# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 08:52:56 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: {[(2-{3-[(4-fluorobenzene-1-carbonyl)amino]phenyl}thieno[2,3-d]pyrimidin-4-yl)amino]methylene}bis(phosphonic acid)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)C(Nc1nc(nc2sccc12)c3cccc(NC(=O)c4ccc(F)cc4)c3)[P](O)(O)=O
#
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
 FV9  FV9  '{[(2-{3-[(4-fluorobenzene-1-carbonyl)amino]phenyl}thieno[2,3-d]pyrimidin-4-yl)amino]methylene}bis(phosphonic acid)'  ligand  52  35  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_FV9
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
 FV9  OBD  O  OH1   0  -0.751    6.0596   2.0542   1.3534
 FV9  PBB  P  P     0   1.405    5.5088   0.5521   1.4417
 FV9  OBE  O  O     0  -0.685    6.4910  -0.5477   1.3655
 FV9  OBC  O  OH1   0  -0.730    4.6501   0.4246   2.7839
 FV9  CAB  C  CH1   0  -0.680    4.2937   0.5821   0.0754
 FV9  PBF  P  P     0   1.379    4.8499   1.2833  -1.5247
 FV9  OBH  O  OH1   0  -0.738    5.0231   2.8577  -1.3043
 FV9  OBI  O  OH1   0  -0.738    6.3094   0.6346  -1.6304
 FV9  OBG  O  O     0  -0.684    3.9197   1.0135  -2.6405
 FV9  NAA  N  NH1   0  -0.692    3.8274  -0.7639  -0.1096
 FV9  C4   C  CR6   0   0.579    2.5188  -1.0784  -0.2070
 FV9  N3   N  N     0  -0.504    1.6222  -0.1223  -0.0448
 FV9  C5   C  CR56  0   0.006    2.1056  -2.4078  -0.4521
 FV9  CAI  C  CR15  0  -0.199    2.8253  -3.6231  -0.6588
 FV9  CAJ  C  CR15  0  -0.461    1.9940  -4.6720  -0.8563
 FV9  SAK  S  S2    0   0.228    0.3195  -4.2370  -0.8022
 FV9  C6   C  CR56  0  -0.013    0.7248  -2.5817  -0.5009
 FV9  N1   N  N     0  -0.469   -0.1791  -1.6224  -0.3384
 FV9  C2   C  CR6   0   0.411    0.3226  -0.4212  -0.1136
 FV9  CAL  C  CR6   0  -0.007   -0.6294   0.6962   0.0789
 FV9  CAQ  C  CR16  0  -0.347   -2.0000   0.4405   0.0614
 FV9  CAM  C  CR16  0  -0.305   -0.1645   1.9952   0.2709
 FV9  CAN  C  CR16  0  -0.228   -1.0721   3.0291   0.4384
 FV9  CAO  C  CR16  0  -0.344   -2.4332   2.7788   0.4315
 FV9  CAP  C  CR6   0   0.411   -2.9070   1.4788   0.2471
 FV9  NAR  N  NH1   0  -0.764   -4.2959   1.3016   0.2249
 FV9  CAS  C  C     0   0.528   -4.9940   0.1768   0.5283
 FV9  OAU  O  O     0  -0.458   -4.4748  -0.8697   0.8741
 FV9  CAT  C  CR6   0  -0.058   -6.4769   0.3084   0.4281
 FV9  CAV  C  CR16  0  -0.245   -7.2609  -0.5297   1.2195
 FV9  CAW  C  CR16  0  -0.398   -8.6424  -0.4667   1.1675
 FV9  CAX  C  CR6   0   0.535   -9.2296   0.4321   0.2963
 FV9  FBA  F  F     0  -0.307  -10.5651   0.4957   0.2348
 FV9  CAY  C  CR16  0  -0.397   -8.4849   1.2631  -0.5182
 FV9  CAZ  C  CR16  0  -0.272   -7.1025   1.1971  -0.4446
 FV9  H1   H  HOH1  0   0.511    6.8222   2.2543   1.9164
 FV9  H2   H  HOH1  0   0.498    4.0374   1.1473   2.9757
 FV9  H3   H  HCH1  0   0.361    3.4389   1.1934   0.3821
 FV9  H4   H  HOH1  0   0.494    5.6354   3.1189  -0.6014
 FV9  H5   H  HOH1  0   0.502    6.7231   0.7079  -2.5025
 FV9  H6   H  HNH1  0   0.418    4.5124  -1.4816  -0.2887
 FV9  H7   H  HCR5  0   0.277    3.9018  -3.7187  -0.6617
 FV9  H8   H  HCR5  0   0.308    2.2694  -5.6998  -1.0349
 FV9  H9   H  HCR6  0   0.273   -2.3385  -0.5685  -0.1066
 FV9  H10  H  HCR6  0   0.262    0.8977   2.1927   0.2858
 FV9  H11  H  HCR6  0   0.264   -0.7184   4.0413   0.5828
 FV9  H12  H  HCR6  0   0.275   -3.1331   3.5941   0.5714
 FV9  H13  H  HNH1  0   0.421   -4.8272   2.1531   0.1285
 FV9  H14  H  HCR6  0   0.274   -6.7900  -1.2337   1.8922
 FV9  H15  H  HCR6  0   0.288   -9.2526  -1.1064   1.7908
 FV9  H16  H  HCR6  0   0.290   -8.9728   1.9438  -1.2029
 FV9  H17  H  HCR6  0   0.276   -6.5255   1.8332  -1.1038

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
 FV9  NAA  CAB  single    1.436  0.020  1.436
 FV9  NAA  C4   single    1.349  0.020  1.349
 FV9  CAB  PBF  single    1.833  0.020  1.833
 FV9  CAB  PBB  single    1.829  0.020  1.829
 FV9  OBG  PBF  double    1.478  0.020  1.478
 FV9  OBE  PBB  double    1.477  0.020  1.477
 FV9  OBH  PBF  single    1.599  0.020  1.599
 FV9  OBD  PBB  single    1.602  0.020  1.602
 FV9  PBF  OBI  single    1.601  0.020  1.601
 FV9  CAI  CAJ  aromatic  1.353  0.020  1.353
 FV9  CAI  C5   aromatic  1.427  0.020  1.427
 FV9  PBB  OBC  single    1.598  0.020  1.598
 FV9  C4   C5   aromatic  1.414  0.020  1.414
 FV9  C4   N3   aromatic  1.321  0.020  1.321
 FV9  CAJ  SAK  aromatic  1.731  0.020  1.731
 FV9  C5   C6   aromatic  1.393  0.020  1.393
 FV9  N3   C2   aromatic  1.335  0.020  1.335
 FV9  C6   SAK  aromatic  1.731  0.020  1.731
 FV9  C6   N1   aromatic  1.328  0.020  1.328
 FV9  C2   N1   aromatic  1.321  0.020  1.321
 FV9  C2   CAL  single    1.481  0.020  1.481
 FV9  CAM  CAL  aromatic  1.393  0.020  1.393
 FV9  CAM  CAN  aromatic  1.386  0.020  1.386
 FV9  CAL  CAQ  aromatic  1.394  0.020  1.394
 FV9  CAN  CAO  aromatic  1.384  0.020  1.384
 FV9  CAQ  CAP  aromatic  1.391  0.020  1.391
 FV9  CAO  CAP  aromatic  1.396  0.020  1.396
 FV9  OAU  CAS  double    1.218  0.020  1.218
 FV9  CAP  NAR  single    1.400  0.020  1.400
 FV9  CAS  NAR  single    1.358  0.020  1.358
 FV9  CAS  CAT  single    1.492  0.020  1.492
 FV9  CAZ  CAT  aromatic  1.394  0.020  1.394
 FV9  CAZ  CAY  aromatic  1.386  0.020  1.386
 FV9  CAT  CAV  aromatic  1.394  0.020  1.394
 FV9  CAY  CAX  aromatic  1.382  0.020  1.382
 FV9  CAV  CAW  aromatic  1.384  0.020  1.384
 FV9  CAX  CAW  aromatic  1.383  0.020  1.383
 FV9  CAX  FBA  single    1.338  0.020  1.338
 FV9  OBD  H1   single    0.850  0.020  0.980
 FV9  OBC  H2   single    0.850  0.020  0.980
 FV9  CAB  H3   single    0.970  0.020  1.090
 FV9  OBH  H4   single    0.850  0.020  0.980
 FV9  OBI  H5   single    0.850  0.020  0.980
 FV9  NAA  H6   single    0.860  0.020  1.020
 FV9  CAI  H7   single    0.930  0.020  1.080
 FV9  CAJ  H8   single    0.930  0.020  1.080
 FV9  CAQ  H9   single    0.930  0.020  1.080
 FV9  CAM  H10  single    0.930  0.020  1.080
 FV9  CAN  H11  single    0.930  0.020  1.080
 FV9  CAO  H12  single    0.930  0.020  1.080
 FV9  NAR  H13  single    0.860  0.020  1.020
 FV9  CAV  H14  single    0.930  0.020  1.080
 FV9  CAW  H15  single    0.930  0.020  1.080
 FV9  CAY  H16  single    0.930  0.020  1.080
 FV9  CAZ  H17  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
 FV9  H1   OBD  PBB  115.61  3.000
 FV9  CAB  PBB  OBC  105.77  3.000
 FV9  OBC  PBB  OBE  109.95  3.000
 FV9  CAB  PBB  OBE  114.56  3.000
 FV9  OBC  PBB  OBD  107.80  3.000
 FV9  OBE  PBB  OBD  117.82  3.000
 FV9  CAB  PBB  OBD   99.90  3.000
 FV9  H2   OBC  PBB  116.58  3.000
 FV9  H3   CAB  NAA  107.81  3.000
 FV9  H3   CAB  PBF  105.53  3.000
 FV9  NAA  CAB  PBF  110.15  3.000
 FV9  H3   CAB  PBB  108.58  3.000
 FV9  PBF  CAB  PBB  117.18  3.000
 FV9  NAA  CAB  PBB  107.25  3.000
 FV9  OBG  PBF  OBI  116.75  3.000
 FV9  OBI  PBF  OBH  108.02  3.000
 FV9  OBG  PBF  OBH  110.61  3.000
 FV9  OBI  PBF  CAB  100.32  3.000
 FV9  OBH  PBF  CAB  106.81  3.000
 FV9  OBG  PBF  CAB  113.47  3.000
 FV9  H4   OBH  PBF  115.74  3.000
 FV9  H5   OBI  PBF  114.74  3.000
 FV9  H6   NAA  C4   118.70  3.000
 FV9  H6   NAA  CAB  118.00  3.000
 FV9  C4   NAA  CAB  122.85  3.000
 FV9  C5   C4   N3   120.24  3.000
 FV9  N3   C4   NAA  118.74  3.000
 FV9  C5   C4   NAA  121.01  3.000
 FV9  C2   N3   C4   119.50  3.000
 FV9  C6   C5   CAI  112.87  3.000
 FV9  C6   C5   C4   114.42  3.000
 FV9  CAI  C5   C4   132.72  3.000
 FV9  H7   CAI  CAJ  122.89  3.000
 FV9  H7   CAI  C5   125.30  3.000
 FV9  CAJ  CAI  C5   111.80  3.000
 FV9  H8   CAJ  SAK  119.44  3.000
 FV9  H8   CAJ  CAI  127.30  3.000
 FV9  SAK  CAJ  CAI  113.26  3.000
 FV9  C6   SAK  CAJ   91.11  3.000
 FV9  N1   C6   SAK  123.56  3.000
 FV9  N1   C6   C5   125.48  3.000
 FV9  SAK  C6   C5   110.96  3.000
 FV9  C2   N1   C6   114.78  3.000
 FV9  CAL  C2   N1   117.66  3.000
 FV9  CAL  C2   N3   116.76  3.000
 FV9  N1   C2   N3   125.59  3.000
 FV9  CAM  CAL  CAQ  120.06  3.000
 FV9  CAQ  CAL  C2   119.47  3.000
 FV9  CAM  CAL  C2   120.47  3.000
 FV9  H9   CAQ  CAP  121.00  3.000
 FV9  H9   CAQ  CAL  118.85  3.000
 FV9  CAP  CAQ  CAL  120.15  3.000
 FV9  H10  CAM  CAN  120.38  3.000
 FV9  H10  CAM  CAL  120.03  3.000
 FV9  CAN  CAM  CAL  119.58  3.000
 FV9  H11  CAN  CAO  119.43  3.000
 FV9  H11  CAN  CAM  119.99  3.000
 FV9  CAO  CAN  CAM  120.57  3.000
 FV9  H12  CAO  CAP  119.91  3.000
 FV9  H12  CAO  CAN  119.90  3.000
 FV9  CAP  CAO  CAN  120.19  3.000
 FV9  NAR  CAP  CAO  117.17  3.000
 FV9  NAR  CAP  CAQ  123.37  3.000
 FV9  CAO  CAP  CAQ  119.44  3.000
 FV9  H13  NAR  CAS  116.74  3.000
 FV9  H13  NAR  CAP  114.66  3.000
 FV9  CAS  NAR  CAP  127.67  3.000
 FV9  CAT  CAS  OAU  121.22  3.000
 FV9  CAT  CAS  NAR  115.01  3.000
 FV9  OAU  CAS  NAR  123.76  3.000
 FV9  CAZ  CAT  CAV  119.10  3.000
 FV9  CAV  CAT  CAS  117.89  3.000
 FV9  CAZ  CAT  CAS  122.98  3.000
 FV9  H14  CAV  CAW  119.18  3.000
 FV9  H14  CAV  CAT  119.97  3.000
 FV9  CAW  CAV  CAT  120.85  3.000
 FV9  H15  CAW  CAX  120.52  3.000
 FV9  H15  CAW  CAV  120.97  3.000
 FV9  CAX  CAW  CAV  118.50  3.000
 FV9  CAY  CAX  FBA  118.83  3.000
 FV9  FBA  CAX  CAW  118.92  3.000
 FV9  CAY  CAX  CAW  122.25  3.000
 FV9  H16  CAY  CAZ  120.89  3.000
 FV9  H16  CAY  CAX  120.57  3.000
 FV9  CAZ  CAY  CAX  118.54  3.000
 FV9  H17  CAZ  CAY  118.12  3.000
 FV9  H17  CAZ  CAT  121.11  3.000
 FV9  CAY  CAZ  CAT  120.75  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
 FV9  CONST_01  CAJ  CAI  C5   C4   180.00   0.0  0
 FV9  CONST_02  SAK  C6   C5   C4   180.00   0.0  0
 FV9  CONST_03  N1   C6   C5   C4     0.00   0.0  0
 FV9  CONST_04  N1   C2   N3   C4     0.00   0.0  0
 FV9  CONST_05  CAL  C2   N3   C4   180.00   0.0  0
 FV9  CONST_06  CAI  C5   C4   N3   180.00   0.0  0
 FV9  CONST_07  C6   C5   C4   N3     0.00   0.0  0
 FV9  CONST_08  C6   N1   C2   N3     0.00   0.0  0
 FV9  CONST_09  CAM  CAL  C2   N3     0.00   0.0  0
 FV9  CONST_10  CAQ  CAL  C2   N3   180.00   0.0  0
 FV9  CONST_11  SAK  CAJ  CAI  C5     0.00   0.0  0
 FV9  CONST_12  C2   N3   C4   C5     0.00   0.0  0
 FV9  CONST_13  CAJ  SAK  C6   C5     0.00   0.0  0
 FV9  CONST_14  C2   N1   C6   C5     0.00   0.0  0
 FV9  CONST_15  C6   SAK  CAJ  CAI    0.00   0.0  0
 FV9  CONST_16  SAK  C6   C5   CAI    0.00   0.0  0
 FV9  CONST_17  N1   C6   C5   CAI  180.00   0.0  0
 FV9  CONST_18  C6   C5   CAI  CAJ    0.00   0.0  0
 FV9  CONST_19  N1   C6   SAK  CAJ  180.00   0.0  0
 FV9  CONST_20  C2   N1   C6   SAK  180.00   0.0  0
 FV9  CONST_21  CAL  C2   N1   C6   180.00   0.0  0
 FV9  CONST_22  CAM  CAL  C2   N1   180.00   0.0  0
 FV9  CONST_23  CAQ  CAL  C2   N1     0.00   0.0  0
 FV9  CONST_24  CAN  CAM  CAL  C2   180.00   0.0  0
 FV9  CONST_25  CAP  CAQ  CAL  C2   180.00   0.0  0
 FV9  CONST_26  CAO  CAN  CAM  CAL    0.00   0.0  0
 FV9  CONST_27  CAO  CAP  CAQ  CAL    0.00   0.0  0
 FV9  CONST_28  CAN  CAM  CAL  CAQ    0.00   0.0  0
 FV9  CONST_29  CAN  CAO  CAP  CAQ    0.00   0.0  0
 FV9  CONST_30  CAP  CAQ  CAL  CAM    0.00   0.0  0
 FV9  CONST_31  CAP  CAO  CAN  CAM    0.00   0.0  0
 FV9  CONST_32  CAX  CAY  CAZ  CAT    0.00   0.0  0
 FV9  CONST_33  CAX  CAW  CAV  CAT    0.00   0.0  0
 FV9  CONST_34  CAY  CAZ  CAT  CAV    0.00   0.0  0
 FV9  CONST_35  CAY  CAX  CAW  CAV    0.00   0.0  0
 FV9  CONST_36  CAZ  CAT  CAV  CAW    0.00   0.0  0
 FV9  CONST_37  CAZ  CAY  CAX  CAW    0.00   0.0  0
 FV9  CONST_38  CAI  C5   C4   NAA    0.00   0.0  0
 FV9  CONST_39  C6   C5   C4   NAA  180.00   0.0  0
 FV9  CONST_40  C2   N3   C4   NAA  180.00   0.0  0
 FV9  CONST_41  NAR  CAP  CAQ  CAL  180.00   0.0  0
 FV9  CONST_42  NAR  CAP  CAO  CAN  180.00   0.0  0
 FV9  CONST_43  CAY  CAZ  CAT  CAS  180.00   0.0  0
 FV9  CONST_44  CAW  CAV  CAT  CAS  180.00   0.0  0
 FV9  CONST_45  FBA  CAX  CAW  CAV  180.00   0.0  0
 FV9  CONST_46  CAZ  CAY  CAX  FBA  180.00   0.0  0
 FV9  CONST_47  H7   CAI  C5   C4     0.00   0.0  0
 FV9  CONST_48  H8   CAJ  CAI  C5   180.00   0.0  0
 FV9  CONST_49  H10  CAM  CAL  C2     0.00   0.0  0
 FV9  CONST_50  H9   CAQ  CAL  C2     0.00   0.0  0
 FV9  CONST_51  H11  CAN  CAM  CAL  180.00   0.0  0
 FV9  CONST_52  H12  CAO  CAP  CAQ  180.00   0.0  0
 FV9  CONST_53  H16  CAY  CAZ  CAT  180.00   0.0  0
 FV9  CONST_54  H15  CAW  CAV  CAT  180.00   0.0  0
 FV9  CONST_55  H17  CAZ  CAT  CAV  180.00   0.0  0
 FV9  CONST_56  H14  CAV  CAW  CAX  180.00   0.0  0
 FV9  CONST_57  CAT  CAS  NAR  CAP  180.00   0.0  0
 FV9  CONST_58  C5   C4   NAA  CAB  180.00   0.0  0
 FV9  CONST_59  N3   C4   NAA  CAB    0.00   0.0  0
 FV9  CONST_62  H6   NAA  C4   N3   180.00   0.0  0
 FV9  CONST_64  OAU  CAS  NAR  CAP    0.00   0.0  0
 FV9  Var_01    CAZ  CAT  CAS  NAR   28.61  30.0  2
 FV9  Var_02    C4   NAA  CAB  PBB  131.69  30.0  3
 FV9  Var_03    NAA  CAB  PBB  OBD  172.12  30.0  3
 FV9  Var_04    OBG  PBF  CAB  PBB  167.83  30.0  3

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
 FV9  plan-1  C2   0.020
 FV9  plan-1  CAL  0.020
 FV9  plan-1  CAQ  0.020
 FV9  plan-1  CAM  0.020
 FV9  plan-1  CAN  0.020
 FV9  plan-1  CAO  0.020
 FV9  plan-1  CAP  0.020
 FV9  plan-1  NAR  0.020
 FV9  plan-1  H9   0.020
 FV9  plan-1  H10  0.020
 FV9  plan-1  H11  0.020
 FV9  plan-1  H12  0.020
 FV9  plan-2  CAS  0.020
 FV9  plan-2  CAT  0.020
 FV9  plan-2  CAV  0.020
 FV9  plan-2  CAW  0.020
 FV9  plan-2  CAX  0.020
 FV9  plan-2  FBA  0.020
 FV9  plan-2  CAY  0.020
 FV9  plan-2  CAZ  0.020
 FV9  plan-2  H14  0.020
 FV9  plan-2  H15  0.020
 FV9  plan-2  H16  0.020
 FV9  plan-2  H17  0.020
 FV9  plan-3  NAA  0.020
 FV9  plan-3  C4   0.020
 FV9  plan-3  N3   0.020
 FV9  plan-3  C5   0.020
 FV9  plan-3  CAI  0.020
 FV9  plan-3  CAJ  0.020
 FV9  plan-3  SAK  0.020
 FV9  plan-3  C6   0.020
 FV9  plan-3  N1   0.020
 FV9  plan-3  C2   0.020
 FV9  plan-3  CAL  0.020
 FV9  plan-3  H7   0.020
 FV9  plan-3  H8   0.020
 FV9  plan-4  CAP  0.020
 FV9  plan-4  NAR  0.020
 FV9  plan-4  CAS  0.020
 FV9  plan-4  OAU  0.020
 FV9  plan-4  CAT  0.020
 FV9  plan-4  H13  0.020
 FV9  plan-5  CAB  0.020
 FV9  plan-5  NAA  0.020
 FV9  plan-5  C4   0.020
 FV9  plan-5  H6   0.020

