# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 08:01:22 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 2-[(5,6-dimethyl-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidin-2-yl)sulfanyl]-N-(2-hydroxyethyl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1sc2N=C(NC(=O)c2c1C)SCC(=O)NCCO
#
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
 V30  V30  2-[(5,6-dimethyl-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidin-2-yl)sulfanyl]-N-(2-hydroxyethyl)acetamide  ligand  35  20  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_V30
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
 V30  N1I   N  N     0  -0.437   0.6277   0.2624  -0.0674
 V30  N1J   N  NH1   0  -0.620  -4.4670   0.5516  -0.5822
 V30  N1K   N  NR16  0  -0.701   1.2949  -1.9017   0.4869
 V30  CAA   C  CH3   0  -0.722   5.2688   2.6147  -0.5406
 V30  CAB   C  CH3   0  -0.726   5.5802  -0.4174   0.2188
 V30  OAC   O  O     0  -0.486  -4.0447  -1.4955   0.2868
 V30  OAD   O  O     0  -0.457   3.4437  -2.5861   0.7091
 V30  OAE   O  OH1   0  -0.672  -6.3119   2.2442   0.8562
 V30  CAF   C  CH2   0  -0.154  -6.5838   0.8759   0.6607
 V30  CAG   C  CH2   0  -0.330  -5.9086   0.4266  -0.6191
 V30  CAH   C  CH2   0  -0.685  -2.1905  -0.0379  -0.0936
 V30  SAL   S  S2    0   0.096  -1.2960  -1.5476   0.3353
 V30  SAM   S  S2    0   0.228   2.5244   2.1230  -0.4926
 V30  CAN   C  C     0   0.574  -3.6621  -0.4041  -0.1081
 V30  CAO   C  CR5   0  -0.258   4.1802   1.6128  -0.3350
 V30  CAP   C  CR5   0   0.184   4.2851   0.2967   0.0004
 V30  CAQ   C  CR6   0   0.353   0.3474  -0.9627   0.2300
 V30  CAR   C  CR6   0   0.536   2.6710  -1.6777   0.4624
 V30  CAS   C  CR56  0  -0.030   1.9472   0.5518  -0.1104
 V30  CAT   C  CR56  0  -0.075   2.9953  -0.3158   0.1270
 V30  HN1J  H  HNH1  0   0.410  -4.0661   1.4360  -0.8495
 V30  HN1K  H  HNR6  0   0.432   1.0081  -2.8459   0.7168
 V30  HAA   H  HCH3  0   0.256   4.9279   3.4664  -1.1280
 V30  HAAA  H  HCH3  0   0.260   5.6406   3.0012   0.4098
 V30  HAAB  H  HCH3  0   0.258   6.1120   2.1756  -1.0723
 V30  HAB   H  HCH3  0   0.248   5.6325  -0.8393   1.2223
 V30  HABA  H  HCH3  0   0.247   5.7029  -1.2427  -0.4824
 V30  HABB  H  HCH3  0   0.243   6.4275   0.2545   0.0974
 V30  HOAE  H  HOH1  0   0.457  -6.6705   2.5053   1.7087
 V30  HAF   H  HCH2  0   0.204  -6.2207   0.2648   1.4962
 V30  HAFA  H  HCH2  0   0.205  -7.6594   0.6798   0.5627
 V30  HAG   H  HCH2  0   0.260  -6.2733   1.0157  -1.4615
 V30  HAGA  H  HCH2  0   0.255  -6.1743  -0.6112  -0.8159
 V30  HAH   H  HCH2  0   0.328  -1.9982   0.7374   0.6496
 V30  HAHA  H  HCH2  0   0.321  -1.8615   0.3352  -1.0634

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
 V30  CAQ  N1I   double    1.291  0.020  1.291
 V30  CAS  N1I   single    1.352  0.020  1.352
 V30  CAN  N1J   single    1.336  0.020  1.336
 V30  CAG  N1J   single    1.447  0.020  1.447
 V30  N1J  HN1J  single    0.860  0.020  1.020
 V30  CAR  N1K   single    1.394  0.020  1.394
 V30  N1K  CAQ   single    1.359  0.020  1.359
 V30  N1K  HN1K  single    0.860  0.020  1.020
 V30  CAA  CAO   single    1.494  0.020  1.494
 V30  CAA  HAA   single    0.970  0.020  1.090
 V30  CAA  HAAA  single    0.970  0.020  1.090
 V30  CAA  HAAB  single    0.970  0.020  1.090
 V30  CAB  CAP   single    1.495  0.020  1.495
 V30  CAB  HAB   single    0.970  0.020  1.090
 V30  CAB  HABA  single    0.970  0.020  1.090
 V30  CAB  HABB  single    0.970  0.020  1.090
 V30  OAC  CAN   double    1.222  0.020  1.222
 V30  OAD  CAR   double    1.218  0.020  1.218
 V30  CAF  OAE   single    1.409  0.020  1.409
 V30  OAE  HOAE  single    0.850  0.020  0.980
 V30  CAG  CAF   single    1.515  0.020  1.515
 V30  CAF  HAF   single    0.970  0.020  1.090
 V30  CAF  HAFA  single    0.970  0.020  1.090
 V30  CAG  HAG   single    0.970  0.020  1.090
 V30  CAG  HAGA  single    0.970  0.020  1.090
 V30  SAL  CAH   single    1.806  0.020  1.806
 V30  CAN  CAH   single    1.517  0.020  1.517
 V30  CAH  HAH   single    0.970  0.020  1.090
 V30  CAH  HAHA  single    0.970  0.020  1.090
 V30  CAQ  SAL   single    1.748  0.020  1.748
 V30  CAO  SAM   aromatic  1.740  0.020  1.740
 V30  CAS  SAM   aromatic  1.717  0.020  1.717
 V30  CAP  CAO   aromatic  1.362  0.020  1.362
 V30  CAP  CAT   aromatic  1.433  0.020  1.433
 V30  CAR  CAT   single    1.440  0.020  1.440
 V30  CAT  CAS   aromatic  1.381  0.020  1.381

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
 V30  CAS   N1I  CAQ   114.98  3.000
 V30  HN1J  N1J  CAN   118.84  3.000
 V30  HN1J  N1J  CAG   117.74  3.000
 V30  CAN   N1J  CAG   123.17  3.000
 V30  HN1K  N1K  CAR   115.66  3.000
 V30  HN1K  N1K  CAQ   119.31  3.000
 V30  CAR   N1K  CAQ   125.03  3.000
 V30  HAAB  CAA  HAAA  107.70  3.000
 V30  HAAB  CAA  HAA   107.11  3.000
 V30  HAAA  CAA  HAA   107.42  3.000
 V30  HAAB  CAA  CAO   111.16  3.000
 V30  HAAA  CAA  CAO   111.47  3.000
 V30  HAA   CAA  CAO   111.76  3.000
 V30  HABB  CAB  HABA  107.95  3.000
 V30  HABB  CAB  HAB   107.72  3.000
 V30  HABA  CAB  HAB   107.08  3.000
 V30  HABB  CAB  CAP   111.30  3.000
 V30  HABA  CAB  CAP   111.42  3.000
 V30  HAB   CAB  CAP   111.16  3.000
 V30  HOAE  OAE  CAF   108.36  3.000
 V30  HAFA  CAF  HAF   107.03  3.000
 V30  HAFA  CAF  CAG   107.95  3.000
 V30  HAF   CAF  CAG   109.31  3.000
 V30  HAFA  CAF  OAE   112.03  3.000
 V30  HAF   CAF  OAE   111.81  3.000
 V30  CAG   CAF  OAE   108.61  3.000
 V30  HAGA  CAG  HAG   107.06  3.000
 V30  HAGA  CAG  CAF   109.05  3.000
 V30  HAG   CAG  CAF   110.08  3.000
 V30  HAGA  CAG  N1J   109.26  3.000
 V30  HAG   CAG  N1J   107.82  3.000
 V30  CAF   CAG  N1J   113.37  3.000
 V30  HAHA  CAH  HAH   108.04  3.000
 V30  HAHA  CAH  CAN   111.53  3.000
 V30  HAH   CAH  CAN   110.43  3.000
 V30  HAHA  CAH  SAL   110.36  3.000
 V30  HAH   CAH  SAL   110.18  3.000
 V30  CAN   CAH  SAL   106.32  3.000
 V30  CAQ   SAL  CAH    99.88  3.000
 V30  CAS   SAM  CAO    91.80  3.000
 V30  CAH   CAN  OAC   121.09  3.000
 V30  CAH   CAN  N1J   114.53  3.000
 V30  OAC   CAN  N1J   124.39  3.000
 V30  CAP   CAO  SAM   112.27  3.000
 V30  CAP   CAO  CAA   128.75  3.000
 V30  SAM   CAO  CAA   118.97  3.000
 V30  CAT   CAP  CAO   111.43  3.000
 V30  CAT   CAP  CAB   124.23  3.000
 V30  CAO   CAP  CAB   124.34  3.000
 V30  SAL   CAQ  N1K   114.40  3.000
 V30  SAL   CAQ  N1I   122.38  3.000
 V30  N1K   CAQ  N1I   123.22  3.000
 V30  CAT   CAR  OAD   127.58  3.000
 V30  CAT   CAR  N1K   112.23  3.000
 V30  OAD   CAR  N1K   120.19  3.000
 V30  CAT   CAS  SAM   110.98  3.000
 V30  CAT   CAS  N1I   126.93  3.000
 V30  SAM   CAS  N1I   122.09  3.000
 V30  CAS   CAT  CAR   117.60  3.000
 V30  CAS   CAT  CAP   113.53  3.000
 V30  CAR   CAT  CAP   128.87  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
 V30  CONST_01  CAT   CAP  CAO  SAM     0.00   0.0  0
 V30  CONST_02  CAP   CAT  CAS  SAM     0.00   0.0  0
 V30  CONST_03  CAT   CAS  SAM  CAO     0.00   0.0  0
 V30  CONST_04  CAS   CAT  CAP  CAO     0.00   0.0  0
 V30  CONST_05  CAS   SAM  CAO  CAP     0.00   0.0  0
 V30  CONST_06  CAR   N1K  CAQ  N1I     0.00   0.0  0
 V30  CONST_07  CAS   N1I  CAQ  N1K     0.00   0.0  0
 V30  CONST_08  CAT   CAR  N1K  CAQ     0.00   0.0  0
 V30  CONST_09  CAS   SAM  CAO  CAA   180.00   0.0  0
 V30  CONST_10  CAT   CAP  CAO  CAA   180.00   0.0  0
 V30  CONST_11  SAM   CAO  CAP  CAB   180.00   0.0  0
 V30  CONST_12  CAR   CAT  CAP  CAB     0.00   0.0  0
 V30  CONST_13  CAS   CAT  CAP  CAB   180.00   0.0  0
 V30  CONST_14  CAQ   N1K  CAR  OAD   180.00   0.0  0
 V30  CONST_15  CAS   N1I  CAQ  SAL   180.00   0.0  0
 V30  CONST_16  CAR   N1K  CAQ  SAL   180.00   0.0  0
 V30  CONST_17  HN1K  N1K  CAQ  N1I   180.00   0.0  0
 V30  CONST_18  CAG   N1J  CAN  OAC     0.00   0.0  0
 V30  CONST_19  CAH   CAN  N1J  CAG   180.00   0.0  0
 V30  CONST_20  HN1J  N1J  CAN  OAC   180.00   0.0  0
 V30  Var_01    HAA   CAA  CAO  SAM   -21.60  30.0  2
 V30  Var_02    HAB   CAB  CAP  CAO   121.37  30.0  2
 V30  Var_03    HAH   CAH  SAL  CAQ   -62.87  30.0  3
 V30  Var_04    SAL   CAH  CAN  N1J  -171.48  30.0  3
 V30  Var_05    OAE   CAF  CAG  N1J    62.16  30.0  3
 V30  Var_06    CAN   N1J  CAG  CAF    87.30  30.0  3

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
 V30  plan-1  N1I   0.020
 V30  plan-1  N1K   0.020
 V30  plan-1  CAA   0.020
 V30  plan-1  CAB   0.020
 V30  plan-1  OAD   0.020
 V30  plan-1  SAL   0.020
 V30  plan-1  SAM   0.020
 V30  plan-1  CAO   0.020
 V30  plan-1  CAP   0.020
 V30  plan-1  CAQ   0.020
 V30  plan-1  CAR   0.020
 V30  plan-1  CAS   0.020
 V30  plan-1  CAT   0.020
 V30  plan-1  HN1K  0.020
 V30  plan-2  N1J   0.020
 V30  plan-2  OAC   0.020
 V30  plan-2  CAG   0.020
 V30  plan-2  CAH   0.020
 V30  plan-2  CAN   0.020
 V30  plan-2  HN1J  0.020

