# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 15:52:55 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: [(2R,4R)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-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@@H]1N[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
 CJO  CJO  '[(2R,4R)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzyl)-5-oxoimidazolidin-1-yl]acetic acid'  L-peptide  43  23  .  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 (side chain)
;

data_comp_CJO
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
 CJO  N1    N  NH2    0  -0.794   1.1343   2.0007  -1.8301
 CJO  CA1   C  CH1    0  -0.135   1.5575   2.1036  -0.4449
 CJO  CB1   C  CH1    0   0.049   0.7869   3.1539   0.3809
 CJO  CG1   C  CH3    0  -0.678   1.0624   4.5670  -0.0953
 CJO  OG1   O  OH1    0  -0.700  -0.6069   2.9253   0.3235
 CJO  C1    C  CH1    0   0.094   1.4729   0.7410   0.2594
 CJO  N2    N  NH1    0  -0.657   0.0905   0.2686   0.3591
 CJO  N3    N  NT     0  -0.430   2.1607  -0.3039  -0.4643
 CJO  C2    C  C      0   0.542   1.3215  -1.1521  -1.0619
 CJO  O2    O  O      0  -0.510   1.6164  -2.1059  -1.7679
 CJO  CA2   C  CH1    0  -0.186  -0.0925  -0.7103  -0.7103
 CJO  CA3   C  CH2    0  -0.464   3.5911  -0.4004  -0.5009
 CJO  C3    C  C      0   0.411   4.2166  -0.9500   0.8026
 CJO  OXT   O  OC    -1  -0.619   5.4622  -0.9502   0.8173
 CJO  CB2   C  CH2    0  -0.560  -0.9935  -1.8718  -0.3120
 CJO  CG2   C  CR6    0   0.134  -2.4028  -1.4290  -0.0312
 CJO  CD1   C  CR16   0  -0.292  -3.2974  -1.1996  -1.0724
 CJO  CD2   C  CR16   0  -0.308  -2.8501  -1.2004   1.2671
 CJO  CE1   C  CR16   0  -0.369  -4.5900  -0.7577  -0.8350
 CJO  CE2   C  CR16   0  -0.323  -4.1385  -0.7580   1.5251
 CJO  CZ    C  CR6    0   0.337  -5.0189  -0.5324   0.4708
 CJO  OH    O  OH1    0  -0.635  -6.2656  -0.1071   0.7663
 CJO  O3    O  O      0  -0.592   3.4422  -1.3417   1.6905
 CJO  HN1   H  HNH2   0   0.340   0.1378   2.1685  -1.9019
 CJO  HN1A  H  HNH2   0   0.355   1.5782   2.7201  -2.3843
 CJO  HA1   H  HCH1   0   0.239   2.6120   2.3987  -0.4347
 CJO  HB1   H  HCH1   0   0.187   1.1465   3.0737   1.4201
 CJO  HG1   H  HCH3   0   0.216   0.7734   4.7028  -1.1390
 CJO  HG1A  H  HCH3   0   0.235   0.5126   5.2954   0.5022
 CJO  HG1B  H  HCH3   0   0.225   2.1244   4.7980  -0.0050
 CJO  HOG1  H  HOH1   0   0.449  -0.7207   1.9573   0.4202
 CJO  HA2   H  HCH1   0   0.275  -0.5178  -0.2227  -1.5946
 CJO  HA3   H  HCH2   0   0.259   3.8710  -1.0536  -1.3299
 CJO  HA3A  H  HCH2   0   0.248   4.0237   0.5779  -0.7286
 CJO  HB2   H  HCH2   0   0.266  -0.9823  -2.6012  -1.1241
 CJO  HB2A  H  HCH2   0   0.256  -0.5731  -2.3728   0.5653
 CJO  HD1   H  HCR6   0   0.251  -2.9848  -1.3726  -2.0960
 CJO  HD2   H  HCR6   0   0.245  -2.1832  -1.3767   2.1036
 CJO  HE1   H  HCR6   0   0.268  -5.2644  -0.5955  -1.6684
 CJO  HE2   H  HCR6   0   0.260  -4.4645  -0.5896   2.5441
 CJO  HOH   H  HOH1   0   0.473  -6.7793   0.0081  -0.0406
 CJO  HC1   H  HCH1   0   0.265   1.8946   0.8443   1.2622
 CJO  HN2   H  HNH1   0   0.375  -0.0219  -0.1956   1.2535

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
 CJO  CA1  N1    single    1.452  0.020  1.452
 CJO  N1   HN1   single    0.890  0.020  1.040
 CJO  N1   HN1A  single    0.890  0.020  1.040
 CJO  C1   CA1   single    1.536  0.020  1.536
 CJO  CA1  CB1   single    1.542  0.020  1.542
 CJO  CA1  HA1   single    0.970  0.020  1.090
 CJO  CB1  OG1   single    1.414  0.020  1.414
 CJO  CB1  CG1   single    1.516  0.020  1.516
 CJO  CB1  HB1   single    0.970  0.020  1.090
 CJO  CG1  HG1   single    0.970  0.020  1.090
 CJO  CG1  HG1A  single    0.970  0.020  1.090
 CJO  CG1  HG1B  single    0.970  0.020  1.090
 CJO  OG1  HOG1  single    0.850  0.020  0.980
 CJO  N3   C1    single    1.445  0.020  1.445
 CJO  C1   N2    single    1.464  0.020  1.464
 CJO  CA2  N2    single    1.461  0.020  1.461
 CJO  C2   N3    single    1.335  0.020  1.335
 CJO  CA3  N3    single    1.434  0.020  1.434
 CJO  O2   C2    double    1.223  0.020  1.223
 CJO  C2   CA2   single    1.523  0.020  1.523
 CJO  CB2  CA2   single    1.523  0.020  1.523
 CJO  CA2  HA2   single    0.970  0.020  1.090
 CJO  CA3  C3    single    1.547  0.020  1.547
 CJO  CA3  HA3   single    0.970  0.020  1.090
 CJO  CA3  HA3A  single    0.970  0.020  1.090
 CJO  O3   C3    deloc     1.242  0.020  1.242
 CJO  C3   OXT   deloc     1.246  0.020  1.246
 CJO  CB2  CG2   single    1.504  0.020  1.504
 CJO  CB2  HB2   single    0.970  0.020  1.090
 CJO  CB2  HB2A  single    0.970  0.020  1.090
 CJO  CD2  CG2   aromatic  1.392  0.020  1.392
 CJO  CG2  CD1   aromatic  1.392  0.020  1.392
 CJO  CD1  CE1   aromatic  1.387  0.020  1.387
 CJO  CD1  HD1   single    0.930  0.020  1.080
 CJO  CD2  CE2   aromatic  1.386  0.020  1.386
 CJO  CD2  HD2   single    0.930  0.020  1.080
 CJO  CZ   CE1   aromatic  1.393  0.020  1.393
 CJO  CE1  HE1   single    0.930  0.020  1.080
 CJO  CE2  CZ    aromatic  1.392  0.020  1.392
 CJO  CE2  HE2   single    0.930  0.020  1.080
 CJO  CZ   OH    single    1.350  0.020  1.350
 CJO  OH   HOH   single    0.850  0.020  0.980
 CJO  C1   HC1   single    0.970  0.020  1.090
 CJO  N2   HN2   single    0.890  0.020  1.040

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
 CJO  HN1A  N1   HN1   105.98  3.000
 CJO  HN1A  N1   CA1   110.15  3.000
 CJO  HN1   N1   CA1   110.03  3.000
 CJO  HA1   CA1  C1    106.72  3.000
 CJO  HA1   CA1  CB1   107.02  3.000
 CJO  C1    CA1  CB1   109.34  3.000
 CJO  HA1   CA1  N1    107.98  3.000
 CJO  CB1   CA1  N1    114.42  3.000
 CJO  C1    CA1  N1    111.00  3.000
 CJO  HB1   CB1  OG1   110.37  3.000
 CJO  HB1   CB1  CG1   107.73  3.000
 CJO  OG1   CB1  CG1   108.48  3.000
 CJO  HB1   CB1  CA1   106.99  3.000
 CJO  CG1   CB1  CA1   112.07  3.000
 CJO  OG1   CB1  CA1   111.15  3.000
 CJO  HG1B  CG1  HG1A  107.69  3.000
 CJO  HG1B  CG1  HG1   108.10  3.000
 CJO  HG1A  CG1  HG1   107.90  3.000
 CJO  HG1B  CG1  CB1   110.38  3.000
 CJO  HG1A  CG1  CB1   111.02  3.000
 CJO  HG1   CG1  CB1   111.60  3.000
 CJO  HOG1  OG1  CB1   105.69  3.000
 CJO  HC1   C1   N3    110.14  3.000
 CJO  HC1   C1   N2    109.41  3.000
 CJO  N3    C1   N2    104.49  3.000
 CJO  HC1   C1   CA1   108.40  3.000
 CJO  N2    C1   CA1   111.67  3.000
 CJO  N3    C1   CA1   112.68  3.000
 CJO  HN2   N2   CA2   108.96  3.000
 CJO  HN2   N2   C1    108.21  3.000
 CJO  CA2   N2   C1    106.53  3.000
 CJO  CA3   N3   C2    124.96  3.000
 CJO  CA3   N3   C1    122.42  3.000
 CJO  C2    N3   C1    112.61  3.000
 CJO  CA2   C2   O2    125.71  3.000
 CJO  CA2   C2   N3    107.23  3.000
 CJO  O2    C2   N3    127.07  3.000
 CJO  HA2   CA2  CB2   108.71  3.000
 CJO  HA2   CA2  C2    107.65  3.000
 CJO  CB2   CA2  C2    112.86  3.000
 CJO  HA2   CA2  N2    109.94  3.000
 CJO  CB2   CA2  N2    113.18  3.000
 CJO  C2    CA2  N2    104.31  3.000
 CJO  HA3A  CA3  HA3   106.00  3.000
 CJO  HA3A  CA3  C3    109.47  3.000
 CJO  HA3   CA3  C3    108.88  3.000
 CJO  HA3A  CA3  N3    109.85  3.000
 CJO  HA3   CA3  N3    108.38  3.000
 CJO  C3    CA3  N3    113.94  3.000
 CJO  O3    C3   OXT   127.96  3.000
 CJO  OXT   C3   CA3   114.48  3.000
 CJO  O3    C3   CA3   117.55  3.000
 CJO  HB2A  CB2  HB2   106.65  3.000
 CJO  HB2A  CB2  CG2   110.19  3.000
 CJO  HB2   CB2  CG2   110.20  3.000
 CJO  HB2A  CB2  CA2   109.36  3.000
 CJO  HB2   CB2  CA2   108.00  3.000
 CJO  CG2   CB2  CA2   112.26  3.000
 CJO  CD2   CG2  CD1   117.65  3.000
 CJO  CD1   CG2  CB2   120.75  3.000
 CJO  CD2   CG2  CB2   121.58  3.000
 CJO  HD1   CD1  CE1   118.77  3.000
 CJO  HD1   CD1  CG2   119.65  3.000
 CJO  CE1   CD1  CG2   121.58  3.000
 CJO  HD2   CD2  CE2   118.68  3.000
 CJO  HD2   CD2  CG2   119.68  3.000
 CJO  CE2   CD2  CG2   121.64  3.000
 CJO  HE1   CE1  CZ    120.32  3.000
 CJO  HE1   CE1  CD1   119.73  3.000
 CJO  CZ    CE1  CD1   119.95  3.000
 CJO  HE2   CE2  CZ    119.81  3.000
 CJO  HE2   CE2  CD2   120.29  3.000
 CJO  CZ    CE2  CD2   119.90  3.000
 CJO  OH    CZ   CE2   117.99  3.000
 CJO  OH    CZ   CE1   122.72  3.000
 CJO  CE2   CZ   CE1   119.29  3.000
 CJO  HOH   OH   CZ    110.29  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
 CJO  CONST_01  CZ   CE2  CD2  CG2    0.00   0.0  0
 CJO  CONST_02  CZ   CE1  CD1  CG2    0.00   0.0  0
 CJO  CONST_03  CE2  CD2  CG2  CD1    0.00   0.0  0
 CJO  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 CJO  CONST_05  CE1  CD1  CG2  CD2    0.00   0.0  0
 CJO  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 CJO  CONST_07  CA2  C2   N3   C1     0.00   0.0  0
 CJO  CONST_08  CE2  CD2  CG2  CB2  180.00   0.0  0
 CJO  CONST_09  CE1  CD1  CG2  CB2  180.00   0.0  0
 CJO  CONST_10  OH   CZ   CE1  CD1  180.00   0.0  0
 CJO  CONST_11  OH   CZ   CE2  CD2  180.00   0.0  0
 CJO  CONST_12  O2   C2   N3   C1   180.00   0.0  0
 CJO  CONST_13  CA3  N3   C2   CA2  180.00   0.0  0
 CJO  CONST_14  HE2  CE2  CD2  CG2  180.00   0.0  0
 CJO  CONST_15  HE1  CE1  CD1  CG2  180.00   0.0  0
 CJO  CONST_16  HD2  CD2  CG2  CD1  180.00   0.0  0
 CJO  CONST_17  HD1  CD1  CG2  CD2  180.00   0.0  0
 CJO  CONST_18  CA3  N3   C2   O2     0.00   0.0  0
 CJO  Var_01    CD2  CG2  CB2  CA2  -98.05  30.0  2
 CJO  Var_02    C3   CA3  N3   C1    75.72  30.0  2
 CJO  Var_03    O3   C3   CA3  N3     5.35  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
 CJO  chir_01  CA1  N1   C1   CB1  positiv
 CJO  chir_02  CB1  OG1  CA1  CG1  negativ
 CJO  chir_03  C1   N3   N2   CA1  positiv
 CJO  chir_04  CA2  N2   CB2  C2   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
 CJO  plan-1  CB2  0.020
 CJO  plan-1  CG2  0.020
 CJO  plan-1  CD1  0.020
 CJO  plan-1  CD2  0.020
 CJO  plan-1  CE1  0.020
 CJO  plan-1  CE2  0.020
 CJO  plan-1  CZ   0.020
 CJO  plan-1  OH   0.020
 CJO  plan-1  HD1  0.020
 CJO  plan-1  HD2  0.020
 CJO  plan-1  HE1  0.020
 CJO  plan-1  HE2  0.020
 CJO  plan-2  CA3  0.020
 CJO  plan-2  C3   0.020
 CJO  plan-2  OXT  0.020
 CJO  plan-2  O3   0.020
 CJO  plan-3  C1   0.020
 CJO  plan-3  N3   0.020
 CJO  plan-3  C2   0.020
 CJO  plan-3  O2   0.020
 CJO  plan-3  CA2  0.020
 CJO  plan-3  CA3  0.020

