gromacs.geometry¶
| Type | Status |
|---|---|
| CML extraction template |  |
| HTML5 representation | |
| Attribute | Value |
|---|---|
| source | GROMACS geometry |
| id | gromacs.geometry |
| name | GROMACS geometry |
| xml:base | topTemplate.xml |
Input
(linq)8- (4) with 8 cs countercations in TIP4P water
76416
1LIN Nb1 1 5.810 1.559 0.766 -0.4173 -0.1889 -0.2270
1LIN Nb2 2 6.001 1.401 1.000 -0.1596 0.0263 0.1401
1LIN Nb3 3 6.142 1.515 0.709 0.0276 -0.0019 0.1114
1LIN O4 4 5.652 1.515 0.673 0.0837 -0.4086 0.1651
1LIN O5 5 5.852 1.744 0.694 -0.0227 0.3679 -0.2743
1LIN O6 6 5.952 1.487 0.642 -0.3804 0.3800 -0.0091
1LIN O7 7 5.836 1.394 0.880 0.0079 0.0958 -0.0982
1LIN O8 8 5.737 1.652 0.931 -0.3629 -0.1323 0.4503
1LIN O9 9 5.895 1.521 1.124 0.0201 0.2309 0.0658
1LIN O10 10 6.110 1.357 0.832 -0.1260 -0.1949 0.1862
1LIN O11 11 6.243 1.436 0.572 0.0043 -0.4130 0.0718
1LIN O12 12 5.996 1.235 1.085 -0.1923 0.3103 -0.4478
1LIN O13 13 6.011 1.613 0.885 0.6876 -1.7207 -0.6949
1LIN Nb14 14 6.212 1.668 1.003 0.4424 0.2590 0.1420
1LIN Nb15 15 6.021 1.827 0.771 0.0513 -0.2025 -0.0121
1LIN Nb16 16 5.880 1.713 1.061 0.0255 0.1201 -0.1408
1LIN O17 17 6.370 1.710 1.097 -0.0617 0.3024 0.2917
1LIN O18 18 6.170 1.483 1.076 0.4044 0.4683 -0.2260
1LIN O19 19 6.069 1.741 1.128 -0.9370 0.1656 -0.0906
1LIN O20 20 6.186 1.833 0.888 -0.4769 0.0927 -0.5405
1LIN O21 21 6.285 1.575 0.840 0.2852 -0.1937 0.4972
1LIN O22 22 6.127 1.706 0.646 -0.7172 0.2968 0.1049
1LIN O23 23 5.913 1.871 0.937 -0.2232 -0.0839 -0.2263
1LIN O24 24 5.779 1.791 1.199 -0.3659 -0.2080 -0.4021
1LIN O25 25 6.026 1.991 0.684 0.0687 -0.0672 -0.0522
2LIN Nb1 26 5.260 1.830 6.447 -0.0557 0.2373 -0.3825
2LIN Nb2 27 5.539 1.765 6.629 -0.0777 0.0271 -0.3349
2LIN Nb3 28 5.297 1.526 6.597 -0.0219 0.1647 -0.0619
2LIN O4 29 5.128 1.963 6.446 0.2157 0.2823 0.3355
2LIN O5 30 5.199 1.712 6.291 -0.3053 0.5303 0.0676
2LIN O6 31 5.181 1.691 6.573 0.6073 0.4165 0.0433
2LIN O7 32 5.381 1.888 6.597 0.0880 0.1810 -0.2018
2LIN O8 33 5.396 1.907 6.317 -0.5756 0.3915 -0.1352
2LIN O9 34 5.628 1.856 6.470 -0.0894 0.1755 -0.3962
2LIN O10 35 5.410 1.639 6.723 -0.2246 0.2070 0.1855
2LIN O11 36 5.195 1.425 6.717 0.3458 -0.2283 -0.4530
2LIN O12 37 5.625 1.847 6.774 -0.3264 0.0189 -0.5579
2LIN O13 38 5.428 1.659 6.444 0.5024 0.0886 0.3093
2LIN Nb14 39 5.597 1.487 6.440 -0.2521 -0.1014 0.0850
2LIN Nb15 40 5.318 1.552 6.258 0.0011 -0.1108 -0.0993
2LIN Nb16 41 5.560 1.790 6.290 0.3229 -0.0541 0.2736
2LIN O17 42 5.729 1.353 6.440 0.0074 -0.1950 0.0665
2LIN O18 43 5.658 1.604 6.595 0.1789 0.0952 -0.2046
2LIN O19 44 5.676 1.625 6.316 -0.0861 0.3383 0.1013
2LIN O20 45 5.477 1.429 6.289 -0.6165 0.0135 -0.1116
2LIN O21 46 5.461 1.409 6.569 -0.2265 -0.0314 0.1346
2LIN O22 47 5.230 1.461 6.417 -0.0047 0.1077 -0.5277
2LIN O23 48 5.448 1.677 6.165 -0.2375 -0.1728 0.5415
2LIN O24 49 5.662 1.892 6.170 0.4462 -0.3747 -0.1704
2LIN O25 50 5.233 1.470 6.111 0.0618 -0.2295 0.4029
3LIN Nb1 51 6.750 8.326 5.568 0.4200 0.0374 0.0637
3LIN Nb2 52 6.876 8.011 5.584 -0.1342 -0.0551 -0.0933
3LIN Nb3 53 7.020 8.240 5.378 0.1175 0.0073 -0.0033
3LIN O4 54 6.582 8.400 5.534 -0.1284 0.0558 0.2268
3LIN O5 55 6.865 8.492 5.599 0.4111 -0.1060 -0.4950
3LIN O6 56 6.833 8.318 5.382 -0.3341 0.3604 0.5517
3LIN O7 57 6.714 8.127 5.553 -0.1245 -0.0852 0.3490
3LIN O8 58 6.748 8.303 5.770 -0.3185 -0.0872 -0.0036
3LIN O9 59 6.850 8.042 5.783 -0.1757 -0.6237 -0.0480
3LIN O10 60 6.934 8.057 5.396 -0.3812 -0.2300 -0.3298
3LIN O11 61 7.061 8.247 5.195 -0.3614 -0.3630 -0.5207
3LIN O12 62 6.809 7.837 5.561 -0.5106 -0.1567 -0.4734
3LIN O13 63 6.968 8.232 5.612 0.3980 -0.6783 -0.3094
3LIN Nb14 64 7.186 8.138 5.658 -0.4250 0.2241 -0.1676
3LIN Nb15 65 7.058 8.453 5.642 0.1333 0.0690 -0.5771
3LIN Nb16 66 6.916 8.224 5.847 -0.1387 0.1415 -0.1112
3LIN O17 67 7.353 8.062 5.693 -0.5562 -0.3470 0.3537
3LIN O18 68 7.072 7.972 5.626 0.4653 0.1177 -0.0523
3LIN O19 69 7.104 8.147 5.843 -0.2395 -0.0211 0.1046
3LIN O20 70 7.222 8.336 5.673 0.4193 -0.1168 -0.3051
3LIN O21 71 7.190 8.159 5.456 0.1946 -0.3028 0.1491
3LIN O22 72 7.087 8.421 5.442 -0.5835 -0.0348 0.0941
3LIN O23 73 7.001 8.406 5.829 0.1787 0.0588 -0.2018
3LIN O24 74 6.874 8.217 6.031 -0.2728 0.1975 0.8066
3LIN O25 75 7.129 8.626 5.663 0.0795 -0.0493 0.0525
4LIN Nb1 76 6.378 1.221 5.553 0.2196 0.0239 -0.0272
4LIN Nb2 77 6.504 0.956 5.723 -0.0464 -0.0845 0.0415
4LIN Nb3 78 6.229 0.915 5.526 0.0194 0.0640 0.2128
4LIN O4 79 6.320 1.393 5.598 0.1483 -0.2553 -0.2280
4LIN O5 80 6.349 1.219 5.352 -0.0851 0.1264 -0.0787
4LIN O6 81 6.208 1.114 5.569 -0.1017 -0.0225 0.4543
4LIN O7 82 6.436 1.146 5.732 -0.0598 0.3724 0.0652
4LIN O8 83 6.576 1.252 5.511 0.0719 0.2196 -0.4376
4LIN O9 84 6.679 1.032 5.656 0.1019 -0.2984 0.0839
4LIN O10 85 6.312 0.896 5.711 0.7002 -0.3967 0.3123
4LIN O11 86 6.056 0.850 5.553 -0.0569 -0.1638 -0.0827
4LIN O12 87 6.545 0.918 5.903 0.0803 -0.1563 0.0973
4LIN O13 88 6.452 1.000 5.493 -0.4241 0.0996 -0.1981
4LIN Nb14 89 6.527 0.779 5.432 0.0885 0.1144 -0.0878
4LIN Nb15 90 6.401 1.046 5.262 -0.0467 0.0648 -0.4253
4LIN Nb16 91 6.676 1.085 5.459 0.1055 -0.0733 -0.2142
4LIN O17 92 6.584 0.607 5.385 0.6414 0.0667 -0.1400
4LIN O18 93 6.556 0.781 5.634 -0.5752 -0.1859 0.3018
4LIN O19 94 6.697 0.887 5.416 0.1758 -0.2570 -0.2296
4LIN O20 95 6.471 0.854 5.252 0.0230 0.2680 -0.2407
4LIN O21 96 6.331 0.749 5.473 0.2104 0.3245 0.4100
4LIN O22 97 6.226 0.967 5.329 0.4807 -0.3350 -0.2637
4LIN O23 98 6.595 1.104 5.276 0.0670 -0.0337 0.1302
4LIN O24 99 6.850 1.149 5.433 -0.0403 0.1785 0.2385
4LIN O25 100 6.360 1.081 5.083 -0.3518 0.0005 0.3838
5LIN Nb1 101 6.545 1.221 6.217 0.2087 0.1941 0.0683
5LIN Nb2 102 6.526 1.411 6.503 -0.0695 -0.1723 0.0067
5LIN Nb3 103 6.588 1.559 6.202 -0.4801 -0.2600 -0.0345
5LIN O4 104 6.645 1.073 6.164 0.3211 0.3832 -0.5795
5LIN O5 105 6.432 1.259 6.052 0.1381 -0.2355 -0.1928
5LIN O6 106 6.663 1.376 6.160 -0.5096 -0.3242 -0.0568
5LIN O7 107 6.611 1.251 6.407 0.2488 0.1983 -0.4196
5LIN O8 108 6.380 1.136 6.298 -0.0833 -0.0750 -0.3630
5LIN O9 109 6.364 1.290 6.533 0.0101 -0.0858 -0.3787
5LIN O10 110 6.647 1.530 6.393 0.1150 0.0926 0.4802
5LIN O11 111 6.722 1.673 6.136 0.1472 0.3066 -0.3661
5LIN O12 112 6.609 1.408 6.668 0.0055 0.1294 -0.2185
5LIN O13 113 6.417 1.414 6.286 0.2796 0.3019 0.1002
5LIN Nb14 114 6.286 1.606 6.355 0.0443 0.3950 0.1540
5LIN Nb15 115 6.305 1.417 6.070 -0.1290 0.0838 -0.1548
5LIN Nb16 116 6.244 1.267 6.371 0.3969 0.4392 -0.3288
5LIN O17 117 6.186 1.753 6.409 -0.4569 -0.3400 -0.0641
5LIN O18 118 6.400 1.569 6.519 0.4508 -0.5102 0.2835
5LIN O19 119 6.169 1.452 6.413 0.3934 -0.5910 0.5730
5LIN O20 120 6.221 1.575 6.164 0.0641 -0.4725 -0.4570
5LIN O21 121 6.452 1.691 6.274 -0.3747 -0.4995 -0.3154
5LIN O22 122 6.468 1.538 6.039 -0.6274 0.0907 -0.1016
5LIN O23 123 6.184 1.298 6.180 -0.7045 -0.3482 0.2388
5LIN O24 124 6.110 1.155 6.437 0.0293 -0.0769 -0.1893
5LIN O25 125 6.223 1.418 5.903 0.2876 0.0700 -0.0308
6LIN Nb1 126 6.024 3.540 5.986 -0.1827 -0.4654 -0.6232
6LIN Nb2 127 5.969 3.208 5.936 0.0331 -0.2833 0.2285
6LIN Nb3 128 5.765 3.437 5.788 0.1039 0.0330 -0.0286
6LIN O4 129 6.039 3.650 6.137 -0.5422 -0.1394 0.2485
6LIN O5 130 6.047 3.672 5.833 -0.1022 0.0102 -0.5766
6LIN O6 131 5.824 3.548 5.948 0.0057 -0.4113 -0.1438
6LIN O7 132 5.992 3.359 6.071 -0.4658 0.3420 -0.2258
6LIN O8 133 6.216 3.484 5.953 -0.0334 -0.5255 0.1017
6LIN O9 134 6.170 3.209 5.915 0.0818 -0.5013 -0.0785
6LIN O10 135 5.780 3.274 5.910 0.1728 0.0925 0.7025
6LIN O11 136 5.580 3.469 5.787 0.1575 0.5049 -0.3332
6LIN O12 137 5.941 3.059 6.047 0.3600 -0.1013 0.0031
6LIN O13 138 6.002 3.397 5.793 0.7076 -0.0042 -0.0458
6LIN Nb14 139 5.982 3.255 5.600 -0.2135 -0.0056 0.3288
6LIN Nb15 140 6.036 3.588 5.648 0.1803 0.4974 -0.3566
6LIN Nb16 141 6.238 3.357 5.797 -0.1317 -0.2080 0.0315
6LIN O17 142 5.966 3.145 5.449 -0.2639 -0.0492 0.1303
6LIN O18 143 5.956 3.124 5.752 0.3618 0.3790 -0.2739
6LIN O19 144 6.181 3.247 5.637 -0.0499 -0.1372 -0.3025
6LIN O20 145 6.012 3.437 5.515 0.2975 -0.3812 -0.2701
6LIN O21 146 5.790 3.313 5.632 -0.0896 -0.1640 -0.1874
6LIN O22 147 5.834 3.588 5.670 -0.5374 -0.1608 0.1761
6LIN O23 148 6.225 3.521 5.676 0.1266 0.5164 -0.3799
6LIN O24 149 6.425 3.327 5.799 0.0929 -0.2051 0.3833
6LIN O25 150 6.064 3.736 5.537 0.0110 0.1953 0.4498
7LIN Nb1 151 5.392 8.981 8.811 0.2160 0.0371 0.4946
7LIN Nb2 152 5.460 9.197 9.066 0.1506 -0.1520 -0.1486
7LIN Nb3 153 5.160 9.033 9.054 -0.0336 -0.0299 0.2581
7LIN O4 154 5.393 8.992 8.624 0.2768 -0.1344 0.3170
7LIN O5 155 5.337 8.788 8.841 -0.0885 -0.5277 -0.0285
7LIN O6 156 5.202 9.033 8.856 -0.2866 -0.8342 0.1440
7LIN O7 157 5.449 9.168 8.866 -0.0700 -0.0299 -0.0777
7LIN O8 158 5.581 8.921 8.850 -0.5868 0.4342 -0.8116
7LIN O9 159 5.637 9.101 9.060 0.1580 -0.7041 0.1734
7LIN O10 160 5.257 9.210 9.065 0.1332 -0.2387 -0.0638
7LIN O11 161 4.980 9.086 9.058 -0.1005 -0.2543 0.1529
7LIN O12 162 5.509 9.376 9.081 -0.3187 0.1575 -0.0575
7LIN O13 163 5.392 8.965 9.052 0.2748 0.1677 0.5512
7LIN Nb14 164 5.391 8.949 9.292 0.2491 -0.0478 -0.2873
7LIN Nb15 165 5.323 8.735 9.036 0.0645 0.3476 -0.0818
7LIN Nb16 166 5.623 8.898 9.047 0.1628 0.1145 -0.2619
7LIN O17 167 5.392 8.938 9.478 0.3335 -0.2162 -0.1348
7LIN O18 168 5.447 9.143 9.261 0.7868 -0.2757 0.0569
7LIN O19 169 5.581 8.898 9.246 -0.2426 0.0293 -0.1646
7LIN O20 170 5.334 8.763 9.236 -0.1094 -0.1687 0.0199
7LIN O21 171 5.200 9.010 9.251 0.1673 -0.1235 0.1141
7LIN O22 172 5.145 8.832 9.042 0.5148 -0.0248 -0.1262
7LIN O23 173 5.525 8.720 9.037 -0.0343 0.0226 0.2150
7LIN O24 174 5.803 8.846 9.044 -0.3253 -0.2630 -0.1538
7LIN O25 175 5.273 8.555 9.022 -0.2652 -0.1921 0.0314
8LIN Nb1 176 8.282 8.798 1.404 0.0021 0.1354 -0.6430
8LIN Nb2 177 8.482 8.991 1.206 -0.4517 -0.2695 0.0220
8LIN Nb3 178 8.435 8.661 1.131 0.0796 0.1804 0.1715
8LIN O4 179 8.277 8.756 1.586 0.6006 -0.1353 0.1907
8LIN O5 180 8.125 8.692 1.330 -0.5502 -0.2886 -0.3831
8LIN O6 181 8.403 8.652 1.330 0.1047 -0.2908 -0.1881
8LIN O7 182 8.441 8.923 1.393 0.6428 -0.2866 -0.0264
8LIN O8 183 8.163 8.960 1.392 -0.3339 0.0384 -0.0096
8LIN O9 184 8.328 9.121 1.231 -0.0173 -0.1536 0.2622
8LIN O10 185 8.567 8.811 1.170 0.1547 0.3133 0.1476
8LIN O11 186 8.549 8.516 1.100 0.4554 0.3387 0.5275
8LIN O12 187 8.632 9.099 1.235 0.1353 0.2710 0.2884
8LIN O13 188 8.289 8.849 1.169 0.7890 0.1089 0.3575
8LIN Nb14 189 8.298 8.903 0.932 0.0499 -0.1784 0.4252
8LIN Nb15 190 8.097 8.710 1.130 0.5486 0.1448 0.0238
8LIN Nb16 191 8.144 9.040 1.207 0.0813 -0.1658 0.0761
8LIN O17 192 8.303 8.945 0.750 0.2972 -0.3445 -0.2229
8LIN O18 193 8.454 9.010 1.006 0.3100 0.6401 -0.1811
8LIN O19 194 8.177 9.048 1.005 0.6013 0.2187 0.0235
8LIN O20 195 8.139 8.777 0.943 0.6808 0.2484 -0.4909
8LIN O21 196 8.418 8.739 0.945 0.0975 -0.1240 -0.1372
8LIN O22 197 8.252 8.579 1.105 -0.2247 -0.3236 0.1897
8LIN O23 198 8.013 8.890 1.166 -0.0999 -0.3412 -0.2347
8LIN O24 199 8.031 9.185 1.235 0.0654 0.0428 -0.0522
8LIN O25 200 7.948 8.602 1.102 0.2512 -0.2312 0.3551
9LIN Nb1 201 2.891 6.891 2.488 -0.0221 -0.0137 0.1522
9LIN Nb2 202 2.658 6.657 2.570 0.0821 -0.0207 -0.1581
9LIN Nb3 203 2.580 6.988 2.585 -0.0867 0.1993 0.0606
9LIN O4 204 3.066 6.929 2.543 -0.0143 0.1136 -0.2651
9LIN O5 205 2.858 7.034 2.347 -0.0889 -0.2267 -0.2453
9LIN O6 206 2.780 7.003 2.615 -0.1641 0.4822 -0.4265
9LIN O7 207 2.846 6.729 2.600 -0.1502 0.1397 -0.2172
9LIN O8 208 2.923 6.763 2.332 -0.2277 -0.3032 -0.1894
9LIN O9 209 2.732 6.568 2.402 -0.1505 0.0785 -0.1437
9LIN O10 210 2.591 6.810 2.683 -0.1541 0.1129 0.1363
9LIN O11 211 2.512 7.101 2.720 -0.2460 -0.3867 0.6128
9LIN O12 212 2.649 6.513 2.690 0.1890 0.2904 -0.5468
9LIN O13 213 2.666 6.841 2.417 -0.4410 0.3065 0.6241
9LIN Nb14 214 2.441 6.791 2.344 -0.0074 -0.1578 0.0933
9LIN Nb15 215 2.675 7.026 2.261 -0.0973 -0.1064 0.1654
9LIN Nb16 216 2.754 6.695 2.246 0.1233 -0.0113 -0.0552
9LIN O17 217 2.267 6.753 2.288 -0.2192 -0.0989 0.2713
9LIN O18 218 2.475 6.648 2.483 -0.3368 0.2132 -0.1107
9LIN O19 219 2.553 6.680 2.216 0.6042 0.3515 -0.7637
9LIN O20 220 2.488 6.954 2.230 -0.2218 0.3674 -0.2409
9LIN O21 221 2.410 6.920 2.498 0.1851 0.2043 -0.1555
9LIN O22 222 2.601 7.114 2.429 -0.3492 0.1031 0.1268
9LIN O23 223 2.742 6.872 2.148 -0.3681 0.1387 0.3875
9LIN O24 224 2.820 6.581 2.112 -0.2502 -0.1068 0.0906
9LIN O25 225 2.683 7.169 2.140 0.2271 -0.1442 0.0521
10LIN Nb1 226 4.810 1.772 6.875 -0.0883 -0.2924 -0.3441
10LIN Nb2 227 4.721 1.980 7.130 -0.0114 -0.0972 0.1610
10LIN Nb3 228 4.523 1.713 7.050 -0.0641 -0.1979 -0.3613
10LIN O4 229 4.855 1.794 6.695 -0.1655 0.0243 -0.4433
10LIN O5 230 4.829 1.570 6.898 0.0002 0.1716 -0.4838
10LIN O6 231 4.611 1.742 6.867 0.4753 0.0878 -0.0464
10LIN O7 232 4.774 1.962 6.936 -0.1251 -0.2526 -0.2390
10LIN O8 233 4.992 1.786 6.966 0.0874 0.3752 -0.0747
10LIN O9 234 4.918 1.960 7.174 0.3279 -0.0574 -0.4848
10LIN O10 235 4.537 1.914 7.076 0.3561 0.2438 0.2863
10LIN O11 236 4.342 1.692 7.001 -0.2438 0.3069 0.2586
10LIN O12 237 4.693 2.163 7.148 0.0723 -0.0031 0.1024
10LIN O13 238 4.755 1.740 7.107 -0.5803 -0.9459 0.3685
10LIN Nb14 239 4.698 1.711 7.341 0.2914 0.0228 0.4613
10LIN Nb15 240 4.789 1.502 7.085 -0.1124 0.1379 -0.0714
10LIN Nb16 241 4.986 1.768 7.168 0.3481 0.1418 0.3491
10LIN O17 242 4.655 1.686 7.521 -0.2896 0.2738 0.3482
10LIN O18 243 4.680 1.911 7.317 0.0960 -0.4610 -0.2184
10LIN O19 244 4.898 1.738 7.349 0.2500 -0.2457 -0.0466
10LIN O20 245 4.736 1.520 7.281 0.0851 0.4945 0.4460
10LIN O21 246 4.517 1.696 7.249 0.1204 0.7805 0.3589
10LIN O22 247 4.591 1.522 7.041 -0.1275 -0.2444 0.1186
10LIN O23 248 4.973 1.568 7.140 0.5541 0.0354 -0.3086
10LIN O24 249 5.167 1.789 7.214 0.1666 -0.2001 0.3113
10LIN O25 250 4.816 1.319 7.067 -0.3755 0.1881 0.0857
11LIN Nb1 251 3.406 7.274 1.883 -0.3580 0.0275 -0.4085
11LIN Nb2 252 3.317 7.395 1.577 0.1644 0.2414 -0.2734
11LIN Nb3 253 3.272 7.064 1.651 -0.1380 -0.2062 -0.1216
11LIN O4 254 3.564 7.275 1.984 -0.2236 -0.3731 -0.5218
11LIN O5 255 3.278 7.175 2.004 -0.2706 -0.0441 -0.1344
11LIN O6 256 3.427 7.104 1.776 -0.5786 0.0170 -0.6796
11LIN O7 257 3.463 7.376 1.716 0.0049 -0.0125 -0.4272
11LIN O8 258 3.315 7.445 1.943 -0.2025 0.0191 -0.1390
11LIN O9 259 3.242 7.545 1.691 0.4205 0.2907 0.3599
11LIN O10 260 3.353 7.202 1.525 -0.0378 0.0086 -0.5225
11LIN O11 261 3.323 6.903 1.572 0.0627 0.1756 -0.2964
11LIN O12 262 3.403 7.487 1.438 -0.3205 0.3584 0.0990
11LIN O13 263 3.204 7.272 1.752 0.5994 -0.6366 0.0402
11LIN Nb14 264 3.002 7.271 1.622 0.0637 -0.1397 -0.0501
11LIN Nb15 265 3.092 7.151 1.928 0.0405 -0.3499 0.4030
11LIN Nb16 266 3.137 7.482 1.852 -0.0900 0.0217 0.0354
11LIN O17 267 2.844 7.271 1.520 -0.0983 0.3608 -0.4324
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Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9
O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4
O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25
Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21
O22 O23 O24 O25 LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI
LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI</array>
</property>
</propertyList>
</molecule>
</module>
</comment>
Template definition
<templateList id="geometry"> <template name="geometry lines" pattern=".*" endPattern="~"> <record repeat="2" /> <templateList> <template name="atoms" id="solvent" pattern="\s*[0-9]+(SOL|LIG)\s+.*" endPattern="\s*[0-9]+((?!SOL|LIG).)+" endPattern2="\s*[0-9]+\.[0-9]+.*" endPattern3="~" repeat="*" endOffset="0"> <record id="atoms" repeat="*">{A5,gm:residueNumber}{A5,gm:residueName}{A5,gm:atomName}{I5,cc:serial}{F8.3,cc:x3}{F8.3,cc:y3}{F8.3,cc:z3}.*</record>
</template> <template name="atoms" id="molecule" pattern="\s*[0-9]+((?!SOL|LIG).)+[A-Za-z]+.*" endPattern="\s*[0-9]+(SOL|LIG)\s+.*" endPattern2="\s*[0-9]+\.[0-9]+.*" endPattern3="~" repeat="*" endOffset="0"> <record id="atoms" repeat="*">{A5,gm:residueNumber}{A5,gm:residueName}{A5,gm:atomName}{I5,cc:serial}{F8.3,cc:x3}{F8.3,cc:y3}{F8.3,cc:z3}.*</record>
</template> <template id="lattice" pattern="\s*[0-9]+\.[0-9]+\s*[0-9]+\.[0-9]+\s*[0-9]+\.[0-9]+.*" endPattern=".*" endPattern2="~" endOffset="0" repeat="*"> <record id="vectors">{1_9F,x:lattice}</record> <transform process="split" xpath=".//cml:array[@dictRef='x:lattice']" dictRef="x:lattice" /> <transform process="operateScalar" xpath=".//cml:scalar" args="operator=multiply operand=10" /> <transform process="pullup" xpath=".//cml:scalar" repeat="2" /> <transform process="addChild" xpath="." elementName="cml:scalar" dictRef="x:lattice" value="0.00000" /> <transform process="addChild" xpath="." elementName="cml:scalar" dictRef="x:lattice" value="0.00000" /> <transform process="addChild" xpath="." elementName="cml:scalar" dictRef="x:lattice" value="0.00000" /> <transform process="addChild" xpath="." elementName="cml:scalar" dictRef="x:lattice" value="0.00000" /> <transform process="addChild" xpath="." elementName="cml:scalar" dictRef="x:lattice" value="0.00000" /> <transform process="addChild" xpath="." elementName="cml:scalar" dictRef="x:lattice" value="0.00000" /> <transform process="addChild" xpath="." elementName="cml:list" dictRef="lattice1" /> <transform process="copy" xpath="./cml:scalar[@dictRef='x:lattice' and position() = 1]" to="//cml:list[@dictRef='lattice1']" /> <transform process="copy" xpath="./cml:scalar[@dictRef='x:lattice' and position() = 4]" to="//cml:list[@dictRef='lattice1']" /> <transform process="copy" xpath="./cml:scalar[@dictRef='x:lattice' and position() = 5]" to="//cml:list[@dictRef='lattice1']" /> <transform process="addChild" xpath="." elementName="cml:list" dictRef="lattice2" /> <transform process="copy" xpath="./cml:scalar[@dictRef='x:lattice' and position() = 6]" to="//cml:list[@dictRef='lattice2']" /> <transform process="copy" xpath="./cml:scalar[@dictRef='x:lattice' and position() = 2]" to="//cml:list[@dictRef='lattice2']" /> <transform process="copy" xpath="./cml:scalar[@dictRef='x:lattice' and position() = 7]" to="//cml:list[@dictRef='lattice2']" /> <transform process="addChild" xpath="." elementName="cml:list" dictRef="lattice3" /> <transform process="copy" xpath="./cml:scalar[@dictRef='x:lattice' and position() = 8]" to="//cml:list[@dictRef='lattice3']" /> <transform process="copy" xpath="./cml:scalar[@dictRef='x:lattice' and position() = 9]" to="//cml:list[@dictRef='lattice3']" /> <transform process="copy" xpath="./cml:scalar[@dictRef='x:lattice' and position() = 3]" to="//cml:list[@dictRef='lattice3']" /> <transform process="createArray" xpath="." from="./cml:list[@dictRef='lattice1']/cml:scalar" dataType="xsd:double" dictRef="cc:lattice" /> <transform process="createArray" xpath="." from="./cml:list[@dictRef='lattice2']/cml:scalar" dataType="xsd:double" dictRef="cc:lattice" /> <transform process="createArray" xpath="." from="./cml:list[@dictRef='lattice3']/cml:scalar" dataType="xsd:double" dictRef="cc:lattice" /> <transform process="pullup" xpath=".//cml:array" /> <transform process="delete" xpath=".//cml:scalar" /> <transform process="delete" xpath=".//cml:list" />
</template>
</templateList> <transform process="delete" xpath="/cml:module/cml:module/cml:module[@cmlx:templateRef='molecule']/preceding-sibling::cml:module[@cmlx:templateRef='solvent']" /> <transform process="delete" xpath="/cml:module/cml:module/cml:module[@cmlx:templateRef='molecule']/following-sibling::cml:module[@cmlx:templateRef='solvent']" /> <transform process="setValue" xpath="/cml:module/cml:module/cml:module[@cmlx:templateRef='solvent']//cml:scalar[@dictRef='gm:atomName' and (text() = 'HW1' or text() = 'HW2')]" value="H" /> <transform process="setValue" xpath="/cml:module/cml:module/cml:module[@cmlx:templateRef='solvent']//cml:scalar[@dictRef='gm:atomName' and text() = 'OW']" value="O" /> <transform process="addChild" xpath="/cml:module/cml:module/cml:module/cml:list[@cmlx:templateRef='atoms']/cml:list" elementName="cml:scalar" dictRef="cc:elementType" /> <transform process="addAttribute" xpath="//cml:scalar[@dictRef='cc:elementType']" name="dataType" value="xsd:string" /> <transform process="setValue" xpath="//cml:scalar[@dictRef='cc:elementType']" value="$string(replace(preceding-sibling::cml:scalar[@dictRef='gm:atomName'], '[0-9]',''))" /> <transform process="setValue" xpath="//cml:scalar[@dictRef='cc:elementType']" value="$string(concat(upper-case(substring(./text(), 1, 1)), lower-case(substring(./text(), 2))))" /> <transform process="operateScalar" xpath=".//cml:scalar[@dictRef='cc:x3']" args="operator=multiply operand=10" /> <transform process="operateScalar" xpath=".//cml:scalar[@dictRef='cc:y3']" args="operator=multiply operand=10" /> <transform process="operateScalar" xpath=".//cml:scalar[@dictRef='cc:z3']" args="operator=multiply operand=10" /> <transform process="setValue" xpath=".//cml:scalar[@dictRef='cc:x3']" value="$number(round-half-to-even(./text(), 2))" /> <transform process="setValue" xpath=".//cml:scalar[@dictRef='cc:y3']" value="$number(round-half-to-even(./text(), 2))" /> <transform process="setValue" xpath=".//cml:scalar[@dictRef='cc:z3']" value="$number(round-half-to-even(./text(), 2))" /> <transform process="createArray" xpath="." from="//cml:scalar[@dictRef='cc:serial']" dataType="xsd:integer" dictRef="cc:serial" /> <transform process="createArray" xpath="." from="//cml:scalar[@dictRef='cc:elementType']" dataType="xsd:string" dictRef="cc:elementType" /> <transform process="createArray" xpath="." from="//cml:scalar[@dictRef='cc:x3']" dataType="xsd:double" dictRef="cc:x3" /> <transform process="createArray" xpath="." from="//cml:scalar[@dictRef='cc:y3']" dataType="xsd:double" dictRef="cc:y3" /> <transform process="createArray" xpath="." from="//cml:scalar[@dictRef='cc:z3']" dataType="xsd:double" dictRef="cc:z3" /> <transform process="createArray" xpath="." from="//cml:scalar[@dictRef='gm:residueNumber']" dataType="xsd:integer" dictRef="gm:residueNumber" /> <transform process="createArray" xpath="." from="//cml:scalar[@dictRef='gm:residueName']" dataType="xsd:integer" dictRef="gm:residueName" /> <transform process="createArray" xpath="." from="//cml:scalar[@dictRef='gm:atomName']" dataType="xsd:string" dictRef="gm:atomName" /> <transform process="pullup" xpath="//cml:list[@cmlx:templateRef='atoms']/cml:list/cml:array" /> <transform process="delete" xpath="//cml:list[count(*)=0]" /> <transform process="addChild" xpath="." elementName="cml:list" dictRef="cc:properties" /> <transform process="move" xpath="//cml:array[@dictRef='gm:residueNumber']" to="//cml:list[@dictRef='cc:properties']" /> <transform process="move" xpath="//cml:array[@dictRef='gm:residueName']" to="//cml:list[@dictRef='cc:properties']" /> <transform process="move" xpath="//cml:array[@dictRef='gm:atomName']" to="//cml:list[@dictRef='cc:properties']" /> <transform process="pullup" xpath="//cml:list[@dictRef='cc:properties']" repeat="2" />
</template>
</templateList>
<transform process="createMolecule" xpath="//cml:module[@cmlx:templateRef='solvent']/cml:list[@cmlx:templateRef='atoms']/cml:array" from="." id="solvent" connect="no" />
<transform process="createMolecule" xpath="//cml:module[@cmlx:templateRef='molecule']/cml:list[@cmlx:templateRef='atoms']/cml:array" from="." id="molecule" connect="no" />
<transform process="createCrystal" xpath="//cml:molecule[@id='solvent']/cml:atomArray" lattice=".//cml:module[@cmlx:templateRef='lattice']" id="coordinates" connect="no" />
<transform process="createCrystal" xpath="//cml:molecule[@id='molecule']/cml:atomArray" lattice=".//cml:module[@cmlx:templateRef='lattice']" id="coordinates" connect="no" />
<transform process="delete" xpath="//cml:module[@cmlx:templateRef='solvent']/preceding::cml:list[@dictRef='cc:properties']" />
<transform process="delete" xpath="//cml:scalar[@dictRef='cc:serial']" />
<transform process="delete" xpath="//cml:scalar[@dictRef='cc:atomicNumber']" />
<transform process="addChild" xpath="//cml:molecule" elementName="cml:propertyList" />
<transform process="move" xpath="//cml:list[@dictRef='cc:properties']/cml:array" to="//cml:molecule/cml:propertyList" />
<transform process="createWrapperProperty" xpath="//cml:molecule/cml:propertyList/*" />
<transform process="createWrapper" xpath="//cml:molecule/cml:propertyList/cml:module" elementName="cml:property" />
<transform process="move" xpath="//cml:molecule[@id='coordinates']" to="/cml:module" />
<transform process="delete" xpath="//cml:module" />
<transform process="delete" xpath="//cml:list" />