# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jun  4 16:03:01 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: ({[6-(4-cyclopropylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino}methanediyl)bis(phosphonic acid)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)C(Nc1ncnc2sc(cc12)c3ccc(cc3)C4CC4)[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
 YL2  YL2  '({[6-(4-cyclopropylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino}methanediyl)bis(phosphonic acid)'  ligand  45  28  .  2022-11-18  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_YL2
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
 YL2  OAU  O  OH1   0  -0.730   2.4692  -2.4049   1.9510
 YL2  PAS  P  P     0   1.385   3.6802  -2.0903   0.9548
 YL2  OAV  O  OH1   0  -0.730   4.9999  -1.9373   1.8341
 YL2  OAW  O  O     0  -0.689   3.6878  -3.0631  -0.1563
 YL2  CAR  C  CH1   0  -0.673   3.4282  -0.3473   0.4405
 YL2  PAT  P  P     0   1.370   4.6133   0.1107  -0.9000
 YL2  OAX  O  OH1   0  -0.740   3.7301  -0.2557  -2.1850
 YL2  OAZ  O  OH1   0  -0.765   4.7070   1.6958  -0.8012
 YL2  OAY  O  O     0  -0.693   5.9404  -0.5403  -0.8171
 YL2  NAJ  N  NH1   0  -0.675   2.0406  -0.1363   0.1140
 YL2  C4   C  CR6   0   0.608   1.4571   1.0739   0.0602
 YL2  N3   N  N     0  -0.579   2.2130   2.1681   0.1238
 YL2  C2   C  CR16  0   0.091   1.6204   3.3674   0.1054
 YL2  N1   N  N     0  -0.424   0.3356   3.6094   0.0164
 YL2  C6   C  CR56  0  -0.020  -0.4195   2.5126  -0.0594
 YL2  SAE  S  S2    0   0.240  -2.1412   2.5485  -0.1602
 YL2  C5   C  CR56  0   0.059   0.0530   1.2043  -0.0449
 YL2  CAC  C  CR15  0  -0.274  -0.9899   0.2374  -0.0959
 YL2  CAD  C  CR5   0  -0.197  -2.2254   0.8041  -0.1609
 YL2  CAK  C  CR6   0   0.125  -3.5190   0.1297  -0.2134
 YL2  CAP  C  CR16  0  -0.306  -3.6100  -1.1890  -0.6626
 YL2  CAO  C  CR16  0  -0.303  -4.8272  -1.8465  -0.6844
 YL2  CAL  C  CR16  0  -0.299  -4.6939   0.7642   0.1971
 YL2  CAM  C  CR16  0  -0.337  -5.9095   0.1045   0.1661
 YL2  CAN  C  CR6   0   0.215  -6.0019  -1.2174  -0.2708
 YL2  CAQ  C  CH1   0  -0.370  -7.2817  -1.9589  -0.3106
 YL2  CBA  C  CH2   0  -0.476  -8.3599  -1.7130   0.7116
 YL2  CBB  C  CH2   0  -0.474  -8.5677  -1.2755  -0.6968
 YL2  H1   H  HOH1  0   0.498   2.4180  -1.8682   2.7534
 YL2  H2   H  HOH1  0   0.506   5.5170  -2.7500   1.9315
 YL2  H3   H  HCH1  0   0.354   3.6901   0.2758   1.3039
 YL2  H4   H  HOH1  0   0.499   4.2105  -0.2051  -3.0234
 YL2  H5   H  HOH1  0   0.497   3.8558   2.0708  -0.4387
 YL2  H6   H  HNH1  0   0.426   1.4889  -0.9261  -0.1811
 YL2  H7   H  HCR6  0   0.278   2.2851   4.2207   0.1625
 YL2  H8   H  HCR5  0   0.277  -0.8407  -0.8326  -0.0584
 YL2  H9   H  HCR6  0   0.258  -2.7256  -1.7072  -1.0112
 YL2  H10  H  HCR6  0   0.256  -4.8666  -2.8699  -1.0378
 YL2  H11  H  HCR6  0   0.255  -4.6683   1.7824   0.5675
 YL2  H12  H  HCR6  0   0.256  -6.7931   0.6350   0.5001
 YL2  H13  H  HCH1  0   0.264  -7.1797  -2.9855  -0.6436
 YL2  H14  H  HCH2  0   0.263  -8.9070  -2.5742   1.0726
 YL2  H15  H  HCH2  0   0.255  -8.1774  -0.9552   1.4640
 YL2  H16  H  HCH2  0   0.255  -8.5245  -0.2159  -0.9172
 YL2  H17  H  HCH2  0   0.263  -9.2600  -1.8310  -1.3161

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
 YL2  OAW  PAS  double    1.477  0.020  1.477
 YL2  OAU  PAS  single    1.599  0.020  1.599
 YL2  C2   N1   aromatic  1.310  0.020  1.310
 YL2  C2   N3   aromatic  1.338  0.020  1.338
 YL2  PAS  OAV  single    1.593  0.020  1.593
 YL2  PAS  CAR  single    1.835  0.020  1.835
 YL2  N1   C6   aromatic  1.334  0.020  1.334
 YL2  N3   C4   aromatic  1.331  0.020  1.331
 YL2  C6   SAE  aromatic  1.725  0.020  1.725
 YL2  C6   C5   aromatic  1.391  0.020  1.391
 YL2  SAE  CAD  aromatic  1.746  0.020  1.746
 YL2  CAR  NAJ  single    1.441  0.020  1.441
 YL2  CAR  PAT  single    1.847  0.020  1.847
 YL2  C4   C5   aromatic  1.414  0.020  1.414
 YL2  C4   NAJ  single    1.345  0.020  1.345
 YL2  C5   CAC  aromatic  1.423  0.020  1.423
 YL2  OAY  PAT  double    1.480  0.020  1.480
 YL2  CAD  CAC  aromatic  1.361  0.020  1.361
 YL2  CAD  CAK  single    1.460  0.020  1.460
 YL2  CAP  CAO  aromatic  1.384  0.020  1.384
 YL2  CAP  CAK  aromatic  1.396  0.020  1.396
 YL2  PAT  OAX  single    1.602  0.020  1.602
 YL2  PAT  OAZ  single    1.591  0.020  1.591
 YL2  CAO  CAN  aromatic  1.395  0.020  1.395
 YL2  CAK  CAL  aromatic  1.397  0.020  1.397
 YL2  CAN  CAQ  single    1.480  0.020  1.480
 YL2  CAN  CAM  aromatic  1.395  0.020  1.395
 YL2  CAL  CAM  aromatic  1.383  0.020  1.383
 YL2  CAQ  CBB  single    1.507  0.020  1.507
 YL2  CAQ  CBA  single    1.506  0.020  1.506
 YL2  CBB  CBA  single    1.489  0.020  1.489
 YL2  OAU  H1   single    0.850  0.020  0.980
 YL2  OAV  H2   single    0.850  0.020  0.980
 YL2  CAR  H3   single    0.970  0.020  1.090
 YL2  OAX  H4   single    0.850  0.020  0.980
 YL2  OAZ  H5   single    0.850  0.020  0.980
 YL2  NAJ  H6   single    0.860  0.020  1.020
 YL2  C2   H7   single    0.930  0.020  1.080
 YL2  CAC  H8   single    0.930  0.020  1.080
 YL2  CAP  H9   single    0.930  0.020  1.080
 YL2  CAO  H10  single    0.930  0.020  1.080
 YL2  CAL  H11  single    0.930  0.020  1.080
 YL2  CAM  H12  single    0.930  0.020  1.080
 YL2  CAQ  H13  single    0.970  0.020  1.090
 YL2  CBA  H14  single    0.970  0.020  1.090
 YL2  CBA  H15  single    0.970  0.020  1.090
 YL2  CBB  H16  single    0.970  0.020  1.090
 YL2  CBB  H17  single    0.970  0.020  1.090

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
 YL2  H1   OAU  PAS  116.61  3.000
 YL2  CAR  PAS  OAW  114.56  3.000
 YL2  CAR  PAS  OAV  100.21  3.000
 YL2  OAW  PAS  OAV  118.31  3.000
 YL2  CAR  PAS  OAU  104.92  3.000
 YL2  OAV  PAS  OAU  107.60  3.000
 YL2  OAW  PAS  OAU  110.06  3.000
 YL2  H2   OAV  PAS  114.67  3.000
 YL2  H3   CAR  NAJ  108.97  3.000
 YL2  H3   CAR  PAT  106.10  3.000
 YL2  NAJ  CAR  PAT  114.66  3.000
 YL2  H3   CAR  PAS  106.64  3.000
 YL2  PAT  CAR  PAS  110.54  3.000
 YL2  NAJ  CAR  PAS  109.57  3.000
 YL2  OAY  PAT  OAZ  112.45  3.000
 YL2  OAZ  PAT  OAX  108.07  3.000
 YL2  OAY  PAT  OAX  116.02  3.000
 YL2  OAZ  PAT  CAR  103.87  3.000
 YL2  OAX  PAT  CAR   99.88  3.000
 YL2  OAY  PAT  CAR  115.18  3.000
 YL2  H4   OAX  PAT  114.16  3.000
 YL2  H5   OAZ  PAT  110.28  3.000
 YL2  H6   NAJ  C4   117.14  3.000
 YL2  H6   NAJ  CAR  118.60  3.000
 YL2  C4   NAJ  CAR  123.97  3.000
 YL2  C5   C4   N3   119.44  3.000
 YL2  C5   C4   NAJ  121.12  3.000
 YL2  N3   C4   NAJ  119.43  3.000
 YL2  C2   N3   C4   118.99  3.000
 YL2  H7   C2   N1   117.37  3.000
 YL2  H7   C2   N3   115.70  3.000
 YL2  N1   C2   N3   126.92  3.000
 YL2  C6   N1   C2   114.02  3.000
 YL2  C5   C6   SAE  111.05  3.000
 YL2  C5   C6   N1   125.49  3.000
 YL2  SAE  C6   N1   123.45  3.000
 YL2  CAD  SAE  C6    91.56  3.000
 YL2  CAC  C5   C6   112.94  3.000
 YL2  CAC  C5   C4   131.89  3.000
 YL2  C6   C5   C4   115.13  3.000
 YL2  H8   CAC  CAD  122.63  3.000
 YL2  H8   CAC  C5   124.76  3.000
 YL2  CAD  CAC  C5   112.59  3.000
 YL2  CAK  CAD  CAC  127.87  3.000
 YL2  CAK  CAD  SAE  120.28  3.000
 YL2  CAC  CAD  SAE  111.85  3.000
 YL2  CAL  CAK  CAP  117.95  3.000
 YL2  CAL  CAK  CAD  121.66  3.000
 YL2  CAP  CAK  CAD  120.38  3.000
 YL2  H9   CAP  CAO  119.09  3.000
 YL2  H9   CAP  CAK  120.16  3.000
 YL2  CAO  CAP  CAK  120.75  3.000
 YL2  H10  CAO  CAN  119.47  3.000
 YL2  H10  CAO  CAP  119.08  3.000
 YL2  CAN  CAO  CAP  121.45  3.000
 YL2  H11  CAL  CAM  118.46  3.000
 YL2  H11  CAL  CAK  120.48  3.000
 YL2  CAM  CAL  CAK  121.05  3.000
 YL2  H12  CAM  CAN  120.43  3.000
 YL2  H12  CAM  CAL  118.44  3.000
 YL2  CAN  CAM  CAL  121.13  3.000
 YL2  CAQ  CAN  CAM  122.71  3.000
 YL2  CAM  CAN  CAO  117.66  3.000
 YL2  CAQ  CAN  CAO  119.62  3.000
 YL2  H13  CAQ  CBB  115.54  3.000
 YL2  H13  CAQ  CBA  115.50  3.000
 YL2  CBB  CAQ  CBA   59.26  3.000
 YL2  H13  CAQ  CAN  113.67  3.000
 YL2  CBA  CAQ  CAN  121.28  3.000
 YL2  CBB  CAQ  CAN  121.19  3.000
 YL2  H15  CBA  H14  114.22  3.000
 YL2  H15  CBA  CBB  118.34  3.000
 YL2  H14  CBA  CBB  118.59  3.000
 YL2  H15  CBA  CAQ  117.71  3.000
 YL2  H14  CBA  CAQ  117.28  3.000
 YL2  CBB  CBA  CAQ   60.39  3.000
 YL2  H17  CBB  H16  114.28  3.000
 YL2  H17  CBB  CBA  118.66  3.000
 YL2  H16  CBB  CBA  118.31  3.000
 YL2  H17  CBB  CAQ  117.38  3.000
 YL2  H16  CBB  CAQ  117.50  3.000
 YL2  CBA  CBB  CAQ   60.35  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
 YL2  CONST_01  N1   C2   N3   C4      0.00   0.0  0
 YL2  CONST_02  N1   C6   C5   C4      0.00   0.0  0
 YL2  CONST_03  SAE  C6   C5   C4    180.00   0.0  0
 YL2  CONST_04  CAD  CAC  C5   C4    180.00   0.0  0
 YL2  CONST_05  C6   N1   C2   N3      0.00   0.0  0
 YL2  CONST_06  C6   C5   C4   N3      0.00   0.0  0
 YL2  CONST_07  CAC  C5   C4   N3    180.00   0.0  0
 YL2  CONST_08  SAE  C6   N1   C2    180.00   0.0  0
 YL2  CONST_09  C5   C6   N1   C2      0.00   0.0  0
 YL2  CONST_10  C5   C4   N3   C2      0.00   0.0  0
 YL2  CONST_11  CAD  SAE  C6   N1    180.00   0.0  0
 YL2  CONST_12  CAC  C5   C6   N1    180.00   0.0  0
 YL2  CONST_13  CAC  CAD  SAE  C6      0.00   0.0  0
 YL2  CONST_14  CAK  CAD  SAE  C6    180.00   0.0  0
 YL2  CONST_15  CAD  CAC  C5   C6      0.00   0.0  0
 YL2  CONST_16  CAC  C5   C6   SAE     0.00   0.0  0
 YL2  CONST_17  C5   CAC  CAD  SAE     0.00   0.0  0
 YL2  CONST_20  CAD  SAE  C6   C5      0.00   0.0  0
 YL2  CONST_21  CAK  CAD  CAC  C5    180.00   0.0  0
 YL2  CONST_24  CAO  CAP  CAK  CAD   180.00   0.0  0
 YL2  CONST_25  CAM  CAL  CAK  CAD   180.00   0.0  0
 YL2  CONST_26  CAN  CAO  CAP  CAK     0.00   0.0  0
 YL2  CONST_27  CAN  CAM  CAL  CAK     0.00   0.0  0
 YL2  CONST_28  CAM  CAN  CAO  CAP     0.00   0.0  0
 YL2  CONST_29  CAM  CAL  CAK  CAP     0.00   0.0  0
 YL2  CONST_30  CAL  CAK  CAP  CAO     0.00   0.0  0
 YL2  CONST_31  CAL  CAM  CAN  CAO     0.00   0.0  0
 YL2  CONST_32  CAQ  CAN  CAO  CAP   180.00   0.0  0
 YL2  CONST_33  CAQ  CAN  CAM  CAL   180.00   0.0  0
 YL2  CONST_34  C2   N3   C4   NAJ   180.00   0.0  0
 YL2  CONST_35  C6   C5   C4   NAJ   180.00   0.0  0
 YL2  CONST_36  CAC  C5   C4   NAJ     0.00   0.0  0
 YL2  CONST_37  H7   C2   N3   C4    180.00   0.0  0
 YL2  CONST_38  H8   CAC  C5   C4      0.00   0.0  0
 YL2  CONST_39  H9   CAP  CAK  CAD     0.00   0.0  0
 YL2  CONST_40  H11  CAL  CAK  CAD     0.00   0.0  0
 YL2  CONST_41  H10  CAO  CAP  CAK   180.00   0.0  0
 YL2  CONST_42  H12  CAM  CAL  CAK   180.00   0.0  0
 YL2  CONST_43  N3   C4   NAJ  CAR     0.00   0.0  0
 YL2  CONST_44  C5   C4   NAJ  CAR   180.00   0.0  0
 YL2  Var_01    CBB  CAQ  CAN  CAO  -142.65  30.0  2
 YL2  Var_02    CBA  CBB  CAQ  CAN  -110.25  30.0  1
 YL2  Var_03    C4   NAJ  CAR  PAS   160.98  30.0  3
 YL2  Var_04    NAJ  CAR  PAS  OAU   -44.85  30.0  3
 YL2  Var_05    OAY  PAT  CAR  PAS   -33.59  30.0  3

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
 YL2  chir_01  CAQ  CAN  CBB  CBA  both

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
 YL2  plan-1  CAD  0.020
 YL2  plan-1  CAK  0.020
 YL2  plan-1  CAP  0.020
 YL2  plan-1  CAO  0.020
 YL2  plan-1  CAL  0.020
 YL2  plan-1  CAM  0.020
 YL2  plan-1  CAN  0.020
 YL2  plan-1  CAQ  0.020
 YL2  plan-1  H9   0.020
 YL2  plan-1  H10  0.020
 YL2  plan-1  H11  0.020
 YL2  plan-1  H12  0.020
 YL2  plan-2  NAJ  0.020
 YL2  plan-2  C4   0.020
 YL2  plan-2  N3   0.020
 YL2  plan-2  C2   0.020
 YL2  plan-2  N1   0.020
 YL2  plan-2  C6   0.020
 YL2  plan-2  SAE  0.020
 YL2  plan-2  C5   0.020
 YL2  plan-2  CAC  0.020
 YL2  plan-2  CAD  0.020
 YL2  plan-2  CAK  0.020
 YL2  plan-2  H7   0.020
 YL2  plan-2  H8   0.020
 YL2  plan-3  CAR  0.020
 YL2  plan-3  NAJ  0.020
 YL2  plan-3  C4   0.020
 YL2  plan-3  H6   0.020

