# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 22:20:15 2020
#   Inital geometry file: a 44 line input string
#   Ligand name: (2~{R},3~{R})-2-azanyl-3-selanyl-butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]([SeH])[C@H](N)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
 T9E  T9E  '(2~{R},3~{R})-2-azanyl-3-selanyl-butanoic acid'  L-peptide  16  8  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_T9E
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
 T9E  N     N   NH2    0  -0.785  -0.7914   1.3970   1.4731
 T9E  CA    C   CH1    0  -0.208  -1.0294   1.0024   0.0956
 T9E  CB    C   CH1    0  -0.344   0.2843   0.8434  -0.6793
 T9E  CG2   C   CH3    0  -0.639   1.1569   2.0826  -0.6304
 T9E  SEG   SE  SE     0  -0.233   1.2561  -0.7448   0.0278
 T9E  C     C   C      0   0.395  -1.8719  -0.2833  -0.0893
 T9E  O     O   O      0  -0.598  -1.8255  -1.1178   0.8381
 T9E  H     H   HNH2   0   0.340  -1.6447   1.7970   1.8438
 T9E  H2    H   HNH2   0   0.332  -0.6433   0.5557   2.0190
 T9E  HA    H   HCH1   0   0.231  -1.5509   1.8275  -0.4025
 T9E  HB    H   HCH1   0   0.264   0.0346   0.6140  -1.7170
 T9E  HG21  H   HCH3   0   0.229   2.0594   1.9662  -1.2316
 T9E  HG22  H   HCH3   0   0.228   0.6009   2.9303  -1.0398
 T9E  HG23  H   HCH3   0   0.233   1.4440   2.3311   0.3893
 T9E  HG1   H   H      0   0.165   2.5240  -0.3942  -0.5988
 T9E  OXT   O   OC    -1  -0.609  -2.4845  -0.3985  -1.1685

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
 T9E  SEG  CB    single  1.992  0.020  1.992
 T9E  CG2  CB    single  1.516  0.020  1.516
 T9E  CB   CA    single  1.540  0.027  1.540
 T9E  O    C     deloc   1.231  0.020  1.231
 T9E  CA   C     single  1.525  0.021  1.525
 T9E  CA   N     single  1.458  0.019  1.458
 T9E  N    H     single  0.860  0.020  0.860
 T9E  N    H2    single  0.868  0.020  1.013
 T9E  CA   HA    single  0.970  0.020  0.970
 T9E  CB   HB    single  0.939  0.020  1.096
 T9E  CG2  HG21  single  0.939  0.020  1.096
 T9E  CG2  HG22  single  0.939  0.020  1.096
 T9E  CG2  HG23  single  0.939  0.020  1.096
 T9E  SEG  HG1   single  1.444  0.020  1.000
 T9E  C    OXT   deloc   1.246  0.020  1.246

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
 T9E  H2    N    H     104.70  3.000
 T9E  H2    N    CA    108.01  3.000
 T9E  H     N    CA    114.00  3.000
 T9E  HA    CA   C     109.00  3.000
 T9E  HA    CA   CB    109.00  3.000
 T9E  C     CA   CB    109.10  2.200
 T9E  HA    CA   N     110.00  3.000
 T9E  C     CA   N     111.00  2.800
 T9E  CB    CA   N     111.50  1.700
 T9E  HB    CB   SEG   106.35  3.000
 T9E  HB    CB   CG2   109.51  3.000
 T9E  SEG   CB   CG2   111.06  3.000
 T9E  HB    CB   CA    107.83  3.000
 T9E  CG2   CB   CA    113.08  3.000
 T9E  SEG   CB   CA    108.74  3.000
 T9E  HG23  CG2  HG22  107.94  3.000
 T9E  HG23  CG2  HG21  108.82  3.000
 T9E  HG22  CG2  HG21  107.29  3.000
 T9E  HG23  CG2  CB    111.63  3.000
 T9E  HG22  CG2  CB    109.20  3.000
 T9E  HG21  CG2  CB    111.79  3.000
 T9E  HG1   SEG  CB     94.59  3.000
 T9E  OXT   C    O     126.85  3.000
 T9E  OXT   C    CA    116.59  3.000
 T9E  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
 T9E  chir_01  CA  CB   C   N    negativ
 T9E  chir_02  CB  SEG  CA  CG2  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
 T9E  plan-1  CA   0.020
 T9E  plan-1  C    0.020
 T9E  plan-1  O    0.020
 T9E  plan-1  OXT  0.020

