# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jun  4 01:54:20 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  49  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 OK
;

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  -0.267  -4.5154   1.0214  -0.2873
 YF7  CAA  C   CR6   0  -0.083  -5.7054   1.7236  -0.2559
 YF7  CLA  CL  CL    0  -0.122  -5.7035   3.3606  -0.8318
 YF7  CAB  C   CR6   0   0.155  -6.8972   1.1647   0.2056
 YF7  CAG  C   CH3   0  -0.721  -8.1824   1.9302   0.2281
 YF7  CAC  C   CR16  0  -0.298  -6.8310  -0.1544   0.6459
 YF7  CAD  C   CR16  0  -0.296  -5.6493  -0.8756   0.6345
 YF7  CAE  C   CR6   0   0.127  -4.4695  -0.2972   0.1678
 YF7  CAI  C   CR5   0  -0.204  -3.2054  -1.0292   0.1531
 YF7  SAJ  S   S2    0   0.227  -3.2015  -2.7754   0.1621
 YF7  CAM  C   CR15  0  -0.270  -1.9448  -0.5189   0.1306
 YF7  C5   C   CR56  0   0.050  -0.9425  -1.5303   0.1231
 YF7  C6   C   CR56  0  -0.023  -1.4740  -2.8162   0.1453
 YF7  N1   N   N     0  -0.435  -0.7682  -3.9448   0.1497
 YF7  C2   C   CR16  0   0.047   0.5356  -3.7495   0.1314
 YF7  N3   N   N     0  -0.472   1.1825  -2.5893   0.1040
 YF7  C4   C   CR6   0   0.559   0.4731  -1.4663   0.0986
 YF7  NAR  N   NH1   0  -0.679   1.1115  -0.2842   0.0893
 YF7  CAS  C   CH1   0  -0.371   2.5389  -0.1245  -0.0326
 YF7  PBB  P   P     0   1.384   2.9391   0.2742  -1.7799
 YF7  OBD  O   OH1   0  -0.733   4.5119   0.0465  -1.9950
 YF7  OBE  O   OH1   0  -0.736   2.1901  -0.9247  -2.5382
 YF7  OBC  O   O     0  -0.707   2.5596   1.6464  -2.1911
 YF7  CAT  C   CH2   0  -0.522   3.0134   0.9800   0.9215
 YF7  CAU  C   CR6   0   0.122   4.4978   1.2132   0.8834
 YF7  CAZ  C   CR16  0  -0.463   5.3644   0.2572   1.4077
 YF7  CAY  C   CR6   0   0.542   6.7250   0.4788   1.3474
 YF7  FBA  F   F     0  -0.317   7.5532  -0.4501   1.8548
 YF7  CAX  C   CR16  0  -0.422   7.2680   1.6213   0.7909
 YF7  CAW  C   CR16  0  -0.226   6.3974   2.5712   0.2770
 YF7  CAV  C   CR16  0  -0.298   5.0247   2.3703   0.3197
 YF7  H1   H   HCR6  0   0.279  -3.6267   1.4970  -0.6801
 YF7  H2   H   HCH3  0   0.254  -8.4601   2.2740  -0.7693
 YF7  H3   H   HCH3  0   0.254  -8.9930   1.3117   0.6083
 YF7  H4   H   HCH3  0   0.254  -8.1087   2.8145   0.8633
 YF7  H5   H   HCR6  0   0.266  -7.7327  -0.6275   1.0140
 YF7  H6   H   HCR6  0   0.260  -5.6562  -1.8914   1.0104
 YF7  H7   H   HCR5  0   0.276  -1.7468   0.5438   0.1418
 YF7  H8   H   HCR6  0   0.260   1.1578  -4.6377   0.1376
 YF7  H9   H   HNH1  0   0.415   0.5541   0.5543   0.0425
 YF7  H10  H   HCH1  0   0.314   3.0092  -1.0734   0.2324
 YF7  H11  H   HOH1  0   0.490   4.8420  -0.8362  -1.7824
 YF7  H12  H   HOH1  0   0.496   2.0642  -0.7721  -3.4853
 YF7  H13  H   HCH2  0   0.272   2.4907   1.9102   0.6885
 YF7  H14  H   HCH2  0   0.286   2.7071   0.6847   1.9273
 YF7  H15  H   HCR6  0   0.274   4.9847  -0.6509   1.8611
 YF7  H16  H   HCR6  0   0.278   8.3399   1.7664   0.7632
 YF7  H17  H   HCR6  0   0.267   6.7967   3.4760  -0.1612
 YF7  H18  H   HCR6  0   0.255   4.3586   3.1172  -0.0930

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  double    1.482  0.020  1.482
 YF7  OBD  PBB  single    1.604  0.020  1.604
 YF7  PBB  OBE  single    1.604  0.020  1.604
 YF7  PBB  CAS  single    1.836  0.020  1.836
 YF7  CAS  NAR  single    1.442  0.020  1.442
 YF7  CAS  CAT  single    1.535  0.020  1.535
 YF7  NAR  C4   single    1.343  0.020  1.343
 YF7  C4   N3   aromatic  1.328  0.020  1.328
 YF7  C4   C5   aromatic  1.417  0.020  1.417
 YF7  CAT  CAU  single    1.503  0.020  1.503
 YF7  N3   C2   aromatic  1.329  0.020  1.329
 YF7  CAM  C5   aromatic  1.424  0.020  1.424
 YF7  CAM  CAI  aromatic  1.360  0.020  1.360
 YF7  C5   C6   aromatic  1.392  0.020  1.392
 YF7  C2   N1   aromatic  1.318  0.020  1.318
 YF7  CAD  CAC  aromatic  1.384  0.020  1.384
 YF7  CAD  CAE  aromatic  1.394  0.020  1.394
 YF7  CAI  CAE  single    1.461  0.020  1.461
 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  1.331  0.020  1.331
 YF7  C6   SAJ  aromatic  1.728  0.020  1.728
 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  1.391  0.020  1.391
 YF7  CAU  CAZ  aromatic  1.393  0.020  1.393
 YF7  CAA  CLA  single    1.735  0.020  1.735
 YF7  CAV  CAW  aromatic  1.388  0.020  1.388
 YF7  CAZ  CAY  aromatic  1.380  0.020  1.380
 YF7  CAW  CAX  aromatic  1.387  0.020  1.387
 YF7  CAY  CAX  aromatic  1.382  0.020  1.382
 YF7  CAY  FBA  single    1.344  0.020  1.344
 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    0.860  0.020  1.020
 YF7  CAS  H10  single    0.970  0.020  1.090
 YF7  OBD  H11  single    0.850  0.020  0.980
 YF7  OBE  H12  single    0.850  0.020  0.980
 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  120.44  3.000
 YF7  H1   CAF  CAA  119.49  3.000
 YF7  CAE  CAF  CAA  120.06  3.000
 YF7  CAB  CAA  CLA  119.26  3.000
 YF7  CLA  CAA  CAF  118.08  3.000
 YF7  CAB  CAA  CAF  122.66  3.000
 YF7  CAC  CAB  CAG  121.39  3.000
 YF7  CAG  CAB  CAA  122.27  3.000
 YF7  CAC  CAB  CAA  116.34  3.000
 YF7  H4   CAG  H3   107.91  3.000
 YF7  H4   CAG  H2   107.09  3.000
 YF7  H3   CAG  H2   107.99  3.000
 YF7  H4   CAG  CAB  111.43  3.000
 YF7  H3   CAG  CAB  110.76  3.000
 YF7  H2   CAG  CAB  111.48  3.000
 YF7  H5   CAC  CAD  119.08  3.000
 YF7  H5   CAC  CAB  118.81  3.000
 YF7  CAD  CAC  CAB  122.11  3.000
 YF7  H6   CAD  CAE  120.70  3.000
 YF7  H6   CAD  CAC  118.70  3.000
 YF7  CAE  CAD  CAC  120.59  3.000
 YF7  CAI  CAE  CAD  121.85  3.000
 YF7  CAI  CAE  CAF  119.91  3.000
 YF7  CAD  CAE  CAF  118.24  3.000
 YF7  CAM  CAI  SAJ  111.91  3.000
 YF7  SAJ  CAI  CAE  120.19  3.000
 YF7  CAM  CAI  CAE  127.89  3.000
 YF7  C6   SAJ  CAI   91.48  3.000
 YF7  H7   CAM  C5   124.71  3.000
 YF7  H7   CAM  CAI  122.57  3.000
 YF7  C5   CAM  CAI  112.70  3.000
 YF7  C4   C5   C6   115.05  3.000
 YF7  C6   C5   CAM  112.80  3.000
 YF7  C4   C5   CAM  132.15  3.000
 YF7  N1   C6   C5   125.52  3.000
 YF7  N1   C6   SAJ  123.37  3.000
 YF7  C5   C6   SAJ  111.11  3.000
 YF7  C2   N1   C6   113.50  3.000
 YF7  H8   C2   N3   115.85  3.000
 YF7  H8   C2   N1   116.48  3.000
 YF7  N3   C2   N1   127.67  3.000
 YF7  C4   N3   C2   118.57  3.000
 YF7  NAR  C4   N3   119.35  3.000
 YF7  N3   C4   C5   119.68  3.000
 YF7  NAR  C4   C5   120.96  3.000
 YF7  H9   NAR  CAS  116.84  3.000
 YF7  H9   NAR  C4   118.00  3.000
 YF7  CAS  NAR  C4   124.65  3.000
 YF7  H10  CAS  CAT  109.97  3.000
 YF7  H10  CAS  PBB  109.01  3.000
 YF7  CAT  CAS  PBB  111.59  3.000
 YF7  H10  CAS  NAR  108.04  3.000
 YF7  CAT  CAS  NAR  109.47  3.000
 YF7  PBB  CAS  NAR  108.68  3.000
 YF7  OBC  PBB  OBE  116.19  3.000
 YF7  OBE  PBB  OBD  106.76  3.000
 YF7  OBC  PBB  OBD  110.20  3.000
 YF7  OBE  PBB  CAS  100.71  3.000
 YF7  OBD  PBB  CAS  108.09  3.000
 YF7  OBC  PBB  CAS  114.16  3.000
 YF7  H11  OBD  PBB  115.81  3.000
 YF7  H12  OBE  PBB  113.94  3.000
 YF7  H14  CAT  H13  107.01  3.000
 YF7  H14  CAT  CAU  110.02  3.000
 YF7  H13  CAT  CAU  109.58  3.000
 YF7  H14  CAT  CAS  106.93  3.000
 YF7  H13  CAT  CAS  109.41  3.000
 YF7  CAU  CAT  CAS  113.65  3.000
 YF7  CAV  CAU  CAZ  119.20  3.000
 YF7  CAZ  CAU  CAT  119.90  3.000
 YF7  CAV  CAU  CAT  120.90  3.000
 YF7  H15  CAZ  CAY  119.89  3.000
 YF7  H15  CAZ  CAU  120.98  3.000
 YF7  CAY  CAZ  CAU  119.13  3.000
 YF7  CAX  CAY  FBA  118.77  3.000
 YF7  FBA  CAY  CAZ  118.69  3.000
 YF7  CAX  CAY  CAZ  122.53  3.000
 YF7  H16  CAX  CAW  121.36  3.000
 YF7  H16  CAX  CAY  120.69  3.000
 YF7  CAW  CAX  CAY  117.95  3.000
 YF7  H17  CAW  CAV  119.91  3.000
 YF7  H17  CAW  CAX  119.41  3.000
 YF7  CAV  CAW  CAX  120.68  3.000
 YF7  H18  CAV  CAW  119.79  3.000
 YF7  H18  CAV  CAU  119.70  3.000
 YF7  CAW  CAV  CAU  120.50  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_58  CAS  NAR  C4   C5   180.00   0.0  0
 YF7  CONST_59  CAS  NAR  C4   N3     0.00   0.0  0
 YF7  CONST_60  H9   NAR  C4   C5     0.00   0.0  0
 YF7  Var_01    CAV  CAU  CAT  CAS  109.16  30.0  2
 YF7  Var_02    H2   CAG  CAB  CAA   58.87  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

