# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Oct 22 14:03:04 2020
#
#   Inital geometry file: a 110 line input string
#   Ligand name: [[(2R,5S)-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxy-phosphoryl] phosphono hydrogen phosphate
#   CSD Mogul values: True
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3CC[C@H](CO[P@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O3
#
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
DAD        DAD '[[(2R,5S)-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxy-phosphoryl] phosphono hydrogen phosphate' ligand 41 29 .
2020-10-22 2020-10-22
;
CIF prepared directly in eLBOW
;
#
data_comp_DAD
#
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
DAD         PG     P   P      0    .       1.1540    0.2820   -6.5950
DAD         O1G    O   O      0    .      -0.2030    0.0960   -7.1540
DAD         O2G    O   OP    -1    .       2.0430    1.1480   -7.6220
DAD         O3G    O   OP    -1    .       1.8430   -1.1540   -6.3690
DAD         PB     P   P      0    .       0.1560    0.1400   -4.2150
DAD         O1B    O   O      0    .       0.8050   -1.1780   -4.0440
DAD         O2B    O   OP    -1    .      -1.3030   -0.0600   -4.8630
DAD         O3B    O   O2     0    .       1.0530    1.0570   -5.1880
DAD         PA     P   P      0    .      -0.8900   -0.1080   -1.8650
DAD         O1A    O   O      0    .      -0.2250   -1.4230   -1.7290
DAD         O2A    O   OP    -1    .      -2.3330   -0.3040   -2.5520
DAD         O3A    O   O2     0    .       0.0130    0.8580   -2.7810
DAD        O5'     O   O2     0    .      -1.0750    0.5520   -0.4080
DAD        C5'     C   CH2    0    .      -1.8810   -0.3480    0.3530
DAD        C4'     C   CH1    0    .      -2.0960    0.2220    1.7570
DAD        O4'     O   O2     0    .      -0.8410    0.3050    2.4670
DAD        C3'     C   CH2    0    .      -2.9670   -0.7350    2.5990
DAD        C2'     C   CH2    0    .      -2.3630   -0.6400    4.0180
DAD        C1'     C   CH1    0    .      -1.1990    0.3630    3.8650
DAD         N9     N   NR5    0    .      -0.0640   -0.0400    4.6990
DAD         C8     C   CR15   0    .       0.9460   -0.8790    4.3350
DAD         N7     N   N      0    .       1.7850   -1.0170    5.3200
DAD         C5     C   CR56   0    .       1.3700   -0.2740    6.3740
DAD         C6     C   CR6    0    .       1.8530   -0.0450    7.6740
DAD         N6     N   NH2    0    .       3.0220   -0.6450    8.1100
DAD         N1     N   N      0    .       1.1650    0.7630    8.4720
DAD         C2     C   CR16   0    .       0.0490    1.3390    8.0640
DAD         N3     N   N      0    .      -0.4440    1.1500    6.8590
DAD         C4     C   CR56   0    .       0.1750    0.3570    5.9910
DAD        H5'1    H   HCH2   0    .      -1.3790   -1.3120    0.4270
DAD        H5'2    H   HCH2   0    .      -2.8460   -0.4770   -0.1370
DAD        H4'     H   HCH1   0    .      -2.5620    1.2060    1.6980
DAD        H3'1    H   HCH2   0    .      -2.8920   -1.7540    2.2190
DAD        H3'2    H   HCH2   0    .      -4.0050   -0.4030    2.6040
DAD        H2'1    H   HCH2   0    .      -1.9890   -1.6130    4.3400
DAD        H2'2    H   HCH2   0    .      -3.1030   -0.2620    4.7240
DAD        H1'     H   HCH1   0    .      -1.5270    1.3670    4.1310
DAD         H8     H   HCR5   0    .       1.0370   -1.3580    3.3720
DAD        HN61    H   HNH2   0    .       3.3480   -0.4760    9.0080
DAD        HN62    H   HNH2   0    .       3.5130   -1.2370    7.5190
DAD         H2     H   HCR6   0    .      -0.4780    1.9900    8.7460
#
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
DAD   PG      O1G   deloc         1.491 0.020     1.491
DAD   PG      O2G   deloc         1.533 0.032     1.533
DAD   PG      O3G   deloc         1.533 0.028     1.533
DAD   PG      O3B   single        1.600 0.028     1.600
DAD   PB      O1B   deloc         1.477 0.022     1.477
DAD   PB      O2B   deloc         1.529 0.022     1.529
DAD   PB      O3B   single        1.592 0.030     1.592
DAD   PB      O3A   single        1.592 0.011     1.592
DAD   PA      O1A   deloc         1.477 0.011     1.477
DAD   PA      O2A   deloc         1.529 0.022     1.529
DAD   PA      O3A   single        1.592 0.030     1.592
DAD   PA     O5'    single        1.579 0.011     1.579
DAD  O5'     C5'    single        1.443 0.010     1.443
DAD  C5'     C4'    single        1.504 0.015     1.504
DAD  C5'     H5'1   single        0.970 0.015     1.090
DAD  C5'     H5'2   single        0.970 0.015     1.090
DAD  C4'     O4'    single        1.445 0.015     1.445
DAD  C4'     C3'    single        1.521 0.011     1.521
DAD  C4'     H4'    single        0.970 0.027     1.090
DAD  O4'     C1'    single        1.418 0.027     1.418
DAD  C3'     C2'    single        1.539 0.013     1.539
DAD  C3'     H3'1   single        0.970 0.017     1.090
DAD  C3'     H3'2   single        0.970 0.017     1.090
DAD  C2'     C1'    single        1.520 0.017     1.520
DAD  C2'     H2'1   single        0.970 0.010     1.090
DAD  C2'     H2'2   single        0.970 0.010     1.090
DAD  C1'      N9    single        1.457 0.010     1.457
DAD  C1'     H1'    single        0.970 0.011     1.090
DAD   N9      C8    aromatic      1.370 0.011     1.370
DAD   N9      C4    aromatic      1.374 0.010     1.374
DAD   C8      N7    aromatic      1.310 0.010     1.310
DAD   C8      H8    single        0.930 0.010     1.080
DAD   N7      C5    aromatic      1.387 0.010     1.387
DAD   C5      C6    aromatic      1.409 0.010     1.409
DAD   C5      C4    aromatic      1.388 0.010     1.388
DAD   C6      N6    single        1.337 0.011     1.337
DAD   C6      N1    aromatic      1.350 0.014     1.350
DAD   N6     HN61   single        0.860 0.010     1.020
DAD   N6     HN62   single        0.860 0.010     1.020
DAD   N1      C2    aromatic      1.334 0.010     1.334
DAD   C2      N3    aromatic      1.334 0.011     1.334
DAD   C2      H2    single        0.930 0.011     1.080
DAD   N3      C4    aromatic      1.338 0.011     1.338
#
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
DAD   O3B     PG      O3G         104.48 1.135
DAD   O3B     PG      O2G         104.48 1.135
DAD   O3G     PG      O2G         108.70 2.785
DAD   O3B     PG      O1G         110.47 1.644
DAD   O3G     PG      O1G         113.32 2.534
DAD   O2G     PG      O1G         113.32 2.534
DAD   O3A     PB      O3B         101.57 1.536
DAD   O3A     PB      O2B         106.94 1.880
DAD   O3B     PB      O2B         106.94 1.880
DAD   O3A     PB      O1B         111.24 2.719
DAD   O3B     PB      O1B         111.24 2.719
DAD   O2B     PB      O1B         114.42 3.527
DAD   PB      O3B     PG          139.87 1.000
DAD  O5'      PA      O3A         102.67 2.380
DAD  O5'      PA      O2A         108.07 2.651
DAD   O3A     PA      O2A         106.94 1.880
DAD  O5'      PA      O1A         110.65 3.490
DAD   O3A     PA      O1A         111.24 2.719
DAD   O2A     PA      O1A         114.42 3.527
DAD   PA      O3A     PB          136.83 1.000
DAD  C5'     O5'      PA          121.27 1.000
DAD  H5'2    C5'     H5'1         109.50 3.000
DAD  H5'2    C5'     C4'          109.40 3.000
DAD  H5'1    C5'     C4'          109.39 3.000
DAD  H5'2    C5'     O5'          109.56 3.000
DAD  H5'1    C5'     O5'          109.50 3.000
DAD  C4'     C5'     O5'          107.83 2.029
DAD  H4'     C4'     C3'          127.79 3.000
DAD  H4'     C4'     O4'          127.79 3.000
DAD  C3'     C4'     O4'          104.42 1.238
DAD  H4'     C4'     C5'          127.79 3.000
DAD  C3'     C4'     C5'          114.99 2.697
DAD  O4'     C4'     C5'          109.99 1.587
DAD  C1'     O4'     C4'          110.05 1.000
DAD  H3'2    C3'     H3'1         110.60 3.000
DAD  H3'2    C3'     C2'          110.45 3.000
DAD  H3'1    C3'     C2'          110.53 3.000
DAD  H3'2    C3'     C4'          110.55 3.000
DAD  H3'1    C3'     C4'          110.52 3.000
DAD  C2'     C3'     C4'          102.63 1.568
DAD  H2'2    C2'     H2'1         110.53 3.000
DAD  H2'2    C2'     C1'          110.52 3.000
DAD  H2'1    C2'     C1'          110.50 3.000
DAD  H2'2    C2'     C3'          110.53 3.000
DAD  H2'1    C2'     C3'          110.50 3.000
DAD  C1'     C2'     C3'          102.93 1.282
DAD  H1'     C1'      N9          122.98 3.000
DAD  H1'     C1'     C2'          122.98 3.000
DAD   N9     C1'     C2'          114.05 1.000
DAD  H1'     C1'     O4'          122.98 3.000
DAD   N9     C1'     O4'          108.17 1.038
DAD  C2'     C1'     O4'          106.88 1.000
DAD   C4      N9      C8          105.72 1.000
DAD   C4      N9     C1'          126.78 2.496
DAD   C8      N9     C1'          126.87 2.531
DAD   H8      C8      N7          122.96 3.000
DAD   H8      C8      N9          122.96 3.000
DAD   N7      C8      N9          114.08 1.000
DAD   C5      N7      C8          103.68 1.000
DAD   C4      C5      C6          116.99 1.000
DAD   C4      C5      N7          110.69 1.000
DAD   C6      C5      N7          132.07 1.184
DAD   N1      C6      N6          118.11 1.227
DAD   N1      C6      C5          117.60 1.000
DAD   N6      C6      C5          123.59 1.076
DAD  HN62     N6     HN61         120.01 3.000
DAD  HN62     N6      C6          120.00 3.000
DAD  HN61     N6      C6          119.98 3.000
DAD   C2      N1      C6          118.58 1.047
DAD   H2      C2      N3          115.66 3.000
DAD   H2      C2      N1          115.66 3.000
DAD   N3      C2      N1          128.69 1.000
DAD   C4      N3      C2          112.03 2.344
DAD   N3      C4      C5          126.80 1.000
DAD   N3      C4      N9          127.04 1.148
DAD   C5      C4      N9          105.76 1.000
#
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
DAD CONST_01       C5      N7      C8      N9           -0.20   0.0 0
DAD CONST_02       N7      C5      C4      N9           -0.45   0.0 0
DAD CONST_03       C6      C5      C4      N9         -179.68   0.0 0
DAD CONST_04       C2      N3      C4      N9         -179.96   0.0 0
DAD CONST_05       C5      C4      N9      C8            0.33   0.0 0
DAD CONST_06       N3      C4      N9      C8          179.99   0.0 0
DAD CONST_07       C6      C5      N7      C8          179.44   0.0 0
DAD CONST_08       C4      C5      N7      C8            0.40   0.0 0
DAD CONST_09       C4      N9      C8      N7           -0.10   0.0 0
DAD CONST_10       N1      C6      C5      N7         -179.51   0.0 0
DAD CONST_11       N3      C4      C5      N7          179.83   0.0 0
DAD CONST_12       C2      N1      C6      C5            0.24   0.0 0
DAD CONST_13       C2      N3      C4      C5           -0.33   0.0 0
DAD CONST_14       N3      C4      C5      C6            0.60   0.0 0
DAD CONST_15       N3      C2      N1      C6            0.05   0.0 0
DAD CONST_16       C4      C5      C6      N1           -0.55   0.0 0
DAD CONST_17       C4      N3      C2      N1           -0.00   0.0 0
DAD CONST_18       N7      C8      N9     C1'         -180.00   0.0 0
DAD CONST_19       C5      C4      N9     C1'         -179.77   0.0 0
DAD CONST_20       N3      C4      N9     C1'           -0.11   0.0 0
DAD CONST_21       N6      C6      C5      N7            0.71   0.0 0
DAD CONST_22       C4      C5      C6      N6          179.67   0.0 0
DAD CONST_23       C2      N1      C6      N6         -179.99   0.0 0
DAD CONST_24       H8      C8      N9     C1'            0.03   0.0 0
DAD CONST_25       H2      C2      N1      C6         -179.93   0.0 0
DAD CONST_26      HN61     N6      C6      C5          179.70   0.0 0
DAD CONST_27      HN62     N6      C6      C5           -0.55   0.0 0
DAD Var_01        C1'     C2'     C3'     C4'            0.00  30.0 1
DAD Var_02        C4'     C5'     O5'      PA          179.97  30.0 3
DAD Var_03         O1B     PB      O3B     PG           59.97  30.0 1
DAD Var_04         O1A     PA      O3A     PB           60.03  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
DAD chir_03  C4'     C5'     O4'     C3'    positiv
DAD chir_04  C1'     O4'      N9     C2'    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
DAD plan-1    C1' 0.020
DAD plan-1     N9 0.020
DAD plan-1     C8 0.020
DAD plan-1     N7 0.020
DAD plan-1     C5 0.020
DAD plan-1     C6 0.020
DAD plan-1     N6 0.020
DAD plan-1     N1 0.020
DAD plan-1     C2 0.020
DAD plan-1     N3 0.020
DAD plan-1     C4 0.020
DAD plan-1     H8 0.020
DAD plan-1     H2 0.020
DAD plan-2     C6 0.020
DAD plan-2     N6 0.020
DAD plan-2   HN61 0.020
DAD plan-2   HN62 0.020
