# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 06:57:52 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: 6-(2,2,2-trifluoroethyl)-4-{4-[5-(trifluoromethyl)-1,3,4-thiadiazol-2-yl]piperazin-1-yl}thieno[2,3-d]pyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)Cc1sc2ncnc(N3CCN(CC3)c4sc(nn4)C(F)(F)F)c2c1
#
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
 59V  59V  6-(2,2,2-trifluoroethyl)-4-{4-[5-(trifluoromethyl)-1,3,4-thiadiazol-2-yl]piperazin-1-yl}thieno[2,3-d]pyrimidine  ligand  41  29  .  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_59V
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
 59V  C4   C  CR56  0  -0.025  -3.5900   1.9311   1.0275
 59V  C5   C  CR56  0   0.054  -2.8173   1.4118  -0.0147
 59V  C6   C  CR6   0   0.524  -1.5162   1.9739  -0.1276
 59V  N1   N  N     0  -0.469  -1.1805   2.9831   0.6727
 59V  N3   N  N     0  -0.428  -3.2271   2.9012   1.8616
 59V  FAA  F  F     0  -0.300  -4.9132  -2.6003   0.1116
 59V  CBB  C  CT    0   0.989  -6.0424  -1.9035  -0.0600
 59V  FAB  F  F     0  -0.304  -6.9364  -2.7293  -0.6170
 59V  FAC  F  F     0  -0.308  -6.4993  -1.5991   1.1647
 59V  CAT  C  CR5   0  -0.167  -4.8038   0.2455  -0.3202
 59V  SAS  S  S2    0   0.244  -5.1571   1.2052   1.0854
 59V  CAH  C  CR15  0  -0.242  -3.5532   0.4587  -0.7904
 59V  C2   C  CR16  0   0.048  -2.0327   3.3924   1.6026
 59V  NBA  N  NT    0  -0.486  -0.6034   1.5719  -1.0486
 59V  CAL  C  CH2   0  -0.353  -0.4117   0.1824  -1.4236
 59V  CAJ  C  CH2   0  -0.293   0.7355  -0.4375  -0.6390
 59V  CAK  C  CH2   0  -0.333   0.6064   2.3420  -1.2661
 59V  CAI  C  CH2   0  -0.319   1.7772   1.7937  -0.4691
 59V  NAZ  N  NT    0  -0.496   1.9409   0.3741  -0.7410
 59V  CAU  C  CR5   0   0.385   3.1324  -0.2217  -0.6215
 59V  SAR  S  S2    0   0.203   4.6138   0.6800  -0.4353
 59V  NAP  N  N     0  -0.337   3.3192  -1.5205  -0.6501
 59V  NAQ  N  N     0  -0.205   4.6081  -1.8598  -0.5567
 59V  CAV  C  CR5   0  -0.215   5.4017  -0.8588  -0.4411
 59V  CBC  C  CT    0   1.074   6.8780  -0.9898  -0.2967
 59V  FAE  F  F     0  -0.305   7.2805  -0.6263   0.9261
 59V  FAF  F  F     0  -0.291   7.2737  -2.2388  -0.5048
 59V  FAD  F  F     0  -0.305   7.5147  -0.1956  -1.1637
 59V  H1   H  HCH2  0   0.316  -5.5040  -0.9819  -1.8951
 59V  H2   H  HCH2  0   0.317  -6.7905  -0.1639  -1.0191
 59V  H3   H  HCR5  0   0.287  -3.2012  -0.0263  -1.6888
 59V  H4   H  HCR6  0   0.261  -1.6984   4.2150   2.2253
 59V  H5   H  HCH2  0   0.282  -1.2948  -0.4142  -1.2249
 59V  H6   H  HCH2  0   0.269  -0.2100   0.1286  -2.4957
 59V  H7   H  HCH2  0   0.257   0.4503  -0.5453   0.4137
 59V  H8   H  HCH2  0   0.289   0.9358  -1.4310  -1.0325
 59V  H9   H  HCH2  0   0.271   0.8404   2.2914  -2.3325
 59V  H10  H  HCH2  0   0.286   0.4465   3.3835  -1.0051
 59V  H11  H  HCH2  0   0.277   2.6728   2.3381  -0.7729
 59V  H12  H  HCH2  0   0.266   1.6238   1.9623   0.6019
 59V  CAM  C  CH2   0  -0.716  -5.8285  -0.6687  -0.9014

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
 59V  FAD  CBC  single    1.337  0.020  1.337
 59V  FAE  CBC  single    1.338  0.020  1.338
 59V  CBC  FAF  single    1.327  0.020  1.327
 59V  CBC  CAV  single    1.489  0.020  1.489
 59V  SAR  CAV  aromatic  1.729  0.020  1.729
 59V  SAR  CAU  aromatic  1.744  0.020  1.744
 59V  CAM  CAT  single    1.491  0.020  1.491
 59V  CAM  CBB  single    1.509  0.020  1.509
 59V  CAV  NAQ  aromatic  1.283  0.020  1.283
 59V  SAS  CAT  aromatic  1.738  0.020  1.738
 59V  SAS  C4   aromatic  1.728  0.020  1.728
 59V  CAT  CAH  aromatic  1.353  0.020  1.353
 59V  CAJ  CAL  single    1.522  0.020  1.522
 59V  CAJ  NAZ  single    1.457  0.020  1.457
 59V  FAB  CBB  single    1.338  0.020  1.338
 59V  C4   N3   aromatic  1.330  0.020  1.330
 59V  C4   C5   aromatic  1.398  0.020  1.398
 59V  CAH  C5   aromatic  1.432  0.020  1.432
 59V  N3   C2   aromatic  1.317  0.020  1.317
 59V  C5   C6   aromatic  1.422  0.020  1.422
 59V  CBB  FAC  single    1.342  0.020  1.342
 59V  CBB  FAA  single    1.338  0.020  1.338
 59V  CAL  NBA  single    1.452  0.020  1.452
 59V  CAU  NAZ  single    1.338  0.020  1.338
 59V  CAU  NAP  aromatic  1.312  0.020  1.312
 59V  C2   N1   aromatic  1.326  0.020  1.326
 59V  NAQ  NAP  aromatic  1.336  0.020  1.336
 59V  C6   N1   aromatic  1.331  0.020  1.331
 59V  C6   NBA  single    1.358  0.020  1.358
 59V  NAZ  CAI  single    1.455  0.020  1.455
 59V  NBA  CAK  single    1.450  0.020  1.450
 59V  CAK  CAI  single    1.519  0.020  1.519
 59V  CAM  H1   single    0.970  0.020  1.090
 59V  CAM  H2   single    0.970  0.020  1.090
 59V  CAH  H3   single    0.930  0.020  1.080
 59V  C2   H4   single    0.930  0.020  1.080
 59V  CAL  H5   single    0.970  0.020  1.090
 59V  CAL  H6   single    0.970  0.020  1.090
 59V  CAJ  H7   single    0.970  0.020  1.090
 59V  CAJ  H8   single    0.970  0.020  1.090
 59V  CAK  H9   single    0.970  0.020  1.090
 59V  CAK  H10  single    0.970  0.020  1.090
 59V  CAI  H11  single    0.970  0.020  1.090
 59V  CAI  H12  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
 59V  SAS  C4   N3   122.20  3.000
 59V  N3   C4   C5   126.01  3.000
 59V  SAS  C4   C5   111.74  3.000
 59V  CAH  C5   C6   133.65  3.000
 59V  C6   C5   C4   114.73  3.000
 59V  CAH  C5   C4   111.53  3.000
 59V  NBA  C6   N1   117.57  3.000
 59V  NBA  C6   C5   123.51  3.000
 59V  N1   C6   C5   118.87  3.000
 59V  C2   N1   C6   119.57  3.000
 59V  C2   N3   C4   113.34  3.000
 59V  CAM  CBB  FAC  111.80  3.000
 59V  FAC  CBB  FAB  107.00  3.000
 59V  CAM  CBB  FAB  111.55  3.000
 59V  FAC  CBB  FAA  106.77  3.000
 59V  FAB  CBB  FAA  107.21  3.000
 59V  CAM  CBB  FAA  112.21  3.000
 59V  CAH  CAT  SAS  112.45  3.000
 59V  CAH  CAT  CAM  126.61  3.000
 59V  SAS  CAT  CAM  120.92  3.000
 59V  CAT  SAS  C4    91.17  3.000
 59V  H3   CAH  CAT  121.30  3.000
 59V  H3   CAH  C5   125.59  3.000
 59V  CAT  CAH  C5   113.05  3.000
 59V  H4   C2   N3   116.71  3.000
 59V  H4   C2   N1   116.01  3.000
 59V  N3   C2   N1   127.27  3.000
 59V  CAK  NBA  CAL  111.05  3.000
 59V  CAK  NBA  C6   120.36  3.000
 59V  CAL  NBA  C6   123.18  3.000
 59V  H6   CAL  H5   107.65  3.000
 59V  H6   CAL  CAJ  110.29  3.000
 59V  H5   CAL  CAJ  107.18  3.000
 59V  H6   CAL  NBA  108.97  3.000
 59V  H5   CAL  NBA  111.83  3.000
 59V  CAJ  CAL  NBA  110.87  3.000
 59V  H8   CAJ  H7   107.80  3.000
 59V  H8   CAJ  NAZ  109.35  3.000
 59V  H7   CAJ  NAZ  109.72  3.000
 59V  H8   CAJ  CAL  108.94  3.000
 59V  H7   CAJ  CAL  109.83  3.000
 59V  NAZ  CAJ  CAL  111.14  3.000
 59V  H10  CAK  H9   108.09  3.000
 59V  H10  CAK  CAI  109.50  3.000
 59V  H9   CAK  CAI  109.29  3.000
 59V  H10  CAK  NBA  110.51  3.000
 59V  H9   CAK  NBA  107.48  3.000
 59V  CAI  CAK  NBA  111.88  3.000
 59V  H12  CAI  H11  108.09  3.000
 59V  H12  CAI  NAZ  110.42  3.000
 59V  H11  CAI  NAZ  110.03  3.000
 59V  H12  CAI  CAK  110.47  3.000
 59V  H11  CAI  CAK  107.85  3.000
 59V  NAZ  CAI  CAK  109.93  3.000
 59V  CAU  NAZ  CAI  121.22  3.000
 59V  CAI  NAZ  CAJ  115.95  3.000
 59V  CAU  NAZ  CAJ  118.86  3.000
 59V  NAP  CAU  SAR  113.14  3.000
 59V  NAP  CAU  NAZ  124.45  3.000
 59V  SAR  CAU  NAZ  122.40  3.000
 59V  CAV  SAR  CAU   85.79  3.000
 59V  NAQ  NAP  CAU  112.77  3.000
 59V  CAV  NAQ  NAP  113.89  3.000
 59V  CBC  CAV  NAQ  123.60  3.000
 59V  NAQ  CAV  SAR  114.39  3.000
 59V  CBC  CAV  SAR  122.00  3.000
 59V  FAD  CBC  FAF  108.39  3.000
 59V  FAF  CBC  FAE  108.03  3.000
 59V  FAD  CBC  FAE  106.74  3.000
 59V  FAF  CBC  CAV  111.31  3.000
 59V  FAE  CBC  CAV  111.29  3.000
 59V  FAD  CBC  CAV  110.91  3.000
 59V  H2   CAM  H1   107.23  3.000
 59V  H2   CAM  CAT  111.33  3.000
 59V  H1   CAM  CAT  109.06  3.000
 59V  H2   CAM  CBB  108.26  3.000
 59V  H1   CAM  CBB  108.35  3.000
 59V  CAT  CAM  CBB  112.44  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
 59V  CONST_01  CAH  CAT  SAS  C4      0.00   0.0  0
 59V  CONST_02  N1   C2   N3   C4      0.00   0.0  0
 59V  CONST_03  CAT  CAH  C5   C4      0.00   0.0  0
 59V  CONST_04  N1   C6   C5   C4      0.00   0.0  0
 59V  CONST_05  CAT  SAS  C4   C5      0.00   0.0  0
 59V  CONST_06  C2   N3   C4   C5      0.00   0.0  0
 59V  CONST_07  SAS  CAT  CAH  C5      0.00   0.0  0
 59V  CONST_08  C2   N1   C6   C5      0.00   0.0  0
 59V  CONST_09  SAS  C4   C5   C6    180.00   0.0  0
 59V  CONST_10  N3   C4   C5   C6      0.00   0.0  0
 59V  CONST_11  CAT  CAH  C5   C6    180.00   0.0  0
 59V  CONST_12  N3   C2   N1   C6      0.00   0.0  0
 59V  CONST_13  CAH  C5   C6   N1    180.00   0.0  0
 59V  CONST_14  CAT  SAS  C4   N3    180.00   0.0  0
 59V  CONST_15  CAH  C5   C4   N3    180.00   0.0  0
 59V  CONST_16  C2   N3   C4   SAS   180.00   0.0  0
 59V  CONST_17  CAH  C5   C4   SAS     0.00   0.0  0
 59V  CONST_18  NAQ  CAV  SAR  CAU     0.00   0.0  0
 59V  CONST_19  CAV  NAQ  NAP  CAU     0.00   0.0  0
 59V  CONST_20  NAP  NAQ  CAV  SAR     0.00   0.0  0
 59V  CONST_21  NAQ  NAP  CAU  SAR     0.00   0.0  0
 59V  CONST_22  CAV  SAR  CAU  NAP     0.00   0.0  0
 59V  CONST_23  NBA  C6   C5   C4    180.00   0.0  0
 59V  CONST_24  NBA  C6   C5   CAH     0.00   0.0  0
 59V  CONST_25  NBA  C6   N1   C2    180.00   0.0  0
 59V  CONST_26  CAV  SAR  CAU  NAZ   180.00   0.0  0
 59V  CONST_27  NAQ  NAP  CAU  NAZ   180.00   0.0  0
 59V  CONST_28  CAM  CAT  SAS  C4    180.00   0.0  0
 59V  CONST_29  CAM  CAT  CAH  C5    180.00   0.0  0
 59V  CONST_30  CBC  CAV  SAR  CAU   180.00   0.0  0
 59V  CONST_31  CBC  CAV  NAQ  NAP   180.00   0.0  0
 59V  CONST_32  H4   C2   N3   C4    180.00   0.0  0
 59V  CONST_33  H3   CAH  C5   C4    180.00   0.0  0
 59V  Var_01    CAL  NBA  C6   C5    -39.40  30.0  2
 59V  Var_02    CAJ  CAL  NBA  C6    -96.07  30.0  1
 59V  Var_03    CAI  CAK  NBA  C6     95.80  30.0  1
 59V  Var_04    NAZ  CAJ  CAL  NBA   -52.19  30.0  1
 59V  Var_05    NAZ  CAI  CAK  NBA    53.14  30.0  1
 59V  Var_06    CAU  NAZ  CAJ  CAL  -152.56  30.0  1
 59V  Var_07    SAR  CAU  NAZ  CAJ  -168.53  30.0  1
 59V  Var_08    CAK  CAI  NAZ  CAJ   -49.49  30.0  1
 59V  Var_09    SAS  CAT  CAM  CBB   -73.59  30.0  2
 59V  Var_10    FAD  CBC  CAV  SAR   -50.99  30.0  3
 59V  Var_11    CAT  CAM  CBB  FAA   -57.88  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
 59V  plan-1  NAZ  0.020
 59V  plan-1  CAU  0.020
 59V  plan-1  SAR  0.020
 59V  plan-1  NAP  0.020
 59V  plan-1  NAQ  0.020
 59V  plan-1  CAV  0.020
 59V  plan-1  CBC  0.020
 59V  plan-2  C4   0.020
 59V  plan-2  C5   0.020
 59V  plan-2  C6   0.020
 59V  plan-2  N1   0.020
 59V  plan-2  N3   0.020
 59V  plan-2  CAT  0.020
 59V  plan-2  SAS  0.020
 59V  plan-2  CAH  0.020
 59V  plan-2  C2   0.020
 59V  plan-2  NBA  0.020
 59V  plan-2  H3   0.020
 59V  plan-2  H4   0.020
 59V  plan-2  CAM  0.020

