# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 22:21:35 2020
#   Inital geometry file: a 43 line input string
#   Ligand name: 3-(oxido-lambda~4~-selanyl)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](C[Se@H]=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
 UOX  UOX  3-(oxido-lambda~4~-selanyl)-L-alanine  L-peptide  14  8  .  2022-07-22  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_UOX
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
 UOX  N   N   NH2    0  -0.779  -1.1896   1.7996  -0.1302
 UOX  CA  C   CH1    0  -0.235  -1.1891   0.3692  -0.3531
 UOX  CB  C   CH2    0  -0.659  -0.1255  -0.4290   0.4137
 UOX  SE  SE  SE     0   0.671   1.7175  -0.0494  -0.1442
 UOX  OD  O   O      0  -0.812   2.6693  -0.8757   0.9197
 UOX  C   C   C      0   0.420  -2.5651  -0.2558   0.0229
 UOX  O   O   O      0  -0.591  -3.3437   0.4449   0.6904
 UOX  H1  H   HNH2   0   0.336  -1.3906   2.0009   0.8402
 UOX  H2  H   HNH2   0   0.331  -0.2978   2.2230  -0.3495
 UOX  H4  H   HCH1   0   0.238  -1.0413   0.1951  -1.4250
 UOX  H5  H   HCH2   0   0.281  -0.1820  -0.2490   1.4909
 UOX  H6  H   HCH2   0   0.281  -0.2479  -1.4981   0.2321
 UOX  O1  O   OC    -1  -0.613  -2.7431  -1.4274  -0.3626
 UOX  H3  H   H      0   0.132   1.6699   1.3408   0.3754

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
 UOX  OD  SE  double  1.649  0.020  1.649
 UOX  SE  CB  single  1.963  0.020  1.963
 UOX  O   C   deloc   1.231  0.020  1.231
 UOX  C   CA  single  1.525  0.033  1.525
 UOX  CB  CA  single  1.521  0.020  1.521
 UOX  CA  N   single  1.458  0.020  1.458
 UOX  N   H1  single  0.868  0.020  1.013
 UOX  N   H2  single  0.868  0.020  1.013
 UOX  CA  H4  single  0.939  0.020  1.096
 UOX  CB  H5  single  0.939  0.020  1.096
 UOX  CB  H6  single  0.939  0.020  1.096
 UOX  C   O1  deloc   1.246  0.020  1.246
 UOX  SE  H3  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
 UOX  H2  N   H1  107.46  3.000
 UOX  H2  N   CA  112.33  3.000
 UOX  H1  N   CA  110.15  3.000
 UOX  H4  CA  C   106.95  3.000
 UOX  H4  CA  CB  108.21  3.000
 UOX  C   CA  CB  110.50  1.500
 UOX  H4  CA  N   107.91  3.000
 UOX  CB  CA  N   110.40  1.500
 UOX  C   CA  N   111.00  2.800
 UOX  H6  CB  H5  108.62  3.000
 UOX  H6  CB  SE  104.33  3.000
 UOX  H5  CB  SE  107.26  3.000
 UOX  H6  CB  CA  110.40  3.000
 UOX  H5  CB  CA  111.76  3.000
 UOX  SE  CB  CA  114.09  3.000
 UOX  H3  SE  OD  105.18  3.000
 UOX  H3  SE  CB   92.95  3.000
 UOX  OD  SE  CB  105.16  3.000
 UOX  O1  C   O   127.38  3.000
 UOX  O1  C   CA  115.39  3.000
 UOX  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
 UOX  Var_01  OD  SE  CB  CA  173.66  30.0  2

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
 UOX  chir_01  CA  C  CB  N  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
 UOX  plan-1  CA  0.020
 UOX  plan-1  C   0.020
 UOX  plan-1  O   0.020
 UOX  plan-1  O1  0.020
 UOX  plan-2  CB  0.020
 UOX  plan-2  SE  0.020
 UOX  plan-2  OD  0.020
 UOX  plan-2  H3  0.020

