//////////////////////////////////////// // ***** Supporting Information ***** // //////////////////////////////////////// // ***** .PQR format description ***** // Column 1: Indicates and atom Column 2: Atom index Column 3: Atomic symbol Column 4: Residue label (here, all are unknown) Column 5: Residue index Column 6: x coordinate (Angstroms) Column 7: y coordinate (Angstroms) Column 8: z coordinate (Angstroms) Column 9: Atomic charge Column 10: Atomic radius (Angstroms) // ***** THG atoms .PQR file ***** // ATOM 1 Na UNK 1 -19.655000 -23.331000 -11.628000 1.180000 1.9500 ATOM 2 Na UNK 1 11.045000 -7.906000 20.975000 1.280000 1.5300 ATOM 3 Na UNK 1 -19.791000 26.918000 -9.685000 -0.720000 1.1800 ATOM 4 Na UNK 1 -4.178000 7.954000 2.882000 -1.890000 1.0200 ATOM 5 Na UNK 1 0.001000 -0.732000 -0.573000 -1.980000 1.4300 ATOM 6 Na UNK 1 2.545000 -0.076000 -4.433000 -0.240000 1.5600 ATOM 7 Na UNK 1 -24.484000 -12.237000 18.033000 -1.880000 1.3300 ATOM 8 Na UNK 1 -13.783000 0.505000 -4.231000 0.020000 1.0800 ATOM 9 Na UNK 1 21.323000 5.452000 -9.906000 1.800000 1.5900 ATOM 10 Na UNK 1 21.194000 -6.942000 15.258000 0.300000 1.9400 ATOM 11 Na UNK 1 2.385000 -16.218000 -30.961000 0.990000 1.6900 ATOM 12 Na UNK 1 2.508000 2.139000 11.519000 0.070000 0.9200 ATOM 13 Na UNK 1 -17.811000 10.847000 12.941000 -0.550000 0.7600 ATOM 14 Na UNK 1 -16.464000 4.930000 15.543000 0.480000 1.0400 ATOM 15 Na UNK 1 -29.617000 -12.835000 17.896000 0.190000 0.9500 ATOM 16 Na UNK 1 8.407000 10.263000 -19.518000 -0.510000 1.2400 ATOM 17 Na UNK 1 -11.861000 -18.446000 -10.512000 -0.460000 1.1000 ATOM 18 Na UNK 1 20.471000 11.542000 14.301000 -1.570000 0.5300 ATOM 19 Na UNK 1 0.434000 -0.315000 27.878000 1.710000 1.9100 ATOM 20 Na UNK 1 3.055000 2.462000 8.383000 1.850000 0.9700 // ***** Alanine dipeptide (AA) .PQR file ***** // ATOM 1 N UNK 1 0.000000 0.000000 0.000000 0.141400 1.8750 ATOM 2 C UNK 1 0.000000 0.000000 1.500000 0.128100 1.9080 ATOM 3 C UNK 1 1.412520 0.000000 2.033747 0.616300 1.9080 ATOM 4 O UNK 1 2.282886 -0.727569 1.584852 -0.572200 1.6612 ATOM 5 H UNK 1 -0.679879 0.679879 -0.340483 0.199700 0.6000 ATOM 6 H UNK 1 -0.277258 -0.920652 -0.340483 0.199700 0.6000 ATOM 7 H UNK 1 0.920652 0.277258 -0.340483 0.199700 0.6000 ATOM 8 H UNK 1 -0.504720 0.916552 1.870526 0.088900 1.3870 ATOM 9 C UNK 1 -0.697507 -1.273116 2.014063 -0.182500 1.9080 ATOM 10 H UNK 1 -0.696576 -1.271417 3.124061 0.060300 1.4870 ATOM 11 H UNK 1 -0.151445 -2.166786 1.646273 0.060300 1.4870 ATOM 12 H UNK 1 -1.744597 -1.293939 1.646273 0.060300 1.4870 ATOM 13 N UNK 1 1.587270 0.874126 3.034230 -0.382100 1.8240 ATOM 14 C UNK 1 2.886035 1.023156 3.684307 -0.153200 1.9080 ATOM 15 C UNK 1 2.752791 1.072544 5.187605 0.773100 1.9080 ATOM 16 O UNK 1 1.847974 1.798264 5.653583 -0.805500 1.6612 ATOM 17 H UNK 1 0.785643 1.432258 3.327969 0.268100 0.6000 ATOM 18 H UNK 1 3.530648 0.156855 3.427216 0.106700 1.3870 ATOM 19 C UNK 1 3.542145 2.338985 3.226363 -0.182500 1.9080 ATOM 20 H UNK 1 4.529295 2.450603 3.721515 0.060300 1.4870 ATOM 21 H UNK 1 2.890549 3.192861 3.506397 0.060300 1.4870 ATOM 22 H UNK 1 3.682208 2.317508 2.125444 0.060300 1.4870 ATOM 23 O UNK 1 3.557457 0.383945 5.851567 -0.805500 1.6612 // ***** Thymine dinucleotide (TpT) .PQR file ***** // ATOM 1 O UNK 1 0.000000 0.000000 0.000000 -0.631800 3.1210 ATOM 2 C UNK 1 0.000000 0.000000 1.440000 -0.006900 3.3080 ATOM 3 C UNK 1 1.427423 0.000000 1.962363 0.162900 3.3080 ATOM 4 O UNK 1 1.924453 -1.372676 1.980293 -0.369100 3.0837 ATOM 5 C UNK 1 2.866758 -1.556753 0.934073 0.068000 3.3080 ATOM 6 C UNK 1 2.435730 0.816736 1.151710 0.071300 3.3080 ATOM 7 C UNK 1 2.832568 -0.159062 0.042099 -0.085400 3.3080 ATOM 8 O UNK 1 3.554295 1.211441 1.932365 -0.523200 3.0837 ATOM 9 H UNK 1 -0.918053 0.000000 -0.280677 0.442200 1.4001 ATOM 10 H UNK 1 -0.520597 -0.885828 1.803849 0.075400 2.7870 ATOM 11 H UNK 1 -0.520597 0.885828 1.803849 0.075400 2.7870 ATOM 12 H UNK 1 1.435560 0.337148 2.998879 0.117600 2.7870 ATOM 13 H UNK 1 3.838325 -1.808062 1.359516 0.180400 2.6870 ATOM 14 H UNK 1 1.936098 1.681209 0.714498 0.098500 2.7870 ATOM 15 H UNK 1 2.031585 -0.217259 -0.694882 0.071800 2.8870 ATOM 16 H UNK 1 3.838626 0.075227 -0.305832 0.071800 2.8870 ATOM 17 N UNK 1 2.474231 -2.760890 0.168322 -0.023900 3.2240 ATOM 18 C UNK 1 3.115370 -3.932085 0.475148 0.567700 3.3080 ATOM 19 O UNK 1 3.975980 -4.010522 1.336309 -0.588100 3.0612 ATOM 20 N UNK 1 2.722448 -5.032098 -0.259688 -0.434000 3.2240 ATOM 21 C UNK 1 1.763668 -5.054101 -1.251987 0.519400 3.3080 ATOM 22 O UNK 1 1.497905 -6.101153 -1.840166 -0.556300 3.0612 ATOM 23 C UNK 1 1.146824 -3.777158 -1.502027 0.002500 3.3080 ATOM 24 C UNK 1 0.092408 -3.713979 -2.567022 -0.226900 3.3080 ATOM 25 C UNK 1 1.508399 -2.692041 -0.803898 -0.220900 3.3080 ATOM 26 H UNK 1 3.177163 -5.898371 -0.052795 0.342000 2.0000 ATOM 27 H UNK 1 -0.043142 -4.703321 -3.003975 0.077000 2.8870 ATOM 28 H UNK 1 0.400223 -3.012723 -3.342644 0.077000 2.8870 ATOM 29 H UNK 1 -0.847410 -3.377775 -2.129062 0.077000 2.8870 ATOM 30 H UNK 1 1.030878 -1.745547 -1.010107 0.260700 2.8090 ATOM 31 P UNK 1 4.945025 1.509927 1.199715 1.165900 3.5000 ATOM 32 O UNK 1 4.678174 1.880838 -0.207983 -0.776100 3.0612 ATOM 33 O UNK 1 5.626338 2.624779 1.894925 -0.776100 3.0612 ATOM 34 O UNK 1 5.703046 0.109294 1.353436 -0.495400 3.0837 ATOM 35 C UNK 1 5.699764 -0.549445 2.633925 -0.006900 3.3080 ATOM 36 C UNK 1 7.006450 -1.298253 2.839489 0.162900 3.3080 ATOM 37 O UNK 1 6.911920 -2.601814 2.188803 -0.369100 3.0837 ATOM 38 C UNK 1 7.703952 -2.609688 1.010234 0.068000 3.3080 ATOM 39 C UNK 1 8.259344 -0.622459 2.278722 0.071300 3.3080 ATOM 40 C UNK 1 8.234572 -1.051237 0.810241 -0.085400 3.3080 ATOM 41 O UNK 1 9.440568 -1.057682 2.935755 -0.654900 3.1210 ATOM 42 H UNK 1 4.867074 -1.251311 2.679895 0.075400 2.7870 ATOM 43 H UNK 1 5.576799 0.191424 3.423920 0.075400 2.7870 ATOM 44 H UNK 1 7.146603 -1.500768 3.901301 0.117600 2.7870 ATOM 45 H UNK 1 8.492507 -3.355987 1.106768 0.180400 2.6870 ATOM 46 H UNK 1 8.148859 0.459983 2.343619 0.098500 2.7870 ATOM 47 H UNK 1 7.479038 -0.475395 0.275756 0.071800 2.8870 ATOM 48 H UNK 1 9.251023 -1.060627 0.416745 0.071800 2.8870 ATOM 49 H UNK 1 10.253146 -0.658975 2.615835 0.439600 1.4001 ATOM 50 N UNK 1 6.863668 -3.099766 -0.105179 -0.023900 3.2240 ATOM 51 C UNK 1 6.981233 -4.422883 -0.440499 0.567700 3.3080 ATOM 52 O UNK 1 7.736382 -5.188096 0.136215 -0.588100 3.0612 ATOM 53 N UNK 1 6.182229 -4.842170 -1.484621 -0.434000 3.2240 ATOM 54 C UNK 1 5.297194 -4.063695 -2.202319 0.519400 3.3080 ATOM 55 O UNK 1 4.635581 -4.552360 -3.116854 -0.556300 3.0612 ATOM 56 C UNK 1 5.244122 -2.689118 -1.776499 0.002500 3.3080 ATOM 57 C UNK 1 4.305750 -1.773860 -2.505719 -0.226900 3.3080 ATOM 58 C UNK 1 6.008521 -2.253973 -0.765587 -0.220900 3.3080 ATOM 59 H UNK 1 6.251362 -5.804673 -1.746931 0.342000 2.0000 ATOM 60 H UNK 1 3.786218 -2.331220 -3.285165 0.077000 2.8870 ATOM 61 H UNK 1 4.870476 -0.957929 -2.956763 0.077000 2.8870 ATOM 62 H UNK 1 3.578326 -1.364738 -1.804596 0.077000 2.8870 ATOM 63 H UNK 1 5.950626 -1.218309 -0.464842 0.260700 2.8090