# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 00:05:08 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: [(2R,3aR,4R,6R,6aR)-6-(6-amino-9H-purin-9-yl)-2-oxido-2-sulfanyltetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-4-yl]methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO)[C@H]4O[P@](S)(=O)O[C@@H]34
#
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
 QQY  QQY  '[(2R,3aR,4R,6R,6aR)-6-(6-amino-9H-purin-9-yl)-2-oxido-2-sulfanyltetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-4-yl]methanol'  ligand  34  22  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QQY
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
 QQY  OP3   O  O     0  -0.631   3.5576   2.2906   1.6561
 QQY  S1P   S  S2    0  -0.337   3.9767   1.3471  -1.1546
 QQY  O5'   O  OH1   0  -0.664   2.1230  -3.8284  -1.2368
 QQY  C5'   C  CH2   0  -0.155   2.1444  -3.1442  -0.0124
 QQY  C4'   C  CH1   0  -0.001   1.7637  -1.7050  -0.2522
 QQY  O4'   O  O2    0  -0.483   0.4172  -1.6245  -0.6853
 QQY  C3'   C  CR15  0  -0.044   1.7873  -0.8568   1.0220
 QQY  O3'   O  O     0  -0.566   3.0310  -0.2180   1.2524
 QQY  C2'   C  CR15  0  -0.068   0.7519   0.2350   0.7289
 QQY  O2'   O  O     0  -0.579   1.4996   1.3499   0.2463
 QQY  C1'   C  CH1   0   0.187  -0.1150  -0.3630  -0.3933
 QQY  N9    N  NR5   0  -0.544  -1.4889  -0.5433  -0.0114
 QQY  C8    C  CR15  0   0.114  -2.0049  -1.4924   0.8330
 QQY  N7    N  N     0  -0.445  -3.2850  -1.3726   1.0137
 QQY  C5    C  CR56  0  -0.006  -3.6403  -0.2854   0.2568
 QQY  C6    C  CR6   0   0.464  -4.8683   0.3625   0.0239
 QQY  N6    N  NH2   0  -0.815  -6.0116  -0.0354   0.5806
 QQY  N1    N  N     0  -0.473  -4.8695   1.4263  -0.7882
 QQY  C2    C  CR16  0   0.048  -3.7270   1.8255  -1.3387
 QQY  C4    C  CR56  0   0.494  -2.5374   0.2470  -0.3894
 QQY  N3    N  N     0  -0.457  -2.5204   1.3029  -1.1973
 QQY  P     P  P     0   1.240   3.0497   1.3001   0.6952
 QQY  H1P   H  HSH1  0   0.281   5.1681   1.7417  -0.6866
 QQY  H5'   H  HOH1  0   0.462   2.4143  -4.7315  -1.0817
 QQY  H5'1  H  HCH2  0   0.208   1.4510  -3.5788   0.7212
 QQY  H5'2  H  HCH2  0   0.219   3.1411  -3.1468   0.4470
 QQY  H4'   H  HCH1  0   0.252   2.4357  -1.2702  -1.0061
 QQY  H3'   H  HCR5  0   0.313   1.5311  -1.4413   1.9076
 QQY  H1'   H  HCH1  0   0.291  -0.1118   0.3043  -1.2624
 QQY  H2'   H  HCR5  0   0.325   0.1655   0.5433   1.5954
 QQY  H8    H  HCR5  0   0.298  -1.3874  -2.2583   1.2774
 QQY  H61N  H  HNH2  0   0.413  -6.0501  -0.8525   1.1640
 QQY  H62N  H  HNH2  0   0.405  -6.8705   0.4439   0.3727
 QQY  H2    H  HCR6  0   0.255  -3.7984   2.6935  -1.9850

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
 QQY  OP3  P     double    1.471  0.020  1.471
 QQY  S1P  P     single    2.070  0.020  2.070
 QQY  O5'  C5'   single    1.403  0.020  1.403
 QQY  C5'  C4'   single    1.508  0.020  1.508
 QQY  C4'  O4'   single    1.417  0.020  1.417
 QQY  C4'  C3'   single    1.531  0.020  1.531
 QQY  O4'  C1'   single    1.400  0.020  1.400
 QQY  C3'  O3'   single    1.417  0.020  1.417
 QQY  C3'  C2'   single    1.533  0.020  1.533
 QQY  O3'  P     single    1.617  0.020  1.617
 QQY  C2'  O2'   single    1.426  0.020  1.426
 QQY  C2'  C1'   single    1.539  0.020  1.539
 QQY  O2'  P     single    1.615  0.020  1.615
 QQY  C1'  N9    single    1.437  0.020  1.437
 QQY  N9   C8    aromatic  1.371  0.020  1.371
 QQY  N9   C4    aromatic  1.366  0.020  1.366
 QQY  C8   N7    aromatic  1.298  0.020  1.298
 QQY  N7   C5    aromatic  1.372  0.020  1.372
 QQY  C5   C6    aromatic  1.408  0.020  1.408
 QQY  C5   C4    aromatic  1.385  0.020  1.385
 QQY  N3   C4    aromatic  1.330  0.020  1.330
 QQY  C6   N6    single    1.332  0.020  1.332
 QQY  C6   N1    aromatic  1.338  0.020  1.338
 QQY  N1   C2    aromatic  1.330  0.020  1.330
 QQY  C2   N3    aromatic  1.323  0.020  1.323
 QQY  S1P  H1P   single    1.200  0.020  1.300
 QQY  O5'  H5'   single    0.850  0.020  0.980
 QQY  C5'  H5'1  single    0.970  0.020  1.090
 QQY  C5'  H5'2  single    0.970  0.020  1.090
 QQY  C4'  H4'   single    0.970  0.020  1.090
 QQY  C3'  H3'   single    0.970  0.020  1.090
 QQY  C1'  H1'   single    0.970  0.020  1.090
 QQY  C2'  H2'   single    0.970  0.020  1.090
 QQY  C8   H8    single    0.930  0.020  1.080
 QQY  N6   H61N  single    0.860  0.020  1.020
 QQY  N6   H62N  single    0.860  0.020  1.020
 QQY  C2   H2    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
 QQY  H1P   S1P  P      95.33  3.000
 QQY  H5'   O5'  C5'   108.22  3.000
 QQY  H5'2  C5'  H5'1  107.02  3.000
 QQY  H5'2  C5'  C4'   107.35  3.000
 QQY  H5'1  C5'  C4'   108.92  3.000
 QQY  H5'2  C5'  O5'   112.21  3.000
 QQY  H5'1  C5'  O5'   112.34  3.000
 QQY  C4'   C5'  O5'   108.84  3.000
 QQY  H4'   C4'  C3'   110.00  3.000
 QQY  H4'   C4'  O4'   110.41  3.000
 QQY  C3'   C4'  O4'   103.75  3.000
 QQY  H4'   C4'  C5'   109.40  3.000
 QQY  C3'   C4'  C5'   113.12  3.000
 QQY  O4'   C4'  C5'   110.05  3.000
 QQY  C1'   O4'  C4'   110.41  3.000
 QQY  H3'   C3'  C2'   112.21  3.000
 QQY  H3'   C3'  O3'   108.39  3.000
 QQY  C2'   C3'  O3'   107.63  3.000
 QQY  H3'   C3'  C4'   112.02  3.000
 QQY  C2'   C3'  C4'   103.01  3.000
 QQY  O3'   C3'  C4'   113.49  3.000
 QQY  P     O3'  C3'   112.17  3.000
 QQY  H2'   C2'  C1'   112.72  3.000
 QQY  H2'   C2'  O2'   109.25  3.000
 QQY  C1'   C2'  O2'   110.63  3.000
 QQY  H2'   C2'  C3'   114.36  3.000
 QQY  C1'   C2'  C3'   104.07  3.000
 QQY  O2'   C2'  C3'   105.50  3.000
 QQY  P     O2'  C2'   112.65  3.000
 QQY  H1'   C1'  N9    106.85  3.000
 QQY  H1'   C1'  C2'   109.89  3.000
 QQY  N9    C1'  C2'   113.17  3.000
 QQY  H1'   C1'  O4'   112.47  3.000
 QQY  N9    C1'  O4'   107.80  3.000
 QQY  C2'   C1'  O4'   106.75  3.000
 QQY  C4    N9   C8    106.37  3.000
 QQY  C4    N9   C1'   125.98  3.000
 QQY  C8    N9   C1'   127.60  3.000
 QQY  H8    C8   N7    124.90  3.000
 QQY  H8    C8   N9    121.96  3.000
 QQY  N7    C8   N9    113.14  3.000
 QQY  C5    N7   C8    104.58  3.000
 QQY  C4    C5   C6    116.14  3.000
 QQY  C4    C5   N7    110.85  3.000
 QQY  C6    C5   N7    133.00  3.000
 QQY  N1    C6   N6    119.35  3.000
 QQY  N1    C6   C5    117.84  3.000
 QQY  N6    C6   C5    122.81  3.000
 QQY  H62N  N6   H61N  118.36  3.000
 QQY  H62N  N6   C6    120.28  3.000
 QQY  H61N  N6   C6    121.22  3.000
 QQY  C2    N1   C6    119.28  3.000
 QQY  H2    C2   N3    116.11  3.000
 QQY  H2    C2   N1    115.50  3.000
 QQY  N3    C2   N1    128.39  3.000
 QQY  N3    C4   C5    126.80  3.000
 QQY  N3    C4   N9    128.14  3.000
 QQY  C5    C4   N9    105.06  3.000
 QQY  C4    N3   C2    111.54  3.000
 QQY  O2'   P    O3'    96.52  3.000
 QQY  O2'   P    S1P   100.42  3.000
 QQY  O3'   P    S1P   109.54  3.000
 QQY  O2'   P    OP3   119.50  3.000
 QQY  O3'   P    OP3   114.28  3.000
 QQY  S1P   P    OP3   114.46  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
 QQY  CONST_01  C5    N7  C8   N9     0.00   0.0  0
 QQY  CONST_02  N7    C5  C4   N9     0.00   0.0  0
 QQY  CONST_03  C6    C5  C4   N9   180.00   0.0  0
 QQY  CONST_04  C2    N3  C4   N9   180.00   0.0  0
 QQY  CONST_05  C5    C4  N9   C8     0.00   0.0  0
 QQY  CONST_06  N3    C4  N9   C8   180.00   0.0  0
 QQY  CONST_07  C6    C5  N7   C8   180.00   0.0  0
 QQY  CONST_08  C4    C5  N7   C8     0.00   0.0  0
 QQY  CONST_09  C4    N9  C8   N7     0.00   0.0  0
 QQY  CONST_10  N1    C6  C5   N7   180.00   0.0  0
 QQY  CONST_11  N3    C4  C5   N7   180.00   0.0  0
 QQY  CONST_12  C2    N1  C6   C5     0.00   0.0  0
 QQY  CONST_13  C2    N3  C4   C5     0.00   0.0  0
 QQY  CONST_14  N3    C4  C5   C6     0.00   0.0  0
 QQY  CONST_15  N3    C2  N1   C6     0.00   0.0  0
 QQY  CONST_16  C4    C5  C6   N1     0.00   0.0  0
 QQY  CONST_17  C4    N3  C2   N1     0.00   0.0  0
 QQY  CONST_18  N7    C8  N9   C1'  180.00   0.0  0
 QQY  CONST_19  C5    C4  N9   C1'  180.00   0.0  0
 QQY  CONST_20  N3    C4  N9   C1'    0.00   0.0  0
 QQY  CONST_21  N6    C6  C5   N7     0.00   0.0  0
 QQY  CONST_22  C4    C5  C6   N6   180.00   0.0  0
 QQY  CONST_23  C2    N1  C6   N6   180.00   0.0  0
 QQY  CONST_24  H8    C8  N9   C1'    0.00   0.0  0
 QQY  CONST_25  H2    C2  N1   C6   180.00   0.0  0
 QQY  CONST_26  H61N  N6  C6   C5     0.00   0.0  0
 QQY  CONST_27  H62N  N6  C6   C5   180.00   0.0  0
 QQY  Var_01    O2'   P   O3'  C3'    4.83  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
 QQY  chir_01  C4'  C5'  O4'  C3'  negativ
 QQY  chir_02  C3'  O3'  C2'  C4'  negativ
 QQY  chir_03  C2'  O2'  C1'  C3'  negativ
 QQY  chir_04  C1'  O4'  N9   C2'  negativ
 QQY  chir_05  P    S1P  O3'  O2'  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
 QQY  plan-1  C1'   0.020
 QQY  plan-1  N9    0.020
 QQY  plan-1  C8    0.020
 QQY  plan-1  N7    0.020
 QQY  plan-1  C5    0.020
 QQY  plan-1  C6    0.020
 QQY  plan-1  N6    0.020
 QQY  plan-1  N1    0.020
 QQY  plan-1  C2    0.020
 QQY  plan-1  C4    0.020
 QQY  plan-1  N3    0.020
 QQY  plan-1  H8    0.020
 QQY  plan-1  H2    0.020
 QQY  plan-2  C6    0.020
 QQY  plan-2  N6    0.020
 QQY  plan-2  H61N  0.020
 QQY  plan-2  H62N  0.020

