# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 07:56:07 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-fluoroethyl)thieno[2,3-d]pyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)CN=C(S1)N2CCN(CC2)c3ncnc4sc(CCF)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
 59X  59X  4-[4-(5,5-dimethyl-4,5-dihydro-1,3-thiazol-2-yl)piperazin-1-yl]-6-(2-fluoroethyl)thieno[2,3-d]pyrimidine  ligand  47  25  .  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_59X
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
 59X  C4   C  CR56  0  -0.025  -3.8741  -1.4272  -0.2455
 59X  C5   C  CR56  0   0.049  -2.6435  -0.7986  -0.0475
 59X  C6   C  CR6   0   0.522  -1.5160  -1.6606  -0.1054
 59X  N1   N  N     0  -0.470  -1.6966  -2.9364  -0.4370
 59X  N3   N  N     0  -0.427  -4.0550  -2.7164  -0.5186
 59X  FAC  F  F     0  -0.375  -5.5436   4.2281  -1.0662
 59X  CAF  C  CH2   0   0.010  -5.0980   2.9154  -1.1867
 59X  CAS  C  CR5   0  -0.170  -4.0781   1.0290   0.0701
 59X  SAQ  S  S2    0   0.222  -5.1822  -0.2982  -0.1644
 59X  CAE  C  CR15  0  -0.242  -2.7887   0.6186   0.1019
 59X  C2   C  CR16  0   0.045  -2.9288  -3.3908  -0.6284
 59X  NAX  N  NT    0  -0.500  -0.2469  -1.2339   0.1186
 59X  CAK  C  CH2   0  -0.330   0.0880  -0.3180   1.1982
 59X  CAI  C  CH2   0  -0.288   1.2483   0.5743   0.8084
 59X  CAJ  C  CH2   0  -0.301   0.8806  -2.0805  -0.2247
 59X  CAH  C  CH2   0  -0.303   2.0541  -1.2115  -0.6431
 59X  NAW  N  NT    0  -0.492   2.3747  -0.2381   0.3849
 59X  CAR  C  CR5   0   0.359   3.6244   0.2634   0.5440
 59X  SAP  S  S2    0   0.008   5.0172  -0.7076  -0.0047
 59X  CAY  C  CR5   0  -0.242   6.1031   0.7530   0.2624
 59X  CAA  C  CH3   0  -0.639   7.4665   0.3189   0.7735
 59X  CAB  C  CH3   0  -0.616   6.2242   1.5306  -1.0415
 59X  CAL  C  CH2   0  -0.257   5.3074   1.5427   1.3176
 59X  NAM  N  N     0  -0.449   3.8908   1.3707   1.1132
 59X  H1   H  HCH2  0   0.209  -5.9330   2.3072  -1.5391
 59X  H2   H  HCH2  0   0.217  -4.3035   2.8882  -1.9334
 59X  H3   H  HCH2  0   0.274  -3.7736   3.0709   0.4959
 59X  H4   H  HCH2  0   0.275  -5.3890   2.4972   0.9001
 59X  H5   H  HCR5  0   0.275  -1.9746   1.3225   0.1927
 59X  H6   H  HCR6  0   0.259  -3.0139  -4.4397  -0.8911
 59X  H7   H  HCH2  0   0.274  -0.7620   0.2943   1.4811
 59X  H8   H  HCH2  0   0.257   0.3658  -0.9024   2.0840
 59X  H9   H  HCH2  0   0.238   0.9456   1.2636   0.0109
 59X  H10  H  HCH2  0   0.269   1.5432   1.1707   1.6685
 59X  H11  H  HCH2  0   0.239   1.1641  -2.7134   0.6245
 59X  H12  H  HCH2  0   0.274   0.6186  -2.7335  -1.0528
 59X  H13  H  HCH2  0   0.270   2.9070  -1.8633  -0.8284
 59X  H14  H  HCH2  0   0.242   1.8123  -0.7085  -1.5871
 59X  H15  H  HCH3  0   0.243   8.0122  -0.2595   0.0275
 59X  H16  H  HCH3  0   0.242   8.0656   1.2016   1.0067
 59X  H17  H  HCH3  0   0.241   7.3825  -0.2797   1.6804
 59X  H18  H  HCH3  0   0.238   5.2523   1.8753  -1.3959
 59X  H19  H  HCH3  0   0.235   6.8581   2.4080  -0.8918
 59X  H20  H  HCH3  0   0.240   6.6765   0.9209  -1.8239
 59X  H21  H  HCH2  0   0.235   5.5822   1.1962   2.3219
 59X  H22  H  HCH2  0   0.237   5.5782   2.6006   1.2634
 59X  CAG  C  CH2   0  -0.571  -4.5888   2.4282   0.1588

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
 59X  CAI  CAK  single    1.515  0.020  1.515
 59X  CAI  NAW  single    1.452  0.020  1.452
 59X  CAK  NAX  single    1.455  0.020  1.455
 59X  NAM  CAL  single    1.442  0.020  1.442
 59X  NAM  CAR  double    1.273  0.020  1.273
 59X  NAX  C6   single    1.358  0.020  1.358
 59X  NAX  CAJ  single    1.451  0.020  1.451
 59X  N1   C6   aromatic  1.331  0.020  1.331
 59X  N1   C2   aromatic  1.327  0.020  1.327
 59X  C6   C5   aromatic  1.420  0.020  1.420
 59X  C2   N3   aromatic  1.317  0.020  1.317
 59X  NAW  CAR  single    1.356  0.020  1.356
 59X  NAW  CAH  single    1.452  0.020  1.452
 59X  CAL  CAY  single    1.540  0.020  1.540
 59X  CAJ  CAH  single    1.519  0.020  1.519
 59X  CAR  SAP  single    1.784  0.020  1.784
 59X  FAC  CAF  single    1.391  0.020  1.391
 59X  C5   C4   aromatic  1.396  0.020  1.396
 59X  C5   CAE  aromatic  1.432  0.020  1.432
 59X  CAF  CAG  single    1.519  0.020  1.519
 59X  N3   C4   aromatic  1.330  0.020  1.330
 59X  C4   SAQ  aromatic  1.730  0.020  1.730
 59X  CAE  CAS  aromatic  1.354  0.020  1.354
 59X  CAS  SAQ  aromatic  1.742  0.020  1.742
 59X  CAS  CAG  single    1.492  0.020  1.492
 59X  CAB  CAY  single    1.523  0.020  1.523
 59X  CAY  SAP  single    1.839  0.020  1.839
 59X  CAY  CAA  single    1.519  0.020  1.519
 59X  CAF  H1   single    0.970  0.020  1.090
 59X  CAF  H2   single    0.970  0.020  1.090
 59X  CAG  H3   single    0.970  0.020  1.090
 59X  CAG  H4   single    0.970  0.020  1.090
 59X  CAE  H5   single    0.930  0.020  1.080
 59X  C2   H6   single    0.930  0.020  1.080
 59X  CAK  H7   single    0.970  0.020  1.090
 59X  CAK  H8   single    0.970  0.020  1.090
 59X  CAI  H9   single    0.970  0.020  1.090
 59X  CAI  H10  single    0.970  0.020  1.090
 59X  CAJ  H11  single    0.970  0.020  1.090
 59X  CAJ  H12  single    0.970  0.020  1.090
 59X  CAH  H13  single    0.970  0.020  1.090
 59X  CAH  H14  single    0.970  0.020  1.090
 59X  CAA  H15  single    0.970  0.020  1.090
 59X  CAA  H16  single    0.970  0.020  1.090
 59X  CAA  H17  single    0.970  0.020  1.090
 59X  CAB  H18  single    0.970  0.020  1.090
 59X  CAB  H19  single    0.970  0.020  1.090
 59X  CAB  H20  single    0.970  0.020  1.090
 59X  CAL  H21  single    0.970  0.020  1.090
 59X  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
 59X  SAQ  C4   N3   122.64  3.000
 59X  SAQ  C4   C5   111.47  3.000
 59X  N3   C4   C5   125.83  3.000
 59X  CAE  C5   C6   133.24  3.000
 59X  CAE  C5   C4   111.78  3.000
 59X  C6   C5   C4   114.88  3.000
 59X  NAX  C6   N1   118.00  3.000
 59X  N1   C6   C5   118.97  3.000
 59X  NAX  C6   C5   123.00  3.000
 59X  C2   N1   C6   119.36  3.000
 59X  C2   N3   C4   113.40  3.000
 59X  H2   CAF  H1   108.80  3.000
 59X  H2   CAF  CAG  110.75  3.000
 59X  H1   CAF  CAG  111.33  3.000
 59X  H2   CAF  FAC  108.42  3.000
 59X  H1   CAF  FAC  107.98  3.000
 59X  CAG  CAF  FAC  109.47  3.000
 59X  CAE  CAS  SAQ  112.08  3.000
 59X  SAQ  CAS  CAG  120.36  3.000
 59X  CAE  CAS  CAG  127.52  3.000
 59X  CAS  SAQ  C4    91.39  3.000
 59X  H5   CAE  CAS  121.49  3.000
 59X  H5   CAE  C5   125.25  3.000
 59X  CAS  CAE  C5   113.21  3.000
 59X  H6   C2   N3   116.63  3.000
 59X  H6   C2   N1   116.03  3.000
 59X  N3   C2   N1   127.33  3.000
 59X  CAJ  NAX  CAK  111.35  3.000
 59X  CAJ  NAX  C6   120.26  3.000
 59X  CAK  NAX  C6   122.38  3.000
 59X  H8   CAK  H7   106.77  3.000
 59X  H8   CAK  CAI  109.13  3.000
 59X  H7   CAK  CAI  109.55  3.000
 59X  H8   CAK  NAX  108.79  3.000
 59X  H7   CAK  NAX  111.62  3.000
 59X  CAI  CAK  NAX  110.87  3.000
 59X  H10  CAI  H9   107.77  3.000
 59X  H10  CAI  NAW  109.10  3.000
 59X  H9   CAI  NAW  110.71  3.000
 59X  H10  CAI  CAK  109.11  3.000
 59X  H9   CAI  CAK  110.24  3.000
 59X  NAW  CAI  CAK  109.86  3.000
 59X  H12  CAJ  H11  107.80  3.000
 59X  H12  CAJ  CAH  108.67  3.000
 59X  H11  CAJ  CAH  110.11  3.000
 59X  H12  CAJ  NAX  110.09  3.000
 59X  H11  CAJ  NAX  110.76  3.000
 59X  CAH  CAJ  NAX  109.37  3.000
 59X  H14  CAH  H13  107.50  3.000
 59X  H14  CAH  NAW  110.54  3.000
 59X  H13  CAH  NAW  110.42  3.000
 59X  H14  CAH  CAJ  109.22  3.000
 59X  H13  CAH  CAJ  108.02  3.000
 59X  NAW  CAH  CAJ  111.05  3.000
 59X  CAR  NAW  CAH  122.32  3.000
 59X  CAH  NAW  CAI  114.23  3.000
 59X  CAR  NAW  CAI  118.28  3.000
 59X  NAM  CAR  SAP  116.58  3.000
 59X  SAP  CAR  NAW  118.82  3.000
 59X  NAM  CAR  NAW  124.54  3.000
 59X  CAY  SAP  CAR   89.09  3.000
 59X  CAL  CAY  CAB  111.47  3.000
 59X  CAB  CAY  CAA  111.26  3.000
 59X  CAL  CAY  CAA  112.32  3.000
 59X  CAA  CAY  SAP  110.60  3.000
 59X  CAB  CAY  SAP  109.15  3.000
 59X  CAL  CAY  SAP  101.63  3.000
 59X  H17  CAA  H16  107.97  3.000
 59X  H17  CAA  H15  108.45  3.000
 59X  H16  CAA  H15  107.48  3.000
 59X  H17  CAA  CAY  111.57  3.000
 59X  H16  CAA  CAY  109.47  3.000
 59X  H15  CAA  CAY  111.75  3.000
 59X  H20  CAB  H19  107.86  3.000
 59X  H20  CAB  H18  108.26  3.000
 59X  H19  CAB  H18  107.92  3.000
 59X  H20  CAB  CAY  111.22  3.000
 59X  H19  CAB  CAY  109.80  3.000
 59X  H18  CAB  CAY  111.64  3.000
 59X  H22  CAL  H21  106.79  3.000
 59X  H22  CAL  NAM  110.59  3.000
 59X  H21  CAL  NAM  109.77  3.000
 59X  H22  CAL  CAY  109.53  3.000
 59X  H21  CAL  CAY  109.63  3.000
 59X  NAM  CAL  CAY  110.46  3.000
 59X  CAL  NAM  CAR  111.88  3.000
 59X  H4   CAG  H3   107.47  3.000
 59X  H4   CAG  CAS  110.50  3.000
 59X  H3   CAG  CAS  108.36  3.000
 59X  H4   CAG  CAF  109.58  3.000
 59X  H3   CAG  CAF  109.58  3.000
 59X  CAS  CAG  CAF  111.28  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
 59X  CONST_01  N1   C6   C5   C4      0.00   0.0  0
 59X  CONST_02  CAS  CAE  C5   C4      0.00   0.0  0
 59X  CONST_03  N1   C2   N3   C4      0.00   0.0  0
 59X  CONST_04  CAE  CAS  SAQ  C4      0.00   0.0  0
 59X  CONST_05  C2   N1   C6   C5      0.00   0.0  0
 59X  CONST_06  C2   N3   C4   C5      0.00   0.0  0
 59X  CONST_07  CAS  SAQ  C4   C5      0.00   0.0  0
 59X  CONST_08  SAQ  CAS  CAE  C5      0.00   0.0  0
 59X  CONST_09  N3   C2   N1   C6      0.00   0.0  0
 59X  CONST_10  N3   C4   C5   C6      0.00   0.0  0
 59X  CONST_11  SAQ  C4   C5   C6    180.00   0.0  0
 59X  CONST_12  CAS  CAE  C5   C6    180.00   0.0  0
 59X  CONST_13  CAE  C5   C6   N1    180.00   0.0  0
 59X  CONST_14  CAE  C5   C4   N3    180.00   0.0  0
 59X  CONST_15  CAS  SAQ  C4   N3    180.00   0.0  0
 59X  CONST_16  CAE  C5   C4   SAQ     0.00   0.0  0
 59X  CONST_17  C2   N3   C4   SAQ   180.00   0.0  0
 59X  CONST_18  NAX  C6   C5   C4    180.00   0.0  0
 59X  CONST_19  NAX  C6   C5   CAE     0.00   0.0  0
 59X  CONST_20  NAX  C6   N1   C2    180.00   0.0  0
 59X  CONST_21  NAM  CAR  NAW  CAI     0.00   0.0  0
 59X  CONST_22  SAP  CAR  NAW  CAI   180.00   0.0  0
 59X  CONST_25  CAL  NAM  CAR  NAW   180.00   0.0  0
 59X  CONST_26  CAL  NAM  CAR  SAP     0.00   0.0  0
 59X  CONST_27  CAG  CAS  SAQ  C4    180.00   0.0  0
 59X  CONST_28  CAG  CAS  CAE  C5    180.00   0.0  0
 59X  CONST_29  H5   CAE  C5   C4    180.00   0.0  0
 59X  CONST_30  H6   C2   N3   C4    180.00   0.0  0
 59X  Var_01    CAK  NAX  C6   C5     42.62  30.0  1
 59X  Var_02    CAI  CAK  NAX  C6   -147.84  30.0  1
 59X  Var_03    CAH  CAJ  NAX  C6    147.79  30.0  1
 59X  Var_04    NAW  CAI  CAK  NAX   -54.44  30.0  1
 59X  Var_05    NAW  CAH  CAJ  NAX    54.90  30.0  1
 59X  Var_06    CAR  NAW  CAI  CAK  -152.21  30.0  1
 59X  Var_07    CAJ  CAH  NAW  CAI   -53.43  30.0  1
 59X  Var_08    CAY  CAL  NAM  CAR    27.00  30.0  1
 59X  Var_09    CAL  CAY  SAP  CAR    24.64  30.0  1
 59X  Var_10    NAM  CAL  CAY  SAP   -33.43  30.0  1
 59X  Var_11    NAM  CAR  SAP  CAY   -12.84  30.0  1
 59X  Var_12    CAE  CAS  CAG  CAF   107.03  30.0  2
 59X  Var_13    H18  CAB  CAY  SAP    59.67  30.0  3
 59X  Var_14    H15  CAA  CAY  SAP    65.87  30.0  3
 59X  Var_15    CAS  CAG  CAF  FAC  -179.02  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
 59X  plan-1  CAI  0.020
 59X  plan-1  CAH  0.020
 59X  plan-1  NAW  0.020
 59X  plan-1  CAR  0.020
 59X  plan-1  SAP  0.020
 59X  plan-1  CAL  0.020
 59X  plan-1  NAM  0.020
 59X  plan-2  C4   0.020
 59X  plan-2  C5   0.020
 59X  plan-2  C6   0.020
 59X  plan-2  N1   0.020
 59X  plan-2  N3   0.020
 59X  plan-2  CAS  0.020
 59X  plan-2  SAQ  0.020
 59X  plan-2  CAE  0.020
 59X  plan-2  C2   0.020
 59X  plan-2  NAX  0.020
 59X  plan-2  H5   0.020
 59X  plan-2  H6   0.020
 59X  plan-2  CAG  0.020

