# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 14:07:40 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: [(1R)-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
 YL6  YL6  '[(1R)-1-{[6-(3-chloro-4-methylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino}-2-(3-fluorophenyl)ethyl]phosphonic acid'  ligand  47  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 PERFECT
;

data_comp_YL6
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
 YL6  CAP  C   CR16   0  -0.280  -3.8313  -0.3925   0.9512
 YL6  CAQ  C   CR6    0  -0.079  -5.1290  -0.2623   1.4068
 YL6  CL   CL  CL     0  -0.123  -5.4073  -0.3684   3.1172
 YL6  CAR  C   CR6    0   0.147  -6.2124  -0.0585   0.5523
 YL6  CAW  C   CH3    0  -0.721  -7.6150   0.0817   1.0540
 YL6  CAS  C   CR16   0  -0.296  -5.9174   0.0066  -0.8063
 YL6  CAT  C   CR16   0  -0.306  -4.6248  -0.1174  -1.2868
 YL6  CAO  C   CR6    0   0.146  -3.5537  -0.3177  -0.4158
 YL6  CAM  C   CR5    0  -0.203  -2.1808  -0.4441  -0.8963
 YL6  SAN  S   S2     0   0.196  -1.8560  -0.5515  -2.6113
 YL6  CAL  C   CR15   0  -0.289  -1.0309  -0.4894  -0.1684
 YL6  C5   C   CR56   0   0.062   0.1341  -0.6132  -0.9748
 YL6  C6   C   CR56   0  -0.032  -0.1512  -0.6542  -2.3329
 YL6  N1   N   N      0  -0.455   0.7451  -0.7498  -3.3138
 YL6  C2   C   CR16   0   0.040   1.9900  -0.8113  -2.8697
 YL6  N3   N   N      0  -0.457   2.4168  -0.7819  -1.6183
 YL6  C4   C   CR6    0   0.539   1.5172  -0.6645  -0.6352
 YL6  NAB  N   NH1    0  -0.640   1.9175  -0.6061   0.6284
 YL6  CAC  C   CH1    0  -0.364   3.2786  -0.4990   1.1114
 YL6  PAA  P   P      0   1.185   3.3625  -1.4710   2.7206
 YL6  OAD  O   O      0  -0.896   2.1125  -0.9671   3.4619
 YL6  OAU  O   OP    -1  -0.891   3.2890  -2.9405   2.3035
 YL6  OAE  O   OP    -1  -0.889   4.6891  -1.0618   3.3637
 YL6  CAV  C   CH2    0  -0.507   3.6531   0.9797   1.3166
 YL6  CAX  C   CR6    0   0.166   3.4861   1.7840   0.0633
 YL6  CAY  C   CR16   0  -0.473   2.2630   2.3784  -0.2371
 YL6  CAZ  C   CR6    0   0.541   2.0968   3.0128  -1.4520
 YL6  FBD  F   F      0  -0.323   0.9036   3.5721  -1.7303
 YL6  CBA  C   CR16   0  -0.431   3.1061   3.1015  -2.3893
 YL6  CBB  C   CR16   0  -0.223   4.3322   2.5272  -2.0764
 YL6  CBC  C   CR16   0  -0.311   4.5198   1.8769  -0.8672
 YL6  H1   H   HCR6   0   0.277  -3.0375  -0.5560   1.6671
 YL6  H2   H   HCH3   0   0.253  -7.7125   0.9238   1.7408
 YL6  H3   H   HCH3   0   0.253  -8.3043   0.2413   0.2273
 YL6  H4   H   HCH3   0   0.253  -7.9376  -0.8104   1.5932
 YL6  H5   H   HCR6   0   0.265  -6.7258   0.1603  -1.5099
 YL6  H6   H   HCR6   0   0.258  -4.4667  -0.0486  -2.3561
 YL6  H7   H   HCR5   0   0.271  -1.0142  -0.4297   0.9112
 YL6  H8   H   HCR6   0   0.245   2.7613  -0.8980  -3.6283
 YL6  H9   H   HNH1   0   0.378   1.2232  -0.5637   1.3623
 YL6  H10  H   HCH1   0   0.228   3.9431  -0.9315   0.3621
 YL6  H13  H   HCH2   0   0.225   3.0302   1.3858   2.1185
 YL6  H14  H   HCH2   0   0.237   4.6864   1.0196   1.6625
 YL6  H15  H   HCR6   0   0.260   1.4412   2.3372   0.4672
 YL6  H16  H   HCR6   0   0.268   2.9443   3.6102  -3.3308
 YL6  H17  H   HCR6   0   0.257   5.1442   2.5893  -2.7894
 YL6  H18  H   HCR6   0   0.240   5.4783   1.4232  -0.6446

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
 YL6  N1   C2   aromatic  1.323  0.020  1.323
 YL6  N1   C6   aromatic  1.332  0.020  1.332
 YL6  SAN  C6   aromatic  1.730  0.020  1.730
 YL6  SAN  CAM  aromatic  1.749  0.020  1.749
 YL6  OAD  PAA  deloc     1.538  0.020  1.538
 YL6  C2   N3   aromatic  1.323  0.020  1.323
 YL6  C6   C5   aromatic  1.388  0.020  1.388
 YL6  CAT  CAS  aromatic  1.385  0.020  1.385
 YL6  CAT  CAO  aromatic  1.395  0.020  1.395
 YL6  CAM  CAO  single    1.460  0.020  1.460
 YL6  CAM  CAL  aromatic  1.362  0.020  1.362
 YL6  N3   C4   aromatic  1.338  0.020  1.338
 YL6  CAS  CAR  aromatic  1.392  0.020  1.392
 YL6  C5   CAL  aromatic  1.422  0.020  1.422
 YL6  C5   C4   aromatic  1.425  0.020  1.425
 YL6  CAO  CAP  aromatic  1.397  0.020  1.397
 YL6  OAE  PAA  deloc     1.530  0.020  1.530
 YL6  CAR  CAW  single    1.496  0.020  1.496
 YL6  CAR  CAQ  aromatic  1.395  0.020  1.395
 YL6  CAP  CAQ  aromatic  1.382  0.020  1.382
 YL6  C4   NAB  single    1.327  0.020  1.327
 YL6  CAQ  CL   single    1.736  0.020  1.736
 YL6  PAA  OAU  deloc     1.529  0.020  1.529
 YL6  PAA  CAC  single    1.882  0.020  1.882
 YL6  NAB  CAC  single    1.448  0.020  1.448
 YL6  CAC  CAV  single    1.539  0.020  1.539
 YL6  CAV  CAX  single    1.499  0.020  1.499
 YL6  CBC  CAX  aromatic  1.394  0.020  1.394
 YL6  CBC  CBB  aromatic  1.386  0.020  1.386
 YL6  CAX  CAY  aromatic  1.393  0.020  1.393
 YL6  CBB  CBA  aromatic  1.390  0.020  1.390
 YL6  CAY  CAZ  aromatic  1.381  0.020  1.381
 YL6  CBA  CAZ  aromatic  1.380  0.020  1.380
 YL6  CAZ  FBD  single    1.347  0.020  1.347
 YL6  CAP  H1   single    0.930  0.020  1.080
 YL6  CAW  H2   single    0.970  0.020  1.090
 YL6  CAW  H3   single    0.970  0.020  1.090
 YL6  CAW  H4   single    0.970  0.020  1.090
 YL6  CAS  H5   single    0.930  0.020  1.080
 YL6  CAT  H6   single    0.930  0.020  1.080
 YL6  CAL  H7   single    0.930  0.020  1.080
 YL6  C2   H8   single    0.930  0.020  1.080
 YL6  NAB  H9   single    0.860  0.020  1.020
 YL6  CAC  H10  single    0.970  0.020  1.090
 YL6  CAV  H13  single    0.970  0.020  1.090
 YL6  CAV  H14  single    0.970  0.020  1.090
 YL6  CAY  H15  single    0.930  0.020  1.080
 YL6  CBA  H16  single    0.930  0.020  1.080
 YL6  CBB  H17  single    0.930  0.020  1.080
 YL6  CBC  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
 YL6  H1   CAP  CAO  120.67  3.000
 YL6  H1   CAP  CAQ  119.04  3.000
 YL6  CAO  CAP  CAQ  120.29  3.000
 YL6  CAR  CAQ  CL   119.21  3.000
 YL6  CL   CAQ  CAP  118.02  3.000
 YL6  CAR  CAQ  CAP  122.77  3.000
 YL6  CAS  CAR  CAW  121.44  3.000
 YL6  CAW  CAR  CAQ  122.44  3.000
 YL6  CAS  CAR  CAQ  116.12  3.000
 YL6  H4   CAW  H3   107.94  3.000
 YL6  H4   CAW  H2   107.07  3.000
 YL6  H3   CAW  H2   107.96  3.000
 YL6  H4   CAW  CAR  111.49  3.000
 YL6  H3   CAW  CAR  110.66  3.000
 YL6  H2   CAW  CAR  111.54  3.000
 YL6  H5   CAS  CAT  118.96  3.000
 YL6  H5   CAS  CAR  118.86  3.000
 YL6  CAT  CAS  CAR  122.18  3.000
 YL6  H6   CAT  CAO  120.90  3.000
 YL6  H6   CAT  CAS  118.24  3.000
 YL6  CAO  CAT  CAS  120.86  3.000
 YL6  CAM  CAO  CAT  121.93  3.000
 YL6  CAM  CAO  CAP  120.28  3.000
 YL6  CAT  CAO  CAP  117.78  3.000
 YL6  CAL  CAM  SAN  111.43  3.000
 YL6  CAL  CAM  CAO  128.39  3.000
 YL6  SAN  CAM  CAO  120.18  3.000
 YL6  C6   SAN  CAM   91.65  3.000
 YL6  H7   CAL  C5   123.93  3.000
 YL6  H7   CAL  CAM  123.02  3.000
 YL6  C5   CAL  CAM  113.05  3.000
 YL6  C4   C5   C6   115.56  3.000
 YL6  C4   C5   CAL  131.53  3.000
 YL6  C6   C5   CAL  112.88  3.000
 YL6  N1   C6   C5   125.74  3.000
 YL6  C5   C6   SAN  110.98  3.000
 YL6  N1   C6   SAN  123.27  3.000
 YL6  C2   N1   C6   112.90  3.000
 YL6  H8   C2   N3   115.71  3.000
 YL6  H8   C2   N1   115.96  3.000
 YL6  N3   C2   N1   128.33  3.000
 YL6  C4   N3   C2   118.70  3.000
 YL6  NAB  C4   N3   120.06  3.000
 YL6  NAB  C4   C5   121.21  3.000
 YL6  N3   C4   C5   118.73  3.000
 YL6  H9   NAB  CAC  113.59  3.000
 YL6  H9   NAB  C4   119.07  3.000
 YL6  CAC  NAB  C4   127.19  3.000
 YL6  H10  CAC  CAV  108.92  3.000
 YL6  H10  CAC  PAA  110.82  3.000
 YL6  CAV  CAC  PAA  111.80  3.000
 YL6  H10  CAC  NAB  108.31  3.000
 YL6  CAV  CAC  NAB  110.13  3.000
 YL6  PAA  CAC  NAB  106.79  3.000
 YL6  OAE  PAA  OAU  114.41  3.000
 YL6  OAU  PAA  OAD  114.03  3.000
 YL6  OAE  PAA  OAD  114.48  3.000
 YL6  OAU  PAA  CAC  105.13  3.000
 YL6  OAE  PAA  CAC  105.07  3.000
 YL6  OAD  PAA  CAC  101.93  3.000
 YL6  H14  CAV  H13  107.07  3.000
 YL6  H14  CAV  CAX  110.56  3.000
 YL6  H13  CAV  CAX  110.52  3.000
 YL6  H14  CAV  CAC  107.94  3.000
 YL6  H13  CAV  CAC  108.42  3.000
 YL6  CAX  CAV  CAC  112.15  3.000
 YL6  CBC  CAX  CAY  118.61  3.000
 YL6  CAY  CAX  CAV  120.48  3.000
 YL6  CBC  CAX  CAV  120.76  3.000
 YL6  H15  CAY  CAZ  119.89  3.000
 YL6  H15  CAY  CAX  120.66  3.000
 YL6  CAZ  CAY  CAX  119.45  3.000
 YL6  CBA  CAZ  FBD  118.74  3.000
 YL6  FBD  CAZ  CAY  118.64  3.000
 YL6  CBA  CAZ  CAY  122.62  3.000
 YL6  H16  CBA  CBB  121.47  3.000
 YL6  H16  CBA  CAZ  120.77  3.000
 YL6  CBB  CBA  CAZ  117.76  3.000
 YL6  H17  CBB  CBC  120.01  3.000
 YL6  H17  CBB  CBA  119.33  3.000
 YL6  CBC  CBB  CBA  120.66  3.000
 YL6  H18  CBC  CBB  119.70  3.000
 YL6  H18  CBC  CAX  119.40  3.000
 YL6  CBB  CBC  CAX  120.89  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
 YL6  CONST_01  CAS  CAT  CAO  CAP    0.00   0.0  0
 YL6  CONST_02  SAN  CAM  CAO  CAP  180.00   0.0  0
 YL6  CONST_03  CAL  CAM  CAO  CAP    0.00   0.0  0
 YL6  CONST_04  CAS  CAR  CAQ  CAP    0.00   0.0  0
 YL6  CONST_05  CAT  CAS  CAR  CAQ    0.00   0.0  0
 YL6  CONST_06  CAT  CAO  CAP  CAQ    0.00   0.0  0
 YL6  CONST_07  CAM  CAO  CAP  CAQ  180.00   0.0  0
 YL6  CONST_08  CAO  CAT  CAS  CAR    0.00   0.0  0
 YL6  CONST_09  CAO  CAP  CAQ  CAR    0.00   0.0  0
 YL6  CONST_10  CAM  CAO  CAT  CAS  180.00   0.0  0
 YL6  CONST_11  SAN  CAM  CAO  CAT    0.00   0.0  0
 YL6  CONST_12  CAL  CAM  CAO  CAT  180.00   0.0  0
 YL6  CONST_13  C6   SAN  CAM  CAO  180.00   0.0  0
 YL6  CONST_14  C5   CAL  CAM  CAO  180.00   0.0  0
 YL6  CONST_15  N1   C6   SAN  CAM  180.00   0.0  0
 YL6  CONST_16  C5   C6   SAN  CAM    0.00   0.0  0
 YL6  CONST_17  C6   C5   CAL  CAM    0.00   0.0  0
 YL6  CONST_18  C4   C5   CAL  CAM  180.00   0.0  0
 YL6  CONST_19  C2   N1   C6   SAN  180.00   0.0  0
 YL6  CONST_20  CAL  C5   C6   SAN    0.00   0.0  0
 YL6  CONST_21  C4   C5   C6   SAN  180.00   0.0  0
 YL6  CONST_22  C5   CAL  CAM  SAN    0.00   0.0  0
 YL6  CONST_23  C6   SAN  CAM  CAL    0.00   0.0  0
 YL6  CONST_24  N1   C6   C5   CAL  180.00   0.0  0
 YL6  CONST_25  N3   C4   C5   CAL  180.00   0.0  0
 YL6  CONST_26  C2   N1   C6   C5     0.00   0.0  0
 YL6  CONST_27  C2   N3   C4   C5     0.00   0.0  0
 YL6  CONST_28  N3   C2   N1   C6     0.00   0.0  0
 YL6  CONST_29  N3   C4   C5   C6     0.00   0.0  0
 YL6  CONST_30  C4   N3   C2   N1     0.00   0.0  0
 YL6  CONST_31  C4   C5   C6   N1     0.00   0.0  0
 YL6  CONST_32  CBA  CBB  CBC  CAX    0.00   0.0  0
 YL6  CONST_33  CBA  CAZ  CAY  CAX    0.00   0.0  0
 YL6  CONST_34  CBB  CBC  CAX  CAY    0.00   0.0  0
 YL6  CONST_35  CBB  CBA  CAZ  CAY    0.00   0.0  0
 YL6  CONST_36  CBC  CAX  CAY  CAZ    0.00   0.0  0
 YL6  CONST_37  CBC  CBB  CBA  CAZ    0.00   0.0  0
 YL6  CONST_38  CAW  CAR  CAQ  CAP  180.00   0.0  0
 YL6  CONST_39  CAS  CAR  CAQ  CL   180.00   0.0  0
 YL6  CONST_40  CAO  CAP  CAQ  CL   180.00   0.0  0
 YL6  CONST_41  CAT  CAS  CAR  CAW  180.00   0.0  0
 YL6  CONST_42  NAB  C4   C5   CAL    0.00   0.0  0
 YL6  CONST_43  NAB  C4   C5   C6   180.00   0.0  0
 YL6  CONST_44  NAB  C4   N3   C2   180.00   0.0  0
 YL6  CONST_45  CBB  CBC  CAX  CAV  180.00   0.0  0
 YL6  CONST_46  CAZ  CAY  CAX  CAV  180.00   0.0  0
 YL6  CONST_47  FBD  CAZ  CAY  CAX  180.00   0.0  0
 YL6  CONST_48  CBB  CBA  CAZ  FBD  180.00   0.0  0
 YL6  CONST_49  H6   CAT  CAO  CAP  180.00   0.0  0
 YL6  CONST_50  H5   CAS  CAR  CAQ  180.00   0.0  0
 YL6  CONST_51  H1   CAP  CAQ  CAR  180.00   0.0  0
 YL6  CONST_52  H7   CAL  CAM  CAO    0.00   0.0  0
 YL6  CONST_53  H8   C2   N1   C6   180.00   0.0  0
 YL6  CONST_54  H17  CBB  CBC  CAX  180.00   0.0  0
 YL6  CONST_55  H18  CBC  CAX  CAY  180.00   0.0  0
 YL6  CONST_56  H16  CBA  CAZ  CAY  180.00   0.0  0
 YL6  CONST_57  H15  CAY  CAZ  CBA  180.00   0.0  0
 YL6  CONST_58  CAC  NAB  C4   C5   180.00   0.0  0
 YL6  CONST_59  CAC  NAB  C4   N3     0.00   0.0  0
 YL6  CONST_60  H9   NAB  C4   C5     0.00   0.0  0
 YL6  Var_01    CBC  CAX  CAV  CAC  -87.30  30.0  2
 YL6  Var_02    H2   CAW  CAR  CAQ   59.33  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
 YL6  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
 YL6  plan-1  CAP  0.020
 YL6  plan-1  CAQ  0.020
 YL6  plan-1  CL   0.020
 YL6  plan-1  CAR  0.020
 YL6  plan-1  CAW  0.020
 YL6  plan-1  CAS  0.020
 YL6  plan-1  CAT  0.020
 YL6  plan-1  CAO  0.020
 YL6  plan-1  CAM  0.020
 YL6  plan-1  H1   0.020
 YL6  plan-1  H5   0.020
 YL6  plan-1  H6   0.020
 YL6  plan-2  CAV  0.020
 YL6  plan-2  CAX  0.020
 YL6  plan-2  CAY  0.020
 YL6  plan-2  CAZ  0.020
 YL6  plan-2  FBD  0.020
 YL6  plan-2  CBA  0.020
 YL6  plan-2  CBB  0.020
 YL6  plan-2  CBC  0.020
 YL6  plan-2  H15  0.020
 YL6  plan-2  H16  0.020
 YL6  plan-2  H17  0.020
 YL6  plan-2  H18  0.020
 YL6  plan-3  CAO  0.020
 YL6  plan-3  CAM  0.020
 YL6  plan-3  SAN  0.020
 YL6  plan-3  CAL  0.020
 YL6  plan-3  C5   0.020
 YL6  plan-3  C6   0.020
 YL6  plan-3  N1   0.020
 YL6  plan-3  C2   0.020
 YL6  plan-3  N3   0.020
 YL6  plan-3  C4   0.020
 YL6  plan-3  NAB  0.020
 YL6  plan-3  H7   0.020
 YL6  plan-3  H8   0.020
 YL6  plan-4  C4   0.020
 YL6  plan-4  NAB  0.020
 YL6  plan-4  CAC  0.020
 YL6  plan-4  H9   0.020

