# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 20:59:07 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 5-[(4-{[6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl]amino}piperidin-1-yl)methyl]-1H-indole-2-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)Cc1sc2ncnc(NC3CCN(CC3)Cc4ccc5[nH]c(cc5c4)C#N)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
 3XY  3XY  5-[(4-{[6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl]amino}piperidin-1-yl)methyl]-1H-indole-2-carbonitrile  ligand  54  33  .  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_3XY
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
 3XY  C4   C  CR56  0  -0.027  -4.9957  -1.5874  -0.3399
 3XY  C5   C  CR56  0   0.030  -3.8628  -0.8725   0.0311
 3XY  C6   C  CR6   0   0.539  -2.6244  -1.4593  -0.3434
 3XY  N1   N  N     0  -0.476  -2.6246  -2.6162  -1.0063
 3XY  N3   N  N     0  -0.440  -4.9994  -2.7443  -1.0026
 3XY  FAB  F  F     0  -0.306  -7.6411   2.1264  -0.2835
 3XY  CBG  C  CT    0   0.990  -6.7232   2.6693   0.5297
 3XY  FAC  F  F     0  -0.302  -5.7571   3.1624  -0.2547
 3XY  FAD  F  F     0  -0.305  -7.3059   3.7093   1.1392
 3XY  CAY  C  CR5   0  -0.171  -5.5101   0.5187   0.8701
 3XY  SAV  S  S2    0   0.235  -6.4367  -0.7762   0.1667
 3XY  CAK  C  CR15  0  -0.231  -4.1766   0.3355   0.7228
 3XY  C2   C  CR16  0   0.044  -3.7910  -3.1815  -1.2963
 3XY  NAT  N  NH1   0  -0.671  -1.4592  -0.8696  -0.0613
 3XY  CBE  C  CH1   0  -0.067  -0.1576  -1.4380  -0.3541
 3XY  CAM  C  CH2   0  -0.452   0.8797  -0.3287  -0.4548
 3XY  CAO  C  CH2   0  -0.280   2.2599  -0.9141  -0.7082
 3XY  CAL  C  CH2   0  -0.436   0.2831  -2.4555   0.6944
 3XY  CAN  C  CH2   0  -0.286   1.6842  -2.9607   0.3883
 3XY  NBF  N  NT    0  -0.411   2.6317  -1.8628   0.3245
 3XY  CAP  C  CH2   0  -0.331   3.9895  -2.3426   0.1552
 3XY  CAW  C  CR6   0   0.082   5.0084  -1.2524   0.3540
 3XY  CAI  C  CR16  0  -0.394   5.9334  -0.9606  -0.6218
 3XY  CBA  C  CR56  0   0.080   6.8775   0.0546  -0.3965
 3XY  CAJ  C  CR15  0  -0.372   7.9357   0.5954  -1.1721
 3XY  CAX  C  CR5   0   0.305   8.5055   1.5825  -0.4078
 3XY  CAE  C  CSP   0   0.018   9.5948   2.4174  -0.7385
 3XY  NAA  N  NS    0  -0.244  10.4898   3.0898  -1.0159
 3XY  NAU  N  NR15  0  -0.718   7.8554   1.6809   0.7953
 3XY  CBB  C  CR56  0   0.350   6.8578   0.7597   0.8257
 3XY  CAH  C  CR16  0  -0.292   5.9196   0.4747   1.8234
 3XY  CAG  C  CR16  0  -0.288   5.0109  -0.5243   1.5675
 3XY  H1   H  HCH2  0   0.316  -5.4794   2.1838   2.1795
 3XY  H2   H  HCH2  0   0.314  -7.0190   1.3402   2.1595
 3XY  H3   H  HCR5  0   0.277  -3.4505   1.0424   1.1014
 3XY  H4   H  HCR6  0   0.256  -3.7376  -4.1195  -1.8387
 3XY  H5   H  HNH1  0   0.403  -1.4767  -0.0422   0.5140
 3XY  H6   H  HCH1  0   0.243  -0.2258  -1.9421  -1.3219
 3XY  H7   H  HCH2  0   0.248   0.6271   0.3602  -1.2636
 3XY  H8   H  HCH2  0   0.228   0.8961   0.2493   0.4753
 3XY  H9   H  HCH2  0   0.191   2.2762  -1.3858  -1.7077
 3XY  H10  H  HCH2  0   0.249   2.9931  -0.1061  -0.7329
 3XY  H11  H  HCH2  0   0.222   0.2735  -1.9856   1.6823
 3XY  H12  H  HCH2  0   0.243  -0.4135  -3.2958   0.7214
 3XY  H13  H  HCH2  0   0.240   2.0012  -3.6544   1.1704
 3XY  H14  H  HCH2  0   0.191   1.6688  -3.5376  -0.5542
 3XY  H16  H  HCH2  0   0.247   4.1573  -3.1298   0.8971
 3XY  H17  H  HCH2  0   0.212   4.1453  -2.8095  -0.8322
 3XY  H18  H  HCR6  0   0.251   5.9314  -1.5065  -1.5579
 3XY  H19  H  HCR5  0   0.275   8.2455   0.3070  -2.1635
 3XY  H20  H  HNR5  0   0.426   8.0902   2.3248   1.5340
 3XY  H21  H  HCR6  0   0.267   5.9087   1.0197   2.7584
 3XY  H22  H  HCR6  0   0.249   4.2650  -0.7618   2.3156
 3XY  CAQ  C  CH2   0  -0.719  -6.1903   1.6708   1.5291

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
 3XY  CAN  CAL  single    1.521  0.020  1.521
 3XY  CAN  NBF  single    1.452  0.020  1.452
 3XY  CAL  CBE  single    1.526  0.020  1.526
 3XY  CAP  NBF  single    1.450  0.020  1.450
 3XY  CAP  CAW  single    1.505  0.020  1.505
 3XY  NBF  CAO  single    1.451  0.020  1.451
 3XY  FAD  CBG  single    1.339  0.020  1.339
 3XY  CAW  CAG  aromatic  1.415  0.020  1.415
 3XY  CAW  CAI  aromatic  1.376  0.020  1.376
 3XY  CAG  CAH  aromatic  1.375  0.020  1.375
 3XY  CBE  NAT  single    1.450  0.020  1.450
 3XY  CBE  CAM  single    1.522  0.020  1.522
 3XY  N1   C2   aromatic  1.328  0.020  1.328
 3XY  N1   C6   aromatic  1.333  0.020  1.333
 3XY  CAI  CBA  aromatic  1.405  0.020  1.405
 3XY  NAT  C6   single    1.336  0.020  1.336
 3XY  FAC  CBG  single    1.339  0.020  1.339
 3XY  C2   N3   aromatic  1.318  0.020  1.318
 3XY  C6   C5   aromatic  1.421  0.020  1.421
 3XY  CAH  CBB  aromatic  1.399  0.020  1.399
 3XY  CAO  CAM  single    1.520  0.020  1.520
 3XY  CBG  FAB  single    1.341  0.020  1.341
 3XY  CBG  CAQ  single    1.510  0.020  1.510
 3XY  N3   C4   aromatic  1.333  0.020  1.333
 3XY  C5   C4   aromatic  1.390  0.020  1.390
 3XY  C5   CAK  aromatic  1.427  0.020  1.427
 3XY  C4   SAV  aromatic  1.730  0.020  1.730
 3XY  CBA  CBB  aromatic  1.411  0.020  1.411
 3XY  CBA  CAJ  aromatic  1.419  0.020  1.419
 3XY  CAK  CAY  aromatic  1.354  0.020  1.354
 3XY  CBB  NAU  aromatic  1.358  0.020  1.358
 3XY  CAY  SAV  aromatic  1.741  0.020  1.741
 3XY  CAY  CAQ  single    1.491  0.020  1.491
 3XY  CAJ  CAX  aromatic  1.372  0.020  1.372
 3XY  NAU  CAX  aromatic  1.371  0.020  1.371
 3XY  CAX  CAE  single    1.412  0.020  1.412
 3XY  CAE  NAA  triple    1.153  0.020  1.153
 3XY  CAQ  H1   single    0.970  0.020  1.090
 3XY  CAQ  H2   single    0.970  0.020  1.090
 3XY  CAK  H3   single    0.930  0.020  1.080
 3XY  C2   H4   single    0.930  0.020  1.080
 3XY  NAT  H5   single    0.860  0.020  1.020
 3XY  CBE  H6   single    0.970  0.020  1.090
 3XY  CAM  H7   single    0.970  0.020  1.090
 3XY  CAM  H8   single    0.970  0.020  1.090
 3XY  CAO  H9   single    0.970  0.020  1.090
 3XY  CAO  H10  single    0.970  0.020  1.090
 3XY  CAL  H11  single    0.970  0.020  1.090
 3XY  CAL  H12  single    0.970  0.020  1.090
 3XY  CAN  H13  single    0.970  0.020  1.090
 3XY  CAN  H14  single    0.970  0.020  1.090
 3XY  CAP  H16  single    0.970  0.020  1.090
 3XY  CAP  H17  single    0.970  0.020  1.090
 3XY  CAI  H18  single    0.930  0.020  1.080
 3XY  CAJ  H19  single    0.930  0.020  1.080
 3XY  NAU  H20  single    0.860  0.020  1.020
 3XY  CAH  H21  single    0.930  0.020  1.080
 3XY  CAG  H22  single    0.930  0.020  1.080

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
 3XY  SAV  C4   N3   123.38  3.000
 3XY  SAV  C4   C5   111.08  3.000
 3XY  N3   C4   C5   125.53  3.000
 3XY  CAK  C5   C6   132.01  3.000
 3XY  CAK  C5   C4   112.67  3.000
 3XY  C6   C5   C4   115.32  3.000
 3XY  NAT  C6   N1   119.21  3.000
 3XY  NAT  C6   C5   121.48  3.000
 3XY  N1   C6   C5   119.30  3.000
 3XY  C2   N1   C6   118.55  3.000
 3XY  C2   N3   C4   113.33  3.000
 3XY  CAQ  CBG  FAD  111.47  3.000
 3XY  CAQ  CBG  FAC  112.13  3.000
 3XY  FAD  CBG  FAC  107.14  3.000
 3XY  CAQ  CBG  FAB  112.04  3.000
 3XY  FAC  CBG  FAB  106.73  3.000
 3XY  FAD  CBG  FAB  107.01  3.000
 3XY  CAK  CAY  SAV  112.31  3.000
 3XY  SAV  CAY  CAQ  120.69  3.000
 3XY  CAK  CAY  CAQ  127.00  3.000
 3XY  CAY  SAV  C4    91.36  3.000
 3XY  H3   CAK  CAY  122.31  3.000
 3XY  H3   CAK  C5   125.11  3.000
 3XY  CAY  CAK  C5   112.58  3.000
 3XY  H4   C2   N3   116.31  3.000
 3XY  H4   C2   N1   115.72  3.000
 3XY  N3   C2   N1   127.97  3.000
 3XY  H5   NAT  CBE  116.91  3.000
 3XY  H5   NAT  C6   117.88  3.000
 3XY  CBE  NAT  C6   124.56  3.000
 3XY  H6   CBE  CAL  108.59  3.000
 3XY  H6   CBE  CAM  108.66  3.000
 3XY  CAL  CBE  CAM  109.55  3.000
 3XY  H6   CBE  NAT  107.66  3.000
 3XY  CAM  CBE  NAT  109.84  3.000
 3XY  CAL  CBE  NAT  112.45  3.000
 3XY  H8   CAM  H7   107.43  3.000
 3XY  H8   CAM  CAO  109.34  3.000
 3XY  H7   CAM  CAO  109.23  3.000
 3XY  H8   CAM  CBE  109.79  3.000
 3XY  H7   CAM  CBE  110.55  3.000
 3XY  CAO  CAM  CBE  110.43  3.000
 3XY  H10  CAO  H9   106.60  3.000
 3XY  H10  CAO  NBF  109.15  3.000
 3XY  H9   CAO  NBF  111.15  3.000
 3XY  H10  CAO  CAM  109.18  3.000
 3XY  H9   CAO  CAM  109.17  3.000
 3XY  NBF  CAO  CAM  111.45  3.000
 3XY  H12  CAL  H11  107.62  3.000
 3XY  H12  CAL  CAN  109.70  3.000
 3XY  H11  CAL  CAN  109.42  3.000
 3XY  H12  CAL  CBE  110.24  3.000
 3XY  H11  CAL  CBE  109.36  3.000
 3XY  CAN  CAL  CBE  110.44  3.000
 3XY  H14  CAN  H13  106.45  3.000
 3XY  H14  CAN  NBF  111.50  3.000
 3XY  H13  CAN  NBF  108.80  3.000
 3XY  H14  CAN  CAL  109.41  3.000
 3XY  H13  CAN  CAL  109.53  3.000
 3XY  NBF  CAN  CAL  111.04  3.000
 3XY  CAP  NBF  CAN  111.47  3.000
 3XY  CAP  NBF  CAO  111.92  3.000
 3XY  CAN  NBF  CAO  111.01  3.000
 3XY  H17  CAP  H16  106.30  3.000
 3XY  H17  CAP  CAW  109.21  3.000
 3XY  H16  CAP  CAW  109.12  3.000
 3XY  H17  CAP  NBF  112.14  3.000
 3XY  H16  CAP  NBF  107.60  3.000
 3XY  CAW  CAP  NBF  112.25  3.000
 3XY  CAG  CAW  CAI  119.86  3.000
 3XY  CAI  CAW  CAP  120.99  3.000
 3XY  CAG  CAW  CAP  119.15  3.000
 3XY  H18  CAI  CBA  120.26  3.000
 3XY  H18  CAI  CAW  120.31  3.000
 3XY  CBA  CAI  CAW  119.43  3.000
 3XY  CBB  CBA  CAJ  107.06  3.000
 3XY  CAJ  CBA  CAI  133.55  3.000
 3XY  CBB  CBA  CAI  119.39  3.000
 3XY  H19  CAJ  CAX  125.83  3.000
 3XY  H19  CAJ  CBA  127.95  3.000
 3XY  CAX  CAJ  CBA  106.22  3.000
 3XY  NAU  CAX  CAE  121.94  3.000
 3XY  CAE  CAX  CAJ  127.97  3.000
 3XY  NAU  CAX  CAJ  110.09  3.000
 3XY  NAA  CAE  CAX  180.00  3.000
 3XY  H20  NAU  CBB  126.03  3.000
 3XY  H20  NAU  CAX  125.35  3.000
 3XY  CBB  NAU  CAX  108.62  3.000
 3XY  CAH  CBB  NAU  130.30  3.000
 3XY  NAU  CBB  CBA  108.02  3.000
 3XY  CAH  CBB  CBA  121.69  3.000
 3XY  H21  CAH  CAG  121.34  3.000
 3XY  H21  CAH  CBB  121.36  3.000
 3XY  CAG  CAH  CBB  117.30  3.000
 3XY  H22  CAG  CAH  119.09  3.000
 3XY  H22  CAG  CAW  118.58  3.000
 3XY  CAH  CAG  CAW  122.33  3.000
 3XY  H2   CAQ  H1   107.00  3.000
 3XY  H2   CAQ  CAY  111.54  3.000
 3XY  H1   CAQ  CAY  109.22  3.000
 3XY  H2   CAQ  CBG  108.32  3.000
 3XY  H1   CAQ  CBG  108.27  3.000
 3XY  CAY  CAQ  CBG  112.29  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
 3XY  CONST_01  N1   C2   N3   C4     0.00   0.0  0
 3XY  CONST_02  N1   C6   C5   C4     0.00   0.0  0
 3XY  CONST_03  CAY  CAK  C5   C4     0.00   0.0  0
 3XY  CONST_04  CAK  CAY  SAV  C4     0.00   0.0  0
 3XY  CONST_05  C2   N1   C6   C5     0.00   0.0  0
 3XY  CONST_06  C2   N3   C4   C5     0.00   0.0  0
 3XY  CONST_07  CAY  SAV  C4   C5     0.00   0.0  0
 3XY  CONST_08  SAV  CAY  CAK  C5     0.00   0.0  0
 3XY  CONST_09  N3   C2   N1   C6     0.00   0.0  0
 3XY  CONST_10  N3   C4   C5   C6     0.00   0.0  0
 3XY  CONST_11  SAV  C4   C5   C6   180.00   0.0  0
 3XY  CONST_12  CAY  CAK  C5   C6   180.00   0.0  0
 3XY  CONST_13  CAK  C5   C6   N1   180.00   0.0  0
 3XY  CONST_14  CAK  C5   C4   N3   180.00   0.0  0
 3XY  CONST_15  CAY  SAV  C4   N3   180.00   0.0  0
 3XY  CONST_16  C2   N3   C4   SAV  180.00   0.0  0
 3XY  CONST_17  CAK  C5   C4   SAV    0.00   0.0  0
 3XY  CONST_18  CBB  CAH  CAG  CAW    0.00   0.0  0
 3XY  CONST_19  CBB  CBA  CAI  CAW    0.00   0.0  0
 3XY  CONST_20  CAJ  CBA  CAI  CAW  180.00   0.0  0
 3XY  CONST_21  CAH  CAG  CAW  CAI    0.00   0.0  0
 3XY  CONST_22  CAH  CBB  CBA  CAI    0.00   0.0  0
 3XY  CONST_23  NAU  CBB  CBA  CAI  180.00   0.0  0
 3XY  CONST_24  CAX  CAJ  CBA  CAI  180.00   0.0  0
 3XY  CONST_25  CAG  CAW  CAI  CBA    0.00   0.0  0
 3XY  CONST_26  CAG  CAH  CBB  CBA    0.00   0.0  0
 3XY  CONST_27  CAX  NAU  CBB  CBA    0.00   0.0  0
 3XY  CONST_28  NAU  CAX  CAJ  CBA    0.00   0.0  0
 3XY  CONST_29  CAH  CBB  CBA  CAJ  180.00   0.0  0
 3XY  CONST_30  NAU  CBB  CBA  CAJ    0.00   0.0  0
 3XY  CONST_31  CBB  NAU  CAX  CAJ    0.00   0.0  0
 3XY  CONST_32  CBB  CBA  CAJ  CAX    0.00   0.0  0
 3XY  CONST_33  CAH  CBB  NAU  CAX  180.00   0.0  0
 3XY  CONST_34  CAG  CAH  CBB  NAU  180.00   0.0  0
 3XY  CONST_35  NAT  C6   C5   C4   180.00   0.0  0
 3XY  CONST_36  CAQ  CAY  SAV  C4   180.00   0.0  0
 3XY  CONST_37  CAQ  CAY  CAK  C5   180.00   0.0  0
 3XY  CONST_38  NAT  C6   C5   CAK    0.00   0.0  0
 3XY  CONST_39  NAT  C6   N1   C2   180.00   0.0  0
 3XY  CONST_40  CAH  CAG  CAW  CAP  180.00   0.0  0
 3XY  CONST_41  CBA  CAI  CAW  CAP  180.00   0.0  0
 3XY  CONST_42  CAE  CAX  CAJ  CBA  180.00   0.0  0
 3XY  CONST_43  CBB  NAU  CAX  CAE  180.00   0.0  0
 3XY  CONST_44  CBE  NAT  C6   C5   180.00   0.0  0
 3XY  CONST_45  CBE  NAT  C6   N1     0.00   0.0  0
 3XY  CONST_46  H4   C2   N3   C4   180.00   0.0  0
 3XY  CONST_47  H3   CAK  C5   C4   180.00   0.0  0
 3XY  CONST_48  H21  CAH  CAG  CAW  180.00   0.0  0
 3XY  CONST_49  H22  CAG  CAW  CAI  180.00   0.0  0
 3XY  CONST_50  H19  CAJ  CBA  CAI    0.00   0.0  0
 3XY  CONST_51  H20  NAU  CBB  CBA  180.00   0.0  0
 3XY  CONST_52  H18  CAI  CBA  CAJ    0.00   0.0  0
 3XY  CONST_53  H5   NAT  C6   C5     0.00   0.0  0
 3XY  Var_01    NBF  CAN  CAL  CBE   57.38  30.0  1
 3XY  Var_02    NBF  CAO  CAM  CBE  -56.87  30.0  1
 3XY  Var_03    CAN  NBF  CAO  CAM   59.59  30.0  1
 3XY  Var_04    CAL  CAN  NBF  CAO  -59.76  30.0  1
 3XY  Var_05    CAW  CAP  NBF  CAO   66.13  30.0  2
 3XY  Var_06    CAG  CAW  CAP  NBF   55.90  30.0  2
 3XY  Var_07    CAK  CAY  CAQ  CBG  100.66  30.0  1
 3XY  Var_08    CAY  CAQ  CBG  FAB   61.38  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 3XY  chir_01  CBE  CAL  NAT  CAM  negativ

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
 3XY  plan-1  C4   0.020
 3XY  plan-1  C5   0.020
 3XY  plan-1  C6   0.020
 3XY  plan-1  N1   0.020
 3XY  plan-1  N3   0.020
 3XY  plan-1  CAY  0.020
 3XY  plan-1  SAV  0.020
 3XY  plan-1  CAK  0.020
 3XY  plan-1  C2   0.020
 3XY  plan-1  NAT  0.020
 3XY  plan-1  H3   0.020
 3XY  plan-1  H4   0.020
 3XY  plan-1  CAQ  0.020
 3XY  plan-2  CAP  0.020
 3XY  plan-2  CAW  0.020
 3XY  plan-2  CAI  0.020
 3XY  plan-2  CBA  0.020
 3XY  plan-2  CAJ  0.020
 3XY  plan-2  CAX  0.020
 3XY  plan-2  CAE  0.020
 3XY  plan-2  NAA  0.020
 3XY  plan-2  NAU  0.020
 3XY  plan-2  CBB  0.020
 3XY  plan-2  CAH  0.020
 3XY  plan-2  CAG  0.020
 3XY  plan-2  H18  0.020
 3XY  plan-2  H19  0.020
 3XY  plan-2  H20  0.020
 3XY  plan-2  H21  0.020
 3XY  plan-2  H22  0.020
 3XY  plan-3  C6   0.020
 3XY  plan-3  NAT  0.020
 3XY  plan-3  CBE  0.020
 3XY  plan-3  H5   0.020

