# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 03:39:38 2022
#   Inital geometry file: a 102 line input string
#   Ligand name: 3-[(1R)-4-hydroxy-6-oxo-3-(2-pyridin-2-ylhydrazino)cyclohexa-2,4-dien-1-yl]-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](C[C@@H]1C=C(NNc2ccccn2)C(=CC1=O)O)C(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
 PAQ  PAQ  3-[(1R)-4-hydroxy-6-oxo-3-(2-pyridin-2-ylhydrazino)cyclohexa-2,4-dien-1-yl]-L-alanine  L-peptide  37  22  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_PAQ
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
 PAQ  N    N  NH2    0  -0.807  67.3791  76.2277  -3.4674
 PAQ  CA   C  CH1    0  -0.224  66.2068  75.4891  -3.0208
 PAQ  CB   C  CH2    0  -0.401  66.4412  74.8252  -1.6647
 PAQ  CG   C  CR16   0  -0.447  67.5842  73.7895  -1.6333
 PAQ  CD1  C  CR6    0   0.417  67.3279  72.6504  -2.6084
 PAQ  O2   O  O      0  -0.469  66.2391  72.0868  -2.6130
 PAQ  CD2  C  CR16   0  -0.193  68.9198  74.4387  -1.7333
 PAQ  CE1  C  CR16   0  -0.518  68.4027  72.2524  -3.4758
 PAQ  CE2  C  CR6    0   0.185  69.8653  74.0346  -2.5813
 PAQ  CZ   C  CR6    0   0.400  69.6067  72.8812  -3.4431
 PAQ  OH   O  OH1    0  -0.591  70.6070  72.4523  -4.1992
 PAQ  N1   N  NH1    0  -0.598  71.1621  74.5874  -2.7326
 PAQ  N2   N  NH1    0  -0.508  71.7160  75.1939  -1.6249
 PAQ  C1   C  CR6    0   0.457  71.6186  76.5558  -1.4273
 PAQ  C2   C  CR16   0  -0.402  70.6301  77.3399  -2.0364
 PAQ  C3   C  CR16   0  -0.153  70.6020  78.6884  -1.7366
 PAQ  C4   C  CR16   0  -0.351  71.5356  79.2242  -0.8561
 PAQ  C5   C  CR16   0  -0.064  72.4691  78.3580  -0.3154
 PAQ  N3   N  N      0  -0.457  72.5199  77.0607  -0.5907
 PAQ  C    C  C      0   0.417  64.9551  76.4128  -2.9740
 PAQ  O    O  O      0  -0.597  65.0447  77.5119  -3.5567
 PAQ  OXT  O  OC    -1  -0.600  63.9547  75.9579  -2.3879
 PAQ  H    H  HNH2   0   0.337  67.0500  76.9959  -4.0392
 PAQ  H2   H  HNH2   0   0.337  67.9664  75.6478  -4.0503
 PAQ  HA   H  HCH1   0   0.206  65.9405  74.6936  -3.7359
 PAQ  HB2  H  HCH2   0   0.224  66.6585  75.5938  -0.9170
 PAQ  HB3  H  HCH2   0   0.233  65.5277  74.3266  -1.3483
 PAQ  HG   H  HCR6   0   0.300  67.5436  73.3299  -0.6339
 PAQ  HD2  H  HCR6   0   0.276  69.0994  75.2653  -1.0572
 PAQ  HE1  H  HCR6   0   0.257  68.2550  71.4068  -4.1367
 PAQ  HH   H  HOH1   0   0.476  71.4101  72.9461  -3.9559
 PAQ  HN1  H  HNH1   0   0.394  71.2527  75.1563  -3.5716
 PAQ  HN2  H  HNH1   0   0.388  72.6103  74.8040  -1.3639
 PAQ  HC2  H  HCR6   0   0.291  69.8865  76.9150  -2.6983
 PAQ  H3   H  HCR6   0   0.268  69.8465  79.3189  -2.1880
 PAQ  H4   H  HCR6   0   0.260  71.5403  80.2739  -0.5994
 PAQ  H5   H  HCR6   0   0.258  73.2206  78.7261   0.3750

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
 PAQ  N    CA   single    1.458  0.019  1.458
 PAQ  N    H    single    0.860  0.020  0.860
 PAQ  N    H2   single    0.890  0.020  1.040
 PAQ  CA   CB   single    1.530  0.020  1.530
 PAQ  CA   C    single    1.525  0.021  1.525
 PAQ  CA   HA   single    0.970  0.020  0.970
 PAQ  CB   CG   single    1.543  0.020  1.543
 PAQ  CB   HB2  single    0.970  0.020  1.090
 PAQ  CB   HB3  single    0.970  0.020  1.090
 PAQ  CG   CD1  single    1.521  0.020  1.521
 PAQ  CG   CD2  single    1.488  0.020  1.488
 PAQ  CG   HG   single    0.970  0.020  1.090
 PAQ  CD1  O2   double    1.226  0.020  1.226
 PAQ  CD1  CE1  single    1.437  0.020  1.437
 PAQ  CD2  CE2  double    1.333  0.020  1.333
 PAQ  CD2  HD2  single    0.930  0.020  1.080
 PAQ  CE1  CZ   double    1.359  0.020  1.359
 PAQ  CE1  HE1  single    0.930  0.020  1.080
 PAQ  CE2  CZ   single    1.463  0.020  1.463
 PAQ  CE2  N1   single    1.418  0.020  1.418
 PAQ  CZ   OH   single    1.325  0.020  1.325
 PAQ  OH   HH   single    0.850  0.020  0.980
 PAQ  N1   N2   single    1.379  0.020  1.379
 PAQ  N1   HN1  single    0.890  0.020  1.040
 PAQ  N2   C1   single    1.380  0.020  1.380
 PAQ  N2   HN2  single    0.890  0.020  1.040
 PAQ  C1   C2   aromatic  1.401  0.020  1.401
 PAQ  C1   N3   aromatic  1.329  0.020  1.329
 PAQ  C2   C3   aromatic  1.382  0.020  1.382
 PAQ  C2   HC2  single    0.930  0.020  1.080
 PAQ  C3   C4   aromatic  1.391  0.020  1.391
 PAQ  C3   H3   single    0.930  0.020  1.080
 PAQ  C4   C5   aromatic  1.384  0.020  1.384
 PAQ  C4   H4   single    0.930  0.020  1.080
 PAQ  C5   N3   aromatic  1.327  0.020  1.327
 PAQ  C5   H5   single    0.930  0.020  1.080
 PAQ  C    O    deloc     1.231  0.020  1.231
 PAQ  C    OXT  deloc     1.245  0.020  1.245

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
 PAQ  H2   N    H    107.37  3.000
 PAQ  H2   N    CA   110.73  3.000
 PAQ  H    N    CA   114.00  3.000
 PAQ  HA   CA   C    109.00  3.000
 PAQ  HA   CA   CB   109.00  3.000
 PAQ  C    CA   CB   110.10  1.900
 PAQ  HA   CA   N    110.00  3.000
 PAQ  C    CA   N    111.00  2.800
 PAQ  CB   CA   N    110.50  1.700
 PAQ  HB3  CB   HB2  106.86  3.000
 PAQ  HB3  CB   CG   107.97  3.000
 PAQ  HB2  CB   CG   108.09  3.000
 PAQ  HB3  CB   CA   109.18  3.000
 PAQ  HB2  CB   CA   109.37  3.000
 PAQ  CG   CB   CA   115.05  3.000
 PAQ  HG   CG   CD2  106.03  3.000
 PAQ  HG   CG   CD1  105.26  3.000
 PAQ  CD2  CG   CD1  115.77  3.000
 PAQ  HG   CG   CB   105.75  3.000
 PAQ  CD2  CG   CB   111.75  3.000
 PAQ  CD1  CG   CB   111.40  3.000
 PAQ  CE1  CD1  O2   122.31  3.000
 PAQ  CE1  CD1  CG   117.91  3.000
 PAQ  O2   CD1  CG   119.75  3.000
 PAQ  HD2  CD2  CE2  120.73  3.000
 PAQ  HD2  CD2  CG   116.10  3.000
 PAQ  CE2  CD2  CG   123.17  3.000
 PAQ  HE1  CE1  CZ   119.78  3.000
 PAQ  HE1  CE1  CD1  118.84  3.000
 PAQ  CZ   CE1  CD1  121.33  3.000
 PAQ  N1   CE2  CZ   113.97  3.000
 PAQ  N1   CE2  CD2  126.77  3.000
 PAQ  CZ   CE2  CD2  119.24  3.000
 PAQ  OH   CZ   CE2  117.24  3.000
 PAQ  OH   CZ   CE1  120.36  3.000
 PAQ  CE2  CZ   CE1  122.40  3.000
 PAQ  HH   OH   CZ   108.42  3.000
 PAQ  HN1  N1   N2   112.37  3.000
 PAQ  HN1  N1   CE2  112.79  3.000
 PAQ  N2   N1   CE2  116.95  3.000
 PAQ  HN2  N2   C1   113.99  3.000
 PAQ  HN2  N2   N1   113.17  3.000
 PAQ  C1   N2   N1   121.39  3.000
 PAQ  N3   C1   C2   122.64  3.000
 PAQ  N3   C1   N2   114.66  3.000
 PAQ  C2   C1   N2   122.68  3.000
 PAQ  HC2  C2   C3   120.12  3.000
 PAQ  HC2  C2   C1   122.06  3.000
 PAQ  C3   C2   C1   117.79  3.000
 PAQ  H3   C3   C4   120.54  3.000
 PAQ  H3   C3   C2   119.48  3.000
 PAQ  C4   C3   C2   119.98  3.000
 PAQ  H4   C4   C5   120.82  3.000
 PAQ  H4   C4   C3   121.84  3.000
 PAQ  C5   C4   C3   117.34  3.000
 PAQ  H5   C5   N3   115.92  3.000
 PAQ  H5   C5   C4   120.25  3.000
 PAQ  N3   C5   C4   123.83  3.000
 PAQ  C5   N3   C1   118.42  3.000
 PAQ  OXT  C    O    126.82  3.000
 PAQ  OXT  C    CA   116.32  3.000
 PAQ  O    C    CA   120.80  1.700

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
 PAQ  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 PAQ  CONST_02  C4   C5   N3   C1     0.00   0.0  0
 PAQ  CONST_03  C5   N3   C1   C2     0.00   0.0  0
 PAQ  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 PAQ  CONST_05  N3   C1   C2   C3     0.00   0.0  0
 PAQ  CONST_06  N3   C5   C4   C3     0.00   0.0  0
 PAQ  CONST_07  C3   C2   C1   N2   180.00   0.0  0
 PAQ  CONST_08  C5   N3   C1   N2   180.00   0.0  0
 PAQ  CONST_09  H3   C3   C2   C1   180.00   0.0  0
 PAQ  CONST_10  H5   C5   N3   C1   180.00   0.0  0
 PAQ  CONST_11  H4   C4   C3   C2   180.00   0.0  0
 PAQ  CONST_12  HC2  C2   C3   C4   180.00   0.0  0
 PAQ  Var_01    CZ   CE1  CD1  CG    -0.85  30.0  1
 PAQ  Var_02    CZ   CE2  CD2  CG    -1.37  30.0  1
 PAQ  Var_03    CE2  CZ   CE1  CD1   -3.12  30.0  1
 PAQ  Var_04    CE1  CZ   CE2  CD2    4.33  30.0  1
 PAQ  Var_05    N2   N1   CE2  CD2   27.97  30.0  2

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
 PAQ  chir_01  CA  N    CB   C   negativ
 PAQ  chir_02  CG  CD2  CD1  CB  positiv

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
 PAQ  plan-1  N2   0.020
 PAQ  plan-1  C1   0.020
 PAQ  plan-1  C2   0.020
 PAQ  plan-1  C3   0.020
 PAQ  plan-1  C4   0.020
 PAQ  plan-1  C5   0.020
 PAQ  plan-1  N3   0.020
 PAQ  plan-1  HC2  0.020
 PAQ  plan-1  H3   0.020
 PAQ  plan-1  H4   0.020
 PAQ  plan-1  H5   0.020
 PAQ  plan-2  N1   0.020
 PAQ  plan-2  N2   0.020
 PAQ  plan-2  C1   0.020
 PAQ  plan-2  HN2  0.020
 PAQ  plan-3  CG   0.020
 PAQ  plan-3  CD1  0.020
 PAQ  plan-3  O2   0.020
 PAQ  plan-3  CE1  0.020
 PAQ  plan-4  CA   0.020
 PAQ  plan-4  C    0.020
 PAQ  plan-4  O    0.020
 PAQ  plan-4  OXT  0.020

