# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 03:29:36 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: (2R)-2-[(3S)-3-amino-2,5-dioxopyrrolidin-1-yl]-3-sulfanylpropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1CC(=O)N([C@@H](CS)C(O)=O)C1=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
 SIC  SIC  '(2R)-2-[(3S)-3-amino-2,5-dioxopyrrolidin-1-yl]-3-sulfanylpropanoic acid'  L-peptide  24  14  .  2022-07-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SIC
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
 SIC  N    N  NH2   0  -0.780   3.7778   0.3122  -0.5358
 SIC  C3   C  CR15  0  -0.223   2.5837  -0.2616   0.0229
 SIC  C2   C  CR5   0   0.557   1.3297  -0.1755  -0.8396
 SIC  O2   O  O     0  -0.413   1.2519  -0.3135  -2.0333
 SIC  C4   C  CH2   0  -0.595   2.1460   0.3676   1.3417
 SIC  C5   C  CR5   0   0.573   0.6440   0.3766   1.2902
 SIC  O5   O  O     0  -0.422  -0.1300   0.6311   2.1775
 SIC  N1   N  NR5   0  -0.543   0.2574   0.0699  -0.0027
 SIC  CA   C  CH1   0  -0.235  -1.1125   0.1259  -0.4484
 SIC  CB   C  CH2   0  -0.557  -2.0069  -0.9006   0.2475
 SIC  SG   S  S2    0  -0.237  -1.1418  -2.5059   0.2351
 SIC  C    C  C     0   0.575  -1.6170   1.5595  -0.3403
 SIC  O    O  O     0  -0.421  -0.8930   2.5121  -0.2361
 SIC  HN   H  HNH2  0   0.363   4.0478  -0.1848  -1.3744
 SIC  HNA  H  HNH2  0   0.354   3.6221   1.2765  -0.8026
 SIC  H3   H  HCR5  0   0.309   2.7592  -1.3317   0.1772
 SIC  H4   H  HCH2  0   0.306   2.5060  -0.1554   2.2258
 SIC  H4A  H  HCH2  0   0.306   2.4830   1.4061   1.4125
 SIC  HA   H  HCH1  0   0.340  -1.0981  -0.1105  -1.5179
 SIC  HB   H  HCH2  0   0.289  -2.2378  -0.6082   1.2688
 SIC  HBA  H  HCH2  0   0.305  -2.9362  -0.9969  -0.3090
 SIC  HSG  H  HSH1  0   0.237  -2.2119  -3.2591   0.5084
 SIC  OXT  O  OH1   0  -0.581  -2.9320   1.6176  -0.4328
 SIC  HXT  H  HOH1  0   0.493  -3.2324   2.5396  -0.4113

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
 SIC  N    HN   single  0.890  0.020  1.040
 SIC  N    HNA  single  0.890  0.020  1.040
 SIC  C3   N    single  1.438  0.020  1.438
 SIC  C3   H3   single  0.970  0.020  1.090
 SIC  C2   C3   single  1.524  0.020  1.524
 SIC  C2   O2   double  1.204  0.020  1.204
 SIC  C4   C3   single  1.525  0.020  1.525
 SIC  C4   H4   single  0.970  0.020  1.090
 SIC  C4   H4A  single  0.970  0.020  1.090
 SIC  C5   C4   single  1.503  0.020  1.503
 SIC  C5   N1   single  1.384  0.020  1.384
 SIC  O5   C5   double  1.205  0.020  1.205
 SIC  N1   C2   single  1.382  0.020  1.382
 SIC  CA   N1   single  1.442  0.020  1.442
 SIC  CA   C    single  1.524  0.020  1.524
 SIC  CA   HA   single  0.970  0.020  1.090
 SIC  CB   CA   single  1.529  0.020  1.529
 SIC  CB   HB   single  0.970  0.020  1.090
 SIC  CB   HBA  single  0.970  0.020  1.090
 SIC  SG   CB   single  1.824  0.020  1.824
 SIC  SG   HSG  single  1.200  0.020  1.300
 SIC  C    O    double  1.201  0.020  1.201
 SIC  C    OXT  single  1.320  0.020  1.320
 SIC  OXT  HXT  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
 SIC  HNA  N    HN  106.89  3.000
 SIC  HNA  N    C3  110.77  3.000
 SIC  HN   N    C3  110.35  3.000
 SIC  H3   C3   C4  109.09  3.000
 SIC  C4   C3   C2  103.29  3.000
 SIC  H3   C3   C2  105.46  3.000
 SIC  C4   C3   N   114.19  3.000
 SIC  C2   C3   N   116.16  3.000
 SIC  H3   C3   N   108.15  3.000
 SIC  N1   C2   O2  124.78  3.000
 SIC  N1   C2   C3  107.80  3.000
 SIC  O2   C2   C3  127.42  3.000
 SIC  H4A  C4   H4  107.55  3.000
 SIC  H4A  C4   C5  107.72  3.000
 SIC  H4   C4   C5  111.18  3.000
 SIC  C5   C4   C3  105.05  3.000
 SIC  H4A  C4   C3  111.04  3.000
 SIC  H4   C4   C3  114.15  3.000
 SIC  N1   C5   O5  123.74  3.000
 SIC  O5   C5   C4  128.18  3.000
 SIC  N1   C5   C4  108.05  3.000
 SIC  CA   N1   C5  123.07  3.000
 SIC  CA   N1   C2  123.84  3.000
 SIC  C5   N1   C2  112.85  3.000
 SIC  HA   CA   C   106.06  3.000
 SIC  HA   CA   CB  107.88  3.000
 SIC  C    CA   CB  113.94  3.000
 SIC  CB   CA   N1  112.90  3.000
 SIC  HA   CA   N1  106.31  3.000
 SIC  C    CA   N1  109.22  3.000
 SIC  HBA  CB   HB  108.85  3.000
 SIC  HBA  CB   SG  108.90  3.000
 SIC  HB   CB   SG  110.12  3.000
 SIC  SG   CB   CA  108.08  3.000
 SIC  HBA  CB   CA  109.05  3.000
 SIC  HB   CB   CA  111.79  3.000
 SIC  HSG  SG   CB   96.59  3.000
 SIC  OXT  C    O   124.88  3.000
 SIC  OXT  C    CA  111.50  3.000
 SIC  O    C    CA  123.56  3.000
 SIC  HXT  OXT  C   110.43  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
 SIC  CONST_01  C5   N1   C2  C3    0.00   0.0  0
 SIC  CONST_02  CA   N1   C2  C3  180.00   0.0  0
 SIC  CONST_03  C5   N1   C2  O2  180.00   0.0  0
 SIC  CONST_04  CA   N1   C2  O2    0.00   0.0  0
 SIC  CONST_05  HXT  OXT  C   CA  180.00   0.0  0
 SIC  Var_01    N1   C5   C4  C3  -11.59  30.0  1
 SIC  Var_02    C4   C5   N1  C2    1.23  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
 SIC  chir_01  C3  N   C2  C4  positiv
 SIC  chir_02  CA  N1  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
 SIC  plan-1  C4   0.020
 SIC  plan-1  C5   0.020
 SIC  plan-1  O5   0.020
 SIC  plan-1  N1   0.020
 SIC  plan-2  C3   0.020
 SIC  plan-2  C2   0.020
 SIC  plan-2  O2   0.020
 SIC  plan-2  C5   0.020
 SIC  plan-2  N1   0.020
 SIC  plan-2  CA   0.020
 SIC  plan-3  CA   0.020
 SIC  plan-3  C    0.020
 SIC  plan-3  O    0.020
 SIC  plan-3  OXT  0.020
 SIC  plan-3  HXT  0.020

