data_G5F
# 
_chem_comp.id                                    G5F 
_chem_comp.name                                  "[(2~{S},3~{S},4~{R})-4-[(2~{S},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-5-[[(2~{S},3~{R})-2,3-bis(oxidanyl)butoxy]-oxidanyl-phosphoryl]oxy-2,3-bis(oxidanyl)pentyl] [(2~{R},3~{S},4~{S})-2,3,4,5-tetrakis(oxidanyl)pentyl] hydrogen phosphate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C23 H47 N O24 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-01-27 
_chem_comp.pdbx_modified_date                    2022-08-26 
_chem_comp.pdbx_ambiguous_flag                   N 
_chem_comp.pdbx_release_status                   REL 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        783.559 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     G5F 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   Y 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        7QXD 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
# 
loop_
_chem_comp_atom.comp_id 
_chem_comp_atom.atom_id 
_chem_comp_atom.alt_atom_id 
_chem_comp_atom.type_symbol 
_chem_comp_atom.charge 
_chem_comp_atom.pdbx_align 
_chem_comp_atom.pdbx_aromatic_flag 
_chem_comp_atom.pdbx_leaving_atom_flag 
_chem_comp_atom.pdbx_stereo_config 
_chem_comp_atom.model_Cartn_x 
_chem_comp_atom.model_Cartn_y 
_chem_comp_atom.model_Cartn_z 
_chem_comp_atom.pdbx_model_Cartn_x_ideal 
_chem_comp_atom.pdbx_model_Cartn_y_ideal 
_chem_comp_atom.pdbx_model_Cartn_z_ideal 
_chem_comp_atom.pdbx_component_atom_id 
_chem_comp_atom.pdbx_component_comp_id 
_chem_comp_atom.pdbx_ordinal 
G5F C2  C1  C 0 1 N N R 4.850  -24.824 -61.815 2.294   2.890  -1.497 C2  G5F 1  
G5F C4  C2  C 0 1 N N S 3.099  -26.575 -62.329 1.463   0.705  -0.623 C4  G5F 2  
G5F C5  C3  C 0 1 N N R 5.267  -26.867 -63.185 1.295   2.645  0.777  C5  G5F 3  
G5F C6  C4  C 0 1 N N N 6.215  -27.983 -63.555 0.404   3.306  1.830  C6  G5F 4  
G5F C7  C5  C 0 1 N N R 1.249  -28.056 -62.649 0.686   -1.438 0.120  C7  G5F 5  
G5F C8  C6  C 0 1 N N N 0.114  -27.226 -63.204 1.908   -2.359 0.120  C8  G5F 6  
G5F C9  C7  C 0 1 N N S 0.768  -29.253 -61.836 -0.584  -2.274 -0.046 C9  G5F 7  
G5F C10 C8  C 0 1 N N S 1.902  -30.043 -61.177 -1.806  -1.353 -0.046 C10 G5F 8  
G5F C11 C9  C 0 1 N N N 2.842  -30.656 -62.179 -3.076  -2.190 -0.212 C11 G5F 9  
G5F C12 C10 C 0 1 N N N 6.883  -31.839 -62.782 -8.177  -0.886 0.167  C12 G5F 10 
G5F O14 O1  O 0 1 N N N 12.016 -32.092 -61.748 -13.151 2.558  1.596  O14 G5F 11 
G5F C15 C11 C 0 1 N N S 9.919  -32.561 -62.884 -11.035 1.559  0.990  C15 G5F 12 
G5F C16 C12 C 0 1 N N N -3.821 -27.879 -63.003 7.054   -1.316 0.656  C16 G5F 13 
G5F C17 C13 C 0 1 N N S -4.517 -28.584 -64.162 7.800   0.005  0.861  C17 G5F 14 
G5F C18 C14 C 0 1 N N R -5.578 -27.735 -64.874 9.300   -0.271 0.984  C18 G5F 15 
G5F C19 C15 C 0 1 N N N -6.320 -28.457 -66.009 10.045  1.050  1.189  C19 G5F 16 
G5F C20 C16 C 0 1 N N N 1.568  -24.541 -60.289 1.905   -0.031 -3.699 C20 G5F 17 
G5F O21 O2  O 0 1 N N N 5.312  -33.234 -60.767 -5.983  -2.442 -1.710 O21 G5F 18 
G5F O22 O3  O 0 1 N N N -2.808 -25.909 -61.012 4.630   -3.256 1.714  O22 G5F 19 
G5F C1  C17 C 0 1 N N S 5.881  -25.869 -62.209 1.451   3.583  -0.423 C1  G5F 20 
G5F C3  C18 C 0 1 N N R 3.547  -25.475 -61.355 1.626   1.565  -1.879 C3  G5F 21 
G5F O1  O4  O 0 1 N N N 4.143  -27.501 -62.562 0.696   1.420  0.347  O1  G5F 22 
G5F O2  O5  O 0 1 N N N 2.024  -27.231 -61.758 0.790   -0.510 -0.962 O2  G5F 23 
G5F N1  N1  N 0 1 N N N 2.465  -24.517 -61.281 2.461   0.858  -2.852 N1  G5F 24 
G5F O3  O6  O 0 1 N N N 5.400  -23.985 -60.805 2.383   3.730  -2.650 O3  G5F 25 
G5F O4  O7  O 0 1 N N N 7.032  -25.255 -62.786 2.102   4.785  -0.007 O4  G5F 26 
G5F O5  O8  O 0 1 N N N 5.626  -28.841 -64.554 0.352   2.481  2.996  O5  G5F 27 
G5F O6  O9  O 0 1 N N N -0.688 -26.778 -62.080 3.083   -1.592 0.391  O6  G5F 28 
G5F O7  O10 O 0 1 N N N 3.964  -31.237 -61.465 -4.222  -1.344 -0.096 O7  G5F 29 
G5F P1  P1  P 0 1 N N N 4.545  -32.669 -61.936 -5.731  -1.891 -0.218 P1  G5F 30 
G5F O8  O11 O 0 1 N N N 5.566  -32.308 -63.125 -6.762  -0.695 0.093  O8  G5F 31 
G5F C13 C19 C 0 1 N N R 7.729  -31.885 -64.028 -8.856  0.450  0.477  C13 G5F 32 
G5F C14 C20 C 0 1 N N S 9.175  -31.507 -63.712 -10.356 0.224  0.679  C14 G5F 33 
G5F P2  P2  P 0 1 N N N -2.053 -25.984 -62.301 4.554   -2.241 0.466  P2  G5F 34 
G5F O9  O12 O 0 1 N N N -2.820 -26.892 -63.398 5.646   -1.073 0.658  O9  G5F 35 
G5F C21 C21 C 0 1 N N N 0.390  -23.637 -60.467 2.764   -0.758 -4.700 C21 G5F 36 
G5F O10 O13 O 0 1 N N N 1.677  -25.301 -59.325 0.712   -0.245 -3.655 O10 G5F 37 
G5F O11 O14 O 0 1 N N N 0.030  -30.069 -62.714 -0.688  -3.203 1.035  O11 G5F 38 
G5F O12 O15 O 0 1 N N N 1.375  -31.099 -60.366 -1.702  -0.425 -1.128 O12 G5F 39 
G5F C22 C22 C 0 1 N N N 11.426 -32.437 -63.001 -12.535 1.333  1.192  C22 G5F 40 
G5F O15 O16 O 0 1 N N N -3.555 -29.010 -65.129 7.563   0.864  -0.256 O15 G5F 41 
G5F O17 O17 O 0 1 N N N -6.543 -27.296 -63.924 9.536   -1.130 2.101  O17 G5F 42 
G5F O18 O18 O 0 1 N N N 9.152  -30.246 -63.029 -10.559 -0.679 1.768  O18 G5F 43 
G5F O19 O19 O 0 1 N N N 9.513  -33.878 -63.280 -10.832 2.462  -0.099 O19 G5F 44 
G5F O20 O20 O 0 1 N N N 7.201  -30.998 -65.023 -8.653  1.352  -0.612 O20 G5F 45 
G5F O23 O21 O 0 1 N N N 3.386  -33.385 -62.581 -5.939  -2.987 0.754  O23 G5F 46 
G5F O24 O22 O 0 1 N N N -1.785 -24.723 -63.097 4.834   -2.977 -0.787 O24 G5F 47 
G5F H1  H1  H 0 1 N N N 4.627  -24.218 -62.705 3.293   2.696  -1.110 H1  G5F 48 
G5F H2  H2  H 0 1 N N N 2.801  -26.099 -63.275 2.445   0.473  -0.212 H2  G5F 49 
G5F H3  H3  H 0 1 N N N 4.954  -26.336 -64.096 2.275   2.438  1.207  H3  G5F 50 
G5F H4  H4  H 0 1 N N N 6.442  -28.577 -62.657 0.815   4.281  2.093  H4  G5F 51 
G5F H5  H5  H 0 1 N N N 7.145  -27.550 -63.953 -0.602  3.432  1.428  H5  G5F 52 
G5F H6  H6  H 0 1 N N N 1.876  -28.414 -63.479 0.642   -0.893 1.063  H6  G5F 53 
G5F H7  H7  H 0 1 N N N 0.514  -26.359 -63.749 1.787   -3.123 0.888  H7  G5F 54 
G5F H8  H8  H 0 1 N N N -0.499 -27.835 -63.884 2.002   -2.837 -0.855 H8  G5F 55 
G5F H9  H9  H 0 1 N N N 0.108  -28.879 -61.039 -0.540  -2.819 -0.989 H9  G5F 56 
G5F H10 H10 H 0 1 N N N 2.475  -29.350 -60.544 -1.850  -0.808 0.897  H10 G5F 57 
G5F H11 H11 H 0 1 N N N 3.204  -29.881 -62.870 -3.072  -2.664 -1.193 H11 G5F 58 
G5F H12 H12 H 0 1 N N N 2.319  -31.439 -62.747 -3.109  -2.956 0.562  H12 G5F 59 
G5F H13 H13 H 0 1 N N N 7.321  -32.487 -62.009 -8.542  -1.266 -0.787 H13 G5F 60 
G5F H14 H14 H 0 1 N N N 6.826  -30.807 -62.406 -8.406  -1.602 0.955  H14 G5F 61 
G5F H15 H15 H 0 1 N N N 12.958 -32.021 -61.850 -14.104 2.489  1.743  H15 G5F 62 
G5F H16 H16 H 0 1 N N N 9.649  -32.407 -61.829 -10.606 1.983  1.898  H16 G5F 63 
G5F H17 H17 H 0 1 N N N -4.588 -27.367 -62.404 7.346   -1.753 -0.299 H17 G5F 64 
G5F H18 H18 H 0 1 N N N -3.324 -28.643 -62.387 7.305   -2.004 1.463  H18 G5F 65 
G5F H19 H19 H 0 1 N N N -5.024 -29.471 -63.754 7.443   0.486  1.771  H19 G5F 66 
G5F H20 H20 H 0 1 N N N -5.072 -26.860 -65.307 9.657   -0.752 0.073  H20 G5F 67 
G5F H21 H21 H 0 1 N N N -7.057 -27.775 -66.458 9.688   1.531  2.099  H21 G5F 68 
G5F H24 H24 H 0 1 N N N 4.948  -34.078 -60.527 -5.864  -1.776 -2.401 H24 G5F 69 
G5F H25 H25 H 0 1 N N N -3.046 -25.006 -60.836 4.457   -2.841 2.570  H25 G5F 70 
G5F H26 H26 H 0 1 N N N 6.176  -26.417 -61.302 0.468   3.822  -0.828 H26 G5F 71 
G5F H27 H27 H 0 1 N N N 3.710  -25.928 -60.366 0.646   1.763  -2.314 H27 G5F 72 
G5F H28 H28 H 0 1 N N N 2.386  -23.818 -61.991 3.415   1.030  -2.888 H28 G5F 73 
G5F H29 H29 H 0 1 N N N 4.760  -23.329 -60.554 2.797   4.587  -2.481 H29 G5F 74 
G5F H30 H30 H 0 1 N N N 7.404  -24.636 -62.169 1.625   5.274  0.678  H30 G5F 75 
G5F H31 H31 H 0 1 N N N 6.235  -29.536 -64.774 -0.197  2.840  3.707  H31 G5F 76 
G5F H32 H32 H 0 1 N N N 7.721  -32.914 -64.415 -8.427  0.873  1.385  H32 G5F 77 
G5F H33 H33 H 0 1 N N N 9.710  -31.390 -64.666 -10.785 -0.200 -0.229 H33 G5F 78 
G5F H34 H34 H 0 1 N N N -0.309 -23.775 -59.629 2.143   -1.430 -5.293 H34 G5F 79 
G5F H35 H35 H 0 1 N N N 0.731  -22.591 -60.492 3.247   -0.035 -5.358 H35 G5F 80 
G5F H36 H36 H 0 1 N N N -0.119 -23.880 -61.412 3.524   -1.336 -4.175 H36 G5F 81 
G5F H37 H37 H 0 1 N N N -0.290 -30.831 -62.245 -0.732  -2.787 1.907  H37 G5F 82 
G5F H38 H38 H 0 1 N N N 0.777  -30.737 -59.723 -1.658  -0.840 -2.000 H38 G5F 83 
G5F H39 H39 H 0 1 N N N 11.840 -33.398 -63.339 -12.688 0.578  1.963  H39 G5F 84 
G5F H40 H40 H 0 1 N N N 11.665 -31.655 -63.737 -12.980 0.994  0.257  H40 G5F 85 
G5F H41 H41 H 0 1 N N N -2.890 -29.538 -64.703 7.856   0.499  -1.102 H41 G5F 86 
G5F H42 H42 H 0 1 N N N -6.105 -26.846 -63.212 9.243   -0.765 2.947  H42 G5F 87 
G5F H43 H43 H 0 1 N N N 10.040 -29.983 -62.818 -10.202 -0.366 2.611  H43 G5F 88 
G5F H44 H44 H 0 1 N N N 9.979  -34.523 -62.761 -11.189 2.149  -0.941 H44 G5F 89 
G5F H45 H45 H 0 1 N N N 6.302  -31.237 -65.216 -9.010  1.039  -1.454 H45 G5F 90 
G5F C23 C23 C 0 1 N N N ?      ?       ?       11.545  0.775  1.311  C23 G5F 91 
G5F O13 O23 O 0 1 N N N ?      ?       ?       9.809   1.909  0.072  O13 G5F 92 
G5F O16 O24 O 0 1 N N N ?      ?       ?       12.229  1.991  1.618  O16 G5F 93 
G5F H22 H22 H 0 1 N N N ?      ?       ?       11.718  0.050  2.107  H22 G5F 94 
G5F H23 H23 H 0 1 N N N ?      ?       ?       11.920  0.375  0.369  H23 G5F 95 
G5F H46 H46 H 0 1 N N N ?      ?       ?       10.102  1.544  -0.775 H46 G5F 96 
G5F H47 H47 H 0 1 N N N ?      ?       ?       13.187  1.891  1.711  H47 G5F 97 
# 
loop_
_chem_comp_bond.comp_id 
_chem_comp_bond.atom_id_1 
_chem_comp_bond.atom_id_2 
_chem_comp_bond.value_order 
_chem_comp_bond.pdbx_aromatic_flag 
_chem_comp_bond.pdbx_stereo_config 
_chem_comp_bond.pdbx_ordinal 
G5F C19 C18 SING N N 1  
G5F O15 C17 SING N N 2  
G5F O20 C13 SING N N 3  
G5F C18 C17 SING N N 4  
G5F C18 O17 SING N N 5  
G5F O5  C6  SING N N 6  
G5F C17 C16 SING N N 7  
G5F C13 C14 SING N N 8  
G5F C13 C12 SING N N 9  
G5F C14 O18 SING N N 10 
G5F C14 C15 SING N N 11 
G5F C6  C5  SING N N 12 
G5F O9  C16 SING N N 13 
G5F O9  P2  SING N N 14 
G5F O19 C15 SING N N 15 
G5F C8  C7  SING N N 16 
G5F C8  O6  SING N N 17 
G5F C5  O1  SING N N 18 
G5F C5  C1  SING N N 19 
G5F O8  C12 SING N N 20 
G5F O8  P1  SING N N 21 
G5F O24 P2  DOUB N N 22 
G5F C22 C15 SING N N 23 
G5F C22 O14 SING N N 24 
G5F O4  C1  SING N N 25 
G5F O11 C9  SING N N 26 
G5F C7  C9  SING N N 27 
G5F C7  O2  SING N N 28 
G5F O23 P1  DOUB N N 29 
G5F O1  C4  SING N N 30 
G5F C4  O2  SING N N 31 
G5F C4  C3  SING N N 32 
G5F P2  O6  SING N N 33 
G5F P2  O22 SING N N 34 
G5F C1  C2  SING N N 35 
G5F C11 O7  SING N N 36 
G5F C11 C10 SING N N 37 
G5F P1  O7  SING N N 38 
G5F P1  O21 SING N N 39 
G5F C9  C10 SING N N 40 
G5F C2  C3  SING N N 41 
G5F C2  O3  SING N N 42 
G5F C3  N1  SING N N 43 
G5F N1  C20 SING N N 44 
G5F C10 O12 SING N N 45 
G5F C21 C20 SING N N 46 
G5F C20 O10 DOUB N N 47 
G5F C2  H1  SING N N 48 
G5F C4  H2  SING N N 49 
G5F C5  H3  SING N N 50 
G5F C6  H4  SING N N 51 
G5F C6  H5  SING N N 52 
G5F C7  H6  SING N N 53 
G5F C8  H7  SING N N 54 
G5F C8  H8  SING N N 55 
G5F C9  H9  SING N N 56 
G5F C10 H10 SING N N 57 
G5F C11 H11 SING N N 58 
G5F C11 H12 SING N N 59 
G5F C12 H13 SING N N 60 
G5F C12 H14 SING N N 61 
G5F O14 H15 SING N N 62 
G5F C15 H16 SING N N 63 
G5F C16 H17 SING N N 64 
G5F C16 H18 SING N N 65 
G5F C17 H19 SING N N 66 
G5F C18 H20 SING N N 67 
G5F C19 H21 SING N N 68 
G5F O21 H24 SING N N 69 
G5F O22 H25 SING N N 70 
G5F C1  H26 SING N N 71 
G5F C3  H27 SING N N 72 
G5F N1  H28 SING N N 73 
G5F O3  H29 SING N N 74 
G5F O4  H30 SING N N 75 
G5F O5  H31 SING N N 76 
G5F C13 H32 SING N N 77 
G5F C14 H33 SING N N 78 
G5F C21 H34 SING N N 79 
G5F C21 H35 SING N N 80 
G5F C21 H36 SING N N 81 
G5F O11 H37 SING N N 82 
G5F O12 H38 SING N N 83 
G5F C22 H39 SING N N 84 
G5F C22 H40 SING N N 85 
G5F O15 H41 SING N N 86 
G5F O17 H42 SING N N 87 
G5F O18 H43 SING N N 88 
G5F O19 H44 SING N N 89 
G5F O20 H45 SING N N 90 
G5F C23 C19 SING N N 91 
G5F O13 C19 SING N N 92 
G5F O16 C23 SING N N 93 
G5F C23 H22 SING N N 94 
G5F C23 H23 SING N N 95 
G5F O13 H46 SING N N 96 
G5F O16 H47 SING N N 97 
# 
loop_
_pdbx_chem_comp_descriptor.comp_id 
_pdbx_chem_comp_descriptor.type 
_pdbx_chem_comp_descriptor.program 
_pdbx_chem_comp_descriptor.program_version 
_pdbx_chem_comp_descriptor.descriptor 
G5F InChI            InChI                1.06  "InChI=1S/C23H47NO24P2/c1-9(28)24-17-22(38)21(37)15(4-27)47-23(17)48-16(8-46-50(41,42)44-6-13(32)19(35)11(30)3-26)20(36)14(33)7-45-49(39,40)43-5-12(31)18(34)10(29)2-25/h10-23,25-27,29-38H,2-8H2,1H3,(H,24,28)(H,39,40)(H,41,42)/t10-,11?,12+,13-,14-,15+,16+,17+,18-,19+,20-,21+,22+,23-/m0/s1" 
G5F InChIKey         InChI                1.06  CTFVIOIQZHDZBZ-OLJBVLMTSA-N                                                                                                                                                                                                                                                                       
G5F SMILES_CANONICAL CACTVS               3.385 "CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@H]1O[C@H](CO[P](O)(=O)OC[C@H](O)[C@H](O)C(O)CO)[C@@H](O)[C@@H](O)CO[P](O)(=O)OC[C@@H](O)[C@@H](O)[C@@H](O)CO"                                                                                                                                       
G5F SMILES           CACTVS               3.385 "CC(=O)N[CH]1[CH](O)[CH](O)[CH](CO)O[CH]1O[CH](CO[P](O)(=O)OC[CH](O)[CH](O)C(O)CO)[CH](O)[CH](O)CO[P](O)(=O)OC[CH](O)[CH](O)[CH](O)CO"                                                                                                                                                            
G5F SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@H]1O[C@H](COP(=O)(O)OC[C@@H]([C@@H]([C@H](CO)O)O)O)[C@H]([C@H](COP(=O)(O)OC[C@H]([C@H]([C@H](CO)O)O)O)O)O)CO)O)O"                                                                                                                                           
G5F SMILES           "OpenEye OEToolkits" 2.0.7 "CC(=O)NC1C(C(C(OC1OC(COP(=O)(O)OCC(C(C(CO)O)O)O)C(C(COP(=O)(O)OCC(C(C(CO)O)O)O)O)O)CO)O)O"                                                                                                                                                                                                       
# 
_pdbx_chem_comp_identifier.comp_id           G5F 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.7 
_pdbx_chem_comp_identifier.identifier        "[(2~{R},3~{S},4~{S})-2-[(2~{S},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-3,4-bis(oxidanyl)-5-[oxidanyl-[(2~{R},3~{S},4~{S})-2,3,4,5-tetrakis(oxidanyl)pentoxy]phosphoryl]oxy-pentyl] [(2~{S},3~{R},4~{S})-2,3,4,5-tetrakis(oxidanyl)pentyl] hydrogen phosphate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
G5F "Create component"  2022-01-27 PDBE 
G5F "Modify descriptor" 2022-08-22 RCSB 
G5F "Initial release"   2022-08-31 RCSB 
# 
