# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 05:18:45 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: 4-{4-[5-(fluoromethyl)-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: FCc1sc(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
 59M  59M  4-{4-[5-(fluoromethyl)-1,3,4-thiadiazol-2-yl]piperazin-1-yl}-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidine  ligand  41  27  .  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_59M
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
 59M  C4   C  CR56  0  -0.026  -2.9414  -1.9430  -0.9554
 59M  C5   C  CR56  0   0.054  -2.1412  -1.4428   0.0751
 59M  C6   C  CR6   0   0.524  -0.8669  -2.0629   0.1941
 59M  N1   N  N     0  -0.469  -0.5829  -3.1017  -0.5886
 59M  N3   N  N     0  -0.428  -2.6278  -2.9437  -1.7732
 59M  FAB  F  F     0  -0.307  -5.7064   1.6974  -1.1383
 59M  CBA  C  CT    0   0.989  -5.2307   2.0093   0.0770
 59M  FAC  F  F     0  -0.301  -4.0805   2.6652  -0.1157
 59M  FAD  F  F     0  -0.304  -6.0929   2.8745   0.6243
 59M  CAS  C  CR5   0  -0.167  -4.0704  -0.1809   0.3681
 59M  SAR  S  S2    0   0.243  -4.4735  -1.1465  -1.0203
 59M  CAF  C  CR15  0  -0.243  -2.8291  -0.4446   0.8376
 59M  C2   C  CR16  0   0.047  -1.4573  -3.4867  -1.5081
 59M  NAZ  N  NT    0  -0.485   0.0675  -1.6876   1.1040
 59M  CAK  C  CH2   0  -0.341   1.2485  -2.5038   1.3233
 59M  CAI  C  CH2   0  -0.301   2.4286  -2.0213   0.5017
 59M  CAJ  C  CH2   0  -0.348   0.3229  -0.3039   1.4567
 59M  CAH  C  CH2   0  -0.300   1.4896   0.2555   0.6527
 59M  NAY  N  NT    0  -0.493   2.6577  -0.6019   0.7479
 59M  CAU  C  CR5   0   0.364   3.8829  -0.1052   0.4974
 59M  SAQ  S  S2    0   0.161   4.2104   1.6040   0.4405
 59M  NAP  N  N     0  -0.345   4.9462  -0.8372   0.2918
 59M  NAO  N  N     0  -0.222   6.0545  -0.1027   0.0989
 59M  CAT  C  CR5   0   0.005   5.8655   1.1677   0.1468
 59M  CAG  C  CH2   0  -0.053   6.9325   2.1810  -0.0419
 59M  FAA  F  F     0  -0.369   6.6364   2.9683  -1.1491
 59M  H1   H  HCH2  0   0.315  -4.7013   1.1067   1.9237
 59M  H2   H  HCH2  0   0.317  -6.0296   0.3199   1.0843
 59M  H3   H  HCR5  0   0.286  -2.4512   0.0372   1.7269
 59M  H4   H  HCR6  0   0.261  -1.1650  -4.3353  -2.1170
 59M  H5   H  HCH2  0   0.267   1.4935  -2.4437   2.3868
 59M  H6   H  HCH2  0   0.282   1.0405  -3.5424   1.0846
 59M  H7   H  HCH2  0   0.279   3.3178  -2.5790   0.7865
 59M  H8   H  HCH2  0   0.251   2.2467  -2.1965  -0.5643
 59M  H9   H  HCH2  0   0.282  -0.5349   0.3299   1.2629
 59M  H10  H  HCH2  0   0.269   0.5416  -0.2449   2.5251
 59M  H11  H  HCH2  0   0.257   1.1905   0.3857  -0.3943
 59M  H12  H  HCH2  0   0.278   1.7170   1.2426   1.0584
 59M  H17  H  HCH2  0   0.240   7.0175   2.8374   0.8240
 59M  H18  H  HCH2  0   0.247   7.8818   1.6710  -0.2026
 59M  CAL  C  CH2   0  -0.716  -5.0512   0.7850   0.9413

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
 59M  C4   C5   aromatic  1.397  0.020  1.397
 59M  C4   N3   aromatic  1.330  0.020  1.330
 59M  C4   SAR  aromatic  1.728  0.020  1.728
 59M  C5   C6   aromatic  1.422  0.020  1.422
 59M  C5   CAF  aromatic  1.432  0.020  1.432
 59M  C6   N1   aromatic  1.331  0.020  1.331
 59M  C6   NAZ  single    1.357  0.020  1.357
 59M  N1   C2   aromatic  1.326  0.020  1.326
 59M  N3   C2   aromatic  1.317  0.020  1.317
 59M  FAB  CBA  single    1.342  0.020  1.342
 59M  CBA  FAC  single    1.338  0.020  1.338
 59M  CBA  FAD  single    1.338  0.020  1.338
 59M  CBA  CAL  single    1.509  0.020  1.509
 59M  CAL  CAS  single    1.491  0.020  1.491
 59M  CAS  SAR  aromatic  1.739  0.020  1.739
 59M  CAS  CAF  aromatic  1.353  0.020  1.353
 59M  NAZ  CAK  single    1.452  0.020  1.452
 59M  NAZ  CAJ  single    1.451  0.020  1.451
 59M  CAK  CAI  single    1.517  0.020  1.517
 59M  CAI  NAY  single    1.459  0.020  1.459
 59M  CAJ  CAH  single    1.523  0.020  1.523
 59M  CAH  NAY  single    1.452  0.020  1.452
 59M  NAY  CAU  single    1.346  0.020  1.346
 59M  CAU  SAQ  aromatic  1.741  0.020  1.741
 59M  CAU  NAP  aromatic  1.307  0.020  1.307
 59M  SAQ  CAT  aromatic  1.737  0.020  1.737
 59M  NAP  NAO  aromatic  1.343  0.020  1.343
 59M  NAO  CAT  aromatic  1.285  0.020  1.285
 59M  CAT  CAG  single    1.484  0.020  1.484
 59M  CAG  FAA  single    1.390  0.020  1.390
 59M  CAL  H1   single    0.970  0.020  1.090
 59M  CAL  H2   single    0.970  0.020  1.090
 59M  CAF  H3   single    0.930  0.020  1.080
 59M  C2   H4   single    0.930  0.020  1.080
 59M  CAK  H5   single    0.970  0.020  1.090
 59M  CAK  H6   single    0.970  0.020  1.090
 59M  CAI  H7   single    0.970  0.020  1.090
 59M  CAI  H8   single    0.970  0.020  1.090
 59M  CAJ  H9   single    0.970  0.020  1.090
 59M  CAJ  H10  single    0.970  0.020  1.090
 59M  CAH  H11  single    0.970  0.020  1.090
 59M  CAH  H12  single    0.970  0.020  1.090
 59M  CAG  H17  single    0.970  0.020  1.090
 59M  CAG  H18  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
 59M  SAR  C4   N3   122.20  3.000
 59M  SAR  C4   C5   111.74  3.000
 59M  N3   C4   C5   126.01  3.000
 59M  CAF  C5   C6   133.61  3.000
 59M  CAF  C5   C4   111.54  3.000
 59M  C6   C5   C4   114.75  3.000
 59M  NAZ  C6   N1   117.58  3.000
 59M  NAZ  C6   C5   123.54  3.000
 59M  N1   C6   C5   118.83  3.000
 59M  C2   N1   C6   119.58  3.000
 59M  C2   N3   C4   113.33  3.000
 59M  CAL  CBA  FAD  111.52  3.000
 59M  CAL  CBA  FAC  112.20  3.000
 59M  FAD  CBA  FAC  107.20  3.000
 59M  CAL  CBA  FAB  111.86  3.000
 59M  FAD  CBA  FAB  106.99  3.000
 59M  FAC  CBA  FAB  106.75  3.000
 59M  CAF  CAS  SAR  112.43  3.000
 59M  CAF  CAS  CAL  126.61  3.000
 59M  SAR  CAS  CAL  120.95  3.000
 59M  CAS  SAR  C4    91.17  3.000
 59M  H3   CAF  CAS  121.33  3.000
 59M  H3   CAF  C5   125.55  3.000
 59M  CAS  CAF  C5   113.07  3.000
 59M  H4   C2   N3   116.68  3.000
 59M  H4   C2   N1   116.03  3.000
 59M  N3   C2   N1   127.28  3.000
 59M  CAJ  NAZ  CAK  110.87  3.000
 59M  CAJ  NAZ  C6   123.23  3.000
 59M  CAK  NAZ  C6   120.38  3.000
 59M  H6   CAK  H5   108.03  3.000
 59M  H6   CAK  CAI  109.53  3.000
 59M  H5   CAK  CAI  109.58  3.000
 59M  H6   CAK  NAZ  110.41  3.000
 59M  H5   CAK  NAZ  107.36  3.000
 59M  CAI  CAK  NAZ  111.85  3.000
 59M  H8   CAI  H7   107.97  3.000
 59M  H8   CAI  NAY  110.23  3.000
 59M  H7   CAI  NAY  109.05  3.000
 59M  H8   CAI  CAK  110.31  3.000
 59M  H7   CAI  CAK  109.34  3.000
 59M  NAY  CAI  CAK  109.90  3.000
 59M  H10  CAJ  H9   107.56  3.000
 59M  H10  CAJ  CAH  110.07  3.000
 59M  H9   CAJ  CAH  107.28  3.000
 59M  H10  CAJ  NAZ  108.94  3.000
 59M  H9   CAJ  NAZ  112.02  3.000
 59M  CAH  CAJ  NAZ  110.90  3.000
 59M  H12  CAH  H11  107.72  3.000
 59M  H12  CAH  NAY  110.00  3.000
 59M  H11  CAH  NAY  110.62  3.000
 59M  H12  CAH  CAJ  107.19  3.000
 59M  H11  CAH  CAJ  109.79  3.000
 59M  NAY  CAH  CAJ  111.39  3.000
 59M  CAU  NAY  CAH  120.15  3.000
 59M  CAU  NAY  CAI  118.08  3.000
 59M  CAH  NAY  CAI  115.92  3.000
 59M  NAP  CAU  SAQ  113.05  3.000
 59M  NAP  CAU  NAY  124.28  3.000
 59M  SAQ  CAU  NAY  122.66  3.000
 59M  CAT  SAQ  CAU   86.45  3.000
 59M  NAO  NAP  CAU  112.80  3.000
 59M  CAT  NAO  NAP  114.44  3.000
 59M  CAG  CAT  NAO  124.37  3.000
 59M  CAG  CAT  SAQ  122.37  3.000
 59M  NAO  CAT  SAQ  113.26  3.000
 59M  H18  CAG  H17  109.34  3.000
 59M  H18  CAG  FAA  109.46  3.000
 59M  H17  CAG  FAA  107.95  3.000
 59M  H18  CAG  CAT  109.01  3.000
 59M  H17  CAG  CAT  111.49  3.000
 59M  FAA  CAG  CAT  109.57  3.000
 59M  H2   CAL  H1   107.14  3.000
 59M  H2   CAL  CAS  111.32  3.000
 59M  H1   CAL  CAS  109.03  3.000
 59M  H2   CAL  CBA  108.28  3.000
 59M  H1   CAL  CBA  108.33  3.000
 59M  CAS  CAL  CBA  112.56  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
 59M  CONST_01  N1   C6   C5   C4     0.00   0.0  0
 59M  CONST_02  CAS  CAF  C5   C4     0.00   0.0  0
 59M  CONST_03  N1   C2   N3   C4     0.00   0.0  0
 59M  CONST_04  CAF  CAS  SAR  C4     0.00   0.0  0
 59M  CONST_05  C2   N3   C4   C5     0.00   0.0  0
 59M  CONST_06  CAS  SAR  C4   C5     0.00   0.0  0
 59M  CONST_07  C2   N1   C6   C5     0.00   0.0  0
 59M  CONST_08  SAR  CAS  CAF  C5     0.00   0.0  0
 59M  CONST_09  N3   C4   C5   C6     0.00   0.0  0
 59M  CONST_10  SAR  C4   C5   C6   180.00   0.0  0
 59M  CONST_11  CAS  CAF  C5   C6   180.00   0.0  0
 59M  CONST_12  N3   C2   N1   C6     0.00   0.0  0
 59M  CONST_13  CAF  C5   C6   N1   180.00   0.0  0
 59M  CONST_14  CAF  C5   C4   N3   180.00   0.0  0
 59M  CONST_15  CAS  SAR  C4   N3   180.00   0.0  0
 59M  CONST_16  CAF  C5   C4   SAR    0.00   0.0  0
 59M  CONST_17  C2   N3   C4   SAR  180.00   0.0  0
 59M  CONST_18  NAO  CAT  SAQ  CAU    0.00   0.0  0
 59M  CONST_19  CAT  NAO  NAP  CAU    0.00   0.0  0
 59M  CONST_20  NAO  NAP  CAU  SAQ    0.00   0.0  0
 59M  CONST_21  NAP  NAO  CAT  SAQ    0.00   0.0  0
 59M  CONST_22  CAT  SAQ  CAU  NAP    0.00   0.0  0
 59M  CONST_23  NAZ  C6   C5   C4   180.00   0.0  0
 59M  CONST_24  NAZ  C6   C5   CAF    0.00   0.0  0
 59M  CONST_25  NAZ  C6   N1   C2   180.00   0.0  0
 59M  CONST_26  CAT  SAQ  CAU  NAY  180.00   0.0  0
 59M  CONST_27  NAO  NAP  CAU  NAY  180.00   0.0  0
 59M  CONST_28  CAL  CAS  SAR  C4   180.00   0.0  0
 59M  CONST_29  CAL  CAS  CAF  C5   180.00   0.0  0
 59M  CONST_30  CAG  CAT  SAQ  CAU  180.00   0.0  0
 59M  CONST_31  CAG  CAT  NAO  NAP  180.00   0.0  0
 59M  CONST_32  H3   CAF  C5   C4   180.00   0.0  0
 59M  CONST_33  H4   C2   N3   C4   180.00   0.0  0
 59M  Var_01    CAK  NAZ  C6   C5   169.46  30.0  2
 59M  Var_02    CAI  CAK  NAZ  C6    95.18  30.0  1
 59M  Var_03    CAH  CAJ  NAZ  C6   -95.84  30.0  1
 59M  Var_04    NAY  CAI  CAK  NAZ   53.40  30.0  1
 59M  Var_05    NAY  CAH  CAJ  NAZ  -51.98  30.0  1
 59M  Var_06    CAH  NAY  CAI  CAK  -49.32  30.0  1
 59M  Var_07    CAJ  CAH  NAY  CAI   49.13  30.0  1
 59M  Var_08    SAQ  CAU  NAY  CAI  167.50  30.0  2
 59M  Var_09    SAR  CAS  CAL  CBA  -73.00  30.0  2
 59M  Var_10    FAA  CAG  CAT  SAQ  -60.67  30.0  2
 59M  Var_11    CAS  CAL  CBA  FAB   61.55  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
 59M  plan-1  NAY  0.020
 59M  plan-1  CAU  0.020
 59M  plan-1  SAQ  0.020
 59M  plan-1  NAP  0.020
 59M  plan-1  NAO  0.020
 59M  plan-1  CAT  0.020
 59M  plan-1  CAG  0.020
 59M  plan-2  C4   0.020
 59M  plan-2  C5   0.020
 59M  plan-2  C6   0.020
 59M  plan-2  N1   0.020
 59M  plan-2  N3   0.020
 59M  plan-2  CAS  0.020
 59M  plan-2  SAR  0.020
 59M  plan-2  CAF  0.020
 59M  plan-2  C2   0.020
 59M  plan-2  NAZ  0.020
 59M  plan-2  H3   0.020
 59M  plan-2  H4   0.020
 59M  plan-2  CAL  0.020

