# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 18:44:00 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: [(2R,4Z)-2-[(1R)-1-amino-3-(methylsulfanyl)propyl]-2-hydroxy-4-(4-hydroxybenzylidene)-5-oxoimidazolidin-1-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCC[C@@H](N)[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
 EYG  EYG  '[(2R,4Z)-2-[(1R)-1-amino-3-(methylsulfanyl)propyl]-2-hydroxy-4-(4-hydroxybenzylidene)-5-oxoimidazolidin-1-yl]acetic acid'  L-peptide  46  25  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EYG
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
 EYG  C     C  C     0   0.579  -3.4854  -2.3145   0.6671
 EYG  O     O  O     0  -0.443  -3.0083  -2.0476   1.7383
 EYG  N1    N  NH2   0  -0.798  -3.2700   0.3119  -0.2717
 EYG  C2    C  C     0   0.536  -0.3396  -2.5209   0.0117
 EYG  O2    O  O     0  -0.462  -0.3262  -3.6350   0.4965
 EYG  N3    N  NT    0  -0.541  -1.4044  -1.8950  -0.5372
 EYG  CB    C  CH2   0  -0.443  -1.3895   1.9492  -0.5265
 EYG  CE    C  CH3   0  -0.746  -2.4989   5.6578   0.9495
 EYG  CG    C  CH2   0  -0.541  -2.0852   3.0010   0.3251
 EYG  CZ    C  CR6   0   0.347   5.5843   0.5129   0.1561
 EYG  C13   C  CT    0   0.632  -1.1149  -0.5451  -0.9998
 EYG  O13   O  OH1   0  -0.628  -1.5121  -0.3595  -2.3150
 EYG  N23   N  NH1   0  -0.755   0.3255  -0.5074  -0.8583
 EYG  CA3   C  CH1   0  -0.092  -1.8428   0.5271  -0.1588
 EYG  CAG   C  CH2   0  -0.414  -2.6984  -2.5009  -0.6093
 EYG  CAR   C  C     0   0.217   0.7980  -1.5833  -0.1326
 EYG  CB2   C  C1    0  -0.388   2.0152  -1.8272   0.3726
 EYG  CD1   C  CR16  0  -0.319   3.4168  -0.0455  -0.7267
 EYG  CD2   C  CR16  0  -0.278   4.2477  -1.1961   1.1924
 EYG  CE1   C  CR16  0  -0.291   4.5773   0.7034  -0.7867
 EYG  CE2   C  CR16  0  -0.345   5.4124  -0.4515   1.1455
 EYG  CG2   C  CR6   0   0.155   3.2132  -1.0079   0.2713
 EYG  HN11  H  HNH2  0   0.379  -3.7612   0.7222   0.5104
 EYG  HN12  H  HNH2  0   0.369  -3.6384   0.7289  -1.1182
 EYG  OXT   O  OH1   0  -0.569  -4.7711  -2.5709   0.4700
 EYG  HB    H  HCH2  0   0.257  -1.5905   2.1432  -1.5824
 EYG  HBA   H  HCH2  0   0.212  -0.3108   2.0642  -0.3796
 EYG  HE    H  HCH3  0   0.245  -3.5615   5.5151   0.7566
 EYG  HEA   H  HCH3  0   0.245  -2.2946   5.4446   1.9980
 EYG  HEB   H  HCH3  0   0.261  -2.2525   6.7002   0.7569
 EYG  HG    H  HCH2  0   0.244  -3.1663   2.9609   0.1798
 EYG  HGA   H  HCH2  0   0.242  -1.8845   2.8313   1.3862
 EYG  HOH   H  HOH1  0   0.443   7.3207   1.0347   0.7426
 EYG  HO13  H  HOH1  0   0.433  -0.9861  -0.9325  -2.8837
 EYG  HN23  H  HNH1  0   0.378   0.7413   0.3965  -0.6952
 EYG  H13   H  HCH1  0   0.239  -1.5608   0.3318   0.8804
 EYG  HAG   H  HCH2  0   0.284  -2.5788  -3.5746  -0.7825
 EYG  HAGA  H  HCH2  0   0.291  -3.2516  -2.1002  -1.4545
 EYG  HB2   H  H     0   0.237   2.0995  -2.7455   0.9422
 EYG  HD1   H  HCR6  0   0.240   2.6826   0.1010  -1.5076
 EYG  HD2   H  HCR6  0   0.233   4.1394  -1.9413   1.9704
 EYG  HE1   H  HCR6  0   0.256   4.7117   1.4339  -1.5737
 EYG  HE2   H  HCR6  0   0.238   6.1840  -0.6301   1.8856
 EYG  HXT   H  HOH1  0   0.452  -5.2506  -2.4743   1.3027
 EYG  OH    O  OH1   0  -0.601   6.6917   1.2725   0.0559
 EYG  SD    S  S2    0   0.014  -1.4862   4.6452  -0.1463

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
 EYG  O    C     double    1.203  0.020  1.203
 EYG  CA3  N1    single    1.448  0.020  1.448
 EYG  N1   HN11  single    0.890  0.020  1.040
 EYG  C2   CAR   single    1.481  0.020  1.481
 EYG  C2   N3    single    1.352  0.020  1.352
 EYG  O2   C2    double    1.215  0.020  1.215
 EYG  N3   C13   single    1.456  0.020  1.456
 EYG  CB   CG    single    1.522  0.020  1.522
 EYG  SD   CE    single    1.803  0.020  1.803
 EYG  CG   SD    single    1.812  0.020  1.812
 EYG  CZ   OH    single    1.347  0.020  1.347
 EYG  CZ   CE1   aromatic  1.393  0.020  1.393
 EYG  C13  O13   single    1.386  0.020  1.386
 EYG  C13  CA3   single    1.545  0.020  1.545
 EYG  N23  C13   single    1.448  0.020  1.448
 EYG  CA3  CB    single    1.537  0.020  1.537
 EYG  CAG  C     single    1.511  0.020  1.511
 EYG  CAG  N3    single    1.431  0.020  1.431
 EYG  CAR  N23   single    1.381  0.020  1.381
 EYG  CB2  CAR   double    1.340  0.020  1.340
 EYG  CB2  CG2   single    1.455  0.020  1.455
 EYG  CD1  CE1   aromatic  1.382  0.020  1.382
 EYG  CD2  CE2   aromatic  1.383  0.020  1.383
 EYG  CD2  CG2   aromatic  1.398  0.020  1.398
 EYG  CE2  CZ    aromatic  1.392  0.020  1.392
 EYG  CG2  CD1   aromatic  1.401  0.020  1.401
 EYG  C    OXT   single    1.326  0.020  1.326
 EYG  N1   HN12  single    0.890  0.020  1.040
 EYG  CB   HB    single    0.970  0.020  1.090
 EYG  CB   HBA   single    0.970  0.020  1.090
 EYG  CE   HE    single    0.970  0.020  1.090
 EYG  CE   HEA   single    0.970  0.020  1.090
 EYG  CE   HEB   single    0.970  0.020  1.090
 EYG  CG   HG    single    0.970  0.020  1.090
 EYG  CG   HGA   single    0.970  0.020  1.090
 EYG  OH   HOH   single    0.850  0.020  0.980
 EYG  O13  HO13  single    0.850  0.020  0.980
 EYG  N23  HN23  single    0.890  0.020  1.040
 EYG  CA3  H13   single    0.970  0.020  1.090
 EYG  CAG  HAG   single    0.970  0.020  1.090
 EYG  CAG  HAGA  single    0.970  0.020  1.090
 EYG  CB2  HB2   single    0.930  0.020  1.080
 EYG  CD1  HD1   single    0.930  0.020  1.080
 EYG  CD2  HD2   single    0.930  0.020  1.080
 EYG  CE1  HE1   single    0.930  0.020  1.080
 EYG  CE2  HE2   single    0.930  0.020  1.080
 EYG  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
 EYG  OXT   C    CAG   110.83  3.000
 EYG  OXT   C    O     124.07  3.000
 EYG  CAG   C    O     124.96  3.000
 EYG  HN12  N1   HN11  107.63  3.000
 EYG  HN12  N1   CA3   111.26  3.000
 EYG  HN11  N1   CA3   111.00  3.000
 EYG  CAR   C2   N3    105.80  3.000
 EYG  N3    C2   O2    126.53  3.000
 EYG  CAR   C2   O2    127.65  3.000
 EYG  CAG   N3   C13   123.81  3.000
 EYG  CAG   N3   C2    122.47  3.000
 EYG  C13   N3   C2    113.69  3.000
 EYG  HBA   CB   HB    107.00  3.000
 EYG  HBA   CB   CA3   110.83  3.000
 EYG  HB    CB   CA3   109.95  3.000
 EYG  HBA   CB   CG    107.63  3.000
 EYG  HB    CB   CG    109.52  3.000
 EYG  CA3   CB   CG    111.76  3.000
 EYG  HEB   CE   HEA   108.38  3.000
 EYG  HEB   CE   HE    108.36  3.000
 EYG  HEA   CE   HE    109.13  3.000
 EYG  HEB   CE   SD    107.65  3.000
 EYG  HEA   CE   SD    111.69  3.000
 EYG  HE    CE   SD    111.51  3.000
 EYG  HGA   CG   HG    107.78  3.000
 EYG  HGA   CG   SD    109.43  3.000
 EYG  HG    CG   SD    109.03  3.000
 EYG  HGA   CG   CB    110.61  3.000
 EYG  HG    CG   CB    110.67  3.000
 EYG  SD    CG   CB    109.29  3.000
 EYG  CE2   CZ   CE1   119.12  3.000
 EYG  CE2   CZ   OH    123.03  3.000
 EYG  CE1   CZ   OH    117.85  3.000
 EYG  CA3   C13  N23   113.42  3.000
 EYG  N23   C13  O13   111.98  3.000
 EYG  CA3   C13  O13   106.77  3.000
 EYG  N23   C13  N3    101.00  3.000
 EYG  CA3   C13  N3    112.13  3.000
 EYG  O13   C13  N3    111.63  3.000
 EYG  HO13  O13  C13   108.90  3.000
 EYG  HN23  N23  CAR   118.18  3.000
 EYG  HN23  N23  C13   116.71  3.000
 EYG  CAR   N23  C13   111.80  3.000
 EYG  H13   CA3  C13   105.76  3.000
 EYG  H13   CA3  CB    108.43  3.000
 EYG  C13   CA3  CB    111.89  3.000
 EYG  H13   CA3  N1    107.55  3.000
 EYG  CB    CA3  N1    114.18  3.000
 EYG  C13   CA3  N1    108.60  3.000
 EYG  HAGA  CAG  HAG   107.12  3.000
 EYG  HAGA  CAG  N3    110.09  3.000
 EYG  HAG   CAG  N3    108.95  3.000
 EYG  HAGA  CAG  C     110.26  3.000
 EYG  HAG   CAG  C     108.16  3.000
 EYG  N3    CAG  C     112.10  3.000
 EYG  CB2   CAR  N23   130.58  3.000
 EYG  CB2   CAR  C2    123.07  3.000
 EYG  N23   CAR  C2    106.35  3.000
 EYG  HB2   CB2  CG2   116.72  3.000
 EYG  HB2   CB2  CAR   115.02  3.000
 EYG  CG2   CB2  CAR   128.25  3.000
 EYG  HD1   CD1  CG2   120.56  3.000
 EYG  HD1   CD1  CE1   117.71  3.000
 EYG  CG2   CD1  CE1   121.67  3.000
 EYG  HD2   CD2  CG2   119.48  3.000
 EYG  HD2   CD2  CE2   118.63  3.000
 EYG  CG2   CD2  CE2   121.89  3.000
 EYG  HE1   CE1  CD1   120.10  3.000
 EYG  HE1   CE1  CZ    119.66  3.000
 EYG  CD1   CE1  CZ    120.23  3.000
 EYG  HE2   CE2  CD2   119.18  3.000
 EYG  HE2   CE2  CZ    120.76  3.000
 EYG  CD2   CE2  CZ    120.06  3.000
 EYG  CD2   CG2  CD1   117.01  3.000
 EYG  CD1   CG2  CB2   123.78  3.000
 EYG  CD2   CG2  CB2   119.19  3.000
 EYG  HXT   OXT  C     109.51  3.000
 EYG  HOH   OH   CZ    110.21  3.000
 EYG  CG    SD   CE     99.54  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
 EYG  CONST_01  CG2  CD1  CE1  CZ     0.00   0.0  0
 EYG  CONST_02  CG2  CD2  CE2  CZ     0.00   0.0  0
 EYG  CONST_03  CE2  CZ   CE1  CD1    0.00   0.0  0
 EYG  CONST_04  CE2  CD2  CG2  CD1    0.00   0.0  0
 EYG  CONST_05  CE1  CZ   CE2  CD2    0.00   0.0  0
 EYG  CONST_06  CE1  CD1  CG2  CD2    0.00   0.0  0
 EYG  CONST_07  CAR  C2   N3   C13    0.00   0.0  0
 EYG  CONST_08  CD1  CE1  CZ   OH   180.00   0.0  0
 EYG  CONST_09  CD2  CE2  CZ   OH   180.00   0.0  0
 EYG  CONST_10  CE2  CD2  CG2  CB2  180.00   0.0  0
 EYG  CONST_11  CE1  CD1  CG2  CB2  180.00   0.0  0
 EYG  CONST_12  C13  N3   C2   O2   180.00   0.0  0
 EYG  CONST_13  CAR  C2   N3   CAG  180.00   0.0  0
 EYG  CONST_14  HD1  CD1  CE1  CZ   180.00   0.0  0
 EYG  CONST_15  HD2  CD2  CE2  CZ   180.00   0.0  0
 EYG  CONST_16  HE2  CE2  CZ   CE1  180.00   0.0  0
 EYG  CONST_17  HE1  CE1  CZ   CE2  180.00   0.0  0
 EYG  CONST_18  CAG  N3   C2   O2     0.00   0.0  0
 EYG  CONST_19  HXT  OXT  C    O      0.00   0.0  0
 EYG  Var_01    C13  N23  CAR  C2    10.63  30.0  1
 EYG  Var_02    N23  CAR  C2   N3    -4.57  30.0  1
 EYG  Var_03    CG2  CB2  CAR  C2   178.36  30.0  2
 EYG  Var_04    CD2  CG2  CB2  CAR  159.72  30.0  2
 EYG  Var_05    C2   N3   CAG  C     84.30  30.0  3
 EYG  Var_06    N3   CAG  C    O    -20.02  30.0  1
 EYG  Var_07    CA3  CB   CG   SD   179.20  30.0  2
 EYG  Var_08    HG   CG   SD   CE    56.93  30.0  1
 EYG  Var_09    HE   CE   SD   CG   -60.19  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
 EYG  chir_01  C13  N3  CA3  N23  negativ
 EYG  chir_02  CA3  N1  CB   C13  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
 EYG  plan-1  CZ    0.020
 EYG  plan-1  CB2   0.020
 EYG  plan-1  CD1   0.020
 EYG  plan-1  CD2   0.020
 EYG  plan-1  CE1   0.020
 EYG  plan-1  CE2   0.020
 EYG  plan-1  CG2   0.020
 EYG  plan-1  HD1   0.020
 EYG  plan-1  HD2   0.020
 EYG  plan-1  HE1   0.020
 EYG  plan-1  HE2   0.020
 EYG  plan-1  OH    0.020
 EYG  plan-2  C13   0.020
 EYG  plan-2  N23   0.020
 EYG  plan-2  CAR   0.020
 EYG  plan-2  HN23  0.020
 EYG  plan-3  C     0.020
 EYG  plan-3  O     0.020
 EYG  plan-3  CAG   0.020
 EYG  plan-3  OXT   0.020
 EYG  plan-3  HXT   0.020
 EYG  plan-4  C2    0.020
 EYG  plan-4  O2    0.020
 EYG  plan-4  N3    0.020
 EYG  plan-4  C13   0.020
 EYG  plan-4  CAG   0.020
 EYG  plan-4  CAR   0.020

