###################################################################### ########################################################################## ### ### ### Tinker --- Software Tools for Molecular Design ### ## ## ## Version 25.6 December 2025 ## ## ## ## Copyright (c) Jay William Ponder 1990-2025 ## ### All Rights Reserved ### ### ### ########################################################################## ###################################################################### Enter Name to be Used for Output Files : Enter Title : Enter One Residue Name per Line as the Standard Three-Letter Code, and optionally, Phi-Psi-Omega Angles (3F), Chi Angles (4F), Disulfide Partner if CYX Residue (I), and D/L Chirality (A1) If Only Residue Names are Entered, the Default is to Build an Extended Conformation Using L-Amino Acids and Zwitterionic Termini Standard Amino Acids: GLY, ALA, VAL, LEU, ILE, SER, THR, CYS, CYX, PRO, PHE, TYR, TRP, HIS, ASP, ASN, GLU, GLN, MET, LYS, ARG, ORN, AIB Alternative Protonation States: CYD, TYD, HID, HIE, HIP, ASH, GLH, LYD N-Terminal Cap Residues: H2N=Deprotonated, FOR=Formyl, ACE=Acetyl, PCA=Pyroglutamic Acid C-Terminal Cap Residues: COH=Protonated, NH2=Amide, NME=N-MethylAmide Use Residue Name=MOL to Start a New Chain, and Use to End Input Enter Residue 1 : Enter Residue 2 : Enter Residue 3 : Enter Residue 4 : Enter Residue 5 : Enter Residue 6 : Cyclize the Polypeptide Chain [N] : ###################################################################### ########################################################################## ### ### ### Tinker --- Software Tools for Molecular Design ### ## ## ## Version 25.6 December 2025 ## ## ## ## Copyright (c) Jay William Ponder 1990-2025 ## ### All Rights Reserved ### ### ### ########################################################################## ###################################################################### Limited Memory BFGS Quasi-Newton Optimization : QN Iter F Value G RMS F Move X Move Angle FG Call Comment 0 86.2696 232.8492 1 100 -228.0620 1.2944 0.1247 0.0063 79.11 102 Success 200 -235.6510 1.0427 0.0807 0.0134 84.33 203 Success 300 -240.8223 0.8679 0.0304 0.0113 83.74 303 Success 400 -242.2394 0.2571 0.0020 0.0024 82.17 403 Success 500 -242.5452 0.2138 0.0027 0.0025 85.55 503 Success 600 -242.6815 0.0687 0.0003 0.0006 85.12 603 Success 700 -242.6995 0.0337 0.0001 0.0003 83.44 703 Success 800 -242.7046 0.0129 0.0000 0.0002 85.25 803 Success 900 -242.7056 0.0068 0.0000 0.0001 85.51 903 Success 1000 -242.7057 0.0018 0.0000 0.0000 83.46 1003 Success 1100 -242.7057 0.0012 0.0000 0.0000 83.53 1103 Success 1200 -242.7057 0.0003 0.0000 0.0000 84.27 1203 Success 1300 -242.7057 0.0001 0.0000 0.0000 79.85 1304 Success 1400 -242.7057 0.0000 0.0000 0.0000 80.64 1404 Success 1442 -242.7057 0.0000 0.0000 0.0000 77.00 1446 SmallGrad LBFGS -- Normal Termination due to SmallGrad Final Function Value : -242.70570313 Final RMS Gradient : 0.00000998 Final Gradient Norm : 0.00008646 ###################################################################### ########################################################################## ### ### ### Tinker --- Software Tools for Molecular Design ### ## ## ## Version 25.6 December 2025 ## ## ## ## Copyright (c) Jay William Ponder 1990-2025 ## ### All Rights Reserved ### ### ### ########################################################################## ###################################################################### Eigenvalues of the Hessian Matrix : 1 -0.000 2 -0.000 3 0.000 4 0.000 5 0.000 6 0.000 7 0.077 8 0.095 9 0.203 10 0.224 11 0.294 12 0.378 13 0.600 14 0.834 15 1.021 16 1.267 17 2.133 18 2.219 19 2.826 20 3.500 21 3.911 22 4.223 23 4.730 24 5.369 25 5.883 26 6.418 27 8.359 28 8.602 29 10.221 30 10.764 31 11.481 32 12.574 33 17.905 34 18.612 35 19.751 36 22.128 37 23.243 38 24.470 39 25.205 40 29.053 41 29.921 42 33.489 43 35.056 44 36.397 45 39.847 46 40.355 47 40.771 48 43.265 49 44.995 50 47.225 51 49.075 52 49.955 53 52.253 54 56.407 55 58.713 56 63.260 57 65.072 58 66.118 59 68.775 60 70.694 61 74.833 62 76.972 63 77.380 64 81.675 65 85.144 66 89.422 67 94.632 68 95.861 69 96.536 70 97.466 71 97.884 72 99.535 73 104.535 74 105.435 75 105.635 76 107.300 77 113.198 78 113.352 79 113.479 80 114.435 81 116.006 82 116.819 83 117.820 84 119.463 85 125.023 86 125.255 87 127.663 88 131.114 89 134.971 90 138.108 91 140.019 92 143.560 93 149.539 94 158.786 95 159.657 96 161.847 97 171.665 98 173.785 99 177.983 100 182.848 101 187.574 102 188.956 103 191.515 104 192.775 105 193.810 106 203.515 107 204.922 108 213.166 109 217.014 110 222.107 111 228.359 112 231.043 113 232.763 114 241.762 115 245.627 116 252.371 117 253.662 118 254.947 119 260.605 120 273.474 121 277.852 122 286.031 123 295.874 124 308.864 125 317.694 126 322.034 127 336.354 128 351.400 129 352.948 130 388.327 131 389.388 132 396.766 133 416.018 134 427.546 135 443.461 136 456.637 137 481.494 138 488.001 139 491.107 140 513.211 141 519.584 142 528.492 143 546.648 144 553.451 145 560.980 146 562.286 147 566.459 148 581.001 149 610.584 150 611.899 151 625.621 152 632.261 153 649.787 154 653.702 155 737.446 156 768.360 157 789.242 158 798.220 159 899.715 160 910.731 161 922.203 162 952.094 163 1023.350 164 1081.642 165 1164.182 166 1189.554 167 1209.540 168 1317.861 169 1386.660 170 1418.404 171 1418.544 172 1445.631 173 1465.230 174 1480.027 175 1536.794 176 1543.116 177 1583.461 178 1615.059 179 1622.144 180 1650.400 181 1678.091 182 1707.071 183 1722.937 184 1747.014 185 1780.924 186 1802.147 187 1824.479 188 1830.548 189 1866.644 190 1881.453 191 1910.975 192 1954.378 193 1961.008 194 2102.368 195 2139.194 196 2141.720 197 2144.664 198 2200.141 199 2215.266 200 2242.847 201 2253.128 202 2300.904 203 2346.105 204 2360.242 205 2381.517 206 2439.391 207 2489.892 208 2547.777 209 2623.415 210 2668.525 211 2690.210 212 2695.262 213 2735.361 214 2758.850 215 2953.236 216 2978.774 217 3137.413 218 3163.156 219 3179.434 220 3212.553 221 3217.330 222 3227.194 223 3239.917 224 3281.066 225 3601.712 Vibrational Frequencies (cm-1) : 1 -0.010 2 -0.007 3 0.000 4 0.000 5 0.000 6 0.020 7 11.705 8 13.691 9 19.040 10 23.058 11 26.951 12 28.144 13 35.626 14 41.579 15 48.471 16 50.933 17 64.180 18 72.371 19 78.242 20 79.287 21 89.316 22 95.833 23 102.065 24 107.063 25 110.830 26 117.890 27 134.317 28 143.319 29 159.908 30 168.170 31 176.657 32 189.109 33 199.604 34 202.465 35 212.601 36 214.615 37 222.941 38 245.237 39 262.038 40 272.613 41 290.035 42 292.547 43 302.460 44 323.761 45 329.559 46 336.633 47 344.767 48 353.374 49 368.036 50 377.798 51 406.530 52 415.372 53 418.749 54 425.307 55 427.629 56 428.285 57 432.747 58 464.125 59 480.896 60 484.278 61 498.010 62 516.209 63 543.416 64 564.918 65 566.502 66 587.159 67 597.757 68 599.286 69 620.539 70 624.417 71 624.720 72 629.888 73 649.891 74 663.095 75 670.852 76 699.307 77 701.167 78 705.933 79 706.864 80 709.492 81 715.001 82 717.836 83 744.250 84 750.208 85 755.637 86 760.126 87 788.149 88 795.301 89 804.471 90 823.027 91 827.932 92 831.731 93 836.220 94 839.845 95 850.703 96 861.186 97 862.226 98 864.611 99 880.658 100 890.426 101 900.336 102 913.650 103 918.450 104 941.550 105 950.535 106 952.380 107 953.591 108 958.554 109 968.405 110 977.850 111 978.006 112 981.297 113 984.009 114 989.865 115 997.139 116 1009.348 117 1012.779 118 1025.705 119 1036.770 120 1041.341 121 1073.214 122 1079.262 123 1090.325 124 1095.289 125 1099.829 126 1104.627 127 1116.817 128 1119.289 129 1125.762 130 1127.758 131 1136.043 132 1144.330 133 1159.548 134 1167.425 135 1175.190 136 1178.038 137 1184.175 138 1189.728 139 1191.463 140 1191.726 141 1216.240 142 1230.237 143 1237.019 144 1242.147 145 1272.249 146 1275.859 147 1298.766 148 1302.248 149 1304.272 150 1316.367 151 1327.797 152 1331.022 153 1336.046 154 1347.910 155 1348.952 156 1351.090 157 1359.840 158 1364.141 159 1372.936 160 1375.570 161 1378.897 162 1381.575 163 1397.671 164 1422.752 165 1448.108 166 1449.424 167 1468.486 168 1469.799 169 1472.409 170 1493.699 171 1546.588 172 1559.262 173 1578.058 174 1595.952 175 1599.050 176 1614.410 177 1621.553 178 1638.085 179 1645.892 180 1688.984 181 1696.512 182 1699.906 183 1701.932 184 1715.279 185 1718.109 186 1728.856 187 1729.012 188 1751.056 189 1789.463 190 1800.904 191 2867.898 192 2910.654 193 2914.268 194 2914.480 195 2914.707 196 2915.288 197 2920.617 198 2948.310 199 2949.116 200 2955.495 201 2974.863 202 2975.313 203 2975.731 204 2976.856 205 2977.145 206 2978.197 207 2979.217 208 2980.154 209 3063.397 210 3063.658 211 3063.985 212 3064.088 213 3064.519 214 3065.455 215 3065.503 216 3066.872 217 3066.953 218 3202.805 219 3271.222 220 3298.499 221 3299.562 222 3307.279 223 3314.097 224 3347.267 225 3709.870 Vibrational Normal Mode 7 with Frequency 11.705 cm-1 Atom Delta X Delta Y Delta Z 1 0.009190 -0.004562 -0.022104 2 0.009343 -0.006889 -0.025366 3 0.005379 0.012471 -0.003539 4 0.027514 0.045622 -0.008660 5 -0.020659 -0.004711 -0.008850 6 0.015509 -0.021705 -0.044475 7 0.029041 0.013754 -0.006161 8 -0.008729 -0.020494 -0.032664 9 0.039875 -0.011633 -0.046459 10 0.060727 -0.029500 -0.065247 11 0.058271 -0.069541 -0.069827 12 0.081818 -0.007595 -0.079462 13 0.076550 -0.087883 -0.088747 14 0.100281 -0.025678 -0.098235 15 0.097464 -0.065963 -0.103035 16 0.114960 -0.083612 -0.121653 17 0.050533 0.014126 -0.049634 18 0.038242 -0.028436 -0.048261 19 0.042081 -0.086989 -0.059313 20 0.083911 0.023017 -0.076144 21 0.074103 -0.118922 -0.092214 22 0.116396 -0.008759 -0.109193 23 0.109568 -0.113337 -0.125993 24 -0.023138 -0.009912 0.022730 25 -0.033016 -0.008311 0.051839 26 -0.063874 -0.016958 0.055008 27 -0.053792 -0.031007 0.076653 28 -0.037910 -0.026900 0.024010 29 -0.028802 -0.006653 0.057011 30 -0.022194 -0.003955 0.066997 31 -0.099044 -0.009670 0.033227 32 -0.129149 -0.020679 0.033680 33 -0.108816 0.002050 0.022453 34 -0.124117 0.025126 0.006902 35 -0.104004 0.003158 0.014409 36 -0.164695 -0.017430 0.017924 37 -0.131788 -0.050352 0.059182 38 -0.072042 -0.004013 0.032691 39 -0.039727 0.020194 0.031214 40 -0.044055 -0.000108 0.017877 41 -0.042443 -0.000631 -0.000368 42 -0.061585 -0.024627 0.043933 43 -0.046193 0.051823 0.059308 44 0.013634 0.026660 0.009303 45 0.063682 0.080168 0.016206 46 0.051223 0.135233 0.036311 47 0.125266 0.076615 0.006018 48 0.099999 0.186190 0.045600 49 0.174069 0.127580 0.015250 50 0.161461 0.182329 0.035120 51 0.032277 -0.013190 -0.019139 52 0.001803 0.030410 0.016472 53 0.004327 0.138757 0.045271 54 0.135052 0.035074 -0.009045 55 0.090178 0.228287 0.060965 56 0.221050 0.124556 0.007066 57 0.198802 0.221332 0.042246 58 -0.050007 -0.013910 0.026960 59 -0.047230 -0.026115 0.023160 60 -0.050716 -0.026652 0.028375 61 -0.036839 -0.030554 0.028279 62 -0.049748 -0.012990 0.038489 63 -0.042352 -0.023874 0.014978 64 -0.045507 -0.038307 0.022776 65 -0.039932 -0.035980 0.009403 66 -0.037466 -0.055850 0.005904 67 -0.030059 -0.047661 -0.010724 68 -0.043377 -0.049669 0.021210 69 -0.049698 -0.039329 0.033509 70 -0.041240 -0.025171 0.011551 71 -0.035201 -0.032802 -0.001561 72 -0.027763 -0.057947 -0.014579 73 -0.032294 -0.036146 -0.007106 74 -0.025469 -0.043766 -0.020920 75 -0.062038 -0.020480 0.029252 Vibrational Normal Mode 8 with Frequency 13.691 cm-1 Atom Delta X Delta Y Delta Z 1 0.110258 -0.045613 -0.027508 2 0.072535 -0.046385 -0.020425 3 0.064104 -0.065164 0.015515 4 0.072149 -0.092242 0.046048 5 0.101313 -0.046280 -0.022364 6 0.120311 -0.038854 -0.055975 7 0.131699 -0.051715 -0.007872 8 0.054463 -0.035046 -0.034373 9 0.064984 -0.038472 -0.032836 10 -0.001179 -0.031484 -0.026426 11 -0.049227 -0.009908 -0.075499 12 -0.018845 -0.049335 0.026550 13 -0.115081 -0.006812 -0.072026 14 -0.084754 -0.046354 0.029951 15 -0.133106 -0.025353 -0.019489 16 -0.197629 -0.023471 -0.016170 17 0.091410 -0.056681 -0.008952 18 0.081248 -0.019090 -0.074295 19 -0.036905 0.003829 -0.116561 20 0.016634 -0.066368 0.064331 21 -0.151662 0.009483 -0.110212 22 -0.098714 -0.060647 0.070350 23 -0.224583 -0.006113 -0.048943 24 0.050969 -0.046747 0.008646 25 0.042642 -0.045020 0.032404 26 0.017277 -0.030596 0.028874 27 0.015573 -0.029987 0.030154 28 0.046520 -0.033162 -0.014039 29 0.044114 -0.046501 0.050400 30 0.053169 -0.050252 0.035334 31 -0.000689 -0.019726 0.023840 32 -0.018146 -0.011365 0.021795 33 -0.015528 -0.003514 0.005986 34 -0.018854 0.006315 0.004958 35 -0.000366 -0.018603 0.021109 36 -0.029629 -0.007277 0.022649 37 -0.021487 -0.015738 0.032907 38 -0.007743 -0.007607 -0.001793 39 0.002079 0.000172 -0.000929 40 -0.011009 -0.005130 -0.005718 41 -0.052226 0.002134 -0.009670 42 -0.005003 -0.015345 0.000695 43 0.001153 0.009488 0.015817 44 0.028477 0.004136 -0.012014 45 0.042862 0.008004 0.008667 46 0.056026 0.011549 0.027970 47 0.044677 0.008427 0.011063 48 0.070969 0.015482 0.049529 49 0.059587 0.012369 0.032599 50 0.072807 0.015895 0.051909 51 0.025492 0.001743 -0.032768 52 0.043857 0.006842 -0.014643 53 0.054842 0.011313 0.026568 54 0.034499 0.005765 -0.003405 55 0.081031 0.018176 0.064319 56 0.060797 0.012683 0.034370 57 0.084226 0.018898 0.068492 58 0.019164 -0.013137 -0.004461 59 0.015377 -0.017015 -0.005692 60 0.060434 -0.039682 -0.011767 61 0.067752 -0.040539 -0.010297 62 0.048473 -0.021193 -0.002391 63 -0.016947 -0.039611 -0.011207 64 0.013001 0.038082 0.006726 65 -0.056274 0.090244 -0.009795 66 -0.076192 0.168755 -0.012344 67 -0.175999 0.235123 -0.046500 68 0.019869 0.012164 0.002979 69 0.055416 0.069526 0.032470 70 -0.048160 0.122022 -0.006625 71 -0.107774 0.053078 -0.024023 72 -0.198167 0.286947 -0.050996 73 -0.162316 0.274404 -0.037709 74 -0.230384 0.186170 -0.072328 75 0.083950 -0.049844 -0.013960