# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 10:15:16 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: [(2R,4Z)-2-(aminomethyl)-2-hydroxy-4-(4-hydroxybenzylidene)-5-oxoimidazolidin-1-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@@]1(O)NC(=C\c2ccc(O)cc2)/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
 WCR  WCR  '[(2R,4Z)-2-(aminomethyl)-2-hydroxy-4-(4-hydroxybenzylidene)-5-oxoimidazolidin-1-yl]acetic acid'  L-peptide  35  21  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_WCR
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
 WCR  C1    C  CR5    0   0.596  -1.5716   1.1371   0.1801
 WCR  N1    N  NH2    0  -0.818  -1.4356   3.4856   0.8385
 WCR  O1    O  OH1    0  -0.649  -2.1882   1.6731  -0.9321
 WCR  C2    C  CR5    0   0.529  -1.2816  -1.1405   0.5924
 WCR  N2    N  NR15   0  -0.741  -0.1909   0.7567  -0.0842
 WCR  O2    O  O      0  -0.484  -1.5195  -2.3026   0.8717
 WCR  C3    C  C      0   0.422  -4.1637  -0.8790  -0.7747
 WCR  N3    N  NR5    0  -0.514  -2.1649  -0.1291   0.5334
 WCR  O3    O  O      0  -0.589  -3.3627  -1.2637  -1.6383
 WCR  CZ    C  CR6    0   0.339   5.2489  -0.0630  -0.2614
 WCR  CA1   C  CH2    0  -0.340  -1.6887   2.1480   1.3424
 WCR  CA2   C  CR5    0   0.207   0.0476  -0.5447   0.2919
 WCR  CA3   C  CH2    0  -0.461  -3.5869  -0.3293   0.5509
 WCR  CB2   C  C1     0  -0.418   1.1919  -1.2372   0.4107
 WCR  CD1   C  CR16   0  -0.330   2.8950   0.3251  -0.6074
 WCR  CD2   C  CR16   0  -0.302   3.6147  -1.5491   0.6842
 WCR  CE1   C  CR16   0  -0.362   4.2163   0.6891  -0.8136
 WCR  CE2   C  CR16   0  -0.324   4.9360  -1.1961   0.4873
 WCR  CG2   C  CR6    0   0.155   2.5554  -0.7973   0.1565
 WCR  OXT   O  OC    -1  -0.624  -5.4096  -0.9022  -0.8166
 WCR  HN1   H  HNH2   0   0.378  -1.9228   4.1774   1.3896
 WCR  HO1   H  HOH1   0   0.449  -2.1353   2.6395  -0.7943
 WCR  HN2   H  HNR5   0   0.387   0.5161   1.4503   0.1116
 WCR  HOH   H  HOH1   0   0.474   6.6367   1.0454  -0.9641
 WCR  HA1   H  HCH2   0   0.257  -2.7130   2.1165   1.7181
 WCR  HA3   H  HCH2   0   0.253  -4.0766   0.6116   0.8045
 WCR  HA3A  H  HCH2   0   0.260  -3.8323  -1.0278   1.3548
 WCR  HB2   H  H      0   0.245   1.0768  -2.2541   0.7686
 WCR  HD1   H  HCR6   0   0.251   2.1306   0.9175  -1.0920
 WCR  HD2   H  HCR6   0   0.252   3.3931  -2.4346   1.2682
 WCR  HE1   H  HCR6   0   0.271   4.4392   1.5637  -1.4146
 WCR  HE2   H  HCR6   0   0.263   5.7304  -1.7987   0.9102
 WCR  HN    H  HNH2   0   0.365  -0.4527   3.7207   0.8801
 WCR  HA1A  H  HCH2   0   0.236  -1.0367   1.8347   2.1641
 WCR  OH    O  OH1    0  -0.632   6.5498   0.2505  -0.4262

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
 WCR  O1   C1    single    1.380  0.020  1.380
 WCR  CA1  C1    single    1.545  0.020  1.545
 WCR  C1   N3    single    1.442  0.020  1.442
 WCR  C1   N2    single    1.456  0.020  1.456
 WCR  CA1  N1    single    1.452  0.020  1.452
 WCR  N1   HN1   single    0.890  0.020  1.040
 WCR  O1   HO1   single    0.850  0.020  0.980
 WCR  N3   C2    single    1.344  0.020  1.344
 WCR  C2   CA2   single    1.487  0.020  1.487
 WCR  C2   O2    double    1.219  0.020  1.219
 WCR  N2   CA2   single    1.375  0.020  1.375
 WCR  N2   HN2   single    0.890  0.020  1.040
 WCR  OXT  C3    deloc     1.247  0.020  1.247
 WCR  O3   C3    deloc     1.239  0.020  1.239
 WCR  C3   CA3   single    1.547  0.020  1.547
 WCR  CA3  N3    single    1.436  0.020  1.436
 WCR  CZ   OH    single    1.348  0.020  1.348
 WCR  OH   HOH   single    0.850  0.020  0.980
 WCR  CE2  CZ    aromatic  1.394  0.020  1.394
 WCR  CZ   CE1   aromatic  1.392  0.020  1.392
 WCR  CA1  HA1   single    0.970  0.020  1.090
 WCR  CA2  CB2   double    1.343  0.020  1.343
 WCR  CA3  HA3   single    0.970  0.020  1.090
 WCR  CA3  HA3A  single    0.970  0.020  1.090
 WCR  CB2  CG2   single    1.455  0.020  1.455
 WCR  CB2  HB2   single    0.930  0.020  1.080
 WCR  CG2  CD1   aromatic  1.400  0.020  1.400
 WCR  CD1  CE1   aromatic  1.386  0.020  1.386
 WCR  CD1  HD1   single    0.930  0.020  1.080
 WCR  CD2  CG2   aromatic  1.402  0.020  1.402
 WCR  CD2  CE2   aromatic  1.382  0.020  1.382
 WCR  CD2  HD2   single    0.930  0.020  1.080
 WCR  CE1  HE1   single    0.930  0.020  1.080
 WCR  CE2  HE2   single    0.930  0.020  1.080
 WCR  N1   HN    single    0.890  0.020  1.040
 WCR  CA1  HA1A  single    0.970  0.020  1.090

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
 WCR  CA1   C1   N3   111.04  3.000
 WCR  N3    C1   N2   101.84  3.000
 WCR  CA1   C1   N2   112.29  3.000
 WCR  N2    C1   O1   112.26  3.000
 WCR  N3    C1   O1   110.77  3.000
 WCR  CA1   C1   O1   108.57  3.000
 WCR  HN    N1   HN1  106.69  3.000
 WCR  HN    N1   CA1  111.67  3.000
 WCR  HN1   N1   CA1  110.96  3.000
 WCR  HO1   O1   C1   104.25  3.000
 WCR  CA2   C2   N3   106.08  3.000
 WCR  CA2   C2   O2   127.07  3.000
 WCR  N3    C2   O2   126.82  3.000
 WCR  HN2   N2   CA2  118.40  3.000
 WCR  HN2   N2   C1   116.70  3.000
 WCR  CA2   N2   C1   111.22  3.000
 WCR  OXT   C3   CA3  114.08  3.000
 WCR  CA3   C3   O3   117.82  3.000
 WCR  OXT   C3   O3   128.08  3.000
 WCR  CA3   N3   C2   123.05  3.000
 WCR  CA3   N3   C1   122.18  3.000
 WCR  C2    N3   C1   113.64  3.000
 WCR  CE2   CZ   CE1  119.08  3.000
 WCR  CE1   CZ   OH   122.80  3.000
 WCR  CE2   CZ   OH   118.12  3.000
 WCR  HA1A  CA1  HA1  107.00  3.000
 WCR  HA1A  CA1  N1   114.86  3.000
 WCR  HA1   CA1  N1   108.04  3.000
 WCR  HA1A  CA1  C1   109.41  3.000
 WCR  HA1   CA1  C1   108.13  3.000
 WCR  N1    CA1  C1   109.18  3.000
 WCR  CB2   CA2  N2   131.29  3.000
 WCR  CB2   CA2  C2   122.49  3.000
 WCR  N2    CA2  C2   106.22  3.000
 WCR  HA3A  CA3  HA3  106.24  3.000
 WCR  HA3A  CA3  N3   108.69  3.000
 WCR  HA3   CA3  N3   109.10  3.000
 WCR  HA3A  CA3  C3   108.63  3.000
 WCR  HA3   CA3  C3   109.78  3.000
 WCR  N3    CA3  C3   114.10  3.000
 WCR  HB2   CB2  CG2  116.15  3.000
 WCR  HB2   CB2  CA2  114.99  3.000
 WCR  CG2   CB2  CA2  128.85  3.000
 WCR  HD1   CD1  CG2  120.82  3.000
 WCR  HD1   CD1  CE1  117.60  3.000
 WCR  CG2   CD1  CE1  121.54  3.000
 WCR  HD2   CD2  CG2  119.11  3.000
 WCR  HD2   CD2  CE2  118.76  3.000
 WCR  CG2   CD2  CE2  122.13  3.000
 WCR  HE1   CE1  CD1  119.36  3.000
 WCR  HE1   CE1  CZ   120.22  3.000
 WCR  CD1   CE1  CZ   120.42  3.000
 WCR  HE2   CE2  CD2  120.24  3.000
 WCR  HE2   CE2  CZ   119.83  3.000
 WCR  CD2   CE2  CZ   119.93  3.000
 WCR  CD2   CG2  CD1  116.89  3.000
 WCR  CD2   CG2  CB2  118.69  3.000
 WCR  CD1   CG2  CB2  124.41  3.000
 WCR  HOH   OH   CZ   110.31  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
 WCR  CONST_01  CG2  CD2  CE2  CZ      0.00   0.0  0
 WCR  CONST_02  CG2  CD1  CE1  CZ      0.00   0.0  0
 WCR  CONST_03  CE2  CD2  CG2  CD1     0.00   0.0  0
 WCR  CONST_04  CE2  CZ   CE1  CD1     0.00   0.0  0
 WCR  CONST_05  CE1  CD1  CG2  CD2     0.00   0.0  0
 WCR  CONST_06  CE1  CZ   CE2  CD2     0.00   0.0  0
 WCR  CONST_07  CA2  C2   N3   C1      0.00   0.0  0
 WCR  CONST_08  CD2  CE2  CZ   OH    180.00   0.0  0
 WCR  CONST_09  CD1  CE1  CZ   OH    180.00   0.0  0
 WCR  CONST_10  CE1  CD1  CG2  CB2   180.00   0.0  0
 WCR  CONST_11  CE2  CD2  CG2  CB2   180.00   0.0  0
 WCR  CONST_12  O2   C2   N3   C1    180.00   0.0  0
 WCR  CONST_13  CA3  N3   C2   CA2   180.00   0.0  0
 WCR  CONST_14  HD2  CD2  CE2  CZ    180.00   0.0  0
 WCR  CONST_15  HD1  CD1  CE1  CZ    180.00   0.0  0
 WCR  CONST_16  HE2  CE2  CZ   CE1   180.00   0.0  0
 WCR  CONST_17  HE1  CE1  CZ   CE2   180.00   0.0  0
 WCR  CONST_18  CA3  N3   C2   O2      0.00   0.0  0
 WCR  Var_01    C2   CA2  N2   C1     10.40  30.0  1
 WCR  Var_02    N3   C2   CA2  N2     -7.24  30.0  1
 WCR  Var_03    CG2  CB2  CA2  C2   -179.98  30.0  2
 WCR  Var_04    CD1  CG2  CB2  CA2   -18.43  30.0  2
 WCR  Var_05    C3   CA3  N3   C1     92.82  30.0  2
 WCR  Var_06    OXT  C3   CA3  N3   -171.87  30.0  2
 WCR  Var_07    HN1  N1   CA1  C1    151.89  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
 WCR  chir_01  C1  CA1  N3  N2  positiv

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
 WCR  plan-1  CZ   0.020
 WCR  plan-1  CB2  0.020
 WCR  plan-1  CD1  0.020
 WCR  plan-1  CD2  0.020
 WCR  plan-1  CE1  0.020
 WCR  plan-1  CE2  0.020
 WCR  plan-1  CG2  0.020
 WCR  plan-1  HD1  0.020
 WCR  plan-1  HD2  0.020
 WCR  plan-1  HE1  0.020
 WCR  plan-1  HE2  0.020
 WCR  plan-1  OH   0.020
 WCR  plan-2  C1   0.020
 WCR  plan-2  N2   0.020
 WCR  plan-2  CA2  0.020
 WCR  plan-2  HN2  0.020
 WCR  plan-3  C1   0.020
 WCR  plan-3  C2   0.020
 WCR  plan-3  O2   0.020
 WCR  plan-3  N3   0.020
 WCR  plan-3  CA2  0.020
 WCR  plan-3  CA3  0.020
 WCR  plan-4  C3   0.020
 WCR  plan-4  O3   0.020
 WCR  plan-4  CA3  0.020
 WCR  plan-4  OXT  0.020

