# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 00:38:49 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: [(4Z)-2-[(1R)-1-amino-2-sulfanylethyl]-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](CS)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
 GYC  GYC  '[(4Z)-2-[(1R)-1-amino-2-sulfanylethyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid'  L-peptide  36  22  .  2022-07-25  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GYC
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
 GYC  N     N  NH2    0  -0.772  -1.3003  -2.4027  -1.6006
 GYC  SG1   S  S2     0  -0.235  -3.5841  -3.2860   0.6069
 GYC  CB1   C  CH2    0  -0.593  -2.4117  -1.8985   0.6099
 GYC  CA1   C  CH1    0  -0.199  -2.0203  -1.4340  -0.8043
 GYC  C1    C  CR5    0   0.566  -1.1821  -0.2007  -0.6497
 GYC  N2    N  N      0  -0.488   0.0919  -0.2466  -0.4530
 GYC  N3    N  NR5    0  -0.543  -1.7068   1.0700  -0.6568
 GYC  C2    C  CR5    0   0.532  -0.6804   1.9498  -0.3958
 GYC  O2    O  O      0  -0.456  -0.7816   3.1574  -0.3038
 GYC  CA2   C  CR5    0   0.084   0.5036   1.0691  -0.2914
 GYC  CA3   C  CH2    0  -0.478  -3.0876   1.4776  -0.6927
 GYC  CB2   C  C1     0  -0.389   1.7485   1.5409  -0.0801
 GYC  CG2   C  CR6    0   0.135   2.9997   0.8260   0.0339
 GYC  CD1   C  CR16   0  -0.299   3.1232  -0.5681  -0.0541
 GYC  CD2   C  CR16   0  -0.287   4.1696   1.5704   0.2435
 GYC  CE1   C  CR16   0  -0.361   4.3549  -1.1818   0.0606
 GYC  CE2   C  CR16   0  -0.331   5.4055   0.9678   0.3594
 GYC  CZ    C  CR6    0   0.361   5.5074  -0.4202   0.2667
 GYC  OH    O  OH1    0  -0.620   6.7262  -0.9680   0.3810
 GYC  C     C  C      0   0.424  -3.7117   1.6754   0.7082
 GYC  O     O  O      0  -0.587  -3.0203   1.3562   1.6890
 GYC  OXT   O  OC    -1  -0.607  -4.8666   2.1360   0.6951
 GYC  HN1   H  HNH2   0   0.350  -0.4613  -2.6935  -1.1133
 GYC  HN2   H  HNH2   0   0.350  -1.8732  -3.2287  -1.7198
 GYC  HG1   H  HSH1   0   0.222  -2.7138  -4.2620   0.3258
 GYC  HB11  H  HCH2   0   0.296  -2.8989  -1.0926   1.1595
 GYC  HB12  H  HCH2   0   0.284  -1.5203  -2.1817   1.1717
 GYC  HA1   H  HCH1   0   0.271  -2.9383  -1.1805  -1.3400
 GYC  HA31  H  HCH2   0   0.271  -3.1550   2.4073  -1.2594
 GYC  HA32  H  HCH2   0   0.272  -3.6667   0.7425  -1.2527
 GYC  HB2   H  H      0   0.264   1.8217   2.6200   0.0156
 GYC  HD1   H  HCR6   0   0.278   2.2435  -1.1748  -0.2147
 GYC  HD2   H  HCR6   0   0.262   4.1046   2.6495   0.3155
 GYC  HE1   H  HCR6   0   0.276   4.4239  -2.2614  -0.0116
 GYC  HE2   H  HCR6   0   0.269   6.2941   1.5646   0.5212
 GYC  HOH   H  HOH1   0   0.479   6.6773  -1.9280   0.3056

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
 GYC  N    CA1   single    1.446  0.020  1.446
 GYC  N    HN1   single    0.890  0.020  1.040
 GYC  N    HN2   single    0.890  0.020  1.040
 GYC  SG1  CB1   single    1.816  0.020  1.816
 GYC  SG1  HG1   single    1.200  0.020  1.300
 GYC  CB1  CA1   single    1.539  0.020  1.539
 GYC  CB1  HB11  single    0.970  0.020  1.090
 GYC  CB1  HB12  single    0.970  0.020  1.090
 GYC  CA1  C1    single    1.499  0.020  1.499
 GYC  CA1  HA1   single    0.970  0.020  1.090
 GYC  C1   N2    double    1.290  0.020  1.290
 GYC  C1   N3    single    1.375  0.020  1.375
 GYC  N2   CA2   single    1.388  0.020  1.388
 GYC  N3   C2    single    1.377  0.020  1.377
 GYC  N3   CA3   single    1.440  0.020  1.440
 GYC  C2   O2    double    1.215  0.020  1.215
 GYC  C2   CA2   single    1.479  0.020  1.479
 GYC  CA2  CB2   double    1.348  0.020  1.348
 GYC  CA3  C     single    1.546  0.020  1.546
 GYC  CA3  HA31  single    0.970  0.020  1.090
 GYC  CA3  HA32  single    0.970  0.020  1.090
 GYC  CB2  CG2   single    1.445  0.020  1.445
 GYC  CB2  HB2   single    0.930  0.020  1.080
 GYC  CG2  CD1   aromatic  1.402  0.020  1.402
 GYC  CG2  CD2   aromatic  1.402  0.020  1.402
 GYC  CD1  CE1   aromatic  1.381  0.020  1.381
 GYC  CD1  HD1   single    0.930  0.020  1.080
 GYC  CD2  CE2   aromatic  1.380  0.020  1.380
 GYC  CD2  HD2   single    0.930  0.020  1.080
 GYC  CE1  CZ    aromatic  1.397  0.020  1.397
 GYC  CE1  HE1   single    0.930  0.020  1.080
 GYC  CE2  CZ    aromatic  1.395  0.020  1.395
 GYC  CE2  HE2   single    0.930  0.020  1.080
 GYC  CZ   OH    single    1.341  0.020  1.341
 GYC  OH   HOH   single    0.850  0.020  0.980
 GYC  C    O     deloc     1.242  0.020  1.242
 GYC  C    OXT   deloc     1.243  0.020  1.243

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
 GYC  HN2   N    HN1   106.93  3.000
 GYC  HN2   N    CA1   109.25  3.000
 GYC  HN1   N    CA1   109.86  3.000
 GYC  HG1   SG1  CB1    97.92  3.000
 GYC  HB12  CB1  HB11  107.30  3.000
 GYC  HB12  CB1  CA1   110.10  3.000
 GYC  HB11  CB1  CA1   110.71  3.000
 GYC  HB12  CB1  SG1   109.26  3.000
 GYC  HB11  CB1  SG1   106.09  3.000
 GYC  CA1   CB1  SG1   113.15  3.000
 GYC  HA1   CA1  C1    109.24  3.000
 GYC  HA1   CA1  CB1   107.87  3.000
 GYC  C1    CA1  CB1   107.20  3.000
 GYC  HA1   CA1  N     107.68  3.000
 GYC  C1    CA1  N     109.24  3.000
 GYC  CB1   CA1  N     115.49  3.000
 GYC  N3    C1   N2    114.25  3.000
 GYC  N3    C1   CA1   123.12  3.000
 GYC  N2    C1   CA1   122.59  3.000
 GYC  CA2   N2   C1    106.08  3.000
 GYC  CA3   N3   C2    122.59  3.000
 GYC  CA3   N3   C1    128.88  3.000
 GYC  C2    N3   C1    107.77  3.000
 GYC  CA2   C2   O2    130.76  3.000
 GYC  CA2   C2   N3    103.27  3.000
 GYC  O2    C2   N3    125.96  3.000
 GYC  CB2   CA2  C2    122.81  3.000
 GYC  CB2   CA2  N2    128.61  3.000
 GYC  C2    CA2  N2    108.59  3.000
 GYC  HA32  CA3  HA31  105.96  3.000
 GYC  HA32  CA3  C     109.70  3.000
 GYC  HA31  CA3  C     109.67  3.000
 GYC  HA32  CA3  N3    109.34  3.000
 GYC  HA31  CA3  N3    108.26  3.000
 GYC  C     CA3  N3    113.62  3.000
 GYC  HB2   CB2  CG2   115.22  3.000
 GYC  HB2   CB2  CA2   115.09  3.000
 GYC  CG2   CB2  CA2   129.69  3.000
 GYC  CD2   CG2  CD1   117.62  3.000
 GYC  CD2   CG2  CB2   118.12  3.000
 GYC  CD1   CG2  CB2   124.26  3.000
 GYC  HD1   CD1  CE1   119.27  3.000
 GYC  HD1   CD1  CG2   119.72  3.000
 GYC  CE1   CD1  CG2   121.01  3.000
 GYC  HD2   CD2  CE2   118.89  3.000
 GYC  HD2   CD2  CG2   119.25  3.000
 GYC  CE2   CD2  CG2   121.87  3.000
 GYC  HE1   CE1  CZ    120.03  3.000
 GYC  HE1   CE1  CD1   119.59  3.000
 GYC  CZ    CE1  CD1   120.39  3.000
 GYC  HE2   CE2  CZ    119.91  3.000
 GYC  HE2   CE2  CD2   120.46  3.000
 GYC  CZ    CE2  CD2   119.63  3.000
 GYC  OH    CZ   CE2   117.85  3.000
 GYC  OH    CZ   CE1   122.66  3.000
 GYC  CE2   CZ   CE1   119.49  3.000
 GYC  HOH   OH   CZ    110.73  3.000
 GYC  OXT   C    O     128.36  3.000
 GYC  OXT   C    CA3   114.38  3.000
 GYC  O     C    CA3   117.26  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
 GYC  CONST_01  CZ   CE1  CD1  CG2    0.00   0.0  0
 GYC  CONST_02  CZ   CE2  CD2  CG2    0.00   0.0  0
 GYC  CONST_03  CE2  CD2  CG2  CD1    0.00   0.0  0
 GYC  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 GYC  CONST_05  CE1  CD1  CG2  CD2    0.00   0.0  0
 GYC  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 GYC  CONST_07  C2   CA2  N2   C1     0.00   0.0  0
 GYC  CONST_08  CA2  C2   N3   C1     0.00   0.0  0
 GYC  CONST_09  C2   N3   C1   N2     0.00   0.0  0
 GYC  CONST_10  N3   C2   CA2  N2     0.00   0.0  0
 GYC  CONST_11  CA2  N2   C1   N3     0.00   0.0  0
 GYC  CONST_12  CE1  CD1  CG2  CB2  180.00   0.0  0
 GYC  CONST_13  CE2  CD2  CG2  CB2  180.00   0.0  0
 GYC  CONST_14  OH   CZ   CE1  CD1  180.00   0.0  0
 GYC  CONST_15  OH   CZ   CE2  CD2  180.00   0.0  0
 GYC  CONST_16  CA2  N2   C1   CA1  180.00   0.0  0
 GYC  CONST_17  C2   N3   C1   CA1  180.00   0.0  0
 GYC  CONST_18  O2   C2   N3   C1   180.00   0.0  0
 GYC  CONST_19  CA3  N3   C1   N2   180.00   0.0  0
 GYC  CONST_20  CA3  N3   C2   CA2  180.00   0.0  0
 GYC  CONST_21  HE1  CE1  CD1  CG2  180.00   0.0  0
 GYC  CONST_22  HE2  CE2  CD2  CG2  180.00   0.0  0
 GYC  CONST_23  HD2  CD2  CG2  CD1  180.00   0.0  0
 GYC  CONST_24  HD1  CD1  CG2  CD2  180.00   0.0  0
 GYC  CONST_25  CA3  N3   C1   CA1    0.00   0.0  0
 GYC  CONST_26  CA3  N3   C2   O2     0.00   0.0  0
 GYC  Var_01    CG2  CB2  CA2  N2     0.23  30.0  2
 GYC  Var_02    CD1  CG2  CB2  CA2   -0.51  30.0  2
 GYC  Var_03    C    CA3  N3   C1    91.29  30.0  3
 GYC  Var_04    O    C    CA3  N3    -6.20  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
 GYC  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
 GYC  plan-1  CA1  0.020
 GYC  plan-1  C1   0.020
 GYC  plan-1  N2   0.020
 GYC  plan-1  N3   0.020
 GYC  plan-1  C2   0.020
 GYC  plan-1  O2   0.020
 GYC  plan-1  CA2  0.020
 GYC  plan-1  CA3  0.020
 GYC  plan-1  CB2  0.020
 GYC  plan-2  CB2  0.020
 GYC  plan-2  CG2  0.020
 GYC  plan-2  CD1  0.020
 GYC  plan-2  CD2  0.020
 GYC  plan-2  CE1  0.020
 GYC  plan-2  CE2  0.020
 GYC  plan-2  CZ   0.020
 GYC  plan-2  OH   0.020
 GYC  plan-2  HD1  0.020
 GYC  plan-2  HD2  0.020
 GYC  plan-2  HE1  0.020
 GYC  plan-2  HE2  0.020
 GYC  plan-3  CA3  0.020
 GYC  plan-3  C    0.020
 GYC  plan-3  O    0.020
 GYC  plan-3  OXT  0.020

