# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 22:18:56 2020
#   Inital geometry file: a 58 line input string
#   Ligand name: (3S,5S,7aR)-5-(sulfanylmethyl)tetrahydro[1,3]thiazolo[4,3-b][1,3]thiazole-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H]1CS[C@@H]2CS[C@@H](CS)N12
#
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
 3R9  3R9  '(3S,5S,7aR)-5-(sulfanylmethyl)tetrahydro[1,3]thiazolo[4,3-b][1,3]thiazole-3-carboxylic acid'  ligand  24  13  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3R9
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
 3R9  OXT  O  OH1   0  -0.649  -3.0641  -1.9796   0.7203
 3R9  N    N  NR5   0  -0.395  -0.0714  -0.1313  -0.0355
 3R9  C    C  C     0   0.549  -1.8294  -1.5371   0.9074
 3R9  O    O  O     0  -0.441  -1.1788  -1.7619   1.8917
 3R9  CA   C  CH1   0  -0.137  -1.3343  -0.7672  -0.3079
 3R9  CB   C  CH2   0  -0.578  -2.3093   0.3185  -0.8107
 3R9  SAH  S  S2    0  -0.019  -1.8669   1.8189   0.1153
 3R9  CAM  C  CR15  0  -0.191  -0.2919   1.0411   0.7535
 3R9  CAF  C  CH2   0  -0.555   0.9136   1.9412   0.6248
 3R9  SAG  S  S2    0   0.031   1.4315   1.7763  -1.0977
 3R9  CAJ  C  CR15  0  -0.210   0.7331   0.0981  -1.2338
 3R9  CAD  C  CH2   0  -0.546   1.7886  -0.9837  -1.3593
 3R9  SAC  S  S2    0  -0.225   2.7557  -1.1233   0.1764
 3R9  H1   H  HOH1  0   0.482  -3.3446  -2.5141   1.4782
 3R9  H3   H  HCH1  0   0.277  -1.2037  -1.5181  -1.0955
 3R9  H4   H  HCH2  0   0.323  -2.1572   0.4807  -1.8777
 3R9  H5   H  HCH2  0   0.325  -3.3547   0.0612  -0.6575
 3R9  H6   H  HCR5  0   0.284  -0.4572   0.7786   1.7975
 3R9  H7   H  HCH2  0   0.281   0.6861   2.9827   0.8444
 3R9  H8   H  HCH2  0   0.319   1.7036   1.6031   1.2955
 3R9  H9   H  HCR5  0   0.304   0.1213   0.0785  -2.1457
 3R9  H10  H  HCH2  0   0.274   1.3045  -1.9394  -1.5689
 3R9  H11  H  HCH2  0   0.260   2.4592  -0.7737  -2.1910
 3R9  H12  H  HSH1  0   0.235   3.9669  -1.0083  -0.3771

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
 3R9  CAM  CAF  single  1.510  0.020  1.510
 3R9  CAM  SAH  single  1.869  0.020  1.869
 3R9  CAM  N    single  1.430  0.020  1.430
 3R9  CAF  SAG  single  1.806  0.020  1.806
 3R9  SAC  CAD  single  1.820  0.020  1.820
 3R9  SAH  CB   single  1.818  0.020  1.818
 3R9  CAD  CAJ  single  1.517  0.020  1.517
 3R9  N    CAJ  single  1.461  0.020  1.461
 3R9  N    CA   single  1.440  0.020  1.440
 3R9  CAJ  SAG  single  1.823  0.020  1.823
 3R9  O    C    double  1.201  0.020  1.201
 3R9  CB   CA   single  1.543  0.020  1.543
 3R9  CA   C    single  1.521  0.020  1.521
 3R9  C    OXT  single  1.325  0.020  1.325
 3R9  OXT  H1   single  0.850  0.020  0.980
 3R9  CA   H3   single  0.970  0.020  1.090
 3R9  CB   H4   single  0.970  0.020  1.090
 3R9  CB   H5   single  0.970  0.020  1.090
 3R9  CAM  H6   single  0.970  0.020  1.090
 3R9  CAF  H7   single  0.970  0.020  1.090
 3R9  CAF  H8   single  0.970  0.020  1.090
 3R9  CAJ  H9   single  0.970  0.020  1.090
 3R9  CAD  H10  single  0.970  0.020  1.090
 3R9  CAD  H11  single  0.970  0.020  1.090
 3R9  SAC  H12  single  1.200  0.020  1.300

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
 3R9  H1   OXT  C    110.09  3.000
 3R9  CAJ  N    CAM  114.11  3.000
 3R9  CAJ  N    CA   113.39  3.000
 3R9  CAM  N    CA   109.34  3.000
 3R9  CA   C    O    124.96  3.000
 3R9  CA   C    OXT  111.07  3.000
 3R9  O    C    OXT  123.92  3.000
 3R9  H3   CA   CB   108.85  3.000
 3R9  H3   CA   C    105.43  3.000
 3R9  CB   CA   C    114.25  3.000
 3R9  H3   CA   N    109.51  3.000
 3R9  C    CA   N    110.96  3.000
 3R9  CB   CA   N    107.76  3.000
 3R9  H5   CB   H4   107.90  3.000
 3R9  H5   CB   SAH  110.95  3.000
 3R9  H4   CB   SAH  109.99  3.000
 3R9  H5   CB   CA   113.26  3.000
 3R9  H4   CB   CA   109.60  3.000
 3R9  SAH  CB   CA   105.12  3.000
 3R9  CAM  SAH  CB    92.04  3.000
 3R9  H6   CAM  CAF  110.27  3.000
 3R9  H6   CAM  SAH  107.45  3.000
 3R9  CAF  CAM  SAH  113.31  3.000
 3R9  H6   CAM  N    110.77  3.000
 3R9  SAH  CAM  N    106.42  3.000
 3R9  CAF  CAM  N    108.58  3.000
 3R9  H8   CAF  H7   108.92  3.000
 3R9  H8   CAF  SAG  110.53  3.000
 3R9  H7   CAF  SAG  109.86  3.000
 3R9  H8   CAF  CAM  109.95  3.000
 3R9  H7   CAF  CAM  112.73  3.000
 3R9  SAG  CAF  CAM  104.81  3.000
 3R9  CAJ  SAG  CAF   92.60  3.000
 3R9  H9   CAJ  CAD  107.83  3.000
 3R9  H9   CAJ  SAG  106.97  3.000
 3R9  CAD  CAJ  SAG  113.34  3.000
 3R9  H9   CAJ  N    111.80  3.000
 3R9  SAG  CAJ  N    107.11  3.000
 3R9  CAD  CAJ  N    109.82  3.000
 3R9  H11  CAD  H10  107.18  3.000
 3R9  H11  CAD  SAC  109.39  3.000
 3R9  H10  CAD  SAC  109.30  3.000
 3R9  H11  CAD  CAJ  110.76  3.000
 3R9  H10  CAD  CAJ  109.37  3.000
 3R9  SAC  CAD  CAJ  110.77  3.000
 3R9  H12  SAC  CAD   97.21  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
 3R9  CONST_01  H1  OXT  C    CA    180.00   0.0  0
 3R9  Var_01    H4  CB   SAH  CAM  -106.48  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
 3R9  chir_01  CA   N    CB  C    positiv
 3R9  chir_02  CAM  SAH  N   CAF  negativ
 3R9  chir_03  CAJ  SAG  N   CAD  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
 3R9  plan-1  OXT  0.020
 3R9  plan-1  C    0.020
 3R9  plan-1  O    0.020
 3R9  plan-1  CA   0.020
 3R9  plan-1  H1   0.020

