# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 10:59:51 2022
#   Inital geometry file: a 113 line input string
#   Ligand name: {(4Z)-2-[(1S)-1-amino-3-(methylsulfanyl)propyl]-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: CSCC[C@H](N)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
 CH6  CH6  "{(4Z)-2-[(1S)-1-amino-3-(methylsulfanyl)propyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid"  L-peptide  42  24  .  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_CH6
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
 CH6  N1    N  NH2    0  -0.767  -1.0193   1.7530   2.0548
 CH6  CE    C  CH3    0  -0.764  -5.7582   3.5686  -0.1708
 CH6  SD    S  S2     0  -0.046  -4.4084   2.6713  -0.9669
 CH6  CB1   C  CH2    0  -0.433  -2.3610   1.1979   0.0872
 CH6  CA1   C  CH1    0  -0.214  -1.6011   0.6586   1.3082
 CH6  C1    C  CR5    0   0.537  -0.5821  -0.3480   0.8444
 CH6  N2    N  N      0  -0.495   0.6504  -0.0371   0.6213
 CH6  CD2   C  CR16   0  -0.301   3.5286   0.9216   0.1694
 CH6  CE2   C  CR16   0  -0.361   4.6169   1.7705   0.1261
 CH6  CZ    C  CR6    0   0.360   5.8694   1.2946  -0.2672
 CH6  CE1   C  CR16   0  -0.331   6.0142  -0.0481  -0.6151
 CH6  CD1   C  CR16   0  -0.287   4.9195  -0.8875  -0.5692
 CH6  CG2   C  CR6    0   0.133   3.6522  -0.4314  -0.1790
 CH6  CA2   C  CR5    0   0.090   1.2703  -1.1980   0.1814
 CH6  C2    C  CR5    0   0.533   0.2659  -2.2847   0.1498
 CH6  O2    O  O      0  -0.457   0.3694  -3.4525  -0.1707
 CH6  N3    N  NR5    0  -0.540  -0.8766  -1.6712   0.6112
 CH6  CA3   C  CH2    0  -0.475  -2.1583  -2.3279   0.6152
 CH6  C3    C  C      0   0.423  -2.7930  -2.4559  -0.7897
 CH6  O3    O  O      0  -0.587  -2.2137  -1.8906  -1.7305
 CH6  OXT   O  OC    -1  -0.609  -3.8449  -3.1193  -0.8178
 CH6  HN11  H  HNH2   0   0.353  -0.6339   1.4078   2.9250
 CH6  HN12  H  HNH2   0   0.348  -0.2343   2.1286   1.5350
 CH6  HE1A  H  HCH3   0   0.273  -6.3514   4.0394  -0.9526
 CH6  HE2A  H  HCH3   0   0.260  -6.3994   2.8938   0.3947
 CH6  HE3   H  HCH3   0   0.260  -5.3773   4.3447   0.4920
 CH6  HG11  H  HCH2   0   0.265  -3.2844   2.8290   1.1556
 CH6  HG12  H  HCH2   0   0.257  -4.2814   1.3751   1.0531
 CH6  HB11  H  HCH2   0   0.262  -2.6593   0.3722  -0.5617
 CH6  HB12  H  HCH2   0   0.243  -1.6736   1.8163  -0.4986
 CH6  HA1   H  HCH1   0   0.266  -2.3158   0.1516   1.9643
 CH6  HOH   H  HOH1   0   0.479   6.7371   2.9820  -0.0655
 CH6  HD2   H  HCR6   0   0.279   2.5682   1.3098   0.4769
 CH6  HE2   H  HCR6   0   0.276   4.4932   2.8128   0.3979
 CH6  HE1   H  HCR6   0   0.269   6.9821  -0.4250  -0.9199
 CH6  HD1   H  HCR6   0   0.261   5.0473  -1.9283  -0.8418
 CH6  HA31  H  HCH2   0   0.269  -2.0370  -3.3207   1.0520
 CH6  HA32  H  HCH2   0   0.271  -2.8382  -1.7885   1.2761
 CH6  CB2   C  C1     0  -0.392   2.5606  -1.3802  -0.1627
 CH6  HB2   H  H      0   0.263   2.8186  -2.3885  -0.4722
 CH6  CG1   C  CH2    0  -0.547  -3.5784   2.0060   0.5033
 CH6  OH    O  OH1    0  -0.620   6.9550   2.0802  -0.3281

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
 CH6  CE   SD    single    1.806  0.020  1.806
 CH6  SD   CG1   single    1.815  0.020  1.815
 CH6  CG1  CB1   single    1.519  0.020  1.519
 CH6  OH   CZ    single    1.341  0.020  1.341
 CH6  CB1  CA1   single    1.536  0.020  1.536
 CH6  OXT  C3    deloc     1.244  0.020  1.244
 CH6  CE1  CZ    aromatic  1.395  0.020  1.395
 CH6  CE1  CD1   aromatic  1.380  0.020  1.380
 CH6  CZ   CE2   aromatic  1.396  0.020  1.396
 CH6  CD1  CG2   aromatic  1.402  0.020  1.402
 CH6  CA1  C1    single    1.506  0.020  1.506
 CH6  CA1  N1    single    1.447  0.020  1.447
 CH6  CE2  CD2   aromatic  1.381  0.020  1.381
 CH6  N2   C1    double    1.291  0.020  1.291
 CH6  N2   CA2   single    1.388  0.020  1.388
 CH6  C1   N3    single    1.376  0.020  1.376
 CH6  CG2  CD2   aromatic  1.403  0.020  1.403
 CH6  CG2  CB2   single    1.446  0.020  1.446
 CH6  C3   O3    deloc     1.241  0.020  1.241
 CH6  C3   CA3   single    1.547  0.020  1.547
 CH6  CA2  CB2   double    1.348  0.020  1.348
 CH6  CA2  C2    single    1.480  0.020  1.480
 CH6  N3   C2    single    1.376  0.020  1.376
 CH6  N3   CA3   single    1.440  0.020  1.440
 CH6  C2   O2    double    1.215  0.020  1.215
 CH6  N1   HN11  single    0.890  0.020  1.040
 CH6  N1   HN12  single    0.890  0.020  1.040
 CH6  CE   HE1A  single    0.970  0.020  1.090
 CH6  CE   HE2A  single    0.970  0.020  1.090
 CH6  CE   HE3   single    0.970  0.020  1.090
 CH6  CG1  HG11  single    0.970  0.020  1.090
 CH6  CG1  HG12  single    0.970  0.020  1.090
 CH6  CB1  HB11  single    0.970  0.020  1.090
 CH6  CB1  HB12  single    0.970  0.020  1.090
 CH6  CA1  HA1   single    0.970  0.020  1.090
 CH6  OH   HOH   single    0.850  0.020  0.980
 CH6  CD2  HD2   single    0.930  0.020  1.080
 CH6  CE2  HE2   single    0.930  0.020  1.080
 CH6  CE1  HE1   single    0.930  0.020  1.080
 CH6  CD1  HD1   single    0.930  0.020  1.080
 CH6  CB2  HB2   single    0.930  0.020  1.080
 CH6  CA3  HA31  single    0.970  0.020  1.090
 CH6  CA3  HA32  single    0.970  0.020  1.090

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
 CH6  HN12  N1   HN11  105.80  3.000
 CH6  HN12  N1   CA1   109.09  3.000
 CH6  HN11  N1   CA1   109.80  3.000
 CH6  HE3   CE   HE2A  109.35  3.000
 CH6  HE3   CE   HE1A  108.63  3.000
 CH6  HE2A  CE   HE1A  108.67  3.000
 CH6  HE3   CE   SD    111.15  3.000
 CH6  HE2A  CE   SD    111.17  3.000
 CH6  HE1A  CE   SD    107.80  3.000
 CH6  CG1   SD   CE     99.61  3.000
 CH6  HB12  CB1  HB11  106.31  3.000
 CH6  HB12  CB1  CA1   108.25  3.000
 CH6  HB11  CB1  CA1   110.01  3.000
 CH6  HB12  CB1  CG1   110.45  3.000
 CH6  HB11  CB1  CG1   110.25  3.000
 CH6  CA1   CB1  CG1   111.44  3.000
 CH6  HA1   CA1  C1    108.47  3.000
 CH6  HA1   CA1  CB1   108.43  3.000
 CH6  C1    CA1  CB1   108.95  3.000
 CH6  HA1   CA1  N1    107.67  3.000
 CH6  C1    CA1  N1    113.11  3.000
 CH6  CB1   CA1  N1    110.10  3.000
 CH6  N3    C1   N2    114.01  3.000
 CH6  N3    C1   CA1   123.40  3.000
 CH6  N2    C1   CA1   122.59  3.000
 CH6  CA2   N2   C1    106.26  3.000
 CH6  HD2   CD2  CG2   119.71  3.000
 CH6  HD2   CD2  CE2   119.24  3.000
 CH6  CG2   CD2  CE2   121.05  3.000
 CH6  HE2   CE2  CZ    120.04  3.000
 CH6  HE2   CE2  CD2   119.55  3.000
 CH6  CZ    CE2  CD2   120.41  3.000
 CH6  CE1   CZ   CE2   119.44  3.000
 CH6  CE2   CZ   OH    122.62  3.000
 CH6  CE1   CZ   OH    117.94  3.000
 CH6  HE1   CE1  CD1   120.46  3.000
 CH6  HE1   CE1  CZ    119.88  3.000
 CH6  CD1   CE1  CZ    119.66  3.000
 CH6  HD1   CD1  CG2   119.28  3.000
 CH6  HD1   CD1  CE1   118.83  3.000
 CH6  CG2   CD1  CE1   121.89  3.000
 CH6  CB2   CG2  CD1   118.15  3.000
 CH6  CB2   CG2  CD2   124.30  3.000
 CH6  CD1   CG2  CD2   117.55  3.000
 CH6  C2    CA2  CB2   123.02  3.000
 CH6  C2    CA2  N2    108.53  3.000
 CH6  CB2   CA2  N2    128.44  3.000
 CH6  N3    C2   O2    125.97  3.000
 CH6  O2    C2   CA2   130.79  3.000
 CH6  N3    C2   CA2   103.23  3.000
 CH6  CA3   N3   C2    122.44  3.000
 CH6  CA3   N3   C1    128.96  3.000
 CH6  C2    N3   C1    107.93  3.000
 CH6  HA32  CA3  HA31  106.06  3.000
 CH6  HA32  CA3  C3    109.60  3.000
 CH6  HA31  CA3  C3    109.50  3.000
 CH6  HA32  CA3  N3    109.32  3.000
 CH6  HA31  CA3  N3    108.48  3.000
 CH6  C3    CA3  N3    113.60  3.000
 CH6  OXT   C3   O3    128.35  3.000
 CH6  O3    C3   CA3   117.34  3.000
 CH6  OXT   C3   CA3   114.30  3.000
 CH6  HB2   CB2  CA2   115.20  3.000
 CH6  HB2   CB2  CG2   115.25  3.000
 CH6  CA2   CB2  CG2   129.54  3.000
 CH6  HG12  CG1  HG11  107.95  3.000
 CH6  HG12  CG1  CB1   110.25  3.000
 CH6  HG11  CG1  CB1   110.44  3.000
 CH6  HG12  CG1  SD    108.96  3.000
 CH6  HG11  CG1  SD    109.34  3.000
 CH6  CB1   CG1  SD    109.85  3.000
 CH6  HOH   OH   CZ    110.64  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
 CH6  CONST_01  CE1   CZ   CE2  CD2     0.00   0.0  0
 CH6  CONST_02  CE1   CD1  CG2  CD2     0.00   0.0  0
 CH6  CONST_03  CD1   CE1  CZ   CE2     0.00   0.0  0
 CH6  CONST_04  CD1   CG2  CD2  CE2     0.00   0.0  0
 CH6  CONST_05  CG2   CD1  CE1  CZ      0.00   0.0  0
 CH6  CONST_06  CG2   CD2  CE2  CZ      0.00   0.0  0
 CH6  CONST_07  C2    CA2  N2   C1      0.00   0.0  0
 CH6  CONST_08  CA2   C2   N3   C1      0.00   0.0  0
 CH6  CONST_09  C2    N3   C1   N2      0.00   0.0  0
 CH6  CONST_10  N3    C2   CA2  N2      0.00   0.0  0
 CH6  CONST_11  N3    C1   N2   CA2     0.00   0.0  0
 CH6  CONST_12  CD1   CE1  CZ   OH    180.00   0.0  0
 CH6  CONST_13  CD2   CE2  CZ   OH    180.00   0.0  0
 CH6  CONST_14  CB2   CG2  CD2  CE2   180.00   0.0  0
 CH6  CONST_15  CB2   CG2  CD1  CE1   180.00   0.0  0
 CH6  CONST_16  CA2   N2   C1   CA1   180.00   0.0  0
 CH6  CONST_17  C2    N3   C1   CA1   180.00   0.0  0
 CH6  CONST_18  O2    C2   N3   C1    180.00   0.0  0
 CH6  CONST_19  CA3   N3   C1   N2    180.00   0.0  0
 CH6  CONST_20  CA3   N3   C2   CA2   180.00   0.0  0
 CH6  CONST_21  HD1   CD1  CG2  CD2   180.00   0.0  0
 CH6  CONST_22  HE1   CE1  CZ   CE2   180.00   0.0  0
 CH6  CONST_23  HD1   CD1  CE1  CZ    180.00   0.0  0
 CH6  CONST_24  HD2   CD2  CE2  CZ    180.00   0.0  0
 CH6  CONST_25  HE2   CE2  CZ   CE1   180.00   0.0  0
 CH6  CONST_26  HD2   CD2  CG2  CD1   180.00   0.0  0
 CH6  CONST_27  HE1   CE1  CD1  CG2   180.00   0.0  0
 CH6  CONST_28  HE2   CE2  CD2  CG2   180.00   0.0  0
 CH6  CONST_29  CA3   N3   C1   CA1     0.00   0.0  0
 CH6  CONST_30  CA3   N3   C2   O2      0.00   0.0  0
 CH6  Var_01    CG2   CB2  CA2  N2     -0.36   0.0  2
 CH6  Var_02    C2    CA2  CB2  CG2  -179.71   0.0  2
 CH6  Var_03    CA2   CB2  CG2  CD2    -0.81  30.0  2
 CH6  Var_04    CA2   CB2  CG2  CD1   179.27  30.0  2
 CH6  Var_05    C3    CA3  N3   C1     95.61  30.0  3
 CH6  Var_06    C3    CA3  N3   C2    -73.82  30.0  3
 CH6  Var_07    HB2   CB2  CA2  N2    179.56   0.0  2
 CH6  Var_08    HB2   CB2  CA2  C2      0.22   0.0  2
 CH6  Var_09    HA31  CA3  N3   C1   -142.37  30.0  3
 CH6  Var_10    HA32  CA3  N3   C1    -27.14  30.0  3
 CH6  Var_11    HB2   CB2  CG2  CD2   179.27  30.0  2
 CH6  Var_12    HB2   CB2  CG2  CD1    -0.66  30.0  2
 CH6  Var_13    HA31  CA3  N3   C2     48.19  30.0  3
 CH6  Var_14    HA32  CA3  N3   C2    163.43  30.0  3
 CH6  Var_15    OXT   C3   CA3  N3    174.24  30.0  3
 CH6  Var_16    O3    C3   CA3  N3     -6.29  30.0  3
 CH6  Var_17    CB1   CG1  SD   CE   -179.39  30.0  3
 CH6  Var_18    CA1   CB1  CG1  SD    177.96  30.0  3
 CH6  Var_19    HG11  CG1  SD   CE    -58.04  30.0  3
 CH6  Var_20    HG12  CG1  SD   CE     59.73  30.0  3
 CH6  Var_21    HB11  CB1  CG1  SD    -59.58  30.0  3
 CH6  Var_22    HB12  CB1  CG1  SD     57.61  30.0  3
 CH6  Var_23    HE1A  CE   SD   CG1   179.51  30.0  3
 CH6  Var_24    HE2A  CE   SD   CG1   -61.49  30.0  3
 CH6  Var_25    HE3   CE   SD   CG1    60.56  30.0  3
 CH6  Var_26    HG11  CG1  CB1  CA1    57.28  30.0  2
 CH6  Var_27    HG12  CG1  CB1  CA1   -61.94  30.0  2
 CH6  Var_28    HA31  CA3  C3   O3   -127.74  30.0  3
 CH6  Var_29    HA32  CA3  C3   O3    116.31  30.0  3
 CH6  Var_30    HA31  CA3  C3   OXT    52.79  30.0  3
 CH6  Var_31    HA32  CA3  C3   OXT   -63.16  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
 CH6  chir_01  CA1  CB1  C1  N1  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
 CH6  plan-1  CA1  0.020
 CH6  plan-1  C1   0.020
 CH6  plan-1  N2   0.020
 CH6  plan-1  CG2  0.020
 CH6  plan-1  CA2  0.020
 CH6  plan-1  C2   0.020
 CH6  plan-1  O2   0.020
 CH6  plan-1  N3   0.020
 CH6  plan-1  CA3  0.020
 CH6  plan-1  CB2  0.020
 CH6  plan-1  HB2  0.020
 CH6  plan-2  CD2  0.020
 CH6  plan-2  CE2  0.020
 CH6  plan-2  CZ   0.020
 CH6  plan-2  CE1  0.020
 CH6  plan-2  CD1  0.020
 CH6  plan-2  CG2  0.020
 CH6  plan-2  HD2  0.020
 CH6  plan-2  HE2  0.020
 CH6  plan-2  HE1  0.020
 CH6  plan-2  HD1  0.020
 CH6  plan-2  CB2  0.020
 CH6  plan-2  OH   0.020
 CH6  plan-3  CA3  0.020
 CH6  plan-3  C3   0.020
 CH6  plan-3  O3   0.020
 CH6  plan-3  OXT  0.020

