# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 31 18:26:47 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: (3S,5S,7aR)-2,2-dimethyl-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: CC1(C)S[C@@H]2CS[C@@H](CS)N2[C@H]1C(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
 VC2  VC2  '(3S,5S,7aR)-2,2-dimethyl-5-(sulfanylmethyl)tetrahydro[1,3]thiazolo[4,3-b][1,3]thiazole-3-carboxylic acid'  ligand  30  15  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VC2
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
 VC2  O    O  O     0  -0.420   0.8948  -2.1347  -1.2258
 VC2  C    C  C     0   0.563   1.3203  -1.8155  -0.1462
 VC2  OXT  O  OH1   0  -0.590   2.1269  -2.5756   0.5825
 VC2  CA   C  CH1   0  -0.165   1.0006  -0.5027   0.5564
 VC2  N    N  NR5   0  -0.410  -0.2902  -0.0171   0.1629
 VC2  CB   C  CT    0  -0.223   2.0437   0.6041   0.2465
 VC2  CG2  C  CH3   0  -0.651   3.4743   0.1282   0.0341
 VC2  CG1  C  CH3   0  -0.627   2.0080   1.6496   1.3569
 VC2  SAI  S  S2    0   0.021   1.4181   1.2867  -1.3355
 VC2  CAO  C  CR15  0  -0.165  -0.3190   0.9727  -0.8914
 VC2  CAG  C  CH2   0  -0.550  -1.0551   2.2025  -0.3673
 VC2  SAH  S  S2    0  -0.010  -2.3596   1.5197   0.6846
 VC2  CAK  C  CR15  0  -0.182  -1.3525   0.0571   1.1314
 VC2  CAF  C  CH2   0  -0.541  -2.2211  -1.1967   1.1717
 VC2  SAE  S  S2    0  -0.245  -2.8986  -1.6912  -0.4328
 VC2  H1   H  HOH1  0   0.483   2.3489  -3.3883   0.1029
 VC2  H2   H  HCH1  0   0.298   1.0099  -0.6916   1.6352
 VC2  H4   H  HCH3  0   0.246   3.5720  -0.5672  -0.7992
 VC2  H5   H  HCH3  0   0.253   4.1196   0.9818  -0.1764
 VC2  H6   H  HCH3  0   0.251   3.8542  -0.3536   0.9353
 VC2  H7   H  HCH3  0   0.243   2.4531   1.2438   2.2680
 VC2  H8   H  HCH3  0   0.248   2.5754   2.5335   1.0675
 VC2  H9   H  HCH3  0   0.244   0.9941   1.9664   1.5978
 VC2  H10  H  HCR5  0   0.282  -0.8208   0.6043  -1.7900
 VC2  H11  H  HCH2  0   0.275  -0.3976   2.8568   0.2037
 VC2  H12  H  HCH2  0   0.295  -1.5060   2.7776  -1.1745
 VC2  H13  H  HCR5  0   0.283  -0.9434   0.1993   2.1396
 VC2  H14  H  HCH2  0   0.283  -1.6401  -2.0202   1.5908
 VC2  H15  H  HSH1  0   0.223  -1.7266  -1.9345  -1.0310
 VC2  H3   H  HCH2  0   0.287  -3.0734  -1.0479   1.8369

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
 VC2  O    C    double  1.204  0.020  1.204
 VC2  C    OXT  single  1.326  0.020  1.326
 VC2  C    CA   single  1.523  0.020  1.523
 VC2  CA   N    single  1.434  0.020  1.434
 VC2  CA   CB   single  1.552  0.020  1.552
 VC2  N    CAO  single  1.446  0.020  1.446
 VC2  N    CAK  single  1.439  0.020  1.439
 VC2  CB   CG2  single  1.523  0.020  1.523
 VC2  CB   CG1  single  1.526  0.020  1.526
 VC2  CB   SAI  single  1.833  0.020  1.833
 VC2  SAI  CAO  single  1.820  0.020  1.820
 VC2  CAO  CAG  single  1.526  0.020  1.526
 VC2  CAG  SAH  single  1.810  0.020  1.810
 VC2  SAH  CAK  single  1.831  0.020  1.831
 VC2  CAK  CAF  single  1.526  0.020  1.526
 VC2  CAF  SAE  single  1.810  0.020  1.810
 VC2  OXT  H1   single  0.850  0.020  0.980
 VC2  CA   H2   single  0.970  0.020  1.090
 VC2  CG2  H4   single  0.970  0.020  1.090
 VC2  CG2  H5   single  0.970  0.020  1.090
 VC2  CG2  H6   single  0.970  0.020  1.090
 VC2  CG1  H7   single  0.970  0.020  1.090
 VC2  CG1  H8   single  0.970  0.020  1.090
 VC2  CG1  H9   single  0.970  0.020  1.090
 VC2  CAO  H10  single  0.970  0.020  1.090
 VC2  CAG  H11  single  0.970  0.020  1.090
 VC2  CAG  H12  single  0.970  0.020  1.090
 VC2  CAK  H13  single  0.970  0.020  1.090
 VC2  CAF  H14  single  0.970  0.020  1.090
 VC2  SAE  H15  single  1.200  0.020  1.300
 VC2  CAF  H3   single  0.970  0.020  1.090

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
 VC2  CA   C    OXT  111.60  3.000
 VC2  CA   C    O    124.63  3.000
 VC2  OXT  C    O    123.77  3.000
 VC2  H1   OXT  C    110.35  3.000
 VC2  H2   CA   CB   108.29  3.000
 VC2  H2   CA   N    109.65  3.000
 VC2  CB   CA   N    107.98  3.000
 VC2  H2   CA   C    107.69  3.000
 VC2  CB   CA   C    112.43  3.000
 VC2  N    CA   C    110.75  3.000
 VC2  CAK  N    CAO  116.13  3.000
 VC2  CAK  N    CA   119.81  3.000
 VC2  CAO  N    CA   116.72  3.000
 VC2  SAI  CB   CG1  111.41  3.000
 VC2  SAI  CB   CG2  108.46  3.000
 VC2  CG1  CB   CG2  109.74  3.000
 VC2  SAI  CB   CA   102.03  3.000
 VC2  CG1  CB   CA   109.13  3.000
 VC2  CG2  CB   CA   115.87  3.000
 VC2  H6   CG2  H5   107.41  3.000
 VC2  H6   CG2  H4   108.60  3.000
 VC2  H5   CG2  H4   107.39  3.000
 VC2  H6   CG2  CB   110.50  3.000
 VC2  H5   CG2  CB   109.77  3.000
 VC2  H4   CG2  CB   112.98  3.000
 VC2  H9   CG1  H8   107.91  3.000
 VC2  H9   CG1  H7   107.63  3.000
 VC2  H8   CG1  H7   108.11  3.000
 VC2  H9   CG1  CB   112.46  3.000
 VC2  H8   CG1  CB   110.52  3.000
 VC2  H7   CG1  CB   110.06  3.000
 VC2  CAO  SAI  CB    92.92  3.000
 VC2  H10  CAO  CAG  109.43  3.000
 VC2  H10  CAO  SAI  107.19  3.000
 VC2  CAG  CAO  SAI  113.90  3.000
 VC2  H10  CAO  N    112.19  3.000
 VC2  CAG  CAO  N    108.10  3.000
 VC2  SAI  CAO  N    106.07  3.000
 VC2  H12  CAG  H11  108.74  3.000
 VC2  H12  CAG  SAH  109.37  3.000
 VC2  H11  CAG  SAH  110.92  3.000
 VC2  H12  CAG  CAO  111.76  3.000
 VC2  H11  CAG  CAO  111.90  3.000
 VC2  SAH  CAG  CAO  104.08  3.000
 VC2  CAK  SAH  CAG   92.68  3.000
 VC2  H13  CAK  CAF  107.13  3.000
 VC2  H13  CAK  SAH  109.01  3.000
 VC2  CAF  CAK  SAH  110.47  3.000
 VC2  H13  CAK  N    110.47  3.000
 VC2  CAF  CAK  N    113.30  3.000
 VC2  SAH  CAK  N    106.43  3.000
 VC2  H3   CAF  H14  106.53  3.000
 VC2  H3   CAF  SAE  106.57  3.000
 VC2  H14  CAF  SAE  109.47  3.000
 VC2  H3   CAF  CAK  110.41  3.000
 VC2  H14  CAF  CAK  109.09  3.000
 VC2  SAE  CAF  CAK  114.46  3.000
 VC2  H15  SAE  CAF   96.78  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
 VC2  CONST_01  H1  OXT  C   CA  180.00   0.0  0
 VC2  Var_01    H4  CG2  CB  CA   60.13  30.0  3
 VC2  Var_02    H7  CG1  CB  CA   72.29  30.0  3

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
 VC2  chir_01  CA   C    N  CB   positiv
 VC2  chir_02  CAO  SAI  N  CAG  negativ
 VC2  chir_03  CAK  SAH  N  CAF  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
 VC2  plan-1  O    0.020
 VC2  plan-1  C    0.020
 VC2  plan-1  OXT  0.020
 VC2  plan-1  CA   0.020
 VC2  plan-1  H1   0.020

