# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 07:17:19 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: {(4Z)-2-[(1S)-1,3-diamino-3-oxopropyl]-4-[(4-hydroxyphenyl)methylidene]-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](CC(N)=O)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
 NYG  NYG  '{(4Z)-2-[(1S)-1,3-diamino-3-oxopropyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid'  L-peptide  39  24  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_NYG
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
 NYG  OD1   O  O      0  -0.492   5.4046  -0.3074  -3.5882
 NYG  CG1   C  C      0   0.537   5.7344  -0.2242  -2.4138
 NYG  ND1   N  NH2    0  -0.807   6.0502  -1.2946  -1.6672
 NYG  CB1   C  CH2    0  -0.591   5.8892   1.1122  -1.7226
 NYG  CA1   C  CH1    0  -0.208   4.8582   2.1547  -2.1536
 NYG  N     N  NH2    0  -0.780   5.0873   3.4722  -1.5817
 NYG  C1    C  CR5    0   0.602   3.4721   1.7069  -1.8068
 NYG  N3    N  NR5    0  -0.538   2.3558   2.4446  -2.1318
 NYG  CA3   C  CH2    0  -0.478   2.2883   3.5501  -3.0524
 NYG  C     C  C      0   0.413   2.3004   3.1083  -4.5327
 NYG  O     O  O      0  -0.585   2.4242   1.8953  -4.7622
 NYG  N2    N  N      0  -0.498   3.2172   0.6236  -1.1567
 NYG  CA2   C  CR5    0   0.093   1.8357   0.5560  -1.0438
 NYG  C2    C  CR5    0   0.521   1.2520   1.7394  -1.7159
 NYG  O2    O  O      0  -0.461   0.0898   2.0563  -1.8854
 NYG  CB2   C  C1     0  -0.391   1.0946  -0.3973  -0.4466
 NYG  CG2   C  CR6    0   0.131   1.5250  -1.6049   0.2237
 NYG  CD2   C  CR16   0  -0.286   0.5517  -2.4137   0.8229
 NYG  CE2   C  CR16   0  -0.377   0.8816  -3.5852   1.4777
 NYG  CZ    C  CR6    0   0.357   2.2145  -3.9866   1.5473
 NYG  OH    O  OH1    0  -0.620   2.6019  -5.1127   2.1652
 NYG  CE1   C  CR16   0  -0.317   3.2017  -3.1972   0.9516
 NYG  CD1   C  CR16   0  -0.306   2.8619  -2.0282   0.3034
 NYG  OXT   O  OC    -1  -0.617   2.1919   4.0412  -5.3508
 NYG  HD11  H  HNH2   0   0.403   6.2679  -1.2126  -0.6898
 NYG  HD12  H  HNH2   0   0.396   5.9904  -2.2229  -2.0531
 NYG  HB11  H  HCH2   0   0.284   6.8789   1.4987  -1.9862
 NYG  HB12  H  HCH2   0   0.253   5.8745   0.9996  -0.6371
 NYG  HA1   H  HCH1   0   0.279   4.8969   2.2555  -3.2423
 NYG  HN1   H  HNH2   0   0.362   5.9332   3.8672  -1.9720
 NYG  HN2   H  HNH2   0   0.352   5.2392   3.3937  -0.5831
 NYG  HA31  H  HCH2   0   0.277   3.1230   4.2220  -2.8533
 NYG  HA32  H  HCH2   0   0.263   1.3753   4.1103  -2.8449
 NYG  HB2   H  H      0   0.263   0.0212  -0.2354  -0.4724
 NYG  HD2   H  HCR6   0   0.263  -0.4892  -2.1168   0.7751
 NYG  HE2   H  HCR6   0   0.276   0.1037  -4.1878   1.9319
 NYG  HOH   H  HOH1   0   0.478   1.8406  -5.5793   2.5294
 NYG  HE1   H  HCR6   0   0.265   4.2369  -3.5111   1.0010
 NYG  HD1   H  HCR6   0   0.285   3.6380  -1.4322  -0.1561

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
 NYG  OD1  CG1   double    1.223  0.020  1.223
 NYG  CG1  CB1   single    1.513  0.020  1.513
 NYG  CG1  ND1   single    1.343  0.020  1.343
 NYG  ND1  HD11  single    0.860  0.020  1.020
 NYG  ND1  HD12  single    0.860  0.020  1.020
 NYG  CB1  CA1   single    1.528  0.020  1.528
 NYG  CB1  HB11  single    0.970  0.020  1.090
 NYG  CB1  HB12  single    0.970  0.020  1.090
 NYG  CA1  C1    single    1.497  0.020  1.497
 NYG  CA1  N     single    1.454  0.020  1.454
 NYG  CA1  HA1   single    0.970  0.020  1.090
 NYG  N    HN1   single    0.890  0.020  1.040
 NYG  N    HN2   single    0.890  0.020  1.040
 NYG  C1   N2    double    1.289  0.020  1.289
 NYG  C1   N3    single    1.377  0.020  1.377
 NYG  N3   C2    single    1.374  0.020  1.374
 NYG  N3   CA3   single    1.440  0.020  1.440
 NYG  CA3  C     single    1.545  0.020  1.545
 NYG  CA3  HA31  single    0.970  0.020  1.090
 NYG  CA3  HA32  single    0.970  0.020  1.090
 NYG  C    OXT   deloc     1.245  0.020  1.245
 NYG  C    O     deloc     1.241  0.020  1.241
 NYG  N2   CA2   single    1.388  0.020  1.388
 NYG  CA2  CB2   double    1.347  0.020  1.347
 NYG  CA2  C2    single    1.481  0.020  1.481
 NYG  C2   O2    double    1.217  0.020  1.217
 NYG  CB2  CG2   single    1.447  0.020  1.447
 NYG  CB2  HB2   single    0.930  0.020  1.080
 NYG  CG2  CD1   aromatic  1.405  0.020  1.405
 NYG  CG2  CD2   aromatic  1.400  0.020  1.400
 NYG  CD2  CE2   aromatic  1.382  0.020  1.382
 NYG  CD2  HD2   single    0.930  0.020  1.080
 NYG  CE2  CZ    aromatic  1.394  0.020  1.394
 NYG  CE2  HE2   single    0.930  0.020  1.080
 NYG  CZ   OH    single    1.342  0.020  1.342
 NYG  CZ   CE1   aromatic  1.397  0.020  1.397
 NYG  OH   HOH   single    0.850  0.020  0.980
 NYG  CE1  CD1   aromatic  1.379  0.020  1.379
 NYG  CE1  HE1   single    0.930  0.020  1.080
 NYG  CD1  HD1   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
 NYG  CB1   CG1  ND1   115.23  3.000
 NYG  ND1   CG1  OD1   122.91  3.000
 NYG  CB1   CG1  OD1   121.78  3.000
 NYG  HD12  ND1  HD11  117.44  3.000
 NYG  HD12  ND1  CG1   120.52  3.000
 NYG  HD11  ND1  CG1   121.79  3.000
 NYG  HB12  CB1  HB11  106.75  3.000
 NYG  HB12  CB1  CA1   109.98  3.000
 NYG  HB11  CB1  CA1   107.53  3.000
 NYG  HB12  CB1  CG1   111.22  3.000
 NYG  HB11  CB1  CG1   107.12  3.000
 NYG  CA1   CB1  CG1   113.88  3.000
 NYG  HA1   CA1  C1    106.91  3.000
 NYG  HA1   CA1  N     107.59  3.000
 NYG  C1    CA1  N     109.01  3.000
 NYG  HA1   CA1  CB1   108.64  3.000
 NYG  N     CA1  CB1   113.62  3.000
 NYG  C1    CA1  CB1   110.81  3.000
 NYG  HN2   N    HN1   106.56  3.000
 NYG  HN2   N    CA1   109.94  3.000
 NYG  HN1   N    CA1   109.49  3.000
 NYG  N2    C1   N3    114.14  3.000
 NYG  N3    C1   CA1   122.38  3.000
 NYG  N2    C1   CA1   123.45  3.000
 NYG  C2    N3   CA3   123.35  3.000
 NYG  CA3   N3   C1    126.88  3.000
 NYG  C2    N3   C1    107.74  3.000
 NYG  HA32  CA3  HA31  106.84  3.000
 NYG  HA32  CA3  C     109.61  3.000
 NYG  HA31  CA3  C     110.21  3.000
 NYG  HA32  CA3  N3    108.16  3.000
 NYG  HA31  CA3  N3    108.70  3.000
 NYG  C     CA3  N3    113.12  3.000
 NYG  OXT   C    O     128.28  3.000
 NYG  O     C    CA3   117.23  3.000
 NYG  OXT   C    CA3   114.49  3.000
 NYG  CA2   N2   C1    106.19  3.000
 NYG  CB2   CA2  C2    123.36  3.000
 NYG  C2    CA2  N2    108.45  3.000
 NYG  CB2   CA2  N2    128.18  3.000
 NYG  O2    C2   CA2   130.39  3.000
 NYG  O2    C2   N3    126.26  3.000
 NYG  CA2   C2   N3    103.35  3.000
 NYG  HB2   CB2  CG2   115.44  3.000
 NYG  HB2   CB2  CA2   115.32  3.000
 NYG  CG2   CB2  CA2   129.23  3.000
 NYG  CD1   CG2  CD2   117.60  3.000
 NYG  CD2   CG2  CB2   118.27  3.000
 NYG  CD1   CG2  CB2   124.13  3.000
 NYG  HD2   CD2  CE2   118.85  3.000
 NYG  HD2   CD2  CG2   119.38  3.000
 NYG  CE2   CD2  CG2   121.77  3.000
 NYG  HE2   CE2  CZ    120.36  3.000
 NYG  HE2   CE2  CD2   119.90  3.000
 NYG  CZ    CE2  CD2   119.74  3.000
 NYG  CE1   CZ   OH    117.81  3.000
 NYG  CE1   CZ   CE2   119.45  3.000
 NYG  OH    CZ   CE2   122.74  3.000
 NYG  HOH   OH   CZ    110.62  3.000
 NYG  HE1   CE1  CD1   120.18  3.000
 NYG  HE1   CE1  CZ    119.48  3.000
 NYG  CD1   CE1  CZ    120.34  3.000
 NYG  HD1   CD1  CE1   119.36  3.000
 NYG  HD1   CD1  CG2   119.54  3.000
 NYG  CE1   CD1  CG2   121.10  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
 NYG  CONST_01  CZ    CE1  CD1  CG2    0.00   0.0  0
 NYG  CONST_02  CZ    CE2  CD2  CG2    0.00   0.0  0
 NYG  CONST_03  CE1   CD1  CG2  CD2    0.00   0.0  0
 NYG  CONST_04  CE1   CZ   CE2  CD2    0.00   0.0  0
 NYG  CONST_05  CD1   CG2  CD2  CE2    0.00   0.0  0
 NYG  CONST_06  CD1   CE1  CZ   CE2    0.00   0.0  0
 NYG  CONST_07  C2    CA2  N2   C1     0.00   0.0  0
 NYG  CONST_08  CA2   C2   N3   C1     0.00   0.0  0
 NYG  CONST_09  CA2   N2   C1   N3     0.00   0.0  0
 NYG  CONST_10  N2    CA2  C2   N3     0.00   0.0  0
 NYG  CONST_11  C2    N3   C1   N2     0.00   0.0  0
 NYG  CONST_12  CE1   CD1  CG2  CB2  180.00   0.0  0
 NYG  CONST_13  CE2   CD2  CG2  CB2  180.00   0.0  0
 NYG  CONST_14  OH    CZ   CE2  CD2  180.00   0.0  0
 NYG  CONST_15  CD1   CE1  CZ   OH   180.00   0.0  0
 NYG  CONST_16  CA2   N2   C1   CA1  180.00   0.0  0
 NYG  CONST_17  C2    N3   C1   CA1  180.00   0.0  0
 NYG  CONST_18  O2    C2   N3   C1   180.00   0.0  0
 NYG  CONST_19  N2    C1   N3   CA3  180.00   0.0  0
 NYG  CONST_20  CA2   C2   N3   CA3  180.00   0.0  0
 NYG  CONST_21  HE1   CE1  CD1  CG2  180.00   0.0  0
 NYG  CONST_22  HE2   CE2  CD2  CG2  180.00   0.0  0
 NYG  CONST_23  HD1   CD1  CG2  CD2  180.00   0.0  0
 NYG  CONST_24  HD2   CD2  CE2  CZ   180.00   0.0  0
 NYG  CONST_25  CA3   N3   C1   CA1    0.00   0.0  0
 NYG  CONST_26  O2    C2   N3   CA3    0.00   0.0  0
 NYG  CONST_27  HD11  ND1  CG1  OD1  180.00   0.0  0
 NYG  CONST_28  HD12  ND1  CG1  OD1    0.00   0.0  0
 NYG  Var_01    CG2   CB2  CA2  N2    -0.60  30.0  2
 NYG  Var_02    CD1   CG2  CB2  CA2   -3.43  30.0  2
 NYG  Var_03    C     CA3  N3   C1    76.72  30.0  3
 NYG  Var_04    OXT   C    CA3  N3   177.41  30.0  3
 NYG  Var_05    CA1   CB1  CG1  OD1   37.14  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
 NYG  chir_01  CA1  CB1  C1  N  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
 NYG  plan-1  CA1   0.020
 NYG  plan-1  C1    0.020
 NYG  plan-1  N3    0.020
 NYG  plan-1  CA3   0.020
 NYG  plan-1  N2    0.020
 NYG  plan-1  CA2   0.020
 NYG  plan-1  C2    0.020
 NYG  plan-1  O2    0.020
 NYG  plan-1  CB2   0.020
 NYG  plan-2  CB2   0.020
 NYG  plan-2  CG2   0.020
 NYG  plan-2  CD2   0.020
 NYG  plan-2  CE2   0.020
 NYG  plan-2  CZ    0.020
 NYG  plan-2  OH    0.020
 NYG  plan-2  CE1   0.020
 NYG  plan-2  CD1   0.020
 NYG  plan-2  HD2   0.020
 NYG  plan-2  HE2   0.020
 NYG  plan-2  HE1   0.020
 NYG  plan-2  HD1   0.020
 NYG  plan-3  OD1   0.020
 NYG  plan-3  CG1   0.020
 NYG  plan-3  ND1   0.020
 NYG  plan-3  CB1   0.020
 NYG  plan-3  HD11  0.020
 NYG  plan-3  HD12  0.020
 NYG  plan-4  CA3   0.020
 NYG  plan-4  C     0.020
 NYG  plan-4  O     0.020
 NYG  plan-4  OXT   0.020

