# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 21:15:15 2020
#   Inital geometry file: a 41 line input string
#   Ligand name: (3S)-3-aminopyrrolidine-2,5-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1CC(=O)NC1=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
 SNN  SNN  (3S)-3-aminopyrrolidine-2,5-dione  L-peptide  14  8  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SNN
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
 SNN  N1    N  NH1   0  -0.675   0.6299  -1.0460   0.0738
 SNN  C2    C  C     0   0.540  -0.7020  -0.7120   0.0926
 SNN  C3    C  CH1   0  -0.224  -0.8154   0.7436  -0.3559
 SNN  N3    N  NH2   0  -0.781  -1.7744   1.5511   0.3516
 SNN  C4    C  CH2   0  -0.599   0.6217   1.2538  -0.2639
 SNN  C5    C  C     0   0.545   1.4730   0.0134  -0.1721
 SNN  O2    O  O     0  -0.422  -1.6028  -1.4536   0.3972
 SNN  O5    O  O     0  -0.426   2.6727  -0.0714  -0.2639
 SNN  HN    H  HNH1  0   0.423   0.9682  -1.9824   0.2587
 SNN  H3    H  HCH1  0   0.305  -1.1131   0.7054  -1.4091
 SNN  HN31  H  HNH2  0   0.361  -2.7124   1.2131   0.1813
 SNN  HN32  H  HNH2  0   0.352  -1.6221   1.4939   1.3511
 SNN  H41   H  HCH2  0   0.301   0.9262   1.8790  -1.1015
 SNN  H42   H  HCH2  0   0.301   0.7721   1.8351   0.6505

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
 SNN  N1  C2    single  1.373  0.020  1.373
 SNN  N1  C5    single  1.376  0.020  1.376
 SNN  N1  HN    single  0.860  0.020  1.020
 SNN  C2  C3    single  1.527  0.020  1.527
 SNN  C2  O2    double  1.206  0.020  1.206
 SNN  C3  N3    single  1.440  0.020  1.440
 SNN  C3  C4    single  1.528  0.020  1.528
 SNN  C3  H3    single  0.970  0.020  1.090
 SNN  N3  HN31  single  0.890  0.020  1.040
 SNN  N3  HN32  single  0.890  0.020  1.040
 SNN  C4  C5    single  1.507  0.020  1.507
 SNN  C4  H41   single  0.970  0.020  1.090
 SNN  C4  H42   single  0.970  0.020  1.090
 SNN  C5  O5    double  1.206  0.020  1.206

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
 SNN  HN    N1  C5    122.67  3.000
 SNN  HN    N1  C2    123.12  3.000
 SNN  C5    N1  C2    114.17  3.000
 SNN  O2    C2  C3    127.21  3.000
 SNN  O2    C2  N1    125.34  3.000
 SNN  C3    C2  N1    107.44  3.000
 SNN  H3    C3  C4    108.98  3.000
 SNN  H3    C3  N3    108.13  3.000
 SNN  C4    C3  N3    114.19  3.000
 SNN  H3    C3  C2    105.62  3.000
 SNN  C4    C3  C2    103.34  3.000
 SNN  N3    C3  C2    116.09  3.000
 SNN  HN32  N3  HN31  106.66  3.000
 SNN  HN32  N3  C3    110.68  3.000
 SNN  HN31  N3  C3    110.34  3.000
 SNN  H42   C4  H41   107.43  3.000
 SNN  H42   C4  C5    107.98  3.000
 SNN  H41   C4  C5    111.20  3.000
 SNN  H42   C4  C3    110.92  3.000
 SNN  H41   C4  C3    114.11  3.000
 SNN  C5    C4  C3    105.08  3.000
 SNN  O5    C5  C4    127.95  3.000
 SNN  O5    C5  N1    124.67  3.000
 SNN  C4    C5  N1    107.36  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
 SNN  CONST_01  C5  N1  C2  C3    0.00   0.0  0
 SNN  CONST_02  O2  C2  N1  C5  180.00   0.0  0
 SNN  CONST_03  HN  N1  C2  C3  180.00   0.0  0
 SNN  Var_01    C3  C4  C5  N1  -12.34  30.0  1
 SNN  Var_02    C4  C5  N1  C2    3.34  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
 SNN  chir_01  C3  C2  N3  C4  negativ

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
 SNN  plan-1  N1  0.020
 SNN  plan-1  C4  0.020
 SNN  plan-1  C5  0.020
 SNN  plan-1  O5  0.020
 SNN  plan-2  N1  0.020
 SNN  plan-2  C2  0.020
 SNN  plan-2  C3  0.020
 SNN  plan-2  C5  0.020
 SNN  plan-2  O2  0.020
 SNN  plan-2  HN  0.020

