# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 11:36:36 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  29  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  -0.578   0.6064  -2.0876  -1.2623
 VC2  C    C  C      0   0.437   1.2412  -1.8654  -0.2118
 VC2  OXT  O  OC    -1  -0.607   2.0832  -2.6133   0.3215
 VC2  CA   C  CH1    0  -0.154   0.9695  -0.5307   0.5235
 VC2  N    N  NT     0  -0.407  -0.3020   0.0540   0.1973
 VC2  CB   C  CT     0  -0.209   2.0265   0.5668   0.2358
 VC2  CG2  C  CH3    0  -0.634   3.4476   0.0787  -0.0018
 VC2  CG1  C  CH3    0  -0.623   2.0175   1.5982   1.3609
 VC2  SAI  S  S2     0  -0.019   1.4008   1.3174  -1.3210
 VC2  CAO  C  CH1    0  -0.141  -0.3436   0.9786  -0.8967
 VC2  CAG  C  CH2    0  -0.546  -1.1157   2.2111  -0.4308
 VC2  SAH  S  S2     0  -0.033  -2.4014   1.5445   0.6589
 VC2  CAK  C  CH1    0  -0.167  -1.3778   0.0985   1.1346
 VC2  CAF  C  CH2    0  -0.532  -2.2292  -1.1716   1.1522
 VC2  SAE  S  S2     0  -0.302  -2.7566  -1.7142  -0.4935
 VC2  H2   H  HCH1   0   0.241   0.9915  -0.7385   1.6001
 VC2  H4   H  HCH3   0   0.238   3.5211  -0.5971  -0.8512
 VC2  H5   H  HCH3   0   0.229   4.1096   0.9264  -0.1876
 VC2  H6   H  HCH3   0   0.235   3.8184  -0.4437   0.8802
 VC2  H7   H  HCH3   0   0.230   2.4465   1.1683   2.2694
 VC2  H8   H  HCH3   0   0.234   2.6086   2.4739   1.0917
 VC2  H9   H  HCH3   0   0.238   1.0082   1.9337   1.5984
 VC2  H10  H  HCH1   0   0.258  -0.8170   0.5664  -1.7937
 VC2  H11  H  HCH2   0   0.267  -0.4741   2.9069   0.1096
 VC2  H12  H  HCH2   0   0.284  -1.5834   2.7396  -1.2605
 VC2  H13  H  HCH1   0   0.267  -0.9973   0.2468   2.1543
 VC2  H14  H  HCH2   0   0.273  -1.6566  -1.9708   1.6269
 VC2  H15  H  HSH1   0   0.245  -1.5095  -1.8592  -0.9835
 VC2  H3   H  HCH2   0   0.276  -3.1289  -1.0283   1.7533

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    deloc   1.247  0.020  1.247
 VC2  C    OXT  deloc   1.246  0.020  1.246
 VC2  C    CA   single  1.548  0.020  1.548
 VC2  CA   N    single  1.437  0.020  1.437
 VC2  CA   CB   single  1.551  0.020  1.551
 VC2  N    CAO  single  1.433  0.020  1.433
 VC2  N    CAK  single  1.428  0.020  1.428
 VC2  CB   CG2  single  1.521  0.020  1.521
 VC2  CB   CG1  single  1.526  0.020  1.526
 VC2  CB   SAI  single  1.838  0.020  1.838
 VC2  SAI  CAO  single  1.827  0.020  1.827
 VC2  CAO  CAG  single  1.527  0.020  1.527
 VC2  CAG  SAH  single  1.812  0.020  1.812
 VC2  SAH  CAK  single  1.834  0.020  1.834
 VC2  CAK  CAF  single  1.529  0.020  1.529
 VC2  CAF  SAE  single  1.811  0.020  1.811
 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  115.65  3.000
 VC2  CA   C    O    117.67  3.000
 VC2  OXT  C    O    126.68  3.000
 VC2  H2   CA   CB   107.61  3.000
 VC2  H2   CA   N    108.52  3.000
 VC2  CB   CA   N    105.84  3.000
 VC2  H2   CA   C    107.43  3.000
 VC2  CB   CA   C    113.73  3.000
 VC2  N    CA   C    113.47  3.000
 VC2  CAK  N    CAO  117.34  3.000
 VC2  CAK  N    CA   122.03  3.000
 VC2  CAO  N    CA   117.49  3.000
 VC2  SAI  CB   CG1  110.26  3.000
 VC2  SAI  CB   CG2  108.47  3.000
 VC2  CG1  CB   CG2  109.72  3.000
 VC2  SAI  CB   CA   102.37  3.000
 VC2  CG1  CB   CA   109.73  3.000
 VC2  CG2  CB   CA   116.02  3.000
 VC2  H6   CG2  H5   107.68  3.000
 VC2  H6   CG2  H4   108.12  3.000
 VC2  H5   CG2  H4   107.97  3.000
 VC2  H6   CG2  CB   110.19  3.000
 VC2  H5   CG2  CB   110.12  3.000
 VC2  H4   CG2  CB   112.60  3.000
 VC2  H9   CG1  H8   107.98  3.000
 VC2  H9   CG1  H7   107.67  3.000
 VC2  H8   CG1  H7   107.96  3.000
 VC2  H9   CG1  CB   111.97  3.000
 VC2  H8   CG1  CB   110.95  3.000
 VC2  H7   CG1  CB   110.16  3.000
 VC2  CAO  SAI  CB    93.02  3.000
 VC2  H10  CAO  CAG  109.58  3.000
 VC2  H10  CAO  SAI  107.01  3.000
 VC2  CAG  CAO  SAI  113.82  3.000
 VC2  H10  CAO  N    113.27  3.000
 VC2  CAG  CAO  N    107.61  3.000
 VC2  SAI  CAO  N    105.62  3.000
 VC2  H12  CAG  H11  108.71  3.000
 VC2  H12  CAG  SAH  109.38  3.000
 VC2  H11  CAG  SAH  110.75  3.000
 VC2  H12  CAG  CAO  112.10  3.000
 VC2  H11  CAG  CAO  111.65  3.000
 VC2  SAH  CAG  CAO  104.19  3.000
 VC2  CAK  SAH  CAG   92.87  3.000
 VC2  H13  CAK  CAF  107.12  3.000
 VC2  H13  CAK  SAH  109.13  3.000
 VC2  CAF  CAK  SAH  110.30  3.000
 VC2  H13  CAK  N    110.65  3.000
 VC2  CAF  CAK  N    113.66  3.000
 VC2  SAH  CAK  N    105.95  3.000
 VC2  H3   CAF  H14  106.79  3.000
 VC2  H3   CAF  SAE  107.44  3.000
 VC2  H14  CAF  SAE  109.18  3.000
 VC2  H3   CAF  CAK  110.87  3.000
 VC2  H14  CAF  CAK  108.72  3.000
 VC2  SAE  CAF  CAK  113.61  3.000
 VC2  H15  SAE  CAF   95.34  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  Var_01  H4  CG2  CB  CA  59.80  30.0  3
 VC2  Var_02  H7  CG1  CB  CA  71.43  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

