# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 14:52:43 2020
#   Inital geometry file: a 45 line input string
#   Ligand name: (Z)-2-azanylbut-2-enedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N\C(=C/C(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
 DYA  DYA  '(Z)-2-azanylbut-2-enedioic acid'  L-peptide  14  9  .  2022-03-18  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DYA
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
 DYA  N    N  NH2   0  -0.823  -0.3949   1.6319  0.0970
 DYA  CA   C  C     0   0.257  -0.4401   0.2997  0.0611
 DYA  CB   C  C1    0  -0.523   0.6277  -0.5483  0.0426
 DYA  CG   C  C     0   0.560   1.9910  -0.0765  0.0535
 DYA  OD1  O  OH1   0  -0.611   2.8761  -1.0762  0.0342
 DYA  OD2  O  O     0  -0.491   2.3428   1.0926  0.0774
 DYA  C    C  C     0   0.552  -1.8092  -0.3374  0.0428
 DYA  O    O  O     0  -0.410  -1.9886  -1.5256  0.0182
 DYA  OXT  O  OH1   0  -0.594  -2.7728   0.5635  0.0573
 DYA  HN1  H  HNH2  0   0.416   0.5002   2.0934  0.1030
 DYA  HN2  H  HNH2  0   0.414  -1.2261   2.1950  0.0951
 DYA  HB   H  H     0   0.276   0.4467  -1.6116  0.0174
 DYA  HD1  H  HOH1  0   0.476   3.7737  -0.7142  0.0404
 DYA  HXT  H  HOH1  0   0.499  -3.6434   0.1367  0.0472

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
 DYA  N    CA   single  1.458  0.019  1.458
 DYA  CA   CB   double  1.530  0.020  1.530
 DYA  CA   C    single  1.525  0.021  1.525
 DYA  CB   CG   single  1.443  0.020  1.443
 DYA  CG   OD1  single  1.335  0.020  1.335
 DYA  CG   OD2  double  1.221  0.020  1.221
 DYA  C    O    double  1.231  0.020  1.231
 DYA  C    OXT  single  1.319  0.020  1.319
 DYA  N    HN1  single  0.860  0.020  1.020
 DYA  N    HN2  single  0.860  0.020  1.020
 DYA  CB   HB   single  0.930  0.020  1.080
 DYA  OD1  HD1  single  0.850  0.020  0.980
 DYA  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
 DYA  HN2  N    HN1  118.61  3.000
 DYA  HN2  N    CA   122.16  3.000
 DYA  HN1  N    CA   119.22  3.000
 DYA  C    CA   CB   110.10  1.900
 DYA  C    CA   N    111.00  2.800
 DYA  CB   CA   N    110.50  1.700
 DYA  HB   CB   CG   118.75  3.000
 DYA  HB   CB   CA   118.80  3.000
 DYA  CG   CB   CA   122.45  3.000
 DYA  OD2  CG   OD1  121.74  3.000
 DYA  OD2  CG   CB   125.83  3.000
 DYA  OD1  CG   CB   112.43  3.000
 DYA  HD1  OD1  CG   109.55  3.000
 DYA  OXT  C    O    124.49  3.000
 DYA  OXT  C    CA   111.96  3.000
 DYA  O    C    CA   120.80  1.700
 DYA  HXT  OXT  C    110.80  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
 DYA  CONST_01  HXT  OXT  C   CA   180.00   0.0  0
 DYA  CONST_02  HD1  OD1  CG  CB   180.00   0.0  0
 DYA  Var_01    CG   CB   CA  N     -0.33   0.0  2
 DYA  Var_02    O    C    CA  N   -179.57  30.0  2
 DYA  Var_03    OD1  CG   CB  CA   179.87  30.0  2
 DYA  Var_04    HN1  N    CA  CB     0.64  30.0  2

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
 DYA  plan-1  CB   0.020
 DYA  plan-1  CG   0.020
 DYA  plan-1  OD1  0.020
 DYA  plan-1  OD2  0.020
 DYA  plan-1  HD1  0.020
 DYA  plan-2  CA   0.020
 DYA  plan-2  C    0.020
 DYA  plan-2  O    0.020
 DYA  plan-2  OXT  0.020
 DYA  plan-2  HXT  0.020
 DYA  plan-3  N    0.020
 DYA  plan-3  CA   0.020
 DYA  plan-3  CB   0.020
 DYA  plan-3  CG   0.020
 DYA  plan-3  C    0.020
 DYA  plan-3  HB   0.020

