# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 22:14:54 2020
#   Inital geometry file: a 46 line input string
#   Ligand name: 3-(dioxidoselanyl)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](C[SeH](=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
 SOC  SOC  3-(dioxidoselanyl)-L-alanine  L-peptide  15  9  .  2022-09-22  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_SOC
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
 SOC  N    N   NH2    0  -0.807  62.1519   -8.3843  21.4744
 SOC  CA   C   CH1    0  -0.245  63.1755   -8.0089  22.4259
 SOC  CB   C   CH2    0  -0.658  63.8575   -9.2422  23.0049
 SOC  SE   SE  SE     0   1.207  62.7477  -10.2108  24.2493
 SOC  OD1  O   O      0  -0.735  63.5118  -11.5416  24.7272
 SOC  OD2  O   O      0  -0.732  61.2463  -10.3902  23.7046
 SOC  C    C   C      0   0.438  64.2584   -7.0959  21.7640
 SOC  O    O   O      0  -0.597  65.3295   -6.9783  22.3841
 SOC  OXT  O   OC    -1  -0.589  63.9324   -6.5366  20.7035
 SOC  H    H   HNH2   0   0.343  62.0447   -7.6217  20.8185
 SOC  H2   H   HNH2   0   0.341  61.2635   -8.5216  21.9346
 SOC  HA   H   HCH1   0   0.234  62.7840   -7.4023  23.2611
 SOC  HB2  H   HCH2   0   0.303  64.1242   -9.9541  22.2197
 SOC  HB3  H   HCH2   0   0.307  64.7501   -8.9834  23.5769
 SOC  HE   H   H      0   0.189  62.6972   -9.2677  25.3863

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
 SOC  N   CA   single  1.458  0.020  1.458
 SOC  N   H    single  0.868  0.019  0.868
 SOC  N   H2   single  0.868  0.020  1.013
 SOC  CA  CB   single  1.521  0.020  1.521
 SOC  CA  C    single  1.525  0.033  1.525
 SOC  CA  HA   single  0.939  0.021  0.939
 SOC  CB  SE   single  1.928  0.020  1.928
 SOC  CB  HB2  single  0.939  0.020  1.096
 SOC  CB  HB3  single  0.939  0.020  1.096
 SOC  SE  OD1  double  1.607  0.020  1.607
 SOC  SE  OD2  double  1.607  0.020  1.607
 SOC  C   O    deloc   1.231  0.020  1.231
 SOC  C   OXT  deloc   1.242  0.020  1.242
 SOC  HE  SE   single  1.444  0.020  1.000

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
 SOC  H2   N   H    107.74  3.000
 SOC  H2   N   CA   110.97  3.000
 SOC  H    N   CA   114.00  3.000
 SOC  HA   CA  C    110.00  3.000
 SOC  HA   CA  CB   109.00  3.000
 SOC  C    CA  CB   110.50  1.500
 SOC  HA   CA  N    110.00  3.000
 SOC  C    CA  N    111.00  2.800
 SOC  CB   CA  N    110.40  1.500
 SOC  HB3  CB  HB2  109.36  3.000
 SOC  HB3  CB  SE   104.57  3.000
 SOC  HB2  CB  SE   106.07  3.000
 SOC  HB3  CB  CA   111.92  3.000
 SOC  HB2  CB  CA   111.31  3.000
 SOC  SE   CB  CA   113.22  3.000
 SOC  HE   SE  OD2  107.46  3.000
 SOC  HE   SE  OD1  108.41  3.000
 SOC  OD2  SE  OD1  116.90  3.000
 SOC  HE   SE  CB   101.28  3.000
 SOC  OD2  SE  CB   112.03  3.000
 SOC  OD1  SE  CB   109.52  3.000
 SOC  OXT  C   O    127.53  3.000
 SOC  OXT  C   CA   114.20  3.000
 SOC  O    C   CA   120.80  1.700

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
 SOC  Var_01  OD1  SE  CB  CA  176.20  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
 SOC  chir_01  CA  N  CB  C  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
 SOC  plan-1  CA   0.020
 SOC  plan-1  C    0.020
 SOC  plan-1  O    0.020
 SOC  plan-1  OXT  0.020

