# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 12:58:06 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: [(4Z)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-2-(3,4,5,6-tetrahydropyridin-2-yl)-4,5-dihydro-1H-imidazol-1-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CN1C(=O)C(=C/c2ccc(O)cc2)/N=C1C3=NCCCC3
#
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
 CH7  CH7  '[(4Z)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-2-(3,4,5,6-tetrahydropyridin-2-yl)-4,5-dihydro-1H-imidazol-1-yl]acetic acid'  L-peptide  40  24  .  2022-07-24  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CH7
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
 CH7  NZ    N  N      0  -0.368   1.8650   1.1360   1.9587
 CH7  CA1   C  C      0   0.163   1.9800   0.7667   0.7533
 CH7  CB    C  CH2    0  -0.514   3.0263   1.2020  -0.2322
 CH7  CG    C  CH2    0  -0.447   4.1612   1.9512   0.4491
 CH7  CD    C  CH2    0  -0.476   3.5819   2.9036   1.4839
 CH7  CE    C  CH2    0  -0.315   2.7808   2.1140   2.5070
 CH7  C1    C  C      0   0.548   1.0082  -0.2317   0.2638
 CH7  N2    N  N      0  -0.493   1.3378  -1.1605  -0.5706
 CH7  CD2   C  CR16   0  -0.300   2.3528  -3.3317  -2.4886
 CH7  CE2   C  CR16   0  -0.361   3.2230  -4.0546  -3.2800
 CH7  CZ    C  CR6    0   0.362   2.7846  -5.2010  -3.9467
 CH7  CE1   C  CR16   0  -0.331   1.4578  -5.6097  -3.8107
 CH7  CD1   C  CR16   0  -0.285   0.5967  -4.8791  -3.0180
 CH7  CG2   C  CR6    0   0.134   1.0157  -3.7275  -2.3356
 CH7  CA2   C  C      0   0.097   0.1993  -1.9285  -0.7570
 CH7  C2    C  C      0   0.521  -0.8995  -1.3470   0.0457
 CH7  O2    O  O      0  -0.458  -2.0683  -1.6735   0.1282
 CH7  N3    N  NT     0  -0.542  -0.2957  -0.2995   0.7042
 CH7  CA3   C  CH2    0  -0.460  -1.0180   0.7611   1.3633
 CH7  C3    C  C      0   0.426  -0.9528   2.0940   0.5845
 CH7  O3    O  O      0  -0.585  -0.3620   2.0864  -0.5086
 CH7  OXT   O  OC    -1  -0.611  -1.5218   3.0480   1.1442
 CH7  HB1   H  HCH2   0   0.267   3.3894   0.3275  -0.7745
 CH7  HB2A  H  HCH2   0   0.262   2.5295   1.8347  -0.9743
 CH7  HG1   H  HCH2   0   0.229   4.8317   1.2412   0.9423
 CH7  HG2   H  HCH2   0   0.243   4.7575   2.4855  -0.2916
 CH7  HD1A  H  HCH2   0   0.240   4.3664   3.4682   1.9909
 CH7  HD2A  H  HCH2   0   0.230   2.9329   3.6321   0.9882
 CH7  HE1A  H  HCH2   0   0.238   3.4557   1.5805   3.1857
 CH7  HE2A  H  HCH2   0   0.242   2.1961   2.7833   3.1424
 CH7  HOH   H  HOH1   0   0.479   4.4802  -5.5666  -4.7420
 CH7  HD2   H  HCR6   0   0.281   2.7110  -2.4478  -1.9806
 CH7  HE2   H  HCR6   0   0.277   4.2521  -3.7287  -3.3806
 CH7  HE1   H  HCR6   0   0.270   1.1115  -6.4970  -4.3249
 CH7  HD1   H  HCR6   0   0.262  -0.4312  -5.2072  -2.9212
 CH7  HB2   H  H      0   0.265  -0.9470  -3.4641  -1.5093
 CH7  HA31  H  HCH2   0   0.265  -0.6424   0.9033   2.3746
 CH7  HA32  H  HCH2   0   0.264  -2.0577   0.4404   1.4469
 CH7  CB2   C  C1     0  -0.397   0.0490  -3.0316  -1.5181
 CH7  OH    O  OH1    0  -0.619   3.5908  -5.9389  -4.7230

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
 CH7  NZ   CA1   double    1.266  0.020  1.266
 CH7  NZ   CE    single    1.448  0.020  1.448
 CH7  CA1  CB    single    1.502  0.020  1.502
 CH7  CA1  C1    single    1.477  0.020  1.477
 CH7  CB   CG    single    1.521  0.020  1.521
 CH7  CB   HB1   single    0.970  0.020  1.090
 CH7  CB   HB2A  single    0.970  0.020  1.090
 CH7  CG   CD    single    1.521  0.020  1.521
 CH7  CG   HG1   single    0.970  0.020  1.090
 CH7  CG   HG2   single    0.970  0.020  1.090
 CH7  CD   CE    single    1.521  0.020  1.521
 CH7  CD   HD1A  single    0.970  0.020  1.090
 CH7  CD   HD2A  single    0.970  0.020  1.090
 CH7  CE   HE1A  single    0.970  0.020  1.090
 CH7  CE   HE2A  single    0.970  0.020  1.090
 CH7  C1   N2    double    1.291  0.020  1.291
 CH7  C1   N3    single    1.378  0.020  1.378
 CH7  N2   CA2   single    1.386  0.020  1.386
 CH7  OH   CZ    single    1.341  0.020  1.341
 CH7  OH   HOH   single    0.850  0.020  0.980
 CH7  CD2  CE2   aromatic  1.381  0.020  1.381
 CH7  CD2  CG2   aromatic  1.403  0.020  1.403
 CH7  CD2  HD2   single    0.930  0.020  1.080
 CH7  CE2  CZ    aromatic  1.397  0.020  1.397
 CH7  CE2  HE2   single    0.930  0.020  1.080
 CH7  CZ   CE1   aromatic  1.395  0.020  1.395
 CH7  CE1  CD1   aromatic  1.380  0.020  1.380
 CH7  CE1  HE1   single    0.930  0.020  1.080
 CH7  CD1  CG2   aromatic  1.403  0.020  1.403
 CH7  CD1  HD1   single    0.930  0.020  1.080
 CH7  CG2  CB2   single    1.445  0.020  1.445
 CH7  CB2  CA2   double    1.349  0.020  1.349
 CH7  CB2  HB2   single    0.930  0.020  1.080
 CH7  CA2  C2    single    1.480  0.020  1.480
 CH7  C2   O2    double    1.216  0.020  1.216
 CH7  C2   N3    single    1.377  0.020  1.377
 CH7  N3   CA3   single    1.443  0.020  1.443
 CH7  CA3  C3    single    1.545  0.020  1.545
 CH7  CA3  HA31  single    0.970  0.020  1.090
 CH7  CA3  HA32  single    0.970  0.020  1.090
 CH7  C3   O3    deloc     1.243  0.020  1.243
 CH7  C3   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
 CH7  CE    NZ   CA1   120.01  3.000
 CH7  C1    CA1  CB    115.91  3.000
 CH7  C1    CA1  NZ    116.94  3.000
 CH7  CB    CA1  NZ    127.13  3.000
 CH7  HB2A  CB   HB1   106.10  3.000
 CH7  HB2A  CB   CG    110.96  3.000
 CH7  HB1   CB   CG    111.66  3.000
 CH7  HB2A  CB   CA1   107.24  3.000
 CH7  HB1   CB   CA1   109.00  3.000
 CH7  CG    CB   CA1   111.63  3.000
 CH7  HG2   CG   HG1   106.79  3.000
 CH7  HG2   CG   CD    111.32  3.000
 CH7  HG1   CG   CD    109.46  3.000
 CH7  HG2   CG   CB    110.19  3.000
 CH7  HG1   CG   CB    109.85  3.000
 CH7  CD    CG   CB    109.21  3.000
 CH7  HD2A  CD   HD1A  106.99  3.000
 CH7  HD2A  CD   CE    109.76  3.000
 CH7  HD1A  CD   CE    109.56  3.000
 CH7  HD2A  CD   CG    109.55  3.000
 CH7  HD1A  CD   CG    111.48  3.000
 CH7  CE    CD   CG    109.47  3.000
 CH7  HE2A  CE   HE1A  105.52  3.000
 CH7  HE2A  CE   CD    110.81  3.000
 CH7  HE1A  CE   CD    110.19  3.000
 CH7  HE2A  CE   NZ    107.19  3.000
 CH7  HE1A  CE   NZ    107.17  3.000
 CH7  CD    CE   NZ    115.42  3.000
 CH7  N3    C1   N2    114.37  3.000
 CH7  N3    C1   CA1   123.37  3.000
 CH7  N2    C1   CA1   122.18  3.000
 CH7  CA2   N2   C1    106.01  3.000
 CH7  HD2   CD2  CG2   119.70  3.000
 CH7  HD2   CD2  CE2   119.27  3.000
 CH7  CG2   CD2  CE2   121.03  3.000
 CH7  HE2   CE2  CZ    120.02  3.000
 CH7  HE2   CE2  CD2   119.61  3.000
 CH7  CZ    CE2  CD2   120.37  3.000
 CH7  CE1   CZ   CE2   119.50  3.000
 CH7  CE1   CZ   OH    117.86  3.000
 CH7  CE2   CZ   OH    122.65  3.000
 CH7  HE1   CE1  CD1   120.48  3.000
 CH7  HE1   CE1  CZ    119.88  3.000
 CH7  CD1   CE1  CZ    119.64  3.000
 CH7  HD1   CD1  CG2   119.25  3.000
 CH7  HD1   CD1  CE1   118.89  3.000
 CH7  CG2   CD1  CE1   121.86  3.000
 CH7  CB2   CG2  CD1   118.09  3.000
 CH7  CB2   CG2  CD2   124.31  3.000
 CH7  CD1   CG2  CD2   117.60  3.000
 CH7  C2    CA2  CB2   123.01  3.000
 CH7  C2    CA2  N2    108.62  3.000
 CH7  CB2   CA2  N2    128.37  3.000
 CH7  N3    C2   O2    126.39  3.000
 CH7  N3    C2   CA2   103.46  3.000
 CH7  O2    C2   CA2   130.15  3.000
 CH7  CA3   N3   C2    123.94  3.000
 CH7  CA3   N3   C1    125.71  3.000
 CH7  C2    N3   C1    107.43  3.000
 CH7  HA32  CA3  HA31  107.22  3.000
 CH7  HA32  CA3  C3    109.42  3.000
 CH7  HA31  CA3  C3    109.94  3.000
 CH7  HA32  CA3  N3    107.21  3.000
 CH7  HA31  CA3  N3    110.36  3.000
 CH7  C3    CA3  N3    112.51  3.000
 CH7  OXT   C3   O3    128.17  3.000
 CH7  OXT   C3   CA3   114.55  3.000
 CH7  O3    C3   CA3   117.27  3.000
 CH7  HB2   CB2  CA2   115.05  3.000
 CH7  HB2   CB2  CG2   115.25  3.000
 CH7  CA2   CB2  CG2   129.70  3.000
 CH7  HOH   OH   CZ    110.71  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
 CH7  CONST_01  CE1  CZ   CE2  CD2     0.00   0.0  0
 CH7  CONST_02  CE1  CD1  CG2  CD2     0.00   0.0  0
 CH7  CONST_03  CD1  CG2  CD2  CE2     0.00   0.0  0
 CH7  CONST_04  CD1  CE1  CZ   CE2     0.00   0.0  0
 CH7  CONST_05  CG2  CD2  CE2  CZ      0.00   0.0  0
 CH7  CONST_06  CG2  CD1  CE1  CZ      0.00   0.0  0
 CH7  CONST_07  CA2  N2   C1   CA1   180.00   0.0  0
 CH7  CONST_08  C2   N3   C1   CA1   180.00   0.0  0
 CH7  CONST_09  C2   CA2  N2   C1      0.00   0.0  0
 CH7  CONST_10  CA2  C2   N3   C1      0.00   0.0  0
 CH7  CONST_11  C2   N3   C1   N2      0.00   0.0  0
 CH7  CONST_12  N3   C2   CA2  N2      0.00   0.0  0
 CH7  CONST_13  N3   C1   N2   CA2     0.00   0.0  0
 CH7  CONST_14  CD2  CE2  CZ   OH    180.00   0.0  0
 CH7  CONST_15  CD1  CE1  CZ   OH    180.00   0.0  0
 CH7  CONST_16  CB2  CG2  CD2  CE2   180.00   0.0  0
 CH7  CONST_17  CB2  CG2  CD1  CE1   180.00   0.0  0
 CH7  CONST_19  O2   C2   N3   C1    180.00   0.0  0
 CH7  CONST_22  HD1  CD1  CG2  CD2   180.00   0.0  0
 CH7  CONST_23  HE1  CE1  CZ   CE2   180.00   0.0  0
 CH7  CONST_24  HD2  CD2  CE2  CZ    180.00   0.0  0
 CH7  CONST_25  HE2  CE2  CZ   CE1   180.00   0.0  0
 CH7  CONST_26  CA3  N3   C2   O2      0.00   0.0  0
 CH7  Var_01    CG   CB   CA1  NZ     12.01  30.0  1
 CH7  Var_02    N2   C1   CA1  NZ   -143.56  30.0  2
 CH7  Var_03    CG   CD   CE   NZ    -46.81  30.0  1
 CH7  Var_04    CD   CE   NZ   CA1    15.99  30.0  1
 CH7  Var_05    CD   CG   CB   CA1   -42.08  30.0  1
 CH7  Var_06    CE   CD   CG   CB     59.11  30.0  1
 CH7  Var_07    CG2  CB2  CA2  N2      0.62  30.0  2
 CH7  Var_08    CA2  CB2  CG2  CD2    -0.70  30.0  2
 CH7  Var_09    C3   CA3  N3   C1     51.51  30.0  3
 CH7  Var_10    O3   C3   CA3  N3      3.15  30.0  3

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
 CH7  plan-1  CA1  0.020
 CH7  plan-1  C1   0.020
 CH7  plan-1  N2   0.020
 CH7  plan-1  CA2  0.020
 CH7  plan-1  C2   0.020
 CH7  plan-1  O2   0.020
 CH7  plan-1  N3   0.020
 CH7  plan-1  CA3  0.020
 CH7  plan-1  CB2  0.020
 CH7  plan-2  CD2  0.020
 CH7  plan-2  CE2  0.020
 CH7  plan-2  CZ   0.020
 CH7  plan-2  CE1  0.020
 CH7  plan-2  CD1  0.020
 CH7  plan-2  CG2  0.020
 CH7  plan-2  HD2  0.020
 CH7  plan-2  HE2  0.020
 CH7  plan-2  HE1  0.020
 CH7  plan-2  HD1  0.020
 CH7  plan-2  CB2  0.020
 CH7  plan-2  OH   0.020
 CH7  plan-3  CA3  0.020
 CH7  plan-3  C3   0.020
 CH7  plan-3  O3   0.020
 CH7  plan-3  OXT  0.020

