# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 11:04:17 2022
#   Inital geometry file: a 50 line input string
#   Ligand name: 3-(4-hydroxy-1,2,5-thiadiazol-3-yl)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1nsnc1O)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
 S2P  S2P  3-(4-hydroxy-1,2,5-thiadiazol-3-yl)-L-alanine  L-peptide  18  12  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_S2P
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
 S2P  CD2   C  CR5    0   0.410  102.2559  27.0610  40.3242
 S2P  CG    C  CR5    0   0.149  102.1733  25.9395  41.2364
 S2P  ND1   N  N      0  -0.501  102.2049  24.8010  40.6059
 S2P  CB    C  CH2    0  -0.522  102.1012  26.0504  42.7211
 S2P  CA    C  CH1    0  -0.222  103.4619  26.4067  43.3414
 S2P  OD2   O  OH1    0  -0.588  102.2413  28.3463  40.6645
 S2P  C     C  C      0   0.424  103.3310  26.5846  44.8809
 S2P  OXT   O  OC    -1  -0.590  104.2541  26.1233  45.5780
 S2P  NE2   N  N      0  -0.541  102.3489  26.7311  39.0738
 S2P  N     N  NH2    0  -0.807  104.4429  25.3941  42.9996
 S2P  SE1   S  S2     0   0.502  102.3351  25.0900  38.9932
 S2P  HB    H  HCH2   0   0.254  101.3625  26.8045  43.0021
 S2P  HBA   H  HCH2   0   0.259  101.7596  25.0975  43.1270
 S2P  HA    H  HCH1   0   0.207  103.7518  27.4036  42.9666
 S2P  HOD2  H  HOH1   0   0.492  102.1274  28.4585  41.6157
 S2P  H     H  HNH2   0   0.336  104.8824  25.6078  42.1144
 S2P  H2    H  HNH2   0   0.339  105.1680  25.4138  43.7048
 S2P  O     O  O      0  -0.599  102.3293  27.2113  45.2734

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
 S2P  CD2  CG    aromatic  1.448  0.020  1.448
 S2P  CD2  OD2   single    1.330  0.020  1.330
 S2P  CD2  NE2   aromatic  1.296  0.020  1.296
 S2P  CG   ND1   aromatic  1.302  0.020  1.302
 S2P  CG   CB    single    1.491  0.020  1.491
 S2P  ND1  SE1   aromatic  1.643  0.020  1.643
 S2P  CB   CA    single    1.521  0.033  1.521
 S2P  CA   C     single    1.525  0.021  1.525
 S2P  CA   N     single    1.458  0.019  1.458
 S2P  O    C     deloc     1.231  0.020  1.231
 S2P  C    OXT   deloc     1.245  0.020  1.245
 S2P  NE2  SE1   aromatic  1.643  0.020  1.643
 S2P  CB   HB    single    0.970  0.020  1.090
 S2P  CB   HBA   single    0.970  0.020  1.090
 S2P  CA   HA    single    0.970  0.020  0.970
 S2P  OD2  HOD2  single    0.850  0.020  0.980
 S2P  N    H     single    0.860  0.020  0.860
 S2P  N    H2    single    0.890  0.020  1.040

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
 S2P  NE2   CD2  OD2  119.57  3.000
 S2P  NE2   CD2  CG   114.49  3.000
 S2P  OD2   CD2  CG   125.93  3.000
 S2P  CB    CG   ND1  123.28  3.000
 S2P  CB    CG   CD2  124.93  3.000
 S2P  ND1   CG   CD2  111.77  3.000
 S2P  SE1   ND1  CG   108.87  3.000
 S2P  HBA   CB   HB   107.19  3.000
 S2P  HBA   CB   CA   109.24  3.000
 S2P  HB    CB   CA   109.56  3.000
 S2P  HBA   CB   CG   108.71  3.000
 S2P  HB    CB   CG   109.89  3.000
 S2P  CA    CB   CG   112.11  3.000
 S2P  HA    CA   N    110.00  3.000
 S2P  HA    CA   C    109.00  3.000
 S2P  N     CA   C    111.00  2.800
 S2P  HA    CA   CB   109.00  3.000
 S2P  N     CA   CB   110.40  1.500
 S2P  C     CA   CB   110.50  1.500
 S2P  HOD2  OD2  CD2  111.48  3.000
 S2P  OXT   C    O    127.33  3.000
 S2P  OXT   C    CA   116.70  3.000
 S2P  O     C    CA   120.80  1.700
 S2P  SE1   NE2  CD2  107.51  3.000
 S2P  H2    N    H    107.14  3.000
 S2P  H2    N    CA   107.87  3.000
 S2P  H     N    CA   114.00  3.000
 S2P  NE2   SE1  ND1   97.36  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
 S2P  CONST_01  SE1  ND1  CG   CD2    0.00   0.0  0
 S2P  CONST_02  ND1  SE1  NE2  CD2    0.00   0.0  0
 S2P  CONST_03  SE1  NE2  CD2  CG     0.00   0.0  0
 S2P  CONST_04  NE2  SE1  ND1  CG     0.00   0.0  0
 S2P  CONST_05  NE2  CD2  CG   ND1    0.00   0.0  0
 S2P  CONST_06  OD2  CD2  CG   ND1  180.00   0.0  0
 S2P  CONST_07  NE2  CD2  CG   CB   180.00   0.0  0
 S2P  CONST_08  SE1  ND1  CG   CB   180.00   0.0  0
 S2P  CONST_09  SE1  NE2  CD2  OD2  180.00   0.0  0
 S2P  Var_01    CA   CB   CG   CD2  -75.41  30.0  2

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
 S2P  chir_01  CA  CB  C  N  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
 S2P  plan-1  CD2  0.020
 S2P  plan-1  CG   0.020
 S2P  plan-1  ND1  0.020
 S2P  plan-1  CB   0.020
 S2P  plan-1  OD2  0.020
 S2P  plan-1  NE2  0.020
 S2P  plan-1  SE1  0.020
 S2P  plan-2  CA   0.020
 S2P  plan-2  C    0.020
 S2P  plan-2  OXT  0.020
 S2P  plan-2  O    0.020

