# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jun  4 18:33:38 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  49  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 OK
;

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  -0.264  -3.6727   0.4130   0.7090
 YL6  CAQ  C   CR6   0  -0.084  -4.9626   0.6178   1.1614
 YL6  CL   CL  CL    0  -0.121  -5.1753   1.3938   2.6986
 YL6  CAR  C   CR6   0   0.155  -6.0862   0.2413   0.4257
 YL6  CAW  C   CH3   0  -0.721  -7.4797   0.4807   0.9145
 YL6  CAS  C   CR16  0  -0.297  -5.8449  -0.3685  -0.8027
 YL6  CAT  C   CR16  0  -0.294  -4.5624  -0.5949  -1.2729
 YL6  CAO  C   CR6   0   0.122  -3.4537  -0.2061  -0.5223
 YL6  CAM  C   CR5   0  -0.204  -2.0876  -0.4304  -0.9875
 YL6  SAN  S   S2    0   0.226  -1.7574  -0.5963  -2.6944
 YL6  CAL  C   CR15  0  -0.269  -0.9556  -0.5206  -0.2395
 YL6  C5   C   CR56  0   0.059   0.2092  -0.7292  -1.0311
 YL6  C6   C   CR56  0  -0.022  -0.0666  -0.7943  -2.3934
 YL6  N1   N   N     0  -0.435   0.8358  -0.9656  -3.3562
 YL6  C2   C   CR16  0   0.049   2.0711  -1.0710  -2.9072
 YL6  N3   N   N     0  -0.460   2.4814  -1.0223  -1.6446
 YL6  C4   C   CR6   0   0.556   1.5775  -0.8489  -0.6898
 YL6  NAB  N   NH1   0  -0.686   1.9781  -0.7945   0.5973
 YL6  CAC  C   CH1   0  -0.376   3.3501  -0.5794   0.9930
 YL6  PAA  P   P     0   1.390   3.6905  -1.7328   2.3622
 YL6  OAD  O   O     0  -0.708   2.8461  -1.5040   3.5603
 YL6  OAU  O   OH1   0  -0.740   3.5843  -3.2018   1.7212
 YL6  OAE  O   OH1   0  -0.741   5.2696  -1.5611   2.5363
 YL6  CAV  C   CH2   0  -0.535   3.6151   0.8883   1.3685
 YL6  CAX  C   CR6   0   0.148   3.2453   1.7840   0.2211
 YL6  CAY  C   CR16  0  -0.471   1.9683   2.3306   0.1453
 YL6  CAZ  C   CR6   0   0.545   1.6141   3.0667  -0.9688
 YL6  FBD  F   F     0  -0.317   0.3740   3.5804  -1.0310
 YL6  CBA  C   CR16  0  -0.423   2.4853   3.2932  -2.0152
 YL6  CBB  C   CR16  0  -0.222   3.7629   2.7557  -1.9262
 YL6  CBC  C   CR16  0  -0.299   4.1401   2.0072  -0.8220
 YL6  H1   H   HCR6  0   0.278  -2.8376   0.7518   1.3079
 YL6  H2   H   HCH3  0   0.254  -7.6617   1.5409   1.0959
 YL6  H3   H   HCH3  0   0.254  -8.2080   0.1347   0.1835
 YL6  H4   H   HCH3  0   0.255  -7.6708  -0.0417   1.8532
 YL6  H5   H   HCR6  0   0.266  -6.6889  -0.6796  -1.4057
 YL6  H6   H   HCR6  0   0.260  -4.4365  -1.0936  -2.2262
 YL6  H7   H   HCR5  0   0.276  -0.9631  -0.4635   0.8404
 YL6  H8   H   HCR6  0   0.259   2.8462  -1.2132  -3.6519
 YL6  H9   H   HNH1  0   0.408   1.2718  -0.5965   1.2895
 YL6  H10  H   HCH1  0   0.322   3.9852  -0.8584   0.1511
 YL6  H11  H   HOH1  0   0.496   2.6933  -3.5747   1.7347
 YL6  H12  H   HOH1  0   0.500   5.6231  -1.8948   3.3727
 YL6  H13  H   HCH2  0   0.269   3.0405   1.1541   2.2591
 YL6  H14  H   HCH2  0   0.278   4.6705   1.0047   1.6201
 YL6  H15  H   HCR6  0   0.272   1.2524   2.1841   0.9452
 YL6  H16  H   HCR6  0   0.276   2.1787   3.8763  -2.8735
 YL6  H17  H   HCR6  0   0.265   4.4670   2.9230  -2.7305
 YL6  H18  H   HCR6  0   0.252   5.1367   1.5857  -0.7741

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  1.319  0.020  1.319
 YL6  N1   C6   aromatic  1.331  0.020  1.331
 YL6  SAN  C6   aromatic  1.729  0.020  1.729
 YL6  SAN  CAM  aromatic  1.746  0.020  1.746
 YL6  OAD  PAA  double    1.483  0.020  1.483
 YL6  C2   N3   aromatic  1.328  0.020  1.328
 YL6  C6   C5   aromatic  1.392  0.020  1.392
 YL6  CAT  CAS  aromatic  1.385  0.020  1.385
 YL6  CAT  CAO  aromatic  1.394  0.020  1.394
 YL6  CAM  CAO  single    1.460  0.020  1.460
 YL6  CAM  CAL  aromatic  1.360  0.020  1.360
 YL6  N3   C4   aromatic  1.326  0.020  1.326
 YL6  CAS  CAR  aromatic  1.392  0.020  1.392
 YL6  C5   CAL  aromatic  1.424  0.020  1.424
 YL6  C5   C4   aromatic  1.415  0.020  1.415
 YL6  CAO  CAP  aromatic  1.395  0.020  1.395
 YL6  OAE  PAA  single    1.598  0.020  1.598
 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    1.349  0.020  1.349
 YL6  CAQ  CL   single    1.735  0.020  1.735
 YL6  PAA  OAU  single    1.606  0.020  1.606
 YL6  PAA  CAC  single    1.822  0.020  1.822
 YL6  NAB  CAC  single    1.444  0.020  1.444
 YL6  CAC  CAV  single    1.538  0.020  1.538
 YL6  CAV  CAX  single    1.502  0.020  1.502
 YL6  CBC  CAX  aromatic  1.392  0.020  1.392
 YL6  CBC  CBB  aromatic  1.386  0.020  1.386
 YL6  CAX  CAY  aromatic  1.391  0.020  1.391
 YL6  CBB  CBA  aromatic  1.389  0.020  1.389
 YL6  CAY  CAZ  aromatic  1.381  0.020  1.381
 YL6  CBA  CAZ  aromatic  1.380  0.020  1.380
 YL6  CAZ  FBD  single    1.344  0.020  1.344
 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    0.890  0.020  1.040
 YL6  CAC  H10  single    0.970  0.020  1.090
 YL6  OAU  H11  single    0.850  0.020  0.980
 YL6  OAE  H12  single    0.850  0.020  0.980
 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  120.41  3.000
 YL6  H1   CAP  CAQ  119.52  3.000
 YL6  CAO  CAP  CAQ  120.06  3.000
 YL6  CAR  CAQ  CL   119.30  3.000
 YL6  CL   CAQ  CAP  118.07  3.000
 YL6  CAR  CAQ  CAP  122.63  3.000
 YL6  CAS  CAR  CAW  121.31  3.000
 YL6  CAW  CAR  CAQ  122.33  3.000
 YL6  CAS  CAR  CAQ  116.36  3.000
 YL6  H4   CAW  H3   107.97  3.000
 YL6  H4   CAW  H2   107.03  3.000
 YL6  H3   CAW  H2   108.00  3.000
 YL6  H4   CAW  CAR  111.57  3.000
 YL6  H3   CAW  CAR  110.67  3.000
 YL6  H2   CAW  CAR  111.42  3.000
 YL6  H5   CAS  CAT  119.07  3.000
 YL6  H5   CAS  CAR  118.82  3.000
 YL6  CAT  CAS  CAR  122.12  3.000
 YL6  H6   CAT  CAO  120.65  3.000
 YL6  H6   CAT  CAS  118.80  3.000
 YL6  CAO  CAT  CAS  120.54  3.000
 YL6  CAM  CAO  CAT  121.97  3.000
 YL6  CAM  CAO  CAP  119.74  3.000
 YL6  CAT  CAO  CAP  118.29  3.000
 YL6  CAL  CAM  SAN  111.96  3.000
 YL6  CAL  CAM  CAO  127.85  3.000
 YL6  SAN  CAM  CAO  120.19  3.000
 YL6  C6   SAN  CAM   91.47  3.000
 YL6  H7   CAL  C5   124.65  3.000
 YL6  H7   CAL  CAM  122.69  3.000
 YL6  C5   CAL  CAM  112.64  3.000
 YL6  C4   C5   C6   115.07  3.000
 YL6  C4   C5   CAL  132.02  3.000
 YL6  C6   C5   CAL  112.89  3.000
 YL6  N1   C6   C5   125.45  3.000
 YL6  C5   C6   SAN  111.04  3.000
 YL6  N1   C6   SAN  123.51  3.000
 YL6  C2   N1   C6   113.53  3.000
 YL6  H8   C2   N3   115.90  3.000
 YL6  H8   C2   N1   116.50  3.000
 YL6  N3   C2   N1   127.59  3.000
 YL6  C4   N3   C2   118.59  3.000
 YL6  NAB  C4   N3   119.33  3.000
 YL6  NAB  C4   C5   120.91  3.000
 YL6  N3   C4   C5   119.76  3.000
 YL6  H9   NAB  CAC  116.62  3.000
 YL6  H9   NAB  C4   117.05  3.000
 YL6  CAC  NAB  C4   123.34  3.000
 YL6  H10  CAC  CAV  109.40  3.000
 YL6  H10  CAC  PAA  108.01  3.000
 YL6  CAV  CAC  PAA  112.85  3.000
 YL6  H10  CAC  NAB  107.67  3.000
 YL6  CAV  CAC  NAB  111.89  3.000
 YL6  PAA  CAC  NAB  106.80  3.000
 YL6  OAE  PAA  OAU  101.95  3.000
 YL6  OAU  PAA  OAD  115.19  3.000
 YL6  OAE  PAA  OAD  117.25  3.000
 YL6  OAU  PAA  CAC  105.47  3.000
 YL6  OAE  PAA  CAC  101.45  3.000
 YL6  OAD  PAA  CAC  113.76  3.000
 YL6  H11  OAU  PAA  114.11  3.000
 YL6  H12  OAE  PAA  114.73  3.000
 YL6  H14  CAV  H13  107.14  3.000
 YL6  H14  CAV  CAX  110.53  3.000
 YL6  H13  CAV  CAX  110.38  3.000
 YL6  H14  CAV  CAC  108.95  3.000
 YL6  H13  CAV  CAC  109.91  3.000
 YL6  CAX  CAV  CAC  109.89  3.000
 YL6  CBC  CAX  CAY  119.09  3.000
 YL6  CAY  CAX  CAV  120.13  3.000
 YL6  CBC  CAX  CAV  120.65  3.000
 YL6  H15  CAY  CAZ  119.87  3.000
 YL6  H15  CAY  CAX  120.88  3.000
 YL6  CAZ  CAY  CAX  119.25  3.000
 YL6  CBA  CAZ  FBD  118.99  3.000
 YL6  FBD  CAZ  CAY  118.53  3.000
 YL6  CBA  CAZ  CAY  122.48  3.000
 YL6  H16  CBA  CBB  121.33  3.000
 YL6  H16  CBA  CAZ  120.73  3.000
 YL6  CBB  CBA  CAZ  117.93  3.000
 YL6  H17  CBB  CBC  119.90  3.000
 YL6  H17  CBB  CBA  119.41  3.000
 YL6  CBC  CBB  CBA  120.69  3.000
 YL6  H18  CBC  CBB  119.72  3.000
 YL6  H18  CBC  CAX  119.72  3.000
 YL6  CBB  CBC  CAX  120.55  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_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_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_60  H9   NAB  C4   C5     0.00   0.0  0
 YL6  Var_01    CBC  CAX  CAV  CAC  -83.43  30.0  2
 YL6  Var_02    H2   CAW  CAR  CAQ   58.50  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

