# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 16:31:51 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  41  24  .  2022-07-24  2022-11-17
;
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  -0.380   1.5641   1.5095   1.7206
 CH7  CA1   C  C     0   0.185   1.9758   0.6243   0.9126
 CH7  CB    C  CH2   0  -0.505   3.4121   0.3021   0.5964
 CH7  CG    C  CH2   0  -0.450   4.3535   0.9181   1.6205
 CH7  CD    C  CH2   0  -0.476   3.9204   2.3446   1.9169
 CH7  CE    C  CH2   0  -0.312   2.4938   2.3476   2.4417
 CH7  C1    C  CR5   0   0.543   0.9594  -0.1641   0.1947
 CH7  N2    N  N     0  -0.479   1.2826  -1.0534  -0.6812
 CH7  CD2   C  CR16  0  -0.279   0.5078  -4.3636  -3.6302
 CH7  CE2   C  CR16  0  -0.376   1.3990  -5.1436  -4.3401
 CH7  CZ    C  CR6   0   0.364   2.7678  -4.8972  -4.2346
 CH7  CE1   C  CR16  0  -0.313   3.2214  -3.8616  -3.4117
 CH7  CD1   C  CR16  0  -0.296   2.3240  -3.0933  -2.7033
 CH7  CG2   C  CR6   0   0.133   0.9406  -3.3261  -2.7927
 CH7  CA2   C  CR5   0   0.101   0.1011  -1.5861  -1.1640
 CH7  C2    C  CR5   0   0.536  -1.0294  -0.9165  -0.4952
 CH7  O2    O  O     0  -0.449  -2.2281  -1.0624  -0.6247
 CH7  N3    N  NR5   0  -0.579  -0.4080  -0.0378   0.3726
 CH7  CA3   C  CH2   0  -0.424  -1.1315   0.8655   1.2200
 CH7  C3    C  C     0   0.553  -0.9688   2.2952   0.7636
 CH7  O3    O  O     0  -0.439  -0.6020   2.6177  -0.3358
 CH7  OXT   O  OH1   0  -0.590  -1.3458   3.1430   1.7070
 CH7  HB1   H  HCH2  0   0.268   3.5372  -0.7797   0.5397
 CH7  HB2A  H  HCH2  0   0.265   3.6329   0.6803  -0.4067
 CH7  HG1   H  HCH2  0   0.232   4.3331   0.3284   2.5416
 CH7  HG2   H  HCH2  0   0.247   5.3786   0.8863   1.2500
 CH7  HD1A  H  HCH2  0   0.244   4.5778   2.8165   2.6489
 CH7  HD2A  H  HCH2  0   0.232   3.9785   2.9441   1.0036
 CH7  HE1A  H  HCH2  0   0.247   2.4692   2.0180   3.4862
 CH7  HE2A  H  HCH2  0   0.249   2.0787   3.3581   2.4478
 CH7  HOH   H  HOH1  0   0.481   3.2651  -6.2988  -5.4274
 CH7  HD2   H  HCR6  0   0.268  -0.5524  -4.5661  -3.7220
 CH7  HE2   H  HCR6  0   0.280   1.0333  -5.9436  -4.9736
 CH7  HE1   H  HCR6  0   0.272   4.2837  -3.6675  -3.3347
 CH7  HD1   H  HCR6  0   0.281   2.6942  -2.2986  -2.0717
 CH7  HB2   H  H     0   0.272  -1.0865  -2.8406  -2.2886
 CH7  HA31  H  HCH2  0   0.305  -0.8395   0.7566   2.2613
 CH7  HA32  H  HCH2  0   0.307  -2.1910   0.6032   1.1505
 CH7  HXT   H  HOH1  0   0.484  -1.2850   4.0535   1.3810
 CH7  CB2   C  C1    0  -0.385  -0.0565  -2.5712  -2.0757
 CH7  OH    O  OH1   0  -0.615   3.6857  -5.6134  -4.8952

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    1.267  0.020  1.267
 CH7  NZ   CE    single    1.445  0.020  1.445
 CH7  CA1  CB    single    1.505  0.020  1.505
 CH7  CA1  C1    single    1.473  0.020  1.473
 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    1.520  0.020  1.520
 CH7  CG   HG1   single    0.970  0.020  1.090
 CH7  CG   HG2   single    0.970  0.020  1.090
 CH7  CD   CE    single    1.520  0.020  1.520
 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    1.289  0.020  1.289
 CH7  C1   N3    single    1.385  0.020  1.385
 CH7  N2   CA2   single    1.383  0.020  1.383
 CH7  OH   CZ    single    1.339  0.020  1.339
 CH7  OH   HOH   single    0.850  0.020  0.980
 CH7  CD2  CE2   aromatic  1.381  0.020  1.381
 CH7  CD2  CG2   aromatic  1.402  0.020  1.402
 CH7  CD2  HD2   single    0.930  0.020  1.080
 CH7  CE2  CZ    aromatic  1.395  0.020  1.395
 CH7  CE2  HE2   single    0.930  0.020  1.080
 CH7  CZ   CE1   aromatic  1.398  0.020  1.398
 CH7  CE1  CD1   aromatic  1.377  0.020  1.377
 CH7  CE1  HE1   single    0.930  0.020  1.080
 CH7  CD1  CG2   aromatic  1.406  0.020  1.406
 CH7  CD1  HD1   single    0.930  0.020  1.080
 CH7  CG2  CB2   single    1.442  0.020  1.442
 CH7  CB2  CA2   double    1.351  0.020  1.351
 CH7  CB2  HB2   single    0.930  0.020  1.080
 CH7  CA2  C2    single    1.474  0.020  1.474
 CH7  C2   O2    double    1.214  0.020  1.214
 CH7  C2   N3    single    1.383  0.020  1.383
 CH7  N3   CA3   single    1.434  0.020  1.434
 CH7  CA3  C3    single    1.510  0.020  1.510
 CH7  CA3  HA31  single    0.970  0.020  1.090
 CH7  CA3  HA32  single    0.970  0.020  1.090
 CH7  C3   O3    double    1.203  0.020  1.203
 CH7  C3   OXT   single    1.323  0.020  1.323
 CH7  OXT  HXT   single    0.850  0.020  0.980

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   120.96  3.000
 CH7  C1    CA1  CB    116.19  3.000
 CH7  C1    CA1  NZ    117.41  3.000
 CH7  CB    CA1  NZ    126.40  3.000
 CH7  HB2A  CB   HB1   105.78  3.000
 CH7  HB2A  CB   CG    110.62  3.000
 CH7  HB1   CB   CG    111.45  3.000
 CH7  HB2A  CB   CA1   108.12  3.000
 CH7  HB1   CB   CA1   109.43  3.000
 CH7  CG    CB   CA1   111.24  3.000
 CH7  HG2   CG   HG1   106.73  3.000
 CH7  HG2   CG   CD    111.19  3.000
 CH7  HG1   CG   CD    109.66  3.000
 CH7  HG2   CG   CB    109.95  3.000
 CH7  HG1   CG   CB    109.70  3.000
 CH7  CD    CG   CB    109.57  3.000
 CH7  HD2A  CD   HD1A  106.92  3.000
 CH7  HD2A  CD   CE    109.69  3.000
 CH7  HD1A  CD   CE    109.45  3.000
 CH7  HD2A  CD   CG    109.65  3.000
 CH7  HD1A  CD   CG    111.41  3.000
 CH7  CE    CD   CG    109.67  3.000
 CH7  HE2A  CE   HE1A  105.34  3.000
 CH7  HE2A  CE   CD    111.12  3.000
 CH7  HE1A  CE   CD    110.47  3.000
 CH7  HE2A  CE   NZ    107.16  3.000
 CH7  HE1A  CE   NZ    106.67  3.000
 CH7  CD    CE   NZ    115.50  3.000
 CH7  N3    C1   N2    113.43  3.000
 CH7  N3    C1   CA1   124.75  3.000
 CH7  N2    C1   CA1   121.81  3.000
 CH7  CA2   N2   C1    106.78  3.000
 CH7  HD2   CD2  CG2   119.41  3.000
 CH7  HD2   CD2  CE2   118.85  3.000
 CH7  CG2   CD2  CE2   121.74  3.000
 CH7  HE2   CE2  CZ    120.38  3.000
 CH7  HE2   CE2  CD2   119.97  3.000
 CH7  CZ    CE2  CD2   119.65  3.000
 CH7  CE1   CZ   CE2   119.58  3.000
 CH7  CE1   CZ   OH    117.66  3.000
 CH7  CE2   CZ   OH    122.76  3.000
 CH7  HE1   CE1  CD1   120.18  3.000
 CH7  HE1   CE1  CZ    119.53  3.000
 CH7  CD1   CE1  CZ    120.29  3.000
 CH7  HD1   CD1  CG2   119.74  3.000
 CH7  HD1   CD1  CE1   119.18  3.000
 CH7  CG2   CD1  CE1   121.07  3.000
 CH7  CB2   CG2  CD1   124.22  3.000
 CH7  CB2   CG2  CD2   118.11  3.000
 CH7  CD1   CG2  CD2   117.67  3.000
 CH7  C2    CA2  CB2   123.21  3.000
 CH7  C2    CA2  N2    108.77  3.000
 CH7  CB2   CA2  N2    128.01  3.000
 CH7  N3    C2   O2    125.94  3.000
 CH7  N3    C2   CA2   103.22  3.000
 CH7  O2    C2   CA2   130.83  3.000
 CH7  CA3   N3   C2    122.98  3.000
 CH7  CA3   N3   C1    129.16  3.000
 CH7  C2    N3   C1    107.78  3.000
 CH7  HA32  CA3  HA31  107.28  3.000
 CH7  HA32  CA3  C3    108.20  3.000
 CH7  HA31  CA3  C3    110.83  3.000
 CH7  HA32  CA3  N3    107.46  3.000
 CH7  HA31  CA3  N3    111.55  3.000
 CH7  C3    CA3  N3    111.31  3.000
 CH7  OXT   C3   O3    124.51  3.000
 CH7  OXT   C3   CA3   111.14  3.000
 CH7  O3    C3   CA3   124.27  3.000
 CH7  HXT   OXT  C3    110.14  3.000
 CH7  HB2   CB2  CA2   115.07  3.000
 CH7  HB2   CB2  CG2   115.38  3.000
 CH7  CA2   CB2  CG2   129.54  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_18  CA3  N3   C1   CA1    0.00   0.0  0
 CH7  CONST_19  O2   C2   N3   C1   180.00   0.0  0
 CH7  CONST_20  CA3  N3   C1   N2   180.00   0.0  0
 CH7  CONST_21  CA3  N3   C2   CA2  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  CONST_27  HXT  OXT  C3   CA3  180.00   0.0  0
 CH7  Var_01    CG   CB   CA1  NZ    14.63  30.0  1
 CH7  Var_02    N2   C1   CA1  NZ   177.52  30.0  2
 CH7  Var_03    CG   CD   CE   NZ   -44.77  30.0  1
 CH7  Var_04    CD   CE   NZ   CA1   14.91  30.0  1
 CH7  Var_05    CD   CG   CB   CA1  -43.70  30.0  1
 CH7  Var_06    CE   CD   CG   CB    58.76  30.0  1
 CH7  Var_07    CG2  CB2  CA2  N2    -0.31  30.0  2
 CH7  Var_08    CA2  CB2  CG2  CD2  175.98  30.0  2
 CH7  Var_09    C3   CA3  N3   C1    66.47  30.0  3
 CH7  Var_10    O3   C3   CA3  N3    18.64  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
 CH7  plan-3  HXT  0.020

