# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 01:22:23 2022
#   Inital geometry file: a 71 line input string
#   Ligand name: 3-(4-hydroxy-3-oxocyclohexa-1,4-dien-1-yl)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC1=CC(=O)C(=CC1)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
 DPQ  DPQ  3-(4-hydroxy-3-oxocyclohexa-1,4-dien-1-yl)-L-alanine  L-peptide  24  14  .  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_DPQ
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
 DPQ  OE2   O  O      0  -0.460  -3.2518  -1.6305  25.5394
 DPQ  N     N  NH2    0  -0.784   0.0600   3.0723  26.2301
 DPQ  CA    C  CH1    0  -0.209  -1.1871   3.1886  26.9658
 DPQ  C     C  C      0   0.388  -1.4314   4.5468  27.6837
 DPQ  O     O  O      0  -0.593  -0.4965   5.3691  27.6898
 DPQ  CG    C  CR6    0   0.170  -1.2444   0.6946  27.3638
 DPQ  CD1   C  C      0  -0.542   0.0381  -0.0489  27.4226
 DPQ  CD2   C  CR16   0  -0.406  -2.3195   0.1745  26.7443
 DPQ  CE1   C  CR16   0  -0.332   0.0557  -1.3830  26.7743
 DPQ  CE2   C  CR6    0   0.319  -2.2889  -1.1257  26.1089
 DPQ  CZ    C  CR6    0   0.277  -1.0216  -1.8833  26.1617
 DPQ  OH    O  OH1    0  -0.631  -1.0392  -3.0876  25.5652
 DPQ  OXT   O  OC    -1  -0.611  -2.5581   4.6856  28.2023
 DPQ  HA    H  HCH1   0   0.227  -2.0058   3.0459  26.2523
 DPQ  HD11  H  H      0   0.283   0.8108   0.5966  26.9847
 DPQ  HD12  H  H      0   0.280   0.3382  -0.1424  28.4745
 DPQ  HE1   H  HCR6   0   0.266   0.9789  -1.9497  26.8103
 DPQ  HH    H  HOH1   0   0.459  -1.9301  -3.2162  25.2038
 DPQ  HD2   H  HCR6   0   0.255  -3.2560   0.7211  26.7080
 DPQ  H     H  HNH2   0   0.339   0.0254   3.6822  25.4226
 DPQ  CB    C  CH2    0  -0.516  -1.2920   2.0508  27.9972
 DPQ  HN2   H  HNH2   0   0.326   0.8035   3.4526  26.8048
 DPQ  HB1   H  HCH2   0   0.242  -0.4795   2.1513  28.7238
 DPQ  HB2   H  HCH2   0   0.256  -2.2284   2.1636  28.5438

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
 DPQ  OE2  CE2   double  1.227  0.020  1.227
 DPQ  N    CA    single  1.458  0.019  1.458
 DPQ  N    H     single  0.860  0.020  0.860
 DPQ  N    HN2   single  0.890  0.020  1.040
 DPQ  CA   C     single  1.525  0.021  1.525
 DPQ  CA   CB    single  1.530  0.020  1.530
 DPQ  CA   HA    single  0.970  0.020  0.970
 DPQ  C    O     deloc   1.231  0.020  1.231
 DPQ  C    OXT   deloc   1.248  0.020  1.248
 DPQ  CB   CG    single  1.498  0.020  1.498
 DPQ  CB   HB1   single  0.970  0.020  1.090
 DPQ  CB   HB2   single  0.970  0.020  1.090
 DPQ  CG   CD1   single  1.484  0.020  1.484
 DPQ  CG   CD2   double  1.345  0.020  1.345
 DPQ  CD1  CE1   single  1.483  0.020  1.483
 DPQ  CD1  HD11  single  0.970  0.020  1.090
 DPQ  CD1  HD12  single  0.970  0.020  1.090
 DPQ  CD2  CE2   single  1.448  0.020  1.448
 DPQ  CD2  HD2   single  0.930  0.020  1.080
 DPQ  CE1  CZ    double  1.336  0.020  1.336
 DPQ  CE1  HE1   single  0.930  0.020  1.080
 DPQ  CE2  CZ    single  1.477  0.020  1.477
 DPQ  CZ   OH    single  1.344  0.020  1.344
 DPQ  OH   HH    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
 DPQ  HN2   N    H     104.55  3.000
 DPQ  HN2   N    CA    108.21  3.000
 DPQ  H     N    CA    114.00  3.000
 DPQ  HA    CA   CB    109.00  3.000
 DPQ  HA    CA   C     109.00  3.000
 DPQ  CB    CA   C     110.10  1.900
 DPQ  HA    CA   N     110.00  3.000
 DPQ  CB    CA   N     110.50  1.700
 DPQ  C     CA   N     111.00  2.800
 DPQ  OXT   C    O     127.04  3.000
 DPQ  OXT   C    CA    115.51  3.000
 DPQ  O     C    CA    120.80  1.700
 DPQ  CD2   CG   CD1   121.02  3.000
 DPQ  CD2   CG   CB    121.29  3.000
 DPQ  CD1   CG   CB    117.68  3.000
 DPQ  HD12  CD1  HD11  103.88  3.000
 DPQ  HD12  CD1  CE1   109.81  3.000
 DPQ  HD11  CD1  CE1   110.25  3.000
 DPQ  HD12  CD1  CG    108.48  3.000
 DPQ  HD11  CD1  CG    107.33  3.000
 DPQ  CE1   CD1  CG    116.34  3.000
 DPQ  HD2   CD2  CE2   117.13  3.000
 DPQ  HD2   CD2  CG    120.69  3.000
 DPQ  CE2   CD2  CG    122.17  3.000
 DPQ  HE1   CE1  CZ    120.40  3.000
 DPQ  HE1   CE1  CD1   117.76  3.000
 DPQ  CZ    CE1  CD1   121.83  3.000
 DPQ  CZ    CE2  CD2   117.58  3.000
 DPQ  CZ    CE2  OE2   118.60  3.000
 DPQ  CD2   CE2  OE2   123.82  3.000
 DPQ  OH    CZ   CE2   115.61  3.000
 DPQ  OH    CZ   CE1   123.33  3.000
 DPQ  CE2   CZ   CE1   121.06  3.000
 DPQ  HH    OH   CZ    107.23  3.000
 DPQ  HB2   CB   HB1   107.18  3.000
 DPQ  HB2   CB   CG    109.45  3.000
 DPQ  HB1   CB   CG    109.89  3.000
 DPQ  HB2   CB   CA    108.54  3.000
 DPQ  HB1   CB   CA    109.04  3.000
 DPQ  CG    CB   CA    112.57  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
 DPQ  Var_01  CZ   CE1  CD1  CG     0.51  30.0  1
 DPQ  Var_02  CZ   CE2  CD2  CG     0.12  30.0  1
 DPQ  Var_03  CE2  CD2  CG   CD1    0.11  30.0  1
 DPQ  Var_04  CE1  CD1  CG   CD2   -0.41  30.0  1
 DPQ  Var_05  CE1  CZ   CE2  CD2   -0.02  30.0  1
 DPQ  Var_06  CD1  CG   CB   CA   101.27  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
 DPQ  chir_01  CA  N  C  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
 DPQ  plan-1  OE2  0.020
 DPQ  plan-1  CD2  0.020
 DPQ  plan-1  CE2  0.020
 DPQ  plan-1  CZ   0.020
 DPQ  plan-2  CA   0.020
 DPQ  plan-2  C    0.020
 DPQ  plan-2  O    0.020
 DPQ  plan-2  OXT  0.020

