# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 06:36:02 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(azanyl)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: Nc1nc(N)c2ncn([C@@H]3O[C@H](CO[P](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O)c2n1
#
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
 NYW  NYW  '[[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(azanyl)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid'  ligand  43  28  .  2021-08-15  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NYW
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
 NYW  C6    C  CR6    0   0.457  -5.0007  -2.3869   0.0089
 NYW  C4    C  CR56   0   0.508  -3.8327  -0.3407  -0.2034
 NYW  C2    C  CR6    0   0.527  -5.7433  -0.6161  -1.2698
 NYW  PB    P  P      0   1.167   5.3323  -1.6682  -0.9991
 NYW  O1B   O  OP    -1  -0.909   5.8932  -1.7993   0.4214
 NYW  O2B   O  O      0  -0.911   5.9861  -0.5603  -1.8303
 NYW  O3B   O  OP    -1  -0.921   5.2373  -3.0070  -1.7476
 NYW  PA    P  P      0   1.258   3.2741   0.1398   0.4656
 NYW  O1A   O  OP    -1  -0.823   4.1651   1.3397   0.2617
 NYW  O2A   O  O      0  -0.831   3.1414  -0.4226   1.8602
 NYW  C3A   C  CH2    0  -0.996   3.5442  -1.1509  -0.7714
 NYW  C5'   C  CH2    0  -0.129   1.0836   1.5806   0.7387
 NYW  C4'   C  CR15   0  -0.050   0.0589   2.2872  -0.1292
 NYW  O4'   O  O      0  -0.490  -0.8792   1.3514  -0.6741
 NYW  C3'   C  CR15   0  -0.023  -0.7770   3.2977   0.6424
 NYW  O3'   O  OH1    0  -0.670  -1.2418   4.2768  -0.2514
 NYW  C2'   C  CR15   0  -0.058  -1.9275   2.4152   1.1309
 NYW  O2'   O  OH1    0  -0.655  -3.1147   3.0936   1.4175
 NYW  C1'   C  CR15   0   0.213  -2.1360   1.5000  -0.0774
 NYW  N9    N  NR5    0  -0.546  -2.6682   0.2050   0.2571
 NYW  C8    C  CR15   0   0.097  -2.0771  -0.7537   1.0455
 NYW  N7    N  N      0  -0.448  -2.7707  -1.8459   1.1290
 NYW  C5    C  CR56   0  -0.051  -3.8804  -1.6076   0.3539
 NYW  N6    N  NH2    0  -0.820  -5.1806  -3.6247   0.4799
 NYW  N1    N  N      0  -0.522  -5.9138  -1.8643  -0.8057
 NYW  N3    N  N      0  -0.514  -4.7273   0.2087  -1.0150
 NYW  N2    N  NH2    0  -0.825  -6.7389  -0.1389  -2.0569
 NYW  H3A2  H  HCH2   0   0.211   3.1473  -0.8207  -1.7364
 NYW  H3A1  H  HCH2   0   0.208   2.9506  -2.0221  -0.4763
 NYW  H5'2  H  HCH2   0   0.187   0.5995   1.1430   1.6239
 NYW  H5'1  H  HCH2   0   0.205   1.7806   2.3431   1.1105
 NYW  H4'   H  HCR5   0   0.252   0.5794   2.7692  -0.9629
 NYW  H3'   H  HCR5   0   0.248  -0.2165   3.7413   1.4758
 NYW  HO3'  H  HOH1   0   0.448  -2.0249   4.6855   0.1357
 NYW  H2'   H  HCR5   0   0.248  -1.5838   1.8278   1.9921
 NYW  HO2'  H  HOH1   0   0.469  -3.0656   3.4413   2.3137
 NYW  H1'   H  HCR5   0   0.257  -2.8550   1.9531  -0.7687
 NYW  H8    H  HCR5   0   0.288  -1.1234  -0.5871   1.5243
 NYW  HN61  H  HNH2   0   0.408  -4.4653  -4.0739   1.0238
 NYW  HN62  H  HNH2   0   0.399  -5.9335  -4.1917   0.1303
 NYW  H22   H  HNH2   0   0.388  -7.3697  -0.8060  -2.4665
 NYW  H21   H  HNH2   0   0.388  -6.5473   0.6805  -2.6072
 NYW  O5'   O  O2     0  -0.636   1.7268   0.6008  -0.0254

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
 NYW  N2   C2    single    1.356  0.020  1.356
 NYW  C2   N1    aromatic  1.343  0.020  1.343
 NYW  C2   N3    aromatic  1.333  0.020  1.333
 NYW  N1   C6    aromatic  1.331  0.020  1.331
 NYW  N3   C4    aromatic  1.327  0.020  1.327
 NYW  O2'  C2'   single    1.397  0.020  1.397
 NYW  C6   N6    single    1.337  0.020  1.337
 NYW  C6   C5    aromatic  1.408  0.020  1.408
 NYW  C4   C5    aromatic  1.385  0.020  1.385
 NYW  C4   N9    aromatic  1.366  0.020  1.366
 NYW  C2'  C1'   single    1.530  0.020  1.530
 NYW  C2'  C3'   single    1.530  0.020  1.530
 NYW  C5   N7    aromatic  1.374  0.020  1.374
 NYW  C1'  N9    single    1.440  0.020  1.440
 NYW  C1'  O4'   single    1.399  0.020  1.399
 NYW  N9   C8    aromatic  1.375  0.020  1.375
 NYW  O3'  C3'   single    1.405  0.020  1.405
 NYW  C3'  C4'   single    1.522  0.020  1.522
 NYW  N7   C8    aromatic  1.297  0.020  1.297
 NYW  O4'  C4'   single    1.433  0.020  1.433
 NYW  C4'  C5'   single    1.517  0.020  1.517
 NYW  C5'  O5'   single    1.399  0.020  1.399
 NYW  O5'  PA    single    1.688  0.020  1.688
 NYW  O2A  PA    deloc     1.510  0.020  1.510
 NYW  PA   O1A   deloc     1.508  0.020  1.508
 NYW  PA   C3A   single    1.808  0.020  1.808
 NYW  O2B  PB    deloc     1.532  0.020  1.532
 NYW  C3A  PB    single    1.875  0.020  1.875
 NYW  PB   O3B   deloc     1.537  0.020  1.537
 NYW  PB   O1B   deloc     1.533  0.020  1.533
 NYW  C3A  H3A2  single    0.970  0.020  1.090
 NYW  C3A  H3A1  single    0.970  0.020  1.090
 NYW  C5'  H5'2  single    0.970  0.020  1.090
 NYW  C5'  H5'1  single    0.970  0.020  1.090
 NYW  C4'  H4'   single    0.970  0.020  1.090
 NYW  C3'  H3'   single    0.970  0.020  1.090
 NYW  O3'  HO3'  single    0.850  0.020  0.980
 NYW  C2'  H2'   single    0.970  0.020  1.090
 NYW  O2'  HO2'  single    0.850  0.020  0.980
 NYW  C1'  H1'   single    0.970  0.020  1.090
 NYW  C8   H8    single    0.930  0.020  1.080
 NYW  N6   HN61  single    0.860  0.020  1.020
 NYW  N6   HN62  single    0.860  0.020  1.020
 NYW  N2   H22   single    0.890  0.020  1.040
 NYW  N2   H21   single    0.890  0.020  1.040

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
 NYW  N1    C6   N6    119.15  3.000
 NYW  N6    C6   C5    122.24  3.000
 NYW  N1    C6   C5    118.61  3.000
 NYW  N3    C4   C5    126.99  3.000
 NYW  C5    C4   N9    105.03  3.000
 NYW  N3    C4   N9    127.99  3.000
 NYW  N2    C2   N3    116.93  3.000
 NYW  N3    C2   N1    127.29  3.000
 NYW  N2    C2   N1    115.76  3.000
 NYW  C3A   PB   O3B   103.91  3.000
 NYW  O3B   PB   O2B   113.09  3.000
 NYW  C3A   PB   O2B   105.86  3.000
 NYW  O3B   PB   O1B   113.55  3.000
 NYW  C3A   PB   O1B   105.07  3.000
 NYW  O2B   PB   O1B   114.12  3.000
 NYW  O5'   PA   C3A    97.64  3.000
 NYW  C3A   PA   O2A   112.29  3.000
 NYW  O5'   PA   O2A   106.86  3.000
 NYW  C3A   PA   O1A   112.78  3.000
 NYW  O2A   PA   O1A   118.24  3.000
 NYW  O5'   PA   O1A   106.56  3.000
 NYW  H3A1  C3A  H3A2  106.33  3.000
 NYW  H3A1  C3A  PA    107.62  3.000
 NYW  H3A2  C3A  PA    109.50  3.000
 NYW  H3A1  C3A  PB    109.28  3.000
 NYW  H3A2  C3A  PB    108.78  3.000
 NYW  PA    C3A  PB    114.99  3.000
 NYW  H5'1  C5'  H5'2  106.46  3.000
 NYW  H5'1  C5'  C4'   107.40  3.000
 NYW  H5'2  C5'  C4'   110.39  3.000
 NYW  H5'1  C5'  O5'   112.30  3.000
 NYW  H5'2  C5'  O5'   111.30  3.000
 NYW  C4'   C5'  O5'   108.91  3.000
 NYW  H4'   C4'  C3'   110.79  3.000
 NYW  H4'   C4'  O4'   108.02  3.000
 NYW  C3'   C4'  O4'   105.48  3.000
 NYW  H4'   C4'  C5'   108.63  3.000
 NYW  O4'   C4'  C5'   110.83  3.000
 NYW  C3'   C4'  C5'   112.96  3.000
 NYW  C1'   O4'  C4'   110.89  3.000
 NYW  H3'   C3'  C2'   112.00  3.000
 NYW  H3'   C3'  O3'   111.73  3.000
 NYW  C2'   C3'  O3'   110.88  3.000
 NYW  H3'   C3'  C4'   111.89  3.000
 NYW  O3'   C3'  C4'   108.78  3.000
 NYW  C2'   C3'  C4'   101.07  3.000
 NYW  HO3'  O3'  C3'   107.98  3.000
 NYW  H2'   C2'  C1'   110.01  3.000
 NYW  H2'   C2'  O2'   111.41  3.000
 NYW  C1'   C2'  O2'   109.67  3.000
 NYW  H2'   C2'  C3'   108.89  3.000
 NYW  C1'   C2'  C3'   101.26  3.000
 NYW  O2'   C2'  C3'   115.11  3.000
 NYW  HO2'  O2'  C2'   108.85  3.000
 NYW  H1'   C1'  N9    106.02  3.000
 NYW  H1'   C1'  C2'   109.90  3.000
 NYW  N9    C1'  C2'   113.89  3.000
 NYW  H1'   C1'  O4'   111.36  3.000
 NYW  N9    C1'  O4'   109.61  3.000
 NYW  C2'   C1'  O4'   106.13  3.000
 NYW  C8    N9   C1'   126.98  3.000
 NYW  C8    N9   C4    106.34  3.000
 NYW  C1'   N9   C4    126.60  3.000
 NYW  H8    C8   N7    125.01  3.000
 NYW  H8    C8   N9    121.76  3.000
 NYW  N7    C8   N9    113.23  3.000
 NYW  C5    N7   C8    104.45  3.000
 NYW  N7    C5   C4    110.96  3.000
 NYW  N7    C5   C6    133.22  3.000
 NYW  C4    C5   C6    115.81  3.000
 NYW  HN62  N6   HN61  117.99  3.000
 NYW  HN62  N6   C6    120.05  3.000
 NYW  HN61  N6   C6    120.60  3.000
 NYW  C2    N1   C6    119.31  3.000
 NYW  C2    N3   C4    112.00  3.000
 NYW  H21   N2   H22   115.93  3.000
 NYW  H21   N2   C2    117.68  3.000
 NYW  H22   N2   C2    117.63  3.000
 NYW  C5'   O5'  PA    117.00  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
 NYW  CONST_01  N3    C2   N1   C6     0.00   0.0  0
 NYW  CONST_02  N3    C4   C5   C6     0.00   0.0  0
 NYW  CONST_03  N9    C4   C5   C6   180.00   0.0  0
 NYW  CONST_04  C8    N7   C5   C6   180.00   0.0  0
 NYW  CONST_05  N1    C2   N3   C4     0.00   0.0  0
 NYW  CONST_06  N1    C6   C5   C4     0.00   0.0  0
 NYW  CONST_07  C8    N7   C5   C4     0.00   0.0  0
 NYW  CONST_08  N7    C8   N9   C4     0.00   0.0  0
 NYW  CONST_09  C5    C6   N1   C2     0.00   0.0  0
 NYW  CONST_10  C5    C4   N3   C2     0.00   0.0  0
 NYW  CONST_11  N9    C4   N3   C2   180.00   0.0  0
 NYW  CONST_12  N7    C5   C4   N9     0.00   0.0  0
 NYW  CONST_13  C5    N7   C8   N9     0.00   0.0  0
 NYW  CONST_14  N3    C4   N9   C8   180.00   0.0  0
 NYW  CONST_15  C5    C4   N9   C8     0.00   0.0  0
 NYW  CONST_16  N1    C6   C5   N7   180.00   0.0  0
 NYW  CONST_17  N3    C4   C5   N7   180.00   0.0  0
 NYW  CONST_18  N3    C4   N9   C1'    0.00   0.0  0
 NYW  CONST_19  C5    C4   N9   C1'  180.00   0.0  0
 NYW  CONST_20  N7    C8   N9   C1'  180.00   0.0  0
 NYW  CONST_21  N2    C2   N1   C6   180.00   0.0  0
 NYW  CONST_22  N2    C2   N3   C4   180.00   0.0  0
 NYW  CONST_23  N6    C6   C5   C4   180.00   0.0  0
 NYW  CONST_24  N6    C6   N1   C2   180.00   0.0  0
 NYW  CONST_25  N6    C6   C5   N7     0.00   0.0  0
 NYW  CONST_26  H8    C8   N9   C4   180.00   0.0  0
 NYW  CONST_27  HN61  N6   C6   C5     0.00   0.0  0
 NYW  CONST_28  HN62  N6   C6   C5   180.00   0.0  0
 NYW  Var_01    C4'   C5'  O5'  PA   155.28  30.0  1
 NYW  Var_02    O5'   PA   C3A  PB   162.80  30.0  2
 NYW  Var_03    PA    C3A  PB   O1B   44.14  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
 NYW  chir_02  C4'  C3'  O4'  C5'  positiv
 NYW  chir_03  C3'  O3'  C2'  C4'  negativ
 NYW  chir_04  C2'  O2'  C1'  C3'  negativ
 NYW  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
 NYW  plan-1  C6    0.020
 NYW  plan-1  C4    0.020
 NYW  plan-1  C2    0.020
 NYW  plan-1  C1'   0.020
 NYW  plan-1  N9    0.020
 NYW  plan-1  C8    0.020
 NYW  plan-1  N7    0.020
 NYW  plan-1  C5    0.020
 NYW  plan-1  N6    0.020
 NYW  plan-1  N1    0.020
 NYW  plan-1  N3    0.020
 NYW  plan-1  N2    0.020
 NYW  plan-1  H8    0.020
 NYW  plan-2  C6    0.020
 NYW  plan-2  N6    0.020
 NYW  plan-2  HN61  0.020
 NYW  plan-2  HN62  0.020
 NYW  plan-3  C2    0.020
 NYW  plan-3  N2    0.020
 NYW  plan-3  H22   0.020
 NYW  plan-3  H21   0.020

