# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 08:46:13 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  16  9  .  2022-09-22  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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  -0.799  62.2403   -8.5554  21.2848
 SOC  CA   C   CH1   0  -0.242  63.2317   -8.1418  22.2633
 SOC  CB   C   CH2   0  -0.685  63.8009   -9.3530  22.9927
 SOC  SE   SE  SE    0   1.219  62.6118  -10.0364  24.3470
 SOC  OD1  O   O     0  -0.716  63.2790  -11.3307  25.0155
 SOC  OD2  O   O     0  -0.722  61.1231  -10.1794  23.7581
 SOC  C    C   C     0   0.592  64.3750   -7.4163  21.5600
 SOC  O    O   O     0  -0.431  65.5443   -7.5984  21.7799
 SOC  OXT  O   OH1   0  -0.586  63.9179   -6.5287  20.6944
 SOC  H    H   HNH2  0   0.365  61.7918   -7.7426  20.8828
 SOC  H2   H   HNH2  0   0.361  61.5046   -9.0705  21.7527
 SOC  HA   H   HCH1  0   0.285  62.8489   -7.4175  23.0041
 SOC  HB2  H   HCH2  0   0.328  63.9869  -10.1798  22.3022
 SOC  HB3  H   HCH2  0   0.331  64.7255   -9.1208  23.5231
 SOC  HXT  H   HOH1  0   0.489  64.6540   -6.0673  20.2645
 SOC  HE   H   H     0   0.210  62.6086   -8.9368  25.3309

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  1.927  0.020  1.927
 SOC  CB   HB2  single  0.939  0.020  1.096
 SOC  CB   HB3  single  0.939  0.020  1.096
 SOC  SE   OD1  double  1.602  0.020  1.602
 SOC  SE   OD2  double  1.607  0.020  1.607
 SOC  C    O    double  1.231  0.020  1.231
 SOC  C    OXT  single  1.321  0.020  1.321
 SOC  OXT  HXT  single  0.832  0.020  0.971
 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    105.68  3.000
 SOC  H2   N    CA   109.23  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  108.89  3.000
 SOC  HB3  CB   SE   104.88  3.000
 SOC  HB2  CB   SE   106.30  3.000
 SOC  HB3  CB   CA   112.33  3.000
 SOC  HB2  CB   CA   111.24  3.000
 SOC  SE   CB   CA   112.81  3.000
 SOC  HE   SE   OD2  107.97  3.000
 SOC  HE   SE   OD1  108.95  3.000
 SOC  OD2  SE   OD1  117.82  3.000
 SOC  HE   SE   CB   101.87  3.000
 SOC  OD2  SE   CB   110.21  3.000
 SOC  OD1  SE   CB   108.83  3.000
 SOC  OXT  C    O    123.87  3.000
 SOC  OXT  C    CA   114.20  3.000
 SOC  O    C    CA   120.80  1.700
 SOC  HXT  OXT  C    110.34  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
 SOC  CONST_01  HXT  OXT  C   CA  180.00   0.0  0
 SOC  Var_01    OD1  SE   CB  CA  178.11  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
 SOC  plan-1  HXT  0.020

