# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 02:48:56 2021
#   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  45  28  .  2021-08-15  2022-11-17
;
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   0.066  -15.0727  21.8190  -33.4571
 NYZ  C5    C  CR56  0  -0.038  -14.0042  23.1206  -34.7411
 NYZ  C6    C  CR6   0   0.467  -13.1628  24.0735  -35.3786
 NYZ  PB    P  P     0   1.389  -17.3343  20.8331  -29.7297
 NYZ  O1B   O  O     0  -0.690  -16.0441  20.9934  -30.4448
 NYZ  O2B   O  OH1   0  -0.739  -18.6316  21.2237  -30.5914
 NYZ  O3B   O  OH1   0  -0.731  -17.5363  21.7048  -28.4070
 NYZ  PA    P  P     0   1.405  -18.1226  17.9319  -30.2902
 NYZ  O1A   O  OH1   0  -0.729  -19.7095  18.0689  -30.2043
 NYZ  O2A   O  O     0  -0.693  -17.5375  16.5866  -30.0982
 NYZ  C3A   C  CH2   0  -1.048  -17.6041  19.1687  -29.0741
 NYZ  C5'   C  CH2   0  -0.173  -16.6316  18.3172  -32.4753
 NYZ  C4'   C  CH1   0   0.005  -16.8936  18.6869  -33.9111
 NYZ  O4'   O  O2    0  -0.493  -17.1801  20.0802  -34.0257
 NYZ  C3'   C  CH1   0  -0.033  -15.6893  18.4585  -34.8181
 NYZ  O3'   O  OH1   0  -0.653  -15.6500  17.1292  -35.2449
 NYZ  C2'   C  CH1   0  -0.061  -15.9647  19.4643  -35.9426
 NYZ  O2'   O  OH1   0  -0.659  -16.9472  18.9929  -36.8184
 NYZ  C1'   C  CH1   0   0.169  -16.5735  20.6259  -35.1549
 NYZ  N9    N  NR5   0  -0.534  -15.5455  21.5772  -34.7318
 NYZ  N7    N  N     0  -0.445  -14.1515  22.7326  -33.4361
 NYZ  N6    N  NH2   0  -0.803  -12.2978  24.7885  -34.6674
 NYZ  N1    N  N     0  -0.539  -13.2356  24.2536  -36.6865
 NYZ  C2    C  CR6   0   0.539  -14.0960  23.5612  -37.4711
 NYZ  N3    N  NR16  0  -0.742  -14.9315  22.6073  -36.8765
 NYZ  C4    C  CR56  0   0.648  -14.8646  22.4180  -35.5427
 NYZ  O     O  O     0  -0.513  -14.1780  23.7289  -38.6802
 NYZ  H8    H  HCR5  0   0.317  -15.4651  21.3110  -32.5899
 NYZ  H1    H  HOH1  0   0.486  -18.5512  21.0147  -31.5321
 NYZ  H2    H  HOH1  0   0.501  -17.2667  22.6300  -28.4968
 NYZ  H4    H  HOH1  0   0.502  -20.1962  17.4251  -30.7389
 NYZ  H3A2  H  HCH2  0   0.340  -18.3422  19.1877  -28.2694
 NYZ  H3A1  H  HCH2  0   0.340  -16.6618  18.8338  -28.6350
 NYZ  H5'1  H  HCH2  0   0.260  -16.3732  17.2569  -32.4292
 NYZ  H5'2  H  HCH2  0   0.241  -15.7991  18.8939  -32.0660
 NYZ  H4'   H  HCH1  0   0.260  -17.7504  18.1104  -34.2808
 NYZ  H3'   H  HCH1  0   0.253  -14.7660  18.7461  -34.2983
 NYZ  HO3'  H  HOH1  0   0.472  -14.7531  16.9132  -35.5198
 NYZ  H2'   H  HCH1  0   0.268  -15.0459  19.7513  -36.4698
 NYZ  HO2'  H  HOH1  0   0.456  -16.7673  18.0615  -36.9965
 NYZ  H1'   H  HCH1  0   0.298  -17.3069  21.1789  -35.7499
 NYZ  H61   H  HNH2  0   0.406  -11.7009  25.4616  -35.1175
 NYZ  H62   H  HNH2  0   0.415  -12.2178  24.6686  -33.6725
 NYZ  H3    H  HNR6  0   0.423  -15.5867  22.1199  -37.4708
 NYZ  O5'   O  O2    0  -0.610  -17.8212  18.5834  -31.7334

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    1.223  0.020  1.223
 NYZ  C2   N1    single    1.355  0.020  1.355
 NYZ  C2   N3    single    1.401  0.020  1.401
 NYZ  N1   C6    double    1.322  0.020  1.322
 NYZ  N3   C4    single    1.349  0.020  1.349
 NYZ  O2'  C2'   single    1.398  0.020  1.398
 NYZ  C6   N6    single    1.329  0.020  1.329
 NYZ  C6   C5    single    1.422  0.020  1.422
 NYZ  C4   C5    aromatic  1.370  0.020  1.370
 NYZ  C4   N9    aromatic  1.352  0.020  1.352
 NYZ  C2'  C1'   single    1.530  0.020  1.530
 NYZ  C2'  C3'   single    1.534  0.020  1.534
 NYZ  C5   N7    aromatic  1.369  0.020  1.369
 NYZ  C1'  N9    single    1.463  0.020  1.463
 NYZ  C1'  O4'   single    1.393  0.020  1.393
 NYZ  N9   C8    aromatic  1.381  0.020  1.381
 NYZ  O3'  C3'   single    1.397  0.020  1.397
 NYZ  C3'  C4'   single    1.525  0.020  1.525
 NYZ  O4'  C4'   single    1.427  0.020  1.427
 NYZ  N7   C8    aromatic  1.298  0.020  1.298
 NYZ  C4'  C5'   single    1.506  0.020  1.506
 NYZ  C5'  O5'   single    1.427  0.020  1.427
 NYZ  O5'  PA    single    1.612  0.020  1.612
 NYZ  O2A  PA    double    1.480  0.020  1.480
 NYZ  PA   O1A   single    1.595  0.020  1.595
 NYZ  PA   C3A   single    1.810  0.020  1.810
 NYZ  C3A  PB    single    1.809  0.020  1.809
 NYZ  O1B  PB    double    1.484  0.020  1.484
 NYZ  O2B  PB    single    1.606  0.020  1.606
 NYZ  PB   O3B   single    1.597  0.020  1.597
 NYZ  C8   H8    single    0.930  0.020  1.080
 NYZ  O2B  H1    single    0.850  0.020  0.980
 NYZ  O3B  H2    single    0.850  0.020  0.980
 NYZ  O1A  H4    single    0.850  0.020  0.980
 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    125.21  3.000
 NYZ  H8    C8   N9    122.34  3.000
 NYZ  N7    C8   N9    112.42  3.000
 NYZ  C4    C5   N7    110.17  3.000
 NYZ  N7    C5   C6    132.90  3.000
 NYZ  C4    C5   C6    116.94  3.000
 NYZ  N1    C6   N6    119.47  3.000
 NYZ  N6    C6   C5    120.39  3.000
 NYZ  N1    C6   C5    120.14  3.000
 NYZ  C3A   PB   O3B   100.55  3.000
 NYZ  O3B   PB   O2B   102.09  3.000
 NYZ  C3A   PB   O2B   107.32  3.000
 NYZ  O3B   PB   O1B   116.76  3.000
 NYZ  O2B   PB   O1B   114.68  3.000
 NYZ  C3A   PB   O1B   113.81  3.000
 NYZ  H1    O2B  PB    113.72  3.000
 NYZ  H2    O3B  PB    114.18  3.000
 NYZ  O5'   PA   C3A   105.77  3.000
 NYZ  C3A   PA   O2A   114.88  3.000
 NYZ  O5'   PA   O2A   114.19  3.000
 NYZ  C3A   PA   O1A   100.95  3.000
 NYZ  O2A   PA   O1A   117.68  3.000
 NYZ  O5'   PA   O1A   101.51  3.000
 NYZ  H4    O1A  PA    114.41  3.000
 NYZ  H3A1  C3A  H3A2  106.99  3.000
 NYZ  H3A1  C3A  PA    107.92  3.000
 NYZ  H3A2  C3A  PA    108.26  3.000
 NYZ  H3A1  C3A  PB    107.40  3.000
 NYZ  H3A2  C3A  PB    110.60  3.000
 NYZ  PA    C3A  PB    115.33  3.000
 NYZ  H5'2  C5'  H5'1  108.45  3.000
 NYZ  H5'2  C5'  C4'   111.12  3.000
 NYZ  H5'1  C5'  C4'   108.65  3.000
 NYZ  H5'2  C5'  O5'   110.00  3.000
 NYZ  H5'1  C5'  O5'   110.88  3.000
 NYZ  C4'   C5'  O5'   107.75  3.000
 NYZ  H4'   C4'  C3'   109.74  3.000
 NYZ  H4'   C4'  O4'   109.23  3.000
 NYZ  C3'   C4'  O4'   104.90  3.000
 NYZ  H4'   C4'  C5'   109.16  3.000
 NYZ  O4'   C4'  C5'   110.56  3.000
 NYZ  C3'   C4'  C5'   113.14  3.000
 NYZ  C1'   O4'  C4'   111.11  3.000
 NYZ  H3'   C3'  C2'   109.04  3.000
 NYZ  H3'   C3'  O3'   111.74  3.000
 NYZ  C2'   C3'  O3'   113.90  3.000
 NYZ  H3'   C3'  C4'   110.08  3.000
 NYZ  O3'   C3'  C4'   110.28  3.000
 NYZ  C2'   C3'  C4'   101.31  3.000
 NYZ  HO3'  O3'  C3'   109.09  3.000
 NYZ  H2'   C2'  C1'   112.45  3.000
 NYZ  H2'   C2'  O2'   112.06  3.000
 NYZ  C1'   C2'  O2'   107.39  3.000
 NYZ  H2'   C2'  C3'   111.92  3.000
 NYZ  C1'   C2'  C3'   101.06  3.000
 NYZ  O2'   C2'  C3'   111.37  3.000
 NYZ  HO2'  O2'  C2'   108.06  3.000
 NYZ  H1'   C1'  N9    107.43  3.000
 NYZ  H1'   C1'  C2'   111.74  3.000
 NYZ  N9    C1'  C2'   111.28  3.000
 NYZ  H1'   C1'  O4'   110.30  3.000
 NYZ  N9    C1'  O4'   109.04  3.000
 NYZ  C2'   C1'  O4'   107.05  3.000
 NYZ  C4    N9   C1'   125.78  3.000
 NYZ  C1'   N9   C8    128.42  3.000
 NYZ  C4    N9   C8    105.80  3.000
 NYZ  C5    N7   C8    105.09  3.000
 NYZ  H62   N6   H61   118.39  3.000
 NYZ  H62   N6   C6    121.16  3.000
 NYZ  H61   N6   C6    120.45  3.000
 NYZ  C2    N1   C6    122.56  3.000
 NYZ  O     C2   N3    118.22  3.000
 NYZ  N3    C2   N1    118.76  3.000
 NYZ  O     C2   N1    123.02  3.000
 NYZ  H3    N3   C4    123.12  3.000
 NYZ  H3    N3   C2    117.77  3.000
 NYZ  C4    N3   C2    119.06  3.000
 NYZ  N3    C4   N9    130.94  3.000
 NYZ  N9    C4   C5    106.52  3.000
 NYZ  N3    C4   C5    122.54  3.000
 NYZ  C5'   O5'  PA    123.09  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   180.00   0.0  0
 NYZ  CONST_18  H62  N6   C6   C5     0.00   0.0  0
 NYZ  Var_01    C4'  C5'  O5'  PA   160.92  30.0  1
 NYZ  Var_02    O5'  PA   C3A  PB    14.93  30.0  1
 NYZ  Var_03    PA   C3A  PB   O1B  -77.88  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
 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
 NYZ  chir_06  PA   O2A  O1A  C3A  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
 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

