# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 13:58:10 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: [(2R,4S)-2-[(1S,2R)-1-amino-2-hydroxypropyl]-2-hydroxy-4-(4-hydroxybenzyl)-5-oxoimidazolidin-1-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@H](N)[C@@]1(O)N[C@@H](Cc2ccc(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
 CZO  CZO  '[(2R,4S)-2-[(1S,2R)-1-amino-2-hydroxypropyl]-2-hydroxy-4-(4-hydroxybenzyl)-5-oxoimidazolidin-1-yl]acetic acid'  L-peptide  44  24  .  2022-07-24  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_CZO
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
 CZO  N1    N  NH2    0  -0.790   0.9770  -1.9861   1.7446
 CZO  CA1   C  CH1    0  -0.142   1.5123  -1.9328   0.4002
 CZO  CB1   C  CH1    0   0.063   1.0245  -3.1165  -0.4390
 CZO  CG1   C  CH3    0  -0.689   1.4789  -4.4420   0.1528
 CZO  OG1   O  OH1    0  -0.673  -0.3876  -3.0506  -0.5353
 CZO  C1    C  CT     0   0.596   1.2622  -0.5656  -0.2881
 CZO  N2    N  NH1    0  -0.648  -0.1257  -0.1812  -0.1575
 CZO  N3    N  NT     0  -0.514   1.9157   0.5172   0.4398
 CZO  C2    C  C      0   0.539   1.1376   1.6133   0.5324
 CZO  O2    O  O      0  -0.491   1.4892   2.7049   0.9430
 CZO  CA2   C  CH1    0  -0.181  -0.2436   1.2407   0.0458
 CZO  CA3   C  CH2    0  -0.482   3.3470   0.6305   0.5684
 CZO  C3    C  C      0   0.458   4.0243   1.3455  -0.6214
 CZO  O3    O  O      0  -0.608   3.3746   1.4026  -1.6975
 CZO  CB2   C  CH2    0  -0.509  -1.3219   1.6024   1.0706
 CZO  CG2   C  CR6    0   0.102  -2.6892   1.1694   0.6255
 CZO  CD1   C  CR16   0  -0.286  -3.1658  -0.1099   0.8977
 CZO  CD2   C  CR16   0  -0.299  -3.5100   2.0210  -0.1113
 CZO  CE1   C  CR16   0  -0.373  -4.4151  -0.5244   0.4617
 CZO  CE2   C  CR16   0  -0.324  -4.7602   1.6225  -0.5586
 CZO  CZ    C  CR6    0   0.337  -5.2217   0.3404  -0.2721
 CZO  OH    O  OH1    0  -0.636  -6.4468  -0.0093  -0.7199
 CZO  O     O  OH1    0  -0.715   1.7366  -0.6188  -1.5972
 CZO  OXT   O  OC    -1  -0.576   5.1641   1.7784  -0.4241
 CZO  HN1   H  HNH2   0   0.341   1.4919  -1.3476   2.3380
 CZO  HN1A  H  HNH2   0   0.343   0.0307  -1.6232   1.7109
 CZO  HA1   H  HCH1   0   0.235   2.5979  -2.0651   0.4641
 CZO  HB1   H  HCH1   0   0.205   1.4756  -3.0216  -1.4337
 CZO  HG1   H  HCH3   0   0.224   1.1238  -5.2769  -0.4559
 CZO  HG1A  H  HCH3   0   0.219   2.5682  -4.5021   0.1775
 CZO  HG1B  H  HCH3   0   0.225   1.1085  -4.5710   1.1691
 CZO  HOG1  H  HOH1   0   0.446  -0.6775  -3.7768  -1.0956
 CZO  HN2   H  HNH1   0   0.361  -0.7058  -0.5656  -0.8867
 CZO  HA2   H  HCH1   0   0.265  -0.4333   1.8033  -0.8804
 CZO  HA3   H  HCH2   0   0.268   3.5847   1.1563   1.4935
 CZO  HA3A  H  HCH2   0   0.275   3.7806  -0.3667   0.6716
 CZO  HB2   H  HCH2   0   0.245  -1.0671   1.1264   2.0208
 CZO  HB2A  H  HCH2   0   0.247  -1.3024   2.6820   1.2332
 CZO  HD1   H  HCR6   0   0.251  -2.5546  -0.7991   1.4667
 CZO  HD2   H  HCR6   0   0.246  -3.1708   3.0251  -0.3398
 CZO  HE1   H  HCR6   0   0.265  -4.7603  -1.5254   0.6965
 CZO  HE2   H  HCR6   0   0.259  -5.3805   2.3043  -1.1274
 CZO  HOH   H  HOH1   0   0.472  -6.6468  -0.9173  -0.4671
 CZO  HO    H  HOH1   0   0.451   2.2904   0.1958  -1.7576

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
 CZO  N1   CA1   single    1.448  0.020  1.448
 CZO  CA1  CB1   single    1.531  0.020  1.531
 CZO  CA1  C1    single    1.551  0.020  1.551
 CZO  CB1  CG1   single    1.521  0.020  1.521
 CZO  CB1  OG1   single    1.417  0.020  1.417
 CZO  C1   N2    single    1.446  0.020  1.446
 CZO  C1   N3    single    1.459  0.020  1.459
 CZO  C1   O     single    1.393  0.020  1.393
 CZO  N2   CA2   single    1.441  0.020  1.441
 CZO  N3   C2    single    1.347  0.020  1.347
 CZO  N3   CA3   single    1.442  0.020  1.442
 CZO  C2   O2    double    1.218  0.020  1.218
 CZO  C2   CA2   single    1.511  0.020  1.511
 CZO  CA2  CB2   single    1.531  0.020  1.531
 CZO  CA3  C3    single    1.545  0.020  1.545
 CZO  C3   O3    deloc     1.258  0.020  1.258
 CZO  C3   OXT   deloc     1.235  0.020  1.235
 CZO  CB2  CG2   single    1.502  0.020  1.502
 CZO  CG2  CD1   aromatic  1.392  0.020  1.392
 CZO  CG2  CD2   aromatic  1.394  0.020  1.394
 CZO  CD1  CE1   aromatic  1.387  0.020  1.387
 CZO  CD2  CE2   aromatic  1.386  0.020  1.386
 CZO  CE1  CZ    aromatic  1.392  0.020  1.392
 CZO  CE2  CZ    aromatic  1.392  0.020  1.392
 CZO  CZ   OH    single    1.350  0.020  1.350
 CZO  N1   HN1   single    0.890  0.020  1.040
 CZO  N1   HN1A  single    0.890  0.020  1.040
 CZO  CA1  HA1   single    0.970  0.020  1.090
 CZO  CB1  HB1   single    0.970  0.020  1.090
 CZO  CG1  HG1   single    0.970  0.020  1.090
 CZO  CG1  HG1A  single    0.970  0.020  1.090
 CZO  CG1  HG1B  single    0.970  0.020  1.090
 CZO  OG1  HOG1  single    0.850  0.020  0.980
 CZO  N2   HN2   single    0.890  0.020  1.040
 CZO  CA2  HA2   single    0.970  0.020  1.090
 CZO  CA3  HA3   single    0.970  0.020  1.090
 CZO  CA3  HA3A  single    0.970  0.020  1.090
 CZO  CB2  HB2   single    0.970  0.020  1.090
 CZO  CB2  HB2A  single    0.970  0.020  1.090
 CZO  CD1  HD1   single    0.930  0.020  1.080
 CZO  CD2  HD2   single    0.930  0.020  1.080
 CZO  CE1  HE1   single    0.930  0.020  1.080
 CZO  CE2  HE2   single    0.930  0.020  1.080
 CZO  OH   HOH   single    0.850  0.020  0.980
 CZO  O    HO    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
 CZO  HN1A  N1   HN1   105.57  3.000
 CZO  HN1A  N1   CA1   107.51  3.000
 CZO  HN1   N1   CA1   109.45  3.000
 CZO  HA1   CA1  C1    106.99  3.000
 CZO  HA1   CA1  CB1   104.73  3.000
 CZO  C1    CA1  CB1   112.76  3.000
 CZO  HA1   CA1  N1    107.93  3.000
 CZO  C1    CA1  N1    112.64  3.000
 CZO  CB1   CA1  N1    111.27  3.000
 CZO  HB1   CB1  OG1   110.15  3.000
 CZO  HB1   CB1  CG1   107.79  3.000
 CZO  OG1   CB1  CG1   111.39  3.000
 CZO  HB1   CB1  CA1   107.42  3.000
 CZO  OG1   CB1  CA1   108.59  3.000
 CZO  CG1   CB1  CA1   111.43  3.000
 CZO  HG1B  CG1  HG1A  108.16  3.000
 CZO  HG1B  CG1  HG1   108.58  3.000
 CZO  HG1A  CG1  HG1   107.16  3.000
 CZO  HG1B  CG1  CB1   111.38  3.000
 CZO  HG1A  CG1  CB1   110.79  3.000
 CZO  HG1   CG1  CB1   110.62  3.000
 CZO  HOG1  OG1  CB1   107.75  3.000
 CZO  O     C1   N3    110.16  3.000
 CZO  O     C1   N2    114.94  3.000
 CZO  N3    C1   N2    100.81  3.000
 CZO  O     C1   CA1   109.17  3.000
 CZO  N3    C1   CA1   111.13  3.000
 CZO  N2    C1   CA1   110.43  3.000
 CZO  HN2   N2   CA2   115.55  3.000
 CZO  HN2   N2   C1    112.69  3.000
 CZO  CA2   N2   C1    110.70  3.000
 CZO  CA3   N3   C2    120.22  3.000
 CZO  CA3   N3   C1    123.19  3.000
 CZO  C2    N3   C1    112.29  3.000
 CZO  CA2   C2   O2    126.40  3.000
 CZO  CA2   C2   N3    107.77  3.000
 CZO  O2    C2   N3    125.84  3.000
 CZO  HA2   CA2  CB2   108.74  3.000
 CZO  HA2   CA2  C2    107.62  3.000
 CZO  CB2   CA2  C2    111.72  3.000
 CZO  HA2   CA2  N2    113.57  3.000
 CZO  CB2   CA2  N2    112.65  3.000
 CZO  C2    CA2  N2    102.36  3.000
 CZO  HA3A  CA3  HA3   105.88  3.000
 CZO  HA3A  CA3  C3    108.74  3.000
 CZO  HA3   CA3  C3    109.56  3.000
 CZO  HA3A  CA3  N3    109.32  3.000
 CZO  HA3   CA3  N3    109.27  3.000
 CZO  C3    CA3  N3    113.77  3.000
 CZO  OXT   C3   O3    126.67  3.000
 CZO  OXT   C3   CA3   116.35  3.000
 CZO  O3    C3   CA3   116.96  3.000
 CZO  HB2A  CB2  HB2   107.28  3.000
 CZO  HB2A  CB2  CG2   110.21  3.000
 CZO  HB2   CB2  CG2   110.14  3.000
 CZO  HB2A  CB2  CA2   108.70  3.000
 CZO  HB2   CB2  CA2   108.35  3.000
 CZO  CG2   CB2  CA2   112.01  3.000
 CZO  CD2   CG2  CD1   117.60  3.000
 CZO  CD2   CG2  CB2   121.12  3.000
 CZO  CD1   CG2  CB2   121.25  3.000
 CZO  HD1   CD1  CE1   118.92  3.000
 CZO  HD1   CD1  CG2   119.63  3.000
 CZO  CE1   CD1  CG2   121.45  3.000
 CZO  HD2   CD2  CE2   118.71  3.000
 CZO  HD2   CD2  CG2   119.55  3.000
 CZO  CE2   CD2  CG2   121.74  3.000
 CZO  HE1   CE1  CZ    120.21  3.000
 CZO  HE1   CE1  CD1   119.64  3.000
 CZO  CZ    CE1  CD1   120.15  3.000
 CZO  HE2   CE2  CZ    119.85  3.000
 CZO  HE2   CE2  CD2   120.33  3.000
 CZO  CZ    CE2  CD2   119.82  3.000
 CZO  OH    CZ   CE2   118.10  3.000
 CZO  OH    CZ   CE1   122.66  3.000
 CZO  CE2   CZ   CE1   119.24  3.000
 CZO  HOH   OH   CZ    110.20  3.000
 CZO  HO    O    C1    107.98  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
 CZO  CONST_01  CZ   CE1  CD1  CG2    0.00   0.0  0
 CZO  CONST_02  CZ   CE2  CD2  CG2    0.00   0.0  0
 CZO  CONST_03  CE2  CD2  CG2  CD1    0.00   0.0  0
 CZO  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 CZO  CONST_05  CE1  CD1  CG2  CD2    0.00   0.0  0
 CZO  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 CZO  CONST_07  CA2  C2   N3   C1     0.00   0.0  0
 CZO  CONST_08  CE1  CD1  CG2  CB2  180.00   0.0  0
 CZO  CONST_09  CE2  CD2  CG2  CB2  180.00   0.0  0
 CZO  CONST_10  OH   CZ   CE1  CD1  180.00   0.0  0
 CZO  CONST_11  OH   CZ   CE2  CD2  180.00   0.0  0
 CZO  CONST_12  O2   C2   N3   C1   180.00   0.0  0
 CZO  CONST_13  CA3  N3   C2   CA2  180.00   0.0  0
 CZO  CONST_14  HE1  CE1  CD1  CG2  180.00   0.0  0
 CZO  CONST_15  HE2  CE2  CD2  CG2  180.00   0.0  0
 CZO  CONST_16  HD2  CD2  CG2  CD1  180.00   0.0  0
 CZO  CONST_17  HD1  CD1  CG2  CD2  180.00   0.0  0
 CZO  CONST_18  CA3  N3   C2   O2     0.00   0.0  0
 CZO  Var_01    CD1  CG2  CB2  CA2   87.14  30.0  2
 CZO  Var_02    C3   CA3  N3   C1    85.13  30.0  3
 CZO  Var_03    O3   C3   CA3  N3   -19.67  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
 CZO  chir_01  CA1  N1   CB1  C1   negativ
 CZO  chir_02  CB1  OG1  CA1  CG1  negativ
 CZO  chir_03  C1   N3   N2   CA1  positiv
 CZO  chir_04  CA2  N2   CB2  C2   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
 CZO  plan-1  CB2  0.020
 CZO  plan-1  CG2  0.020
 CZO  plan-1  CD1  0.020
 CZO  plan-1  CD2  0.020
 CZO  plan-1  CE1  0.020
 CZO  plan-1  CE2  0.020
 CZO  plan-1  CZ   0.020
 CZO  plan-1  OH   0.020
 CZO  plan-1  HD1  0.020
 CZO  plan-1  HD2  0.020
 CZO  plan-1  HE1  0.020
 CZO  plan-1  HE2  0.020
 CZO  plan-2  CA3  0.020
 CZO  plan-2  C3   0.020
 CZO  plan-2  O3   0.020
 CZO  plan-2  OXT  0.020
 CZO  plan-3  C1   0.020
 CZO  plan-3  N3   0.020
 CZO  plan-3  C2   0.020
 CZO  plan-3  O2   0.020
 CZO  plan-3  CA2  0.020
 CZO  plan-3  CA3  0.020

