data_XQD
#
_chem_comp.id XQD
_chem_comp.name
"[(2~{R},3~{R},4~{S},5~{S},6~{R})-3-acetamido-5-[[(1~{S})-1-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]-1-oxidanyl-ethyl]amino]-6-methyl-4-oxidanyl-oxan-2-yl] [[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C40 H66 N11 O32 P5 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-12-31
_chem_comp.pdbx_modified_date 2021-02-26
_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 1399.940
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code XQD
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 7L82
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
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.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_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
XQD N1 N1 N 0 1 N N N N N N -17.224 -23.230 19.774 -17.612 2.442 -1.647 N1 XQD 1
XQD N3 N2 N 0 1 N N N N N N -19.434 -23.714 20.545 -17.911 4.382 -2.924 N3 XQD 2
XQD C4 C1 C 0 1 N N N N N N -19.895 -23.308 19.337 -17.655 3.696 -4.057 C4 XQD 3
XQD C5 C2 C 0 1 N N N N N N -19.075 -22.861 18.312 -17.359 2.314 -3.981 C5 XQD 4
XQD C6 C3 C 0 1 N N N N N N -17.731 -22.810 18.539 -17.342 1.711 -2.773 C6 XQD 5
XQD O5P O1 O 0 1 N N N N N N -6.812 -9.496 11.211 -0.284 0.609 -1.755 O5P XQD 6
XQD C5P C4 C 0 1 N N N N N N -6.596 -10.682 10.971 -0.413 0.115 -0.655 C5P XQD 7
XQD C6P C5 C 0 1 N N N N N N -6.709 -11.209 9.516 0.579 -0.910 -0.168 C6P XQD 8
XQD C7P C6 C 0 1 N N N N N N -7.935 -10.440 8.949 1.640 -1.145 -1.245 C7P XQD 9
XQD N8P N3 N 0 1 N N N N N N -8.210 -11.061 7.630 2.604 -2.141 -0.772 N8P XQD 10
XQD C9P C7 C 0 1 N N N N N N -7.854 -10.554 6.449 3.635 -2.509 -1.559 C9P XQD 11
XQD O9P O2 O 0 1 N N N N N N -7.236 -9.453 6.267 3.712 -2.086 -2.693 O9P XQD 12
XQD CAP C8 C 0 1 N N R N N N -8.182 -11.461 5.256 4.691 -3.444 -1.030 CAP XQD 13
XQD OAP O3 O 0 1 N N N N N N -6.930 -11.570 4.551 4.277 -3.962 0.236 OAP XQD 14
XQD CBP C9 C 0 1 N N N N N N -9.322 -10.944 4.353 6.009 -2.685 -0.864 CBP XQD 15
XQD CDP C10 C 0 1 N N N N N N -10.624 -11.085 5.154 6.527 -2.257 -2.239 CDP XQD 16
XQD CEP C11 C 0 1 N N N N N N -9.075 -9.482 3.936 5.778 -1.446 0.002 CEP XQD 17
XQD CCP C12 C 0 1 N N N N N N -9.311 -11.763 3.055 7.039 -3.593 -0.191 CCP XQD 18
XQD O6A O4 O 0 1 N N N N N N -9.529 -13.118 3.449 8.270 -2.884 -0.036 O6A XQD 19
XQD P2A P1 P 0 1 N N N N N N -9.537 -14.219 2.209 9.579 -3.536 0.638 P2A XQD 20
XQD O4E O5 O 0 1 N N N N N N -10.666 -13.807 1.268 9.923 -4.791 -0.067 O4E XQD 21
XQD O5A O6 O 0 1 N N N N N N -9.538 -15.602 2.845 9.283 -3.855 2.188 O5A XQD 22
XQD O3A O7 O 0 1 N N N N N N -8.185 -13.801 1.429 10.810 -2.504 0.528 O3A XQD 23
XQD P1A P2 P 0 1 N N N N N N -6.961 -14.770 1.031 12.410 -2.659 0.612 P1A XQD 24
XQD O1A O8 O 0 1 N N N N N N -6.090 -15.110 2.239 12.849 -2.877 2.145 O1A XQD 25
XQD O2A O9 O 0 1 N N N N N N -7.456 -15.923 0.196 12.836 -3.825 -0.194 O2A XQD 26
XQD O5C O10 O 0 1 N N N N N N -6.166 -13.838 0.043 13.109 -1.327 0.038 O5C XQD 27
XQD C5C C13 C 0 1 N N N N N N -6.869 -13.231 -1.041 14.523 -1.195 -0.118 C5C XQD 28
XQD C4C C14 C 0 1 N N R N N N -5.892 -12.372 -1.815 14.848 0.189 -0.684 C4C XQD 29
XQD C3C C15 C 0 1 N N S N N N -4.460 -12.900 -1.709 16.359 0.308 -0.979 C3C XQD 30
XQD O3C O11 O 0 1 N N N N N N -3.762 -12.463 -2.862 16.618 0.080 -2.366 O3C XQD 31
XQD P3B P3 P 0 1 N N N N N N -3.552 -13.453 -4.176 17.569 -1.106 -2.896 P3B XQD 32
XQD O9A O12 O 0 1 N N N N N N -2.628 -12.542 -4.966 18.896 -1.001 -2.251 O9A XQD 33
XQD O8A O13 O 0 1 N N N N N N -4.939 -13.764 -4.787 16.907 -2.528 -2.532 O8A XQD 34
XQD O7A O14 O 0 1 N N N N N N -2.888 -14.729 -3.779 17.737 -0.986 -4.493 O7A XQD 35
XQD C2C C16 C 0 1 N N R N N N -3.862 -12.163 -0.500 16.702 1.766 -0.597 C2C XQD 36
XQD O2C O15 O 0 1 N N N N N N -2.432 -12.043 -0.495 17.183 2.482 -1.737 O2C XQD 37
XQD O4C O16 O 0 1 N N N N N N -5.851 -11.024 -1.255 14.582 1.210 0.303 O4C XQD 38
XQD C1A C17 C 0 1 N N R N N N -4.565 -10.813 -0.614 15.357 2.354 -0.117 C1A XQD 39
XQD N9A N4 N 0 1 Y N N N N N -4.892 -10.332 0.760 15.572 3.265 1.010 N9A XQD 40
XQD C4A C18 C 0 1 Y N N N N N -4.638 -9.083 1.186 15.844 4.607 0.929 C4A XQD 41
XQD N3A N5 N 0 1 Y N N N N N -4.062 -7.987 0.608 15.995 5.476 -0.065 N3A XQD 42
XQD C2A C19 C 0 1 Y N N N N N -3.953 -6.839 1.303 16.260 6.741 0.183 C2A XQD 43
XQD C8A C20 C 0 1 Y N N N N N -5.514 -11.031 1.745 15.534 2.935 2.333 C8A XQD 44
XQD N7A N6 N 0 1 Y N N N N N -5.668 -10.213 2.840 15.770 3.988 3.061 N7A XQD 45
XQD C5A C21 C 0 1 Y N N N N N -5.149 -8.999 2.481 15.971 5.058 2.254 C5A XQD 46
XQD C6A C22 C 0 1 Y N N N N N -4.948 -7.819 3.177 16.254 6.417 2.468 C6A XQD 47
XQD N6A N7 N 0 1 N N N N N N -5.457 -7.713 4.438 16.391 6.918 3.751 N6A XQD 48
XQD N1A N8 N 0 1 Y N N N N N -4.396 -6.749 2.587 16.389 7.210 1.411 N1A XQD 49
XQD N4P N9 N 0 1 N N N N N N -6.332 -11.548 11.980 -1.443 0.483 0.132 N4P XQD 50
XQD C3P C23 C 0 1 N N N N N N -6.286 -11.261 13.435 -2.407 1.479 -0.341 C3P XQD 51
XQD C2P C24 C 0 1 N N N N N N -6.587 -12.569 14.156 -3.468 1.714 0.736 C2P XQD 52
XQD S1P S1 S 0 1 N N N N N N -6.425 -12.192 15.934 -4.662 2.947 0.150 S1P XQD 53
XQD C C25 C 0 1 N N S N N N -5.570 -13.723 16.552 -5.734 3.196 1.592 C XQD 54
XQD O O17 O 0 1 N N N N N N -4.745 -14.402 15.580 -5.102 2.654 2.754 O XQD 55
XQD CH3 C26 C 0 1 N N N N N N -4.578 -13.230 17.558 -5.977 4.692 1.795 CH3 XQD 56
XQD N4A N10 N 0 1 N N N N N N -6.526 -14.704 17.187 -7.017 2.516 1.371 N4A XQD 57
XQD "C4'" C27 C 0 1 N N S N N N -7.698 -15.159 16.457 -6.814 1.094 1.064 "C4'" XQD 58
XQD "C3'" C28 C 0 1 N N S N N N -7.497 -16.598 16.120 -7.346 0.240 2.219 "C3'" XQD 59
XQD "O3'" O18 O 0 1 N N N N N N -6.289 -16.818 15.308 -6.596 0.518 3.403 "O3'" XQD 60
XQD "C5'" C29 C 0 1 N N R N N N -8.977 -14.997 17.358 -7.572 0.734 -0.217 "C5'" XQD 61
XQD "C6'" C30 C 0 1 N N N N N N -9.493 -13.651 17.870 -7.006 1.540 -1.388 "C6'" XQD 62
XQD "O5'" O19 O 0 1 N N N N N N -10.101 -15.489 16.573 -7.420 -0.662 -0.482 "O5'" XQD 63
XQD "C1'" C31 C 0 1 N N R N N N -9.968 -16.794 16.089 -7.942 -1.510 0.542 "C1'" XQD 64
XQD "C2'" C32 C 0 1 N N R N N N -8.710 -16.977 15.278 -7.200 -1.240 1.854 "C2'" XQD 65
XQD "N2'" N11 N 0 1 N N N N N N -8.631 -18.391 14.887 -7.773 -2.066 2.919 "N2'" XQD 66
XQD "C7'" C33 C 0 1 N N N N N N -8.434 -18.797 13.620 -7.349 -3.334 3.091 "C7'" XQD 67
XQD "C8'" C34 C 0 1 N N N N N N -8.287 -20.306 13.401 -7.939 -4.184 4.187 "C8'" XQD 68
XQD "O7'" O20 O 0 1 N N N N N N -8.408 -17.981 12.686 -6.493 -3.791 2.363 "O7'" XQD 69
XQD "O1'" O21 O 0 1 N N N N N N -9.995 -17.683 17.224 -9.335 -1.242 0.719 "O1'" XQD 70
XQD PB P4 P 0 1 N N N N N N -11.376 -18.268 17.803 -10.487 -2.014 -0.099 PB XQD 71
XQD O2B O22 O 0 1 N N N N N N -10.915 -18.924 19.047 -10.365 -1.656 -1.664 O2B XQD 72
XQD O1B O23 O 0 1 N N N N N N -12.489 -17.285 17.754 -10.331 -3.474 0.087 O1B XQD 73
XQD O3B O24 O 0 1 N N N N N N -11.791 -19.298 16.623 -11.931 -1.555 0.445 O3B XQD 74
XQD PA P5 P 0 1 N N N N N N -11.552 -20.832 16.423 -13.408 -2.192 0.373 PA XQD 75
XQD O4D O25 O 0 1 N N N N N N -12.297 -21.225 15.175 -13.625 -2.783 -0.967 O4D XQD 76
XQD O5B O26 O 0 1 N N N N N N -10.097 -21.151 16.430 -13.553 -3.338 1.494 O5B XQD 77
XQD O6B O27 O 0 1 N N N N N N -12.264 -21.480 17.674 -14.502 -1.041 0.636 O6B XQD 78
XQD C5B C35 C 0 1 N N N N N N -13.639 -21.319 18.064 -15.909 -1.267 0.535 C5B XQD 79
XQD C4B C36 C 0 1 N N R N N N -13.872 -22.158 19.341 -16.658 0.030 0.846 C4B XQD 80
XQD C2B C37 C 0 1 N N S N N N -13.625 -23.644 19.101 -18.177 -0.229 0.845 C2B XQD 81
XQD O4A O28 O 0 1 N N N N N N -12.861 -24.221 20.127 -18.738 0.081 2.122 O4A XQD 82
XQD C3B C38 C 0 1 N N R N N N -15.039 -24.179 19.099 -18.726 0.735 -0.236 C3B XQD 83
XQD "O2'" O29 O 0 1 N N N N N N -15.146 -25.521 19.527 -19.948 1.339 0.193 "O2'" XQD 84
XQD C1B C39 C 0 1 N N R N N N -15.781 -23.241 20.007 -17.593 1.788 -0.336 C1B XQD 85
XQD O4B O30 O 0 1 N N N N N N -15.216 -21.961 19.657 -16.390 1.006 -0.175 O4B XQD 86
XQD C2 C40 C 0 1 N N N N N N -18.070 -23.628 20.758 -17.888 3.756 -1.733 C2 XQD 87
XQD O2 O31 O 0 1 N N N N N N -17.687 -23.999 21.876 -18.120 4.387 -0.720 O2 XQD 88
XQD O4 O32 O 0 1 N N N N N N -21.144 -23.303 19.176 -17.676 4.261 -5.135 O4 XQD 89
XQD H1 H1 H 0 1 N N N N N N -20.052 -24.060 21.251 -18.111 5.330 -2.968 H1 XQD 90
XQD H2 H2 H 0 1 N N N N N N -19.489 -22.562 17.360 -17.148 1.749 -4.877 H2 XQD 91
XQD H3 H3 H 0 1 N N N N N N -17.063 -22.448 17.771 -17.117 0.658 -2.695 H3 XQD 92
XQD H4 H4 H 0 1 N N N N N N -6.885 -12.295 9.503 1.058 -0.548 0.742 H4 XQD 93
XQD H5 H5 H 0 1 N N N N N N -5.800 -10.978 8.942 0.061 -1.846 0.042 H5 XQD 94
XQD H6 H6 H 0 1 N N N N N N -7.699 -9.372 8.831 1.161 -1.506 -2.155 H6 XQD 95
XQD H7 H7 H 0 1 N N N N N N -8.802 -10.552 9.616 2.158 -0.209 -1.455 H7 XQD 96
XQD H8 H8 H 0 1 N N N N N N -8.703 -11.931 7.626 2.501 -2.536 0.108 H8 XQD 97
XQD H9 H9 H 0 1 N N N N N N -8.473 -12.449 5.643 4.831 -4.267 -1.730 H9 XQD 98
XQD H10 H10 H 0 1 N N N N N N -6.362 -10.850 4.800 4.133 -3.284 0.911 H10 XQD 99
XQD H11 H11 H 0 1 N N N N N N -10.562 -10.474 6.067 5.825 -1.556 -2.690 H11 XQD 100
XQD H12 H12 H 0 1 N N N N N N -11.471 -10.742 4.541 7.499 -1.777 -2.127 H12 XQD 101
XQD H13 H13 H 0 1 N N N N N N -10.773 -12.140 5.428 6.626 -3.134 -2.878 H13 XQD 102
XQD H14 H14 H 0 1 N N N N N N -9.072 -8.841 4.830 5.043 -0.798 -0.478 H14 XQD 103
XQD H15 H15 H 0 1 N N N N N N -8.103 -9.405 3.426 5.408 -1.750 0.982 H15 XQD 104
XQD H16 H16 H 0 1 N N N N N N -9.874 -9.156 3.254 6.716 -0.905 0.120 H16 XQD 105
XQD H17 H17 H 0 1 N N N N N N -8.340 -11.663 2.547 6.670 -3.898 0.789 H17 XQD 106
XQD H18 H18 H 0 1 N N N N N N -10.113 -11.426 2.382 7.204 -4.477 -0.808 H18 XQD 107
XQD H19 H19 H 0 1 N N N N N N -10.305 -16.083 2.556 9.050 -3.076 2.712 H19 XQD 108
XQD H20 H20 H 0 1 N N N N N N -5.979 -16.052 2.295 12.601 -2.150 2.733 H20 XQD 109
XQD H21 H21 H 0 1 N N N N N N -7.687 -12.607 -0.652 15.009 -1.315 0.850 H21 XQD 110
XQD H22 H22 H 0 1 N N N N N N -7.283 -14.009 -1.699 14.886 -1.962 -0.803 H22 XQD 111
XQD H23 H23 H 0 1 N N N N N N -6.190 -12.337 -2.873 14.269 0.375 -1.588 H23 XQD 112
XQD H24 H24 H 0 1 N N N N N N -4.438 -13.991 -1.570 16.925 -0.391 -0.363 H24 XQD 113
XQD H25 H25 H 0 1 N N N N N N -5.026 -13.316 -5.620 16.033 -2.666 -2.922 H25 XQD 114
XQD H26 H26 H 0 1 N N N N N N -1.994 -14.735 -4.100 18.299 -1.670 -4.882 H26 XQD 115
XQD H27 H27 H 0 1 N N N N N N -4.201 -12.662 0.419 17.439 1.787 0.205 H27 XQD 116
XQD H28 H28 H 0 1 N N N N N N -2.156 -11.576 0.285 17.414 3.403 -1.554 H28 XQD 117
XQD H29 H29 H 0 1 N N N N N N -3.943 -10.088 -1.159 14.856 2.873 -0.934 H29 XQD 118
XQD H30 H30 H 0 1 N N N N N N -3.506 -5.975 0.834 16.378 7.420 -0.648 H30 XQD 119
XQD H31 H31 H 0 1 N N N N N N -5.835 -12.060 1.679 15.336 1.946 2.719 H31 XQD 120
XQD H32 H32 H 0 1 N N N N N N -5.336 -6.777 4.769 16.290 6.330 4.515 H32 XQD 121
XQD H33 H33 H 0 1 N N N N N N -6.431 -7.938 4.424 16.587 7.859 3.886 H33 XQD 122
XQD H34 H34 H 0 1 N N N N N N -6.146 -12.493 11.712 -1.546 0.088 1.012 H34 XQD 123
XQD H35 H35 H 0 1 N N N N N N -5.288 -10.895 13.717 -1.889 2.415 -0.551 H35 XQD 124
XQD H36 H36 H 0 1 N N N N N N -7.041 -10.504 13.695 -2.887 1.117 -1.251 H36 XQD 125
XQD H37 H37 H 0 1 N N N N N N -7.608 -12.909 13.926 -3.986 0.778 0.946 H37 XQD 126
XQD H38 H38 H 0 1 N N N N N N -5.867 -13.346 13.860 -2.989 2.076 1.645 H38 XQD 127
XQD H39 H39 H 0 1 N N N N N N -4.350 -15.168 15.979 -4.927 1.705 2.699 H39 XQD 128
XQD H40 H40 H 0 1 N N N N N N -5.104 -12.689 18.358 -6.459 5.106 0.909 H40 XQD 129
XQD H41 H41 H 0 1 N N N N N N -4.037 -14.085 17.989 -6.622 4.841 2.662 H41 XQD 130
XQD H42 H42 H 0 1 N N N N N N -3.863 -12.554 17.067 -5.025 5.196 1.959 H42 XQD 131
XQD H43 H43 H 0 1 N N N N N N -6.858 -14.278 18.029 -7.547 2.971 0.642 H43 XQD 132
XQD H45 H45 H 0 1 N N N N N N -7.832 -14.572 15.537 -5.751 0.900 0.925 H45 XQD 133
XQD H46 H46 H 0 1 N N N N N N -7.468 -17.208 17.035 -8.397 0.471 2.390 H46 XQD 134
XQD H47 H47 H 0 1 N N N N N N -5.520 -16.587 15.815 -6.880 0.011 4.176 H47 XQD 135
XQD H48 H48 H 0 1 N N N N N N -8.845 -15.656 18.229 -8.629 0.968 -0.092 H48 XQD 136
XQD H49 H49 H 0 1 N N N N N N -10.397 -13.811 18.475 -5.968 1.253 -1.560 H49 XQD 137
XQD H50 H50 H 0 1 N N N N N N -8.719 -13.172 18.487 -7.592 1.339 -2.285 H50 XQD 138
XQD H51 H51 H 0 1 N N N N N N -9.734 -13.002 17.015 -7.054 2.604 -1.154 H51 XQD 139
XQD H52 H52 H 0 1 N N N N N N -10.824 -17.028 15.439 -7.806 -2.553 0.255 H52 XQD 140
XQD H53 H53 H 0 1 N N N N N N -8.750 -16.337 14.384 -6.144 -1.483 1.731 H53 XQD 141
XQD H54 H54 H 0 1 N N N N N N -8.729 -19.087 15.599 -8.457 -1.701 3.501 H54 XQD 142
XQD H55 H55 H 0 1 N N N N N N -8.162 -20.511 12.327 -8.807 -4.719 3.805 H55 XQD 143
XQD H56 H56 H 0 1 N N N N N N -7.406 -20.672 13.949 -7.193 -4.900 4.532 H56 XQD 144
XQD H57 H57 H 0 1 N N N N N N -9.187 -20.819 13.770 -8.241 -3.546 5.018 H57 XQD 145
XQD H58 H58 H 0 1 N N N N N N -11.436 -18.617 19.779 -10.457 -0.714 -1.861 H58 XQD 146
XQD H59 H59 H 0 1 N N N N N N -9.860 -21.570 15.611 -13.423 -3.021 2.399 H59 XQD 147
XQD H60 H60 H 0 1 N N N N N N -13.847 -20.259 18.270 -16.153 -1.594 -0.476 H60 XQD 148
XQD H61 H61 H 0 1 N N N N N N -14.300 -21.673 17.259 -16.205 -2.038 1.247 H61 XQD 149
XQD H62 H62 H 0 1 N N N N N N -13.210 -21.797 20.142 -16.346 0.414 1.817 H62 XQD 150
XQD H63 H63 H 0 1 N N N N N N -13.162 -23.793 18.114 -18.388 -1.264 0.578 H63 XQD 151
XQD H64 H64 H 0 1 N N N N N N -11.980 -23.867 20.104 -19.693 -0.064 2.178 H64 XQD 152
XQD H65 H65 H 0 1 N N N N N N -15.447 -24.079 18.083 -18.862 0.217 -1.185 H65 XQD 153
XQD H66 H66 H 0 1 N N N N N N -16.057 -25.790 19.501 -20.662 0.708 0.357 H66 XQD 154
XQD H67 H67 H 0 1 N N N N N N -15.564 -23.488 21.057 -17.684 2.526 0.461 H67 XQD 155
#
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
XQD O9A P3B DOUB N N 1
XQD O8A P3B SING N N 2
XQD P3B O7A SING N N 3
XQD P3B O3C SING N N 4
XQD O3C C3C SING N N 5
XQD C4C C3C SING N N 6
XQD C4C O4C SING N N 7
XQD C4C C5C SING N N 8
XQD C3C C2C SING N N 9
XQD O4C C1A SING N N 10
XQD C5C O5C SING N N 11
XQD C1A C2C SING N N 12
XQD C1A N9A SING N N 13
XQD C2C O2C SING N N 14
XQD O5C P1A SING N N 15
XQD O2A P1A DOUB N N 16
XQD N3A C4A DOUB Y N 17
XQD N3A C2A SING Y N 18
XQD N9A C4A SING Y N 19
XQD N9A C8A SING Y N 20
XQD P1A O3A SING N N 21
XQD P1A O1A SING N N 22
XQD C4A C5A SING Y N 23
XQD O4E P2A DOUB N N 24
XQD C2A N1A DOUB Y N 25
XQD O3A P2A SING N N 26
XQD C8A N7A DOUB Y N 27
XQD P2A O5A SING N N 28
XQD P2A O6A SING N N 29
XQD C5A N7A SING Y N 30
XQD C5A C6A DOUB Y N 31
XQD N1A C6A SING Y N 32
XQD CCP O6A SING N N 33
XQD CCP CBP SING N N 34
XQD C6A N6A SING N N 35
XQD CEP CBP SING N N 36
XQD CBP CDP SING N N 37
XQD CBP CAP SING N N 38
XQD OAP CAP SING N N 39
XQD CAP C9P SING N N 40
XQD O9P C9P DOUB N N 41
XQD C9P N8P SING N N 42
XQD N8P C7P SING N N 43
XQD C7P C6P SING N N 44
XQD C6P C5P SING N N 45
XQD C5P O5P DOUB N N 46
XQD C5P N4P SING N N 47
XQD N4P C3P SING N N 48
XQD "O7'" "C7'" DOUB N N 49
XQD "C8'" "C7'" SING N N 50
XQD C3P C2P SING N N 51
XQD "C7'" "N2'" SING N N 52
XQD C2P S1P SING N N 53
XQD "N2'" "C2'" SING N N 54
XQD O4D PA DOUB N N 55
XQD "C2'" "C1'" SING N N 56
XQD "C2'" "C3'" SING N N 57
XQD "O3'" "C3'" SING N N 58
XQD O C SING N N 59
XQD S1P C SING N N 60
XQD "C1'" "O5'" SING N N 61
XQD "C1'" "O1'" SING N N 62
XQD "C3'" "C4'" SING N N 63
XQD PA O5B SING N N 64
XQD PA O3B SING N N 65
XQD PA O6B SING N N 66
XQD "C4'" N4A SING N N 67
XQD "C4'" "C5'" SING N N 68
XQD C N4A SING N N 69
XQD C CH3 SING N N 70
XQD "O5'" "C5'" SING N N 71
XQD O3B PB SING N N 72
XQD "O1'" PB SING N N 73
XQD "C5'" "C6'" SING N N 74
XQD O6B C5B SING N N 75
XQD O1B PB DOUB N N 76
XQD PB O2B SING N N 77
XQD C5B C4B SING N N 78
XQD C5 C6 DOUB N N 79
XQD C5 C4 SING N N 80
XQD C6 N1 SING N N 81
XQD C3B C2B SING N N 82
XQD C3B "O2'" SING N N 83
XQD C3B C1B SING N N 84
XQD C2B C4B SING N N 85
XQD C2B O4A SING N N 86
XQD O4 C4 DOUB N N 87
XQD C4 N3 SING N N 88
XQD C4B O4B SING N N 89
XQD O4B C1B SING N N 90
XQD N1 C1B SING N N 91
XQD N1 C2 SING N N 92
XQD N3 C2 SING N N 93
XQD C2 O2 DOUB N N 94
XQD N3 H1 SING N N 95
XQD C5 H2 SING N N 96
XQD C6 H3 SING N N 97
XQD C6P H4 SING N N 98
XQD C6P H5 SING N N 99
XQD C7P H6 SING N N 100
XQD C7P H7 SING N N 101
XQD N8P H8 SING N N 102
XQD CAP H9 SING N N 103
XQD OAP H10 SING N N 104
XQD CDP H11 SING N N 105
XQD CDP H12 SING N N 106
XQD CDP H13 SING N N 107
XQD CEP H14 SING N N 108
XQD CEP H15 SING N N 109
XQD CEP H16 SING N N 110
XQD CCP H17 SING N N 111
XQD CCP H18 SING N N 112
XQD O5A H19 SING N N 113
XQD O1A H20 SING N N 114
XQD C5C H21 SING N N 115
XQD C5C H22 SING N N 116
XQD C4C H23 SING N N 117
XQD C3C H24 SING N N 118
XQD O8A H25 SING N N 119
XQD O7A H26 SING N N 120
XQD C2C H27 SING N N 121
XQD O2C H28 SING N N 122
XQD C1A H29 SING N N 123
XQD C2A H30 SING N N 124
XQD C8A H31 SING N N 125
XQD N6A H32 SING N N 126
XQD N6A H33 SING N N 127
XQD N4P H34 SING N N 128
XQD C3P H35 SING N N 129
XQD C3P H36 SING N N 130
XQD C2P H37 SING N N 131
XQD C2P H38 SING N N 132
XQD O H39 SING N N 133
XQD CH3 H40 SING N N 134
XQD CH3 H41 SING N N 135
XQD CH3 H42 SING N N 136
XQD N4A H43 SING N N 137
XQD "C4'" H45 SING N N 138
XQD "C3'" H46 SING N N 139
XQD "O3'" H47 SING N N 140
XQD "C5'" H48 SING N N 141
XQD "C6'" H49 SING N N 142
XQD "C6'" H50 SING N N 143
XQD "C6'" H51 SING N N 144
XQD "C1'" H52 SING N N 145
XQD "C2'" H53 SING N N 146
XQD "N2'" H54 SING N N 147
XQD "C8'" H55 SING N N 148
XQD "C8'" H56 SING N N 149
XQD "C8'" H57 SING N N 150
XQD O2B H58 SING N N 151
XQD O5B H59 SING N N 152
XQD C5B H60 SING N N 153
XQD C5B H61 SING N N 154
XQD C4B H62 SING N N 155
XQD C2B H63 SING N N 156
XQD O4A H64 SING N N 157
XQD C3B H65 SING N N 158
XQD "O2'" H66 SING N N 159
XQD C1B H67 SING N N 160
#
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
XQD SMILES ACDLabs 12.01 N6(C5C(C(C(COP(OP(OC4OC(C(NC(SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(O)(=O)OP(O)(=O)OCC1C(C(O)C(O1)n2c3c(nc2)c(N)ncn3)OP(O)(=O)O)(C)O)C(O)C4NC(C)=O)C)(O)=O)(O)=O)O5)O)O)C(NC(C=C6)=O)=O
XQD InChI InChI 1.03 InChI=1S/C40H66N11O32P5S/c1-17-23(27(56)24(47-18(2)52)37(77-17)81-88(72,73)83-86(68,69)74-12-19-26(55)28(57)35(78-19)50-10-7-22(54)48-38(50)61)49-40(5,62)89-11-9-42-21(53)6-8-43-34(60)31(59)39(3,4)14-76-87(70,71)82-85(66,67)75-13-20-30(80-84(63,64)65)29(58)36(79-20)51-16-46-25-32(41)44-15-45-33(25)51/h7,10,15-17,19-20,23-24,26-31,35-37,49,55-59,62H,6,8-9,11-14H2,1-5H3,(H,42,53)(H,43,60)(H,47,52)(H,66,67)(H,68,69)(H,70,71)(H,72,73)(H2,41,44,45)(H,48,54,61)(H2,63,64,65)/t17-,19-,20-,23-,24-,26-,27+,28-,29-,30-,31+,35-,36-,37-,40+/m1/s1
XQD InChIKey InChI 1.03 CHRNLGHDEXUXFL-IOFFXKHASA-N
XQD SMILES_CANONICAL CACTVS 3.385 C[C@H]1O[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@H](NC(C)=O)[C@@H](O)[C@@H]1N[C@@](C)(O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O[P](O)(O)=O)n5cnc6c(N)ncnc56
XQD SMILES CACTVS 3.385 C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH](NC(C)=O)[CH](O)[CH]1N[C](C)(O)SCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O[P](O)(O)=O)n5cnc6c(N)ncnc56
XQD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 C[C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)NC(=O)C)O)N[C@@](C)(O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)OP(=O)(O)O)O
XQD SMILES "OpenEye OEToolkits" 2.0.7 CC1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)NC(=O)C)O)NC(C)(O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)OP(=O)(O)O)O
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
XQD "SYSTEMATIC NAME" ACDLabs 12.01 "(2R,3R,4S,5S,6R)-3-(acetylamino)-5-({(3R,5S,9R,19S)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9,19-tetrahydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-18-thia-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaicosan-19-yl}amino)-4-hydroxy-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)"
XQD "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{R},4~{S},5~{S},6~{R})-3-acetamido-5-[[(1~{S})-1-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]-1-oxidanyl-ethyl]amino]-6-methyl-4-oxidanyl-oxan-2-yl] [[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] 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
XQD 'Create component' 2020-12-31 RCSB
XQD 'Initial release' 2021-03-03 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
XQD N1 N 51.509 5.536 1
XQD N3 N 53.611 4.009 2
XQD C4 C 54.493 5.222 3
XQD C5 C 53.883 6.593 4
XQD C6 C 52.391 6.749 5
XQD O5P O 30.756 -1.562 6
XQD C5P C 30.756 -3.062 7
XQD C6P C 29.457 -3.812 8
XQD C7P C 28.158 -3.062 9
XQD N8P N 26.859 -3.812 10
XQD C9P C 25.560 -3.062 11
XQD O9P O 25.560 -1.562 12
XQD CAP C 24.261 -3.812 13
XQD OAP O 24.261 -5.312 14
XQD CBP C 22.962 -3.062 15
XQD CDP C 23.712 -1.763 16
XQD CEP C 22.212 -4.361 17
XQD CCP C 21.663 -2.312 18
XQD O6A O 20.364 -3.062 19
XQD P2A P 19.065 -2.312 20
XQD O4E O 18.315 -3.611 21
XQD O5A O 19.815 -1.013 22
XQD O3A O 17.766 -1.562 23
XQD P1A P 16.467 -2.312 24
XQD O1A O 17.217 -3.611 25
XQD O2A O 15.717 -1.013 26
XQD O5C O 15.168 -3.062 27
XQD C5C C 13.868 -2.312 28
XQD C4C C 12.569 -3.062 29
XQD C3C C 12.413 -4.554 30
XQD O3C O 13.527 -5.558 31
XQD P3B P 13.216 -7.025 32
XQD O9A O 12.904 -8.492 33
XQD O8A O 14.683 -7.337 34
XQD O7A O 11.748 -6.713 35
XQD C2C C 10.945 -4.866 36
XQD O2C O 10.335 -6.236 37
XQD O4C O 11.199 -2.452 38
XQD C1A C 10.195 -3.567 39
XQD N9A N 8.704 -3.410 40
XQD C4A C 7.707 -4.519 41
XQD N3A N 7.861 -6.011 42
XQD C2A C 6.646 -6.891 43
XQD C8A C 7.959 -2.118 44
XQD N7A N 6.500 -2.424 45
XQD C5A C 6.338 -3.906 46
XQD C6A C 5.123 -4.786 47
XQD N6A N 3.753 -4.173 48
XQD N1A N 5.277 -6.278 49
XQD N4P N 32.055 -3.812 50
XQD C3P C 33.354 -3.062 51
XQD C2P C 34.653 -3.812 52
XQD S1P S 35.952 -3.062 53
XQD C C 37.251 -3.812 54
XQD O O 36.501 -5.111 55
XQD CH3 C 38.001 -2.513 56
XQD N4A N 38.550 -4.562 57
XQD "C4'" C 39.849 -3.812 58
XQD "C3'" C 41.148 -4.562 59
XQD "O3'" O 41.148 -6.062 60
XQD "C5'" C 39.849 -2.312 61
XQD "C6'" C 38.550 -1.562 62
XQD "O5'" O 41.148 -1.562 63
XQD "C1'" C 42.447 -2.312 64
XQD "C2'" C 42.447 -3.812 65
XQD "N2'" N 43.746 -4.562 66
XQD "C7'" C 45.045 -3.812 67
XQD "C8'" C 46.344 -4.562 68
XQD "O7'" O 45.045 -2.312 69
XQD "O1'" O 43.746 -1.562 70
XQD PB P 43.746 -0.062 71
XQD O2B O 42.246 -0.062 72
XQD O1B O 45.246 -0.062 73
XQD O3B O 43.746 1.438 74
XQD PA P 45.045 2.188 75
XQD O4D O 44.295 3.487 76
XQD O5B O 45.795 0.889 77
XQD O6B O 46.344 2.938 78
XQD C5B C 46.344 4.438 79
XQD C4B C 47.644 5.188 80
XQD C2B C 47.800 6.680 81
XQD O4A O 46.685 7.684 82
XQD C3B C 49.267 6.992 83
XQD "O2'" O 49.878 8.362 84
XQD C1B C 50.017 5.692 85
XQD O4B O 49.014 4.578 86
XQD C2 C 52.120 4.165 87
XQD O2 O 51.238 2.952 88
XQD O4 O 55.985 5.065 89
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
XQD O9A P3B DOUBLE NONE 1
XQD O8A P3B SINGLE NONE 2
XQD P3B O7A SINGLE NONE 3
XQD P3B O3C SINGLE NONE 4
XQD C3C O3C SINGLE BEGINWEDGE 5
XQD C4C C3C SINGLE NONE 6
XQD C4C O4C SINGLE NONE 7
XQD C4C C5C SINGLE BEGINDASH 8
XQD C3C C2C SINGLE NONE 9
XQD O4C C1A SINGLE NONE 10
XQD C5C O5C SINGLE NONE 11
XQD C1A C2C SINGLE NONE 12
XQD C1A N9A SINGLE BEGINDASH 13
XQD C2C O2C SINGLE BEGINWEDGE 14
XQD O5C P1A SINGLE NONE 15
XQD O2A P1A DOUBLE NONE 16
XQD N3A C4A DOUBLE NONE 17
XQD N3A C2A SINGLE NONE 18
XQD N9A C4A SINGLE NONE 19
XQD N9A C8A SINGLE NONE 20
XQD P1A O3A SINGLE NONE 21
XQD P1A O1A SINGLE BEGINWEDGE 22
XQD C4A C5A SINGLE NONE 23
XQD O4E P2A DOUBLE NONE 24
XQD C2A N1A DOUBLE NONE 25
XQD O3A P2A SINGLE NONE 26
XQD C8A N7A DOUBLE NONE 27
XQD P2A O5A SINGLE BEGINDASH 28
XQD P2A O6A SINGLE NONE 29
XQD C5A N7A SINGLE NONE 30
XQD C5A C6A DOUBLE NONE 31
XQD N1A C6A SINGLE NONE 32
XQD CCP O6A SINGLE NONE 33
XQD CCP CBP SINGLE NONE 34
XQD C6A N6A SINGLE NONE 35
XQD CEP CBP SINGLE NONE 36
XQD CBP CDP SINGLE NONE 37
XQD CBP CAP SINGLE NONE 38
XQD CAP OAP SINGLE BEGINDASH 39
XQD CAP C9P SINGLE NONE 40
XQD O9P C9P DOUBLE NONE 41
XQD C9P N8P SINGLE NONE 42
XQD N8P C7P SINGLE NONE 43
XQD C7P C6P SINGLE NONE 44
XQD C6P C5P SINGLE NONE 45
XQD C5P O5P DOUBLE NONE 46
XQD C5P N4P SINGLE NONE 47
XQD N4P C3P SINGLE NONE 48
XQD "O7'" "C7'" DOUBLE NONE 49
XQD "C8'" "C7'" SINGLE NONE 50
XQD C3P C2P SINGLE NONE 51
XQD "C7'" "N2'" SINGLE NONE 52
XQD C2P S1P SINGLE NONE 53
XQD "C2'" "N2'" SINGLE BEGINDASH 54
XQD O4D PA DOUBLE NONE 55
XQD "C2'" "C1'" SINGLE NONE 56
XQD "C2'" "C3'" SINGLE NONE 57
XQD "C3'" "O3'" SINGLE BEGINWEDGE 58
XQD O C SINGLE NONE 59
XQD S1P C SINGLE NONE 60
XQD "C1'" "O5'" SINGLE NONE 61
XQD "C1'" "O1'" SINGLE BEGINDASH 62
XQD "C3'" "C4'" SINGLE NONE 63
XQD PA O5B SINGLE BEGINWEDGE 64
XQD PA O3B SINGLE NONE 65
XQD PA O6B SINGLE NONE 66
XQD "C4'" N4A SINGLE BEGINDASH 67
XQD "C4'" "C5'" SINGLE NONE 68
XQD C N4A SINGLE NONE 69
XQD C CH3 SINGLE BEGINDASH 70
XQD "O5'" "C5'" SINGLE NONE 71
XQD O3B PB SINGLE NONE 72
XQD "O1'" PB SINGLE NONE 73
XQD "C5'" "C6'" SINGLE BEGINWEDGE 74
XQD O6B C5B SINGLE NONE 75
XQD O1B PB DOUBLE NONE 76
XQD PB O2B SINGLE BEGINWEDGE 77
XQD C4B C5B SINGLE BEGINDASH 78
XQD C5 C6 DOUBLE NONE 79
XQD C5 C4 SINGLE NONE 80
XQD C6 N1 SINGLE NONE 81
XQD C3B C2B SINGLE NONE 82
XQD C3B "O2'" SINGLE BEGINWEDGE 83
XQD C3B C1B SINGLE NONE 84
XQD C2B C4B SINGLE NONE 85
XQD C2B O4A SINGLE BEGINWEDGE 86
XQD O4 C4 DOUBLE NONE 87
XQD C4 N3 SINGLE NONE 88
XQD C4B O4B SINGLE NONE 89
XQD O4B C1B SINGLE NONE 90
XQD C1B N1 SINGLE BEGINDASH 91
XQD N1 C2 SINGLE NONE 92
XQD N3 C2 SINGLE NONE 93
XQD C2 O2 DOUBLE NONE 94
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
XQD MurckoScaffold S1 scaffold 'O=C(CCCO[PH](=O)O[PH](=O)OC[C@@H]1CC[C@H](n2cnc3cncnc32)O1)NCCC(=O)NCCSCN[C@H]1CC[C@@H](O[PH](=O)O[PH](=O)OC[C@@H]2CC[C@H](n3ccc(=O)[nH]c3=O)O2)OC1' InChI=1S/C34H53N9O17P4S/c44-27(2-1-14-53-61(48)59-62(49)54-19-25-5-7-31(57-25)43-21-39-26-16-35-20-38-33(26)43)36-11-9-28(45)37-12-15-65-22-40-23-3-8-32(52-17-23)58-64(51)60-63(50)55-18-24-4-6-30(56-24)42-13-10-29(46)41-34(42)47/h10,13,16,20-21,23-25,30-32,40,61-64H,1-9,11-12,14-15,17-19,22H2,(H,36,44)(H,37,45)(H,41,46,47)/t23-,24-,25-,30+,31+,32+/m0/s1 CSSJJBDHWNFORP-FSCKRFQUSA-N
XQD adenine F1 fragment 'Nc1ncnc2nc[nH]c12' InChI=1S/C5H5N5/c6-4-3-5(9-1-7-3)10-2-8-4/h1-2H,(H3,6,7,8,9,10) GFFGJBXGBJISGV-UHFFFAOYSA-N
XQD amide F2 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
XQD imidazole F3 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
XQD phosphate F4 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
XQD purine F5 fragment 'c1ncc2[nH]cnc2n1' InChI=1S/C5H4N4/c1-4-5(8-2-6-1)9-3-7-4/h1-3H,(H,6,7,8,9) KDCGOANMDULRCW-UHFFFAOYSA-N
XQD pyranose F6 fragment OC1CCCCO1 InChI=1S/C5H10O2/c6-5-3-1-2-4-7-5/h5-6H,1-4H2 CELWCAITJAEQNL-UHFFFAOYSA-N
XQD pyrimidine F7 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
XQD ribose F8 fragment OCC1OCC(O)C1O InChI=1S/C5H10O4/c6-1-4-5(8)3(7)2-9-4/h3-8H,1-2H2 KZVAAIRBJJYZOW-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
XQD N1 S1 1
XQD N3 S1 1
XQD C4 S1 1
XQD C5 S1 1
XQD C6 S1 1
XQD O5P S1 1
XQD C5P S1 1
XQD C6P S1 1
XQD C7P S1 1
XQD N8P S1 1
XQD C9P S1 1
XQD O9P S1 1
XQD CAP S1 1
XQD CBP S1 1
XQD CCP S1 1
XQD O6A S1 1
XQD P2A S1 1
XQD O4E S1 1
XQD O3A S1 1
XQD P1A S1 1
XQD O2A S1 1
XQD O5C S1 1
XQD C5C S1 1
XQD C4C S1 1
XQD C3C S1 1
XQD C2C S1 1
XQD O4C S1 1
XQD C1A S1 1
XQD N9A S1 1
XQD C4A S1 1
XQD N3A S1 1
XQD C2A S1 1
XQD C8A S1 1
XQD N7A S1 1
XQD C5A S1 1
XQD C6A S1 1
XQD N1A S1 1
XQD N4P S1 1
XQD C3P S1 1
XQD C2P S1 1
XQD S1P S1 1
XQD C S1 1
XQD N4A S1 1
XQD "C4'" S1 1
XQD "C3'" S1 1
XQD "C5'" S1 1
XQD "O5'" S1 1
XQD "C1'" S1 1
XQD "C2'" S1 1
XQD "O1'" S1 1
XQD PB S1 1
XQD O1B S1 1
XQD O3B S1 1
XQD PA S1 1
XQD O4D S1 1
XQD O6B S1 1
XQD C5B S1 1
XQD C4B S1 1
XQD C2B S1 1
XQD C3B S1 1
XQD C1B S1 1
XQD O4B S1 1
XQD C2 S1 1
XQD O2 S1 1
XQD O4 S1 1
XQD N1A F1 1
XQD C6A F1 1
XQD C5A F1 1
XQD C4A F1 1
XQD N3A F1 1
XQD C2A F1 1
XQD N9A F1 1
XQD C8A F1 1
XQD N7A F1 1
XQD N6A F1 1
XQD N8P F2 1
XQD C9P F2 1
XQD O9P F2 1
XQD CAP F2 1
XQD N4P F2 2
XQD C5P F2 2
XQD O5P F2 2
XQD C6P F2 2
XQD "N2'" F2 3
XQD "C7'" F2 3
XQD "O7'" F2 3
XQD "C8'" F2 3
XQD C4A F3 1
XQD C5A F3 1
XQD N7A F3 1
XQD C8A F3 1
XQD N9A F3 1
XQD O6A F4 1
XQD P2A F4 1
XQD O4E F4 1
XQD O3A F4 1
XQD O5A F4 1
XQD O3A F4 2
XQD P1A F4 2
XQD O2A F4 2
XQD O5C F4 2
XQD O1A F4 2
XQD O3C F4 3
XQD P3B F4 3
XQD O9A F4 3
XQD O8A F4 3
XQD O7A F4 3
XQD "O1'" F4 4
XQD PB F4 4
XQD O1B F4 4
XQD O3B F4 4
XQD O2B F4 4
XQD O3B F4 5
XQD PA F4 5
XQD O4D F4 5
XQD O5B F4 5
XQD O6B F4 5
XQD N7A F5 1
XQD C8A F5 1
XQD N9A F5 1
XQD C4A F5 1
XQD C5A F5 1
XQD C6A F5 1
XQD N1A F5 1
XQD C2A F5 1
XQD N3A F5 1
XQD "C4'" F6 1
XQD "C5'" F6 1
XQD "O5'" F6 1
XQD "C1'" F6 1
XQD "C2'" F6 1
XQD "C3'" F6 1
XQD "O1'" F6 1
XQD C5 F7 1
XQD C6 F7 1
XQD N1 F7 1
XQD C2 F7 1
XQD N3 F7 1
XQD C4 F7 1
XQD C5A F7 2
XQD C4A F7 2
XQD N3A F7 2
XQD C2A F7 2
XQD N1A F7 2
XQD C6A F7 2
XQD C2C F8 1
XQD C3C F8 1
XQD C4C F8 1
XQD O4C F8 1
XQD C1A F8 1
XQD C5C F8 1
XQD O5C F8 1
XQD O3C F8 1
XQD O2C F8 1
XQD C3B F8 2
XQD C2B F8 2
XQD C4B F8 2
XQD O4B F8 2
XQD C1B F8 2
XQD C5B F8 2
XQD O6B F8 2
XQD O4A F8 2
XQD "O2'" F8 2
#
_pdbe_chem_comp_rdkit_properties.comp_id XQD
_pdbe_chem_comp_rdkit_properties.exactmw 1399.228
_pdbe_chem_comp_rdkit_properties.amw 1399.950
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 43
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 19
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 49
_pdbe_chem_comp_rdkit_properties.NumHBD 18
_pdbe_chem_comp_rdkit_properties.NumHBA 40
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 89
_pdbe_chem_comp_rdkit_properties.NumAtoms 155
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 49
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 3
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.700
_pdbe_chem_comp_rdkit_properties.NumRings 6
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 3
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 3
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 3
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 6
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 19
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 598.252
_pdbe_chem_comp_rdkit_properties.tpsa 644.220
_pdbe_chem_comp_rdkit_properties.CrippenClogP -4.217
_pdbe_chem_comp_rdkit_properties.CrippenMR 289.790
_pdbe_chem_comp_rdkit_properties.chi0v 45.916
_pdbe_chem_comp_rdkit_properties.chi1v 28.563
_pdbe_chem_comp_rdkit_properties.chi2v 13.753
_pdbe_chem_comp_rdkit_properties.chi3v 13.753
_pdbe_chem_comp_rdkit_properties.chi4v 9.280
_pdbe_chem_comp_rdkit_properties.chi0n 106.628
_pdbe_chem_comp_rdkit_properties.chi1n 51.973
_pdbe_chem_comp_rdkit_properties.chi2n 8.251
_pdbe_chem_comp_rdkit_properties.chi3n 8.251
_pdbe_chem_comp_rdkit_properties.chi4n 5.066
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -3.980
_pdbe_chem_comp_rdkit_properties.kappa1 24.656
_pdbe_chem_comp_rdkit_properties.kappa2 29.537
_pdbe_chem_comp_rdkit_properties.kappa3 20.507
_pdbe_chem_comp_rdkit_properties.Phi 8.183
#
_pdbe_chem_comp_external_mappings.comp_id XQD
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PubChem
_pdbe_chem_comp_external_mappings.resource_id 155803733
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
XQD N1 9.883 6.679 1.176 ETKDGv3 1
XQD N3 8.528 6.647 3.256 ETKDGv3 2
XQD C4 9.188 7.842 3.673 ETKDGv3 3
XQD C5 10.226 8.434 2.820 ETKDGv3 4
XQD C6 10.544 7.871 1.650 ETKDGv3 5
XQD O5P -0.041 -7.812 5.491 ETKDGv3 6
XQD C5P -0.769 -8.334 4.604 ETKDGv3 7
XQD C6P -2.186 -8.708 4.935 ETKDGv3 8
XQD C7P -3.074 -7.467 5.093 ETKDGv3 9
XQD N8P -3.158 -6.701 3.849 ETKDGv3 10
XQD C9P -3.893 -5.471 3.773 ETKDGv3 11
XQD O9P -4.655 -5.132 4.719 ETKDGv3 12
XQD CAP -3.752 -4.579 2.564 ETKDGv3 13
XQD OAP -3.796 -3.237 2.989 ETKDGv3 14
XQD CBP -4.823 -4.844 1.453 ETKDGv3 15
XQD CDP -4.800 -6.333 1.032 ETKDGv3 16
XQD CEP -6.239 -4.483 1.958 ETKDGv3 17
XQD CCP -4.476 -3.972 0.216 ETKDGv3 18
XQD O6A -5.393 -4.200 -0.831 ETKDGv3 19
XQD P2A -4.933 -3.241 -2.166 ETKDGv3 20
XQD O4E -5.901 -3.478 -3.303 ETKDGv3 21
XQD O5A -3.388 -3.704 -2.685 ETKDGv3 22
XQD O3A -4.900 -1.589 -1.746 ETKDGv3 23
XQD P1A -6.494 -1.104 -1.383 ETKDGv3 24
XQD O1A -7.472 -1.210 -2.762 ETKDGv3 25
XQD O2A -7.078 -1.970 -0.289 ETKDGv3 26
XQD O5C -6.478 0.509 -0.834 ETKDGv3 27
XQD C5C -5.819 1.298 -1.796 ETKDGv3 28
XQD C4C -5.940 2.776 -1.411 ETKDGv3 29
XQD C3C -7.393 3.240 -1.365 ETKDGv3 30
XQD O3C -7.932 3.027 -0.073 ETKDGv3 31
XQD P3B -9.609 2.729 -0.193 ETKDGv3 32
XQD O9A -9.845 1.398 -0.871 ETKDGv3 33
XQD O8A -10.365 3.956 -1.080 ETKDGv3 34
XQD O7A -10.272 2.683 1.363 ETKDGv3 35
XQD C2C -7.265 4.710 -1.698 ETKDGv3 36
XQD O2C -7.183 5.514 -0.543 ETKDGv3 37
XQD O4C -5.245 3.571 -2.344 ETKDGv3 38
XQD C1A -5.968 4.772 -2.516 ETKDGv3 39
XQD N9A -6.263 4.960 -3.936 ETKDGv3 40
XQD C4A -6.631 6.173 -4.561 ETKDGv3 41
XQD N3A -6.538 7.378 -4.086 ETKDGv3 42
XQD C2A -7.104 8.451 -4.874 ETKDGv3 43
XQD C8A -6.814 3.971 -4.834 ETKDGv3 44
XQD N7A -7.419 4.455 -5.888 ETKDGv3 45
XQD C5A -7.322 5.867 -5.759 ETKDGv3 46
XQD C6A -7.892 6.836 -6.473 ETKDGv3 47
XQD N6A -8.655 6.559 -7.648 ETKDGv3 48
XQD N1A -7.740 8.192 -5.993 ETKDGv3 49
XQD N4P -0.254 -8.551 3.281 ETKDGv3 50
XQD C3P 1.049 -8.051 2.845 ETKDGv3 51
XQD C2P 1.023 -6.533 2.660 ETKDGv3 52
XQD S1P -0.254 -6.067 1.433 ETKDGv3 53
XQD C 0.205 -4.304 1.165 ETKDGv3 54
XQD O -0.755 -3.794 0.266 ETKDGv3 55
XQD CH3 0.164 -3.551 2.517 ETKDGv3 56
XQD N4A 1.555 -4.257 0.559 ETKDGv3 57
XQD "C4'" 2.013 -2.915 0.115 ETKDGv3 58
XQD "C3'" 3.345 -2.578 0.800 ETKDGv3 59
XQD "O3'" 3.200 -2.652 2.195 ETKDGv3 60
XQD "C5'" 2.231 -2.837 -1.438 ETKDGv3 61
XQD "C6'" 0.924 -2.582 -2.196 ETKDGv3 62
XQD "O5'" 3.220 -1.892 -1.842 ETKDGv3 63
XQD "C1'" 3.263 -0.753 -1.003 ETKDGv3 64
XQD "C2'" 3.813 -1.157 0.394 ETKDGv3 65
XQD "N2'" 5.279 -1.104 0.410 ETKDGv3 66
XQD "C7'" 6.027 -0.512 1.482 ETKDGv3 67
XQD "C8'" 7.521 -0.528 1.447 ETKDGv3 68
XQD "O7'" 5.436 -0.008 2.475 ETKDGv3 69
XQD "O1'" 4.116 0.198 -1.612 ETKDGv3 70
XQD PB 3.586 1.789 -1.272 ETKDGv3 71
XQD O2B 2.112 2.057 -2.058 ETKDGv3 72
XQD O1B 3.386 1.986 0.215 ETKDGv3 73
XQD O3B 4.715 2.924 -1.853 ETKDGv3 74
XQD PA 6.235 2.531 -1.192 ETKDGv3 75
XQD O4D 6.159 2.501 0.320 ETKDGv3 76
XQD O5B 6.749 1.023 -1.769 ETKDGv3 77
XQD O6B 7.347 3.733 -1.667 ETKDGv3 78
XQD C5B 8.639 3.322 -1.283 ETKDGv3 79
XQD C4B 9.629 4.463 -1.545 ETKDGv3 80
XQD C2B 11.056 4.084 -1.107 ETKDGv3 81
XQD O4A 11.993 4.362 -2.123 ETKDGv3 82
XQD C3B 11.277 4.935 0.125 ETKDGv3 83
XQD "O2'" 12.599 5.394 0.235 ETKDGv3 84
XQD C1B 10.316 6.090 -0.102 ETKDGv3 85
XQD O4B 9.211 5.614 -0.836 ETKDGv3 86
XQD C2 8.885 6.048 2.009 ETKDGv3 87
XQD O2 8.329 4.974 1.655 ETKDGv3 88
XQD O4 8.886 8.383 4.769 ETKDGv3 89
XQD H1 7.798 6.209 3.862 ETKDGv3 90
XQD H2 10.739 9.331 3.142 ETKDGv3 91
XQD H3 11.320 8.332 1.050 ETKDGv3 92
XQD H4 -2.193 -9.281 5.886 ETKDGv3 93
XQD H5 -2.608 -9.366 4.145 ETKDGv3 94
XQD H6 -2.669 -6.820 5.901 ETKDGv3 95
XQD H7 -4.095 -7.794 5.388 ETKDGv3 96
XQD H8 -2.646 -7.030 3.000 ETKDGv3 97
XQD H9 -2.750 -4.794 2.128 ETKDGv3 98
XQD H10 -3.113 -2.735 2.472 ETKDGv3 99
XQD H11 -3.784 -6.627 0.690 ETKDGv3 100
XQD H12 -5.515 -6.525 0.203 ETKDGv3 101
XQD H13 -5.094 -6.993 1.875 ETKDGv3 102
XQD H14 -6.997 -4.659 1.165 ETKDGv3 103
XQD H15 -6.293 -3.414 2.255 ETKDGv3 104
XQD H16 -6.521 -5.107 2.832 ETKDGv3 105
XQD H17 -4.497 -2.899 0.512 ETKDGv3 106
XQD H18 -3.444 -4.230 -0.113 ETKDGv3 107
XQD H19 -2.766 -3.091 -2.219 ETKDGv3 108
XQD H20 -8.327 -0.785 -2.498 ETKDGv3 109
XQD H21 -6.255 1.159 -2.813 ETKDGv3 110
XQD H22 -4.737 1.037 -1.827 ETKDGv3 111
XQD H23 -5.465 2.919 -0.413 ETKDGv3 112
XQD H24 -7.957 2.729 -2.185 ETKDGv3 113
XQD H25 -10.219 4.778 -0.548 ETKDGv3 114
XQD H26 -9.734 2.008 1.847 ETKDGv3 115
XQD H27 -8.142 5.046 -2.293 ETKDGv3 116
XQD H28 -6.389 5.226 -0.019 ETKDGv3 117
XQD H29 -5.332 5.618 -2.173 ETKDGv3 118
XQD H30 -7.011 9.473 -4.533 ETKDGv3 119
XQD H31 -6.758 2.908 -4.643 ETKDGv3 120
XQD H32 -9.099 7.342 -8.176 ETKDGv3 121
XQD H33 -8.778 5.582 -7.996 ETKDGv3 122
XQD H34 -0.829 -9.092 2.595 ETKDGv3 123
XQD H35 1.827 -8.329 3.588 ETKDGv3 124
XQD H36 1.321 -8.527 1.878 ETKDGv3 125
XQD H37 2.023 -6.196 2.316 ETKDGv3 126
XQD H38 0.797 -6.055 3.635 ETKDGv3 127
XQD H39 -0.832 -2.812 0.377 ETKDGv3 128
XQD H40 1.032 -3.823 3.150 ETKDGv3 129
XQD H41 0.194 -2.451 2.378 ETKDGv3 130
XQD H42 -0.767 -3.794 3.069 ETKDGv3 131
XQD H43 1.590 -4.948 -0.225 ETKDGv3 132
XQD H45 1.293 -2.123 0.413 ETKDGv3 133
XQD H46 4.095 -3.335 0.465 ETKDGv3 134
XQD H47 4.114 -2.715 2.575 ETKDGv3 135
XQD H48 2.613 -3.821 -1.788 ETKDGv3 136
XQD H49 1.136 -2.458 -3.279 ETKDGv3 137
XQD H50 0.422 -1.663 -1.826 ETKDGv3 138
XQD H51 0.237 -3.445 -2.080 ETKDGv3 139
XQD H52 2.223 -0.358 -0.892 ETKDGv3 140
XQD H53 3.399 -0.429 1.125 ETKDGv3 141
XQD H54 5.803 -1.602 -0.346 ETKDGv3 142
XQD H55 7.932 0.250 2.124 ETKDGv3 143
XQD H56 7.887 -1.524 1.770 ETKDGv3 144
XQD H57 7.879 -0.324 0.416 ETKDGv3 145
XQD H58 2.289 1.833 -3.006 ETKDGv3 146
XQD H59 6.726 1.111 -2.755 ETKDGv3 147
XQD H60 8.679 3.063 -0.200 ETKDGv3 148
XQD H61 8.953 2.440 -1.886 ETKDGv3 149
XQD H62 9.608 4.690 -2.634 ETKDGv3 150
XQD H63 11.145 3.008 -0.840 ETKDGv3 151
XQD H64 11.915 5.323 -2.363 ETKDGv3 152
XQD H65 10.984 4.363 1.036 ETKDGv3 153
XQD H66 13.143 4.614 0.520 ETKDGv3 154
XQD H67 10.814 6.869 -0.725 ETKDGv3 155
#