# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 16:54:54 2022
#   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-hydroxyphenyl)methylidene]-5-oxoimidazolidin-1-yl}acetic acid"  L-peptide  45  25  .  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_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   0.431  -3.4812  -2.4560   0.7614
 EYG  O     O  O      0  -0.597  -2.8918  -1.9628   1.7366
 EYG  N1    N  NH2    0  -0.777  -3.3341   0.3814  -0.4563
 EYG  C2    C  C      0   0.520  -0.3804  -2.4923  -0.0025
 EYG  O2    O  O      0  -0.488  -0.3484  -3.6006   0.5058
 EYG  N3    N  NT     0  -0.520  -1.4383  -1.9027  -0.5826
 EYG  CB    C  CH2    0  -0.457  -1.3957   1.9426  -0.5690
 EYG  CE    C  CH3    0  -0.765  -2.4114   5.6387   1.0330
 EYG  CG    C  CH2    0  -0.547  -2.0638   2.9855   0.3162
 EYG  CZ    C  CR6    0   0.337   5.5679   0.5198   0.1396
 EYG  C13   C  CT     0   0.631  -1.1607  -0.5585  -1.0640
 EYG  O13   O  OH1    0  -0.647  -1.5327  -0.3936  -2.3894
 EYG  N23   N  NH1    0  -0.763   0.2795  -0.4980  -0.8980
 EYG  CA3   C  CH1    0  -0.093  -1.9064   0.5277  -0.2529
 EYG  CAG   C  CH2    0  -0.439  -2.7369  -2.5232  -0.5873
 EYG  CAR   C  C      0   0.223   0.7546  -1.5473  -0.1471
 EYG  CB2   C  C1     0  -0.419   1.9683  -1.7775   0.3781
 EYG  CD1   C  CR16   0  -0.333   3.3830  -0.0058  -0.7264
 EYG  CD2   C  CR16   0  -0.301   4.2112  -1.1669   1.1879
 EYG  CE1   C  CR16   0  -0.315   4.5555   0.7256  -0.7947
 EYG  CE2   C  CR16   0  -0.370   5.3877  -0.4401   1.1330
 EYG  CG2   C  CR6    0   0.153   3.1722  -0.9662   0.2722
 EYG  HN11  H  HNH2   0   0.355  -3.8465   0.7067   0.3501
 EYG  HN12  H  HNH2   0   0.345  -3.6471   0.9194  -1.2543
 EYG  OXT   O  OC    -1  -0.629  -4.6285  -2.9456   0.7355
 EYG  HB    H  HCH2   0   0.244  -1.5820   2.1771  -1.6208
 EYG  HBA   H  HCH2   0   0.232  -0.3163   2.0211  -0.4128
 EYG  HE    H  HCH3   0   0.261  -3.4797   5.5123   0.8615
 EYG  HEA   H  HCH3   0   0.261  -2.1802   5.3888   2.0675
 EYG  HEB   H  HCH3   0   0.273  -2.1531   6.6819   0.8609
 EYG  HG    H  HCH2   0   0.255  -3.1473   2.9747   0.1872
 EYG  HGA   H  HCH2   0   0.261  -1.8486   2.7867   1.3690
 EYG  HOH   H  HOH1   0   0.475   7.3247   1.0133   0.7101
 EYG  HO13  H  HOH1   0   0.452  -1.0317  -1.0146  -2.9327
 EYG  HN23  H  HNH1   0   0.391   0.6981   0.4122  -0.7910
 EYG  H13   H  HCH1   0   0.248  -1.6994   0.3046   0.7964
 EYG  HAG   H  HCH2   0   0.243  -2.6131  -3.5732  -0.8677
 EYG  HAGA  H  HCH2   0   0.256  -3.3431  -2.0565  -1.3590
 EYG  HB2   H  H      0   0.246   2.0484  -2.6843   0.9671
 EYG  HD1   H  HCR6   0   0.251   2.6445   0.1545  -1.5004
 EYG  HD2   H  HCR6   0   0.255   4.0953  -1.9123   1.9654
 EYG  HE1   H  HCR6   0   0.264   4.6935   1.4542  -1.5838
 EYG  HE2   H  HCR6   0   0.271   6.1665  -0.6251   1.8644
 EYG  SD    S  S2     0  -0.043  -1.4447   4.6359  -0.1160
 EYG  OH    O  OH1    0  -0.631   6.6889   1.2593   0.0290

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     deloc     1.242  0.020  1.242
 EYG  CA3  N1    single    1.449  0.020  1.449
 EYG  N1   HN11  single    0.890  0.020  1.040
 EYG  C2   CAR   single    1.484  0.020  1.484
 EYG  C2   N3    single    1.343  0.020  1.343
 EYG  O2   C2    double    1.220  0.020  1.220
 EYG  N3   C13   single    1.455  0.020  1.455
 EYG  CB   CG    single    1.522  0.020  1.522
 EYG  SD   CE    single    1.806  0.020  1.806
 EYG  CG   SD    single    1.815  0.020  1.815
 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    1.547  0.020  1.547
 EYG  N23  C13   single    1.451  0.020  1.451
 EYG  CA3  CB    single    1.537  0.020  1.537
 EYG  CAG  C     single    1.542  0.020  1.542
 EYG  CAG  N3    single    1.439  0.020  1.439
 EYG  CAR  N23   single    1.375  0.020  1.375
 EYG  CB2  CAR   double    1.342  0.020  1.342
 EYG  CB2  CG2   single    1.456  0.020  1.456
 EYG  CD1  CE1   aromatic  1.384  0.020  1.384
 EYG  CD2  CE2   aromatic  1.384  0.020  1.384
 EYG  CD2  CG2   aromatic  1.399  0.020  1.399
 EYG  CE2  CZ    aromatic  1.393  0.020  1.393
 EYG  CG2  CD1   aromatic  1.401  0.020  1.401
 EYG  C    OXT   deloc     1.248  0.020  1.248
 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

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   114.12  3.000
 EYG  OXT   C    O     127.49  3.000
 EYG  CAG   C    O     118.37  3.000
 EYG  HN12  N1   HN11  107.56  3.000
 EYG  HN12  N1   CA3   111.20  3.000
 EYG  HN11  N1   CA3   110.81  3.000
 EYG  CAR   C2   N3    106.31  3.000
 EYG  N3    C2   O2    126.84  3.000
 EYG  CAR   C2   O2    126.81  3.000
 EYG  CAG   N3   C13   124.72  3.000
 EYG  CAG   N3   C2    121.53  3.000
 EYG  C13   N3   C2    113.47  3.000
 EYG  HBA   CB   HB    106.87  3.000
 EYG  HBA   CB   CA3   111.39  3.000
 EYG  HB    CB   CA3   109.79  3.000
 EYG  HBA   CB   CG    107.52  3.000
 EYG  HB    CB   CG    109.73  3.000
 EYG  CA3   CB   CG    111.42  3.000
 EYG  HEB   CE   HEA   108.65  3.000
 EYG  HEB   CE   HE    108.61  3.000
 EYG  HEA   CE   HE    109.34  3.000
 EYG  HEB   CE   SD    107.73  3.000
 EYG  HEA   CE   SD    111.30  3.000
 EYG  HE    CE   SD    111.12  3.000
 EYG  HGA   CG   HG    107.91  3.000
 EYG  HGA   CG   SD    109.13  3.000
 EYG  HG    CG   SD    108.64  3.000
 EYG  HGA   CG   CB    110.44  3.000
 EYG  HG    CG   CB    111.11  3.000
 EYG  SD    CG   CB    109.56  3.000
 EYG  CE2   CZ   CE1   119.08  3.000
 EYG  CE2   CZ   OH    122.97  3.000
 EYG  CE1   CZ   OH    117.94  3.000
 EYG  CA3   C13  N23   112.90  3.000
 EYG  N23   C13  O13   111.76  3.000
 EYG  CA3   C13  O13   106.76  3.000
 EYG  N23   C13  N3    100.96  3.000
 EYG  CA3   C13  N3    112.53  3.000
 EYG  O13   C13  N3    112.03  3.000
 EYG  HO13  O13  C13   108.80  3.000
 EYG  HN23  N23  CAR   119.20  3.000
 EYG  HN23  N23  C13   117.53  3.000
 EYG  CAR   N23  C13   111.94  3.000
 EYG  H13   CA3  C13   105.60  3.000
 EYG  H13   CA3  CB    108.81  3.000
 EYG  C13   CA3  CB    112.22  3.000
 EYG  H13   CA3  N1    107.51  3.000
 EYG  CB    CA3  N1    113.04  3.000
 EYG  C13   CA3  N1    109.29  3.000
 EYG  HAGA  CAG  HAG   107.06  3.000
 EYG  HAGA  CAG  N3    108.70  3.000
 EYG  HAG   CAG  N3    108.21  3.000
 EYG  HAGA  CAG  C     109.46  3.000
 EYG  HAG   CAG  C     108.70  3.000
 EYG  N3    CAG  C     114.45  3.000
 EYG  CB2   CAR  N23   131.07  3.000
 EYG  CB2   CAR  C2    122.97  3.000
 EYG  N23   CAR  C2    105.95  3.000
 EYG  HB2   CB2  CG2   116.40  3.000
 EYG  HB2   CB2  CAR   115.00  3.000
 EYG  CG2   CB2  CAR   128.60  3.000
 EYG  HD1   CD1  CG2   120.58  3.000
 EYG  HD1   CD1  CE1   117.70  3.000
 EYG  CG2   CD1  CE1   121.66  3.000
 EYG  HD2   CD2  CG2   119.27  3.000
 EYG  HD2   CD2  CE2   118.74  3.000
 EYG  CG2   CD2  CE2   122.00  3.000
 EYG  HE1   CE1  CD1   119.98  3.000
 EYG  HE1   CE1  CZ    119.71  3.000
 EYG  CD1   CE1  CZ    120.31  3.000
 EYG  HE2   CE2  CD2   119.62  3.000
 EYG  HE2   CE2  CZ    120.38  3.000
 EYG  CD2   CE2  CZ    120.00  3.000
 EYG  CD2   CG2  CD1   116.93  3.000
 EYG  CD1   CG2  CB2   123.93  3.000
 EYG  CD2   CG2  CB2   119.12  3.000
 EYG  CG    SD   CE     99.84  3.000
 EYG  HOH   OH   CZ    110.53  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  HD2   CD2  CG2  CD1   180.00   0.0  0
 EYG  CONST_17  HD1   CD1  CG2  CD2   180.00   0.0  0
 EYG  CONST_18  HE2   CE2  CZ   CE1   180.00   0.0  0
 EYG  CONST_19  HE1   CE1  CZ   CE2   180.00   0.0  0
 EYG  CONST_20  HE2   CE2  CD2  CG2   180.00   0.0  0
 EYG  CONST_21  HE1   CE1  CD1  CG2   180.00   0.0  0
 EYG  CONST_22  CAG   N3   C2   O2      0.00   0.0  0
 EYG  Var_01    C13   N23  CAR  C2     10.38  30.0  1
 EYG  Var_02    N23   CAR  C2   N3     -4.13  30.0  1
 EYG  Var_03    CG2   CB2  CAR  C2    177.57   0.0  2
 EYG  Var_04    CG2   CB2  CAR  N23    -1.50   0.0  2
 EYG  Var_05    N23   CAR  C2   O2    173.85  30.0  1
 EYG  Var_06    CB2   CAR  C2   N3    176.60  30.0  1
 EYG  Var_07    CB2   CAR  N23  C13  -170.43  30.0  1
 EYG  Var_08    CD2   CG2  CB2  CAR   161.73  30.0  2
 EYG  Var_09    CD1   CG2  CB2  CAR   -20.23  30.0  2
 EYG  Var_10    HN23  N23  CAR  C2    153.12  30.0  1
 EYG  Var_11    C2    N3   CAG  C      75.45  30.0  3
 EYG  Var_12    C13   N3   CAG  C     -98.12  30.0  3
 EYG  Var_13    CB2   CAR  C2   O2     -5.42  30.0  1
 EYG  Var_14    HB2   CB2  CAR  C2     -3.24   0.0  2
 EYG  Var_15    HB2   CB2  CAR  N23   177.69   0.0  2
 EYG  Var_16    HAG   CAG  N3   C2    -45.91  30.0  2
 EYG  Var_17    HAGA  CAG  N3   C2   -161.85  30.0  2
 EYG  Var_18    HAG   CAG  N3   C13   140.52  30.0  2
 EYG  Var_19    HAGA  CAG  N3   C13    24.58  30.0  2
 EYG  Var_20    HN23  N23  CAR  CB2   -27.69  30.0  1
 EYG  Var_21    HB2   CB2  CG2  CD1   160.59  30.0  1
 EYG  Var_22    HB2   CB2  CG2  CD2   -17.45  30.0  1
 EYG  Var_23    N3    CAG  C    O      -4.23  30.0  2
 EYG  Var_24    OXT   C    CAG  N3    177.14  30.0  3
 EYG  Var_25    CE    SD   CG   CB    178.77  30.0  3
 EYG  Var_26    CA3   CB   CG   SD   -179.12  30.0  2
 EYG  Var_27    HAG   CAG  C    O     116.86  30.0  2
 EYG  Var_28    HAGA  CAG  C    O    -126.52  30.0  2
 EYG  Var_29    HB    CB   CG   SD    -57.32  30.0  2
 EYG  Var_30    HBA   CB   CG   SD     58.56  30.0  2
 EYG  Var_31    HG    CG   SD   CE     57.22  30.0  1
 EYG  Var_32    HGA   CG   SD   CE    -60.20  30.0  1
 EYG  Var_33    HE    CE   SD   CG    -59.67  30.0  3
 EYG  Var_34    HEA   CE   SD   CG     62.45  30.0  3
 EYG  Var_35    HEB   CE   SD   CG   -178.53  30.0  3
 EYG  Var_36    HG    CG   CB   CA3   -59.08  30.0  3
 EYG  Var_37    HGA   CG   CB   CA3    60.64  30.0  3
 EYG  Var_38    HAG   CAG  C    OXT   -61.77  30.0  2
 EYG  Var_39    HAGA  CAG  C    OXT    54.86  30.0  2

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-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
 EYG  plan-5  C2    0.020
 EYG  plan-5  N23   0.020
 EYG  plan-5  CAR   0.020
 EYG  plan-5  CB2   0.020
 EYG  plan-5  CG2   0.020
 EYG  plan-5  HB2   0.020

