# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jun 13 12:22:36 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-oxidanylidene-3~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)Nc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O
#
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
 NYZ  NYZ  '[[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-oxidanylidene-3~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid'  ligand  42  28  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NYZ
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
 NYZ  C8    C  CR15   0   0.044   1.5514  -1.0320  -0.1440
 NYZ  C5    C  CR56   0  -0.042   3.5505  -1.7205  -0.3262
 NYZ  C6    C  CR6    0   0.461   4.7756  -2.4101  -0.5318
 NYZ  PB    P  P      0   1.167  -5.1710  -1.9858   0.2752
 NYZ  O1B   O  O      0  -0.908  -4.4182  -3.0721  -0.5007
 NYZ  O2B   O  OP    -1  -0.909  -6.1699  -1.1893  -0.5686
 NYZ  O3B   O  OP    -1  -0.920  -5.7595  -2.4800   1.6055
 NYZ  PA    P  P      0   1.269  -2.6720  -0.2877  -0.4796
 NYZ  O1A   O  OP    -1  -0.818  -3.3262   0.1701  -1.7582
 NYZ  O2A   O  O      0  -0.800  -1.5353  -1.2829  -0.5829
 NYZ  C3A   C  CH2    0  -0.996  -3.8572  -0.7540   0.8012
 NYZ  C5'   C  CH2    0  -0.129  -1.1346   1.8712  -0.4341
 NYZ  C4'   C  CH1    0  -0.048  -0.1046   2.4094   0.5411
 NYZ  O4'   O  O2     0  -0.491   0.6644   1.3345   1.1082
 NYZ  C3'   C  CH1    0  -0.031   0.9122   3.3445  -0.0981
 NYZ  O3'   O  OH1    0  -0.668   1.4042   4.2165   0.8865
 NYZ  C2'   C  CH1    0  -0.045   1.9885   2.3503  -0.5349
 NYZ  O2'   O  OH1    0  -0.657   3.2747   2.8812  -0.6684
 NYZ  C1'   C  CH1    0   0.221   1.9657   1.3601   0.6294
 NYZ  N9    N  NR5    0  -0.536   2.3649   0.0206   0.2323
 NYZ  N7    N  N      0  -0.454   2.2375  -2.0847  -0.4747
 NYZ  N6    N  NH2    0  -0.805   4.7760  -3.6733  -0.9469
 NYZ  N1    N  N      0  -0.541   5.9285  -1.7995  -0.3123
 NYZ  C2    C  CR6    0   0.535   6.0021  -0.5096   0.0964
 NYZ  N3    N  NR16   0  -0.735   4.8148   0.1949   0.3203
 NYZ  C4    C  CR56   0   0.641   3.6352  -0.4214   0.1012
 NYZ  O     O  O      0  -0.518   7.0651   0.0712   0.2780
 NYZ  H8    H  HCR5   0   0.340   0.4674  -0.9594  -0.1539
 NYZ  H3A2  H  HCH2   0   0.212  -4.3521   0.1459   1.1788
 NYZ  H3A1  H  HCH2   0   0.210  -3.2905  -1.1681   1.6411
 NYZ  H5'1  H  HCH2   0   0.193  -0.6339   1.3124  -1.2363
 NYZ  H5'2  H  HCH2   0   0.212  -1.6336   2.7249  -0.9094
 NYZ  H4'   H  HCH1   0   0.259  -0.6263   2.9130   1.3607
 NYZ  H3'   H  HCH1   0   0.252   0.4868   3.8898  -0.9502
 NYZ  HO3'  H  HOH1   0   0.450   2.2444   4.5739   0.5763
 NYZ  H2'   H  HCH1   0   0.259   1.6601   1.8425  -1.4497
 NYZ  HO2'  H  HOH1   0   0.473   3.4092   3.1662  -1.5774
 NYZ  H1'   H  HCH1   0   0.259   2.6683   1.6818   1.4100
 NYZ  H61   H  HNH2   0   0.414   3.9161  -4.1581  -1.1363
 NYZ  H62   H  HNH2   0   0.405   5.6435  -4.1536  -1.1147
 NYZ  H3    H  HNR6   0   0.417   4.8773   1.1797   0.5364
 NYZ  O5'   O  O2     0  -0.639  -2.0525   1.0839   0.2745

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
 NYZ  O    C2    double    1.225  0.020  1.225
 NYZ  C2   N1    single    1.355  0.020  1.355
 NYZ  C2   N3    single    1.399  0.020  1.399
 NYZ  N1   C6    double    1.323  0.020  1.323
 NYZ  N3   C4    single    1.349  0.020  1.349
 NYZ  O2'  C2'   single    1.398  0.020  1.398
 NYZ  C6   N6    single    1.330  0.020  1.330
 NYZ  C6   C5    single    1.421  0.020  1.421
 NYZ  C4   C5    aromatic  1.370  0.020  1.370
 NYZ  C4   N9    aromatic  1.351  0.020  1.351
 NYZ  C2'  C1'   single    1.529  0.020  1.529
 NYZ  C2'  C3'   single    1.529  0.020  1.529
 NYZ  C5   N7    aromatic  1.371  0.020  1.371
 NYZ  C1'  N9    single    1.453  0.020  1.453
 NYZ  C1'  O4'   single    1.387  0.020  1.387
 NYZ  N9   C8    aromatic  1.383  0.020  1.383
 NYZ  O3'  C3'   single    1.404  0.020  1.404
 NYZ  C3'  C4'   single    1.522  0.020  1.522
 NYZ  O4'  C4'   single    1.438  0.020  1.438
 NYZ  N7   C8    aromatic  1.299  0.020  1.299
 NYZ  C4'  C5'   single    1.517  0.020  1.517
 NYZ  C5'  O5'   single    1.402  0.020  1.402
 NYZ  O5'  PA    single    1.683  0.020  1.683
 NYZ  O2A  PA    deloc     1.514  0.020  1.514
 NYZ  PA   O1A   deloc     1.507  0.020  1.507
 NYZ  PA   C3A   single    1.806  0.020  1.806
 NYZ  C3A  PB    single    1.876  0.020  1.876
 NYZ  O1B  PB    deloc     1.532  0.020  1.532
 NYZ  O2B  PB    deloc     1.531  0.020  1.531
 NYZ  PB   O3B   deloc     1.536  0.020  1.536
 NYZ  C8   H8    single    0.930  0.020  1.080
 NYZ  C3A  H3A2  single    0.970  0.020  1.090
 NYZ  C3A  H3A1  single    0.970  0.020  1.090
 NYZ  C5'  H5'1  single    0.970  0.020  1.090
 NYZ  C5'  H5'2  single    0.970  0.020  1.090
 NYZ  C4'  H4'   single    0.970  0.020  1.090
 NYZ  C3'  H3'   single    0.970  0.020  1.090
 NYZ  O3'  HO3'  single    0.850  0.020  0.980
 NYZ  C2'  H2'   single    0.970  0.020  1.090
 NYZ  O2'  HO2'  single    0.850  0.020  0.980
 NYZ  C1'  H1'   single    0.970  0.020  1.090
 NYZ  N6   H61   single    0.860  0.020  1.020
 NYZ  N6   H62   single    0.860  0.020  1.020
 NYZ  N3   H3    single    0.860  0.020  1.020

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
 NYZ  H8    C8   N7    125.36  3.000
 NYZ  H8    C8   N9    122.59  3.000
 NYZ  N7    C8   N9    112.05  3.000
 NYZ  C4    C5   N7    110.18  3.000
 NYZ  N7    C5   C6    132.95  3.000
 NYZ  C4    C5   C6    116.87  3.000
 NYZ  N1    C6   N6    119.34  3.000
 NYZ  N6    C6   C5    120.43  3.000
 NYZ  N1    C6   C5    120.23  3.000
 NYZ  C3A   PB   O3B   103.69  3.000
 NYZ  O3B   PB   O2B   113.24  3.000
 NYZ  C3A   PB   O2B   105.65  3.000
 NYZ  O3B   PB   O1B   113.49  3.000
 NYZ  O2B   PB   O1B   114.22  3.000
 NYZ  C3A   PB   O1B   105.27  3.000
 NYZ  O5'   PA   C3A    97.71  3.000
 NYZ  C3A   PA   O2A   111.79  3.000
 NYZ  O5'   PA   O2A   106.85  3.000
 NYZ  C3A   PA   O1A   113.27  3.000
 NYZ  O2A   PA   O1A   117.87  3.000
 NYZ  O5'   PA   O1A   106.99  3.000
 NYZ  H3A1  C3A  H3A2  106.29  3.000
 NYZ  H3A1  C3A  PA    107.58  3.000
 NYZ  H3A2  C3A  PA    109.22  3.000
 NYZ  H3A1  C3A  PB    109.23  3.000
 NYZ  H3A2  C3A  PB    108.66  3.000
 NYZ  PA    C3A  PB    115.48  3.000
 NYZ  H5'2  C5'  H5'1  106.67  3.000
 NYZ  H5'2  C5'  C4'   108.13  3.000
 NYZ  H5'1  C5'  C4'   109.90  3.000
 NYZ  H5'2  C5'  O5'   110.99  3.000
 NYZ  H5'1  C5'  O5'   112.46  3.000
 NYZ  C4'   C5'  O5'   108.60  3.000
 NYZ  H4'   C4'  C3'   110.50  3.000
 NYZ  H4'   C4'  O4'   107.67  3.000
 NYZ  C3'   C4'  O4'   105.52  3.000
 NYZ  H4'   C4'  C5'   108.72  3.000
 NYZ  O4'   C4'  C5'   110.57  3.000
 NYZ  C3'   C4'  C5'   113.67  3.000
 NYZ  C1'   O4'  C4'   110.60  3.000
 NYZ  H3'   C3'  C2'   111.97  3.000
 NYZ  H3'   C3'  O3'   111.82  3.000
 NYZ  C2'   C3'  O3'   110.95  3.000
 NYZ  H3'   C3'  C4'   111.86  3.000
 NYZ  O3'   C3'  C4'   108.73  3.000
 NYZ  C2'   C3'  C4'   101.00  3.000
 NYZ  HO3'  O3'  C3'   108.05  3.000
 NYZ  H2'   C2'  C1'   109.32  3.000
 NYZ  H2'   C2'  O2'   111.82  3.000
 NYZ  C1'   C2'  O2'   109.42  3.000
 NYZ  H2'   C2'  C3'   109.19  3.000
 NYZ  C1'   C2'  C3'   101.14  3.000
 NYZ  O2'   C2'  C3'   115.34  3.000
 NYZ  HO2'  O2'  C2'   109.36  3.000
 NYZ  H1'   C1'  N9    106.77  3.000
 NYZ  H1'   C1'  C2'   110.00  3.000
 NYZ  N9    C1'  C2'   112.64  3.000
 NYZ  H1'   C1'  O4'   111.11  3.000
 NYZ  N9    C1'  O4'   109.58  3.000
 NYZ  C2'   C1'  O4'   106.79  3.000
 NYZ  C4    N9   C1'   125.89  3.000
 NYZ  C1'   N9   C8    127.92  3.000
 NYZ  C4    N9   C8    106.12  3.000
 NYZ  C5    N7   C8    105.25  3.000
 NYZ  H62   N6   H61   118.44  3.000
 NYZ  H62   N6   C6    120.40  3.000
 NYZ  H61   N6   C6    121.12  3.000
 NYZ  C2    N1   C6    122.46  3.000
 NYZ  O     C2   N3    118.30  3.000
 NYZ  N3    C2   N1    118.80  3.000
 NYZ  O     C2   N1    122.90  3.000
 NYZ  H3    N3   C4    122.30  3.000
 NYZ  H3    N3   C2    118.21  3.000
 NYZ  C4    N3   C2    119.10  3.000
 NYZ  N3    C4   N9    131.06  3.000
 NYZ  N9    C4   C5    106.40  3.000
 NYZ  N3    C4   C5    122.54  3.000
 NYZ  C5'   O5'  PA    118.18  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
 NYZ  CONST_01  C5   C4   N9   C8      0.00   0.0  0
 NYZ  CONST_02  C4   C5   N7   C8      0.00   0.0  0
 NYZ  CONST_03  N9   C8   N7   C5      0.00   0.0  0
 NYZ  CONST_04  N7   C5   C4   N9      0.00   0.0  0
 NYZ  CONST_05  C4   N9   C8   N7      0.00   0.0  0
 NYZ  CONST_06  C1'  N9   C4   C5    180.00   0.0  0
 NYZ  CONST_07  N3   C4   N9   C1'     0.00   0.0  0
 NYZ  CONST_08  N7   C8   N9   C1'   180.00   0.0  0
 NYZ  CONST_09  C2   N1   C6   C5      0.00   0.0  0
 NYZ  CONST_10  N3   C2   N1   C6      0.00   0.0  0
 NYZ  CONST_11  C4   N3   C2   N1      0.00   0.0  0
 NYZ  CONST_12  O    C2   N1   C6    180.00   0.0  0
 NYZ  CONST_13  C2   N1   C6   N6    180.00   0.0  0
 NYZ  CONST_14  O    C2   N3   C4    180.00   0.0  0
 NYZ  CONST_15  H8   C8   N7   C5    180.00   0.0  0
 NYZ  CONST_16  H3   N3   C2   N1    180.00   0.0  0
 NYZ  CONST_17  H61  N6   C6   C5      0.00   0.0  0
 NYZ  CONST_18  H62  N6   C6   C5    180.00   0.0  0
 NYZ  Var_01    C4'  C5'  O5'  PA   -144.04  30.0  1
 NYZ  Var_02    O5'  PA   C3A  PB    164.14  30.0  1
 NYZ  Var_03    PA   C3A  PB   O1B    45.39  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
 NYZ  chir_02  C4'  C3'  O4'  C5'  positiv
 NYZ  chir_03  C3'  O3'  C2'  C4'  negativ
 NYZ  chir_04  C2'  O2'  C1'  C3'  negativ
 NYZ  chir_05  C1'  O4'  N9   C2'  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
 NYZ  plan-1  C8   0.020
 NYZ  plan-1  C5   0.020
 NYZ  plan-1  C6   0.020
 NYZ  plan-1  C1'  0.020
 NYZ  plan-1  N9   0.020
 NYZ  plan-1  N7   0.020
 NYZ  plan-1  N6   0.020
 NYZ  plan-1  N1   0.020
 NYZ  plan-1  C2   0.020
 NYZ  plan-1  N3   0.020
 NYZ  plan-1  C4   0.020
 NYZ  plan-1  O    0.020
 NYZ  plan-1  H8   0.020
 NYZ  plan-1  H61  0.020
 NYZ  plan-1  H62  0.020
 NYZ  plan-1  H3   0.020

