# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jun  4 04:22:27 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: [({4-[4-(cyclopropyloxy)phenyl]pyridin-2-yl}amino)methanediyl]bis(phosphonic acid)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)C(Nc1cc(ccn1)c2ccc(OC3CC3)cc2)[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
 YS1  YS1  '[({4-[4-(cyclopropyloxy)phenyl]pyridin-2-yl}amino)methanediyl]bis(phosphonic acid)'  ligand  44  26  .  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_YS1
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
 YS1  OAJ  O  O     0  -0.681  -4.2063   0.1505  -2.4406
 YS1  PAI  P  P     0   1.403  -4.2780   0.5992  -1.0362
 YS1  OAK  O  OH1   0  -0.753  -4.4762   2.1683  -0.7741
 YS1  OAL  O  OH1   0  -0.742  -5.4441  -0.1805  -0.2686
 YS1  CAH  C  CH1   0  -0.672  -2.7450   0.3336  -0.0683
 YS1  PAM  P  P     0   1.386  -2.6284   1.1548   1.5725
 YS1  OAN  O  OH1   0  -0.736  -2.4914   2.7281   1.3280
 YS1  OAP  O  OH1   0  -0.758  -4.1126   0.8718   2.1229
 YS1  OAO  O  O     0  -0.678  -1.5168   0.6567   2.4085
 YS1  NAG  N  NH1   0  -0.681  -2.5462  -1.0811   0.0496
 YS1  CAD  C  CR6   0   0.527  -1.3172  -1.6905   0.1129
 YS1  CAE  C  CR16  0  -0.460  -0.1190  -1.0213  -0.1582
 YS1  NAC  N  N     0  -0.464  -1.3572  -2.9817   0.4311
 YS1  CAB  C  CR16  0  -0.057  -0.2103  -3.6478   0.4727
 YS1  CAA  C  CR16  0  -0.420   1.0227  -3.0875   0.2052
 YS1  CAF  C  CR6   0   0.199   1.0742  -1.7286  -0.1212
 YS1  CAQ  C  CR6   0   0.066   2.3550  -1.0565  -0.4014
 YS1  CAV  C  CR16  0  -0.293   2.4386  -0.0159  -1.3305
 YS1  CAU  C  CR16  0  -0.333   3.6362   0.6219  -1.5867
 YS1  CAR  C  CR16  0  -0.294   3.5231  -1.4332   0.2566
 YS1  CAS  C  CR16  0  -0.346   4.7332  -0.7986   0.0168
 YS1  CAT  C  CR6   0   0.374   4.7949   0.2392  -0.9097
 YS1  OAW  O  O2    0  -0.467   5.9183   0.9189  -1.2190
 YS1  CAX  C  CH1   0  -0.009   7.0996   0.5889  -0.5485
 YS1  CAY  C  CH2   0  -0.521   8.0561   1.7034  -0.3320
 YS1  CAZ  C  CH2   0  -0.512   7.3184   1.1042   0.8346
 YS1  H1   H  HOH1  0   0.511  -5.1999   2.5914  -1.2590
 YS1  H2   H  HOH1  0   0.495  -5.5882   0.0828   0.6527
 YS1  H3   H  HCH1  0   0.349  -1.9595   0.7716  -0.6913
 YS1  H4   H  HOH1  0   0.495  -3.2026   3.1368   0.8135
 YS1  H5   H  HOH1  0   0.508  -4.2484   1.0458   3.0661
 YS1  H6   H  HNH1  0   0.394  -3.2917  -1.6229   0.4618
 YS1  H7   H  HCR6  0   0.265  -0.1032   0.0392  -0.3647
 YS1  H8   H  HCR6  0   0.262  -0.2809  -4.6989   0.7310
 YS1  H9   H  HCR6  0   0.259   1.9135  -3.6990   0.2376
 YS1  H10  H  HCR6  0   0.258   1.5594   0.2924  -1.8825
 YS1  H11  H  HCR6  0   0.267   3.6824   1.4203  -2.3165
 YS1  H12  H  HCR6  0   0.261   3.4968  -2.2237   0.9958
 YS1  H13  H  HCR6  0   0.282   5.6087  -1.1160   0.5657
 YS1  H14  H  HCH1  0   0.263   7.4967  -0.3911  -0.8014
 YS1  H15  H  HCH2  0   0.262   9.1108   1.4927  -0.4485
 YS1  H16  H  HCH2  0   0.263   7.7553   2.6922  -0.6548
 YS1  H17  H  HCH2  0   0.266   6.5304   1.6969   1.2822
 YS1  H18  H  HCH2  0   0.261   7.8591   0.4748   1.5295

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
 YS1  OAJ  PAI  double    1.476  0.020  1.476
 YS1  OAL  PAI  single    1.599  0.020  1.599
 YS1  PAI  OAK  single    1.603  0.020  1.603
 YS1  PAI  CAH  single    1.832  0.020  1.832
 YS1  CAB  NAC  aromatic  1.327  0.020  1.327
 YS1  CAB  CAA  aromatic  1.381  0.020  1.381
 YS1  NAC  CAD  aromatic  1.330  0.020  1.330
 YS1  CAA  CAF  aromatic  1.398  0.020  1.398
 YS1  OAO  PAM  double    1.477  0.020  1.477
 YS1  CAH  PAM  single    1.839  0.020  1.839
 YS1  CAH  NAG  single    1.433  0.020  1.433
 YS1  CAD  NAG  single    1.373  0.020  1.373
 YS1  CAD  CAE  aromatic  1.399  0.020  1.399
 YS1  CAF  CAE  aromatic  1.388  0.020  1.388
 YS1  CAF  CAQ  single    1.473  0.020  1.473
 YS1  PAM  OAP  single    1.608  0.020  1.608
 YS1  PAM  OAN  single    1.598  0.020  1.598
 YS1  CAQ  CAR  aromatic  1.393  0.020  1.393
 YS1  CAQ  CAV  aromatic  1.398  0.020  1.398
 YS1  CAR  CAS  aromatic  1.387  0.020  1.387
 YS1  CAV  CAU  aromatic  1.381  0.020  1.381
 YS1  CAS  CAT  aromatic  1.393  0.020  1.393
 YS1  CAU  CAT  aromatic  1.396  0.020  1.396
 YS1  CAT  OAW  single    1.349  0.020  1.349
 YS1  OAW  CAX  single    1.398  0.020  1.398
 YS1  CAX  CAY  single    1.485  0.020  1.485
 YS1  CAX  CAZ  single    1.492  0.020  1.492
 YS1  CAY  CAZ  single    1.505  0.020  1.505
 YS1  OAK  H1   single    0.850  0.020  0.980
 YS1  OAL  H2   single    0.850  0.020  0.980
 YS1  CAH  H3   single    0.970  0.020  1.090
 YS1  OAN  H4   single    0.850  0.020  0.980
 YS1  OAP  H5   single    0.850  0.020  0.980
 YS1  NAG  H6   single    0.890  0.020  1.040
 YS1  CAE  H7   single    0.930  0.020  1.080
 YS1  CAB  H8   single    0.930  0.020  1.080
 YS1  CAA  H9   single    0.930  0.020  1.080
 YS1  CAV  H10  single    0.930  0.020  1.080
 YS1  CAU  H11  single    0.930  0.020  1.080
 YS1  CAR  H12  single    0.930  0.020  1.080
 YS1  CAS  H13  single    0.930  0.020  1.080
 YS1  CAX  H14  single    0.970  0.020  1.090
 YS1  CAY  H15  single    0.970  0.020  1.090
 YS1  CAY  H16  single    0.970  0.020  1.090
 YS1  CAZ  H17  single    0.970  0.020  1.090
 YS1  CAZ  H18  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
 YS1  CAH  PAI  OAL  106.61  3.000
 YS1  CAH  PAI  OAK   99.15  3.000
 YS1  OAL  PAI  OAK  107.97  3.000
 YS1  CAH  PAI  OAJ  114.70  3.000
 YS1  OAK  PAI  OAJ  117.33  3.000
 YS1  OAL  PAI  OAJ  110.12  3.000
 YS1  H1   OAK  PAI  115.99  3.000
 YS1  H2   OAL  PAI  115.62  3.000
 YS1  H3   CAH  NAG  110.03  3.000
 YS1  H3   CAH  PAM  106.49  3.000
 YS1  NAG  CAH  PAM  111.01  3.000
 YS1  H3   CAH  PAI  104.00  3.000
 YS1  NAG  CAH  PAI  107.61  3.000
 YS1  PAM  CAH  PAI  117.37  3.000
 YS1  OAO  PAM  OAP  116.20  3.000
 YS1  OAP  PAM  OAN  107.74  3.000
 YS1  OAO  PAM  OAN  110.74  3.000
 YS1  OAN  PAM  CAH  107.97  3.000
 YS1  OAP  PAM  CAH   99.69  3.000
 YS1  OAO  PAM  CAH  113.71  3.000
 YS1  H4   OAN  PAM  115.72  3.000
 YS1  H5   OAP  PAM  115.53  3.000
 YS1  H6   NAG  CAD  113.82  3.000
 YS1  H6   NAG  CAH  117.44  3.000
 YS1  CAD  NAG  CAH  124.46  3.000
 YS1  NAC  CAD  CAE  122.44  3.000
 YS1  CAE  CAD  NAG  123.05  3.000
 YS1  NAC  CAD  NAG  114.51  3.000
 YS1  H7   CAE  CAF  119.52  3.000
 YS1  H7   CAE  CAD  121.27  3.000
 YS1  CAF  CAE  CAD  119.18  3.000
 YS1  CAB  NAC  CAD  117.95  3.000
 YS1  H8   CAB  CAA  119.84  3.000
 YS1  H8   CAB  NAC  115.96  3.000
 YS1  CAA  CAB  NAC  124.20  3.000
 YS1  H9   CAA  CAF  121.76  3.000
 YS1  H9   CAA  CAB  120.04  3.000
 YS1  CAF  CAA  CAB  118.19  3.000
 YS1  CAQ  CAF  CAA  121.31  3.000
 YS1  CAQ  CAF  CAE  120.66  3.000
 YS1  CAA  CAF  CAE  118.03  3.000
 YS1  CAR  CAQ  CAV  117.73  3.000
 YS1  CAV  CAQ  CAF  121.21  3.000
 YS1  CAR  CAQ  CAF  121.06  3.000
 YS1  H10  CAV  CAU  118.56  3.000
 YS1  H10  CAV  CAQ  120.15  3.000
 YS1  CAU  CAV  CAQ  121.28  3.000
 YS1  H11  CAU  CAT  119.60  3.000
 YS1  H11  CAU  CAV  120.18  3.000
 YS1  CAT  CAU  CAV  120.22  3.000
 YS1  H12  CAR  CAS  118.24  3.000
 YS1  H12  CAR  CAQ  119.99  3.000
 YS1  CAS  CAR  CAQ  121.75  3.000
 YS1  H13  CAS  CAT  121.39  3.000
 YS1  H13  CAS  CAR  118.97  3.000
 YS1  CAT  CAS  CAR  119.64  3.000
 YS1  OAW  CAT  CAS  124.40  3.000
 YS1  OAW  CAT  CAU  116.23  3.000
 YS1  CAS  CAT  CAU  119.37  3.000
 YS1  CAX  OAW  CAT  118.35  3.000
 YS1  H14  CAX  CAZ  118.26  3.000
 YS1  H14  CAX  CAY  118.38  3.000
 YS1  CAZ  CAX  CAY   60.73  3.000
 YS1  H14  CAX  OAW  114.19  3.000
 YS1  CAZ  CAX  OAW  119.15  3.000
 YS1  CAY  CAX  OAW  115.93  3.000
 YS1  H16  CAY  H15  114.63  3.000
 YS1  H16  CAY  CAZ  117.29  3.000
 YS1  H15  CAY  CAZ  118.94  3.000
 YS1  H16  CAY  CAX  117.59  3.000
 YS1  H15  CAY  CAX  117.78  3.000
 YS1  CAZ  CAY  CAX   59.88  3.000
 YS1  H18  CAZ  H17  114.60  3.000
 YS1  H18  CAZ  CAY  118.98  3.000
 YS1  H17  CAZ  CAY  117.34  3.000
 YS1  H18  CAZ  CAX  117.88  3.000
 YS1  H17  CAZ  CAX  117.74  3.000
 YS1  CAY  CAZ  CAX   59.39  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
 YS1  CONST_01  CAA  CAB  NAC  CAD     0.00   0.0  0
 YS1  CONST_02  CAA  CAF  CAE  CAD     0.00   0.0  0
 YS1  CONST_03  CAQ  CAF  CAE  CAD   180.00   0.0  0
 YS1  CONST_04  CAB  NAC  CAD  CAE     0.00   0.0  0
 YS1  CONST_05  CAB  CAA  CAF  CAE     0.00   0.0  0
 YS1  CONST_08  CAF  CAA  CAB  NAC     0.00   0.0  0
 YS1  CONST_09  CAF  CAE  CAD  NAC     0.00   0.0  0
 YS1  CONST_10  CAQ  CAF  CAA  CAB   180.00   0.0  0
 YS1  CONST_13  CAS  CAR  CAQ  CAF   180.00   0.0  0
 YS1  CONST_14  CAU  CAV  CAQ  CAF   180.00   0.0  0
 YS1  CONST_15  CAT  CAS  CAR  CAQ     0.00   0.0  0
 YS1  CONST_16  CAT  CAU  CAV  CAQ     0.00   0.0  0
 YS1  CONST_17  CAS  CAR  CAQ  CAV     0.00   0.0  0
 YS1  CONST_18  CAS  CAT  CAU  CAV     0.00   0.0  0
 YS1  CONST_19  CAR  CAQ  CAV  CAU     0.00   0.0  0
 YS1  CONST_20  CAR  CAS  CAT  CAU     0.00   0.0  0
 YS1  CONST_21  CAB  NAC  CAD  NAG   180.00   0.0  0
 YS1  CONST_22  CAF  CAE  CAD  NAG   180.00   0.0  0
 YS1  CONST_23  OAW  CAT  CAU  CAV   180.00   0.0  0
 YS1  CONST_24  OAW  CAT  CAS  CAR   180.00   0.0  0
 YS1  CONST_25  H8   CAB  NAC  CAD   180.00   0.0  0
 YS1  CONST_26  H9   CAA  CAF  CAE   180.00   0.0  0
 YS1  CONST_27  H7   CAE  CAD  NAC   180.00   0.0  0
 YS1  CONST_28  H12  CAR  CAQ  CAF     0.00   0.0  0
 YS1  CONST_29  H10  CAV  CAQ  CAF     0.00   0.0  0
 YS1  CONST_30  H13  CAS  CAR  CAQ   180.00   0.0  0
 YS1  CONST_31  H11  CAU  CAV  CAQ   180.00   0.0  0
 YS1  CONST_32  NAC  CAD  NAG  CAH   180.00   0.0  0
 YS1  CONST_33  CAE  CAD  NAG  CAH     0.00   0.0  0
 YS1  CONST_34  H6   NAG  CAD  CAE   180.00   0.0  0
 YS1  Var_01    CAY  CAX  OAW  CAT  -148.36  30.0  3
 YS1  Var_02    CAZ  CAY  CAX  OAW   110.38  30.0  1
 YS1  Var_03    H17  CAZ  CAY  CAX  -107.63  30.0  1
 YS1  Var_04    CAD  NAG  CAH  PAI   147.97  30.0  3
 YS1  Var_05    PAM  CAH  PAI  OAJ   168.19  30.0  3
 YS1  Var_06    OAO  PAM  CAH  PAI   167.05  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
 YS1  chir_01  CAX  OAW  CAY  CAZ  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
 YS1  plan-1  NAG  0.020
 YS1  plan-1  CAD  0.020
 YS1  plan-1  CAE  0.020
 YS1  plan-1  NAC  0.020
 YS1  plan-1  CAB  0.020
 YS1  plan-1  CAA  0.020
 YS1  plan-1  CAF  0.020
 YS1  plan-1  CAQ  0.020
 YS1  plan-1  H7   0.020
 YS1  plan-1  H8   0.020
 YS1  plan-1  H9   0.020
 YS1  plan-2  CAF  0.020
 YS1  plan-2  CAQ  0.020
 YS1  plan-2  CAV  0.020
 YS1  plan-2  CAU  0.020
 YS1  plan-2  CAR  0.020
 YS1  plan-2  CAS  0.020
 YS1  plan-2  CAT  0.020
 YS1  plan-2  OAW  0.020
 YS1  plan-2  H10  0.020
 YS1  plan-2  H11  0.020
 YS1  plan-2  H12  0.020
 YS1  plan-2  H13  0.020
 YS1  plan-3  CAH  0.020
 YS1  plan-3  NAG  0.020
 YS1  plan-3  CAD  0.020
 YS1  plan-3  H6   0.020

