# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:03:11 2022
#   Inital geometry file: a 109 line input string
#   Ligand name: 4-[4-(5,5-dimethyl-4,5-dihydro-1,3-thiazol-2-yl)piperazin-1-yl]-6-(pentafluoroethyl)thieno[2,3-d]pyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)CN=C(S1)N2CCN(CC2)c3ncnc4sc(cc34)C(F)(F)C(F)(F)F
#
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
 5A1  5A1  4-[4-(5,5-dimethyl-4,5-dihydro-1,3-thiazol-2-yl)piperazin-1-yl]-6-(pentafluoroethyl)thieno[2,3-d]pyrimidine  ligand  47  29  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_5A1
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
 5A1  C4   C  CR56  0  -0.008   2.8955   2.2215  -0.1850
 5A1  C5   C  CR56  0   0.044   1.7122   1.4970  -0.0125
 5A1  C6   C  CR6   0   0.548   0.5152   2.2503  -0.1953
 5A1  N1   N  N     0  -0.470   0.6148   3.5677  -0.3712
 5A1  N3   N  N     0  -0.431   2.9844   3.5223  -0.4401
 5A1  FAC  F  F     0  -0.290   2.7764  -2.7188  -0.7507
 5A1  CBB  C  CT    0   0.940   3.9992  -2.4060  -0.3345
 5A1  FAD  F  F     0  -0.295   4.6189  -3.5242   0.0251
 5A1  FAE  F  F     0  -0.291   4.6656  -1.8614  -1.3477
 5A1  FAF  F  F     0  -0.315   3.2234  -2.0056   1.8258
 5A1  FAG  F  F     0  -0.324   5.1840  -1.2049   1.2731
 5A1  CAU  C  CR5   0  -0.400   3.2972  -0.1129   0.4585
 5A1  SAS  S  S2    0   0.283   4.2982   1.2430   0.0616
 5A1  CAI  C  CR15  0  -0.206   1.9719   0.1534   0.3947
 5A1  C2   C  CR16  0   0.055   1.8117   4.1247  -0.4780
 5A1  NAZ  N  NT    0  -0.494  -0.7195   1.7127  -0.1763
 5A1  CAM  C  CH2   0  -0.312  -1.9068   2.5397  -0.0357
 5A1  CAK  C  CH2   0  -0.302  -2.8653   1.8699   0.9375
 5A1  CAL  C  CH2   0  -0.324  -1.0389   0.3739  -0.6384
 5A1  CAJ  C  CH2   0  -0.304  -1.9788  -0.3176   0.3343
 5A1  NAY  N  NT    0  -0.491  -3.1505   0.5054   0.5368
 5A1  CAT  C  CR5   0   0.364  -4.4245   0.0644   0.4520
 5A1  SAR  S  S2    0   0.002  -4.7160  -1.6776   0.1995
 5A1  CBA  C  CR5   0  -0.241  -6.4735  -1.2990  -0.1859
 5A1  CAA  C  CH3   0  -0.618  -6.6265  -1.1247  -1.6913
 5A1  CAB  C  CH3   0  -0.639  -7.3803  -2.4000   0.3375
 5A1  CAN  C  CH2   0  -0.252  -6.6744   0.0334   0.5596
 5A1  NAO  N  N     0  -0.455  -5.4568   0.8036   0.5614
 5A1  H2   H  HCR5  0   0.294   1.2202  -0.5708   0.6704
 5A1  H3   H  HCR6  0   0.265   1.8238   5.1983  -0.6306
 5A1  H4   H  HCH2  0   0.280  -1.6326   3.5198   0.3433
 5A1  H5   H  HCH2  0   0.247  -2.3888   2.6766  -1.0099
 5A1  H6   H  HCH2  0   0.247  -2.4214   1.8708   1.9392
 5A1  H7   H  HCH2  0   0.278  -3.7944   2.4319   0.9803
 5A1  H8   H  HCH2  0   0.271  -1.5333   0.4558  -1.6130
 5A1  H9   H  HCH2  0   0.272  -0.1444  -0.2183  -0.7947
 5A1  H10  H  HCH2  0   0.276  -2.2545  -1.2851  -0.0815
 5A1  H11  H  HCH2  0   0.250  -1.4687  -0.4962   1.2877
 5A1  H12  H  HCH3  0   0.240  -6.3666  -2.0396  -2.2237
 5A1  H13  H  HCH3  0   0.235  -7.6634  -0.8781  -1.9310
 5A1  H14  H  HCH3  0   0.238  -5.9949  -0.3201  -2.0685
 5A1  H15  H  HCH3  0   0.240  -7.2627  -2.5377   1.4124
 5A1  H16  H  HCH3  0   0.242  -8.4220  -2.1393   0.1396
 5A1  H17  H  HCH3  0   0.243  -7.1834  -3.3528  -0.1549
 5A1  H18  H  HCH2  0   0.235  -7.4861   0.5961   0.0893
 5A1  H19  H  HCH2  0   0.231  -6.9885  -0.1670   1.5922
 5A1  CBC  C  CT    0   0.640   3.9203  -1.4081   0.8371

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
 5A1  C4   C5   aromatic  1.398  0.020  1.398
 5A1  C4   N3   aromatic  1.328  0.020  1.328
 5A1  C4   SAS  aromatic  1.728  0.020  1.728
 5A1  C5   C6   aromatic  1.426  0.020  1.426
 5A1  C5   CAI  aromatic  1.428  0.020  1.428
 5A1  C6   N1   aromatic  1.333  0.020  1.333
 5A1  C6   NAZ  single    1.347  0.020  1.347
 5A1  N1   C2   aromatic  1.324  0.020  1.324
 5A1  N3   C2   aromatic  1.319  0.020  1.319
 5A1  FAC  CBB  single    1.329  0.020  1.329
 5A1  CBB  FAD  single    1.328  0.020  1.328
 5A1  CBB  FAE  single    1.329  0.020  1.329
 5A1  CBB  CBC  single    1.541  0.020  1.541
 5A1  CBC  FAF  single    1.349  0.020  1.349
 5A1  CBC  FAG  single    1.352  0.020  1.352
 5A1  CBC  CAU  single    1.486  0.020  1.486
 5A1  CAU  SAS  aromatic  1.731  0.020  1.731
 5A1  CAU  CAI  aromatic  1.353  0.020  1.353
 5A1  NAZ  CAM  single    1.454  0.020  1.454
 5A1  NAZ  CAL  single    1.452  0.020  1.452
 5A1  CAM  CAK  single    1.521  0.020  1.521
 5A1  CAK  NAY  single    1.450  0.020  1.450
 5A1  CAL  CAJ  single    1.519  0.020  1.519
 5A1  CAJ  NAY  single    1.446  0.020  1.446
 5A1  NAY  CAT  single    1.351  0.020  1.351
 5A1  CAT  SAR  single    1.784  0.020  1.784
 5A1  CAT  NAO  double    1.274  0.020  1.274
 5A1  SAR  CBA  single    1.839  0.020  1.839
 5A1  CBA  CAA  single    1.523  0.020  1.523
 5A1  CBA  CAB  single    1.519  0.020  1.519
 5A1  CBA  CAN  single    1.540  0.020  1.540
 5A1  CAN  NAO  single    1.441  0.020  1.441
 5A1  CAI  H2   single    0.930  0.020  1.080
 5A1  C2   H3   single    0.930  0.020  1.080
 5A1  CAM  H4   single    0.970  0.020  1.090
 5A1  CAM  H5   single    0.970  0.020  1.090
 5A1  CAK  H6   single    0.970  0.020  1.090
 5A1  CAK  H7   single    0.970  0.020  1.090
 5A1  CAL  H8   single    0.970  0.020  1.090
 5A1  CAL  H9   single    0.970  0.020  1.090
 5A1  CAJ  H10  single    0.970  0.020  1.090
 5A1  CAJ  H11  single    0.970  0.020  1.090
 5A1  CAA  H12  single    0.970  0.020  1.090
 5A1  CAA  H13  single    0.970  0.020  1.090
 5A1  CAA  H14  single    0.970  0.020  1.090
 5A1  CAB  H15  single    0.970  0.020  1.090
 5A1  CAB  H16  single    0.970  0.020  1.090
 5A1  CAB  H17  single    0.970  0.020  1.090
 5A1  CAN  H18  single    0.970  0.020  1.090
 5A1  CAN  H19  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
 5A1  SAS  C4   N3   121.84  3.000
 5A1  SAS  C4   C5   112.08  3.000
 5A1  N3   C4   C5   125.99  3.000
 5A1  CAI  C5   C6   133.34  3.000
 5A1  CAI  C5   C4   111.65  3.000
 5A1  C6   C5   C4   114.89  3.000
 5A1  NAZ  C6   N1   117.70  3.000
 5A1  NAZ  C6   C5   123.84  3.000
 5A1  N1   C6   C5   118.44  3.000
 5A1  C2   N1   C6   119.59  3.000
 5A1  C2   N3   C4   113.16  3.000
 5A1  CBC  CBB  FAE  109.86  3.000
 5A1  CBC  CBB  FAD  111.30  3.000
 5A1  FAE  CBB  FAD  108.51  3.000
 5A1  CBC  CBB  FAC  110.08  3.000
 5A1  FAE  CBB  FAC  108.60  3.000
 5A1  FAD  CBB  FAC  108.42  3.000
 5A1  CAI  CAU  SAS  113.66  3.000
 5A1  CAI  CAU  CBC  126.44  3.000
 5A1  SAS  CAU  CBC  119.90  3.000
 5A1  CAU  SAS  C4    90.39  3.000
 5A1  H2   CAI  CAU  122.54  3.000
 5A1  H2   CAI  C5   125.27  3.000
 5A1  CAU  CAI  C5   112.13  3.000
 5A1  H3   C2   N3   116.50  3.000
 5A1  H3   C2   N1   115.96  3.000
 5A1  N3   C2   N1   127.52  3.000
 5A1  CAL  NAZ  CAM  112.06  3.000
 5A1  CAL  NAZ  C6   124.42  3.000
 5A1  CAM  NAZ  C6   121.54  3.000
 5A1  H5   CAM  H4   107.98  3.000
 5A1  H5   CAM  CAK  110.28  3.000
 5A1  H4   CAM  CAK  109.46  3.000
 5A1  H5   CAM  NAZ  110.15  3.000
 5A1  H4   CAM  NAZ  109.93  3.000
 5A1  CAK  CAM  NAZ  109.03  3.000
 5A1  H7   CAK  H6   108.05  3.000
 5A1  H7   CAK  NAY  109.23  3.000
 5A1  H6   CAK  NAY  109.45  3.000
 5A1  H7   CAK  CAM  109.65  3.000
 5A1  H6   CAK  CAM  109.22  3.000
 5A1  NAY  CAK  CAM  111.18  3.000
 5A1  H9   CAL  H8   106.55  3.000
 5A1  H9   CAL  CAJ  110.74  3.000
 5A1  H8   CAL  CAJ  108.92  3.000
 5A1  H9   CAL  NAZ  111.60  3.000
 5A1  H8   CAL  NAZ  108.27  3.000
 5A1  CAJ  CAL  NAZ  110.61  3.000
 5A1  H11  CAJ  H10  107.78  3.000
 5A1  H11  CAJ  NAY  110.36  3.000
 5A1  H10  CAJ  NAY  110.74  3.000
 5A1  H11  CAJ  CAL  110.08  3.000
 5A1  H10  CAJ  CAL  108.46  3.000
 5A1  NAY  CAJ  CAL  109.38  3.000
 5A1  CAT  NAY  CAJ  124.72  3.000
 5A1  CAT  NAY  CAK  120.66  3.000
 5A1  CAJ  NAY  CAK  114.51  3.000
 5A1  NAO  CAT  SAR  116.50  3.000
 5A1  NAO  CAT  NAY  124.69  3.000
 5A1  SAR  CAT  NAY  118.80  3.000
 5A1  CBA  SAR  CAT   89.13  3.000
 5A1  CAN  CBA  CAB  112.48  3.000
 5A1  CAN  CBA  CAA  111.49  3.000
 5A1  CAB  CBA  CAA  111.31  3.000
 5A1  CAN  CBA  SAR  101.62  3.000
 5A1  CAB  CBA  SAR  110.43  3.000
 5A1  CAA  CBA  SAR  109.07  3.000
 5A1  H14  CAA  H13  107.90  3.000
 5A1  H14  CAA  H12  108.20  3.000
 5A1  H13  CAA  H12  107.98  3.000
 5A1  H14  CAA  CBA  111.60  3.000
 5A1  H13  CAA  CBA  109.76  3.000
 5A1  H12  CAA  CBA  111.27  3.000
 5A1  H17  CAB  H16  107.40  3.000
 5A1  H17  CAB  H15  108.38  3.000
 5A1  H16  CAB  H15  108.17  3.000
 5A1  H17  CAB  CBA  111.70  3.000
 5A1  H16  CAB  CBA  109.51  3.000
 5A1  H15  CAB  CBA  111.52  3.000
 5A1  H19  CAN  H18  106.62  3.000
 5A1  H19  CAN  NAO  109.77  3.000
 5A1  H18  CAN  NAO  110.65  3.000
 5A1  H19  CAN  CBA  109.56  3.000
 5A1  H18  CAN  CBA  109.50  3.000
 5A1  NAO  CAN  CBA  110.67  3.000
 5A1  CAN  NAO  CAT  111.99  3.000
 5A1  CAU  CBC  FAG  110.06  3.000
 5A1  CAU  CBC  FAF  110.86  3.000
 5A1  FAG  CBC  FAF  108.24  3.000
 5A1  CAU  CBC  CBB  113.09  3.000
 5A1  FAG  CBC  CBB  107.13  3.000
 5A1  FAF  CBC  CBB  107.26  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
 5A1  CONST_01  N1   C6   C5   C4      0.00   0.0  0
 5A1  CONST_02  CAU  CAI  C5   C4      0.00   0.0  0
 5A1  CONST_03  N1   C2   N3   C4      0.00   0.0  0
 5A1  CONST_04  CAI  CAU  SAS  C4      0.00   0.0  0
 5A1  CONST_05  C2   N3   C4   C5      0.00   0.0  0
 5A1  CONST_06  CAU  SAS  C4   C5      0.00   0.0  0
 5A1  CONST_07  C2   N1   C6   C5      0.00   0.0  0
 5A1  CONST_08  SAS  CAU  CAI  C5      0.00   0.0  0
 5A1  CONST_09  N3   C4   C5   C6      0.00   0.0  0
 5A1  CONST_10  SAS  C4   C5   C6    180.00   0.0  0
 5A1  CONST_11  CAU  CAI  C5   C6    180.00   0.0  0
 5A1  CONST_12  N3   C2   N1   C6      0.00   0.0  0
 5A1  CONST_13  CAI  C5   C6   N1    180.00   0.0  0
 5A1  CONST_14  CAI  C5   C4   N3    180.00   0.0  0
 5A1  CONST_15  CAU  SAS  C4   N3    180.00   0.0  0
 5A1  CONST_16  CAI  C5   C4   SAS     0.00   0.0  0
 5A1  CONST_17  C2   N3   C4   SAS   180.00   0.0  0
 5A1  CONST_18  NAZ  C6   C5   C4    180.00   0.0  0
 5A1  CONST_19  NAZ  C6   C5   CAI     0.00   0.0  0
 5A1  CONST_20  NAZ  C6   N1   C2    180.00   0.0  0
 5A1  CONST_21  SAR  CAT  NAY  CAK   180.00   0.0  0
 5A1  CONST_22  NAO  CAT  NAY  CAK     0.00   0.0  0
 5A1  CONST_23  SAR  CAT  NAY  CAJ     0.00   0.0  0
 5A1  CONST_24  NAO  CAT  NAY  CAJ   180.00   0.0  0
 5A1  CONST_25  CAN  NAO  CAT  NAY   180.00   0.0  0
 5A1  CONST_26  CAN  NAO  CAT  SAR     0.00   0.0  0
 5A1  CONST_27  CBC  CAU  SAS  C4    180.00   0.0  0
 5A1  CONST_28  CBC  CAU  CAI  C5    180.00   0.0  0
 5A1  CONST_29  H2   CAI  C5   C4    180.00   0.0  0
 5A1  CONST_30  H3   C2   N3   C4    180.00   0.0  0
 5A1  Var_01    CAM  NAZ  C6   C5    164.55  30.0  2
 5A1  Var_02    CAK  CAM  NAZ  C6   -137.27  30.0  1
 5A1  Var_03    CAJ  CAL  NAZ  C6    136.38  30.0  1
 5A1  Var_04    NAY  CAK  CAM  NAZ   -53.92  30.0  1
 5A1  Var_05    NAY  CAJ  CAL  NAZ    54.88  30.0  1
 5A1  Var_06    CAJ  NAY  CAK  CAM    53.94  30.0  1
 5A1  Var_07    CAL  CAJ  NAY  CAK   -53.49  30.0  1
 5A1  Var_08    CAN  CBA  SAR  CAT   -24.82  30.0  1
 5A1  Var_09    CBA  CAN  NAO  CAT   -25.78  30.0  1
 5A1  Var_10    NAO  CAN  CBA  SAR    32.95  30.0  1
 5A1  Var_11    NAO  CAT  SAR  CBA    13.82  30.0  1
 5A1  Var_12    SAS  CAU  CBC  CBB   -97.77  30.0  2
 5A1  Var_13    H12  CAA  CBA  SAR    61.74  30.0  3
 5A1  Var_14    H15  CAB  CBA  SAR    57.85  30.0  3
 5A1  Var_15    CAU  CBC  CBB  FAC   -62.79  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
 5A1  plan-1  CAK  0.020
 5A1  plan-1  CAJ  0.020
 5A1  plan-1  NAY  0.020
 5A1  plan-1  CAT  0.020
 5A1  plan-1  SAR  0.020
 5A1  plan-1  CAN  0.020
 5A1  plan-1  NAO  0.020
 5A1  plan-2  C4   0.020
 5A1  plan-2  C5   0.020
 5A1  plan-2  C6   0.020
 5A1  plan-2  N1   0.020
 5A1  plan-2  N3   0.020
 5A1  plan-2  CAU  0.020
 5A1  plan-2  SAS  0.020
 5A1  plan-2  CAI  0.020
 5A1  plan-2  C2   0.020
 5A1  plan-2  NAZ  0.020
 5A1  plan-2  H2   0.020
 5A1  plan-2  H3   0.020
 5A1  plan-2  CBC  0.020

