# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 04:18:48 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: 4-[4-(5-methyl-1,3,4-thiadiazol-2-yl)piperazin-1-yl]-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1sc(nn1)N2CCN(CC2)c3ncnc4sc(CC(F)(F)F)cc34
#
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
 59K  59K  4-[4-(5-methyl-1,3,4-thiadiazol-2-yl)piperazin-1-yl]-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidine  ligand  41  26  .  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_59K
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
 59K  C4   C  CR56  0  -0.025  -2.5113   2.1654   0.6753
 59K  C5   C  CR56  0   0.051  -1.7651   1.4357  -0.2537
 59K  C6   C  CR6   0   0.524  -0.4024   1.8266  -0.3646
 59K  N1   N  N     0  -0.469   0.0161   2.8928   0.3137
 59K  N3   N  N     0  -0.428  -2.0704   3.1925   1.3960
 59K  FAB  F  F     0  -0.307  -5.5976  -1.1979   1.1124
 59K  CAZ  C  CT    0   0.990  -5.2078  -1.5886  -0.1099
 59K  FAC  F  F     0  -0.301  -4.1147  -2.3428   0.0560
 59K  FAD  F  F     0  -0.305  -6.1687  -2.3860  -0.5922
 59K  CAS  C  CR5   0  -0.172  -3.8573   0.4634  -0.5188
 59K  SAQ  S  S2    0   0.242  -4.1512   1.6218   0.7427
 59K  CAF  C  CR15  0  -0.234  -2.5742   0.4802  -0.9474
 59K  C2   C  CR16  0   0.046  -0.8197   3.5137   1.1352
 59K  NAY  N  NT    0  -0.484   0.4916   1.1960  -1.1676
 59K  CAJ  C  CH2   0  -0.333   1.7988   1.7788  -1.4070
 59K  CAH  C  CH2   0  -0.312   2.8482   1.2214  -0.4625
 59K  CAI  C  CH2   0  -0.354   0.5297  -0.2483  -1.3252
 59K  CAG  C  CH2   0  -0.285   1.5537  -0.8702  -0.3865
 59K  NAX  N  NT    0  -0.494   2.8536  -0.2317  -0.5296
 59K  CAT  C  CR5   0   0.351   3.9363  -0.9210  -0.1053
 59K  SAP  S  S2    0   0.134   5.5093  -0.1886   0.0542
 59K  NAO  N  N     0  -0.349   3.9334  -2.1870   0.1945
 59K  NAN  N  N     0  -0.241   5.1572  -2.6510   0.5333
 59K  CAR  C  CR5   0   0.075   6.0873  -1.7653   0.5190
 59K  CAA  C  CH3   0  -0.721   7.5121  -2.0117   0.8552
 59K  H1   H  HCH2  0   0.317  -4.6790  -0.7975  -2.0072
 59K  H2   H  HCH2  0   0.316  -5.8876   0.1389  -1.1429
 59K  H3   H  HCR5  0   0.287  -2.2421  -0.1431  -1.7641
 59K  H4   H  HCR6  0   0.261  -0.4185   4.3733   1.6607
 59K  H5   H  HCH2  0   0.267   2.0781   1.5429  -2.4371
 59K  H6   H  HCH2  0   0.282   1.7561   2.8592  -1.3093
 59K  H7   H  HCH2  0   0.271   3.8189   1.6103  -0.7744
 59K  H8   H  HCH2  0   0.254   2.6601   1.5656   0.5613
 59K  H9   H  HCH2  0   0.279  -0.4304  -0.7010  -1.1029
 59K  H10  H  HCH2  0   0.266   0.7748  -0.4841  -2.3628
 59K  H11  H  HCH2  0   0.244   1.2033  -0.7925   0.6502
 59K  H12  H  HCH2  0   0.279   1.6478  -1.9275  -0.6249
 59K  H13  H  HCH3  0   0.265   7.8363  -1.3886   1.6888
 59K  H14  H  HCH3  0   0.267   7.6432  -3.0557   1.1319
 59K  H15  H  HCH3  0   0.266   8.1624  -1.7938   0.0078
 59K  CAK  C  CH2   0  -0.720  -4.9529  -0.4135  -1.0231

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
 59K  CAA  CAR  single    1.485  0.020  1.485
 59K  SAP  CAR  aromatic  1.742  0.020  1.742
 59K  SAP  CAT  aromatic  1.742  0.020  1.742
 59K  CAK  CAS  single    1.491  0.020  1.491
 59K  CAK  CAZ  single    1.510  0.020  1.510
 59K  SAQ  CAS  aromatic  1.738  0.020  1.738
 59K  SAQ  C4   aromatic  1.729  0.020  1.729
 59K  CAR  NAN  aromatic  1.284  0.020  1.284
 59K  CAS  CAF  aromatic  1.353  0.020  1.353
 59K  CAG  CAI  single    1.522  0.020  1.522
 59K  CAG  NAX  single    1.455  0.020  1.455
 59K  FAD  CAZ  single    1.339  0.020  1.339
 59K  C4   N3   aromatic  1.330  0.020  1.330
 59K  C4   C5   aromatic  1.397  0.020  1.397
 59K  CAF  C5   aromatic  1.431  0.020  1.431
 59K  N3   C2   aromatic  1.317  0.020  1.317
 59K  CAZ  FAB  single    1.341  0.020  1.341
 59K  CAZ  FAC  single    1.338  0.020  1.338
 59K  C5   C6   aromatic  1.422  0.020  1.422
 59K  CAI  NAY  single    1.453  0.020  1.453
 59K  CAT  NAX  single    1.352  0.020  1.352
 59K  CAT  NAO  aromatic  1.301  0.020  1.301
 59K  C2   N1   aromatic  1.326  0.020  1.326
 59K  NAN  NAO  aromatic  1.352  0.020  1.352
 59K  C6   N1   aromatic  1.331  0.020  1.331
 59K  C6   NAY  single    1.357  0.020  1.357
 59K  NAX  CAH  single    1.455  0.020  1.455
 59K  NAY  CAJ  single    1.451  0.020  1.451
 59K  CAJ  CAH  single    1.518  0.020  1.518
 59K  CAK  H1   single    0.970  0.020  1.090
 59K  CAK  H2   single    0.970  0.020  1.090
 59K  CAF  H3   single    0.930  0.020  1.080
 59K  C2   H4   single    0.930  0.020  1.080
 59K  CAJ  H5   single    0.970  0.020  1.090
 59K  CAJ  H6   single    0.970  0.020  1.090
 59K  CAH  H7   single    0.970  0.020  1.090
 59K  CAH  H8   single    0.970  0.020  1.090
 59K  CAI  H9   single    0.970  0.020  1.090
 59K  CAI  H10  single    0.970  0.020  1.090
 59K  CAG  H11  single    0.970  0.020  1.090
 59K  CAG  H12  single    0.970  0.020  1.090
 59K  CAA  H13  single    0.970  0.020  1.090
 59K  CAA  H14  single    0.970  0.020  1.090
 59K  CAA  H15  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
 59K  SAQ  C4   N3   122.42  3.000
 59K  N3   C4   C5   125.91  3.000
 59K  SAQ  C4   C5   111.61  3.000
 59K  CAF  C5   C6   133.42  3.000
 59K  C6   C5   C4   114.84  3.000
 59K  CAF  C5   C4   111.65  3.000
 59K  NAY  C6   N1   117.81  3.000
 59K  NAY  C6   C5   123.35  3.000
 59K  N1   C6   C5   118.80  3.000
 59K  C2   N1   C6   119.50  3.000
 59K  C2   N3   C4   113.31  3.000
 59K  CAK  CAZ  FAD  111.52  3.000
 59K  FAD  CAZ  FAC  107.17  3.000
 59K  CAK  CAZ  FAC  112.07  3.000
 59K  FAC  CAZ  FAB  106.77  3.000
 59K  FAD  CAZ  FAB  107.06  3.000
 59K  CAK  CAZ  FAB  111.93  3.000
 59K  CAF  CAS  SAQ  112.46  3.000
 59K  CAF  CAS  CAK  126.65  3.000
 59K  SAQ  CAS  CAK  120.88  3.000
 59K  CAS  SAQ  C4    91.20  3.000
 59K  H3   CAF  CAS  121.61  3.000
 59K  H3   CAF  C5   125.31  3.000
 59K  CAS  CAF  C5   113.01  3.000
 59K  H4   C2   N3   116.65  3.000
 59K  H4   C2   N1   115.98  3.000
 59K  N3   C2   N1   127.36  3.000
 59K  CAI  NAY  CAJ  110.95  3.000
 59K  CAJ  NAY  C6   120.29  3.000
 59K  CAI  NAY  C6   122.90  3.000
 59K  H6   CAJ  H5   108.03  3.000
 59K  H6   CAJ  CAH  109.68  3.000
 59K  H5   CAJ  CAH  109.30  3.000
 59K  H6   CAJ  NAY  110.45  3.000
 59K  H5   CAJ  NAY  107.40  3.000
 59K  CAH  CAJ  NAY  111.88  3.000
 59K  H8   CAH  H7   107.92  3.000
 59K  H8   CAH  NAX  110.93  3.000
 59K  H7   CAH  NAX  109.85  3.000
 59K  H8   CAH  CAJ  110.31  3.000
 59K  H7   CAH  CAJ  107.83  3.000
 59K  NAX  CAH  CAJ  109.92  3.000
 59K  H10  CAI  H9   107.66  3.000
 59K  H10  CAI  CAG  110.29  3.000
 59K  H9   CAI  CAG  107.38  3.000
 59K  H10  CAI  NAY  108.88  3.000
 59K  H9   CAI  NAY  111.67  3.000
 59K  CAG  CAI  NAY  110.91  3.000
 59K  H12  CAG  H11  107.67  3.000
 59K  H12  CAG  NAX  109.12  3.000
 59K  H11  CAG  NAX  110.31  3.000
 59K  H12  CAG  CAI  108.67  3.000
 59K  H11  CAG  CAI  109.81  3.000
 59K  NAX  CAG  CAI  111.16  3.000
 59K  CAT  NAX  CAG  117.44  3.000
 59K  CAT  NAX  CAH  119.86  3.000
 59K  CAG  NAX  CAH  115.50  3.000
 59K  NAO  CAT  SAP  112.95  3.000
 59K  NAO  CAT  NAX  124.52  3.000
 59K  SAP  CAT  NAX  122.51  3.000
 59K  CAR  SAP  CAT   86.76  3.000
 59K  NAN  NAO  CAT  112.94  3.000
 59K  CAR  NAN  NAO  114.58  3.000
 59K  CAA  CAR  NAN  125.31  3.000
 59K  NAN  CAR  SAP  112.75  3.000
 59K  CAA  CAR  SAP  121.94  3.000
 59K  H15  CAA  H14  108.53  3.000
 59K  H15  CAA  H13  107.62  3.000
 59K  H14  CAA  H13  108.55  3.000
 59K  H15  CAA  CAR  111.30  3.000
 59K  H14  CAA  CAR  109.42  3.000
 59K  H13  CAA  CAR  111.33  3.000
 59K  H2   CAK  H1   107.09  3.000
 59K  H2   CAK  CAS  111.61  3.000
 59K  H1   CAK  CAS  109.12  3.000
 59K  H2   CAK  CAZ  108.39  3.000
 59K  H1   CAK  CAZ  108.29  3.000
 59K  CAS  CAK  CAZ  112.16  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
 59K  CONST_01  CAF  CAS  SAQ  C4     0.00   0.0  0
 59K  CONST_02  N1   C2   N3   C4     0.00   0.0  0
 59K  CONST_03  CAS  CAF  C5   C4     0.00   0.0  0
 59K  CONST_04  N1   C6   C5   C4     0.00   0.0  0
 59K  CONST_05  CAS  SAQ  C4   C5     0.00   0.0  0
 59K  CONST_06  C2   N3   C4   C5     0.00   0.0  0
 59K  CONST_07  SAQ  CAS  CAF  C5     0.00   0.0  0
 59K  CONST_08  C2   N1   C6   C5     0.00   0.0  0
 59K  CONST_09  SAQ  C4   C5   C6   180.00   0.0  0
 59K  CONST_10  N3   C4   C5   C6     0.00   0.0  0
 59K  CONST_11  CAS  CAF  C5   C6   180.00   0.0  0
 59K  CONST_12  N3   C2   N1   C6     0.00   0.0  0
 59K  CONST_13  CAF  C5   C6   N1   180.00   0.0  0
 59K  CONST_14  CAS  SAQ  C4   N3   180.00   0.0  0
 59K  CONST_15  CAF  C5   C4   N3   180.00   0.0  0
 59K  CONST_16  C2   N3   C4   SAQ  180.00   0.0  0
 59K  CONST_17  CAF  C5   C4   SAQ    0.00   0.0  0
 59K  CONST_18  NAN  CAR  SAP  CAT    0.00   0.0  0
 59K  CONST_19  CAR  NAN  NAO  CAT    0.00   0.0  0
 59K  CONST_20  NAO  NAN  CAR  SAP    0.00   0.0  0
 59K  CONST_21  NAN  NAO  CAT  SAP    0.00   0.0  0
 59K  CONST_22  CAR  SAP  CAT  NAO    0.00   0.0  0
 59K  CONST_23  NAY  C6   C5   C4   180.00   0.0  0
 59K  CONST_24  NAY  C6   C5   CAF    0.00   0.0  0
 59K  CONST_25  NAY  C6   N1   C2   180.00   0.0  0
 59K  CONST_26  CAR  SAP  CAT  NAX  180.00   0.0  0
 59K  CONST_27  NAN  NAO  CAT  NAX  180.00   0.0  0
 59K  CONST_28  CAK  CAS  SAQ  C4   180.00   0.0  0
 59K  CONST_29  CAK  CAS  CAF  C5   180.00   0.0  0
 59K  CONST_30  CAA  CAR  SAP  CAT  180.00   0.0  0
 59K  CONST_31  CAA  CAR  NAN  NAO  180.00   0.0  0
 59K  CONST_32  H4   C2   N3   C4   180.00   0.0  0
 59K  CONST_33  H3   CAF  C5   C4   180.00   0.0  0
 59K  Var_01    CAI  NAY  C6   C5   -39.89  30.0  2
 59K  Var_02    CAG  CAI  NAY  C6   -95.44  30.0  1
 59K  Var_03    CAH  CAJ  NAY  C6    95.01  30.0  1
 59K  Var_04    NAX  CAG  CAI  NAY  -52.46  30.0  1
 59K  Var_05    NAX  CAH  CAJ  NAY   53.64  30.0  1
 59K  Var_06    CAG  NAX  CAH  CAJ  -50.31  30.0  1
 59K  Var_07    CAI  CAG  NAX  CAH   50.30  30.0  1
 59K  Var_08    SAP  CAT  NAX  CAH  -19.76  30.0  2
 59K  Var_09    SAQ  CAS  CAK  CAZ  -79.68  30.0  2
 59K  Var_10    H13  CAA  CAR  SAP   59.01  30.0  2
 59K  Var_11    CAS  CAK  CAZ  FAB   61.73  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
 59K  plan-1  NAX  0.020
 59K  plan-1  CAT  0.020
 59K  plan-1  SAP  0.020
 59K  plan-1  NAO  0.020
 59K  plan-1  NAN  0.020
 59K  plan-1  CAR  0.020
 59K  plan-1  CAA  0.020
 59K  plan-2  C4   0.020
 59K  plan-2  C5   0.020
 59K  plan-2  C6   0.020
 59K  plan-2  N1   0.020
 59K  plan-2  N3   0.020
 59K  plan-2  CAS  0.020
 59K  plan-2  SAQ  0.020
 59K  plan-2  CAF  0.020
 59K  plan-2  C2   0.020
 59K  plan-2  NAY  0.020
 59K  plan-2  H3   0.020
 59K  plan-2  H4   0.020
 59K  plan-2  CAK  0.020

