# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 11:53:37 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  47  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 PERFECT
;

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  -0.471   2.0752   2.2947   0.5881
 YL5  CAZ  C  CR6    0   0.541   1.8225   3.3349  -0.2840
 YL5  FBD  F  F      0  -0.324   0.6608   4.0065  -0.1666
 YL5  CBA  C  CR16   0  -0.433   2.7141   3.7168  -1.2660
 YL5  CBB  C  CR16   0  -0.223   3.9119   3.0184  -1.3587
 YL5  CBC  C  CR16   0  -0.314   4.1843   1.9657  -0.4997
 YL5  CAX  C  CR6    0   0.167   3.2671   1.5828   0.4773
 YL5  CAV  C  CH2    0  -0.508   3.5123   0.3752   1.3305
 YL5  CAC  C  CH1    0  -0.361   2.9664  -0.9142   0.6940
 YL5  PAA  P  P      0   1.185   3.1376  -2.3875   1.8533
 YL5  OAD  O  OP    -1  -0.889   4.5676  -2.3056   2.3909
 YL5  OAU  O  O      0  -0.897   2.0459  -2.1004   2.8982
 YL5  OAE  O  OP    -1  -0.892   2.8590  -3.6152   0.9851
 YL5  NAB  N  NH1    0  -0.641   1.5558  -0.7744   0.3987
 YL5  C4   C  CR6    0   0.536   1.0115  -0.3739  -0.7443
 YL5  N3   N  N      0  -0.460   1.7818  -0.1749  -1.8195
 YL5  C2   C  CR16   0   0.038   1.2144   0.2502  -2.9368
 YL5  N1   N  N      0  -0.455  -0.0635   0.5046  -3.1623
 YL5  C6   C  CR56   0  -0.034  -0.8336   0.2805  -2.0974
 YL5  SAN  S  S2     0   0.197  -2.5484   0.5208  -2.0957
 YL5  C5   C  CR56   0   0.052  -0.3927  -0.1605  -0.8569
 YL5  CAL  C  CR15   0  -0.277  -1.4490  -0.3051   0.0868
 YL5  CAM  C  CR5    0  -0.206  -2.6677   0.0161  -0.4267
 YL5  CAO  C  CR6    0   0.130  -3.9652  -0.0145   0.2431
 YL5  CAP  C  CR16   0  -0.312  -4.0422   0.0562   1.6365
 YL5  CAQ  C  CR16   0  -0.276  -5.2649   0.0060   2.2831
 YL5  CAR  C  CR6    0   0.084  -6.4586  -0.1027   1.5710
 YL5  CAW  C  CH3    0  -0.721  -7.7821  -0.1199   2.2761
 YL5  CAS  C  CR16   0  -0.279  -6.3800  -0.1677   0.1823
 YL5  CAT  C  CR16   0  -0.309  -5.1591  -0.1263  -0.4722
 YL5  H1   H  HCR6   0   0.260   1.3414   2.0358   1.3422
 YL5  H2   H  HCR6   0   0.269   2.4885   4.5393  -1.9320
 YL5  H3   H  HCR6   0   0.256   4.6356   3.3039  -2.1113
 YL5  H4   H  HCR6   0   0.241   5.1188   1.4251  -0.5925
 YL5  H5   H  HCH2   0   0.237   4.5806   0.2365   1.5001
 YL5  H6   H  HCH2   0   0.225   3.0456   0.5026   2.3113
 YL5  H7   H  HCH1   0   0.225   3.4934  -1.0977  -0.2435
 YL5  H10  H  HNH1   0   0.377   0.9570  -0.9406   1.1956
 YL5  H11  H  HCR6   0   0.244   1.8861   0.4071  -3.7752
 YL5  H12  H  HCR5   0   0.267  -1.3190  -0.6532   1.1027
 YL5  H13  H  HCR6   0   0.255  -3.1399   0.1647   2.2246
 YL5  H14  H  HCR6   0   0.252  -5.2902   0.0605   3.3649
 YL5  H15  H  HCH3   0   0.250  -8.1676   0.8937   2.4069
 YL5  H16  H  HCH3   0   0.245  -8.5288  -0.6794   1.7136
 YL5  H17  H  HCH3   0   0.245  -7.7011  -0.5646   3.2677
 YL5  H18  H  HCR6   0   0.252  -7.2867  -0.2618  -0.4033
 YL5  H19  H  HCR6   0   0.251  -5.1460  -0.2009  -1.5533

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  deloc     1.538  0.020  1.538
 YL5  OAE  PAA  deloc     1.529  0.020  1.529
 YL5  N1   C2   aromatic  1.322  0.020  1.322
 YL5  N1   C6   aromatic  1.333  0.020  1.333
 YL5  C2   N3   aromatic  1.323  0.020  1.323
 YL5  SAN  C6   aromatic  1.732  0.020  1.732
 YL5  SAN  CAM  aromatic  1.748  0.020  1.748
 YL5  C6   C5   aromatic  1.388  0.020  1.388
 YL5  PAA  CAC  single    1.883  0.020  1.883
 YL5  PAA  OAD  deloc     1.530  0.020  1.530
 YL5  N3   C4   aromatic  1.338  0.020  1.338
 YL5  C5   C4   aromatic  1.425  0.020  1.425
 YL5  C5   CAL  aromatic  1.424  0.020  1.424
 YL5  C4   NAB  single    1.328  0.020  1.328
 YL5  CAM  CAL  aromatic  1.361  0.020  1.361
 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  1.392  0.020  1.392
 YL5  CAR  CAW  single    1.500  0.020  1.500
 YL5  NAB  CAC  single    1.448  0.020  1.448
 YL5  CAC  CAV  single    1.538  0.020  1.538
 YL5  CAV  CAX  single    1.499  0.020  1.499
 YL5  CAY  CAX  aromatic  1.393  0.020  1.393
 YL5  CAY  CAZ  aromatic  1.381  0.020  1.381
 YL5  CAX  CBC  aromatic  1.394  0.020  1.394
 YL5  FBD  CAZ  single    1.347  0.020  1.347
 YL5  CAZ  CBA  aromatic  1.380  0.020  1.380
 YL5  CBC  CBB  aromatic  1.386  0.020  1.386
 YL5  CBA  CBB  aromatic  1.390  0.020  1.390
 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  NAB  H10  single    0.860  0.020  1.020
 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  120.85  3.000
 YL5  H1   CAY  CAZ  119.71  3.000
 YL5  CAX  CAY  CAZ  119.44  3.000
 YL5  CBA  CAZ  FBD  118.76  3.000
 YL5  CBA  CAZ  CAY  122.65  3.000
 YL5  FBD  CAZ  CAY  118.58  3.000
 YL5  H2   CBA  CBB  121.38  3.000
 YL5  H2   CBA  CAZ  120.90  3.000
 YL5  CBB  CBA  CAZ  117.73  3.000
 YL5  H3   CBB  CBC  119.99  3.000
 YL5  H3   CBB  CBA  119.35  3.000
 YL5  CBC  CBB  CBA  120.66  3.000
 YL5  H4   CBC  CAX  119.37  3.000
 YL5  H4   CBC  CBB  119.70  3.000
 YL5  CAX  CBC  CBB  120.92  3.000
 YL5  CAV  CAX  CBC  120.85  3.000
 YL5  CBC  CAX  CAY  118.59  3.000
 YL5  CAV  CAX  CAY  120.43  3.000
 YL5  H6   CAV  H5   107.07  3.000
 YL5  H6   CAV  CAC  108.50  3.000
 YL5  H5   CAV  CAC  107.78  3.000
 YL5  H6   CAV  CAX  110.29  3.000
 YL5  H5   CAV  CAX  110.56  3.000
 YL5  CAC  CAV  CAX  112.45  3.000
 YL5  H7   CAC  NAB  108.15  3.000
 YL5  H7   CAC  PAA  110.71  3.000
 YL5  NAB  CAC  PAA  106.84  3.000
 YL5  H7   CAC  CAV  108.98  3.000
 YL5  NAB  CAC  CAV  110.44  3.000
 YL5  PAA  CAC  CAV  111.65  3.000
 YL5  OAE  PAA  OAU  113.97  3.000
 YL5  OAE  PAA  OAD  114.38  3.000
 YL5  OAU  PAA  OAD  114.50  3.000
 YL5  OAD  PAA  CAC  105.04  3.000
 YL5  OAE  PAA  CAC  105.20  3.000
 YL5  OAU  PAA  CAC  101.99  3.000
 YL5  H10  NAB  C4   119.04  3.000
 YL5  H10  NAB  CAC  113.61  3.000
 YL5  C4   NAB  CAC  127.16  3.000
 YL5  C5   C4   N3   118.80  3.000
 YL5  C5   C4   NAB  121.15  3.000
 YL5  N3   C4   NAB  120.05  3.000
 YL5  C2   N3   C4   118.66  3.000
 YL5  H11  C2   N1   116.01  3.000
 YL5  H11  C2   N3   115.67  3.000
 YL5  N1   C2   N3   128.33  3.000
 YL5  C6   N1   C2   112.94  3.000
 YL5  C5   C6   SAN  110.96  3.000
 YL5  C5   C6   N1   125.70  3.000
 YL5  SAN  C6   N1   123.34  3.000
 YL5  CAM  SAN  C6    91.63  3.000
 YL5  CAL  C5   C6   112.88  3.000
 YL5  CAL  C5   C4   131.57  3.000
 YL5  C6   C5   C4   115.54  3.000
 YL5  H12  CAL  CAM  122.54  3.000
 YL5  H12  CAL  C5   124.47  3.000
 YL5  CAM  CAL  C5   112.98  3.000
 YL5  CAO  CAM  CAL  128.14  3.000
 YL5  CAO  CAM  SAN  120.31  3.000
 YL5  CAL  CAM  SAN  111.55  3.000
 YL5  CAT  CAO  CAP  117.89  3.000
 YL5  CAT  CAO  CAM  121.76  3.000
 YL5  CAP  CAO  CAM  120.35  3.000
 YL5  H13  CAP  CAQ  119.09  3.000
 YL5  H13  CAP  CAO  120.06  3.000
 YL5  CAQ  CAP  CAO  120.85  3.000
 YL5  H14  CAQ  CAR  119.59  3.000
 YL5  H14  CAQ  CAP  119.04  3.000
 YL5  CAR  CAQ  CAP  121.37  3.000
 YL5  CAS  CAR  CAW  121.21  3.000
 YL5  CAW  CAR  CAQ  121.09  3.000
 YL5  CAS  CAR  CAQ  117.69  3.000
 YL5  H17  CAW  H16  108.13  3.000
 YL5  H17  CAW  H15  107.21  3.000
 YL5  H16  CAW  H15  107.24  3.000
 YL5  H17  CAW  CAR  111.52  3.000
 YL5  H16  CAW  CAR  111.59  3.000
 YL5  H15  CAW  CAR  110.92  3.000
 YL5  H18  CAS  CAT  118.99  3.000
 YL5  H18  CAS  CAR  119.72  3.000
 YL5  CAT  CAS  CAR  121.29  3.000
 YL5  H19  CAT  CAS  118.66  3.000
 YL5  H19  CAT  CAO  120.41  3.000
 YL5  CAS  CAT  CAO  120.91  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_57  N3   C4   NAB  CAC    0.00   0.0  0
 YL5  CONST_58  C5   C4   NAB  CAC  180.00   0.0  0
 YL5  CONST_59  H10  NAB  C4   N3   180.00   0.0  0
 YL5  Var_01    CAC  CAV  CAX  CAY   87.43  30.0  3
 YL5  Var_02    H15  CAW  CAR  CAQ   88.87  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

