# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 10:39:20 2020
#   Inital geometry file: a 45 line input string
#   Ligand name: 3-selenino-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](C[Se](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
 SE7  SE7  '3-selenino-L-alanine     '  L-peptide  15  9  .  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_SE7
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
 SE7  N    N   NH2    0  -0.786   1.4279   1.6648   0.5933
 SE7  CA   C   CH1    0  -0.237   1.3492   0.2347   0.3784
 SE7  C    C   C      0   0.420   2.6974  -0.3320  -0.1503
 SE7  O    O   O      0  -0.592   3.5329   0.4861  -0.5700
 SE7  CB   C   CH2    0  -0.658   0.2637  -0.2270  -0.6016
 SE7  SEG  SE  SE     0   1.070  -1.5274   0.1708   0.0618
 SE7  OD1  O   O      0  -0.776  -1.6044  -0.6994   1.4291
 SE7  OD2  O   O      0  -0.779  -2.2778  -0.8303  -1.2090
 SE7  OXT  O   OC    -1  -0.613   2.7995  -1.5738  -0.1293
 SE7  H    H   HNH2   0   0.336   1.6683   2.1332  -0.2703
 SE7  H2   H   HNH2   0   0.338   0.5499   2.0554   0.9113
 SE7  HA   H   HCH1   0   0.236   1.1565  -0.2436   1.3444
 SE7  HB2  H   HCH2   0   0.275   0.3721   0.2667  -1.5725
 SE7  HB3  H   HCH2   0   0.286   0.2987  -1.3095  -0.7470
 SE7  HD2  H   H      0   0.482  -3.1952  -0.5495  -1.3412

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
 SE7  N    CA   single  1.458  0.020  1.458
 SE7  N    H    single  0.868  0.019  0.868
 SE7  N    H2   single  0.890  0.020  1.040
 SE7  CA   C    single  1.525  0.033  1.525
 SE7  CA   CB   single  1.521  0.020  1.521
 SE7  CA   HA   single  0.939  0.021  0.939
 SE7  C    O    deloc   1.231  0.020  1.231
 SE7  C    OXT  deloc   1.246  0.020  1.246
 SE7  CB   SEG  single  1.951  0.020  1.951
 SE7  CB   HB2  single  0.970  0.020  1.090
 SE7  CB   HB3  single  0.970  0.020  1.090
 SE7  SEG  OD1  double  1.623  0.020  1.623
 SE7  SEG  OD2  single  1.783  0.020  1.783
 SE7  OD2  HD2  single  0.850  0.020  0.980

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
 SE7  H2   N    H    107.20  3.000
 SE7  H2   N    CA   112.37  3.000
 SE7  H    N    CA   114.00  3.000
 SE7  HA   CA   CB   109.00  3.000
 SE7  HA   CA   C    110.00  3.000
 SE7  CB   CA   C    110.50  1.500
 SE7  HA   CA   N    110.00  3.000
 SE7  CB   CA   N    110.40  1.500
 SE7  C    CA   N    111.00  2.800
 SE7  OXT  C    O    127.35  3.000
 SE7  OXT  C    CA   114.20  3.000
 SE7  O    C    CA   120.80  1.700
 SE7  HB3  CB   HB2  109.00  3.000
 SE7  HB3  CB   SEG  106.06  3.000
 SE7  HB2  CB   SEG  107.49  3.000
 SE7  HB3  CB   CA   111.14  3.000
 SE7  HB2  CB   CA   111.15  3.000
 SE7  SEG  CB   CA   111.78  3.000
 SE7  OD2  SEG  OD1  106.22  3.000
 SE7  OD2  SEG  CB    91.69  3.000
 SE7  OD1  SEG  CB   102.75  3.000
 SE7  HD2  OD2  SEG  109.46  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
 SE7  Var_01  OD1  SEG  CB  CA  -61.99  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
 SE7  chir_01  CA  N  C  CB  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
 SE7  plan-1  CA   0.020
 SE7  plan-1  C    0.020
 SE7  plan-1  O    0.020
 SE7  plan-1  OXT  0.020
 SE7  plan-2  CB   0.020
 SE7  plan-2  SEG  0.020
 SE7  plan-2  OD1  0.020
 SE7  plan-2  OD2  0.020

