# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 13:45:36 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: {[(2R)-2-[(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)methyl]-3-(2-phosphonoethoxy)propoxy]methyl}phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(C[C@H](COCC[P](O)(O)=O)COC[P](O)(O)=O)cnc2C(=O)N1
#
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
 9YP  9YP  '{[(2R)-2-[(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)methyl]-3-(2-phosphonoethoxy)propoxy]methyl}phosphonic acid'  ligand  49  28  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9YP
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
 9YP  OAE  O  OH1   0  -0.743   6.2179  -1.7652  -1.2116
 9YP  PBA  P  P     0   1.354   5.3576  -2.0081   0.1228
 9YP  OAF  O  O     0  -0.716   5.3704  -3.3852   0.6713
 9YP  OAC  O  OH1   0  -0.750   5.9282  -0.9962   1.2388
 9YP  CAL  C  CH2   0  -0.792   3.7500  -1.3801  -0.3888
 9YP  CAK  C  CH2   0  -0.123   2.7449  -1.3927   0.7513
 9YP  OAS  O  O2    0  -0.470   1.5151  -0.9443   0.2484
 9YP  CAM  C  CH2   0  -0.110   0.5186  -0.8917   1.2319
 9YP  CAY  C  CH1   0  -0.356  -0.7483  -0.2544   0.6757
 9YP  CAN  C  CH2   0  -0.125  -0.5437   1.1945   0.2608
 9YP  OAT  O  O2    0  -0.475   0.1616   1.2556  -0.9604
 9YP  CAO  C  CH2   0  -0.461   0.5635   2.5496  -1.3079
 9YP  PBB  P  P     0   1.358   2.2129   2.9208  -0.6173
 9YP  OAG  O  OH1   0  -0.750   2.3826   4.4263  -1.1599
 9YP  OAH  O  O     0  -0.704   2.3978   2.7219   0.8387
 9YP  OAD  O  OH1   0  -0.741   3.2763   2.0206  -1.4220
 9YP  CAP  C  CH2   0  -0.313  -1.8176  -0.3435   1.7700
 9YP  NAZ  N  NR5   0  -0.495  -3.1290   0.0777   1.3290
 9YP  CAW  C  CR56  0   0.499  -3.9624  -0.6103   0.5068
 9YP  CAJ  N  N     0  -0.511  -3.7351  -1.8251  -0.0133
 9YP  CAU  C  CR6   0   0.682  -4.7166  -2.2531  -0.7669
 9YP  NAA  N  NH2   0  -0.831  -4.6186  -3.4402  -1.3861
 9YP  NAR  N  NR16  0  -0.726  -5.8511  -1.5276  -0.9949
 9YP  CAV  C  CR6   0   0.502  -6.1425  -0.2612  -0.4719
 9YP  OAB  O  O     0  -0.475  -7.1959   0.2929  -0.7387
 9YP  CAX  C  CR56  0  -0.084  -5.0727   0.1997   0.3483
 9YP  NAQ  N  N     0  -0.443  -4.9291   1.3629   1.0589
 9YP  CAI  C  CR15  0   0.080  -3.7659   1.2549   1.6251
 9YP  H1   H  HOH1  0   0.495   7.1052  -2.1495  -1.1862
 9YP  H2   H  HOH1  0   0.488   6.0161  -0.0747   0.9633
 9YP  H3   H  HCH2  0   0.296   3.8529  -0.3673  -0.7846
 9YP  H4   H  HCH2  0   0.291   3.3984  -2.0157  -1.2058
 9YP  H5   H  HCH2  0   0.209   2.6536  -2.4065   1.1651
 9YP  H6   H  HCH2  0   0.208   3.0863  -0.7426   1.5679
 9YP  H7   H  HCH2  0   0.210   0.2869  -1.9028   1.5997
 9YP  H8   H  HCH2  0   0.198   0.8606  -0.3093   2.1018
 9YP  H9   H  HCH1  0   0.261  -1.0947  -0.8368  -0.1853
 9YP  H10  H  HCH2  0   0.221  -1.5132   1.6973   0.1373
 9YP  H11  H  HCH2  0   0.215  -0.0105   1.7230   1.0600
 9YP  H12  H  HCH2  0   0.285   0.6079   2.6219  -2.3984
 9YP  H13  H  HCH2  0   0.257  -0.1438   3.3185  -0.9708
 9YP  H14  H  HOH1  0   0.495   3.1464   4.8990  -0.8016
 9YP  H15  H  HOH1  0   0.488   3.2595   2.1143  -2.3832
 9YP  H16  H  HCH2  0   0.283  -1.8925  -1.3696   2.1316
 9YP  H17  H  HCH2  0   0.277  -1.5440   0.2753   2.6263
 9YP  H18  H  HNH2  0   0.411  -3.8818  -4.0556  -1.0851
 9YP  H19  H  HNH2  0   0.413  -5.4340  -3.8855  -1.7725
 9YP  H20  H  HNR6  0   0.425  -6.5601  -1.9256  -1.5976
 9YP  H21  H  HCR5  0   0.292  -3.3105   1.9868   2.2765

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
 9YP  OAB  CAV  double    1.220  0.020  1.220
 9YP  OAH  PBB  double    1.481  0.020  1.481
 9YP  NAQ  CAI  aromatic  1.298  0.020  1.298
 9YP  NAQ  CAX  aromatic  1.371  0.020  1.371
 9YP  OAD  PBB  single    1.609  0.020  1.609
 9YP  CAV  CAX  single    1.425  0.020  1.425
 9YP  CAV  NAR  single    1.401  0.020  1.401
 9YP  PBB  CAO  single    1.826  0.020  1.826
 9YP  PBB  OAG  single    1.609  0.020  1.609
 9YP  CAI  NAZ  aromatic  1.371  0.020  1.371
 9YP  CAX  CAW  aromatic  1.383  0.020  1.383
 9YP  CAO  OAT  single    1.399  0.020  1.399
 9YP  NAR  CAU  single    1.366  0.020  1.366
 9YP  NAZ  CAW  aromatic  1.358  0.020  1.358
 9YP  NAZ  CAP  single    1.446  0.020  1.446
 9YP  CAW  CAJ  single    1.341  0.020  1.341
 9YP  CAN  OAT  single    1.412  0.020  1.412
 9YP  CAN  CAY  single    1.521  0.020  1.521
 9YP  CAU  CAJ  double    1.309  0.020  1.309
 9YP  CAU  NAA  single    1.342  0.020  1.342
 9YP  CAP  CAY  single    1.533  0.020  1.533
 9YP  CAY  CAM  single    1.523  0.020  1.523
 9YP  CAM  OAS  single    1.401  0.020  1.401
 9YP  OAS  CAK  single    1.402  0.020  1.402
 9YP  CAK  CAL  single    1.520  0.020  1.520
 9YP  OAF  PBA  double    1.482  0.020  1.482
 9YP  CAL  PBA  single    1.800  0.020  1.800
 9YP  OAE  PBA  single    1.606  0.020  1.606
 9YP  PBA  OAC  single    1.611  0.020  1.611
 9YP  OAE  H1   single    0.850  0.020  0.980
 9YP  OAC  H2   single    0.850  0.020  0.980
 9YP  CAL  H3   single    0.970  0.020  1.090
 9YP  CAL  H4   single    0.970  0.020  1.090
 9YP  CAK  H5   single    0.970  0.020  1.090
 9YP  CAK  H6   single    0.970  0.020  1.090
 9YP  CAM  H7   single    0.970  0.020  1.090
 9YP  CAM  H8   single    0.970  0.020  1.090
 9YP  CAY  H9   single    0.970  0.020  1.090
 9YP  CAN  H10  single    0.970  0.020  1.090
 9YP  CAN  H11  single    0.970  0.020  1.090
 9YP  CAO  H12  single    0.970  0.020  1.090
 9YP  CAO  H13  single    0.970  0.020  1.090
 9YP  OAG  H14  single    0.850  0.020  0.980
 9YP  OAD  H15  single    0.850  0.020  0.980
 9YP  CAP  H16  single    0.970  0.020  1.090
 9YP  CAP  H17  single    0.970  0.020  1.090
 9YP  NAA  H18  single    0.890  0.020  1.040
 9YP  NAA  H19  single    0.890  0.020  1.040
 9YP  NAR  H20  single    0.860  0.020  1.020
 9YP  CAI  H21  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
 9YP  H1   OAE  PBA  114.17  3.000
 9YP  CAL  PBA  OAC  107.10  3.000
 9YP  OAC  PBA  OAF  108.91  3.000
 9YP  CAL  PBA  OAF  115.91  3.000
 9YP  OAC  PBA  OAE  106.91  3.000
 9YP  CAL  PBA  OAE  100.92  3.000
 9YP  OAF  PBA  OAE  116.31  3.000
 9YP  H2   OAC  PBA  115.72  3.000
 9YP  H4   CAL  H3   107.38  3.000
 9YP  H4   CAL  CAK  110.06  3.000
 9YP  H3   CAL  CAK  109.98  3.000
 9YP  H4   CAL  PBA  107.27  3.000
 9YP  H3   CAL  PBA  110.02  3.000
 9YP  CAK  CAL  PBA  111.99  3.000
 9YP  H6   CAK  H5   106.98  3.000
 9YP  H6   CAK  OAS  110.49  3.000
 9YP  H5   CAK  OAS  110.93  3.000
 9YP  H6   CAK  CAL  110.32  3.000
 9YP  H5   CAK  CAL  110.19  3.000
 9YP  OAS  CAK  CAL  107.96  3.000
 9YP  CAM  OAS  CAK  112.58  3.000
 9YP  H8   CAM  H7   106.70  3.000
 9YP  H8   CAM  CAY  108.99  3.000
 9YP  H7   CAM  CAY  109.34  3.000
 9YP  H8   CAM  OAS  110.70  3.000
 9YP  H7   CAM  OAS  110.48  3.000
 9YP  CAY  CAM  OAS  110.54  3.000
 9YP  H9   CAY  CAP  108.04  3.000
 9YP  H9   CAY  CAN  109.54  3.000
 9YP  CAP  CAY  CAN  110.12  3.000
 9YP  H9   CAY  CAM  109.11  3.000
 9YP  CAP  CAY  CAM  107.17  3.000
 9YP  CAN  CAY  CAM  112.72  3.000
 9YP  H11  CAN  H10  106.88  3.000
 9YP  H11  CAN  OAT  111.51  3.000
 9YP  H10  CAN  OAT  108.89  3.000
 9YP  H11  CAN  CAY  109.02  3.000
 9YP  H10  CAN  CAY  110.35  3.000
 9YP  OAT  CAN  CAY  110.15  3.000
 9YP  CAO  OAT  CAN  113.48  3.000
 9YP  H13  CAO  H12  106.62  3.000
 9YP  H13  CAO  PBB  108.87  3.000
 9YP  H12  CAO  PBB  109.08  3.000
 9YP  H13  CAO  OAT  112.74  3.000
 9YP  H12  CAO  OAT  108.69  3.000
 9YP  PBB  CAO  OAT  110.70  3.000
 9YP  OAD  PBB  OAH  109.51  3.000
 9YP  OAD  PBB  OAG  106.56  3.000
 9YP  OAH  PBB  OAG  116.35  3.000
 9YP  OAG  PBB  CAO   99.08  3.000
 9YP  OAD  PBB  CAO  107.10  3.000
 9YP  OAH  PBB  CAO  117.21  3.000
 9YP  H14  OAG  PBB  114.56  3.000
 9YP  H15  OAD  PBB  115.59  3.000
 9YP  H17  CAP  H16  106.89  3.000
 9YP  H17  CAP  NAZ  107.54  3.000
 9YP  H16  CAP  NAZ  108.24  3.000
 9YP  H17  CAP  CAY  110.63  3.000
 9YP  H16  CAP  CAY  109.84  3.000
 9YP  NAZ  CAP  CAY  113.45  3.000
 9YP  CAI  NAZ  CAW  106.30  3.000
 9YP  CAW  NAZ  CAP  126.41  3.000
 9YP  CAI  NAZ  CAP  127.27  3.000
 9YP  CAX  CAW  CAJ  128.47  3.000
 9YP  CAJ  CAW  NAZ  126.14  3.000
 9YP  CAX  CAW  NAZ  105.38  3.000
 9YP  CAU  CAJ  CAW  113.10  3.000
 9YP  NAR  CAU  NAA  116.96  3.000
 9YP  NAA  CAU  CAJ  119.99  3.000
 9YP  NAR  CAU  CAJ  123.03  3.000
 9YP  H19  NAA  H18  115.95  3.000
 9YP  H19  NAA  CAU  120.62  3.000
 9YP  H18  NAA  CAU  117.15  3.000
 9YP  H20  NAR  CAV  115.60  3.000
 9YP  H20  NAR  CAU  118.19  3.000
 9YP  CAV  NAR  CAU  126.21  3.000
 9YP  CAX  CAV  OAB  128.87  3.000
 9YP  CAX  CAV  NAR  110.56  3.000
 9YP  OAB  CAV  NAR  120.58  3.000
 9YP  NAQ  CAX  CAV  130.67  3.000
 9YP  CAV  CAX  CAW  118.63  3.000
 9YP  NAQ  CAX  CAW  110.70  3.000
 9YP  CAI  NAQ  CAX  104.44  3.000
 9YP  H21  CAI  NAQ  125.75  3.000
 9YP  H21  CAI  NAZ  121.07  3.000
 9YP  NAQ  CAI  NAZ  113.18  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
 9YP  CONST_01  CAX  NAQ  CAI  NAZ     0.00   0.0  0
 9YP  CONST_02  NAQ  CAX  CAW  NAZ     0.00   0.0  0
 9YP  CONST_03  CAI  NAQ  CAX  CAW     0.00   0.0  0
 9YP  CONST_04  NAQ  CAI  NAZ  CAW     0.00   0.0  0
 9YP  CONST_05  CAI  NAZ  CAW  CAX     0.00   0.0  0
 9YP  CONST_06  NAR  CAU  CAJ  CAW     0.00   0.0  0
 9YP  CONST_07  CAV  NAR  CAU  CAJ     0.00   0.0  0
 9YP  CONST_08  CAX  CAV  NAR  CAU     0.00   0.0  0
 9YP  CONST_09  NAQ  CAI  NAZ  CAP   180.00   0.0  0
 9YP  CONST_10  CAX  CAW  NAZ  CAP   180.00   0.0  0
 9YP  CONST_11  CAJ  CAW  NAZ  CAP     0.00   0.0  0
 9YP  CONST_12  NAA  CAU  CAJ  CAW   180.00   0.0  0
 9YP  CONST_13  OAB  CAV  NAR  CAU   180.00   0.0  0
 9YP  CONST_14  CAV  NAR  CAU  NAA   180.00   0.0  0
 9YP  CONST_15  H21  CAI  NAZ  CAW   180.00   0.0  0
 9YP  CONST_16  H20  NAR  CAU  CAJ   180.00   0.0  0
 9YP  CONST_17  H18  NAA  CAU  CAJ     0.00   0.0  0
 9YP  Var_01    CAI  NAZ  CAP  CAY  -104.88  30.0  2
 9YP  Var_02    CAK  CAL  PBA  OAE  -175.54  30.0  3
 9YP  Var_03    OAS  CAK  CAL  PBA  -177.50  30.0  1
 9YP  Var_04    CAY  CAM  OAS  CAK   173.67  30.0  1
 9YP  Var_05    PBB  CAO  OAT  CAN    89.47  30.0  1
 9YP  Var_06    OAH  PBB  CAO  OAT   -53.56  30.0  2
 9YP  Var_07    H10  CAN  OAT  CAO    67.89  30.0  1

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
 9YP  chir_01  CAY  CAN  CAP  CAM  positiv

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
 9YP  plan-1  CAP  0.020
 9YP  plan-1  NAZ  0.020
 9YP  plan-1  CAW  0.020
 9YP  plan-1  CAJ  0.020
 9YP  plan-1  CAU  0.020
 9YP  plan-1  NAA  0.020
 9YP  plan-1  NAR  0.020
 9YP  plan-1  CAV  0.020
 9YP  plan-1  OAB  0.020
 9YP  plan-1  CAX  0.020
 9YP  plan-1  NAQ  0.020
 9YP  plan-1  CAI  0.020
 9YP  plan-1  H18  0.020
 9YP  plan-1  H19  0.020
 9YP  plan-1  H20  0.020
 9YP  plan-1  H21  0.020

