# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 06:35:15 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  12  9  .  2022-03-18  2022-07-24
;
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  -0.836  -0.3418   1.6063   0.2610
 DYA  CA   C  C      0   0.139  -0.4390   0.2580   0.1150
 DYA  CB   C  C1     0  -0.563   0.6197  -0.5865   0.0567
 DYA  CG   C  C      0   0.416   2.0513  -0.1862   0.0557
 DYA  OD1  O  OC    -1  -0.638   2.8989  -1.1093   0.0185
 DYA  OD2  O  O      0  -0.632   2.3393   1.0425   0.0832
 DYA  C    C  C      0   0.391  -1.8786  -0.2742   0.0412
 DYA  O    O  O      0  -0.587  -2.0407  -1.5067   0.0568
 DYA  OXT  O  OC    -1  -0.609  -2.7706   0.5951  -0.0377
 DYA  HN1  H  HNH2   0   0.370   0.5805   1.9855   0.0986
 DYA  HN2  H  HNH2   0   0.358  -1.1471   2.1411  -0.0148
 DYA  HB   H  H      0   0.193   0.3990  -1.6440  -0.0046

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  1.486  0.020  1.486
 DYA  CG  OD1  deloc   1.254  0.020  1.254
 DYA  CG  OD2  deloc   1.262  0.020  1.262
 DYA  C   O    deloc   1.231  0.020  1.231
 DYA  C   OXT  deloc   1.248  0.020  1.248
 DYA  N   HN1  single  0.890  0.020  1.040
 DYA  N   HN2  single  0.890  0.020  1.040
 DYA  CB  HB   single  0.930  0.020  1.080

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  119.18  3.000
 DYA  HN2  N   CA   116.16  3.000
 DYA  HN1  N   CA   114.85  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   117.36  3.000
 DYA  HB   CB  CA   116.87  3.000
 DYA  CG   CB  CA   125.76  3.000
 DYA  OD2  CG  OD1  124.27  3.000
 DYA  OD2  CG  CB   118.80  3.000
 DYA  OD1  CG  CB   116.93  3.000
 DYA  OXT  C   O    126.74  3.000
 DYA  OXT  C   CA   115.56  3.000
 DYA  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
 DYA  Var_01  CG   CB  CA  N     -4.05   0.0  2
 DYA  Var_02  O    C   CA  N   -172.22  30.0  2
 DYA  Var_03  OD1  CG  CB  CA   178.87  30.0  2
 DYA  Var_04  HN1  N   CA  CB    14.43  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-2  CA   0.020
 DYA  plan-2  C    0.020
 DYA  plan-2  O    0.020
 DYA  plan-2  OXT  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

