📄 dna1.mol
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#==================================================I# Molecular Dynamics Data Base I# Configuration and interaction potential I#==================================================I# B-DNA (strand 1) I#==================================================I# CHARMM force field I#==================================================I# Number of sites 319# X Y Z M Q sigma epsilon FF# (A) (kJ/M) atom# 1 nucl A name O3* 8.60100 1.61000 -16.82957 15.9990 -.550 3.154 .636 ON2 P 8.68900 1.97400 -15.27959 30.9740 1.500 3.831 2.450 P O1P 9.76000 2.96500 -15.05957 15.9990 -.800 3.030 .502 ON3 O2P 8.79000 .72300 -14.48958 15.9990 -.800 3.030 .502 ON3 O5* 7.26400 2.64400 -15.02959 15.9990 -.550 3.154 .636 ON2 C5* 6.78600 3.63900 -15.96957 12.0110 -.080 3.876 .230 CN8 H5* 6.14500 3.23100 -16.76558 1.0080 .090 2.352 .092 HN7 H5** 7.63800 4.12800 -16.46458 1.0080 .090 2.352 .092 HN7 O1* 4.62200 4.16200 -15.02959 15.9990 -.400 3.154 .636 ON6 C1* 4.44900 3.81300 -13.66959 12.0110 .110 4.054 .084 CN6BH1* 3.70300 4.56300 -13.36860 1.0080 .090 2.352 .092 HN6 C2* 5.78100 4.01800 -12.95958 12.0110 -.180 4.054 .084 CN6 H2* 6.30700 3.06600 -12.79257 1.0080 .090 2.352 .092 HN6 H2** 5.46600 4.41700 -11.98459 1.0080 .090 2.352 .092 HN6 C3* 6.45300 5.06000 -13.83958 12.0110 .010 4.054 .084 CN6 H3* 7.54300 5.08400 -13.69359 1.0080 .090 2.352 .092 HN6 C4* 5.97300 4.68300 -15.23958 12.0110 .110 4.054 .084 CN6 H4* 6.05000 5.63900 -15.77957 1.0080 .090 2.352 .092 HN6 # ADENINE 1 atom 19 N1 .32400 .79700 -13.22958 14.0070 -.740 3.297 .837 NN3AC2 .47300 2.11800 -13.23958 12.0110 .530 3.208 .502 CN4 H2 -.47300 2.66800 -13.12958 1.0080 .160 2.352 .092 HN3 N3C 1.57100 2.83400 -13.35959 14.0070 -.690 3.297 .837 NN3AC4 2.64200 2.02700 -13.47958 12.0110 .310 3.208 .502 CN5 C5 2.65900 .66300 -13.47958 12.0110 .230 3.208 .502 CN5 C6 1.41000 .02000 -13.34958 12.0110 .430 3.208 .586 CN2 N6 1.27100 -1.31600 -13.33958 14.0070 -.800 3.297 .837 NN1 HN61 2.04400 -1.94500 -13.42358 1.0080 .400 .400 .192 HN1 HN62 .38500 -1.77100 -13.24759 1.0080 .400 .400 .192 HN1 N7 3.94600 .17900 -13.62958 14.0070 -.630 3.297 .837 NN4 C8 4.67500 1.25300 -13.69958 12.0110 .380 3.208 .502 CN4 H8 5.76900 1.25500 -13.81258 1.0080 .180 2.352 .092 HN3 N9 3.95200 2.41200 -13.61959 14.0070 -.160 3.297 .837 NN2 # 2 nucl - from 33 T O3* 6.01200 6.35800 -13.44958 15.9990 -.550 3.154 .636 ON2 P 5.86900 6.70400 -11.89958 30.9740 1.500 3.831 2.450 P O1P 6.15300 8.13500 -11.67958 15.9990 -.800 3.030 .502 ON3 O2P 6.68700 5.75200 -11.10959 15.9990 -.800 3.030 .502 ON3 O5* 4.32300 6.40900 -11.64958 15.9990 -.550 3.154 .636 ON2 C5* 3.35100 6.93300 -12.58958 12.0110 -.080 3.876 .230 CN8 H5* 3.07300 6.22600 -13.38559 1.0080 .090 2.352 .092 HN7 H5** 3.75300 7.82900 -13.08458 1.0080 .090 2.352 .092 HN7 O1* 1.29300 6.08400 -11.64958 15.9990 -.400 3.154 .636 ON6 C1* 1.35800 5.70100 -10.28958 12.0110 .110 4.054 .084 CN6BH1* .31300 5.86800 -9.98859 1.0080 .090 2.352 .092 HN6 C2* 2.31500 6.64800 -9.57957 12.0110 -.180 4.054 .084 CN6 H2* 3.30000 6.18700 -9.41258 1.0080 .090 2.352 .092 HN6 H2** 1.82500 6.78700 -8.60458 1.0080 .090 2.352 .092 HN6 C3* 2.24600 7.88600 -10.45958 12.0110 .010 4.054 .084 CN6 H3* 3.11400 8.54700 -10.31359 1.0080 .090 2.352 .092 HN6 C4* 2.07900 7.30000 -11.85959 12.0110 .110 4.054 .084 CN6 H4* 1.58000 8.11800 -12.39958 1.0080 .090 2.352 .092 HN6 # T-BASE atom 51 N1C 1.77900 4.27500 -10.23958 14.0070 -.300 3.297 .837 NN2 C2 .78700 3.32800 -10.08958 12.0110 .570 3.208 .586 CN1 O2 -.39300 3.61900 -9.99957 15.9990 -.470 3.029 .502 ON1 N3H 1.22200 2.01900 -10.04959 14.0070 -.460 3.297 .837 NN2UHN3 .41500 1.43900 -9.94258 1.0080 .360 .400 .192 HN2 C4 2.52400 1.58400 -10.13959 12.0110 .540 3.208 .586 CN1 O4 2.79500 .37800 -10.08958 15.9990 -.490 3.029 .502 ON1 C5 3.49300 2.64200 -10.28958 12.0110 -.150 3.208 .754 CN3 C5M 4.92500 2.21400 -10.39958 12.0110 -.110 3.671 .234 CN9 H5M1 5.57800 2.99000 -10.00058 1.0080 .070 2.352 .092 HN7 H5M2 5.18300 2.03800 -11.44359 1.0080 .070 2.352 .092 HN7 H5M3 5.08400 1.29400 -9.83658 1.0080 .070 2.352 .092 HN7 C6 3.10500 3.93200 -10.33958 12.0110 .170 3.208 .754 CN3 H6 3.93300 4.64500 -10.46358 1.0080 .130 2.352 .092 HN3 # 3 nucl - from 65 G O3* 1.12700 8.67700 -10.06958 15.9990 -.550 3.154 .636 ON2 P .80700 8.87300 -8.51958 30.9740 1.500 3.831 2.450 P O1P .19600 10.19800 -8.29959 15.9990 -.800 3.030 .502 ON3 O2P 2.02900 8.58300 -7.72958 15.9990 -.800 3.030 .502 ON3 O5* -.27000 7.72500 -8.26958 15.9990 -.550 3.154 .636 ON2 C5* -1.36400 7.57800 -9.20958 12.0110 -.080 3.876 .230 CN8 H5* -1.17400 6.84300 -10.00558 1.0080 .090 2.352 .092 HN7 H5** -1.56600 8.53900 -9.70457 1.0080 .090 2.352 .092 HN7 O1* -2.53000 5.68200 -8.26958 15.9990 -.400 3.154 .636 ON6 C1* -2.25200 5.41000 -6.90958 12.0110 .110 4.054 .084 CN6BH1* -3.19600 4.93200 -6.60858 1.0080 .090 2.352 .092 HN6 C2* -2.03500 6.73900 -6.19958 12.0110 -.180 4.054 .084 CN6 H2* -.96700 6.94500 -6.03258 1.0080 .090 2.352 .092 HN6 H2** -2.51200 6.56300 -5.22458 1.0080 .090 2.352 .092 HN6 C3* -2.81800 7.70100 -7.07959 12.0110 .010 4.054 .084 CN6 H3* -2.50400 8.74500 -6.93358 1.0080 .090 2.352 .092 HN6 C4* -2.60800 7.12800 -8.47958 12.0110 .110 4.054 .084 CN6 H4* -3.49300 7.49600 -9.01958 1.0080 .090 2.352 .092 HN6 # G - base atom 83 N1H -.72600 .56500 -6.46959 14.0070 -.380 3.297 .837 NN2GHN1 -.45800 -.39500 -6.38757 1.0080 .280 .400 .192 HN2 C2 -2.00000 1.09500 -6.46959 12.0110 .720 3.208 .586 CN2 N2 -3.00200 .22000 -6.33958 14.0070 -.640 3.297 .837 NN1 HN21 -3.96400 .49200 -6.33357 1.0080 .310 .400 .192 HN1 HN22 -2.85600 -.76400 -6.23958 1.0080 .330 .400 .192 HN1 N3C -2.25600 2.39400 -6.59958 14.0070 -.660 3.297 .837 NN3AC4 -1.12300 3.13500 -6.71957 12.0110 .140 3.208 .502 CN5 C5 .18800 2.69300 -6.71957 12.0110 -.080 3.208 .502 CN5 C6 .45900 1.31200 -6.58958 12.0110 .550 3.208 .586 CN1 O6 1.54500 .73300 -6.56958 15.9990 -.470 3.029 .502 ON1 N7 1.06100 3.77400 -6.85957 14.0070 -.690 3.297 .837 NN4 C8 .26900 4.81200 -6.93958 12.0110 .410 3.208 .502 CN4 H8 .64100 5.84100 -7.05858 1.0080 .280 2.352 .092 HN3 N9 -1.07300 4.50400 -6.85957 14.0070 -.100 3.297 .837 NN2 # 4 nucl - from 98 C O3* -4.18900 7.68200 -6.68958 15.9990 -.550 3.154 .636 ON2 P -4.56200 7.65300 -5.13957 30.9740 1.500 3.831 2.450 P O1P -5.83600 8.36500 -4.91959 15.9990 -.800 3.030 .502 ON3 O2P -3.40400 8.13700 -4.34958 15.9990 -.800 3.030 .502 ON3 O5* -4.75900 6.09100 -4.88959 15.9990 -.550 3.154 .636 ON2 C5* -5.55800 5.33000 -5.82958 12.0110 -.080 3.876 .230 CN8 H5* -4.97200 4.84600 -6.62558 1.0080 .090 2.352 .092 HN7 H5** -6.28600 5.98800 -6.32458 1.0080 .090 2.352 .092 HN7 O1* -5.38700 3.11000 -4.88959 15.9990 -.400 3.154 .636 ON6 C1* -5.00200 3.05300 -3.52959 12.0110 .110 4.054 .084 CN6BH1* -5.48400 2.11100 -3.22858 1.0080 .090 2.352 .092 HN6 C2* -5.60800 4.25600 -2.81958 12.0110 -.180 4.054 .084 CN6 H2* -4.86500 5.05000 -2.65259 1.0080 .090 2.352 .092 HN6 H2** -5.89000 3.83300 -1.84459 1.0080 .090 2.352 .092 HN6 C3* -6.80600 4.57300 -3.69958 12.0110 .010 4.054 .084 CN6 H3* -7.16600 5.60300 -3.55357 1.0080 .090 2.352 .092 HN6 C4* -6.30000 4.23300 -5.09958 12.0110 .110 4.054 .084 CN6 H4* -7.23200 4.01100 -5.63957 1.0080 .090 2.352 .092 HN6 # base C atom 116 N1C -3.51500 3.01300 -3.47958 14.0070 -.160 3.297 .837 NN2 C2 -2.90200 1.77100 -3.32958 12.0110 .530 3.208 .586 CN1 O2 -3.61100 .76100 -3.23958 15.9990 -.480 3.029 .502 ON1CN3 -1.54900 1.71400 -3.27959 14.0070 -.670 3.297 .837 NN3 C4 -.81000 2.82600 -3.37958 12.0110 .620 3.208 .586 CN2 N4 .50800 2.71300 -3.32958 14.0070 -.580 3.297 .837 NN1 H41 .97500 1.83600 -3.22058 1.0080 .270 .400 .192 HN1 H42 1.12500 3.49700 -3.39759 1.0080 .310 .400 .192 HN1 C5 -1.41600 4.11300 -3.52959 12.0110 -.100 3.208 .754 CN3 H5 -.80300 5.02300 -3.59958 1.0080 .100 2.352 .092 HN3 C6 -2.77600 4.14700 -3.57958 12.0110 .110 3.208 .754 CN3 H6 -3.31500 5.09800 -3.69359 1.0080 .050 2.352 .092 HN3 # 5 nucl - from 128 A O3* -7.90400 3.75300 -3.30957 15.9990 -.550 3.154 .636 ON2 P -8.18900 3.51000 -1.75958 30.9740 1.500 3.831 2.450 P O1P -9.63800 3.33800 -1.53958 15.9990 -.800 3.030 .502 ON3 O2P -7.53600 4.58200 -.96957 15.9990 -.800 3.030 .502 ON3 O5* -7.43100 2.13100 -1.50958 15.9990 -.550 3.154 .636 ON2 C5* -7.62900 1.04500 -2.44958 12.0110 -.080 3.876 .230 CN8 H5* -6.87100 .99800 -3.24558 1.0080 .090 2.352 .092 HN7 H5** -8.60500 1.15000 -2.94458 1.0080 .090 2.352 .092 HN7 O1* -6.18600 -.65000 -1.50958 15.9990 -.400 3.154 .636 ON6 C1* -5.84100 -.47000 -.14958 12.0110 .110 4.054 .084 CN6BH1* -5.67800 -1.51500 .15143 1.0080 .090 2.352 .092 HN6 C2* -7.03900 .14700 .56041 12.0110 -.180 4.054 .084 CN6 H2* -6.90400 1.22600 .72741 1.0080 .090 2.352 .092 HN6 H2** -7.01900 -.36100 1.53542 1.0080 .090 2.352 .092 HN6 C3* -8.19400 -.30100 -.31958 12.0110 .010 4.054 .084 CN6 H3* -9.09100 .32100 -.17358 1.0080 .090 2.352 .092 HN6 C4* -7.58500 -.27800 -1.71957 12.0110 .110 4.054 .084 CN6 H4* -8.20900 -1.00600 -2.25958 1.0080 .090 2.352 .092 HN6 # ADENINE 5 atom 146 N1 -.73000 -.45500 .29042 14.0070 -.740 3.297 .837 NN3AC2 -1.62800 -1.43500 .28043 12.0110 .530 3.208 .502 CN4 H2 -1.18600 -2.43600 .39041 1.0080 .160 2.352 .092 HN3 N3C -2.93600 -1.36900 .16042 14.0070 -.690 3.297 .837 NN3AC4 -3.32900 -.08700 .04042 12.0110 .310 3.208 .502 CN5 C5 -2.54000 1.02600 .04042 12.0110 .230 3.208 .502 CN5 C6 -1.15200 .81300 .17042 12.0110 .430 3.208 .586 CN2 N6 -.25500 1.81200 .18042 14.0070 -.800 3.297 .837 NN1 HN61 -.51100 2.77500 .09642 1.0080 .400 .400 .192 HN1 HN62 .72900 1.66000 .27242 1.0080 .400 .400 .192 HN1 N7 -3.29800 2.17400 -.10957 14.0070 -.630 3.297 .837 NN4 C8 -4.51800 1.73500 -.17958 12.0110 .380 3.208 .502 CN4 H8 -5.40500 2.37600 -.29259 1.0080 .180 2.352 .092 HN3 N9 -4.61500 .37100 -.09958 14.0070 -.160 3.297 .837 NN2 # 6 nucl - from 160 G O3* -8.60100 -1.61000 .07042 15.9990 -.550 3.154 .636 ON2 P -8.68900 -1.97400 1.62042 30.9740 1.500 3.831 2.450 P O1P -9.76000 -2.96500 1.84042 15.9990 -.800 3.030 .502 ON3 O2P -8.79000 -.72300 2.41042 15.9990 -.800 3.030 .502 ON3 O5* -7.26400 -2.64400 1.87042 15.9990 -.550 3.154 .636 ON2 C5* -6.78600 -3.63900 .93042 12.0110 -.080 3.876 .230 CN8 H5* -6.14500 -3.23100 .13442 1.0080 .090 2.352 .092 HN7 H5** -7.63800 -4.12800 .43542 1.0080 .090 2.352 .092 HN7 O1* -4.62200 -4.16200 1.87042 15.9990 -.400 3.154 .636 ON6 C1* -4.44900 -3.81300 3.23042 12.0110 .110 4.054 .084 CN6BH1* -3.70300 -4.56300 3.53142 1.0080 .090 2.352 .092 HN6 C2* -5.78100 -4.01800 3.94041 12.0110 -.180 4.054 .084 CN6 H2* -6.30700 -3.06600 4.10742 1.0080 .090 2.352 .092 HN6 H2** -5.46600 -4.41700 4.91542 1.0080 .090 2.352 .092 HN6 C3* -6.45300 -5.06000 3.06042 12.0110 .010 4.054 .084 CN6 H3* -7.54300 -5.08400 3.20642 1.0080 .090 2.352 .092 HN6 C4* -5.97300 -4.68300 1.66042 12.0110 .110 4.054 .084 CN6 H4* -6.05000 -5.63900 1.12042 1.0080 .090 2.352 .092 HN6 # G - base atom 178 N1H -.31300 -.86500 3.67042 14.0070 -.380 3.297 .837 NN2GHN1 .51700 -.31400 3.75243 1.0080 .280 .400 .192 HN2 C2 -.42300 -2.24000 3.67042 12.0110 .720 3.208 .586 CN2 N2 .71800 -2.92300 3.80042 14.0070 -.640 3.297 .837 NN1 HN21 .75700 -3.92200 3.80641 1.0080 .310 .400 .192 HN1 HN22 1.60900 -2.48000 3.90042 1.0080 .330 .400 .192 HN1 N3C -1.58000 -2.88600 3.54042 14.0070 -.660 3.297 .837 NN3AC4 -2.63500 -2.03600 3.42042 12.0110 .140 3.208 .502 CN5 C5 -2.62000 -.65300 3.42042 12.0110 -.080 3.208 .502 CN5 C6 -1.39000 .03200 3.55042 12.0110 .550 3.208 .586 CN1 O6 -1.17500 1.24200 3.57042 15.9990 -.470 3.029 .502 ON1 ⌨️ 快捷键说明
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