# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 16:58:28 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  19  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   CT     0  -0.128  -0.8340   0.5525   0.5281
 9SE  C5   C   CH2    0  -0.590   1.1108  -1.1528  -0.4883
 9SE  O    O   O      0  -0.596  -1.4156   2.1964  -1.0989
 9SE  C2A  C   C      0   0.437  -1.8680   1.3888  -0.2654
 9SE  OXT  O   OC    -1  -0.597  -3.0631   1.1627  -0.0088
 9SE  N3   N   NH1    0  -0.563   0.4855   1.0439   0.3784
 9SE  C2B  C   CH3    0  -0.620  -1.2238   0.3657   1.9832
 9SE  SE1  SE  SE     0  -0.078  -0.8338  -1.3036  -0.3692
 9SE  C4   C   CH1    0  -0.201   1.4982   0.0219   0.4438
 9SE  C4A  C   C      0   0.405   2.8836   0.5543   0.0167
 9SE  O41  O   OC    -1  -0.609   3.8683  -0.0454   0.4863
 9SE  O42  O   O      0  -0.601   2.8930   1.4984  -0.7965
 9SE  H1   H   HCH2   0   0.259   1.5914  -2.0813  -0.1783
 9SE  H2   H   HCH2   0   0.249   1.3994  -0.9416  -1.5205
 9SE  H4   H   HNH1   0   0.338   0.5636   1.5550  -0.4942
 9SE  H6   H   HCH3   0   0.222  -0.4964  -0.2425   2.5216
 9SE  H7   H   HCH3   0   0.221  -1.2743   1.3410   2.4759
 9SE  H8   H   HCH3   0   0.226  -2.1975  -0.1086   2.0811
 9SE  H9   H   HCH1   0   0.225   1.5623  -0.3656   1.4644

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  deloc   1.246  0.020  1.246
 9SE  OXT  C2A  deloc   1.243  0.020  1.243
 9SE  C2A  C2   single  1.549  0.020  1.549
 9SE  N3   C2   single  1.416  0.020  1.416
 9SE  N3   C4   single  1.440  0.020  1.440
 9SE  C2B  C2   single  1.518  0.020  1.518
 9SE  C2   SE1  single  2.062  0.020  2.062
 9SE  O42  C4A  deloc   1.246  0.020  1.246
 9SE  C4A  C4   single  1.544  0.020  1.544
 9SE  C4A  O41  deloc   1.245  0.020  1.245
 9SE  C4   C5   single  1.549  0.020  1.549
 9SE  SE1  C5   single  1.954  0.020  1.954
 9SE  C5   H1   single  0.970  0.020  1.090
 9SE  C5   H2   single  0.970  0.020  1.090
 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

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  107.84  3.000
 9SE  SE1  C2   N3   105.45  3.000
 9SE  C2B  C2   N3   112.54  3.000
 9SE  SE1  C2   C2A  105.27  3.000
 9SE  C2B  C2   C2A  112.72  3.000
 9SE  N3   C2   C2A  112.37  3.000
 9SE  H2   C5   H1   108.47  3.000
 9SE  H2   C5   C4   110.86  3.000
 9SE  H1   C5   C4   111.37  3.000
 9SE  H2   C5   SE1  109.60  3.000
 9SE  H1   C5   SE1  110.83  3.000
 9SE  C4   C5   SE1  105.71  3.000
 9SE  OXT  C2A  O    127.24  3.000
 9SE  OXT  C2A  C2   115.97  3.000
 9SE  O    C2A  C2   116.77  3.000
 9SE  H4   N3   C4   110.03  3.000
 9SE  H4   N3   C2   109.72  3.000
 9SE  C4   N3   C2   113.84  3.000
 9SE  H8   C2B  H7   107.88  3.000
 9SE  H8   C2B  H6   108.03  3.000
 9SE  H7   C2B  H6   107.80  3.000
 9SE  H8   C2B  C2   111.71  3.000
 9SE  H7   C2B  C2   109.51  3.000
 9SE  H6   C2B  C2   111.76  3.000
 9SE  C5   SE1  C2    87.54  3.000
 9SE  H9   C4   C4A  109.13  3.000
 9SE  H9   C4   N3   109.57  3.000
 9SE  C4A  C4   N3   111.93  3.000
 9SE  H9   C4   C5   107.92  3.000
 9SE  C4A  C4   C5   108.63  3.000
 9SE  N3   C4   C5   109.57  3.000
 9SE  O42  C4A  O41  127.24  3.000
 9SE  O41  C4A  C4   116.05  3.000
 9SE  O42  C4A  C4   116.64  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  Var_01  C4  C5  SE1  C2  14.02  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-2  C4   0.020
 9SE  plan-2  C4A  0.020
 9SE  plan-2  O41  0.020
 9SE  plan-2  O42  0.020

