# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 01:28:55 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (2~{R},4~{R})-2-methyl-1,3-selenazolidine-2,4-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]1(N[C@@H](C[Se]1)C(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
 9SE  9SE  '(2~{R},4~{R})-2-methyl-1,3-selenazolidine-2,4-dicarboxylic acid'  ligand  21  12  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_9SE
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
 9SE  C2   C   CR5   0  -0.151  -0.8461   0.5323   0.5207
 9SE  C5   C   CH2   0  -0.592   1.0997  -1.1288  -0.5348
 9SE  O    O   O     0  -0.429  -1.5724   2.1492  -1.1045
 9SE  C2A  C   C     0   0.573  -1.8627   1.3106  -0.2895
 9SE  OXT  O   OH1   0  -0.581  -3.0991   0.9487  -0.0008
 9SE  N3   N   NR15  0  -0.561   0.4564   1.0731   0.3260
 9SE  C2B  C   CH3   0  -0.617  -1.2124   0.4198   1.9921
 9SE  SE1  SE  SE    0   0.055  -0.8296  -1.3341  -0.3258
 9SE  C4   C   CR15  0  -0.213   1.4628   0.0451   0.4037
 9SE  C4A  C   C     0   0.545   2.8230   0.6030   0.0464
 9SE  O41  O   OH1   0  -0.585   3.7749  -0.2797   0.2945
 9SE  O42  O   O     0  -0.426   3.0114   1.6940  -0.4258
 9SE  H1   H   HCH2  0   0.293   1.6048  -2.0487  -0.2425
 9SE  H2   H   HCH2  0   0.283   1.3435  -0.9018  -1.5739
 9SE  H3   H   HOH1  0   0.492  -3.7320   1.4373  -0.5498
 9SE  H4   H   HNR5  0   0.371   0.5138   1.5543  -0.5660
 9SE  H6   H   HCH3  0   0.250  -0.4279  -0.0971   2.5434
 9SE  H7   H   HCH3  0   0.250  -1.3257   1.4178   2.4207
 9SE  H8   H   HCH3  0   0.249  -2.1391  -0.1277   2.1477
 9SE  H9   H   HCR5  0   0.304   1.5153  -0.3398   1.4254
 9SE  H10  H   HOH1  0   0.490   4.6410   0.0654   0.0271

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
 9SE  O    C2A  double  1.205  0.020  1.205
 9SE  OXT  C2A  single  1.320  0.020  1.320
 9SE  C2A  C2   single  1.515  0.020  1.515
 9SE  N3   C2   single  1.424  0.020  1.424
 9SE  N3   C4   single  1.441  0.020  1.441
 9SE  C2B  C2   single  1.520  0.020  1.520
 9SE  C2   SE1  single  2.049  0.020  2.049
 9SE  O42  C4A  double  1.204  0.020  1.204
 9SE  C4A  C4   single  1.513  0.020  1.513
 9SE  C4A  O41  single  1.322  0.020  1.322
 9SE  C4   C5   single  1.546  0.020  1.546
 9SE  SE1  C5   single  1.951  0.020  1.951
 9SE  C5   H1   single  0.970  0.020  1.090
 9SE  C5   H2   single  0.970  0.020  1.090
 9SE  OXT  H3   single  0.850  0.020  0.980
 9SE  N3   H4   single  0.890  0.020  1.040
 9SE  C2B  H6   single  0.970  0.020  1.090
 9SE  C2B  H7   single  0.970  0.020  1.090
 9SE  C2B  H8   single  0.970  0.020  1.090
 9SE  C4   H9   single  0.970  0.020  1.090
 9SE  O41  H10  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
 9SE  SE1  C2   C2B  109.53  3.000
 9SE  SE1  C2   N3   106.38  3.000
 9SE  C2B  C2   N3   112.39  3.000
 9SE  SE1  C2   C2A  104.62  3.000
 9SE  C2B  C2   C2A  113.19  3.000
 9SE  N3   C2   C2A  110.22  3.000
 9SE  H2   C5   H1   109.12  3.000
 9SE  H2   C5   C4   111.56  3.000
 9SE  H1   C5   C4   111.68  3.000
 9SE  H2   C5   SE1  110.17  3.000
 9SE  H1   C5   SE1  109.93  3.000
 9SE  C4   C5   SE1  104.30  3.000
 9SE  OXT  C2A  O    124.36  3.000
 9SE  OXT  C2A  C2   111.75  3.000
 9SE  O    C2A  C2   123.89  3.000
 9SE  H3   OXT  C2A  110.44  3.000
 9SE  H4   N3   C4   110.25  3.000
 9SE  H4   N3   C2   110.61  3.000
 9SE  C4   N3   C2   111.14  3.000
 9SE  H8   C2B  H7   108.40  3.000
 9SE  H8   C2B  H6   107.60  3.000
 9SE  H7   C2B  H6   108.04  3.000
 9SE  H8   C2B  C2   112.40  3.000
 9SE  H7   C2B  C2   109.70  3.000
 9SE  H6   C2B  C2   110.57  3.000
 9SE  C5   SE1  C2    87.50  3.000
 9SE  H9   C4   C4A  107.90  3.000
 9SE  H9   C4   N3   109.59  3.000
 9SE  C4A  C4   N3   110.62  3.000
 9SE  H9   C4   C5   108.14  3.000
 9SE  C4A  C4   C5   110.35  3.000
 9SE  N3   C4   C5   110.18  3.000
 9SE  O42  C4A  O41  124.49  3.000
 9SE  O41  C4A  C4   110.91  3.000
 9SE  O42  C4A  C4   124.59  3.000
 9SE  H10  O41  C4A  110.72  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
 9SE  CONST_01  H3   OXT  C2A  C2  180.00   0.0  0
 9SE  CONST_02  H10  O41  C4A  C4  180.00   0.0  0
 9SE  Var_01    C4   C5   SE1  C2   16.24  30.0  1

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
 9SE  chir_01  C2  N3  C2B  SE1  positiv
 9SE  chir_02  C4  N3  C4A  C5   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
 9SE  plan-1  C2   0.020
 9SE  plan-1  O    0.020
 9SE  plan-1  C2A  0.020
 9SE  plan-1  OXT  0.020
 9SE  plan-1  H3   0.020
 9SE  plan-2  C4   0.020
 9SE  plan-2  C4A  0.020
 9SE  plan-2  O41  0.020
 9SE  plan-2  O42  0.020
 9SE  plan-2  H10  0.020

