Check the Examples
Last updated
Last updated
During the next sections, we exemplify the calculation of all atomic features for several molecules as depicted below. The coordinates of all molecules are given in an xmol format. We have furthermore extracted 135 xmol structures for organic molecules and transition metal complexes that have been optimized at the CAM-B3LYP-D3(B)/def2-TZVP level of theory, which can be used for testing purposes as well.
xmol files can be nicely visualized by the atomic simulation environment (ASE). Once you have installed ASE, you can use their GUI to visualize xmol structures
> ase gui <struture.xyz>> cat alanine-glycine.xyz
20
Alanine-Glycine
C 2.081440 0.615100 -0.508430
C 2.742230 1.824030 -1.200820
N 4.117790 1.799870 -1.190410
C 4.943570 2.827040 -1.822060
C 6.440080 2.569360 -1.637600
O 7.351600 3.252270 -2.069090
N 0.610100 0.695090 -0.538780
O 2.095560 2.724940 -1.739670
O 6.705220 1.463410 -0.897460
H 0.303080 1.426060 0.103770
H 0.338420 1.050680 -1.460480
C 2.488753 -0.593400 -1.198448
H 2.416500 0.557400 0.532050
H 4.614100 1.081980 -0.670550
H 4.699850 3.794460 -1.373720
H 4.722890 2.844690 -2.894180
H 7.687400 1.448620 -0.860340
H 2.029201 -1.457008 -0.719999
H 2.170233 -0.542411 -2.238576
H 3.572730 -0.688405 -1.154998> cat toluene.xyz
15
Toluene
C 1.2264 0.0427 0.0670
C 1.0031 -1.3293 0.0600
C -0.2945 -1.8256 -0.0060
C -1.3704 -0.9461 -0.0646
C -1.1511 0.4266 -0.0578
C 0.1497 0.9292 0.0066
C 0.3871 2.3956 -0.0022
H 2.2495 0.4310 0.1211
H 1.8510 -2.0202 0.1071
H -0.4688 -2.9062 -0.0109
H -2.3926 -1.3347 -0.1157
H -2.0006 1.1172 -0.1021
H 0.5024 2.7582 -1.0330
H 1.2994 2.6647 0.5466
H -0.4475 2.9470 0.4506> cat 1-propanol.xyz
12
1-Propanol
C -1.9554949371 0.1467391618 0.0031595607
C -0.5906278346 -0.5279387138 -0.0201649611
C 0.5440986558 0.4958779663 0.0283462055
H 0.4812068385 1.1678478833 -0.8308000219
H 0.4590669813 1.0993020658 0.9450529713
O 1.8195161785 -0.0957487212 -0.0534239359
H 1.9103706588 -0.7338049177 0.6631507673
H -0.5004127933 -1.2028008461 0.8364936998
H -0.4854009629 -1.1250023438 -0.9282499098
H -2.7476736372 -0.5972665554 -0.0242488945
H -2.0700756998 0.8040326560 -0.8554507953
H -2.0722381370 0.7410005769 0.9069567477> cat iridium.xyz
84
Iridium catalyst
N -1.49181 -1.48156 0.11185
C -2.55925 -0.65086 0.01741
C -3.63669 -0.95853 -0.82211
C -3.59854 -2.11761 -1.59315
C -2.49012 -2.96012 -1.49658
C -1.46463 -2.60530 -0.62538
H -0.57322 -3.21385 -0.51297
H -2.41471 -3.87015 -2.08402
H -4.49525 -0.30018 -0.88801
C -2.47894 0.61554 0.78766
N -1.39333 0.76325 1.58960
C -1.20306 1.93753 2.21949
C -2.08626 3.00879 2.10526
C -3.21893 2.85612 1.30652
C -3.41320 1.64844 0.64061
H -4.27050 1.53205 -0.01267
H -1.87758 3.93959 2.62419
H -0.28049 2.01587 2.78307
Ir 0.35370 -0.67818 1.13253
B 0.63450 0.55858 -0.44422
O -0.19362 0.48283 -1.56874
C 0.00925 1.66870 -2.37306
C -0.12589 1.29406 -3.84707
H 0.54017 0.46992 -4.10962
H 0.10628 2.15145 -4.48906
H -1.15307 0.97924 -4.05614
C -1.08750 2.66827 -1.98296
H -1.04174 3.57795 -2.59043
H -2.06373 2.19834 -2.13176
H -1.00491 2.94365 -0.92811
C 1.44490 2.13099 -1.93197
O 1.51878 1.62563 -0.57810
C 2.56600 1.46656 -2.74257
H 2.45531 0.38222 -2.72527
H 2.57615 1.82480 -3.77708
H 3.52951 1.70730 -2.28517
C 1.65520 3.64467 -1.90072
H 0.97315 4.13144 -1.20137
H 2.67882 3.86791 -1.58386
H 1.50754 4.07589 -2.89735
B 1.97704 0.28091 1.93369
O 3.30134 -0.18839 2.05596
C 4.18961 0.95270 2.08716
C 5.41028 0.61571 2.94057
H 5.12723 0.28553 3.94210
H 5.97772 -0.19076 2.46506
H 6.07064 1.48559 3.03269
C 4.62652 1.21165 0.63857
H 5.32497 2.05273 0.57026
H 5.12271 0.31535 0.25696
H 3.75726 1.40183 0.00958
C 3.26470 2.08824 2.66736
O 1.93958 1.62260 2.33545
C 3.45855 3.45935 2.01726
H 3.21728 3.41456 0.95425
H 2.78607 4.18572 2.48532
H 4.48799 3.81473 2.14222
C 3.33461 2.20824 4.19335
H 3.17890 1.23516 4.66796
H 4.29644 2.61252 4.52541
H 2.54125 2.88257 4.52980
B 1.76449 -1.78676 0.19710
O 2.03307 -3.16409 0.35401
C 3.21936 -3.48040 -0.43243
C 4.42712 -3.31243 0.49519
H 4.47520 -2.28621 0.86981
H 4.31350 -3.98399 1.35146
H 5.36388 -3.55980 -0.01437
C 3.12148 -4.91417 -0.93709
H 3.17214 -5.61331 -0.09676
H 3.95389 -5.13536 -1.61486
H 2.18450 -5.08785 -1.47079
C 3.17452 -2.38636 -1.54879
O 2.55530 -1.29078 -0.85499
C 4.53817 -1.93860 -2.07290
H 5.07805 -2.77906 -2.52321
H 4.40428 -1.16942 -2.83979
H 5.15012 -1.51218 -1.27704
C 2.26428 -2.75789 -2.73039
H 1.28052 -3.07825 -2.37716
H 2.12149 -1.87355 -3.35820
H 2.69777 -3.55266 -3.34605
H -4.42174 -2.35615 -2.26100
H -3.93099 3.66765 1.18443
> cat ethane.xyz
8
Ethane
H 0.00 0.00 0.00
C 0.00 0.00 -1.10
H -1.00 0.27 -1.47
H 0.27 -1.00 -1.47
C 1.03 1.03 -1.61
H 1.03 1.03 -2.71
H 2.03 0.76 -1.25
H 0.76 2.03 -1.25
