# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 09:22:36 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: [(1R)-1-{[6-(4-methylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino}-2-phenylethyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1)c2sc3ncnc(N[C@@H](Cc4ccccc4)[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
 KFA  KFA  '[(1R)-1-{[6-(4-methylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino}-2-phenylethyl]phosphonic acid'  ligand  47  29  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KFA
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
 KFA  C5   C  CR56   0   0.050   0.3832  -0.0983  -0.8289
 KFA  C6   C  CR56   0  -0.035   0.8429  -0.6355  -2.0236
 KFA  N1   N  N      0  -0.456   0.0874  -0.9582  -3.0734
 KFA  C2   C  CR16   0   0.040  -1.1957  -0.6980  -2.8836
 KFA  N3   N  N      0  -0.457  -1.7798  -0.1862  -1.8131
 KFA  C4   C  CR6    0   0.539  -1.0248   0.1066  -0.7486
 KFA  CAP  C  CR16   0  -0.311   4.0142  -0.0526   1.7053
 KFA  CAQ  C  CR16   0  -0.277   5.2309   0.0730   2.3536
 KFA  CAR  C  CR6    0   0.084   6.4277   0.1502   1.6429
 KFA  CAW  C  CH3    0  -0.721   7.7457   0.2488   2.3517
 KFA  CAS  C  CR16   0  -0.278   6.3584   0.1038   0.2527
 KFA  CAT  C  CR16   0  -0.309   5.1439  -0.0137  -0.4038
 KFA  CAO  C  CR6    0   0.130   3.9466  -0.0937   0.3104
 KFA  CAM  C  CR5    0  -0.207   2.6562  -0.2035  -0.3645
 KFA  SAN  S  S2     0   0.195   2.5611  -0.8491  -1.9861
 KFA  CAL  C  CR15   0  -0.276   1.4278   0.1421   0.1084
 KFA  NAB  N  NH1    0  -0.640  -1.5855   0.5930   0.3516
 KFA  CAC  C  CH1    0  -0.360  -2.9995   0.7527   0.6197
 KFA  PAA  P  P      0   1.184  -3.1771   2.3048   1.6686
 KFA  OAE  O  O      0  -0.898  -2.0941   2.0907   2.7409
 KFA  OAU  O  OP    -1  -0.893  -2.8869   3.4691   0.7196
 KFA  OAD  O  OP    -1  -0.890  -4.6110   2.2671   2.2007
 KFA  CAV  C  CH2    0  -0.504  -3.5535  -0.4889   1.3381
 KFA  CAX  C  CR6    0   0.151  -3.2951  -1.7586   0.5831
 KFA  CAY  C  CR16   0  -0.300  -4.1940  -2.2130  -0.3795
 KFA  CAZ  C  CR16   0  -0.240  -3.9155  -3.3335  -1.1478
 KFA  CBA  C  CR16   0  -0.276  -2.7224  -4.0230  -0.9684
 KFA  CBB  C  CR16   0  -0.234  -1.8226  -3.5895  -0.0045
 KFA  CBC  C  CR16   0  -0.309  -2.1125  -2.4720   0.7668
 KFA  H1   H  HCR6   0   0.242  -1.8552  -0.9310  -3.7140
 KFA  H4   H  HCH3   0   0.250   8.1661  -0.7428   2.5332
 KFA  H5   H  HCH3   0   0.245   8.4754   0.8064   1.7652
 KFA  H6   H  HCH3   0   0.245   7.6434   0.7385   3.3199
 KFA  H7   H  HCR6   0   0.252   7.2673   0.1706  -0.3334
 KFA  H8   H  HCR6   0   0.251   5.1377  -0.0226  -1.4876
 KFA  H9   H  HCR5   0   0.267   1.2823   0.5761   1.0887
 KFA  H11  H  HNH1   0   0.376  -0.9977   0.8265   1.1400
 KFA  H12  H  HCH1   0   0.223  -3.5173   0.8689  -0.3335
 KFA  H15  H  HCH2   0   0.219  -3.1021  -0.5420   2.3327
 KFA  H16  H  HCH2   0   0.230  -4.6245  -0.3386   1.4822
 KFA  H17  H  HCR6   0   0.233  -5.1231  -1.6752  -0.5347
 KFA  H18  H  HCR6   0   0.242  -4.6294  -3.6712  -1.8890
 KFA  H19  H  HCR6   0   0.243  -2.5008  -4.8958  -1.5696
 KFA  H20  H  HCR6   0   0.242  -0.8923  -4.1223   0.1484
 KFA  H21  H  HCR6   0   0.235  -1.4009  -2.1413   1.5147
 KFA  H2   H  HCR6   0   0.255   3.1100  -0.1333   2.2951
 KFA  H3   H  HCR6   0   0.252   5.2491   0.1019   3.4366

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
 KFA  OAE  PAA  deloc     1.539  0.020  1.539
 KFA  N1   C2   aromatic  1.323  0.020  1.323
 KFA  N1   C6   aromatic  1.333  0.020  1.333
 KFA  C2   N3   aromatic  1.323  0.020  1.323
 KFA  SAN  C6   aromatic  1.732  0.020  1.732
 KFA  SAN  CAM  aromatic  1.748  0.020  1.748
 KFA  C6   C5   aromatic  1.388  0.020  1.388
 KFA  N3   C4   aromatic  1.337  0.020  1.337
 KFA  C5   C4   aromatic  1.425  0.020  1.425
 KFA  C5   CAL  aromatic  1.424  0.020  1.424
 KFA  PAA  OAU  deloc     1.530  0.020  1.530
 KFA  PAA  OAD  deloc     1.530  0.020  1.530
 KFA  PAA  CAC  single    1.882  0.020  1.882
 KFA  CAM  CAO  single    1.460  0.020  1.460
 KFA  CAM  CAL  aromatic  1.361  0.020  1.361
 KFA  C4   NAB  single    1.327  0.020  1.327
 KFA  CAT  CAO  aromatic  1.396  0.020  1.396
 KFA  CAT  CAS  aromatic  1.386  0.020  1.386
 KFA  CAO  CAP  aromatic  1.397  0.020  1.397
 KFA  CAP  CAQ  aromatic  1.384  0.020  1.384
 KFA  CAS  CAR  aromatic  1.393  0.020  1.393
 KFA  CAQ  CAR  aromatic  1.394  0.020  1.394
 KFA  CAR  CAW  single    1.500  0.020  1.500
 KFA  NAB  CAC  single    1.448  0.020  1.448
 KFA  CAC  CAV  single    1.538  0.020  1.538
 KFA  CAV  CAX  single    1.500  0.020  1.500
 KFA  CAX  CBC  aromatic  1.393  0.020  1.393
 KFA  CAX  CAY  aromatic  1.393  0.020  1.393
 KFA  CBC  CBB  aromatic  1.388  0.020  1.388
 KFA  CAY  CAZ  aromatic  1.387  0.020  1.387
 KFA  CBB  CBA  aromatic  1.388  0.020  1.388
 KFA  CAZ  CBA  aromatic  1.390  0.020  1.390
 KFA  C2   H1   single    0.930  0.020  1.080
 KFA  CAP  H2   single    0.930  0.020  1.080
 KFA  CAQ  H3   single    0.930  0.020  1.080
 KFA  CAW  H4   single    0.970  0.020  1.090
 KFA  CAW  H5   single    0.970  0.020  1.090
 KFA  CAW  H6   single    0.970  0.020  1.090
 KFA  CAS  H7   single    0.930  0.020  1.080
 KFA  CAT  H8   single    0.930  0.020  1.080
 KFA  CAL  H9   single    0.930  0.020  1.080
 KFA  NAB  H11  single    0.860  0.020  1.020
 KFA  CAC  H12  single    0.970  0.020  1.090
 KFA  CAV  H15  single    0.970  0.020  1.090
 KFA  CAV  H16  single    0.970  0.020  1.090
 KFA  CAY  H17  single    0.930  0.020  1.080
 KFA  CAZ  H18  single    0.930  0.020  1.080
 KFA  CBA  H19  single    0.930  0.020  1.080
 KFA  CBB  H20  single    0.930  0.020  1.080
 KFA  CBC  H21  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
 KFA  CAL  C5   C4   131.56  3.000
 KFA  CAL  C5   C6   112.88  3.000
 KFA  C4   C5   C6   115.55  3.000
 KFA  SAN  C6   N1   123.34  3.000
 KFA  SAN  C6   C5   110.96  3.000
 KFA  N1   C6   C5   125.71  3.000
 KFA  C2   N1   C6   112.90  3.000
 KFA  H1   C2   N3   115.71  3.000
 KFA  H1   C2   N1   115.93  3.000
 KFA  N3   C2   N1   128.36  3.000
 KFA  C4   N3   C2   118.66  3.000
 KFA  NAB  C4   N3   120.10  3.000
 KFA  NAB  C4   C5   121.12  3.000
 KFA  N3   C4   C5   118.78  3.000
 KFA  H2   CAP  CAO  120.09  3.000
 KFA  H2   CAP  CAQ  119.05  3.000
 KFA  CAO  CAP  CAQ  120.85  3.000
 KFA  H3   CAQ  CAR  119.58  3.000
 KFA  H3   CAQ  CAP  119.04  3.000
 KFA  CAR  CAQ  CAP  121.38  3.000
 KFA  CAS  CAR  CAW  121.17  3.000
 KFA  CAW  CAR  CAQ  121.14  3.000
 KFA  CAS  CAR  CAQ  117.67  3.000
 KFA  H6   CAW  H5   108.13  3.000
 KFA  H6   CAW  H4   107.24  3.000
 KFA  H5   CAW  H4   107.23  3.000
 KFA  H6   CAW  CAR  111.53  3.000
 KFA  H5   CAW  CAR  111.58  3.000
 KFA  H4   CAW  CAR  110.92  3.000
 KFA  H7   CAS  CAT  118.96  3.000
 KFA  H7   CAS  CAR  119.75  3.000
 KFA  CAT  CAS  CAR  121.29  3.000
 KFA  H8   CAT  CAO  120.40  3.000
 KFA  H8   CAT  CAS  118.65  3.000
 KFA  CAO  CAT  CAS  120.94  3.000
 KFA  CAM  CAO  CAT  121.71  3.000
 KFA  CAT  CAO  CAP  117.87  3.000
 KFA  CAM  CAO  CAP  120.42  3.000
 KFA  CAL  CAM  SAN  111.53  3.000
 KFA  CAL  CAM  CAO  128.17  3.000
 KFA  SAN  CAM  CAO  120.30  3.000
 KFA  CAM  SAN  C6    91.63  3.000
 KFA  H9   CAL  CAM  122.56  3.000
 KFA  H9   CAL  C5   124.44  3.000
 KFA  CAM  CAL  C5   112.99  3.000
 KFA  H11  NAB  CAC  113.46  3.000
 KFA  H11  NAB  C4   119.05  3.000
 KFA  CAC  NAB  C4   127.33  3.000
 KFA  H12  CAC  CAV  108.86  3.000
 KFA  H12  CAC  PAA  110.75  3.000
 KFA  CAV  CAC  PAA  111.81  3.000
 KFA  H12  CAC  NAB  108.27  3.000
 KFA  CAV  CAC  NAB  110.45  3.000
 KFA  PAA  CAC  NAB  106.64  3.000
 KFA  OAD  PAA  OAU  114.35  3.000
 KFA  OAD  PAA  OAE  114.44  3.000
 KFA  OAU  PAA  OAE  113.87  3.000
 KFA  OAD  PAA  CAC  105.19  3.000
 KFA  OAU  PAA  CAC  105.31  3.000
 KFA  OAE  PAA  CAC  101.96  3.000
 KFA  H16  CAV  H15  106.97  3.000
 KFA  H16  CAV  CAX  110.63  3.000
 KFA  H15  CAV  CAX  110.22  3.000
 KFA  H16  CAV  CAC  107.70  3.000
 KFA  H15  CAV  CAC  108.38  3.000
 KFA  CAX  CAV  CAC  112.72  3.000
 KFA  CBC  CAX  CAY  118.15  3.000
 KFA  CAY  CAX  CAV  120.85  3.000
 KFA  CBC  CAX  CAV  120.89  3.000
 KFA  H17  CAY  CAZ  119.56  3.000
 KFA  H17  CAY  CAX  119.33  3.000
 KFA  CAZ  CAY  CAX  121.11  3.000
 KFA  H18  CAZ  CBA  119.97  3.000
 KFA  H18  CAZ  CAY  119.91  3.000
 KFA  CBA  CAZ  CAY  120.12  3.000
 KFA  H19  CBA  CBB  120.31  3.000
 KFA  H19  CBA  CAZ  120.27  3.000
 KFA  CBB  CBA  CAZ  119.42  3.000
 KFA  H20  CBB  CBC  119.79  3.000
 KFA  H20  CBB  CBA  120.08  3.000
 KFA  CBC  CBB  CBA  120.12  3.000
 KFA  H21  CBC  CBB  119.46  3.000
 KFA  H21  CBC  CAX  119.47  3.000
 KFA  CBB  CBC  CAX  121.06  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
 KFA  CONST_01  C2   N1   C6   C5     0.00   0.0  0
 KFA  CONST_02  CAM  SAN  C6   C5     0.00   0.0  0
 KFA  CONST_03  C2   N3   C4   C5     0.00   0.0  0
 KFA  CONST_04  SAN  CAM  CAL  C5     0.00   0.0  0
 KFA  CONST_05  CAO  CAM  CAL  C5   180.00   0.0  0
 KFA  CONST_06  N3   C2   N1   C6     0.00   0.0  0
 KFA  CONST_07  CAO  CAM  SAN  C6   180.00   0.0  0
 KFA  CONST_08  CAL  CAM  SAN  C6     0.00   0.0  0
 KFA  CONST_09  N3   C4   C5   C6     0.00   0.0  0
 KFA  CONST_10  CAM  CAL  C5   C6     0.00   0.0  0
 KFA  CONST_11  C4   N3   C2   N1     0.00   0.0  0
 KFA  CONST_12  CAM  SAN  C6   N1   180.00   0.0  0
 KFA  CONST_13  C4   C5   C6   N1     0.00   0.0  0
 KFA  CONST_14  CAL  C5   C6   N1   180.00   0.0  0
 KFA  CONST_15  SAN  C6   N1   C2   180.00   0.0  0
 KFA  CONST_16  CAL  C5   C4   N3   180.00   0.0  0
 KFA  CONST_17  SAN  C6   C5   C4   180.00   0.0  0
 KFA  CONST_18  CAM  CAL  C5   C4   180.00   0.0  0
 KFA  CONST_21  CAS  CAT  CAO  CAP    0.00   0.0  0
 KFA  CONST_22  CAS  CAR  CAQ  CAP    0.00   0.0  0
 KFA  CONST_23  CAM  CAO  CAP  CAQ  180.00   0.0  0
 KFA  CONST_24  CAT  CAO  CAP  CAQ    0.00   0.0  0
 KFA  CONST_25  CAT  CAS  CAR  CAQ    0.00   0.0  0
 KFA  CONST_26  CAO  CAT  CAS  CAR    0.00   0.0  0
 KFA  CONST_27  CAO  CAP  CAQ  CAR    0.00   0.0  0
 KFA  CONST_28  CAM  CAO  CAT  CAS  180.00   0.0  0
 KFA  CONST_31  CAL  C5   C6   SAN    0.00   0.0  0
 KFA  CONST_32  CBA  CBB  CBC  CAX    0.00   0.0  0
 KFA  CONST_33  CBA  CAZ  CAY  CAX    0.00   0.0  0
 KFA  CONST_34  CBB  CBC  CAX  CAY    0.00   0.0  0
 KFA  CONST_35  CBB  CBA  CAZ  CAY    0.00   0.0  0
 KFA  CONST_36  CBC  CAX  CAY  CAZ    0.00   0.0  0
 KFA  CONST_37  CBC  CBB  CBA  CAZ    0.00   0.0  0
 KFA  CONST_38  NAB  C4   C5   C6   180.00   0.0  0
 KFA  CONST_39  NAB  C4   N3   C2   180.00   0.0  0
 KFA  CONST_40  CAW  CAR  CAQ  CAP  180.00   0.0  0
 KFA  CONST_41  CAT  CAS  CAR  CAW  180.00   0.0  0
 KFA  CONST_42  NAB  C4   C5   CAL    0.00   0.0  0
 KFA  CONST_43  CBB  CBC  CAX  CAV  180.00   0.0  0
 KFA  CONST_44  CAZ  CAY  CAX  CAV  180.00   0.0  0
 KFA  CONST_45  H1   C2   N1   C6   180.00   0.0  0
 KFA  CONST_46  H9   CAL  C5   C6   180.00   0.0  0
 KFA  CONST_47  H8   CAT  CAO  CAP  180.00   0.0  0
 KFA  CONST_48  H7   CAS  CAR  CAQ  180.00   0.0  0
 KFA  CONST_49  H2   CAP  CAQ  CAR  180.00   0.0  0
 KFA  CONST_50  H3   CAQ  CAR  CAS  180.00   0.0  0
 KFA  CONST_51  H20  CBB  CBC  CAX  180.00   0.0  0
 KFA  CONST_52  H18  CAZ  CAY  CAX  180.00   0.0  0
 KFA  CONST_53  H21  CBC  CAX  CAY  180.00   0.0  0
 KFA  CONST_54  H19  CBA  CAZ  CAY  180.00   0.0  0
 KFA  CONST_55  H17  CAY  CAZ  CBA  180.00   0.0  0
 KFA  CONST_56  CAC  NAB  C4   C5   180.00   0.0  0
 KFA  CONST_57  CAC  NAB  C4   N3     0.00   0.0  0
 KFA  CONST_58  H11  NAB  C4   C5     0.00   0.0  0
 KFA  Var_01    CBC  CAX  CAV  CAC   87.89  30.0  2
 KFA  Var_02    H4   CAW  CAR  CAQ   90.77  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
 KFA  chir_01  CAC  PAA  NAB  CAV  negativ

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
 KFA  plan-1  CAP  0.020
 KFA  plan-1  CAQ  0.020
 KFA  plan-1  CAR  0.020
 KFA  plan-1  CAW  0.020
 KFA  plan-1  CAS  0.020
 KFA  plan-1  CAT  0.020
 KFA  plan-1  CAO  0.020
 KFA  plan-1  CAM  0.020
 KFA  plan-1  H7   0.020
 KFA  plan-1  H8   0.020
 KFA  plan-1  H2   0.020
 KFA  plan-1  H3   0.020
 KFA  plan-2  CAV  0.020
 KFA  plan-2  CAX  0.020
 KFA  plan-2  CAY  0.020
 KFA  plan-2  CAZ  0.020
 KFA  plan-2  CBA  0.020
 KFA  plan-2  CBB  0.020
 KFA  plan-2  CBC  0.020
 KFA  plan-2  H17  0.020
 KFA  plan-2  H18  0.020
 KFA  plan-2  H19  0.020
 KFA  plan-2  H20  0.020
 KFA  plan-2  H21  0.020
 KFA  plan-3  C5   0.020
 KFA  plan-3  C6   0.020
 KFA  plan-3  N1   0.020
 KFA  plan-3  C2   0.020
 KFA  plan-3  N3   0.020
 KFA  plan-3  C4   0.020
 KFA  plan-3  CAO  0.020
 KFA  plan-3  CAM  0.020
 KFA  plan-3  SAN  0.020
 KFA  plan-3  CAL  0.020
 KFA  plan-3  NAB  0.020
 KFA  plan-3  H1   0.020
 KFA  plan-3  H9   0.020
 KFA  plan-4  C4   0.020
 KFA  plan-4  NAB  0.020
 KFA  plan-4  CAC  0.020
 KFA  plan-4  H11  0.020

