# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-1071 (Mon Jun  5 03:29:00 2012)
#   - file written: Fri Aug 31 12:03:31 2012
#
#   Ligand name: 5'-O-[(S)-hydroxy{[(S)-hydroxy(thiophosphonooxy)phosphoryl]oxy}phosphoryl]adenosine
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[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
AGS        AGS '5'-O-[(S)-hydroxy{[(S)-hydroxy(thiophosphonooxy)phosphoryl]oxy}phosphoryl]adenosine' ligand 47 31 .
2012-08-31 2012-08-31
;
CIF prepared directly in eLBOW
;
#
data_comp_AGS
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
AGS         PG     P   P     .         -3.5411   -6.2158    2.7774
AGS         S1G    S   S1    .         -2.3610   -7.7646    2.6828
AGS         O2G    O   OH1   .         -3.9902   -5.9940    4.2512
AGS         O3G    O   OH1   .         -4.7965   -6.4706    1.8913
AGS         PB     P   P     .         -1.3105   -4.6483    2.7468
AGS         O1B    O   O     .         -1.2917   -4.2861    4.1829
AGS         O2B    O   OH1   .         -0.4890   -5.9003    2.4267
AGS         O3B    O   O2    .         -2.7929   -4.9484    2.2643
AGS         PA     P   P     .         -0.2520   -2.1206    2.5781
AGS         O1A    O   O     .          0.9154   -2.3384    3.4643
AGS         O2A    O   OH1   .         -1.4861   -1.5729    3.3028
AGS         O3A    O   O2    .         -0.6920   -3.4744    1.8762
AGS        O5'     O   O2    .          0.1940   -1.1698    1.3900
AGS        C5'     C   CH2   .          1.1412   -0.0993    1.5871
AGS        C4'     C   CH1   .          1.7078    0.3106    0.2504
AGS        O4'     O   O2    .          0.7185    1.0421   -0.4886
AGS        C3'     C   CH1   .          2.9070    1.2510    0.3153
AGS        O3'     O   OH1   .          4.1238    0.5154    0.3693
AGS        C2'     C   CH1   .          2.7919    2.0799   -0.9783
AGS        O2'     O   OH1   .          3.7834    1.7186   -1.9332
AGS        C1'     C   CH1   .          1.3880    1.7504   -1.5079
AGS         N9     N   NR5   .          0.5917    2.9216   -1.8603
AGS         C8     C   CR15  .          0.0016    3.8153   -1.0049
AGS         N7     N   N     .         -0.6552    4.7772   -1.6082
AGS         C5     C   CR56  .         -0.4834    4.4971   -2.9555
AGS         C6     C   CR6   .         -0.9335    5.1425   -4.1237
AGS         N6     N   NH2   .         -1.6791    6.2498   -4.1205
AGS         N1     N   N     .         -0.5839    4.6021   -5.3136
AGS         C2     C   CR16  .          0.1628    3.4939   -5.3242
AGS         N3     N   N     .          0.6432    2.8008   -4.2887
AGS         C4     C   CR56  .          0.2827    3.3574   -3.1258
AGS        HOG2    H   HOH1  .         -4.5975   -6.5998    4.4693
AGS        H21     H   HOH1  .         -5.1390   -7.2631    2.0854
AGS        HOB2    H   HOH1  .          0.0422   -6.0876    3.1092
AGS        HOA2    H   HOH1  .         -1.2300   -1.0197    3.9445
AGS        H5'1    H   HCH2  .          0.6969    0.6620    1.9992
AGS        H5'2    H   HCH2  .          1.8632   -0.4059    2.1625
AGS        H4'     H   HCH1  .          1.9536   -0.4850   -0.2489
AGS        H3'     H   HCH1  .          2.8295    1.8315    1.0895
AGS        HO3'    H   HOH1  .          4.6312    0.8314    1.0246
AGS        H2'     H   HCH1  .          2.8549    3.0261   -0.7709
AGS        HO2'    H   HOH1  .          4.0225    0.8734   -1.8102
AGS        H1'     H   HCH1  .          1.4738    1.1773   -2.2894
AGS        H8      H   HCR5  .          0.0622    3.7426   -0.0405
AGS        HN61    H   HNH2  .         -1.8863    6.6586   -4.9055
AGS        HN62    H   HNH2  .         -1.9787    6.5954   -3.3349
AGS        H2      H   HCR6  .          0.3866    3.1455   -6.2045
#
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
AGS   PG      S1G   double        1.949 0.020
AGS   PG      O2G   single        1.557 0.020
AGS   PG      O3G   single        1.558 0.020
AGS   PG      O3B   single        1.559 0.020
AGS   PB      O1B   double        1.481 0.020
AGS   PB      O2B   single        1.531 0.016
AGS   PB      O3B   single        1.585 0.027
AGS   PB      O3A   single        1.585 0.027
AGS   PA      O1A   double        1.481 0.027
AGS   PA      O2A   single        1.531 0.016
AGS   PA      O3A   single        1.585 0.027
AGS   PA     O5'    single        1.581 0.027
AGS  O5'     C5'    single        1.442 0.027
AGS  C5'     C4'    single        1.508 0.016
AGS  C4'     O4'    single        1.444 0.012
AGS  C4'     C3'    single        1.526 0.011
AGS  O4'     C1'    single        1.415 0.011
AGS  C3'     O3'    single        1.423 0.011
AGS  C3'     C2'    single        1.530 0.013
AGS  C2'     O2'    single        1.423 0.013
AGS  C2'     C1'    single        1.530 0.013
AGS  C1'      N9    single        1.459 0.014
AGS   N9      C8    aromatic      1.370 0.011
AGS   N9      C4    aromatic      1.374 0.010
AGS   C8      N7    aromatic      1.311 0.010
AGS   N7      C5    aromatic      1.387 0.010
AGS   C5      C6    aromatic      1.409 0.010
AGS   C5      C4    aromatic      1.386 0.010
AGS   C6      N6    single        1.335 0.010
AGS   C6      N1    aromatic      1.351 0.013
AGS   N1      C2    aromatic      1.335 0.010
AGS   C2      N3    aromatic      1.335 0.010
AGS   N3      C4    aromatic      1.340 0.010
AGS   O2G    HOG2   single        0.885 0.012
AGS   O3G    H21    single        0.885 0.012
AGS   O2B    HOB2   single        0.885 0.012
AGS   O2A    HOA2   single        0.885 0.012
AGS  C5'     H5'1   single        0.973 0.012
AGS  C5'     H5'2   single        0.973 0.012
AGS  C4'     H4'    single        0.971 0.012
AGS  C3'     H3'    single        0.971 0.012
AGS  O3'     HO3'   single        0.887 0.012
AGS  C2'     H2'    single        0.971 0.012
AGS  O2'     HO2'   single        0.887 0.012
AGS  C1'     H1'    single        0.973 0.012
AGS   C8     H8     single        0.969 0.012
AGS   N6     HN61   single        0.909 0.012
AGS   N6     HN62   single        0.909 0.012
AGS   C2     H2     single        0.973 0.012
#
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
AGS   O3B     PG      O3G         109.43 3.000
AGS   O3B     PG      O2G         109.53 3.000
AGS   O3G     PG      O2G         109.23 3.000
AGS   O3B     PG      S1G         109.85 3.000
AGS   O3G     PG      S1G         109.29 3.000
AGS   O2G     PG      S1G         109.50 3.000
AGS  HOG2     O2G     PG          109.50 3.000
AGS  H21      O3G     PG          109.50 3.000
AGS   O3A     PB      O3B         109.69 3.000
AGS   O3A     PB      O2B         105.97 3.000
AGS   O3B     PB      O2B         105.97 3.000
AGS   O3A     PB      O1B         109.95 3.000
AGS   O3B     PB      O1B         109.95 3.000
AGS   O2B     PB      O1B         112.09 4.086
AGS  HOB2     O2B     PB          109.50 3.000
AGS   PB      O3B     PG          120.12 3.000
AGS  O5'      PA      O3A         104.35 3.000
AGS  O5'      PA      O2A         110.83 3.000
AGS   O3A     PA      O2A         105.97 3.000
AGS  O5'      PA      O1A         106.70 3.000
AGS   O3A     PA      O1A         109.95 3.000
AGS   O2A     PA      O1A         112.09 4.086
AGS  HOA2     O2A     PA          109.47 3.000
AGS   PA      O3A     PB          119.76 3.000
AGS  C5'     O5'      PA          121.27 3.000
AGS  H5'2    C5'     H5'1         109.57 3.000
AGS  H5'2    C5'     C4'          109.33 3.000
AGS  H5'1    C5'     C4'          109.52 3.000
AGS  H5'2    C5'     O5'          109.52 3.000
AGS  H5'1    C5'     O5'          109.79 3.000
AGS  C4'     C5'     O5'          108.69 2.415
AGS  H4'     C4'     C3'          109.15 3.000
AGS  H4'     C4'     O4'          109.11 3.000
AGS  C3'     C4'     O4'          105.29 1.268
AGS  H4'     C4'     C5'          109.15 3.000
AGS  C3'     C4'     C5'          115.29 1.819
AGS  O4'     C4'     C5'          109.53 1.519
AGS  C1'     O4'     C4'          109.51 1.456
AGS  H3'     C3'     C2'          109.99 3.000
AGS  H3'     C3'     O3'          110.31 3.000
AGS  C2'     C3'     O3'          111.92 2.692
AGS  H3'     C3'     C4'          109.87 3.000
AGS  C2'     C3'     C4'          102.46 0.989
AGS  O3'     C3'     C4'          111.00 2.566
AGS  HO3'    O3'     C3'          109.45 3.000
AGS  H2'     C2'     C1'          110.00 3.000
AGS  H2'     C2'     O2'          110.22 3.000
AGS  C1'     C2'     O2'          110.64 2.749
AGS  H2'     C2'     C3'          109.89 3.000
AGS  C1'     C2'     C3'          101.46 1.185
AGS  O2'     C2'     C3'          111.92 2.692
AGS  HO2'    O2'     C2'          109.68 3.000
AGS  H1'     C1'      N9          109.08 3.000
AGS  H1'     C1'     C2'          108.82 3.000
AGS   N9     C1'     C2'          114.04 1.554
AGS  H1'     C1'     O4'          109.06 3.000
AGS   N9     C1'     O4'          108.44 1.319
AGS  C2'     C1'     O4'          106.47 1.154
AGS   C4      N9      C8          105.70 0.455
AGS   C4      N9     C1'          126.86 1.802
AGS   C8      N9     C1'          126.91 1.916
AGS  H8       C8      N7          122.96 3.000
AGS  H8       C8      N9          123.04 3.000
AGS   N7      C8      N9          114.03 0.699
AGS   C5      N7      C8          103.67 0.426
AGS   C4      C5      C6          117.00 0.672
AGS   C4      C5      N7          110.73 0.452
AGS   C6      C5      N7          132.18 0.930
AGS   N1      C6      N6          118.30 1.194
AGS   N1      C6      C5          117.53 0.763
AGS   N6      C6      C5          123.61 1.028
AGS  HN62     N6     HN61         120.02 3.000
AGS  HN62     N6      C6          120.10 3.000
AGS  HN61     N6      C6          119.88 3.000
AGS   C2      N1      C6          118.64 0.909
AGS  H2       C2      N3          115.67 3.000
AGS  H2       C2      N1          115.64 3.000
AGS   N3      C2      N1          128.80 0.841
AGS   C4      N3      C2          111.53 1.934
AGS   N3      C4      C5          126.80 0.741
AGS   N3      C4      N9          127.16 1.059
AGS   C5      C4      N9          105.77 0.443
#
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
AGS CONST_01       C5      N7      C8      N9           -0.07   0.0 0
AGS CONST_02       N7      C5      C4      N9            0.03   0.0 0
AGS CONST_03       C6      C5      C4      N9         -179.96   0.0 0
AGS CONST_04       C2      N3      C4      N9          179.96   0.0 0
AGS CONST_05       C5      C4      N9      C8           -0.07   0.0 0
AGS CONST_06       N3      C4      N9      C8          179.96   0.0 0
AGS CONST_07       C6      C5      N7      C8         -179.99   0.0 0
AGS CONST_08       C4      C5      N7      C8            0.02   0.0 0
AGS CONST_09       C4      N9      C8      N7            0.09   0.0 0
AGS CONST_10       N1      C6      C5      N7          179.99   0.0 0
AGS CONST_11       N3      C4      C5      N7          180.00   0.0 0
AGS CONST_12       C2      N1      C6      C5            0.02   0.0 0
AGS CONST_13       C2      N3      C4      C5           -0.00   0.0 0
AGS CONST_14       N3      C4      C5      C6            0.01   0.0 0
AGS CONST_15       N3      C2      N1      C6           -0.02   0.0 0
AGS CONST_16       C4      C5      C6      N1           -0.02   0.0 0
AGS CONST_17       C4      N3      C2      N1            0.01   0.0 0
AGS CONST_18       N7      C8      N9     C1'          179.91   0.0 0
AGS CONST_19       C5      C4      N9     C1'         -179.89   0.0 0
AGS CONST_20       N3      C4      N9     C1'            0.14   0.0 0
AGS CONST_21       N6      C6      C5      N7            0.04   0.0 0
AGS CONST_22       C4      C5      C6      N6         -179.97   0.0 0
AGS CONST_23       C2      N1      C6      N6          179.98   0.0 0
AGS CONST_24      H8       C8      N9     C1'           -0.20   0.0 0
AGS CONST_25      H2       C2      N1      C6          179.99   0.0 0
AGS CONST_26      HN61     N6      C6      C5          175.26   0.0 0
AGS CONST_27      HN62     N6      C6      C5           -4.67   0.0 0
AGS Var_01        C2'     C1'     O4'     C4'          -30.46  30.0 1
AGS Var_02        C1'     C2'     C3'     C4'           11.71  30.0 1
AGS Var_03        C2'     C3'     C4'     O4'          -29.68  30.0 1
AGS Var_04        C3'     C2'     C1'     O4'           10.44  30.0 1
AGS Var_05         C8      N9     C1'     O4'           46.16  30.0 2
AGS Var_06        O4'     C4'     C5'     O5'           73.38  30.0 3
AGS Var_07        C4'     C5'     O5'      PA          161.16  30.0 3
AGS Var_08         O1B     PB      O3B     PG          -68.91  30.0 1
AGS Var_09         O1A     PA      O3A     PB           67.73  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
AGS chir_03  C4'     C5'     O4'     C3'    negativ
AGS chir_04  C3'     O3'     C4'     C2'    positiv
AGS chir_05  C2'     O2'     C3'     C1'    positiv
AGS chir_06  C1'     O4'      N9     C2'    negativ
AGS chir_07   PB      O2B     O3B     O3A   both
AGS chir_08   PA      O2A     O3A    O5'    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
AGS plan-1    C1' 0.020
AGS plan-1     N9 0.020
AGS plan-1     C8 0.020
AGS plan-1     N7 0.020
AGS plan-1     C5 0.020
AGS plan-1     C6 0.020
AGS plan-1     N6 0.020
AGS plan-1     N1 0.020
AGS plan-1     C2 0.020
AGS plan-1     N3 0.020
AGS plan-1     C4 0.020
AGS plan-1     H8 0.020
AGS plan-1     H2 0.020
AGS plan-2     C6 0.020
AGS plan-2     N6 0.020
AGS plan-2   HN61 0.020
AGS plan-2   HN62 0.020
