# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 20:22:58 2022
#   Inital geometry file: a 45 line input string
#   Ligand name: D-aspartic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CC(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
 DAS  DAS  'D-aspartic acid          '  D-peptide  14  9  .  2016-04-22  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_DAS
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
 DAS  N    N  NH2    0  -0.802  17.6379  59.9539  30.1943
 DAS  CA   C  CH1    0  -0.200  18.8848  59.8806  30.9468
 DAS  C    C  C      0   0.409  20.1255  60.1219  30.0553
 DAS  O    O  O      0  -0.616  19.9475  60.2135  28.8233
 DAS  CB   C  CH2    0  -0.537  18.8006  60.8154  32.1521
 DAS  CG   C  C      0   0.394  18.4737  62.2787  31.8017
 DAS  OD1  O  O      0  -0.626  17.5502  62.8220  32.4460
 DAS  OD2  O  OC    -1  -0.610  19.1707  62.8222  30.9191
 DAS  OXT  O  OC    -1  -0.626  21.2273  60.1263  30.6443
 DAS  H    H  HNH2   0   0.322  16.9063  59.4838  30.7127
 DAS  H2   H  HNH2   0   0.324  17.7446  59.4511  29.3239
 DAS  HA   H  HCH1   0   0.181  19.0458  58.8666  31.3565
 DAS  HB2  H  HCH2   0   0.184  18.0481  60.4312  32.8482
 DAS  HB3  H  HCH2   0   0.204  19.7553  60.7766  32.6861

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
 DAS  N   CA   single  1.458  0.019  1.458
 DAS  N   H    single  0.860  0.020  0.860
 DAS  N   H2   single  0.890  0.020  1.040
 DAS  CA  C    single  1.525  0.021  1.525
 DAS  CA  CB   single  1.521  0.033  1.521
 DAS  CA  HA   single  0.970  0.020  0.970
 DAS  C   O    deloc   1.231  0.020  1.231
 DAS  C   OXT  deloc   1.249  0.020  1.249
 DAS  CB  CG   single  1.540  0.020  1.540
 DAS  CB  HB2  single  0.970  0.020  1.090
 DAS  CB  HB3  single  0.970  0.020  1.090
 DAS  CG  OD1  deloc   1.250  0.020  1.250
 DAS  CG  OD2  deloc   1.249  0.020  1.249

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
 DAS  H2   N   H    106.63  3.000
 DAS  H2   N   CA   109.21  3.000
 DAS  H    N   CA   114.00  3.000
 DAS  HA   CA  CB   109.00  3.000
 DAS  HA   CA  C    110.00  3.000
 DAS  CB   CA  C    110.50  1.500
 DAS  HA   CA  N    110.00  3.000
 DAS  CB   CA  N    110.40  1.500
 DAS  C    CA  N    111.00  2.800
 DAS  OXT  C   O    126.22  3.000
 DAS  OXT  C   CA   120.80  1.700
 DAS  O    C   CA   120.80  1.700
 DAS  HB3  CB  HB2  106.08  3.000
 DAS  HB3  CB  CG   109.26  3.000
 DAS  HB2  CB  CG   109.41  3.000
 DAS  HB3  CB  CA   108.37  3.000
 DAS  HB2  CB  CA   108.95  3.000
 DAS  CG   CB  CA   114.44  3.000
 DAS  OD2  CG  OD1  125.96  3.000
 DAS  OD2  CG  CB   117.12  3.000
 DAS  OD1  CG  CB   116.91  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
 DAS  Var_01  OD1  CG  CB  CA  130.38  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
 DAS  chir_01  CA  N  C  CB  negativ

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
 DAS  plan-1  CA   0.020
 DAS  plan-1  C    0.020
 DAS  plan-1  O    0.020
 DAS  plan-1  OXT  0.020
 DAS  plan-2  CB   0.020
 DAS  plan-2  CG   0.020
 DAS  plan-2  OD1  0.020
 DAS  plan-2  OD2  0.020

