# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 13:49:08 2022
#   Inital geometry file: a 49 line input string
#   Ligand name: (2S)-2-azanyl-4-(oxidanylamino)-4-oxidanylidene-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
 SD4  SD4  '(2S)-2-azanyl-4-(oxidanylamino)-4-oxidanylidene-butanoic acid'  L-peptide  17  10  .  2012-08-28  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_SD4
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
 SD4  C    C  C      0   0.389  91.4122  40.5903  54.7457
 SD4  N    N  NH2    0  -0.785  93.8217  41.0984  54.0583
 SD4  OXT  O  OC     0  -0.613  90.2472  41.0284  54.8437
 SD4  CA   C  CH1    0  -0.218  92.4563  41.5868  54.1698
 SD4  CB   C  CH2    0  -0.579  91.9967  42.0929  52.8025
 SD4  CG   C  C      0   0.529  92.8935  43.1943  52.2929
 SD4  OD1  O  O      0  -0.480  93.0997  44.2231  52.9130
 SD4  ND2  N  NH1    0  -0.378  93.4636  42.9273  51.0996
 SD4  O    O  O     -1  -0.595  91.8176  39.4581  55.0689
 SD4  H5   H  HCH1   0   0.225  92.4741  42.4494  54.8454
 SD4  H6   H  HCH2   0   0.266  90.9859  42.4954  52.8807
 SD4  H7   H  HCH2   0   0.241  91.9486  41.2576  52.0963
 SD4  H8   H  HOH1   0   0.473  95.0802  43.7613  50.6345
 SD4  H9   H  HNH1   0   0.409  93.1607  42.1600  50.5173
 SD4  H1   H  HNH2   0   0.336  94.1464  40.8300  54.9791
 SD4  OAD  O  OH1    0  -0.545  94.1460  43.9037  50.4347
 SD4  H2   H  HNH2   0   0.325  93.8112  40.2310  53.5330

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
 SD4  OAD  ND2  single  1.364  0.020  1.364
 SD4  ND2  CG   single  1.349  0.020  1.349
 SD4  CG   OD1  double  1.219  0.020  1.219
 SD4  CG   CB   single  1.509  0.020  1.509
 SD4  CB   CA   single  1.530  0.020  1.530
 SD4  N    CA   single  1.458  0.019  1.458
 SD4  CA   C    single  1.525  0.021  1.525
 SD4  C    O    deloc   1.231  0.020  1.231
 SD4  C    OXT  deloc   1.249  0.020  1.249
 SD4  N    H1   single  0.890  0.020  1.040
 SD4  N    H2   single  0.890  0.020  1.040
 SD4  CA   H5   single  0.970  0.020  1.090
 SD4  CB   H6   single  0.970  0.020  1.090
 SD4  CB   H7   single  0.970  0.020  1.090
 SD4  OAD  H8   single  0.850  0.020  0.980
 SD4  ND2  H9   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
 SD4  O    C    CA   120.80  1.700
 SD4  O    C    OXT  127.05  3.000
 SD4  CA   C    OXT  115.53  3.000
 SD4  H2   N    H1   104.34  3.000
 SD4  H2   N    CA   108.49  3.000
 SD4  H1   N    CA   108.69  3.000
 SD4  H5   CA   CB   107.20  3.000
 SD4  H5   CA   N    107.24  3.000
 SD4  CB   CA   N    110.50  1.700
 SD4  H5   CA   C    106.69  3.000
 SD4  N    CA   C    111.00  2.800
 SD4  CB   CA   C    110.10  1.900
 SD4  H7   CB   H6   106.68  3.000
 SD4  H7   CB   CG   111.41  3.000
 SD4  H6   CB   CG   107.80  3.000
 SD4  H7   CB   CA   109.73  3.000
 SD4  H6   CB   CA   109.67  3.000
 SD4  CG   CB   CA   111.41  3.000
 SD4  ND2  CG   OD1  123.07  3.000
 SD4  OD1  CG   CB   123.01  3.000
 SD4  ND2  CG   CB   113.91  3.000
 SD4  H9   ND2  OAD  114.39  3.000
 SD4  H9   ND2  CG   122.26  3.000
 SD4  OAD  ND2  CG   120.05  3.000
 SD4  H8   OAD  ND2  106.11  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
 SD4  CONST_01  OAD  ND2  CG   CB   180.00   0.0  0
 SD4  CONST_02  OD1  CG   ND2  OAD    0.00   0.0  0
 SD4  CONST_03  H9   ND2  CG   CB     0.00   0.0  0
 SD4  Var_01    ND2  CG   CB   CA   121.97  30.0  1

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
 SD4  chir_01  CA  CB  N  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
 SD4  plan-1  CB   0.020
 SD4  plan-1  CG   0.020
 SD4  plan-1  OD1  0.020
 SD4  plan-1  ND2  0.020
 SD4  plan-1  H9   0.020
 SD4  plan-1  OAD  0.020
 SD4  plan-2  C    0.020
 SD4  plan-2  OXT  0.020
 SD4  plan-2  CA   0.020
 SD4  plan-2  O    0.020

