# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 26 17:11:23 2020
#   Inital geometry file: a 49 line input string
#   Ligand name: (2R)-2-azanyl-4-(hydroxyamino)-4-oxo-butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CC(=O)NO)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
 SD3  SD3  '(2R)-2-azanyl-4-(hydroxyamino)-4-oxo-butanoic acid'  ligand  18  10  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SD3
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
 SD3  C     C  C     0   0.551  -2.3225  -0.1239  -0.0895
 SD3  N     N  NH2   0  -0.783  -0.7162   1.6665  -0.3272
 SD3  OXT   O  OH1   0  -0.594  -2.6778  -1.1612   0.6593
 SD3  CA    C  CH1   0  -0.217  -0.9297   0.3654   0.2584
 SD3  CB    C  CH2   0  -0.606   0.0911  -0.7120  -0.1508
 SD3  CG    C  C     0   0.533   1.4867  -0.3262   0.2890
 SD3  OAD   O  OH1   0  -0.543   3.7438  -0.4679  -0.3192
 SD3  OD1   O  O     0  -0.474   1.7260   0.1594   1.3802
 SD3  ND2   N  NH1   0  -0.373   2.4248  -0.5573  -0.6467
 SD3  O     O  O     0  -0.432  -3.0222   0.3479  -0.9476
 SD3  HN    H  HNH2  0   0.359   0.1291   2.0774   0.0457
 SD3  HNA   H  HNH2  0   0.348  -0.5936   1.5972  -1.3297
 SD3  HA    H  HCH1  0   0.285  -0.8857   0.4740   1.3455
 SD3  HB    H  HCH2  0   0.293  -0.1422  -1.6690   0.3237
 SD3  HBA   H  HCH2  0   0.272   0.0441  -0.8750  -1.2310
 SD3  HOAD  H  HOH1  0   0.479   4.0420   0.3924  -0.6418
 SD3  HND2  H  HNH1  0   0.418   2.2311  -1.1021  -1.4753
 SD3  H8    H  HOH1  0   0.483  -3.5567  -1.4757   0.3994

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
 SD3  C    OXT   single  1.328  0.020  1.328
 SD3  C    CA    single  1.517  0.020  1.517
 SD3  C    O     double  1.204  0.020  1.204
 SD3  N    CA    single  1.443  0.020  1.443
 SD3  N    HN    single  0.890  0.020  1.040
 SD3  N    HNA   single  0.890  0.020  1.040
 SD3  CA   CB    single  1.540  0.020  1.540
 SD3  CA   HA    single  0.970  0.020  1.090
 SD3  CB   CG    single  1.513  0.020  1.513
 SD3  CB   HB    single  0.970  0.020  1.090
 SD3  CB   HBA   single  0.970  0.020  1.090
 SD3  CG   OD1   double  1.218  0.020  1.218
 SD3  CG   ND2   single  1.345  0.020  1.345
 SD3  OAD  ND2   single  1.362  0.020  1.362
 SD3  OAD  HOAD  single  0.850  0.020  0.980
 SD3  ND2  HND2  single  0.890  0.020  1.040
 SD3  OXT  H8    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
 SD3  O     C    CA   124.82  3.000
 SD3  O     C    OXT  123.55  3.000
 SD3  CA    C    OXT  111.62  3.000
 SD3  HNA   N    HN   106.97  3.000
 SD3  HNA   N    CA   110.98  3.000
 SD3  HN    N    CA   109.91  3.000
 SD3  H8    OXT  C    110.18  3.000
 SD3  HA    CA   CB   107.88  3.000
 SD3  HA    CA   N    107.94  3.000
 SD3  CB    CA   N    115.16  3.000
 SD3  HA    CA   C    107.28  3.000
 SD3  CB    CA   C    108.79  3.000
 SD3  N     CA   C    109.50  3.000
 SD3  HBA   CB   HB   106.80  3.000
 SD3  HBA   CB   CG   111.39  3.000
 SD3  HB    CB   CG   107.09  3.000
 SD3  HBA   CB   CA   109.78  3.000
 SD3  HB    CB   CA   110.84  3.000
 SD3  CG    CB   CA   110.85  3.000
 SD3  ND2   CG   OD1  123.69  3.000
 SD3  ND2   CG   CB   113.41  3.000
 SD3  OD1   CG   CB   122.90  3.000
 SD3  HOAD  OAD  ND2  106.10  3.000
 SD3  HND2  ND2  OAD  114.72  3.000
 SD3  HND2  ND2  CG   121.97  3.000
 SD3  OAD   ND2  CG   119.80  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
 SD3  CONST_01  OAD   ND2  CG   CB   180.00   0.0  0
 SD3  CONST_02  OD1   CG   ND2  OAD    0.00   0.0  0
 SD3  CONST_03  HND2  ND2  CG   CB     0.00   0.0  0
 SD3  CONST_04  H8    OXT  C    CA   180.00   0.0  0
 SD3  Var_01    OD1   CG   CB   CA    42.33  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
 SD3  chir_01  CA  C  N  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
 SD3  plan-1  CB    0.020
 SD3  plan-1  CG    0.020
 SD3  plan-1  OAD   0.020
 SD3  plan-1  OD1   0.020
 SD3  plan-1  ND2   0.020
 SD3  plan-1  HND2  0.020
 SD3  plan-2  C     0.020
 SD3  plan-2  OXT   0.020
 SD3  plan-2  CA    0.020
 SD3  plan-2  O     0.020
 SD3  plan-2  H8    0.020

