# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 31 04:35:10 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  15  8  .  2022-07-22  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.782  -1.1877   1.8168  -0.1574
 UOX  CA  C   CH1   0  -0.231  -1.2458   0.3925  -0.3684
 UOX  CB  C   CH2   0  -0.671  -0.2010  -0.4443   0.3876
 UOX  SE  SE  SE    0   0.689   1.6393  -0.0033  -0.1456
 UOX  OD  O   O     0  -0.800   2.5795  -0.9577   0.8093
 UOX  C   C   C     0   0.559  -2.6254  -0.1189   0.0256
 UOX  O   O   O     0  -0.426  -3.4302   0.5098   0.6596
 UOX  H1  H   HNH2  0   0.355  -1.0793   2.0498   0.8213
 UOX  H2  H   HNH2  0   0.365  -0.4203   2.2350  -0.6636
 UOX  H4  H   HCH1  0   0.299  -1.1329   0.2072  -1.4414
 UOX  H5  H   HCH2  0   0.301  -0.2750  -0.3017   1.4686
 UOX  H6  H   HCH2  0   0.302  -0.2997  -1.5096   0.1713
 UOX  O1  O   OH1   0  -0.592  -2.8253  -1.3590  -0.4015
 UOX  H3  H   H     0   0.147   1.5950   1.3139   0.5360
 UOX  H7  H   HOH1  0   0.486  -3.6938  -1.6778  -0.1126

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  1.645  0.020  1.645
 UOX  SE  CB  single  1.966  0.020  1.966
 UOX  O   C   double  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  single  1.327  0.020  1.327
 UOX  SE  H3  single  1.444  0.020  1.000
 UOX  O1  H7  single  0.832  0.020  0.971

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  107.94  3.000
 UOX  H2  N   CA  111.50  3.000
 UOX  H1  N   CA  111.94  3.000
 UOX  H4  CA  C   106.87  3.000
 UOX  H4  CA  CB  108.65  3.000
 UOX  C   CA  CB  110.50  1.500
 UOX  H4  CA  N   107.86  3.000
 UOX  CB  CA  N   110.40  1.500
 UOX  C   CA  N   111.00  2.800
 UOX  H6  CB  H5  108.50  3.000
 UOX  H6  CB  SE  104.47  3.000
 UOX  H5  CB  SE  107.60  3.000
 UOX  H6  CB  CA  111.86  3.000
 UOX  H5  CB  CA  111.68  3.000
 UOX  SE  CB  CA  112.37  3.000
 UOX  H3  SE  OD  105.39  3.000
 UOX  H3  SE  CB   92.67  3.000
 UOX  OD  SE  CB  104.32  3.000
 UOX  O1  C   O   123.90  3.000
 UOX  O1  C   CA  111.53  3.000
 UOX  O   C   CA  120.80  1.700
 UOX  H7  O1  C   110.28  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
 UOX  CONST_01  H7  O1  C   CA  180.00   0.0  0
 UOX  Var_01    OD  SE  CB  CA  177.98  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-1  H7  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

