# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 21:13:23 2022
#   Inital geometry file: a 101 line input string
#   Ligand name: [(4Z)-2-[(1R)-1-amino-2-hydroxyethyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CO)C1=N\C(=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
 GYS  GYS  "[(4Z)-2-(1-AMINO-2-HYDROXYETHYL)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID"  L-peptide  36  22  .  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_GYS
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
 GYS  N     N  NH2    0  -0.781  -1.1989  -2.7802  -1.5784
 GYS  OG1   O  OH1    0  -0.669  -3.2688  -3.5156   0.3358
 GYS  CB1   C  CH2    0  -0.149  -2.4783  -2.3686   0.5440
 GYS  CA1   C  CH1    0  -0.251  -2.0312  -1.8580  -0.8309
 GYS  C1    C  CR5    0   0.558  -1.2942  -0.5688  -0.6397
 GYS  N2    N  N      0  -0.492  -0.0240  -0.5196  -0.4194
 GYS  N3    N  NR5    0  -0.543  -1.9101   0.6603  -0.6608
 GYS  C2    C  CR5    0   0.530  -0.9566   1.6142  -0.3857
 GYS  O2    O  O      0  -0.457  -1.1485   2.8117  -0.3038
 GYS  CA2   C  CR5    0   0.084   0.2870   0.8235  -0.2563
 GYS  CA3   C  CH2    0  -0.475  -3.3155   0.9676  -0.7293
 GYS  CB2   C  C1     0  -0.388   1.4900   1.3884  -0.0320
 GYS  CG2   C  CR6    0   0.136   2.7914   0.7734   0.0967
 GYS  CD1   C  CR16   0  -0.286   3.8963   1.6062   0.3141
 GYS  CD2   C  CR16   0  -0.301   3.0257  -0.6089   0.0133
 GYS  CE1   C  CR16   0  -0.376   5.1752   1.0997   0.4435
 GYS  CE2   C  CR16   0  -0.314   4.2979  -1.1255   0.1419
 GYS  CZ    C  CR6    0   0.358   5.3859  -0.2755   0.3582
 GYS  OH    O  OH1    0  -0.619   6.6002  -0.8326   0.4745
 GYS  C     C  C      0   0.423  -3.9743   1.1677   0.6555
 GYS  O     O  O      0  -0.588  -3.2740   0.9494   1.6568
 GYS  OXT   O  OC    -1  -0.609  -5.1642   1.5268   0.6092
 GYS  HN1   H  HNH2   0   0.346  -0.3472  -2.9620  -1.0606
 GYS  HN2   H  HNH2   0   0.354  -1.6817  -3.6667  -1.6508
 GYS  HA1   H  HCH1   0   0.263  -2.9308  -1.6663  -1.4246
 GYS  HB11  H  HCH2   0   0.212  -3.0279  -1.5842   1.0785
 GYS  HB12  H  HCH2   0   0.202  -1.5794  -2.5937   1.1333
 GYS  HG1   H  HOH1   0   0.459  -3.4080  -3.9442   1.1846
 GYS  HB2   H  H      0   0.264   1.4782   2.4705   0.0598
 GYS  HD2   H  HCR6   0   0.275   2.1971  -1.2822  -0.1539
 GYS  HE2   H  HCR6   0   0.269   4.4599  -2.1941   0.0753
 GYS  HOH   H  HOH1   0   0.479   7.2720  -0.1564   0.6202
 GYS  HE1   H  HCR6   0   0.277   6.0085   1.7725   0.6097
 GYS  HD1   H  HCR6   0   0.264   3.7501   2.6775   0.3819
 GYS  HA31  H  HCH2   0   0.270  -3.4404   1.8720  -1.3268
 GYS  HA32  H  HCH2   0   0.271  -3.8328   0.1753  -1.2716

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
 GYS  N    CA1   single    1.450  0.020  1.450
 GYS  N    HN1   single    0.890  0.020  1.040
 GYS  N    HN2   single    0.890  0.020  1.040
 GYS  OG1  CB1   single    1.408  0.020  1.408
 GYS  OG1  HG1   single    0.850  0.020  0.980
 GYS  CB1  CA1   single    1.533  0.020  1.533
 GYS  CB1  HB11  single    0.970  0.020  1.090
 GYS  CB1  HB12  single    0.970  0.020  1.090
 GYS  CA1  C1    single    1.497  0.020  1.497
 GYS  CA1  HA1   single    0.970  0.020  1.090
 GYS  C1   N2    double    1.290  0.020  1.290
 GYS  C1   N3    single    1.375  0.020  1.375
 GYS  N2   CA2   single    1.388  0.020  1.388
 GYS  N3   C2    single    1.377  0.020  1.377
 GYS  N3   CA3   single    1.440  0.020  1.440
 GYS  C2   CA2   single    1.479  0.020  1.479
 GYS  C2   O2    double    1.216  0.020  1.216
 GYS  CA2  CB2   double    1.348  0.020  1.348
 GYS  CA3  C     single    1.547  0.020  1.547
 GYS  CA3  HA31  single    0.970  0.020  1.090
 GYS  CA3  HA32  single    0.970  0.020  1.090
 GYS  CB2  CG2   single    1.445  0.020  1.445
 GYS  CB2  HB2   single    0.930  0.020  1.080
 GYS  CG2  CD2   aromatic  1.404  0.020  1.404
 GYS  CG2  CD1   aromatic  1.401  0.020  1.401
 GYS  CD1  CE1   aromatic  1.382  0.020  1.382
 GYS  CD1  HD1   single    0.930  0.020  1.080
 GYS  CD2  CE2   aromatic  1.379  0.020  1.379
 GYS  CD2  HD2   single    0.930  0.020  1.080
 GYS  CE1  CZ    aromatic  1.394  0.020  1.394
 GYS  CE1  HE1   single    0.930  0.020  1.080
 GYS  CE2  CZ    aromatic  1.398  0.020  1.398
 GYS  CE2  HE2   single    0.930  0.020  1.080
 GYS  CZ   OH    single    1.341  0.020  1.341
 GYS  OH   HOH   single    0.850  0.020  0.980
 GYS  C    O     deloc     1.241  0.020  1.241
 GYS  C    OXT   deloc     1.244  0.020  1.244

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
 GYS  HN2   N    HN1   106.29  3.000
 GYS  HN2   N    CA1   108.67  3.000
 GYS  HN1   N    CA1   109.47  3.000
 GYS  HG1   OG1  CB1   108.29  3.000
 GYS  HB12  CB1  HB11  107.17  3.000
 GYS  HB12  CB1  CA1   108.10  3.000
 GYS  HB11  CB1  CA1   110.18  3.000
 GYS  HB12  CB1  OG1   111.82  3.000
 GYS  HB11  CB1  OG1   111.92  3.000
 GYS  CA1   CB1  OG1   107.59  3.000
 GYS  HA1   CA1  C1    108.84  3.000
 GYS  HA1   CA1  CB1   107.76  3.000
 GYS  C1    CA1  CB1   108.40  3.000
 GYS  HA1   CA1  N     107.67  3.000
 GYS  C1    CA1  N     109.33  3.000
 GYS  CB1   CA1  N     114.70  3.000
 GYS  N3    C1   N2    114.18  3.000
 GYS  N3    C1   CA1   123.18  3.000
 GYS  N2    C1   CA1   122.63  3.000
 GYS  CA2   N2   C1    106.11  3.000
 GYS  CA3   N3   C2    122.52  3.000
 GYS  CA3   N3   C1    128.95  3.000
 GYS  C2    N3   C1    107.82  3.000
 GYS  CA2   C2   O2    130.79  3.000
 GYS  O2    C2   N3    125.93  3.000
 GYS  CA2   C2   N3    103.26  3.000
 GYS  CB2   CA2  C2    122.74  3.000
 GYS  CB2   CA2  N2    128.68  3.000
 GYS  C2    CA2  N2    108.57  3.000
 GYS  HA32  CA3  HA31  106.00  3.000
 GYS  HA32  CA3  C     109.71  3.000
 GYS  HA31  CA3  C     109.53  3.000
 GYS  HA32  CA3  N3    109.36  3.000
 GYS  HA31  CA3  N3    108.34  3.000
 GYS  C     CA3  N3    113.62  3.000
 GYS  HB2   CB2  CG2   115.23  3.000
 GYS  HB2   CB2  CA2   114.96  3.000
 GYS  CG2   CB2  CA2   129.81  3.000
 GYS  CD2   CG2  CD1   117.57  3.000
 GYS  CD1   CG2  CB2   118.11  3.000
 GYS  CD2   CG2  CB2   124.32  3.000
 GYS  HD1   CD1  CE1   118.79  3.000
 GYS  HD1   CD1  CG2   119.42  3.000
 GYS  CE1   CD1  CG2   121.79  3.000
 GYS  HD2   CD2  CE2   119.23  3.000
 GYS  HD2   CD2  CG2   119.64  3.000
 GYS  CE2   CD2  CG2   121.13  3.000
 GYS  HE1   CE1  CZ    120.37  3.000
 GYS  HE1   CE1  CD1   119.90  3.000
 GYS  CZ    CE1  CD1   119.73  3.000
 GYS  HE2   CE2  CZ    119.55  3.000
 GYS  HE2   CE2  CD2   120.13  3.000
 GYS  CZ    CE2  CD2   120.32  3.000
 GYS  OH    CZ   CE2   117.76  3.000
 GYS  OH    CZ   CE1   122.78  3.000
 GYS  CE2   CZ   CE1   119.46  3.000
 GYS  HOH   OH   CZ    110.65  3.000
 GYS  OXT   C    O     128.36  3.000
 GYS  OXT   C    CA3   114.31  3.000
 GYS  O     C    CA3   117.34  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
 GYS  CONST_01  CZ    CE2  CD2  CG2     0.00   0.0  0
 GYS  CONST_02  CZ    CE1  CD1  CG2     0.00   0.0  0
 GYS  CONST_03  CE2   CD2  CG2  CD1     0.00   0.0  0
 GYS  CONST_04  CE2   CZ   CE1  CD1     0.00   0.0  0
 GYS  CONST_05  CE1   CD1  CG2  CD2     0.00   0.0  0
 GYS  CONST_06  CE1   CZ   CE2  CD2     0.00   0.0  0
 GYS  CONST_07  C2    CA2  N2   C1      0.00   0.0  0
 GYS  CONST_08  CA2   C2   N3   C1      0.00   0.0  0
 GYS  CONST_09  C2    N3   C1   N2      0.00   0.0  0
 GYS  CONST_10  N3    C2   CA2  N2      0.00   0.0  0
 GYS  CONST_11  CA2   N2   C1   N3      0.00   0.0  0
 GYS  CONST_12  CE2   CD2  CG2  CB2   180.00   0.0  0
 GYS  CONST_13  CE1   CD1  CG2  CB2   180.00   0.0  0
 GYS  CONST_14  OH    CZ   CE1  CD1   180.00   0.0  0
 GYS  CONST_15  OH    CZ   CE2  CD2   180.00   0.0  0
 GYS  CONST_16  CA2   N2   C1   CA1   180.00   0.0  0
 GYS  CONST_17  C2    N3   C1   CA1   180.00   0.0  0
 GYS  CONST_18  O2    C2   N3   C1    180.00   0.0  0
 GYS  CONST_19  CA3   N3   C1   N2    180.00   0.0  0
 GYS  CONST_20  CA3   N3   C2   CA2   180.00   0.0  0
 GYS  CONST_21  HE2   CE2  CD2  CG2   180.00   0.0  0
 GYS  CONST_22  HE1   CE1  CD1  CG2   180.00   0.0  0
 GYS  CONST_23  HD2   CD2  CG2  CD1   180.00   0.0  0
 GYS  CONST_24  HD1   CD1  CG2  CD2   180.00   0.0  0
 GYS  CONST_25  HE2   CE2  CZ   CE1   180.00   0.0  0
 GYS  CONST_26  HE1   CE1  CZ   CE2   180.00   0.0  0
 GYS  CONST_27  HD1   CD1  CE1  CZ    180.00   0.0  0
 GYS  CONST_28  HD2   CD2  CE2  CZ    180.00   0.0  0
 GYS  CONST_29  CA3   N3   C1   CA1     0.00   0.0  0
 GYS  CONST_30  CA3   N3   C2   O2      0.00   0.0  0
 GYS  Var_01    CG2   CB2  CA2  N2      0.32   0.0  2
 GYS  Var_02    CG2   CB2  CA2  C2   -178.85   0.0  2
 GYS  Var_03    CD2   CG2  CB2  CA2    -0.57  30.0  2
 GYS  Var_04    CD1   CG2  CB2  CA2   179.18  30.0  2
 GYS  Var_05    C     CA3  N3   C1     93.28  30.0  3
 GYS  Var_06    C     CA3  N3   C2    -75.84  30.0  3
 GYS  Var_07    HB2   CB2  CA2  N2    179.91   0.0  2
 GYS  Var_08    HB2   CB2  CA2  C2      0.73   0.0  2
 GYS  Var_09    HA31  CA3  N3   C1   -144.75  30.0  3
 GYS  Var_10    HA32  CA3  N3   C1    -29.66  30.0  3
 GYS  Var_11    HA31  CA3  N3   C2     46.13  30.0  3
 GYS  Var_12    HA32  CA3  N3   C2    161.22  30.0  3
 GYS  Var_13    HB2   CB2  CG2  CD1    -0.40  30.0  2
 GYS  Var_14    HB2   CB2  CG2  CD2   179.85  30.0  2
 GYS  Var_15    O     C    CA3  N3     -5.25  30.0  3
 GYS  Var_16    OXT   C    CA3  N3    175.14  30.0  3
 GYS  Var_17    HA31  CA3  C    O    -126.55  30.0  2
 GYS  Var_18    HA32  CA3  C    O     117.50  30.0  2
 GYS  Var_19    HA31  CA3  C    OXT    53.84  30.0  2
 GYS  Var_20    HA32  CA3  C    OXT   -62.11  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
 GYS  chir_01  CA1  N  CB1  C1  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
 GYS  plan-1  CA1  0.020
 GYS  plan-1  C1   0.020
 GYS  plan-1  N2   0.020
 GYS  plan-1  N3   0.020
 GYS  plan-1  C2   0.020
 GYS  plan-1  O2   0.020
 GYS  plan-1  CA2  0.020
 GYS  plan-1  CA3  0.020
 GYS  plan-1  CB2  0.020
 GYS  plan-1  CG2  0.020
 GYS  plan-1  HB2  0.020
 GYS  plan-2  CB2  0.020
 GYS  plan-2  CG2  0.020
 GYS  plan-2  CD1  0.020
 GYS  plan-2  CD2  0.020
 GYS  plan-2  CE1  0.020
 GYS  plan-2  CE2  0.020
 GYS  plan-2  CZ   0.020
 GYS  plan-2  OH   0.020
 GYS  plan-2  HD2  0.020
 GYS  plan-2  HE2  0.020
 GYS  plan-2  HE1  0.020
 GYS  plan-2  HD1  0.020
 GYS  plan-3  CA3  0.020
 GYS  plan-3  C    0.020
 GYS  plan-3  O    0.020
 GYS  plan-3  OXT  0.020

