# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 09:37:25 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  49  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 OK
;

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  OH1   0  -0.742  -4.8495  -0.9939   1.0290
 KF7  CAM  C  CR5   0  -0.200   3.4017  -0.3621   0.0228
 KF7  CAO  C  CR6   0   0.128   4.5665   0.5073  -0.1221
 KF7  CAL  C  CR15  0  -0.268   2.0941  -0.0013   0.1273
 KF7  NAB  N  NH1   0  -0.678  -0.9744  -0.1390   0.3554
 KF7  CAP  C  CR16  0  -0.304   5.8453   0.0869   0.2429
 KF7  CAQ  C  CR16  0  -0.283   6.9372   0.9290   0.0978
 KF7  CAR  C  CR6   0   0.088   6.7944   2.2170  -0.4095
 KF7  CAW  C  CH3   0  -0.723   7.9774   3.1204  -0.5900
 KF7  CAS  C  CR16  0  -0.272   5.5129   2.6359  -0.7689
 KF7  CAT  C  CR16  0  -0.308   4.4199   1.7994  -0.6349
 KF7  SAN  S  S2    0   0.239   3.6013  -2.0970   0.0520
 KF7  C5   C  CR56  0   0.068   1.2246  -1.1225   0.2414
 KF7  C6   C  CR56  0  -0.023   1.9017  -2.3377   0.2195
 KF7  N1   N  N     0  -0.427   1.3369  -3.5443   0.2953
 KF7  C2   C  CR16  0   0.090   0.0315  -3.5143   0.4107
 KF7  N3   N  N     0  -0.589  -0.7447  -2.4273   0.4470
 KF7  C4   C  CR6   0   0.594  -0.1827  -1.2211   0.3510
 KF7  CAC  C  CH1   0  -0.364  -2.3962  -0.1537   0.0566
 KF7  PAA  P  P     0   1.363  -3.3817  -0.5873   1.5541
 KF7  OAE  O  O     0  -0.707  -3.3677   0.4766   2.5877
 KF7  OAU  O  OH1   0  -0.772  -2.8380  -2.0055   2.0120
 KF7  CAV  C  CH2   0  -0.556  -2.7798   1.2280  -0.4880
 KF7  CAX  C  CR6   0   0.080  -4.2257   1.3272  -0.8873
 KF7  CAY  C  CR16  0  -0.283  -4.6840   0.6873  -2.0372
 KF7  CAZ  C  CR16  0  -0.239  -6.0230   0.7440  -2.3933
 KF7  CBA  C  CR16  0  -0.261  -6.9268   1.4437  -1.6024
 KF7  CBB  C  CR16  0  -0.238  -6.4801   2.0916  -0.4593
 KF7  CBC  C  CR16  0  -0.336  -5.1365   2.0339  -0.1049
 KF7  H1   H  HOH1  0   0.490  -5.4314  -0.2372   0.8713
 KF7  H2   H  HCR5  0   0.277   1.7705   1.0302   0.1429
 KF7  H3   H  HNH1  0   0.427  -0.5284   0.7649   0.3632
 KF7  H4   H  HCR6  0   0.255   6.0024  -0.9002   0.6620
 KF7  H5   H  HCR6  0   0.256   7.9175   0.5741   0.3914
 KF7  H6   H  HCH3  0   0.252   8.2565   3.1904  -1.6432
 KF7  H7   H  HCH3  0   0.247   7.7622   4.1328  -0.2478
 KF7  H8   H  HCH3  0   0.246   8.8471   2.7567  -0.0443
 KF7  H9   H  HCR6  0   0.255   5.3671   3.6318  -1.1705
 KF7  H10  H  HCR6  0   0.258   3.4453   2.1517  -0.9473
 KF7  H11  H  HCR6  0   0.276  -0.4832  -4.4636   0.4953
 KF7  H12  H  HCH1  0   0.309  -2.5903  -0.9129  -0.7089
 KF7  H13  H  HOH1  0   0.500  -2.1163  -2.3527   1.4064
 KF7  H14  H  HCH2  0   0.280  -2.5486   1.9877   0.2624
 KF7  H15  H  HCH2  0   0.290  -2.1428   1.4268  -1.3535
 KF7  H16  H  HCR6  0   0.257  -3.9869   0.1354  -2.6576
 KF7  H17  H  HCR6  0   0.261  -6.3631   0.2420  -3.2896
 KF7  H18  H  HCR6  0   0.261  -7.9720   1.4865  -1.8790
 KF7  H19  H  HCR6  0   0.263  -7.1746   2.6452   0.1589
 KF7  H20  H  HCR6  0   0.264  -4.7954   2.5410   0.7901

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  double    1.483  0.020  1.483
 KF7  OAU  PAA  single    1.586  0.020  1.586
 KF7  PAA  OAD  single    1.611  0.020  1.611
 KF7  PAA  CAC  single    1.844  0.020  1.844
 KF7  CAC  NAB  single    1.453  0.020  1.453
 KF7  CAC  CAV  single    1.534  0.020  1.534
 KF7  NAB  C4   single    1.341  0.020  1.341
 KF7  CAV  CAX  single    1.503  0.020  1.503
 KF7  C4   N3   aromatic  1.334  0.020  1.334
 KF7  C4   C5   aromatic  1.415  0.020  1.415
 KF7  N3   C2   aromatic  1.336  0.020  1.336
 KF7  C5   CAL  aromatic  1.423  0.020  1.423
 KF7  C5   C6   aromatic  1.391  0.020  1.391
 KF7  C2   N1   aromatic  1.311  0.020  1.311
 KF7  CAL  CAM  aromatic  1.360  0.020  1.360
 KF7  CAT  CAS  aromatic  1.383  0.020  1.383
 KF7  CAT  CAO  aromatic  1.398  0.020  1.398
 KF7  C6   N1   aromatic  1.334  0.020  1.334
 KF7  C6   SAN  aromatic  1.725  0.020  1.725
 KF7  CAS  CAR  aromatic  1.395  0.020  1.395
 KF7  CAM  CAO  single    1.461  0.020  1.461
 KF7  CAM  SAN  aromatic  1.747  0.020  1.747
 KF7  CAO  CAP  aromatic  1.395  0.020  1.395
 KF7  CAR  CAW  single    1.499  0.020  1.499
 KF7  CAR  CAQ  aromatic  1.392  0.020  1.392
 KF7  CAX  CBC  aromatic  1.393  0.020  1.393
 KF7  CAX  CAY  aromatic  1.393  0.020  1.393
 KF7  CAP  CAQ  aromatic  1.386  0.020  1.386
 KF7  CBC  CBB  aromatic  1.391  0.020  1.391
 KF7  CAY  CAZ  aromatic  1.387  0.020  1.387
 KF7  CBB  CBA  aromatic  1.388  0.020  1.388
 KF7  CAZ  CBA  aromatic  1.390  0.020  1.390
 KF7  OAD  H1   single    0.850  0.020  0.980
 KF7  CAL  H2   single    0.930  0.020  1.080
 KF7  NAB  H3   single    0.860  0.020  1.020
 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  OAU  H13  single    0.850  0.020  0.980
 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  H1   OAD  PAA  113.81  3.000
 KF7  SAN  CAM  CAL  111.84  3.000
 KF7  SAN  CAM  CAO  120.12  3.000
 KF7  CAL  CAM  CAO  128.04  3.000
 KF7  CAT  CAO  CAP  118.08  3.000
 KF7  CAP  CAO  CAM  121.72  3.000
 KF7  CAT  CAO  CAM  120.20  3.000
 KF7  H2   CAL  C5   124.58  3.000
 KF7  H2   CAL  CAM  122.81  3.000
 KF7  C5   CAL  CAM  112.60  3.000
 KF7  H3   NAB  CAC  116.34  3.000
 KF7  H3   NAB  C4   117.54  3.000
 KF7  CAC  NAB  C4   124.68  3.000
 KF7  H4   CAP  CAQ  118.65  3.000
 KF7  H4   CAP  CAO  120.57  3.000
 KF7  CAQ  CAP  CAO  120.77  3.000
 KF7  H5   CAQ  CAR  119.67  3.000
 KF7  H5   CAQ  CAP  119.04  3.000
 KF7  CAR  CAQ  CAP  121.29  3.000
 KF7  CAS  CAR  CAW  120.84  3.000
 KF7  CAW  CAR  CAQ  121.37  3.000
 KF7  CAS  CAR  CAQ  117.78  3.000
 KF7  H8   CAW  H7   108.09  3.000
 KF7  H8   CAW  H6   107.49  3.000
 KF7  H7   CAW  H6   107.08  3.000
 KF7  H8   CAW  CAR  111.62  3.000
 KF7  H7   CAW  CAR  111.47  3.000
 KF7  H6   CAW  CAR  110.88  3.000
 KF7  H9   CAS  CAT  119.05  3.000
 KF7  H9   CAS  CAR  119.67  3.000
 KF7  CAT  CAS  CAR  121.28  3.000
 KF7  H10  CAT  CAS  119.13  3.000
 KF7  H10  CAT  CAO  120.08  3.000
 KF7  CAS  CAT  CAO  120.79  3.000
 KF7  C6   SAN  CAM   91.59  3.000
 KF7  C4   C5   C6   115.11  3.000
 KF7  C6   C5   CAL  112.92  3.000
 KF7  C4   C5   CAL  131.96  3.000
 KF7  N1   C6   C5   125.65  3.000
 KF7  N1   C6   SAN  123.29  3.000
 KF7  C5   C6   SAN  111.05  3.000
 KF7  C2   N1   C6   113.94  3.000
 KF7  H11  C2   N3   115.77  3.000
 KF7  H11  C2   N1   117.39  3.000
 KF7  N3   C2   N1   126.84  3.000
 KF7  C4   N3   C2   119.26  3.000
 KF7  N3   C4   C5   119.18  3.000
 KF7  C5   C4   NAB  122.09  3.000
 KF7  N3   C4   NAB  118.73  3.000
 KF7  H12  CAC  CAV  109.39  3.000
 KF7  H12  CAC  PAA  108.04  3.000
 KF7  CAV  CAC  PAA  111.50  3.000
 KF7  H12  CAC  NAB  108.91  3.000
 KF7  CAV  CAC  NAB  107.97  3.000
 KF7  PAA  CAC  NAB  110.99  3.000
 KF7  OAU  PAA  OAE  115.90  3.000
 KF7  OAU  PAA  CAC  105.16  3.000
 KF7  OAE  PAA  CAC  113.08  3.000
 KF7  CAC  PAA  OAD  106.35  3.000
 KF7  OAU  PAA  OAD  100.41  3.000
 KF7  OAE  PAA  OAD  114.62  3.000
 KF7  H13  OAU  PAA  112.42  3.000
 KF7  H15  CAV  H14  107.11  3.000
 KF7  H15  CAV  CAX  109.77  3.000
 KF7  H14  CAV  CAX  109.88  3.000
 KF7  H15  CAV  CAC  107.42  3.000
 KF7  H14  CAV  CAC  109.25  3.000
 KF7  CAX  CAV  CAC  113.22  3.000
 KF7  CBC  CAX  CAY  118.77  3.000
 KF7  CAY  CAX  CAV  120.35  3.000
 KF7  CBC  CAX  CAV  120.87  3.000
 KF7  H16  CAY  CAZ  119.65  3.000
 KF7  H16  CAY  CAX  119.64  3.000
 KF7  CAZ  CAY  CAX  120.71  3.000
 KF7  H17  CAZ  CBA  120.04  3.000
 KF7  H17  CAZ  CAY  119.81  3.000
 KF7  CBA  CAZ  CAY  120.16  3.000
 KF7  H18  CBA  CBB  120.20  3.000
 KF7  H18  CBA  CAZ  120.17  3.000
 KF7  CBB  CBA  CAZ  119.63  3.000
 KF7  H19  CBB  CBC  119.72  3.000
 KF7  H19  CBB  CBA  120.19  3.000
 KF7  CBC  CBB  CBA  120.10  3.000
 KF7  H20  CBC  CBB  119.68  3.000
 KF7  H20  CBC  CAX  119.69  3.000
 KF7  CBB  CBC  CAX  120.63  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_58  H3   NAB  C4   C5     0.00   0.0  0
 KF7  Var_01    CBC  CAX  CAV  CAC  106.10  30.0  2
 KF7  Var_02    H6   CAW  CAR  CAQ  104.46  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

