# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:02:58 2022
#   Inital geometry file: a 109 line input string
#   Ligand name: 6-(2,2-difluoroethyl)-4-[4-(5,5-dimethyl-4,5-dihydro-1,3-thiazol-2-yl)piperazin-1-yl]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)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
 5A0  5A0  6-(2,2-difluoroethyl)-4-[4-(5,5-dimethyl-4,5-dihydro-1,3-thiazol-2-yl)piperazin-1-yl]thieno[2,3-d]pyrimidine  ligand  47  26  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_5A0
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
 5A0  C4   C  CR56  0  -0.027  -3.5135  -1.7606   0.1563
 5A0  C5   C  CR56  0   0.049  -2.3310  -1.0179   0.1998
 5A0  C6   C  CR6   0   0.528  -1.1422  -1.7781   0.0196
 5A0  N1   N  N     0  -0.473  -1.2344  -3.1043  -0.0589
 5A0  N3   N  N     0  -0.429  -3.6023  -3.0803   0.0140
 5A0  FAC  F  F     0  -0.342  -6.1686   1.8135  -0.7522
 5A0  CAW  C  CH1   0   0.545  -5.1546   2.6025  -0.2916
 5A0  FAD  F  F     0  -0.341  -5.7180   3.7946   0.0511
 5A0  CAS  C  CR5   0  -0.167  -3.9053   0.6452   0.6133
 5A0  SAQ  S  S2    0   0.236  -4.9046  -0.7593   0.3826
 5A0  CAF  C  CR15  0  -0.244  -2.5869   0.3606   0.4954
 5A0  C2   C  CR16  0   0.046  -2.4301  -3.6778  -0.0511
 5A0  NAY  N  NT    0  -0.499   0.0954  -1.2298  -0.0413
 5A0  CAJ  C  CH2   0  -0.330   0.3759   0.0384  -0.6936
 5A0  CAH  C  CH2   0  -0.291   1.4432   0.8030   0.0650
 5A0  CAI  C  CH2   0  -0.302   1.2799  -2.0658   0.0355
 5A0  CAG  C  CH2   0  -0.305   2.3748  -1.3286   0.7902
 5A0  NAX  N  NT    0  -0.491   2.6256  -0.0272   0.2043
 5A0  CAR  C  CR5   0   0.358   3.8452   0.5627   0.2102
 5A0  SAP  S  S2    0   0.005   5.2826  -0.4299   0.5713
 5A0  CAZ  C  CR5   0  -0.244   6.3377   0.9019  -0.1373
 5A0  CAA  C  CH3   0  -0.640   7.6513   1.0034   0.6183
 5A0  CAB  C  CH3   0  -0.615   6.5700   0.6186  -1.6154
 5A0  CAK  C  CH2   0  -0.252   5.4476   2.1401   0.0675
 5A0  NAM  N  N     0  -0.451   4.0544   1.7906  -0.0567
 5A0  H1   H  HCH1  0   0.204  -4.4539   2.7709  -1.1100
 5A0  H2   H  HCH2  0   0.296  -3.7261   2.6407   1.2756
 5A0  H3   H  HCH2  0   0.295  -5.2572   1.8901   1.7194
 5A0  H4   H  HCR5  0   0.277  -1.8344   1.1180   0.6586
 5A0  H5   H  HCR6  0   0.259  -2.4393  -4.7602  -0.1208
 5A0  H6   H  HCH2  0   0.261   0.7311  -0.1607  -1.7119
 5A0  H7   H  HCH2  0   0.274  -0.5186   0.6436  -0.7851
 5A0  H8   H  HCH2  0   0.274   1.7035   1.7032  -0.4859
 5A0  H9   H  HCH2  0   0.240   1.0651   1.1050   1.0493
 5A0  H10  H  HCH2  0   0.277   1.0495  -2.9875   0.5619
 5A0  H11  H  HCH2  0   0.242   1.6296  -2.3309  -0.9687
 5A0  H12  H  HCH2  0   0.244   2.0853  -1.2262   1.8426
 5A0  H13  H  HCH2  0   0.271   3.2749  -1.9417   0.7540
 5A0  H16  H  HCH3  0   0.243   8.2560   0.1034   0.5046
 5A0  H17  H  HCH3  0   0.241   8.2320   1.8393   0.2232
 5A0  H18  H  HCH3  0   0.241   7.4888   1.1776   1.6819
 5A0  H19  H  HCH3  0   0.238   5.6326   0.5865  -2.1720
 5A0  H20  H  HCH3  0   0.235   7.1902   1.4063  -2.0494
 5A0  H21  H  HCH3  0   0.240   7.0847  -0.3312  -1.7612
 5A0  H22  H  HCH2  0   0.233   5.6327   2.5658   1.0621
 5A0  H23  H  HCH2  0   0.236   5.7196   2.9105  -0.6594
 5A0  CAL  C  CH2   0  -0.640  -4.5131   1.9723   0.9221

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
 5A0  CAA  CAZ  single    1.519  0.020  1.519
 5A0  SAP  CAZ  single    1.841  0.020  1.841
 5A0  SAP  CAR  single    1.784  0.020  1.784
 5A0  CAL  CAS  single    1.492  0.020  1.492
 5A0  CAL  CAW  single    1.511  0.020  1.511
 5A0  CAZ  CAB  single    1.523  0.020  1.523
 5A0  CAZ  CAK  single    1.539  0.020  1.539
 5A0  SAQ  CAS  aromatic  1.739  0.020  1.739
 5A0  SAQ  C4   aromatic  1.729  0.020  1.729
 5A0  CAS  CAF  aromatic  1.354  0.020  1.354
 5A0  CAH  CAJ  single    1.516  0.020  1.516
 5A0  CAH  NAX  single    1.451  0.020  1.451
 5A0  C4   N3   aromatic  1.330  0.020  1.330
 5A0  C4   C5   aromatic  1.397  0.020  1.397
 5A0  CAF  C5   aromatic  1.433  0.020  1.433
 5A0  FAD  CAW  single    1.362  0.020  1.362
 5A0  N3   C2   aromatic  1.317  0.020  1.317
 5A0  C5   C6   aromatic  1.423  0.020  1.423
 5A0  CAW  FAC  single    1.365  0.020  1.365
 5A0  CAR  NAX  single    1.355  0.020  1.355
 5A0  CAR  NAM  double    1.274  0.020  1.274
 5A0  CAJ  NAY  single    1.453  0.020  1.453
 5A0  CAK  NAM  single    1.442  0.020  1.442
 5A0  C2   N1   aromatic  1.326  0.020  1.326
 5A0  NAX  CAG  single    1.449  0.020  1.449
 5A0  C6   N1   aromatic  1.332  0.020  1.332
 5A0  C6   NAY  single    1.355  0.020  1.355
 5A0  NAY  CAI  single    1.452  0.020  1.452
 5A0  CAI  CAG  single    1.521  0.020  1.521
 5A0  CAW  H1   single    0.970  0.020  1.090
 5A0  CAL  H2   single    0.970  0.020  1.090
 5A0  CAL  H3   single    0.970  0.020  1.090
 5A0  CAF  H4   single    0.930  0.020  1.080
 5A0  C2   H5   single    0.930  0.020  1.080
 5A0  CAJ  H6   single    0.970  0.020  1.090
 5A0  CAJ  H7   single    0.970  0.020  1.090
 5A0  CAH  H8   single    0.970  0.020  1.090
 5A0  CAH  H9   single    0.970  0.020  1.090
 5A0  CAI  H10  single    0.970  0.020  1.090
 5A0  CAI  H11  single    0.970  0.020  1.090
 5A0  CAG  H12  single    0.970  0.020  1.090
 5A0  CAG  H13  single    0.970  0.020  1.090
 5A0  CAA  H16  single    0.970  0.020  1.090
 5A0  CAA  H17  single    0.970  0.020  1.090
 5A0  CAA  H18  single    0.970  0.020  1.090
 5A0  CAB  H19  single    0.970  0.020  1.090
 5A0  CAB  H20  single    0.970  0.020  1.090
 5A0  CAB  H21  single    0.970  0.020  1.090
 5A0  CAK  H22  single    0.970  0.020  1.090
 5A0  CAK  H23  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
 5A0  SAQ  C4   N3   122.33  3.000
 5A0  N3   C4   C5   125.96  3.000
 5A0  SAQ  C4   C5   111.66  3.000
 5A0  CAF  C5   C6   133.59  3.000
 5A0  C6   C5   C4   114.79  3.000
 5A0  CAF  C5   C4   111.51  3.000
 5A0  NAY  C6   N1   117.62  3.000
 5A0  NAY  C6   C5   123.56  3.000
 5A0  N1   C6   C5   118.80  3.000
 5A0  C2   N1   C6   119.52  3.000
 5A0  C2   N3   C4   113.32  3.000
 5A0  H1   CAW  CAL  113.24  3.000
 5A0  H1   CAW  FAD  108.62  3.000
 5A0  CAL  CAW  FAD  109.79  3.000
 5A0  H1   CAW  FAC  108.26  3.000
 5A0  FAD  CAW  FAC  106.47  3.000
 5A0  CAL  CAW  FAC  110.21  3.000
 5A0  CAF  CAS  SAQ  112.22  3.000
 5A0  CAF  CAS  CAL  126.99  3.000
 5A0  SAQ  CAS  CAL  120.78  3.000
 5A0  CAS  SAQ  C4    91.30  3.000
 5A0  H4   CAF  CAS  121.19  3.000
 5A0  H4   CAF  C5   125.55  3.000
 5A0  CAS  CAF  C5   113.21  3.000
 5A0  H5   C2   N3   116.63  3.000
 5A0  H5   C2   N1   116.02  3.000
 5A0  N3   C2   N1   127.34  3.000
 5A0  CAI  NAY  CAJ  111.64  3.000
 5A0  CAI  NAY  C6   120.65  3.000
 5A0  CAJ  NAY  C6   123.34  3.000
 5A0  H7   CAJ  H6   106.87  3.000
 5A0  H7   CAJ  CAH  109.97  3.000
 5A0  H6   CAJ  CAH  109.16  3.000
 5A0  H7   CAJ  NAY  111.46  3.000
 5A0  H6   CAJ  NAY  108.71  3.000
 5A0  CAH  CAJ  NAY  110.57  3.000
 5A0  H9   CAH  H8   108.02  3.000
 5A0  H9   CAH  NAX  110.62  3.000
 5A0  H8   CAH  NAX  109.10  3.000
 5A0  H9   CAH  CAJ  110.19  3.000
 5A0  H8   CAH  CAJ  109.43  3.000
 5A0  NAX  CAH  CAJ  109.45  3.000
 5A0  H11  CAI  H10  107.85  3.000
 5A0  H11  CAI  CAG  110.01  3.000
 5A0  H10  CAI  CAG  108.88  3.000
 5A0  H11  CAI  NAY  110.56  3.000
 5A0  H10  CAI  NAY  109.96  3.000
 5A0  CAG  CAI  NAY  109.55  3.000
 5A0  H13  CAG  H12  107.62  3.000
 5A0  H13  CAG  NAX  110.42  3.000
 5A0  H12  CAG  NAX  110.48  3.000
 5A0  H13  CAG  CAI  107.79  3.000
 5A0  H12  CAG  CAI  109.37  3.000
 5A0  NAX  CAG  CAI  111.06  3.000
 5A0  CAR  NAX  CAG  123.03  3.000
 5A0  CAG  NAX  CAH  114.30  3.000
 5A0  CAR  NAX  CAH  119.00  3.000
 5A0  NAM  CAR  SAP  116.51  3.000
 5A0  NAM  CAR  NAX  124.51  3.000
 5A0  SAP  CAR  NAX  118.95  3.000
 5A0  CAZ  SAP  CAR   88.93  3.000
 5A0  CAK  CAZ  CAB  111.54  3.000
 5A0  CAK  CAZ  CAA  112.35  3.000
 5A0  CAB  CAZ  CAA  111.31  3.000
 5A0  CAK  CAZ  SAP  101.50  3.000
 5A0  CAB  CAZ  SAP  109.06  3.000
 5A0  CAA  CAZ  SAP  110.64  3.000
 5A0  H18  CAA  H17  108.06  3.000
 5A0  H18  CAA  H16  108.45  3.000
 5A0  H17  CAA  H16  107.42  3.000
 5A0  H18  CAA  CAZ  111.54  3.000
 5A0  H17  CAA  CAZ  109.33  3.000
 5A0  H16  CAA  CAZ  111.88  3.000
 5A0  H21  CAB  H20  107.88  3.000
 5A0  H21  CAB  H19  108.17  3.000
 5A0  H20  CAB  H19  107.84  3.000
 5A0  H21  CAB  CAZ  111.34  3.000
 5A0  H20  CAB  CAZ  109.76  3.000
 5A0  H19  CAB  CAZ  111.70  3.000
 5A0  H23  CAK  H22  106.69  3.000
 5A0  H23  CAK  NAM  110.72  3.000
 5A0  H22  CAK  NAM  109.58  3.000
 5A0  H23  CAK  CAZ  109.54  3.000
 5A0  H22  CAK  CAZ  109.58  3.000
 5A0  NAM  CAK  CAZ  110.64  3.000
 5A0  CAK  NAM  CAR  111.98  3.000
 5A0  H3   CAL  H2   107.50  3.000
 5A0  H3   CAL  CAS  111.18  3.000
 5A0  H2   CAL  CAS  108.54  3.000
 5A0  H3   CAL  CAW  109.15  3.000
 5A0  H2   CAL  CAW  108.12  3.000
 5A0  CAS  CAL  CAW  112.20  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
 5A0  CONST_01  CAF  CAS  SAQ  C4      0.00   0.0  0
 5A0  CONST_02  N1   C2   N3   C4      0.00   0.0  0
 5A0  CONST_03  CAS  CAF  C5   C4      0.00   0.0  0
 5A0  CONST_04  N1   C6   C5   C4      0.00   0.0  0
 5A0  CONST_05  CAS  SAQ  C4   C5      0.00   0.0  0
 5A0  CONST_06  C2   N3   C4   C5      0.00   0.0  0
 5A0  CONST_07  SAQ  CAS  CAF  C5      0.00   0.0  0
 5A0  CONST_08  C2   N1   C6   C5      0.00   0.0  0
 5A0  CONST_09  SAQ  C4   C5   C6    180.00   0.0  0
 5A0  CONST_10  N3   C4   C5   C6      0.00   0.0  0
 5A0  CONST_11  CAS  CAF  C5   C6    180.00   0.0  0
 5A0  CONST_12  N3   C2   N1   C6      0.00   0.0  0
 5A0  CONST_13  CAF  C5   C6   N1    180.00   0.0  0
 5A0  CONST_14  CAS  SAQ  C4   N3    180.00   0.0  0
 5A0  CONST_15  CAF  C5   C4   N3    180.00   0.0  0
 5A0  CONST_16  C2   N3   C4   SAQ   180.00   0.0  0
 5A0  CONST_17  CAF  C5   C4   SAQ     0.00   0.0  0
 5A0  CONST_18  NAY  C6   C5   C4    180.00   0.0  0
 5A0  CONST_19  NAY  C6   C5   CAF     0.00   0.0  0
 5A0  CONST_20  NAY  C6   N1   C2    180.00   0.0  0
 5A0  CONST_21  SAP  CAR  NAX  CAH   180.00   0.0  0
 5A0  CONST_22  NAM  CAR  NAX  CAH     0.00   0.0  0
 5A0  CONST_24  NAM  CAR  NAX  CAG   180.00   0.0  0
 5A0  CONST_25  CAK  NAM  CAR  NAX   180.00   0.0  0
 5A0  CONST_26  CAK  NAM  CAR  SAP     0.00   0.0  0
 5A0  CONST_27  CAL  CAS  SAQ  C4    180.00   0.0  0
 5A0  CONST_28  CAL  CAS  CAF  C5    180.00   0.0  0
 5A0  CONST_29  H5   C2   N3   C4    180.00   0.0  0
 5A0  CONST_30  H4   CAF  C5   C4    180.00   0.0  0
 5A0  Var_01    CAJ  NAY  C6   C5    -37.57  30.0  2
 5A0  Var_02    CAH  CAJ  NAY  C6    143.82  30.0  1
 5A0  Var_03    CAG  CAI  NAY  C6   -144.63  30.0  1
 5A0  Var_04    NAX  CAH  CAJ  NAY    55.35  30.0  1
 5A0  Var_05    NAX  CAG  CAI  NAY   -53.94  30.0  1
 5A0  Var_06    CAR  NAX  CAH  CAJ   147.29  30.0  1
 5A0  Var_07    CAI  CAG  NAX  CAH    53.59  30.0  1
 5A0  Var_08    CAK  CAZ  SAP  CAR    25.64  30.0  1
 5A0  Var_09    CAZ  CAK  NAM  CAR    25.27  30.0  1
 5A0  Var_10    NAM  CAK  CAZ  SAP   -33.32  30.0  1
 5A0  Var_11    NAM  CAR  SAP  CAZ   -15.10  30.0  1
 5A0  Var_12    SAQ  CAS  CAL  CAW   -74.92  30.0  2
 5A0  Var_13    H16  CAA  CAZ  SAP    64.74  30.0  3
 5A0  Var_14    H19  CAB  CAZ  SAP    60.07  30.0  3
 5A0  Var_15    CAS  CAL  CAW  FAC    61.70  30.0  1

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
 5A0  plan-1  CAH  0.020
 5A0  plan-1  CAG  0.020
 5A0  plan-1  NAX  0.020
 5A0  plan-1  CAR  0.020
 5A0  plan-1  SAP  0.020
 5A0  plan-1  CAK  0.020
 5A0  plan-1  NAM  0.020
 5A0  plan-2  C4   0.020
 5A0  plan-2  C5   0.020
 5A0  plan-2  C6   0.020
 5A0  plan-2  N1   0.020
 5A0  plan-2  N3   0.020
 5A0  plan-2  CAS  0.020
 5A0  plan-2  SAQ  0.020
 5A0  plan-2  CAF  0.020
 5A0  plan-2  C2   0.020
 5A0  plan-2  NAY  0.020
 5A0  plan-2  H4   0.020
 5A0  plan-2  H5   0.020
 5A0  plan-2  CAL  0.020

