# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 10:40:44 2020
#   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-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)CN=C(S1)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
 0RT  0RT  4-[4-(5,5-dimethyl-4,5-dihydro-1,3-thiazol-2-yl)piperazin-1-yl]-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidine  ligand  47  27  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_0RT
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
 0RT  FAC  F  F     0  -0.307   5.6037   2.0382   1.1903
 0RT  CAZ  C  CT    0   0.988   4.5744   2.6708   0.6068
 0RT  FAD  F  F     0  -0.301   3.6161   2.7851   1.5342
 0RT  FAE  F  F     0  -0.305   4.9914   3.9089   0.3140
 0RT  CAM  C  CH2   0  -0.716   4.0901   1.9474  -0.6262
 0RT  CAT  C  CR5   0  -0.171   3.5533   0.5895  -0.3232
 0RT  SAR  S  S2    0   0.239   4.6101  -0.7131   0.1340
 0RT  CAG  C  CR15  0  -0.231   2.2541   0.2129  -0.3523
 0RT  C5   C  CR56  0   0.039   2.0609  -1.1658  -0.0171
 0RT  C4   C  CR56  0  -0.024   3.2670  -1.7870   0.3152
 0RT  N3   N  N     0  -0.432   3.4067  -3.0253   0.7803
 0RT  C2   C  CR16  0   0.048   2.2580  -3.6486   0.9523
 0RT  N1   N  N     0  -0.472   1.0466  -3.2024   0.6538
 0RT  C6   C  CR6   0   0.533   0.9068  -1.9876   0.1223
 0RT  NAY  N  NT    0  -0.496  -0.3369  -1.5945  -0.2237
 0RT  CAK  C  CH2   0  -0.307  -1.5188  -2.2939   0.2413
 0RT  CAI  C  CH2   0  -0.300  -2.5538  -1.2759   0.6961
 0RT  CAJ  C  CH2   0  -0.337  -0.6453  -0.7047  -1.3273
 0RT  CAH  C  CH2   0  -0.287  -1.6582   0.3416  -0.9054
 0RT  NAX  N  NT    0  -0.494  -2.8311  -0.3140  -0.3545
 0RT  CAS  C  CR5   0   0.363  -4.0422   0.2661  -0.5255
 0RT  SAQ  S  S2    0   0.005  -5.4837  -0.5243   0.1701
 0RT  CBA  C  CR5   0  -0.242  -6.4599   0.9871  -0.2121
 0RT  CAA  C  CH3   0  -0.640  -7.8764   0.6202  -0.6213
 0RT  CAB  C  CH3   0  -0.616  -6.4568   1.9083   1.0010
 0RT  CAL  C  CH2   0  -0.256  -5.6521   1.5896  -1.3751
 0RT  NAN  N  N     0  -0.452  -4.2459   1.3286  -1.1981
 0RT  H1   H  HCH2  0   0.315   3.3018   2.5457  -1.0856
 0RT  H2   H  HCH2  0   0.316   4.9147   1.8981  -1.3415
 0RT  H3   H  HCR5  0   0.279   1.4709   0.9201  -0.5811
 0RT  H4   H  HCR6  0   0.259   2.3065  -4.6467   1.3743
 0RT  H5   H  HCH2  0   0.245  -1.9343  -2.9136  -0.5606
 0RT  H6   H  HCH2  0   0.280  -1.2671  -2.9440   1.0739
 0RT  H7   H  HCH2  0   0.272  -3.4612  -1.8135   0.9681
 0RT  H8   H  HCH2  0   0.244  -2.1910  -0.7675   1.5970
 0RT  H9   H  HCH2  0   0.276   0.2461  -0.2320  -1.7242
 0RT  H10  H  HCH2  0   0.266  -1.0702  -1.3033  -2.1411
 0RT  H11  H  HCH2  0   0.240  -1.2125   1.0219  -0.1693
 0RT  H12  H  HCH2  0   0.272  -1.9543   0.9303  -1.7702
 0RT  H15  H  HCH3  0   0.243  -8.4335   0.1752   0.2034
 0RT  H16  H  HCH3  0   0.242  -8.4099   1.5225  -0.9276
 0RT  H17  H  HCH3  0   0.241  -7.8845  -0.0762  -1.4595
 0RT  H18  H  HCH3  0   0.238  -5.4440   2.1941   1.2856
 0RT  H19  H  HCH3  0   0.235  -7.0117   2.8208   0.7700
 0RT  H20  H  HCH3  0   0.240  -6.9319   1.4343   1.8598
 0RT  H21  H  HCH2  0   0.234  -5.9940   1.1567  -2.3237
 0RT  H22  H  HCH2  0   0.236  -5.8402   2.6653  -1.4342

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
 0RT  CAH  CAJ  single    1.516  0.020  1.516
 0RT  CAH  NAX  single    1.452  0.020  1.452
 0RT  CAJ  NAY  single    1.451  0.020  1.451
 0RT  FAD  CAZ  single    1.338  0.020  1.338
 0RT  NAN  CAL  single    1.441  0.020  1.441
 0RT  NAN  CAS  double    1.274  0.020  1.274
 0RT  NAY  C6   single    1.349  0.020  1.349
 0RT  NAY  CAK  single    1.450  0.020  1.450
 0RT  N1   C6   aromatic  1.333  0.020  1.333
 0RT  N1   C2   aromatic  1.325  0.020  1.325
 0RT  C6   C5   aromatic  1.424  0.020  1.424
 0RT  NAX  CAS  single    1.354  0.020  1.354
 0RT  NAX  CAI  single    1.451  0.020  1.451
 0RT  C2   N3   aromatic  1.318  0.020  1.318
 0RT  CAL  CBA  single    1.539  0.020  1.539
 0RT  FAC  CAZ  single    1.342  0.020  1.342
 0RT  CAK  CAI  single    1.521  0.020  1.521
 0RT  CAS  SAQ  single    1.785  0.020  1.785
 0RT  C5   CAG  aromatic  1.432  0.020  1.432
 0RT  C5   C4   aromatic  1.397  0.020  1.397
 0RT  N3   C4   aromatic  1.330  0.020  1.330
 0RT  CAZ  FAE  single    1.339  0.020  1.339
 0RT  CAZ  CAM  single    1.509  0.020  1.509
 0RT  CAG  CAT  aromatic  1.353  0.020  1.353
 0RT  C4   SAR  aromatic  1.729  0.020  1.729
 0RT  CAT  SAR  aromatic  1.739  0.020  1.739
 0RT  CAT  CAM  single    1.491  0.020  1.491
 0RT  CAB  CBA  single    1.523  0.020  1.523
 0RT  CBA  SAQ  single    1.839  0.020  1.839
 0RT  CBA  CAA  single    1.519  0.020  1.519
 0RT  CAM  H1   single    0.970  0.020  1.090
 0RT  CAM  H2   single    0.970  0.020  1.090
 0RT  CAG  H3   single    0.930  0.020  1.080
 0RT  C2   H4   single    0.930  0.020  1.080
 0RT  CAK  H5   single    0.970  0.020  1.090
 0RT  CAK  H6   single    0.970  0.020  1.090
 0RT  CAI  H7   single    0.970  0.020  1.090
 0RT  CAI  H8   single    0.970  0.020  1.090
 0RT  CAJ  H9   single    0.970  0.020  1.090
 0RT  CAJ  H10  single    0.970  0.020  1.090
 0RT  CAH  H11  single    0.970  0.020  1.090
 0RT  CAH  H12  single    0.970  0.020  1.090
 0RT  CAA  H15  single    0.970  0.020  1.090
 0RT  CAA  H16  single    0.970  0.020  1.090
 0RT  CAA  H17  single    0.970  0.020  1.090
 0RT  CAB  H18  single    0.970  0.020  1.090
 0RT  CAB  H19  single    0.970  0.020  1.090
 0RT  CAB  H20  single    0.970  0.020  1.090
 0RT  CAL  H21  single    0.970  0.020  1.090
 0RT  CAL  H22  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
 0RT  CAM  CAZ  FAE  111.38  3.000
 0RT  CAM  CAZ  FAD  112.16  3.000
 0RT  FAE  CAZ  FAD  107.19  3.000
 0RT  CAM  CAZ  FAC  112.05  3.000
 0RT  FAE  CAZ  FAC  106.99  3.000
 0RT  FAD  CAZ  FAC  106.75  3.000
 0RT  H2   CAM  H1   107.11  3.000
 0RT  H2   CAM  CAT  111.32  3.000
 0RT  H1   CAM  CAT  108.95  3.000
 0RT  H2   CAM  CAZ  108.31  3.000
 0RT  H1   CAM  CAZ  108.24  3.000
 0RT  CAT  CAM  CAZ  112.71  3.000
 0RT  CAG  CAT  SAR  112.38  3.000
 0RT  SAR  CAT  CAM  121.12  3.000
 0RT  CAG  CAT  CAM  126.50  3.000
 0RT  C4   SAR  CAT   91.19  3.000
 0RT  H3   CAG  C5   125.62  3.000
 0RT  H3   CAG  CAT  121.25  3.000
 0RT  C5   CAG  CAT  113.11  3.000
 0RT  C6   C5   C4   114.83  3.000
 0RT  C4   C5   CAG  111.55  3.000
 0RT  C6   C5   CAG  133.48  3.000
 0RT  N3   C4   C5   126.01  3.000
 0RT  N3   C4   SAR  122.23  3.000
 0RT  C5   C4   SAR  111.69  3.000
 0RT  C2   N3   C4   113.22  3.000
 0RT  H4   C2   N1   116.00  3.000
 0RT  H4   C2   N3   116.54  3.000
 0RT  N1   C2   N3   127.45  3.000
 0RT  C6   N1   C2   119.50  3.000
 0RT  NAY  C6   N1   117.66  3.000
 0RT  N1   C6   C5   118.68  3.000
 0RT  NAY  C6   C5   123.63  3.000
 0RT  CAJ  NAY  CAK  111.50  3.000
 0RT  CAK  NAY  C6   121.90  3.000
 0RT  CAJ  NAY  C6   124.73  3.000
 0RT  H6   CAK  H5   108.09  3.000
 0RT  H6   CAK  CAI  109.21  3.000
 0RT  H5   CAK  CAI  109.84  3.000
 0RT  H6   CAK  NAY  110.23  3.000
 0RT  H5   CAK  NAY  110.33  3.000
 0RT  CAI  CAK  NAY  109.13  3.000
 0RT  H8   CAI  H7   107.42  3.000
 0RT  H8   CAI  NAX  110.54  3.000
 0RT  H7   CAI  NAX  110.41  3.000
 0RT  H8   CAI  CAK  109.33  3.000
 0RT  H7   CAI  CAK  108.13  3.000
 0RT  NAX  CAI  CAK  110.92  3.000
 0RT  H10  CAJ  H9   106.55  3.000
 0RT  H10  CAJ  CAH  108.94  3.000
 0RT  H9   CAJ  CAH  110.50  3.000
 0RT  H10  CAJ  NAY  108.20  3.000
 0RT  H9   CAJ  NAY  111.79  3.000
 0RT  CAH  CAJ  NAY  110.71  3.000
 0RT  H12  CAH  H11  107.98  3.000
 0RT  H12  CAH  NAX  109.04  3.000
 0RT  H11  CAH  NAX  110.70  3.000
 0RT  H12  CAH  CAJ  109.53  3.000
 0RT  H11  CAH  CAJ  110.07  3.000
 0RT  NAX  CAH  CAJ  109.48  3.000
 0RT  CAS  NAX  CAH  118.76  3.000
 0RT  CAS  NAX  CAI  123.12  3.000
 0RT  CAH  NAX  CAI  114.81  3.000
 0RT  NAN  CAS  SAQ  116.48  3.000
 0RT  SAQ  CAS  NAX  118.92  3.000
 0RT  NAN  CAS  NAX  124.55  3.000
 0RT  CBA  SAQ  CAS   89.07  3.000
 0RT  CAL  CBA  CAB  111.35  3.000
 0RT  CAB  CBA  CAA  111.25  3.000
 0RT  CAL  CBA  CAA  112.36  3.000
 0RT  CAA  CBA  SAQ  110.63  3.000
 0RT  CAB  CBA  SAQ  109.29  3.000
 0RT  CAL  CBA  SAQ  101.55  3.000
 0RT  H17  CAA  H16  107.98  3.000
 0RT  H17  CAA  H15  108.50  3.000
 0RT  H16  CAA  H15  107.44  3.000
 0RT  H17  CAA  CBA  111.62  3.000
 0RT  H16  CAA  CBA  109.35  3.000
 0RT  H15  CAA  CBA  111.79  3.000
 0RT  H20  CAB  H19  107.96  3.000
 0RT  H20  CAB  H18  108.25  3.000
 0RT  H19  CAB  H18  107.94  3.000
 0RT  H20  CAB  CBA  111.32  3.000
 0RT  H19  CAB  CBA  109.61  3.000
 0RT  H18  CAB  CBA  111.61  3.000
 0RT  H22  CAL  H21  106.72  3.000
 0RT  H22  CAL  NAN  110.65  3.000
 0RT  H21  CAL  NAN  109.79  3.000
 0RT  H22  CAL  CBA  109.62  3.000
 0RT  H21  CAL  CBA  109.59  3.000
 0RT  NAN  CAL  CBA  110.39  3.000
 0RT  CAL  NAN  CAS  111.83  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
 0RT  CONST_01  C6   C5   CAG  CAT   180.00   0.0  0
 0RT  CONST_02  C4   C5   CAG  CAT     0.00   0.0  0
 0RT  CONST_03  C5   C4   SAR  CAT     0.00   0.0  0
 0RT  CONST_04  N3   C4   SAR  CAT   180.00   0.0  0
 0RT  CONST_05  C6   C5   C4   SAR   180.00   0.0  0
 0RT  CONST_06  CAG  C5   C4   SAR     0.00   0.0  0
 0RT  CONST_07  C2   N3   C4   SAR   180.00   0.0  0
 0RT  CONST_08  C5   CAG  CAT  SAR     0.00   0.0  0
 0RT  CONST_09  N1   C6   C5   CAG   180.00   0.0  0
 0RT  CONST_10  N3   C4   C5   CAG   180.00   0.0  0
 0RT  CONST_11  C4   SAR  CAT  CAG     0.00   0.0  0
 0RT  CONST_12  C2   N1   C6   C5      0.00   0.0  0
 0RT  CONST_13  C2   N3   C4   C5      0.00   0.0  0
 0RT  CONST_14  N1   C6   C5   C4      0.00   0.0  0
 0RT  CONST_15  N1   C2   N3   C4      0.00   0.0  0
 0RT  CONST_16  C6   N1   C2   N3      0.00   0.0  0
 0RT  CONST_17  C6   C5   C4   N3      0.00   0.0  0
 0RT  CONST_18  NAY  C6   C5   CAG     0.00   0.0  0
 0RT  CONST_19  NAY  C6   C5   C4    180.00   0.0  0
 0RT  CONST_20  NAY  C6   N1   C2    180.00   0.0  0
 0RT  CONST_23  NAN  CAS  NAX  CAH     0.00   0.0  0
 0RT  CONST_24  SAQ  CAS  NAX  CAH   180.00   0.0  0
 0RT  CONST_25  CAL  NAN  CAS  NAX   180.00   0.0  0
 0RT  CONST_26  CAL  NAN  CAS  SAQ     0.00   0.0  0
 0RT  CONST_27  C5   CAG  CAT  CAM   180.00   0.0  0
 0RT  CONST_28  C4   SAR  CAT  CAM   180.00   0.0  0
 0RT  CONST_29  H3   CAG  CAT  SAR   180.00   0.0  0
 0RT  CONST_30  H4   C2   N3   C4    180.00   0.0  0
 0RT  Var_01    CAJ  NAY  C6   C5     33.34  30.0  2
 0RT  Var_02    CAH  CAJ  NAY  C6   -135.03  30.0  1
 0RT  Var_03    CAI  CAK  NAY  C6    135.50  30.0  1
 0RT  Var_04    NAX  CAH  CAJ  NAY   -54.53  30.0  1
 0RT  Var_05    NAX  CAI  CAK  NAY    54.44  30.0  1
 0RT  Var_06    CAH  NAX  CAI  CAK   -52.97  30.0  1
 0RT  Var_07    CAJ  CAH  NAX  CAI    52.28  30.0  1
 0RT  Var_08    CBA  CAL  NAN  CAS    27.57  30.0  1
 0RT  Var_09    CAL  CBA  SAQ  CAS    24.91  30.0  1
 0RT  Var_10    NAN  CAL  CBA  SAQ   -33.93  30.0  1
 0RT  Var_11    NAN  CAS  SAQ  CBA   -12.81  30.0  1
 0RT  Var_12    CAG  CAT  CAM  CAZ   108.03  30.0  1
 0RT  Var_13    H18  CAB  CBA  SAQ    58.87  30.0  3
 0RT  Var_14    H15  CAA  CBA  SAQ    66.10  30.0  3
 0RT  Var_15    CAT  CAM  CAZ  FAC    63.13  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
 0RT  plan-1  CAI  0.020
 0RT  plan-1  CAH  0.020
 0RT  plan-1  NAX  0.020
 0RT  plan-1  CAS  0.020
 0RT  plan-1  SAQ  0.020
 0RT  plan-1  CAL  0.020
 0RT  plan-1  NAN  0.020
 0RT  plan-2  CAM  0.020
 0RT  plan-2  CAT  0.020
 0RT  plan-2  SAR  0.020
 0RT  plan-2  CAG  0.020
 0RT  plan-2  C5   0.020
 0RT  plan-2  C4   0.020
 0RT  plan-2  N3   0.020
 0RT  plan-2  C2   0.020
 0RT  plan-2  N1   0.020
 0RT  plan-2  C6   0.020
 0RT  plan-2  NAY  0.020
 0RT  plan-2  H3   0.020
 0RT  plan-2  H4   0.020

