📄 dna2.mol
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#==================================================I# Molecular Dynamics Data Base I# Configuration and interaction potential I#==================================================I# B-DNA (strand 2) CHARMM I#==================================================I# Number of sites 316# X Y Z M Q sigma epsilon# (A) (kJ/M)# 1 nucl C O3* -8.60100 1.61000 -12.94958 15.9990 -.550 3.154 .636 ON2 P -8.68900 1.97400 -14.49959 30.9740 1.500 3.831 2.450 P O1P -9.76000 2.96500 -14.71957 15.9990 -.800 3.030 .502 ON3 O2P -8.79000 .72300 -15.28958 15.9990 -.800 3.030 .502 ON3 O5* -7.26400 2.64400 -14.74959 15.9990 -.550 3.154 .636 ON2 C5* -6.78600 3.63900 -13.80959 12.0110 -.080 3.876 .230 CN8 H5* -6.14500 3.23100 -13.01358 1.0080 .090 2.352 .092 HN7 H5** -7.63800 4.12800 -13.31459 1.0080 .090 2.352 .092 HN7 O1* -4.62200 4.16200 -14.74959 15.9990 -.400 3.154 .636 ON6 C1* -4.44900 3.81300 -16.10957 12.0110 .110 4.054 .084 CN6BH1* -3.70300 4.56300 -16.41058 1.0080 .090 2.352 .092 HN6 C2* -5.78100 4.01800 -16.81958 12.0110 -.180 4.054 .084 CN6 H2* -6.30700 3.06600 -16.98657 1.0080 .090 2.352 .092 HN6 H2** -5.46600 4.41700 -17.79457 1.0080 .090 2.352 .092 HN6 C3* -6.45300 5.06000 -15.93958 12.0110 .010 4.054 .084 CN6 H3* -7.54300 5.08400 -16.08559 1.0080 .090 2.352 .092 HN6 C4* -5.97300 4.68300 -14.53958 12.0110 .110 4.054 .084 CN6 H4* -6.05000 5.63900 -13.99957 1.0080 .090 2.352 .092 HN6 # base C atom 19 N1C -3.95200 2.41200 -16.15958 14.0070 -.160 3.297 .837 NN2 C2 -2.58100 2.21300 -16.30959 12.0110 .530 3.208 .586 CN1 O2 -1.83900 3.19900 -16.39958 15.9990 -.480 3.029 .502 ON1CN3 -2.10900 .94300 -16.35957 14.0070 -.670 3.297 .837 NN3 C4 -2.93800 -.10300 -16.25958 12.0110 .620 3.208 .586 CN2 N4 -2.42300 -1.32100 -16.30959 14.0070 -.580 3.297 .837 NN1 H41 -1.44400 -1.49500 -16.41858 1.0080 .270 .400 .192 HN1 H42 -2.97800 -2.15000 -16.24158 1.0080 .310 .400 .192 HN1 C5 -4.34900 .07600 -16.10957 12.0110 -.100 3.208 .754 CN3 H5 -5.02500 -.78900 -16.03958 1.0080 .100 2.352 .092 HN3 C6 -4.80200 1.35900 -16.05959 12.0110 .110 3.208 .754 CN3 H6 -5.87300 1.57700 -15.94557 1.0080 .050 2.352 .092 HN3 # 2 nucl - from 31 T O3* -7.90400 -3.75300 -9.56958 15.9990 -.550 3.154 .636 ON2 P -8.18900 -3.51000 -11.11959 30.9740 1.500 3.831 2.450 P O1P -9.63800 -3.33800 -11.33958 15.9990 -.800 3.030 .502 ON3 O2P -7.53600 -4.58200 -11.90958 15.9990 -.800 3.030 .502 ON3 O5* -7.43100 -2.13100 -11.36959 15.9990 -.550 3.154 .636 ON2 C5* -7.62900 -1.04500 -10.42958 12.0110 -.080 3.876 .230 CN8 H5* -6.87100 -.99800 -9.63358 1.0080 .090 2.352 .092 HN7 H5** -8.60500 -1.15000 -9.93459 1.0080 .090 2.352 .092 HN7 O1* -6.18600 .65000 -11.36959 15.9990 -.400 3.154 .636 ON6 C1* -5.84100 .47000 -12.72958 12.0110 .110 4.054 .084 CN6BH1* -5.67800 1.51500 -13.03058 1.0080 .090 2.352 .092 HN6 C2* -7.03900 -.14700 -13.43959 12.0110 -.180 4.054 .084 CN6 H2* -6.90400 -1.22600 -13.60658 1.0080 .090 2.352 .092 HN6 H2** -7.01900 .36100 -14.41458 1.0080 .090 2.352 .092 HN6 C3* -8.19400 .30100 -12.55959 12.0110 .010 4.054 .084 CN6 H3* -9.09100 -.32100 -12.70558 1.0080 .090 2.352 .092 HN6 C4* -7.58500 .27800 -11.15958 12.0110 .110 4.054 .084 CN6 H4* -8.20900 1.00600 -10.61959 1.0080 .090 2.352 .092 HN6 # T-BASE atom 49 N1C -4.61500 -.37100 -12.77957 14.0070 -.300 3.297 .837 NN2 C2 -3.40800 .28000 -12.92958 12.0110 .570 3.208 .586 CN1 O2 -3.32000 1.49200 -13.01958 15.9990 -.470 3.029 .502 ON1 N3H -2.29800 -.53900 -12.96957 14.0070 -.460 3.297 .837 NN2UHN3 -1.49600 .05000 -13.07658 1.0080 .360 .400 .192 HN2 C4 -2.28600 -1.91200 -12.87958 12.0110 .540 3.208 .586 CN1 O4 -1.22300 -2.54100 -12.92958 15.9990 -.490 3.029 .502 ON1 C5 -3.59200 -2.50600 -12.72958 12.0110 -.150 3.208 .754 CN3 C5M -3.62700 -4.00000 -12.61959 12.0110 -.110 3.671 .234 CN9 H5M1 -4.56700 -4.38200 -13.01859 1.0080 .070 2.352 .092 HN7 H5M2 -3.54000 -4.29900 -11.57558 1.0080 .070 2.352 .092 HN7 H5M3 -2.80100 -4.43500 -13.18259 1.0080 .070 2.352 .092 HN7 C6 -4.69900 -1.73800 -12.67958 12.0110 .170 3.208 .754 CN3 H6 -5.63300 -2.30600 -12.55557 1.0080 .130 2.352 .092 HN3 # 3 nucl - from 63 A O3* -4.18900 -7.68200 -6.18958 15.9990 -.550 3.154 .636 ON2 P -4.56200 -7.65300 -7.73958 30.9740 1.500 3.831 2.450 P O1P -5.83600 -8.36500 -7.95958 15.9990 -.800 3.030 .502 ON3 O2P -3.40400 -8.13700 -8.52957 15.9990 -.800 3.030 .502 ON3 O5* -4.75900 -6.09100 -7.98958 15.9990 -.550 3.154 .636 ON2 C5* -5.55800 -5.33000 -7.04958 12.0110 -.080 3.876 .230 CN8 H5* -4.97200 -4.84600 -6.25357 1.0080 .090 2.352 .092 HN7 H5** -6.28600 -5.98800 -6.55458 1.0080 .090 2.352 .092 HN7 O1* -5.38700 -3.11000 -7.98958 15.9990 -.400 3.154 .636 ON6 C1* -5.00200 -3.05300 -9.34958 12.0110 .110 4.054 .084 CN6BH1* -5.48400 -2.11100 -9.65057 1.0080 .090 2.352 .092 HN6 C2* -5.60800 -4.25600 -10.05959 12.0110 -.180 4.054 .084 CN6 H2* -4.86500 -5.05000 -10.22658 1.0080 .090 2.352 .092 HN6 H2** -5.89000 -3.83300 -11.03458 1.0080 .090 2.352 .092 HN6 C3* -6.80600 -4.57300 -9.17958 12.0110 .010 4.054 .084 CN6 H3* -7.16600 -5.60300 -9.32558 1.0080 .090 2.352 .092 HN6 C4* -6.30000 -4.23300 -7.77959 12.0110 .110 4.054 .084 CN6 H4* -7.23200 -4.01100 -7.23958 1.0080 .090 2.352 .092 HN6 # ADENINE 3 atom 81 N1 -.85800 -.06100 -9.78958 14.0070 -.740 3.297 .837 NN3AC2 -2.16000 .20400 -9.77959 12.0110 .530 3.208 .502 CN4 H2 -2.39200 1.27400 -9.88959 1.0080 .160 2.352 .092 HN3 N3C -3.18100 -.61800 -9.65958 14.0070 -.690 3.297 .837 NN3AC4 -2.74400 -1.88600 -9.53958 12.0110 .310 3.208 .502 CN5 C5 -1.45200 -2.32400 -9.53958 12.0110 .230 3.208 .502 CN5 C6 -.45400 -1.33500 -9.66959 12.0110 .430 3.208 .586 CN2 N6 .85900 -1.61600 -9.67958 14.0070 -.800 3.297 .837 NN1 HN61 1.21800 -2.54500 -9.59558 1.0080 .400 .400 .192 HN1 HN62 1.56600 -.91400 -9.77158 1.0080 .400 .400 .192 HN1 N7 -1.39000 -3.69700 -9.38957 14.0070 -.630 3.297 .837 NN4 C8 -2.63600 -4.05900 -9.31958 12.0110 .380 3.208 .502 CN4 H8 -2.97600 -5.09900 -9.20657 1.0080 .180 2.352 .092 HN3 N9 -3.51500 -3.01300 -9.39958 14.0070 -.160 3.297 .837 NN2 # 4 nucl - from 95 C O3* 1.12700 -8.67700 -2.80959 15.9990 -.550 3.154 .636 ON2 P .80700 -8.87300 -4.35957 30.9740 1.500 3.831 2.450 P O1P .19600 -10.19800 -4.57958 15.9990 -.800 3.030 .502 ON3 O2P 2.02900 -8.58300 -5.14958 15.9990 -.800 3.030 .502 ON3 O5* -.27000 -7.72500 -4.60957 15.9990 -.550 3.154 .636 ON2 C5* -1.36400 -7.57800 -3.66959 12.0110 -.080 3.876 .230 CN8 H5* -1.17400 -6.84300 -2.87358 1.0080 .090 2.352 .092 HN7 H5** -1.56600 -8.53900 -3.17458 1.0080 .090 2.352 .092 HN7 O1* -2.53000 -5.68200 -4.60957 15.9990 -.400 3.154 .636 ON6 C1* -2.25200 -5.41000 -5.96959 12.0110 .110 4.054 .084 CN6BH1* -3.19600 -4.93200 -6.27058 1.0080 .090 2.352 .092 HN6 C2* -2.03500 -6.73900 -6.67958 12.0110 -.180 4.054 .084 CN6 H2* -.96700 -6.94500 -6.84657 1.0080 .090 2.352 .092 HN6 H2** -2.51200 -6.56300 -7.65459 1.0080 .090 2.352 .092 HN6 C3* -2.81800 -7.70100 -5.79958 12.0110 .010 4.054 .084 CN6 H3* -2.50400 -8.74500 -5.94557 1.0080 .090 2.352 .092 HN6 C4* -2.60800 -7.12800 -4.39958 12.0110 .110 4.054 .084 CN6 H4* -3.49300 -7.49600 -3.85959 1.0080 .090 2.352 .092 HN6 # base C atom 113 N1C -1.07300 -4.50400 -6.01958 14.0070 -.160 3.297 .837 NN2 C2 -1.30700 -3.13900 -6.16957 12.0110 .530 3.208 .586 CN1 O2 -2.47400 -2.73800 -6.25958 15.9990 -.480 3.029 .502 ON1CN3 -.24600 -2.29700 -6.21959 14.0070 -.670 3.297 .837 NN3 C4 1.00600 -2.76300 -6.11959 12.0110 .620 3.208 .586 CN2 N4 2.00500 -1.89600 -6.16957 14.0070 -.580 3.297 .837 NN1 H41 1.86800 -.91200 -6.27858 1.0080 .270 .400 .192 HN1 H42 2.96500 -2.16800 -6.10158 1.0080 .310 .400 .192 HN1 C5 1.27200 -4.16000 -5.96959 12.0110 -.100 3.208 .754 CN3 H5 2.30300 -4.53600 -5.89958 1.0080 .100 2.352 .092 HN3 C6 .19200 -4.98600 -5.91957 12.0110 .110 3.208 .754 CN3 H6 .31500 -6.07300 -5.80559 1.0080 .050 2.352 .092 HN3 # 5 nucl - from 125 G O3* 6.01200 -6.35800 .57042 15.9990 -.550 3.154 .636 ON2 P 5.86900 -6.70400 -.97958 30.9740 1.500 3.831 2.450 P O1P 6.15300 -8.13500 -1.19958 15.9990 -.800 3.030 .502 ON3 O2P 6.68700 -5.75200 -1.76958 15.9990 -.800 3.030 .502 ON3 O5* 4.32300 -6.40900 -1.22958 15.9990 -.550 3.154 .636 ON2 C5* 3.35100 -6.93300 -.28958 12.0110 -.080 3.876 .230 CN8 H5* 3.07300 -6.22600 .50642 1.0080 .090 2.352 .092 HN7 H5** 3.75300 -7.82900 .20543 1.0080 .090 2.352 .092 HN7 O1* 1.29300 -6.08400 -1.22958 15.9990 -.400 3.154 .636 ON6 C1* 1.35800 -5.70100 -2.58958 12.0110 .110 4.054 .084 CN6BH1* .31300 -5.86800 -2.89058 1.0080 .090 2.352 .092 HN6 C2* 2.31500 -6.64800 -3.29958 12.0110 -.180 4.054 .084 CN6 H2* 3.30000 -6.18700 -3.46659 1.0080 .090 2.352 .092 HN6 H2** 1.82500 -6.78700 -4.27458 1.0080 .090 2.352 .092 HN6 C3* 2.24600 -7.88600 -2.41957 12.0110 .010 4.054 .084 CN6 H3* 3.11400 -8.54700 -2.56558 1.0080 .090 2.352 .092 HN6 C4* 2.07900 -7.30000 -1.01958 12.0110 .110 4.054 .084 CN6 H4* 1.58000 -8.11800 -.47958 1.0080 .090 2.352 .092 HN6 # G - base atom 143 N1H -.25500 -.88400 -3.02957 14.0070 -.380 3.297 .837 NN2GHN1 -.60300 .05000 -3.11159 1.0080 .280 .400 .192 HN2 C2 -.97400 -2.06100 -3.02957 12.0110 .720 3.208 .586 CN2 N2 -2.29900 -1.94300 -3.15958 14.0070 -.640 3.297 .837 NN1 HN21 -2.91800 -2.72800 -3.16557 1.0080 .310 .400 .192 HN1 HN22 -2.76000 -1.06100 -3.25958 1.0080 .330 .400 .192 HN1 N3C -.41800 -3.26300 -2.89958 14.0070 -.660 3.297 .837 NN3AC4 .93500 -3.19600 -2.77957 12.0110 .140 3.208 .502 CN5 C5 1.73500 -2.06800 -2.77957 12.0110 -.080 3.208 .502 CN5 C6 1.14300 -.79100 -2.90958 12.0110 .550 3.208 .586 CN1 O6 1.68100 .31500 -2.92958 15.9990 -.470 3.029 .502 ON1 N7 3.07600 -2.43000 -2.63959 14.0070 -.690 3.297 .837 NN4 C8 3.04600 -3.73500 -2.55959 12.0110 .410 3.208 .502 CN4 H8 3.95200 -4.34800 -2.44058 1.0080 .280 2.352 .092 HN3 N9 1.77900 -4.27500 -2.63959 14.0070 -.100 3.297 .837 NN2 # 6 nucl - from 158 T O3* 8.60100 -1.61000 3.95042 15.9990 -.550 3.154 .636 ON2 P 8.68900 -1.97400 2.40042 30.9740 1.500 3.831 2.450 P O1P 9.76000 -2.96500 2.18042 15.9990 -.800 3.030 .502 ON3 O2P 8.79000 -.72300 1.61041 15.9990 -.800 3.030 .502 ON3 O5* 7.26400 -2.64400 2.15042 15.9990 -.550 3.154 .636 ON2 C5* 6.78600 -3.63900 3.09042 12.0110 -.080 3.876 .230 CN8 H5* 6.14500 -3.23100 3.88641 1.0080 .090 2.352 .092 HN7 H5** 7.63800 -4.12800 3.58542 1.0080 .090 2.352 .092 HN7 O1* 4.62200 -4.16200 2.15042 15.9990 -.400 3.154 .636 ON6 C1* 4.44900 -3.81300 .79042 12.0110 .110 4.054 .084 CN6BH1* 3.70300 -4.56300 .48943 1.0080 .090 2.352 .092 HN6 C2* 5.78100 -4.01800 .08043 12.0110 -.180 4.054 .084 CN6 H2* 6.30700 -3.06600 -.08658 1.0080 .090 2.352 .092 HN6 H2** 5.46600 -4.41700 -.89458 1.0080 .090 2.352 .092 HN6 C3* 6.45300 -5.06000 .96042 12.0110 .010 4.054 .084 CN6 H3* 7.54300 -5.08400 .81442 1.0080 .090 2.352 .092 HN6 C4* 5.97300 -4.68300 2.36043 12.0110 .110 4.054 .084 CN6 H4* 6.05000 -5.63900 2.90042 1.0080 .090 2.352 .092 HN6 # T-BASE atom 176 N1C 3.95200 -2.41200 .74042 14.0070 -.300 3.297 .837 NN2 C2 2.59300 -2.23000 .59042 12.0110 .570 3.208 .586 CN1 O2 1.80900 -3.15900 .50043 15.9990 -.470 3.029 .502 ON1 N3H 2.17600 -.91400 .55041 14.0070 -.460 3.297 .837 NN2UHN3 1.18100 -.92000 .44342 1.0080 .360 .400 .192 HN2 C4 2.97300 .20300 .64041 12.0110 .540 3.208 .586 CN1 O4 2.48300 1.33700 .59042 15.9990 -.490 3.029 .502 ON1 C5 4.37900 -.08400 .79042 12.0110 -.150 3.208 .754 CN3 C5M 5.28600 1.10400 .90042 12.0110 -.110 3.671 .234 CN9 H5M1 6.27000 .86000 .50142 1.0080 .070 2.352 .092 HN7 H5M2 5.39100 1.39800 1.94441 1.0080 .070 2.352 .092 HN7 H5M3 4.87300 1.94100 .33742 1.0080 .070 2.352 .092 HN7 C6 4.82300 -1.35600 .84042 12.0110 .170 3.208 .754 CN3 H6 5.91200 -1.44600 .96442 1.0080 .130 2.352 .092 HN3 # 7 nucl - from 190 C O3* 7.90400 3.75300 7.33041 15.9990 -.550 3.154 .636 ON2 ⌨️ 快捷键说明
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