# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 08:11:28 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: [(1S)-1-{[6-(3-chloro-4-methylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino}-2-(3-fluorophenyl)ethyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1Cl)c2sc3ncnc(N[C@H](Cc4cccc(F)c4)[P](O)(O)=O)c3c2
#
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
 YF7  YF7  '[(1S)-1-{[6-(3-chloro-4-methylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino}-2-(3-fluorophenyl)ethyl]phosphonic acid'  ligand  47  31  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YF7
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
 YF7  CAF  C   CR16   0  -0.271  -4.5033   1.0120  -0.2816
 YF7  CAA  C   CR6    0  -0.082  -5.6948   1.7116  -0.3147
 YF7  CLA  CL  CL     0  -0.124  -5.6653   3.3495  -0.8893
 YF7  CAB  C   CR6    0   0.153  -6.9096   1.1500   0.0777
 YF7  CAG  C   CH3    0  -0.721  -8.1967   1.9111   0.0247
 YF7  CAC  C   CR16   0  -0.298  -6.8643  -0.1694   0.5198
 YF7  CAD  C   CR16   0  -0.299  -5.6820  -0.8879   0.5732
 YF7  CAE  C   CR6    0   0.130  -4.4785  -0.3082   0.1721
 YF7  CAI  C   CR5    0  -0.207  -3.2163  -1.0409   0.2172
 YF7  SAJ  S   S2     0   0.206  -3.2136  -2.7872   0.2413
 YF7  CAM  C   CR15   0  -0.273  -1.9525  -0.5364   0.2359
 YF7  C5   C   CR56   0   0.031  -0.9512  -1.5476   0.2716
 YF7  C6   C   CR56   0  -0.030  -1.4847  -2.8302   0.2814
 YF7  N1   N   N      0  -0.451  -0.7844  -3.9640   0.3061
 YF7  C2   C   CR16   0   0.039   0.5219  -3.7629   0.3149
 YF7  N3   N   N      0  -0.474   1.1751  -2.6110   0.3022
 YF7  C4   C   CR6    0   0.539   0.4723  -1.4719   0.2836
 YF7  NAR  N   NH1    0  -0.637   1.1016  -0.3028   0.3151
 YF7  CAS  C   CH1    0  -0.350   2.4995  -0.0859  -0.0285
 YF7  PBB  P   P      0   1.187   2.5135   0.6432  -1.7676
 YF7  OBD  O   OP    -1  -0.874   3.9705   0.6427  -2.2256
 YF7  OBE  O   OP    -1  -0.888   1.6142  -0.3115  -2.5589
 YF7  OBC  O   O      0  -0.898   1.9012   2.0372  -1.5529
 YF7  CAT  C   CH2    0  -0.506   3.1140   0.8083   1.0540
 YF7  CAU  C   CR6    0   0.158   4.5851   1.0587   0.8973
 YF7  CAZ  C   CR16   0  -0.482   5.5072   0.1912   1.4753
 YF7  CAY  C   CR6    0   0.528   6.8588   0.4480   1.3406
 YF7  FBA  F   F      0  -0.325   7.7370  -0.4057   1.9043
 YF7  CAX  C   CR16   0  -0.433   7.3400   1.5484   0.6620
 YF7  CAW  C   CR16   0  -0.242   6.4124   2.4111   0.0867
 YF7  CAV  C   CR16   0  -0.265   5.0538   2.1637   0.1905
 YF7  H1   H   HCR6   0   0.278  -3.5953   1.4901  -0.6241
 YF7  H2   H   HCH3   0   0.253  -8.4198   2.2473  -0.9890
 YF7  H3   H   HCH3   0   0.253  -9.0250   1.2918   0.3631
 YF7  H4   H   HCH3   0   0.253  -8.1617   2.8002   0.6564
 YF7  H5   H   HCR6   0   0.264  -7.7842  -0.6454   0.8358
 YF7  H6   H   HCR6   0   0.258  -5.7079  -1.9047   0.9456
 YF7  H7   H   HCR5   0   0.271  -1.7518   0.5261   0.2445
 YF7  H8   H   HCR6   0   0.249   1.1405  -4.6548   0.3349
 YF7  H9   H   HNH1   0   0.380   0.5294   0.5182   0.1777
 YF7  H10  H   HCH1   0   0.230   2.9975  -1.0558  -0.0219
 YF7  H13  H   HCH2   0   0.228   2.5865   1.7647   1.0461
 YF7  H14  H   HCH2   0   0.228   2.9332   0.3561   2.0340
 YF7  H15  H   HCR6   0   0.260   5.1753  -0.6774   2.0328
 YF7  H16  H   HCR6   0   0.268   8.4038   1.7319   0.5861
 YF7  H17  H   HCR6   0   0.254   6.7648   3.2814  -0.4519
 YF7  H18  H   HCR6   0   0.234   4.3376   2.8225  -0.2823

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
 YF7  OBC  PBB  deloc     1.538  0.020  1.538
 YF7  OBD  PBB  deloc     1.527  0.020  1.527
 YF7  PBB  OBE  deloc     1.532  0.020  1.532
 YF7  PBB  CAS  single    1.886  0.020  1.886
 YF7  CAS  NAR  single    1.456  0.020  1.456
 YF7  CAS  CAT  single    1.533  0.020  1.533
 YF7  NAR  C4   single    1.328  0.020  1.328
 YF7  C4   N3   aromatic  1.339  0.020  1.339
 YF7  C4   C5   aromatic  1.426  0.020  1.426
 YF7  CAT  CAU  single    1.500  0.020  1.500
 YF7  N3   C2   aromatic  1.324  0.020  1.324
 YF7  CAM  C5   aromatic  1.423  0.020  1.423
 YF7  CAM  CAI  aromatic  1.361  0.020  1.361
 YF7  C5   C6   aromatic  1.389  0.020  1.389
 YF7  C2   N1   aromatic  1.322  0.020  1.322
 YF7  CAD  CAC  aromatic  1.385  0.020  1.385
 YF7  CAD  CAE  aromatic  1.395  0.020  1.395
 YF7  CAI  CAE  single    1.460  0.020  1.460
 YF7  CAI  SAJ  aromatic  1.746  0.020  1.746
 YF7  CAC  CAB  aromatic  1.392  0.020  1.392
 YF7  CAE  CAF  aromatic  1.396  0.020  1.396
 YF7  C6   N1   aromatic  1.333  0.020  1.333
 YF7  C6   SAJ  aromatic  1.730  0.020  1.730
 YF7  CAB  CAG  single    1.496  0.020  1.496
 YF7  CAB  CAA  aromatic  1.395  0.020  1.395
 YF7  CAF  CAA  aromatic  1.382  0.020  1.382
 YF7  CAU  CAV  aromatic  1.393  0.020  1.393
 YF7  CAU  CAZ  aromatic  1.392  0.020  1.392
 YF7  CAA  CLA  single    1.736  0.020  1.736
 YF7  CAV  CAW  aromatic  1.385  0.020  1.385
 YF7  CAZ  CAY  aromatic  1.382  0.020  1.382
 YF7  CAW  CAX  aromatic  1.391  0.020  1.391
 YF7  CAY  CAX  aromatic  1.380  0.020  1.380
 YF7  CAY  FBA  single    1.348  0.020  1.348
 YF7  CAF  H1   single    0.930  0.020  1.080
 YF7  CAG  H2   single    0.970  0.020  1.090
 YF7  CAG  H3   single    0.970  0.020  1.090
 YF7  CAG  H4   single    0.970  0.020  1.090
 YF7  CAC  H5   single    0.930  0.020  1.080
 YF7  CAD  H6   single    0.930  0.020  1.080
 YF7  CAM  H7   single    0.930  0.020  1.080
 YF7  C2   H8   single    0.930  0.020  1.080
 YF7  NAR  H9   single    0.890  0.020  1.040
 YF7  CAS  H10  single    0.970  0.020  1.090
 YF7  CAT  H13  single    0.970  0.020  1.090
 YF7  CAT  H14  single    0.970  0.020  1.090
 YF7  CAZ  H15  single    0.930  0.020  1.080
 YF7  CAX  H16  single    0.930  0.020  1.080
 YF7  CAW  H17  single    0.930  0.020  1.080
 YF7  CAV  H18  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
 YF7  H1   CAF  CAE  120.38  3.000
 YF7  H1   CAF  CAA  119.49  3.000
 YF7  CAE  CAF  CAA  120.12  3.000
 YF7  CAB  CAA  CLA  119.20  3.000
 YF7  CLA  CAA  CAF  118.09  3.000
 YF7  CAB  CAA  CAF  122.70  3.000
 YF7  CAC  CAB  CAG  121.42  3.000
 YF7  CAG  CAB  CAA  122.30  3.000
 YF7  CAC  CAB  CAA  116.27  3.000
 YF7  H4   CAG  H3   107.94  3.000
 YF7  H4   CAG  H2   107.06  3.000
 YF7  H3   CAG  H2   107.98  3.000
 YF7  H4   CAG  CAB  111.49  3.000
 YF7  H3   CAG  CAB  110.75  3.000
 YF7  H2   CAG  CAB  111.44  3.000
 YF7  H5   CAC  CAD  119.08  3.000
 YF7  H5   CAC  CAB  118.79  3.000
 YF7  CAD  CAC  CAB  122.13  3.000
 YF7  H6   CAD  CAE  120.64  3.000
 YF7  H6   CAD  CAC  118.68  3.000
 YF7  CAE  CAD  CAC  120.67  3.000
 YF7  CAI  CAE  CAD  121.90  3.000
 YF7  CAI  CAE  CAF  120.00  3.000
 YF7  CAD  CAE  CAF  118.11  3.000
 YF7  CAM  CAI  SAJ  111.66  3.000
 YF7  SAJ  CAI  CAE  120.24  3.000
 YF7  CAM  CAI  CAE  128.11  3.000
 YF7  C6   SAJ  CAI   91.53  3.000
 YF7  H7   CAM  C5   124.56  3.000
 YF7  H7   CAM  CAI  122.46  3.000
 YF7  C5   CAM  CAI  112.97  3.000
 YF7  C4   C5   C6   115.62  3.000
 YF7  C6   C5   CAM  112.70  3.000
 YF7  C4   C5   CAM  131.67  3.000
 YF7  N1   C6   C5   125.71  3.000
 YF7  N1   C6   SAJ  123.14  3.000
 YF7  C5   C6   SAJ  111.14  3.000
 YF7  C2   N1   C6   112.96  3.000
 YF7  H8   C2   N3   115.70  3.000
 YF7  H8   C2   N1   116.00  3.000
 YF7  N3   C2   N1   128.30  3.000
 YF7  C4   N3   C2   118.78  3.000
 YF7  NAR  C4   N3   120.00  3.000
 YF7  N3   C4   C5   118.63  3.000
 YF7  NAR  C4   C5   121.34  3.000
 YF7  H9   NAR  CAS  113.00  3.000
 YF7  H9   NAR  C4   116.35  3.000
 YF7  CAS  NAR  C4   125.48  3.000
 YF7  H10  CAS  CAT  109.37  3.000
 YF7  H10  CAS  PBB  110.25  3.000
 YF7  CAT  CAS  PBB  115.01  3.000
 YF7  H10  CAS  NAR  107.74  3.000
 YF7  CAT  CAS  NAR  107.77  3.000
 YF7  PBB  CAS  NAR  106.40  3.000
 YF7  OBC  PBB  OBE  113.79  3.000
 YF7  OBE  PBB  OBD  113.89  3.000
 YF7  OBC  PBB  OBD  114.96  3.000
 YF7  OBE  PBB  CAS  103.36  3.000
 YF7  OBD  PBB  CAS  106.47  3.000
 YF7  OBC  PBB  CAS  102.64  3.000
 YF7  H14  CAT  H13  106.77  3.000
 YF7  H14  CAT  CAU  108.93  3.000
 YF7  H13  CAT  CAU  109.06  3.000
 YF7  H14  CAT  CAS  108.97  3.000
 YF7  H13  CAT  CAS  108.19  3.000
 YF7  CAU  CAT  CAS  114.63  3.000
 YF7  CAV  CAU  CAZ  118.84  3.000
 YF7  CAZ  CAU  CAT  120.14  3.000
 YF7  CAV  CAU  CAT  121.02  3.000
 YF7  H15  CAZ  CAY  119.89  3.000
 YF7  H15  CAZ  CAU  120.67  3.000
 YF7  CAY  CAZ  CAU  119.44  3.000
 YF7  CAX  CAY  FBA  118.91  3.000
 YF7  FBA  CAY  CAZ  118.59  3.000
 YF7  CAX  CAY  CAZ  122.49  3.000
 YF7  H16  CAX  CAW  121.41  3.000
 YF7  H16  CAX  CAY  120.84  3.000
 YF7  CAW  CAX  CAY  117.74  3.000
 YF7  H17  CAW  CAV  120.02  3.000
 YF7  H17  CAW  CAX  119.16  3.000
 YF7  CAV  CAW  CAX  120.82  3.000
 YF7  H18  CAV  CAW  120.52  3.000
 YF7  H18  CAV  CAU  118.82  3.000
 YF7  CAW  CAV  CAU  120.66  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
 YF7  CONST_01  CAC  CAD  CAE  CAF    0.00   0.0  0
 YF7  CONST_04  CAC  CAB  CAA  CAF    0.00   0.0  0
 YF7  CONST_05  CAD  CAC  CAB  CAA    0.00   0.0  0
 YF7  CONST_06  CAD  CAE  CAF  CAA    0.00   0.0  0
 YF7  CONST_07  CAI  CAE  CAF  CAA  180.00   0.0  0
 YF7  CONST_08  CAE  CAD  CAC  CAB    0.00   0.0  0
 YF7  CONST_09  CAE  CAF  CAA  CAB    0.00   0.0  0
 YF7  CONST_10  CAI  CAE  CAD  CAC  180.00   0.0  0
 YF7  CONST_13  C5   CAM  CAI  CAE  180.00   0.0  0
 YF7  CONST_14  C6   SAJ  CAI  CAE  180.00   0.0  0
 YF7  CONST_15  C4   C5   CAM  CAI  180.00   0.0  0
 YF7  CONST_16  C6   C5   CAM  CAI    0.00   0.0  0
 YF7  CONST_17  C5   C6   SAJ  CAI    0.00   0.0  0
 YF7  CONST_18  N1   C6   SAJ  CAI  180.00   0.0  0
 YF7  CONST_19  C5   CAM  CAI  SAJ    0.00   0.0  0
 YF7  CONST_20  C4   C5   C6   SAJ  180.00   0.0  0
 YF7  CONST_21  CAM  C5   C6   SAJ    0.00   0.0  0
 YF7  CONST_22  C2   N1   C6   SAJ  180.00   0.0  0
 YF7  CONST_23  N3   C4   C5   CAM  180.00   0.0  0
 YF7  CONST_24  N1   C6   C5   CAM  180.00   0.0  0
 YF7  CONST_25  C6   SAJ  CAI  CAM    0.00   0.0  0
 YF7  CONST_26  C2   N3   C4   C5     0.00   0.0  0
 YF7  CONST_27  C2   N1   C6   C5     0.00   0.0  0
 YF7  CONST_28  N3   C4   C5   C6     0.00   0.0  0
 YF7  CONST_29  N3   C2   N1   C6     0.00   0.0  0
 YF7  CONST_30  C4   N3   C2   N1     0.00   0.0  0
 YF7  CONST_31  C4   C5   C6   N1     0.00   0.0  0
 YF7  CONST_32  CAX  CAW  CAV  CAU    0.00   0.0  0
 YF7  CONST_33  CAX  CAY  CAZ  CAU    0.00   0.0  0
 YF7  CONST_34  CAW  CAV  CAU  CAZ    0.00   0.0  0
 YF7  CONST_35  CAW  CAX  CAY  CAZ    0.00   0.0  0
 YF7  CONST_36  CAV  CAU  CAZ  CAY    0.00   0.0  0
 YF7  CONST_37  CAV  CAW  CAX  CAY    0.00   0.0  0
 YF7  CONST_38  CAG  CAB  CAA  CAF  180.00   0.0  0
 YF7  CONST_39  CAC  CAB  CAA  CLA  180.00   0.0  0
 YF7  CONST_40  CAE  CAF  CAA  CLA  180.00   0.0  0
 YF7  CONST_41  CAD  CAC  CAB  CAG  180.00   0.0  0
 YF7  CONST_42  NAR  C4   C5   CAM    0.00   0.0  0
 YF7  CONST_43  NAR  C4   C5   C6   180.00   0.0  0
 YF7  CONST_44  NAR  C4   N3   C2   180.00   0.0  0
 YF7  CONST_45  CAW  CAV  CAU  CAT  180.00   0.0  0
 YF7  CONST_46  CAY  CAZ  CAU  CAT  180.00   0.0  0
 YF7  CONST_47  FBA  CAY  CAZ  CAU  180.00   0.0  0
 YF7  CONST_48  CAW  CAX  CAY  FBA  180.00   0.0  0
 YF7  CONST_49  H6   CAD  CAE  CAF  180.00   0.0  0
 YF7  CONST_50  H5   CAC  CAB  CAA  180.00   0.0  0
 YF7  CONST_51  H1   CAF  CAA  CAB  180.00   0.0  0
 YF7  CONST_52  H7   CAM  CAI  CAE    0.00   0.0  0
 YF7  CONST_53  H8   C2   N1   C6   180.00   0.0  0
 YF7  CONST_54  H17  CAW  CAV  CAU  180.00   0.0  0
 YF7  CONST_55  H18  CAV  CAU  CAZ  180.00   0.0  0
 YF7  CONST_56  H16  CAX  CAY  CAZ  180.00   0.0  0
 YF7  CONST_57  H15  CAZ  CAY  CAX  180.00   0.0  0
 YF7  CONST_60  H9   NAR  C4   C5     0.00   0.0  0
 YF7  Var_01    CAV  CAU  CAT  CAS   91.82  30.0  2
 YF7  Var_02    H2   CAG  CAB  CAA   59.20  30.0  2

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
 YF7  chir_01  CAS  PBB  NAR  CAT  positiv

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
 YF7  plan-1  CAF  0.020
 YF7  plan-1  CAA  0.020
 YF7  plan-1  CLA  0.020
 YF7  plan-1  CAB  0.020
 YF7  plan-1  CAG  0.020
 YF7  plan-1  CAC  0.020
 YF7  plan-1  CAD  0.020
 YF7  plan-1  CAE  0.020
 YF7  plan-1  CAI  0.020
 YF7  plan-1  H1   0.020
 YF7  plan-1  H5   0.020
 YF7  plan-1  H6   0.020
 YF7  plan-2  CAT  0.020
 YF7  plan-2  CAU  0.020
 YF7  plan-2  CAZ  0.020
 YF7  plan-2  CAY  0.020
 YF7  plan-2  FBA  0.020
 YF7  plan-2  CAX  0.020
 YF7  plan-2  CAW  0.020
 YF7  plan-2  CAV  0.020
 YF7  plan-2  H15  0.020
 YF7  plan-2  H16  0.020
 YF7  plan-2  H17  0.020
 YF7  plan-2  H18  0.020
 YF7  plan-3  CAE  0.020
 YF7  plan-3  CAI  0.020
 YF7  plan-3  SAJ  0.020
 YF7  plan-3  CAM  0.020
 YF7  plan-3  C5   0.020
 YF7  plan-3  C6   0.020
 YF7  plan-3  N1   0.020
 YF7  plan-3  C2   0.020
 YF7  plan-3  N3   0.020
 YF7  plan-3  C4   0.020
 YF7  plan-3  NAR  0.020
 YF7  plan-3  H7   0.020
 YF7  plan-3  H8   0.020
 YF7  plan-4  C4   0.020
 YF7  plan-4  NAR  0.020
 YF7  plan-4  CAS  0.020
 YF7  plan-4  H9   0.020

