# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jun  5 19:59:10 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: [(1R)-2-(3-fluorophenyl)-1-{[6-(4-methylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino}ethyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1)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
 YL5  YL5  '[(1R)-2-(3-fluorophenyl)-1-{[6-(4-methylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino}ethyl]phosphonic acid'  ligand  49  30  .  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_YL5
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
 YL5  CAY  C  CR16  0  -0.480   1.2506   1.7504   1.2904
 YL5  CAZ  C  CR6   0   0.555   0.4506   2.6500   0.6130
 YL5  FBD  F  F     0  -0.316  -0.7690   2.9235   1.1048
 YL5  CBA  C  CR16  0  -0.418   0.8567   3.2692  -0.5514
 YL5  CBB  C  CR16  0  -0.221   2.1221   2.9715  -1.0409
 YL5  CBC  C  CR16  0  -0.293   2.9412   2.0659  -0.3837
 YL5  CAX  C  CR6   0   0.133   2.5086   1.4401   0.7823
 YL5  CAV  C  CH2   0  -0.535   3.3244   0.3497   1.4192
 YL5  CAC  C  CH1   0  -0.391   3.1847  -0.9535   0.6058
 YL5  PAA  P  P     0   1.392   3.8133  -2.4082   1.5036
 YL5  OAD  O  OH1   0  -0.743   5.3853  -2.1434   1.6430
 YL5  OAU  O  O     0  -0.707   3.0741  -2.6803   2.7603
 YL5  OAE  O  OH1   0  -0.739   3.8386  -3.5892   0.4174
 YL5  NAB  N  NH1   0  -0.680   1.8038  -1.2360   0.2679
 YL5  C4   C  CR6   0   0.531   1.2769  -0.8405  -0.9207
 YL5  N3   N  N     0  -0.456   2.0675  -0.7785  -1.9827
 YL5  C2   C  CR16  0   0.046   1.5493  -0.3762  -3.1379
 YL5  N1   N  N     0  -0.431   0.3045  -0.0113  -3.3743
 YL5  C6   C  CR56  0  -0.019  -0.4830  -0.0773  -2.3048
 YL5  SAN  S  S2    0   0.221  -2.1446   0.4026  -2.3082
 YL5  C5   C  CR56  0   0.059  -0.0873  -0.4965  -1.0369
 YL5  CAL  C  CR15  0  -0.261  -1.1392  -0.4296  -0.0787
 YL5  CAM  C  CR5   0  -0.198  -2.3018   0.0318  -0.6085
 YL5  CAO  C  CR6   0   0.113  -3.5740   0.2460   0.0757
 YL5  CAP  C  CR16  0  -0.297  -3.5932   0.5627   1.4359
 YL5  CAQ  C  CR16  0  -0.277  -4.7926   0.7360   2.1045
 YL5  CAR  C  CR6   0   0.088  -6.0142   0.6182   1.4429
 YL5  CAW  C  CH3   0  -0.722  -7.3088   0.8424   2.1658
 YL5  CAS  C  CR16  0  -0.281  -5.9906   0.3133   0.0839
 YL5  CAT  C  CR16  0  -0.302  -4.7944   0.1292  -0.5910
 YL5  H1   H  HCR6  0   0.275   0.8899   1.2812   2.1980
 YL5  H2   H  HCR6  0   0.276   0.2051   3.9646  -1.0633
 YL5  H3   H  HCR6  0   0.265   2.4637   3.4464  -1.9510
 YL5  H4   H  HCR6  0   0.254   3.9158   1.8267  -0.7912
 YL5  H5   H  HCH2  0   0.280   4.3798   0.6233   1.4653
 YL5  H6   H  HCH2  0   0.267   2.9873   0.1870   2.4456
 YL5  H7   H  HCH1  0   0.319   3.7435  -0.8646  -0.3270
 YL5  H8   H  HOH1  0   0.501   5.7030  -2.1693   2.5553
 YL5  H9   H  HOH1  0   0.496   2.9630  -3.9199   0.1772
 YL5  H10  H  HNH1  0   0.405   1.1667  -1.2221   1.0507
 YL5  H11  H  HCR6  0   0.259   2.2326  -0.3433  -3.9791
 YL5  H12  H  HCR5  0   0.277  -1.0494  -0.7271   0.9571
 YL5  H13  H  HCR6  0   0.252  -2.6629   0.6910   1.9742
 YL5  H14  H  HCR6  0   0.253  -4.7773   0.9760   3.1610
 YL5  H15  H  HCH3  0   0.252  -7.5897   1.8976   2.1416
 YL5  H16  H  HCH3  0   0.246  -8.1238   0.2796   1.7120
 YL5  H17  H  HCH3  0   0.246  -7.2364   0.5523   3.2135
 YL5  H18  H  HCR6  0   0.254  -6.9225   0.2056  -0.4582
 YL5  H19  H  HCR6  0   0.254  -4.8220  -0.1294  -1.6430

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
 YL5  OAU  PAA  double    1.483  0.020  1.483
 YL5  OAE  PAA  single    1.605  0.020  1.605
 YL5  N1   C2   aromatic  1.319  0.020  1.319
 YL5  N1   C6   aromatic  1.330  0.020  1.330
 YL5  C2   N3   aromatic  1.329  0.020  1.329
 YL5  SAN  C6   aromatic  1.729  0.020  1.729
 YL5  SAN  CAM  aromatic  1.747  0.020  1.747
 YL5  C6   C5   aromatic  1.393  0.020  1.393
 YL5  PAA  CAC  single    1.821  0.020  1.821
 YL5  PAA  OAD  single    1.600  0.020  1.600
 YL5  N3   C4   aromatic  1.325  0.020  1.325
 YL5  C5   C4   aromatic  1.412  0.020  1.412
 YL5  C5   CAL  aromatic  1.424  0.020  1.424
 YL5  C4   NAB  single    1.359  0.020  1.359
 YL5  CAM  CAL  aromatic  1.358  0.020  1.358
 YL5  CAM  CAO  single    1.460  0.020  1.460
 YL5  CAP  CAO  aromatic  1.397  0.020  1.397
 YL5  CAP  CAQ  aromatic  1.384  0.020  1.384
 YL5  CAO  CAT  aromatic  1.396  0.020  1.396
 YL5  CAQ  CAR  aromatic  1.394  0.020  1.394
 YL5  CAT  CAS  aromatic  1.386  0.020  1.386
 YL5  CAR  CAS  aromatic  1.393  0.020  1.393
 YL5  CAR  CAW  single    1.500  0.020  1.500
 YL5  NAB  CAC  single    1.449  0.020  1.449
 YL5  CAC  CAV  single    1.543  0.020  1.543
 YL5  CAV  CAX  single    1.503  0.020  1.503
 YL5  CAY  CAX  aromatic  1.392  0.020  1.392
 YL5  CAY  CAZ  aromatic  1.381  0.020  1.381
 YL5  CAX  CBC  aromatic  1.392  0.020  1.392
 YL5  FBD  CAZ  single    1.343  0.020  1.343
 YL5  CAZ  CBA  aromatic  1.380  0.020  1.380
 YL5  CBC  CBB  aromatic  1.387  0.020  1.387
 YL5  CBA  CBB  aromatic  1.389  0.020  1.389
 YL5  CAY  H1   single    0.930  0.020  1.080
 YL5  CBA  H2   single    0.930  0.020  1.080
 YL5  CBB  H3   single    0.930  0.020  1.080
 YL5  CBC  H4   single    0.930  0.020  1.080
 YL5  CAV  H5   single    0.970  0.020  1.090
 YL5  CAV  H6   single    0.970  0.020  1.090
 YL5  CAC  H7   single    0.970  0.020  1.090
 YL5  OAD  H8   single    0.850  0.020  0.980
 YL5  OAE  H9   single    0.850  0.020  0.980
 YL5  NAB  H10  single    0.890  0.020  1.040
 YL5  C2   H11  single    0.930  0.020  1.080
 YL5  CAL  H12  single    0.930  0.020  1.080
 YL5  CAP  H13  single    0.930  0.020  1.080
 YL5  CAQ  H14  single    0.930  0.020  1.080
 YL5  CAW  H15  single    0.970  0.020  1.090
 YL5  CAW  H16  single    0.970  0.020  1.090
 YL5  CAW  H17  single    0.970  0.020  1.090
 YL5  CAS  H18  single    0.930  0.020  1.080
 YL5  CAT  H19  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
 YL5  H1   CAY  CAX  120.68  3.000
 YL5  H1   CAY  CAZ  120.00  3.000
 YL5  CAX  CAY  CAZ  119.32  3.000
 YL5  CBA  CAZ  FBD  119.00  3.000
 YL5  CBA  CAZ  CAY  122.38  3.000
 YL5  FBD  CAZ  CAY  118.61  3.000
 YL5  H2   CBA  CBB  121.32  3.000
 YL5  H2   CBA  CAZ  120.69  3.000
 YL5  CBB  CBA  CAZ  117.99  3.000
 YL5  H3   CBB  CBC  119.92  3.000
 YL5  H3   CBB  CBA  119.34  3.000
 YL5  CBC  CBB  CBA  120.73  3.000
 YL5  H4   CBC  CAX  119.70  3.000
 YL5  H4   CBC  CBB  119.83  3.000
 YL5  CAX  CBC  CBB  120.46  3.000
 YL5  CAV  CAX  CBC  120.81  3.000
 YL5  CBC  CAX  CAY  119.11  3.000
 YL5  CAV  CAX  CAY  119.83  3.000
 YL5  H6   CAV  H5   107.22  3.000
 YL5  H6   CAV  CAC  109.98  3.000
 YL5  H5   CAV  CAC  108.76  3.000
 YL5  H6   CAV  CAX  109.80  3.000
 YL5  H5   CAV  CAX  111.15  3.000
 YL5  CAC  CAV  CAX  109.89  3.000
 YL5  H7   CAC  NAB  107.73  3.000
 YL5  H7   CAC  PAA  108.05  3.000
 YL5  NAB  CAC  PAA  106.74  3.000
 YL5  H7   CAC  CAV  109.61  3.000
 YL5  NAB  CAC  CAV  111.95  3.000
 YL5  PAA  CAC  CAV  112.56  3.000
 YL5  OAE  PAA  OAU  116.51  3.000
 YL5  OAE  PAA  OAD   99.52  3.000
 YL5  OAU  PAA  OAD  116.50  3.000
 YL5  OAD  PAA  CAC  104.46  3.000
 YL5  OAE  PAA  CAC  105.05  3.000
 YL5  OAU  PAA  CAC  113.09  3.000
 YL5  H8   OAD  PAA  113.62  3.000
 YL5  H9   OAE  PAA  113.94  3.000
 YL5  H10  NAB  C4   115.44  3.000
 YL5  H10  NAB  CAC  114.70  3.000
 YL5  C4   NAB  CAC  121.10  3.000
 YL5  C5   C4   N3   119.94  3.000
 YL5  C5   C4   NAB  121.17  3.000
 YL5  N3   C4   NAB  118.89  3.000
 YL5  C2   N3   C4   118.57  3.000
 YL5  H11  C2   N1   116.58  3.000
 YL5  H11  C2   N3   115.98  3.000
 YL5  N1   C2   N3   127.44  3.000
 YL5  C6   N1   C2   113.65  3.000
 YL5  C5   C6   SAN  110.99  3.000
 YL5  C5   C6   N1   125.37  3.000
 YL5  SAN  C6   N1   123.61  3.000
 YL5  CAM  SAN  C6    91.47  3.000
 YL5  CAL  C5   C6   112.85  3.000
 YL5  CAL  C5   C4   132.04  3.000
 YL5  C6   C5   C4   115.01  3.000
 YL5  H12  CAL  CAM  122.55  3.000
 YL5  H12  CAL  C5   124.75  3.000
 YL5  CAM  CAL  C5   112.68  3.000
 YL5  CAO  CAM  CAL  127.78  3.000
 YL5  CAO  CAM  SAN  120.21  3.000
 YL5  CAL  CAM  SAN  112.00  3.000
 YL5  CAT  CAO  CAP  118.18  3.000
 YL5  CAT  CAO  CAM  121.72  3.000
 YL5  CAP  CAO  CAM  120.10  3.000
 YL5  H13  CAP  CAQ  119.32  3.000
 YL5  H13  CAP  CAO  119.96  3.000
 YL5  CAQ  CAP  CAO  120.72  3.000
 YL5  H14  CAQ  CAR  119.59  3.000
 YL5  H14  CAQ  CAP  119.11  3.000
 YL5  CAR  CAQ  CAP  121.30  3.000
 YL5  CAS  CAR  CAW  121.18  3.000
 YL5  CAW  CAR  CAQ  121.00  3.000
 YL5  CAS  CAR  CAQ  117.81  3.000
 YL5  H17  CAW  H16  108.22  3.000
 YL5  H17  CAW  H15  107.20  3.000
 YL5  H16  CAW  H15  107.31  3.000
 YL5  H17  CAW  CAR  111.49  3.000
 YL5  H16  CAW  CAR  111.58  3.000
 YL5  H15  CAW  CAR  110.84  3.000
 YL5  H18  CAS  CAT  119.05  3.000
 YL5  H18  CAS  CAR  119.69  3.000
 YL5  CAT  CAS  CAR  121.26  3.000
 YL5  H19  CAT  CAS  118.85  3.000
 YL5  H19  CAT  CAO  120.40  3.000
 YL5  CAS  CAT  CAO  120.74  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
 YL5  CONST_01  CBB  CBC  CAX  CAY    0.00   0.0  0
 YL5  CONST_02  CBB  CBA  CAZ  CAY    0.00   0.0  0
 YL5  CONST_03  CBC  CAX  CAY  CAZ    0.00   0.0  0
 YL5  CONST_04  CBC  CBB  CBA  CAZ    0.00   0.0  0
 YL5  CONST_05  CAX  CAY  CAZ  CBA    0.00   0.0  0
 YL5  CONST_06  CAX  CBC  CBB  CBA    0.00   0.0  0
 YL5  CONST_07  N1   C2   N3   C4     0.00   0.0  0
 YL5  CONST_08  N1   C6   C5   C4     0.00   0.0  0
 YL5  CONST_09  SAN  C6   C5   C4   180.00   0.0  0
 YL5  CONST_10  CAM  CAL  C5   C4   180.00   0.0  0
 YL5  CONST_11  C6   N1   C2   N3     0.00   0.0  0
 YL5  CONST_12  C6   C5   C4   N3     0.00   0.0  0
 YL5  CONST_13  CAL  C5   C4   N3   180.00   0.0  0
 YL5  CONST_14  SAN  C6   N1   C2   180.00   0.0  0
 YL5  CONST_15  C5   C6   N1   C2     0.00   0.0  0
 YL5  CONST_16  C5   C4   N3   C2     0.00   0.0  0
 YL5  CONST_17  CAM  SAN  C6   N1   180.00   0.0  0
 YL5  CONST_18  CAL  C5   C6   N1   180.00   0.0  0
 YL5  CONST_19  CAL  CAM  SAN  C6     0.00   0.0  0
 YL5  CONST_20  CAO  CAM  SAN  C6   180.00   0.0  0
 YL5  CONST_21  CAM  CAL  C5   C6     0.00   0.0  0
 YL5  CONST_22  CAL  C5   C6   SAN    0.00   0.0  0
 YL5  CONST_23  C5   CAL  CAM  SAN    0.00   0.0  0
 YL5  CONST_26  CAM  SAN  C6   C5     0.00   0.0  0
 YL5  CONST_27  CAO  CAM  CAL  C5   180.00   0.0  0
 YL5  CONST_30  CAQ  CAP  CAO  CAM  180.00   0.0  0
 YL5  CONST_31  CAS  CAT  CAO  CAM  180.00   0.0  0
 YL5  CONST_32  CAR  CAQ  CAP  CAO    0.00   0.0  0
 YL5  CONST_33  CAR  CAS  CAT  CAO    0.00   0.0  0
 YL5  CONST_34  CAS  CAT  CAO  CAP    0.00   0.0  0
 YL5  CONST_35  CAS  CAR  CAQ  CAP    0.00   0.0  0
 YL5  CONST_36  CAT  CAO  CAP  CAQ    0.00   0.0  0
 YL5  CONST_37  CAT  CAS  CAR  CAQ    0.00   0.0  0
 YL5  CONST_38  CAV  CAX  CAY  CAZ  180.00   0.0  0
 YL5  CONST_39  CAX  CAY  CAZ  FBD  180.00   0.0  0
 YL5  CONST_40  CBB  CBA  CAZ  FBD  180.00   0.0  0
 YL5  CONST_41  CAV  CAX  CBC  CBB  180.00   0.0  0
 YL5  CONST_42  C2   N3   C4   NAB  180.00   0.0  0
 YL5  CONST_43  C6   C5   C4   NAB  180.00   0.0  0
 YL5  CONST_44  CAL  C5   C4   NAB    0.00   0.0  0
 YL5  CONST_45  CAW  CAR  CAQ  CAP  180.00   0.0  0
 YL5  CONST_46  CAT  CAS  CAR  CAW  180.00   0.0  0
 YL5  CONST_47  H4   CBC  CAX  CAY  180.00   0.0  0
 YL5  CONST_48  H2   CBA  CAZ  CAY  180.00   0.0  0
 YL5  CONST_49  H3   CBB  CBA  CAZ  180.00   0.0  0
 YL5  CONST_50  H1   CAY  CAZ  CBA  180.00   0.0  0
 YL5  CONST_51  H11  C2   N3   C4   180.00   0.0  0
 YL5  CONST_52  H12  CAL  C5   C4     0.00   0.0  0
 YL5  CONST_53  H13  CAP  CAO  CAM    0.00   0.0  0
 YL5  CONST_54  H19  CAT  CAO  CAM    0.00   0.0  0
 YL5  CONST_55  H14  CAQ  CAP  CAO  180.00   0.0  0
 YL5  CONST_56  H18  CAS  CAT  CAO  180.00   0.0  0
 YL5  CONST_59  H10  NAB  C4   N3   180.00   0.0  0
 YL5  Var_01    CAC  CAV  CAX  CAY   99.16  30.0  2
 YL5  Var_02    H15  CAW  CAR  CAQ   87.92  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
 YL5  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
 YL5  plan-1  CAY  0.020
 YL5  plan-1  CAZ  0.020
 YL5  plan-1  FBD  0.020
 YL5  plan-1  CBA  0.020
 YL5  plan-1  CBB  0.020
 YL5  plan-1  CBC  0.020
 YL5  plan-1  CAX  0.020
 YL5  plan-1  CAV  0.020
 YL5  plan-1  H1   0.020
 YL5  plan-1  H2   0.020
 YL5  plan-1  H3   0.020
 YL5  plan-1  H4   0.020
 YL5  plan-2  CAM  0.020
 YL5  plan-2  CAO  0.020
 YL5  plan-2  CAP  0.020
 YL5  plan-2  CAQ  0.020
 YL5  plan-2  CAR  0.020
 YL5  plan-2  CAW  0.020
 YL5  plan-2  CAS  0.020
 YL5  plan-2  CAT  0.020
 YL5  plan-2  H13  0.020
 YL5  plan-2  H14  0.020
 YL5  plan-2  H18  0.020
 YL5  plan-2  H19  0.020
 YL5  plan-3  NAB  0.020
 YL5  plan-3  C4   0.020
 YL5  plan-3  N3   0.020
 YL5  plan-3  C2   0.020
 YL5  plan-3  N1   0.020
 YL5  plan-3  C6   0.020
 YL5  plan-3  SAN  0.020
 YL5  plan-3  C5   0.020
 YL5  plan-3  CAL  0.020
 YL5  plan-3  CAM  0.020
 YL5  plan-3  CAO  0.020
 YL5  plan-3  H11  0.020
 YL5  plan-3  H12  0.020
 YL5  plan-4  CAC  0.020
 YL5  plan-4  NAB  0.020
 YL5  plan-4  C4   0.020
 YL5  plan-4  H10  0.020

