# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 09:03:29 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: [(1S)-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
 KF7  KF7  '[(1S)-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_KF7
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
 KF7  OAD  O  OP    -1  -0.879  -4.2323   0.0946   1.8551
 KF7  CAM  C  CR5    0  -0.205   3.4182  -0.4041  -0.0345
 KF7  CAO  C  CR6    0   0.135   4.5910   0.4660  -0.0336
 KF7  CAL  C  CR15   0  -0.278   2.1076  -0.0458  -0.1157
 KF7  NAB  N  NH1    0  -0.641  -0.9444  -0.1515  -0.3244
 KF7  CAP  C  CR16   0  -0.311   5.8572  -0.0076  -0.3786
 KF7  CAQ  C  CR16   0  -0.283   6.9552   0.8395  -0.3949
 KF7  CAR  C  CR6    0   0.084   6.8327   2.1881  -0.0757
 KF7  CAW  C  CH3    0  -0.723   8.0113   3.1146  -0.1230
 KF7  CAS  C  CR16   0  -0.271   5.5669   2.6584   0.2763
 KF7  CAT  C  CR16   0  -0.315   4.4690   1.8181   0.3028
 KF7  SAN  S  S2     0   0.199   3.6031  -2.1398   0.0542
 KF7  C5   C  CR56   0   0.031   1.2231  -1.1618  -0.1180
 KF7  C6   C  CR56   0  -0.034   1.8909  -2.3768  -0.0403
 KF7  N1   N  N      0  -0.453   1.3189  -3.5811  -0.0447
 KF7  C2   C  CR16   0   0.035   0.0022  -3.5254  -0.1500
 KF7  N3   N  N      0  -0.474  -0.7696  -2.4532  -0.2334
 KF7  C4   C  CR6    0   0.545  -0.1973  -1.2438  -0.2085
 KF7  CAC  C  CH1    0  -0.345  -2.3899  -0.0978  -0.1567
 KF7  PAA  P  P      0   1.186  -2.7442   0.3661   1.6375
 KF7  OAE  O  O      0  -0.898  -2.3376   1.8469   1.7031
 KF7  OAU  O  OP    -1  -0.886  -1.8230  -0.5584   2.4402
 KF7  CAV  C  CH2    0  -0.509  -2.9318   0.8891  -1.1973
 KF7  CAX  C  CR6    0   0.142  -4.4296   0.9781  -1.2652
 KF7  CAY  C  CR16   0  -0.328  -5.1489   0.1680  -2.1397
 KF7  CAZ  C  CR16   0  -0.247  -6.5333   0.2611  -2.2312
 KF7  CBA  C  CR16   0  -0.279  -7.2188   1.1809  -1.4500
 KF7  CBB  C  CR16   0  -0.257  -6.5104   1.9953  -0.5727
 KF7  CBC  C  CR16   0  -0.256  -5.1322   1.8843  -0.4734
 KF7  H2   H  HCR5   0   0.268   1.7909   0.9848  -0.2018
 KF7  H3   H  HNH1   0   0.383  -0.4813   0.7271  -0.1456
 KF7  H4   H  HCR6   0   0.252   6.0001  -1.0459  -0.6542
 KF7  H5   H  HCR6   0   0.253   7.9237   0.4398  -0.6702
 KF7  H6   H  HCH3   0   0.250   7.9633   3.7616  -1.0012
 KF7  H7   H  HCH3   0   0.246   8.0423   3.7640   0.7522
 KF7  H8   H  HCH3   0   0.245   8.9512   2.5664  -0.1707
 KF7  H9   H  HCR6   0   0.252   5.4378   3.7008   0.5434
 KF7  H10  H  HCR6   0   0.255   3.5083   2.2170   0.6029
 KF7  H11  H  HCR6   0   0.247  -0.5134  -4.4807  -0.1702
 KF7  H12  H  HCH1   0   0.226  -2.7785  -1.0944  -0.3709
 KF7  H14  H  HCH2   0   0.225  -2.5239   1.8791  -0.9764
 KF7  H15  H  HCH2   0   0.223  -2.5516   0.6036  -2.1832
 KF7  H16  H  HCR6   0   0.235  -4.6194  -0.5415  -2.7668
 KF7  H17  H  HCR6   0   0.243  -7.0736  -0.3763  -2.9201
 KF7  H18  H  HCR6   0   0.244  -8.2954   1.2677  -1.5268
 KF7  H19  H  HCR6   0   0.241  -7.0395   2.7157   0.0392
 KF7  H20  H  HCR6   0   0.229  -4.5807   2.5014   0.2239

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
 KF7  OAE  PAA  deloc     1.537  0.020  1.537
 KF7  OAU  PAA  deloc     1.532  0.020  1.532
 KF7  PAA  OAD  deloc     1.528  0.020  1.528
 KF7  PAA  CAC  single    1.887  0.020  1.887
 KF7  CAC  NAB  single    1.456  0.020  1.456
 KF7  CAC  CAV  single    1.533  0.020  1.533
 KF7  NAB  C4   single    1.328  0.020  1.328
 KF7  CAV  CAX  single    1.502  0.020  1.502
 KF7  C4   N3   aromatic  1.338  0.020  1.338
 KF7  C4   C5   aromatic  1.426  0.020  1.426
 KF7  N3   C2   aromatic  1.324  0.020  1.324
 KF7  C5   CAL  aromatic  1.424  0.020  1.424
 KF7  C5   C6   aromatic  1.389  0.020  1.389
 KF7  C2   N1   aromatic  1.322  0.020  1.322
 KF7  CAL  CAM  aromatic  1.361  0.020  1.361
 KF7  CAT  CAS  aromatic  1.383  0.020  1.383
 KF7  CAT  CAO  aromatic  1.399  0.020  1.399
 KF7  C6   N1   aromatic  1.333  0.020  1.333
 KF7  C6   SAN  aromatic  1.731  0.020  1.731
 KF7  CAS  CAR  aromatic  1.396  0.020  1.396
 KF7  CAM  CAO  single    1.460  0.020  1.460
 KF7  CAM  SAN  aromatic  1.748  0.020  1.748
 KF7  CAO  CAP  aromatic  1.395  0.020  1.395
 KF7  CAR  CAW  single    1.500  0.020  1.500
 KF7  CAR  CAQ  aromatic  1.391  0.020  1.391
 KF7  CAX  CBC  aromatic  1.393  0.020  1.393
 KF7  CAX  CAY  aromatic  1.392  0.020  1.392
 KF7  CAP  CAQ  aromatic  1.387  0.020  1.387
 KF7  CBC  CBB  aromatic  1.386  0.020  1.386
 KF7  CAY  CAZ  aromatic  1.391  0.020  1.391
 KF7  CBB  CBA  aromatic  1.391  0.020  1.391
 KF7  CAZ  CBA  aromatic  1.388  0.020  1.388
 KF7  CAL  H2   single    0.930  0.020  1.080
 KF7  NAB  H3   single    0.890  0.020  1.040
 KF7  CAP  H4   single    0.930  0.020  1.080
 KF7  CAQ  H5   single    0.930  0.020  1.080
 KF7  CAW  H6   single    0.970  0.020  1.090
 KF7  CAW  H7   single    0.970  0.020  1.090
 KF7  CAW  H8   single    0.970  0.020  1.090
 KF7  CAS  H9   single    0.930  0.020  1.080
 KF7  CAT  H10  single    0.930  0.020  1.080
 KF7  C2   H11  single    0.930  0.020  1.080
 KF7  CAC  H12  single    0.970  0.020  1.090
 KF7  CAV  H14  single    0.970  0.020  1.090
 KF7  CAV  H15  single    0.970  0.020  1.090
 KF7  CAY  H16  single    0.930  0.020  1.080
 KF7  CAZ  H17  single    0.930  0.020  1.080
 KF7  CBA  H18  single    0.930  0.020  1.080
 KF7  CBB  H19  single    0.930  0.020  1.080
 KF7  CBC  H20  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
 KF7  SAN  CAM  CAL  111.49  3.000
 KF7  SAN  CAM  CAO  120.45  3.000
 KF7  CAL  CAM  CAO  128.06  3.000
 KF7  CAT  CAO  CAP  117.83  3.000
 KF7  CAP  CAO  CAM  121.77  3.000
 KF7  CAT  CAO  CAM  120.40  3.000
 KF7  H2   CAL  C5   124.38  3.000
 KF7  H2   CAL  CAM  122.52  3.000
 KF7  C5   CAL  CAM  113.07  3.000
 KF7  H3   NAB  CAC  113.77  3.000
 KF7  H3   NAB  C4   116.25  3.000
 KF7  CAC  NAB  C4   125.35  3.000
 KF7  H4   CAP  CAQ  118.55  3.000
 KF7  H4   CAP  CAO  120.51  3.000
 KF7  CAQ  CAP  CAO  120.93  3.000
 KF7  H5   CAQ  CAR  119.64  3.000
 KF7  H5   CAQ  CAP  119.04  3.000
 KF7  CAR  CAQ  CAP  121.31  3.000
 KF7  CAS  CAR  CAW  120.83  3.000
 KF7  CAW  CAR  CAQ  121.49  3.000
 KF7  CAS  CAR  CAQ  117.67  3.000
 KF7  H8   CAW  H7   108.09  3.000
 KF7  H8   CAW  H6   107.52  3.000
 KF7  H7   CAW  H6   107.09  3.000
 KF7  H8   CAW  CAR  111.62  3.000
 KF7  H7   CAW  CAR  111.40  3.000
 KF7  H6   CAW  CAR  110.91  3.000
 KF7  H9   CAS  CAT  119.03  3.000
 KF7  H9   CAS  CAR  119.62  3.000
 KF7  CAT  CAS  CAR  121.35  3.000
 KF7  H10  CAT  CAS  119.07  3.000
 KF7  H10  CAT  CAO  120.02  3.000
 KF7  CAS  CAT  CAO  120.90  3.000
 KF7  C6   SAN  CAM   91.64  3.000
 KF7  C4   C5   C6   115.62  3.000
 KF7  C6   C5   CAL  112.76  3.000
 KF7  C4   C5   CAL  131.61  3.000
 KF7  N1   C6   C5   125.72  3.000
 KF7  N1   C6   SAN  123.24  3.000
 KF7  C5   C6   SAN  111.04  3.000
 KF7  C2   N1   C6   112.92  3.000
 KF7  H11  C2   N3   115.76  3.000
 KF7  H11  C2   N1   115.94  3.000
 KF7  N3   C2   N1   128.30  3.000
 KF7  C4   N3   C2   118.78  3.000
 KF7  N3   C4   C5   118.64  3.000
 KF7  C5   C4   NAB  121.24  3.000
 KF7  N3   C4   NAB  120.06  3.000
 KF7  H12  CAC  CAV  109.20  3.000
 KF7  H12  CAC  PAA  110.15  3.000
 KF7  CAV  CAC  PAA  114.88  3.000
 KF7  H12  CAC  NAB  107.29  3.000
 KF7  CAV  CAC  NAB  107.24  3.000
 KF7  PAA  CAC  NAB  107.76  3.000
 KF7  OAU  PAA  OAE  113.58  3.000
 KF7  OAU  PAA  CAC  103.70  3.000
 KF7  OAE  PAA  CAC  103.17  3.000
 KF7  CAC  PAA  OAD  105.93  3.000
 KF7  OAU  PAA  OAD  113.81  3.000
 KF7  OAE  PAA  OAD  115.00  3.000
 KF7  H15  CAV  H14  106.77  3.000
 KF7  H15  CAV  CAX  108.73  3.000
 KF7  H14  CAV  CAX  109.12  3.000
 KF7  H15  CAV  CAC  108.71  3.000
 KF7  H14  CAV  CAC  108.30  3.000
 KF7  CAX  CAV  CAC  114.92  3.000
 KF7  CBC  CAX  CAY  118.35  3.000
 KF7  CAY  CAX  CAV  120.61  3.000
 KF7  CBC  CAX  CAV  121.04  3.000
 KF7  H16  CAY  CAZ  119.45  3.000
 KF7  H16  CAY  CAX  119.43  3.000
 KF7  CAZ  CAY  CAX  121.11  3.000
 KF7  H17  CAZ  CBA  120.11  3.000
 KF7  H17  CAZ  CAY  119.95  3.000
 KF7  CBA  CAZ  CAY  119.94  3.000
 KF7  H18  CBA  CBB  120.28  3.000
 KF7  H18  CBA  CAZ  120.28  3.000
 KF7  CBB  CBA  CAZ  119.44  3.000
 KF7  H19  CBB  CBC  119.90  3.000
 KF7  H19  CBB  CBA  119.80  3.000
 KF7  CBC  CBB  CBA  120.30  3.000
 KF7  H20  CBC  CBB  120.47  3.000
 KF7  H20  CBC  CAX  118.69  3.000
 KF7  CBB  CBC  CAX  120.84  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
 KF7  CONST_01  C4   C5   CAL  CAM  180.00   0.0  0
 KF7  CONST_02  C6   C5   CAL  CAM    0.00   0.0  0
 KF7  CONST_03  CAS  CAT  CAO  CAM  180.00   0.0  0
 KF7  CONST_04  CAQ  CAP  CAO  CAM  180.00   0.0  0
 KF7  CONST_05  C5   C6   SAN  CAM    0.00   0.0  0
 KF7  CONST_06  N1   C6   SAN  CAM  180.00   0.0  0
 KF7  CONST_07  CAR  CAS  CAT  CAO    0.00   0.0  0
 KF7  CONST_08  C5   CAL  CAM  CAO  180.00   0.0  0
 KF7  CONST_09  C6   SAN  CAM  CAO  180.00   0.0  0
 KF7  CONST_10  CAR  CAQ  CAP  CAO    0.00   0.0  0
 KF7  CONST_11  N3   C4   C5   CAL  180.00   0.0  0
 KF7  CONST_12  N1   C6   C5   CAL  180.00   0.0  0
 KF7  CONST_13  SAN  C6   C5   CAL    0.00   0.0  0
 KF7  CONST_16  C6   SAN  CAM  CAL    0.00   0.0  0
 KF7  CONST_17  CAS  CAT  CAO  CAP    0.00   0.0  0
 KF7  CONST_19  CAS  CAR  CAQ  CAP    0.00   0.0  0
 KF7  CONST_20  CAT  CAS  CAR  CAQ    0.00   0.0  0
 KF7  CONST_21  CAT  CAO  CAP  CAQ    0.00   0.0  0
 KF7  CONST_23  C4   C5   C6   SAN  180.00   0.0  0
 KF7  CONST_24  C2   N1   C6   SAN  180.00   0.0  0
 KF7  CONST_25  C5   CAL  CAM  SAN    0.00   0.0  0
 KF7  CONST_26  C2   N3   C4   C5     0.00   0.0  0
 KF7  CONST_27  C2   N1   C6   C5     0.00   0.0  0
 KF7  CONST_28  N3   C4   C5   C6     0.00   0.0  0
 KF7  CONST_29  N3   C2   N1   C6     0.00   0.0  0
 KF7  CONST_30  C4   N3   C2   N1     0.00   0.0  0
 KF7  CONST_31  C4   C5   C6   N1     0.00   0.0  0
 KF7  CONST_32  CBA  CBB  CBC  CAX    0.00   0.0  0
 KF7  CONST_33  CBA  CAZ  CAY  CAX    0.00   0.0  0
 KF7  CONST_34  CBB  CBC  CAX  CAY    0.00   0.0  0
 KF7  CONST_35  CBB  CBA  CAZ  CAY    0.00   0.0  0
 KF7  CONST_36  CBC  CAX  CAY  CAZ    0.00   0.0  0
 KF7  CONST_37  CBC  CBB  CBA  CAZ    0.00   0.0  0
 KF7  CONST_38  NAB  C4   C5   CAL    0.00   0.0  0
 KF7  CONST_39  C2   N3   C4   NAB  180.00   0.0  0
 KF7  CONST_40  C6   C5   C4   NAB  180.00   0.0  0
 KF7  CONST_41  CAW  CAR  CAQ  CAP  180.00   0.0  0
 KF7  CONST_42  CAT  CAS  CAR  CAW  180.00   0.0  0
 KF7  CONST_43  CBB  CBC  CAX  CAV  180.00   0.0  0
 KF7  CONST_44  CAZ  CAY  CAX  CAV  180.00   0.0  0
 KF7  CONST_45  H10  CAT  CAO  CAM    0.00   0.0  0
 KF7  CONST_46  H4   CAP  CAO  CAM    0.00   0.0  0
 KF7  CONST_47  H9   CAS  CAT  CAO  180.00   0.0  0
 KF7  CONST_48  H2   CAL  CAM  CAO    0.00   0.0  0
 KF7  CONST_49  H5   CAQ  CAP  CAO  180.00   0.0  0
 KF7  CONST_50  H11  C2   N1   C6   180.00   0.0  0
 KF7  CONST_51  H19  CBB  CBC  CAX  180.00   0.0  0
 KF7  CONST_52  H17  CAZ  CAY  CAX  180.00   0.0  0
 KF7  CONST_53  H20  CBC  CAX  CAY  180.00   0.0  0
 KF7  CONST_54  H18  CBA  CAZ  CAY  180.00   0.0  0
 KF7  CONST_55  H16  CAY  CAZ  CBA  180.00   0.0  0
 KF7  CONST_56  CAC  NAB  C4   C5   180.00   0.0  0
 KF7  CONST_58  H3   NAB  C4   C5     0.00   0.0  0
 KF7  Var_01    CBC  CAX  CAV  CAC   89.55  30.0  2
 KF7  Var_02    H6   CAW  CAR  CAQ  105.08  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
 KF7  chir_01  CAC  PAA  NAB  CAV  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
 KF7  plan-1  CAM  0.020
 KF7  plan-1  CAO  0.020
 KF7  plan-1  CAP  0.020
 KF7  plan-1  CAQ  0.020
 KF7  plan-1  CAR  0.020
 KF7  plan-1  CAW  0.020
 KF7  plan-1  CAS  0.020
 KF7  plan-1  CAT  0.020
 KF7  plan-1  H4   0.020
 KF7  plan-1  H5   0.020
 KF7  plan-1  H9   0.020
 KF7  plan-1  H10  0.020
 KF7  plan-2  CAV  0.020
 KF7  plan-2  CAX  0.020
 KF7  plan-2  CAY  0.020
 KF7  plan-2  CAZ  0.020
 KF7  plan-2  CBA  0.020
 KF7  plan-2  CBB  0.020
 KF7  plan-2  CBC  0.020
 KF7  plan-2  H16  0.020
 KF7  plan-2  H17  0.020
 KF7  plan-2  H18  0.020
 KF7  plan-2  H19  0.020
 KF7  plan-2  H20  0.020
 KF7  plan-3  CAM  0.020
 KF7  plan-3  CAO  0.020
 KF7  plan-3  CAL  0.020
 KF7  plan-3  NAB  0.020
 KF7  plan-3  SAN  0.020
 KF7  plan-3  C5   0.020
 KF7  plan-3  C6   0.020
 KF7  plan-3  N1   0.020
 KF7  plan-3  C2   0.020
 KF7  plan-3  N3   0.020
 KF7  plan-3  C4   0.020
 KF7  plan-3  H2   0.020
 KF7  plan-3  H11  0.020
 KF7  plan-4  NAB  0.020
 KF7  plan-4  C4   0.020
 KF7  plan-4  CAC  0.020
 KF7  plan-4  H3   0.020

