Step 3. Renumbering of Atoms
It will be re-emphasize that there is a strict rule concerning the ordering of the atoms, based on their QM, MM, or LI atom type designation. All QM and LI atoms must come before any MM atoms. This rule also applies to the dummy atoms. All atoms in the QM model system shown in Figure 5-3b and their equivalent LI atoms in the real system must come first. Given below are the Cartesian coordinates of the initial geometry with the atoms renumbered. Although the optimization will be performed in internal coordinates, this is a complex example, and it might help the reader to examine the 3D structure of the complex with their favorite molecule viewer.
Pd 0.00000 0.00000 0.00000 N 2.18381 0.00000 0.00000 P -0.19353 2.33087 0.00000 Si -2.09382 -0.72920 0.40993 Cl -3.11786 -1.66043 -1.19030 Cl -3.49847 0.77293 1.00006 Cl -2.26795 -2.09058 2.02296 C 1.00751 3.35326 -0.90266 C 2.19320 2.92863 -1.63738 C 2.55933 1.49397 -1.90948 N 3.04680 0.78384 -0.70880 C 4.30216 0.71267 -0.18548 C 4.25805 -0.16196 0.88628 C 2.91893 -0.57760 0.96569 Xx 0.74788 -1.69468 -1.67891 C 1.00986 -2.06361 -1.18981 C 0.48590 -1.32574 -2.16801 H 0.42486 -2.82737 -0.67948 H 2.04440 -1.93825 -0.86750 H 1.06712 -0.55943 -2.68284 H -0.54392 -1.46716 -2.49409 C -0.02313 3.09172 1.69751 C -1.80681 3.04317 -0.56800 C 1.06326 4.78500 -0.83878 C 2.90531 4.10963 -2.00851 H 1.82015 0.84892 -1.41063 C 2.56571 1.10455 -3.38246 H 5.13150 1.27389 -0.59600 H 5.08293 -0.44584 1.52605 C 2.28008 -1.58274 1.88382 Fe 1.04114 4.20972 -2.75447 H 3.29128 1.69565 -3.95722 H 2.82573 0.03883 -3.48724 H 1.57260 1.26129 -3.82619 C 2.23262 5.27491 -1.51096 H 3.82950 4.13635 -2.57654 H 2.53722 6.31008 -1.62736 H 0.35288 5.41923 -0.32204 C -0.36634 3.33949 -3.93243 C -0.80398 4.62382 -3.46691 C 0.14944 5.60144 -3.90508 C 1.17457 4.92275 -4.64218 C 0.85084 3.52607 -4.66695 H 1.38331 2.75840 -5.21594 H -0.88905 2.39926 -3.80335 H -1.70862 4.82843 -2.90699 H 0.10418 6.66814 -3.70967 H 2.03573 5.38561 -5.11158 C -2.52881 2.31699 -1.52071 C -3.74190 2.80302 -2.01422 C -4.24163 4.02394 -1.55340 C -3.52216 4.75609 -0.60549 C -2.30668 4.26891 -0.11529 H -2.14465 1.36750 -1.87729 H -4.29443 2.23258 -2.75379 H -5.18572 4.40286 -1.93263 H -3.90891 5.70542 -0.24710 H -1.76468 4.85404 0.61704 C -1.11030 3.12908 2.57588 C -0.97634 3.68572 3.85061 C 0.25426 4.20707 4.25852 C 1.35020 4.15676 3.39277 C 1.21425 3.58782 2.12359 H -2.06730 2.72549 2.27375 H -1.82678 3.71355 4.52356 H 0.35921 4.64813 5.24539 H 2.30826 4.55806 3.70733 H 2.08227 3.52803 1.47710 C 2.71278 -2.91472 1.84328 C 2.09262 -3.86832 2.66014 C 1.02394 -3.51226 3.48850 C 0.62539 -2.17333 3.54762 C 1.26348 -1.20208 2.77018 C 3.85077 -3.34061 0.90256 H 2.44054 -4.89548 2.65117 C 0.28665 -4.56067 4.32981 H -0.18696 -1.88618 4.20708 C 0.83254 0.25922 2.93922 H 4.81150 -3.02160 1.33267 H 3.72469 -2.87842 -0.08835 H 3.87528 -4.43158 0.76399 H 1.55468 0.95128 2.48757 H 0.75353 0.50536 4.00860 H -0.15276 0.39937 2.47265 H -0.79950 -4.40165 4.25848 H 0.51050 -5.58360 3.99174 H 0.59686 -4.45719 5.38063 Xx 1.88038 4.09028 -1.37966 Xx 0.20091 4.40271 -4.12271
