# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 14:53:58 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  23  14  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.778   3.5818   0.7571  -0.5427
 SIC  C3   C  CR15   0  -0.231   2.6756  -0.2221   0.0204
 SIC  C2   C  CR5    0   0.554   1.3870  -0.3835  -0.7801
 SIC  O2   O  O      0  -0.438   1.3122  -0.6499  -1.9562
 SIC  C4   C  CH2    0  -0.596   2.1892   0.1555   1.4149
 SIC  C5   C  CR5    0   0.566   0.6911   0.2474   1.3092
 SIC  O5   O  O      0  -0.437  -0.0779   0.5916   2.1729
 SIC  N1   N  NR5    0  -0.518   0.3128  -0.1452   0.0427
 SIC  CA   C  CH1    0  -0.246  -1.0433  -0.0059  -0.4459
 SIC  CB   C  CH2    0  -0.550  -2.0382  -0.8750   0.3088
 SIC  SG   S  S2     0  -0.263  -1.3729  -2.5714   0.4383
 SIC  C    C  C      0   0.445  -1.4515   1.4964  -0.4904
 SIC  O    O  O      0  -0.586  -0.5211   2.3146  -0.5369
 SIC  HN   H  HNH2   0   0.359   3.8671   0.4716  -1.4710
 SIC  HNA  H  HNH2   0   0.350   3.1138   1.6500  -0.6486
 SIC  H3   H  HCR5   0   0.297   3.1843  -1.1888   0.0314
 SIC  H4   H  HCH2   0   0.304   2.4517  -0.5871   2.1696
 SIC  H4A  H  HCH2   0   0.297   2.5940   1.1120   1.7489
 SIC  HA   H  HCH1   0   0.284  -1.0176  -0.3562  -1.4815
 SIC  HB   H  HCH2   0   0.272  -2.2481  -0.4843   1.3012
 SIC  HBA  H  HCH2   0   0.282  -2.9671  -0.9020  -0.2549
 SIC  HSG  H  HSH1   0   0.222  -2.5070  -3.1673   0.8220
 SIC  OXT  O  OC    -1  -0.592  -2.6744   1.7136  -0.5222

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  1.448  0.020  1.448
 SIC  C3  H3   single  0.970  0.020  1.090
 SIC  C2  C3   single  1.526  0.020  1.526
 SIC  C2  O2   double  1.208  0.020  1.208
 SIC  C4  C3   single  1.524  0.020  1.524
 SIC  C4  H4   single  0.970  0.020  1.090
 SIC  C4  H4A  single  0.970  0.020  1.090
 SIC  C5  C4   single  1.505  0.020  1.505
 SIC  C5  N1   single  1.379  0.020  1.379
 SIC  O5  C5   double  1.207  0.020  1.207
 SIC  N1  C2   single  1.374  0.020  1.374
 SIC  CA  N1   single  1.448  0.020  1.448
 SIC  CA  C    single  1.557  0.020  1.557
 SIC  CA  HA   single  0.970  0.020  1.090
 SIC  CB  CA   single  1.521  0.020  1.521
 SIC  CB  HB   single  0.970  0.020  1.090
 SIC  CB  HBA  single  0.970  0.020  1.090
 SIC  SG  CB   single  1.827  0.020  1.827
 SIC  SG  HSG  single  1.200  0.020  1.300
 SIC  C   O    deloc   1.240  0.020  1.240
 SIC  C   OXT  deloc   1.242  0.020  1.242

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  106.43  3.000
 SIC  HNA  N   C3  110.33  3.000
 SIC  HN   N   C3  110.02  3.000
 SIC  H3   C3  C4  111.01  3.000
 SIC  C4   C3  C2  103.69  3.000
 SIC  H3   C3  C2  107.76  3.000
 SIC  C4   C3  N   112.82  3.000
 SIC  C2   C3  N   113.33  3.000
 SIC  H3   C3  N   108.12  3.000
 SIC  N1   C2  O2  124.94  3.000
 SIC  N1   C2  C3  109.14  3.000
 SIC  O2   C2  C3  125.90  3.000
 SIC  H4A  C4  H4  107.20  3.000
 SIC  H4A  C4  C5  109.71  3.000
 SIC  H4   C4  C5  109.25  3.000
 SIC  C5   C4  C3  105.58  3.000
 SIC  H4A  C4  C3  112.26  3.000
 SIC  H4   C4  C3  112.80  3.000
 SIC  N1   C5  O5  124.33  3.000
 SIC  O5   C5  C4  126.99  3.000
 SIC  N1   C5  C4  108.68  3.000
 SIC  CA   N1  C5  122.64  3.000
 SIC  CA   N1  C2  123.14  3.000
 SIC  C5   N1  C2  112.64  3.000
 SIC  HA   CA  C   106.74  3.000
 SIC  HA   CA  CB  107.59  3.000
 SIC  C    CA  CB  113.19  3.000
 SIC  CB   CA  N1  112.96  3.000
 SIC  HA   CA  N1  105.47  3.000
 SIC  C    CA  N1  110.36  3.000
 SIC  HBA  CB  HB  108.50  3.000
 SIC  HBA  CB  SG  108.97  3.000
 SIC  HB   CB  SG  109.84  3.000
 SIC  SG   CB  CA  109.11  3.000
 SIC  HBA  CB  CA  108.41  3.000
 SIC  HB   CB  CA  111.96  3.000
 SIC  HSG  SG  CB   97.19  3.000
 SIC  OXT  C   O   128.48  3.000
 SIC  OXT  C   CA  115.30  3.000
 SIC  O    C   CA  116.17  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  Var_01    N1  C5  C4  C3    4.86  30.0  1
 SIC  Var_02    C4  C5  N1  C2   -5.52  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

