# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 05:39:36 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: 4-{4-[5-(difluoromethyl)-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: FC(F)c1sc(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
 59Q  59Q  4-{4-[5-(difluoromethyl)-1,3,4-thiadiazol-2-yl]piperazin-1-yl}-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidine  ligand  41  28  .  2022-07-23  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_59Q
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
 59Q  C4   C  CR56  0  -0.023  -3.8079  -1.8636  -0.0164
 59Q  C5   C  CR56  0   0.042  -2.5871  -1.2209   0.2023
 59Q  C6   C  CR6   0   0.533  -1.4396  -2.0384   0.0088
 59Q  N1   N  N     0  -0.471  -1.6018  -3.2751  -0.4570
 59Q  N3   N  N     0  -0.429  -3.9663  -3.1213  -0.4190
 59Q  FAC  F  F     0  -0.307  -6.1668   1.9293  -0.9305
 59Q  CBB  C  CT    0   0.989  -5.1291   2.5864  -0.3913
 59Q  FAD  F  F     0  -0.301  -4.1989   2.6908  -1.3478
 59Q  FAE  F  F     0  -0.305  -5.5520   3.8259  -0.1134
 59Q  CAS  C  CR5   0  -0.171  -4.0705   0.5322   0.5539
 59Q  SAR  S  S2    0   0.242  -5.1446  -0.7939   0.2221
 59Q  CAG  C  CR15  0  -0.228  -2.7687   0.1676   0.5009
 59Q  C2   C  CR16  0   0.049  -2.8277  -3.7438  -0.6469
 59Q  NBA  N  NT    0  -0.499  -0.1761  -1.6137   0.2389
 59Q  CAK  C  CH2   0  -0.342   0.1995  -0.7060   1.3057
 59Q  CAI  C  CH2   0  -0.293   1.1740   0.3364   0.7990
 59Q  CAJ  C  CH2   0  -0.310   0.9730  -2.3395  -0.2610
 59Q  CAH  C  CH2   0  -0.310   1.9907  -1.3510  -0.8087
 59Q  NAZ  N  NT    0  -0.499   2.3098  -0.3253   0.1701
 59Q  CAU  C  CR5   0   0.375   3.5058   0.2778   0.1895
 59Q  SAQ  S  S2    0   0.182   4.8670  -0.3080  -0.7281
 59Q  NAP  N  N     0  -0.343   3.7842   1.3416   0.9034
 59Q  NAO  N  N     0  -0.218   5.0634   1.7201   0.7891
 59Q  CAT  C  CR5   0  -0.061   5.7591   0.9887  -0.0040
 59Q  CAY  C  CH1   0   0.515   7.1961   1.2281  -0.2799
 59Q  FAA  F  F     0  -0.335   7.9233   0.1287   0.0532
 59Q  FAB  F  F     0  -0.336   7.3875   1.4181  -1.6128
 59Q  H1   H  HCH2  0   0.315  -3.7989   2.5085   1.2590
 59Q  H2   H  HCH2  0   0.317  -5.3989   1.8621   1.5873
 59Q  H3   H  HCR5  0   0.279  -1.9773   0.8884   0.6436
 59Q  H4   H  HCR6  0   0.260  -2.8958  -4.7600  -1.0197
 59Q  H5   H  HCH2  0   0.283  -0.6648  -0.2239   1.7485
 59Q  H6   H  HCH2  0   0.272   0.6767  -1.2875   2.1029
 59Q  H7   H  HCH2  0   0.255   0.6815   1.0020   0.0813
 59Q  H8   H  HCH2  0   0.284   1.5257   0.9373   1.6336
 59Q  H9   H  HCH2  0   0.251   1.4253  -2.9364   0.5386
 59Q  H10  H  HCH2  0   0.286   0.6783  -3.0144  -1.0590
 59Q  H11  H  HCH2  0   0.276   2.8894  -1.9131  -1.0668
 59Q  H12  H  HCH2  0   0.263   1.6073  -0.8927  -1.7267
 59Q  H13  H  HCH1  0   0.233   7.5665   2.0930   0.2699
 59Q  CAL  C  CH2   0  -0.718  -4.6001   1.8960   0.8425

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
 59Q  FAB  CAY  single    1.360  0.020  1.360
 59Q  FAA  CAY  single    1.360  0.020  1.360
 59Q  CAY  CAT  single    1.483  0.020  1.483
 59Q  SAQ  CAT  aromatic  1.733  0.020  1.733
 59Q  SAQ  CAU  aromatic  1.743  0.020  1.743
 59Q  CAL  CAS  single    1.491  0.020  1.491
 59Q  CAL  CBB  single    1.510  0.020  1.510
 59Q  SAR  CAS  aromatic  1.738  0.020  1.738
 59Q  SAR  C4   aromatic  1.729  0.020  1.729
 59Q  CAS  CAG  aromatic  1.353  0.020  1.353
 59Q  CAT  NAO  aromatic  1.284  0.020  1.284
 59Q  C4   N3   aromatic  1.330  0.020  1.330
 59Q  C4   C5   aromatic  1.397  0.020  1.397
 59Q  CAI  CAK  single    1.514  0.020  1.514
 59Q  CAI  NAZ  single    1.457  0.020  1.457
 59Q  FAC  CBB  single    1.341  0.020  1.341
 59Q  CAG  C5   aromatic  1.432  0.020  1.432
 59Q  N3   C2   aromatic  1.318  0.020  1.318
 59Q  CBB  FAD  single    1.338  0.020  1.338
 59Q  CBB  FAE  single    1.339  0.020  1.339
 59Q  C5   C6   aromatic  1.422  0.020  1.422
 59Q  CAK  NBA  single    1.450  0.020  1.450
 59Q  CAU  NAZ  single    1.340  0.020  1.340
 59Q  CAU  NAP  aromatic  1.311  0.020  1.311
 59Q  C2   N1   aromatic  1.326  0.020  1.326
 59Q  C6   N1   aromatic  1.331  0.020  1.331
 59Q  C6   NBA  single    1.353  0.020  1.353
 59Q  NAO  NAP  aromatic  1.339  0.020  1.339
 59Q  NAZ  CAH  single    1.453  0.020  1.453
 59Q  NBA  CAJ  single    1.448  0.020  1.448
 59Q  CAJ  CAH  single    1.521  0.020  1.521
 59Q  CAL  H1   single    0.970  0.020  1.090
 59Q  CAL  H2   single    0.970  0.020  1.090
 59Q  CAG  H3   single    0.930  0.020  1.080
 59Q  C2   H4   single    0.930  0.020  1.080
 59Q  CAK  H5   single    0.970  0.020  1.090
 59Q  CAK  H6   single    0.970  0.020  1.090
 59Q  CAI  H7   single    0.970  0.020  1.090
 59Q  CAI  H8   single    0.970  0.020  1.090
 59Q  CAJ  H9   single    0.970  0.020  1.090
 59Q  CAJ  H10  single    0.970  0.020  1.090
 59Q  CAH  H11  single    0.970  0.020  1.090
 59Q  CAH  H12  single    0.970  0.020  1.090
 59Q  CAY  H13  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
 59Q  SAR  C4   N3   122.33  3.000
 59Q  N3   C4   C5   125.91  3.000
 59Q  SAR  C4   C5   111.68  3.000
 59Q  CAG  C5   C6   133.48  3.000
 59Q  C6   C5   C4   114.79  3.000
 59Q  CAG  C5   C4   111.59  3.000
 59Q  NBA  C6   N1   117.70  3.000
 59Q  NBA  C6   C5   123.37  3.000
 59Q  N1   C6   C5   118.90  3.000
 59Q  C2   N1   C6   119.40  3.000
 59Q  C2   N3   C4   113.34  3.000
 59Q  CAL  CBB  FAE  111.37  3.000
 59Q  FAE  CBB  FAD  107.20  3.000
 59Q  CAL  CBB  FAD  112.10  3.000
 59Q  FAE  CBB  FAC  107.02  3.000
 59Q  FAD  CBB  FAC  106.77  3.000
 59Q  CAL  CBB  FAC  112.07  3.000
 59Q  CAG  CAS  SAR  112.42  3.000
 59Q  CAG  CAS  CAL  126.56  3.000
 59Q  SAR  CAS  CAL  121.01  3.000
 59Q  CAS  SAR  C4    91.18  3.000
 59Q  H3   CAG  CAS  121.34  3.000
 59Q  H3   CAG  C5   125.58  3.000
 59Q  CAS  CAG  C5   113.05  3.000
 59Q  H4   C2   N3   116.60  3.000
 59Q  H4   C2   N1   116.01  3.000
 59Q  N3   C2   N1   127.39  3.000
 59Q  CAJ  NBA  CAK  111.23  3.000
 59Q  CAJ  NBA  C6   121.68  3.000
 59Q  CAK  NBA  C6   124.30  3.000
 59Q  H6   CAK  H5   106.62  3.000
 59Q  H6   CAK  CAI  109.17  3.000
 59Q  H5   CAK  CAI  110.10  3.000
 59Q  H6   CAK  NBA  108.40  3.000
 59Q  H5   CAK  NBA  111.86  3.000
 59Q  CAI  CAK  NBA  110.57  3.000
 59Q  H8   CAI  H7   108.21  3.000
 59Q  H8   CAI  NAZ  109.28  3.000
 59Q  H7   CAI  NAZ  110.09  3.000
 59Q  H8   CAI  CAK  109.38  3.000
 59Q  H7   CAI  CAK  110.37  3.000
 59Q  NAZ  CAI  CAK  109.48  3.000
 59Q  H10  CAJ  H9   108.05  3.000
 59Q  H10  CAJ  CAH  108.72  3.000
 59Q  H9   CAJ  CAH  109.92  3.000
 59Q  H10  CAJ  NBA  110.47  3.000
 59Q  H9   CAJ  NBA  110.41  3.000
 59Q  CAH  CAJ  NBA  109.24  3.000
 59Q  H12  CAH  H11  107.80  3.000
 59Q  H12  CAH  NAZ  110.25  3.000
 59Q  H11  CAH  NAZ  110.01  3.000
 59Q  H12  CAH  CAJ  109.85  3.000
 59Q  H11  CAH  CAJ  107.55  3.000
 59Q  NAZ  CAH  CAJ  111.29  3.000
 59Q  CAU  NAZ  CAH  121.57  3.000
 59Q  CAH  NAZ  CAI  116.11  3.000
 59Q  CAU  NAZ  CAI  119.03  3.000
 59Q  NAP  CAU  SAQ  113.18  3.000
 59Q  NAP  CAU  NAZ  124.24  3.000
 59Q  SAQ  CAU  NAZ  122.57  3.000
 59Q  CAT  SAQ  CAU   86.01  3.000
 59Q  NAO  NAP  CAU  112.69  3.000
 59Q  CAT  NAO  NAP  114.17  3.000
 59Q  CAY  CAT  NAO  123.25  3.000
 59Q  NAO  CAT  SAQ  113.93  3.000
 59Q  CAY  CAT  SAQ  122.82  3.000
 59Q  H13  CAY  FAB  109.62  3.000
 59Q  H13  CAY  FAA  109.66  3.000
 59Q  FAB  CAY  FAA  106.14  3.000
 59Q  H13  CAY  CAT  111.32  3.000
 59Q  FAA  CAY  CAT  110.01  3.000
 59Q  FAB  CAY  CAT  109.96  3.000
 59Q  H2   CAL  H1   107.10  3.000
 59Q  H2   CAL  CAS  111.29  3.000
 59Q  H1   CAL  CAS  109.05  3.000
 59Q  H2   CAL  CBB  108.37  3.000
 59Q  H1   CAL  CBB  108.22  3.000
 59Q  CAS  CAL  CBB  112.61  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
 59Q  CONST_01  CAG  CAS  SAR  C4      0.00   0.0  0
 59Q  CONST_02  N1   C2   N3   C4      0.00   0.0  0
 59Q  CONST_03  CAS  CAG  C5   C4      0.00   0.0  0
 59Q  CONST_04  N1   C6   C5   C4      0.00   0.0  0
 59Q  CONST_05  CAS  SAR  C4   C5      0.00   0.0  0
 59Q  CONST_06  C2   N3   C4   C5      0.00   0.0  0
 59Q  CONST_07  SAR  CAS  CAG  C5      0.00   0.0  0
 59Q  CONST_08  C2   N1   C6   C5      0.00   0.0  0
 59Q  CONST_09  SAR  C4   C5   C6    180.00   0.0  0
 59Q  CONST_10  N3   C4   C5   C6      0.00   0.0  0
 59Q  CONST_11  CAS  CAG  C5   C6    180.00   0.0  0
 59Q  CONST_12  N3   C2   N1   C6      0.00   0.0  0
 59Q  CONST_13  CAG  C5   C6   N1    180.00   0.0  0
 59Q  CONST_14  CAS  SAR  C4   N3    180.00   0.0  0
 59Q  CONST_15  CAG  C5   C4   N3    180.00   0.0  0
 59Q  CONST_16  C2   N3   C4   SAR   180.00   0.0  0
 59Q  CONST_17  CAG  C5   C4   SAR     0.00   0.0  0
 59Q  CONST_18  NAO  CAT  SAQ  CAU     0.00   0.0  0
 59Q  CONST_19  CAT  NAO  NAP  CAU     0.00   0.0  0
 59Q  CONST_20  NAP  NAO  CAT  SAQ     0.00   0.0  0
 59Q  CONST_21  NAO  NAP  CAU  SAQ     0.00   0.0  0
 59Q  CONST_22  CAT  SAQ  CAU  NAP     0.00   0.0  0
 59Q  CONST_23  NBA  C6   C5   C4    180.00   0.0  0
 59Q  CONST_24  NBA  C6   C5   CAG     0.00   0.0  0
 59Q  CONST_25  NBA  C6   N1   C2    180.00   0.0  0
 59Q  CONST_26  CAT  SAQ  CAU  NAZ   180.00   0.0  0
 59Q  CONST_27  NAO  NAP  CAU  NAZ   180.00   0.0  0
 59Q  CONST_28  CAL  CAS  SAR  C4    180.00   0.0  0
 59Q  CONST_29  CAL  CAS  CAG  C5    180.00   0.0  0
 59Q  CONST_30  CAY  CAT  SAQ  CAU   180.00   0.0  0
 59Q  CONST_31  CAY  CAT  NAO  NAP   180.00   0.0  0
 59Q  CONST_32  H4   C2   N3   C4    180.00   0.0  0
 59Q  CONST_33  H3   CAG  C5   C4    180.00   0.0  0
 59Q  Var_01    CAK  NBA  C6   C5     35.60  30.0  2
 59Q  Var_02    CAI  CAK  NBA  C6   -136.64  30.0  1
 59Q  Var_03    CAH  CAJ  NBA  C6    137.76  30.0  1
 59Q  Var_04    NAZ  CAI  CAK  NBA   -54.14  30.0  1
 59Q  Var_05    NAZ  CAH  CAJ  NBA    52.82  30.0  1
 59Q  Var_06    CAU  NAZ  CAI  CAK  -150.56  30.0  1
 59Q  Var_07    SAQ  CAU  NAZ  CAI  -170.76  30.0  1
 59Q  Var_08    CAJ  CAH  NAZ  CAI   -49.66  30.0  1
 59Q  Var_09    SAR  CAS  CAL  CBB   -73.72  30.0  2
 59Q  Var_10    FAB  CAY  CAT  SAQ    58.08  30.0  2
 59Q  Var_11    CAS  CAL  CBB  FAC    62.46  30.0  2

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
 59Q  plan-1  NAZ  0.020
 59Q  plan-1  CAU  0.020
 59Q  plan-1  SAQ  0.020
 59Q  plan-1  NAP  0.020
 59Q  plan-1  NAO  0.020
 59Q  plan-1  CAT  0.020
 59Q  plan-1  CAY  0.020
 59Q  plan-2  C4   0.020
 59Q  plan-2  C5   0.020
 59Q  plan-2  C6   0.020
 59Q  plan-2  N1   0.020
 59Q  plan-2  N3   0.020
 59Q  plan-2  CAS  0.020
 59Q  plan-2  SAR  0.020
 59Q  plan-2  CAG  0.020
 59Q  plan-2  C2   0.020
 59Q  plan-2  NBA  0.020
 59Q  plan-2  H3   0.020
 59Q  plan-2  H4   0.020
 59Q  plan-2  CAL  0.020

