  13.5946
 M3V  HG22  H  HCH3  0   0.229  73.3445  -4.9428  11.9598
 M3V  HG23  H  HCH3  0   0.224  74.9271  -4.7199  12.7163
 M3V  HG1   H  HOH1  0   0.451  73.6303  -3.6598  15.3689
 M3V  H14   H  HCR6  0   0.297  71.9159  -1.1730  16.2510
 M3V  H15   H  HCR6  0   0.276  69.5403   2.3760  16.6910
 M3V  H16   H  HCR6  0   0.284  71.4038  -1.7935  18.5702
 M3V  H17   H  HCR6  0   0.287  69.0235   1.7530  19.0084
 M3V  H18   H  HCH2  0   0.321  73.7681  -0.6016  10.3434
 M3V  H19   H  HCH2  0   0.328  73.2485   1.0618  10.2898
 M3V  OXT   O  OH1   0  -0.578  70.8093  -0.9570  10.3889
 M3V  HXT   H  HOH1  0   0.493  70.0864  -1.2187   9.7975
 M3V  CA3   C  CH2   0  -0.469  72.9332   0.0599  10.5815
 M3V  CB2   C  C1    0  -0.395  71.0107   1.0827  14.9362

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     double    1.203  0.020  1.203
 M3V  C    CA3   single    1.516  0.020  1.516
 M3V  CA3  N3    single    1.435  0.020  1.435
 M3V  N3   C2    single    1.381  0.020  1.381
 M3V  N3   C1    single    1.387  0.020  1.387
 M3V  O2   C2    double    1.210  0.020  1.210
 M3V  CA   N     single    1.458  0.020  1.458
 M3V  CA   C1    single    1.500  0.020  1.500
 M3V  CA   CB1   single    1.532  0.020  1.532
 M3V  C2   CA2   single    1.483  0.020  1.483
 M3V  CG1  CB1   single    1.525  0.020  1.525
 M3V  C1   N2    double    1.285  0.020  1.285
 M3V  CB1  OG1   single    1.408  0.020  1.408
 M3V  CA2  N2    single    1.385  0.020  1.385
 M3V  CA2  CB2   double    1.344  0.020  1.344
 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  1.381  0.020  1.381
 M3V  CE1  CZ    aromatic  1.396  0.020  1.396
 M3V  CE2  CZ    aromatic  1.394  0.020  1.394
 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   single    1.320  0.020  1.320
 M3V  OXT  HXT   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
 M3V  H2    N    H     105.09  3.000
 M3V  H2    N    CA    111.25  3.000
 M3V  H     N    CA    109.24  3.000
 M3V  HA    CA   C1    106.33  3.000
 M3V  HA    CA   CB1   105.73  3.000
 M3V  C1    CA   CB1   111.53  3.000
 M3V  HA    CA   N     113.20  3.000
 M3V  CB1   CA   N     111.11  3.000
 M3V  C1    CA   N     108.86  3.000
 M3V  OXT   C    CA3   112.66  3.000
 M3V  OXT   C    O     124.99  3.000
 M3V  CA3   C    O     122.33  3.000
 M3V  H8    CB1  OG1   110.94  3.000
 M3V  H8    CB1  CG1   107.68  3.000
 M3V  OG1   CB1  CG1   111.22  3.000
 M3V  H8    CB1  CA    106.62  3.000
 M3V  OG1   CB1  CA    108.95  3.000
 M3V  CG1   CB1  CA    111.32  3.000
 M3V  HG23  CG1  HG22  108.26  3.000
 M3V  HG23  CG1  HG21  107.43  3.000
 M3V  HG22  CG1  HG21  107.41  3.000
 M3V  HG23  CG1  CB1   112.25  3.000
 M3V  HG22  CG1  CB1   111.29  3.000
 M3V  HG21  CG1  CB1   110.01  3.000
 M3V  HG1   OG1  CB1   107.74  3.000
 M3V  CD2   CG2  CD1   118.71  3.000
 M3V  CD2   CG2  CB2   117.53  3.000
 M3V  CD1   CG2  CB2   123.76  3.000
 M3V  H14   CD1  CE1   119.61  3.000
 M3V  H14   CD1  CG2   119.97  3.000
 M3V  CE1   CD1  CG2   120.42  3.000
 M3V  H15   CD2  CE2   119.17  3.000
 M3V  H15   CD2  CG2   119.59  3.000
 M3V  CE2   CD2  CG2   121.23  3.000
 M3V  H16   CE1  CZ    119.99  3.000
 M3V  H16   CE1  CD1   120.01  3.000
 M3V  CZ    CE1  CD1   120.00  3.000
 M3V  H17   CE2  CZ    120.38  3.000
 M3V  H17   CE2  CD2   120.35  3.000
 M3V  CZ    CE2  CD2   119.27  3.000
 M3V  CN    CZ   CE2   119.85  3.000
 M3V  CN    CZ   CE1   119.78  3.000
 M3V  CE2   CZ   CE1   120.37  3.000
 M3V  N3    C1   N2    113.43  3.000
 M3V  N2    C1   CA    125.73  3.000
 M3V  N3    C1   CA    120.85  3.000
 M3V  O2    C2   N3    125.86  3.000
 M3V  O2    C2   CA2   131.29  3.000
 M3V  N3    C2   CA2   102.84  3.000
 M3V  N2    CA2  C2    108.67  3.000
 M3V  N2    CA2  CB2   127.92  3.000
 M3V  C2    CA2  CB2   123.41  3.000
 M3V  N40   CN   CZ    180.00  3.000
 M3V  CA2   N2   C1    106.92  3.000
 M3V  CA3   N3   C2    122.16  3.000
 M3V  C2    N3   C1    108.09  3.000
 M3V  CA3   N3   C1    128.64  3.000
 M3V  HXT   OXT  C     110.41  3.000
 M3V  H19   CA3  H18   106.10  3.000
 M3V  H19   CA3  N3    109.67  3.000
 M3V  H18   CA3  N3    110.51  3.000
 M3V  H19   CA3  C     108.46  3.000
 M3V  H18   CA3  C     107.57  3.000
 M3V  N3    CA3  C     114.18  3.000
 M3V  H9    CB2  CA2   115.99  3.000
 M3V  H9    CB2  CG2   115.66  3.000
 M3V  CA2   CB2  CG2   128.35  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_20  N2   C1   N3   CA3  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_25  CA3  N3   C1   CA     0.00   0.0  0
 M3V  CONST_26  O2   C2   N3   CA3    0.00   0.0  0
 M3V  CONST_27  HXT  OXT  C    O      0.00   0.0  0
 M3V  Var_01    C2   CA2  CB2  CG2  179.94   0.0  2
 M3V  Var_02    CA2  CB2  CG2  CD1    3.87  30.0  2
 M3V  Var_03    C2   N3   CA3  C    -74.56  30.0  3
 M3V  Var_04    N3   CA3  C    O    166.20  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  HXT  0.020
 M3V  plan-3  CA3  0.020

