# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:59:03 2022
#   Inital geometry file: a 47 line input string
#   Ligand name: (3S)-3-hydroxy-D-aspartic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]([C@H](O)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
 999  999  '(3S)-3-hydroxy-D-aspartic acid'  D-peptide  15  10  .  2016-04-22  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_999
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
 999  OD2  O  OC    -1  -0.612  1.4887  -52.4150  -19.1740
 999  CG   C  C      0   0.390  1.5709  -53.5802  -19.6017
 999  OD1  O  O      0  -0.633  0.6238  -54.3349  -19.9141
 999  CB   C  CH1    0  -0.056  2.9664  -54.1649  -19.8809
 999  OB   O  OH1    0  -0.687  4.0022  -53.2518  -19.5987
 999  CA   C  CH1    0  -0.254  3.2768  -55.4976  -19.1870
 999  N    N  NH2    0  -0.819  4.5752  -55.9398  -19.6902
 999  C    C  C      0   0.410  3.3122  -55.3968  -17.6394
 999  OXT  O  OC    -1  -0.595  2.3460  -54.8342  -17.0930
 999  O    O  O      0  -0.606  4.2838  -55.9278  -17.0609
 999  HB   H  HCH1   0   0.167  2.9617  -54.3922  -20.9642
 999  H3   H  HOH1   0   0.421  4.8013  -53.7957  -19.6687
 999  HA   H  HCH1   0   0.201  2.4695  -56.2006  -19.4371
 999  H    H  HNH2   0   0.340  4.9970  -56.5504  -19.0036
 999  H2   H  HNH2   0   0.334  4.4652  -56.4623  -20.5492

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
 999  CB   OB   single  1.409  0.020  1.409
 999  CB   CG   single  1.539  0.020  1.539
 999  CB   CA   single  1.530  0.020  1.530
 999  OD1  CG   deloc   1.251  0.020  1.251
 999  CG   OD2  deloc   1.244  0.020  1.244
 999  N    CA   single  1.458  0.019  1.458
 999  CA   C    single  1.525  0.021  1.525
 999  C    O    deloc   1.231  0.020  1.231
 999  C    OXT  deloc   1.244  0.020  1.244
 999  CB   HB   single  0.970  0.020  1.090
 999  OB   H3   single  0.850  0.020  0.980
 999  CA   HA   single  0.970  0.020  0.970
 999  N    H    single  0.860  0.020  0.860
 999  N    H2   single  0.890  0.020  1.040

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
 999  CB   CG  OD1  114.35  3.000
 999  OD1  CG  OD2  126.95  3.000
 999  CB   CG  OD2  118.57  3.000
 999  HB   CB  CA   105.37  3.000
 999  HB   CB  OB   109.40  3.000
 999  CA   CB  OB   108.88  3.000
 999  HB   CB  CG   104.58  3.000
 999  CA   CB  CG   115.56  3.000
 999  OB   CB  CG   112.59  3.000
 999  H3   OB  CB   103.17  3.000
 999  HA   CA  C    109.00  3.000
 999  HA   CA  N    110.00  3.000
 999  C    CA  N    111.00  2.800
 999  HA   CA  CB   109.00  3.000
 999  C    CA  CB   110.10  1.900
 999  N    CA  CB   110.50  1.700
 999  H2   N   H    108.07  3.000
 999  H2   N   CA   110.62  3.000
 999  H    N   CA   114.00  3.000
 999  O    C   OXT  126.35  3.000
 999  OXT  C   CA   116.72  3.000
 999  O    C   CA   120.80  1.700

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
 999  chir_01  CB  OB  CG  CA  positiv
 999  chir_02  CA  N   CB  C   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
 999  plan-1  OD2  0.020
 999  plan-1  CG   0.020
 999  plan-1  OD1  0.020
 999  plan-1  CB   0.020
 999  plan-2  CA   0.020
 999  plan-2  C    0.020
 999  plan-2  OXT  0.020
 999  plan-2  O    0.020

