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Commit 7b96df79 by Peter Eastman
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Added templates for DNA, RNA, and terminal groups

parent a991e13e
Showing with 192 additions and 0 deletions
templates/A.pdb 0 → 100644
ATOM 1 P A A 1 -2.114 -1.179 3.781 1.00 0.00
ATOM 2 OP1 A A 1 -1.822 -1.633 5.165 1.00 0.00
ATOM 3 OP2 A A 1 -3.263 -0.267 3.555 1.00 0.00
ATOM 4 O5' A A 1 -0.800 -0.568 3.129 1.00 0.00
ATOM 5 C5' A A 1 0.456 -1.202 3.303 1.00 0.00
ATOM 6 C4' A A 1 1.422 -0.825 2.211 1.00 0.00
ATOM 7 O4' A A 1 0.959 -1.348 0.941 1.00 0.00
ATOM 8 C3' A A 1 1.591 0.662 1.951 1.00 0.00
ATOM 9 O3' A A 1 2.443 1.298 2.889 1.00 0.00
ATOM 10 C2' A A 1 2.123 0.687 0.523 1.00 0.00
ATOM 11 O2' A A 1 3.512 0.395 0.500 1.00 0.00
ATOM 12 C1' A A 1 1.371 -0.491 -0.105 1.00 0.00
ATOM 13 N9 A A 1 0.184 -0.049 -0.863 1.00 0.00
ATOM 14 C8 A A 1 -1.080 0.283 -0.428 1.00 0.00
ATOM 15 N7 A A 1 -1.892 0.655 -1.393 1.00 0.00
ATOM 16 C5 A A 1 -1.105 0.569 -2.537 1.00 0.00
ATOM 17 C6 A A 1 -1.360 0.829 -3.900 1.00 0.00
ATOM 18 N6 A A 1 -2.535 1.248 -4.391 1.00 0.00
ATOM 19 N1 A A 1 -0.337 0.635 -4.764 1.00 0.00
ATOM 20 C2 A A 1 0.851 0.217 -4.302 1.00 0.00
ATOM 21 N3 A A 1 1.212 -0.058 -3.054 1.00 0.00
ATOM 22 C4 A A 1 0.177 0.144 -2.219 1.00 0.00
TER 23 A A 1
END
templates/ACE.pdb 0 → 100644
ATOM 1 C ACE A 1 0.336 0.267 -0.194 1.00 0.00
ATOM 2 O ACE A 1 -0.134 -0.667 -0.918 1.00 0.00
ATOM 3 CH3 ACE A 1 -0.201 0.401 1.112 1.00 0.00
TER 4 ACE A 1
END
templates/C.pdb 0 → 100644
ATOM 1 P C A 1 -2.563 1.193 2.810 1.00 0.00
ATOM 2 OP1 C A 1 -2.884 2.401 2.011 1.00 0.00
ATOM 3 OP2 C A 1 -2.477 1.317 4.283 1.00 0.00
ATOM 4 O5' C A 1 -1.243 0.497 2.246 1.00 0.00
ATOM 5 C5' C A 1 -0.850 -0.791 2.702 1.00 0.00
ATOM 6 C4' C A 1 0.199 -1.413 1.809 1.00 0.00
ATOM 7 O4' C A 1 -0.344 -1.649 0.484 1.00 0.00
ATOM 8 C3' C A 1 1.442 -0.581 1.550 1.00 0.00
ATOM 9 O3' C A 1 2.367 -0.613 2.625 1.00 0.00
ATOM 10 C2' C A 1 1.975 -1.189 0.255 1.00 0.00
ATOM 11 O2' C A 1 2.641 -2.418 0.508 1.00 0.00
ATOM 12 C1' C A 1 0.675 -1.498 -0.484 1.00 0.00
ATOM 13 N1 C A 1 0.289 -0.415 -1.415 1.00 0.00
ATOM 14 C2 C A 1 0.999 -0.291 -2.603 1.00 0.00
ATOM 15 O2 C A 1 1.926 -1.086 -2.824 1.00 0.00
ATOM 16 N3 C A 1 0.659 0.687 -3.476 1.00 0.00
ATOM 17 C4 C A 1 -0.344 1.523 -3.212 1.00 0.00
ATOM 18 N4 C A 1 -0.627 2.463 -4.117 1.00 0.00
ATOM 19 C5 C A 1 -1.092 1.422 -2.008 1.00 0.00
ATOM 20 C6 C A 1 -0.741 0.447 -1.154 1.00 0.00
TER 21 C A 1
END
templates/DA.pdb 0 → 100644
ATOM 1 P DA A 1 3.455 -3.048 -0.447 1.00 0.00
ATOM 2 OP1 DA A 1 3.367 -2.804 -1.906 1.00 0.00
ATOM 3 OP2 DA A 1 3.853 -4.386 0.047 1.00 0.00
ATOM 4 O5' DA A 1 2.057 -2.670 0.231 1.00 0.00
ATOM 5 C5' DA A 1 1.984 -2.545 1.646 1.00 0.00
ATOM 6 C4' DA A 1 0.732 -1.793 2.062 1.00 0.00
ATOM 7 O4' DA A 1 0.860 -0.386 1.748 1.00 0.00
ATOM 8 C3' DA A 1 -0.540 -2.217 1.345 1.00 0.00
ATOM 9 O3' DA A 1 -1.083 -3.380 1.961 1.00 0.00
ATOM 10 C2' DA A 1 -1.428 -0.996 1.557 1.00 0.00
ATOM 11 C1' DA A 1 -0.430 0.158 1.535 1.00 0.00
ATOM 12 N9 DA A 1 -0.431 0.892 0.273 1.00 0.00
ATOM 13 C8 DA A 1 0.420 0.716 -0.781 1.00 0.00
ATOM 14 N7 DA A 1 0.190 1.518 -1.793 1.00 0.00
ATOM 15 C5 DA A 1 -0.891 2.276 -1.375 1.00 0.00
ATOM 16 C6 DA A 1 -1.617 3.311 -1.997 1.00 0.00
ATOM 17 N6 DA A 1 -1.340 3.769 -3.223 1.00 0.00
ATOM 18 N1 DA A 1 -2.641 3.854 -1.304 1.00 0.00
ATOM 19 C2 DA A 1 -2.916 3.391 -0.077 1.00 0.00
ATOM 20 N3 DA A 1 -2.303 2.427 0.609 1.00 0.00
ATOM 21 C4 DA A 1 -1.289 1.903 -0.103 1.00 0.00
TER 22 DA A 1
END
templates/DC.pdb 0 → 100644
ATOM 1 P DC A 1 0.295 -2.226 -3.343 1.00 0.00
ATOM 2 OP1 DC A 1 1.043 -3.343 -3.965 1.00 0.00
ATOM 3 OP2 DC A 1 -1.169 -2.387 -3.225 1.00 0.00
ATOM 4 O5' DC A 1 0.883 -1.865 -1.892 1.00 0.00
ATOM 5 C5' DC A 1 2.189 -1.294 -1.719 1.00 0.00
ATOM 6 C4' DC A 1 2.331 -0.489 -0.428 1.00 0.00
ATOM 7 O4' DC A 1 1.384 0.603 -0.437 1.00 0.00
ATOM 8 C3' DC A 1 2.062 -1.218 0.887 1.00 0.00
ATOM 9 O3' DC A 1 3.255 -1.815 1.397 1.00 0.00
ATOM 10 C2' DC A 1 1.590 -0.107 1.824 1.00 0.00
ATOM 11 C1' DC A 1 1.067 0.976 0.890 1.00 0.00
ATOM 12 N1 DC A 1 -0.402 1.178 0.991 1.00 0.00
ATOM 13 C2 DC A 1 -0.894 2.298 1.673 1.00 0.00
ATOM 14 O2 DC A 1 -0.091 3.098 2.179 1.00 0.00
ATOM 15 N3 DC A 1 -2.241 2.473 1.753 1.00 0.00
ATOM 16 C4 DC A 1 -3.071 1.588 1.193 1.00 0.00
ATOM 17 N4 DC A 1 -4.387 1.805 1.302 1.00 0.00
ATOM 18 C5 DC A 1 -2.582 0.441 0.498 1.00 0.00
ATOM 19 C6 DC A 1 -1.255 0.277 0.423 1.00 0.00
TER 20 DC A 1
END
templates/DG.pdb 0 → 100644
ATOM 1 P DG A 1 1.161 1.329 -4.498 1.00 0.00
ATOM 2 OP1 DG A 1 1.796 0.851 -5.745 1.00 0.00
ATOM 3 OP2 DG A 1 -0.048 2.176 -4.567 1.00 0.00
ATOM 4 O5' DG A 1 0.805 0.084 -3.560 1.00 0.00
ATOM 5 C5' DG A 1 1.762 -0.946 -3.341 1.00 0.00
ATOM 6 C4' DG A 1 1.846 -1.326 -1.871 1.00 0.00
ATOM 7 O4' DG A 1 1.636 -0.145 -1.058 1.00 0.00
ATOM 8 C3' DG A 1 0.791 -2.290 -1.343 1.00 0.00
ATOM 9 O3' DG A 1 1.106 -3.631 -1.683 1.00 0.00
ATOM 10 C2' DG A 1 0.949 -2.063 0.154 1.00 0.00
ATOM 11 C1' DG A 1 1.187 -0.555 0.219 1.00 0.00
ATOM 12 N9 DG A 1 -0.028 0.159 0.606 1.00 0.00
ATOM 13 C8 DG A 1 -0.940 0.835 -0.171 1.00 0.00
ATOM 14 N7 DG A 1 -1.931 1.350 0.512 1.00 0.00
ATOM 15 C5 DG A 1 -1.657 0.985 1.826 1.00 0.00
ATOM 16 C6 DG A 1 -2.358 1.244 3.030 1.00 0.00
ATOM 17 O6 DG A 1 -3.413 1.875 3.205 1.00 0.00
ATOM 18 N1 DG A 1 -1.704 0.676 4.123 1.00 0.00
ATOM 19 C2 DG A 1 -0.533 -0.046 4.077 1.00 0.00
ATOM 20 N2 DG A 1 -0.051 -0.517 5.237 1.00 0.00
ATOM 21 N3 DG A 1 0.126 -0.294 2.961 1.00 0.00
ATOM 22 C4 DG A 1 -0.493 0.251 1.889 1.00 0.00
TER 23 DG A 1
END
templates/DT.pdb 0 → 100644
ATOM 1 P DT A 1 -1.137 0.745 4.665 1.00 0.00
ATOM 2 OP1 DT A 1 -2.403 1.211 5.278 1.00 0.00
ATOM 3 OP2 DT A 1 -0.705 -0.655 4.875 1.00 0.00
ATOM 4 O5' DT A 1 -1.190 1.013 3.082 1.00 0.00
ATOM 5 C5' DT A 1 -1.958 0.196 2.186 1.00 0.00
ATOM 6 C4' DT A 1 -2.031 0.805 0.789 1.00 0.00
ATOM 7 O4' DT A 1 -0.707 0.882 0.198 1.00 0.00
ATOM 8 C3' DT A 1 -2.890 0.053 -0.226 1.00 0.00
ATOM 9 O3' DT A 1 -3.701 0.978 -0.945 1.00 0.00
ATOM 10 C2' DT A 1 -1.866 -0.623 -1.137 1.00 0.00
ATOM 11 C1' DT A 1 -0.766 0.430 -1.140 1.00 0.00
ATOM 12 N1 DT A 1 0.603 -0.035 -1.562 1.00 0.00
ATOM 13 C2 DT A 1 0.971 0.054 -2.892 1.00 0.00
ATOM 14 O2 DT A 1 0.235 0.484 -3.765 1.00 0.00
ATOM 15 N3 DT A 1 2.244 -0.389 -3.167 1.00 0.00
ATOM 16 C4 DT A 1 3.169 -0.897 -2.270 1.00 0.00
ATOM 17 O4 DT A 1 4.288 -1.269 -2.619 1.00 0.00
ATOM 18 C5 DT A 1 2.725 -0.959 -0.899 1.00 0.00
ATOM 19 C7 DT A 1 3.643 -1.492 0.163 1.00 0.00
ATOM 20 C6 DT A 1 1.484 -0.529 -0.617 1.00 0.00
TER 21 DT A 1
END
templates/G.pdb 0 → 100644
ATOM 1 P G A 1 -3.890 3.026 0.738 1.00 0.00
ATOM 2 OP1 G A 1 -3.347 3.996 -0.254 1.00 0.00
ATOM 3 OP2 G A 1 -4.455 3.555 2.014 1.00 0.00
ATOM 4 O5' G A 1 -2.795 1.882 1.048 1.00 0.00
ATOM 5 C5' G A 1 -2.835 1.119 2.259 1.00 0.00
ATOM 6 C4' G A 1 -1.720 0.091 2.340 1.00 0.00
ATOM 7 O4' G A 1 -1.679 -0.704 1.121 1.00 0.00
ATOM 8 C3' G A 1 -0.295 0.626 2.465 1.00 0.00
ATOM 9 O3' G A 1 0.046 1.086 3.774 1.00 0.00
ATOM 10 C2' G A 1 0.547 -0.561 1.985 1.00 0.00
ATOM 11 O2' G A 1 0.709 -1.536 3.011 1.00 0.00
ATOM 12 C1' G A 1 -0.344 -1.143 0.879 1.00 0.00
ATOM 13 N9 G A 1 0.102 -0.691 -0.466 1.00 0.00
ATOM 14 C8 G A 1 -0.447 0.259 -1.306 1.00 0.00
ATOM 15 N7 G A 1 0.226 0.442 -2.421 1.00 0.00
ATOM 16 C5 G A 1 1.309 -0.426 -2.320 1.00 0.00
ATOM 17 C6 G A 1 2.388 -0.666 -3.222 1.00 0.00
ATOM 18 O6 G A 1 2.613 -0.146 -4.319 1.00 0.00
ATOM 19 N1 G A 1 3.267 -1.620 -2.739 1.00 0.00
ATOM 20 C2 G A 1 3.122 -2.258 -1.538 1.00 0.00
ATOM 21 N2 G A 1 4.078 -3.144 -1.251 1.00 0.00
ATOM 22 N3 G A 1 2.135 -2.053 -0.678 1.00 0.00
ATOM 23 C4 G A 1 1.254 -1.125 -1.124 1.00 0.00
TER 24 G A 1
END
templates/NME.pdb 0 → 100644
ATOM 1 N NME A 1 -0.237 0.562 -0.354 1.00 0.00
ATOM 2 C NME A 1 0.237 -0.562 0.354 1.00 0.00
TER 3 NME A 1
END
templates/U.pdb 0 → 100644
ATOM 1 P U A 1 -2.970 2.321 1.674 1.00 0.00
ATOM 2 OP1 U A 1 -3.135 2.909 3.025 1.00 0.00
ATOM 3 OP2 U A 1 -2.966 3.228 0.497 1.00 0.00
ATOM 4 O5' U A 1 -1.680 1.388 1.645 1.00 0.00
ATOM 5 C5' U A 1 -1.521 0.343 2.591 1.00 0.00
ATOM 6 C4' U A 1 -0.530 -0.696 2.122 1.00 0.00
ATOM 7 O4' U A 1 -0.826 -1.099 0.762 1.00 0.00
ATOM 8 C3' U A 1 0.920 -0.260 2.055 1.00 0.00
ATOM 9 O3' U A 1 1.543 -0.233 3.324 1.00 0.00
ATOM 10 C2' U A 1 1.525 -1.281 1.095 1.00 0.00
ATOM 11 O2' U A 1 1.808 -2.499 1.766 1.00 0.00
ATOM 12 C1' U A 1 0.363 -1.523 0.127 1.00 0.00
ATOM 13 N1 U A 1 0.530 -0.786 -1.143 1.00 0.00
ATOM 14 C2 U A 1 1.310 -1.432 -2.070 1.00 0.00
ATOM 15 O2 U A 1 1.807 -2.523 -1.850 1.00 0.00
ATOM 16 N3 U A 1 1.479 -0.763 -3.254 1.00 0.00
ATOM 17 C4 U A 1 0.967 0.464 -3.613 1.00 0.00
ATOM 18 O4 U A 1 1.230 0.911 -4.736 1.00 0.00
ATOM 19 C5 U A 1 0.166 1.079 -2.595 1.00 0.00
ATOM 20 C6 U A 1 -0.019 0.448 -1.423 1.00 0.00
TER 21 U A 1
END
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