Atomic coordinate data

Coordinate atomic coordinate data MODEL, AEOM, SIC ATOM... 

Figure 2-114. Atomic coordinate data section of the analy2ed PD B file.

The most obvious data in a typical 3D structure record are the atomic coordinate data, the locations in space of the atoms of a molecule represented by (x, y, z) triples, and distances along each axis to some arbitrary origin in space. The coordinate data for each atom are attached to a list of labeling information in the structure record such as that derived from the protein or nucleic acid sequence. 

Tel. 800-232-2224, 203-335-0906, fax 203-336-2481 Display and manipulation of 3D models using keyboard input. Molecular Animator for creating and displaying 3D models. Molecular Graphics for display and manipulation of atomic coordinate data. ChemFile II for creating databases of 2D chemical structures with associated text. PCs and Macintosh. 

Much of our current knowledge of bonding geometry of atoms has been derived from crystal structure determinations. Atomic coordinate data that have been published are included in databases, as will be described in more detail in Chapter 16. For organic compounds the Cambridge Structural Database " can be accessed by computer. Similar data for inorganic compounds are found in the Inorganic Crystal Structure Database. Comparisons with other experimental methods, such as... 

Moving responsibility for the force computation away from the patches required a move away from pure message-driven execution to dependency-driven execution in which patches control the data (atomic coordinates) needed for compute objects to execute. A compute object, upon creation, registers this dependency with those patches from which it needs data. The patch then triggers force calculation by notifying its dependent compute objects when the next timestep s data is available. Once a compute object has received notification from all of the patches it depends on, it is placed in a prioritized queue for eventual execution. 

The different internal and external file formats make it necessary to have programs which convert one format into another. One of the first conversion programs for chemical structure information was Babel (around 1992). It supports almost 50 data formats for input and output of chemical structure information [61]. CLIFF is another file format converter based on the CACTVS technology and which supports nearly the same number of file formats [29]. In contrast to Babel, the program is more comprehensive it is able to convert chemical reaction information, and can calculate missing atom coordinates [29]. 

The PDB contains 20 254 experimentally determined 3D structures (November, 2002) of macromolecules (nucleic adds, proteins, and viruses). In addition, it contains data on complexes of proteins with small-molecule ligands. Besides information on the structure, e.g., sequence details (primary and secondary structure information, etc.), atomic coordinates, crystallization conditions, structure factors. 

The Brookhaven Protein Data Bank, PDB (http //www.pdb.bnl.gov), is the primary store of experimentally determined atomic coordinates of proteins. Each coordinate set has a unique identification code that can be... 

In contrast to single-crystal work, a fiber-diffraction pattern contains much fewer reflections going up to about 3 A resolution. This is a major drawback and it arises either as a result of accidental overlap of reflections that have the same / value and the same Bragg angle 0, or because of systematic superposition of hkl and its counterparts (-h-kl, h-kl, and -hkl, as in an orthorhombic system, for example). Sometimes, two or more adjacent reflections might be too close to separate analytically. Under such circumstances, these reflections have to be considered individually in structure-factor calculation and compounded properly for comparison with the observed composite reflection. Unobserved reflections that are too weak to see are assigned threshold values, based on the lowest measured intensities. Nevertheless, the number of available X-ray data is far fewer than the number of atomic coordinates in a repeat of the helix. Thus, X-ray data alone is inadequate to solve a fiber structure. 

Vibrational spectroscopy is of utmost importance in many areas of chemical research and the application of electronic structure methods for the calculation of harmonic frequencies has been of great value for the interpretation of complex experimental spectra. Numerous unusual molecules have been identified by comparison of computed and observed frequencies. Another standard use of harmonic frequencies in first principles computations is the derivation of thermochemical and kinetic data by statistical thermodynamics for which the frequencies are an important ingredient (see, e. g., Hehre et al. 1986). The theoretical evaluation of harmonic vibrational frequencies is efficiently done in modem programs by evaluation of analytic second derivatives of the total energy with respect to cartesian coordinates (see, e. g., Johnson and Frisch, 1994, for the corresponding DFT implementation and Stratman etal., 1997, for further developments). Alternatively, if the second derivatives are not available analytically, they are obtained by numerical differentiation of analytic first derivatives (i. e., by evaluating gradient differences obtained after finite displacements of atomic coordinates). In the past two decades, most of these calculations have been carried... 

Every space group listed in the family tree corresponds to a structure. Since the space group symbol itself states only symmetry, and gives no information about the atomic positions, additional information concerning these is necessary for every member of the family tree (Wyckoff symbol, site symmetry, atomic coordinates). The value of information of a tree is rather restricted without these data. In simple cases the data can be included in the family tree in more complicated cases an additional table is convenient. The following examples show how specifications can be made for the site occupations. Because they are more informative, it is advisable to label the space groups with their full Hermann-Mauguin symbols. 

The crystal data compared to expected values assuming no distortions are summarized in Table 18.1. Inspection of the atomic coordinates reveals that the distortions of the packing of spheres are only marginal. As expected, the greatest deviations are observed for the molecular compounds PI3 and NMe3. 

P212121 Z = 4 D = 1.25 R = 0.069 number of intensities not reported. This analysis was to confirm a configuration derived from n.m.r. data. The pyranoid rings are slightly distorted 4Q, due to fusion to the trioxacyclooctane ring, which has an almost ideal, boat-chair conformation. The overall molecule has a convex, sickle conformation. There is an error in the atomic coordinates reported, which do not correspond to the structure given in the paper. 

With data averaged in point group m, the first refinements were carried out to estimate the atomic coordinates and anisotropic thermal motion parameters IP s. We have started with the atomic coordinates and equivalent isotropic thermal parameters of Joswig et al. [14] determined by neutron diffraction at room temperature. The high order X-ray data (0.9 < s < 1.28A-1) were used in this case in order not to alter these parameters by the valence electron density contributing to low order structure factors. Hydrogen atoms of the water molecules were refined isotropically with all data and the distance O-H were kept fixed at 0.95 A until the end of the multipolar refinement. The inspection of the residual Fourier maps has revealed anharmonic thermal motion features around the Ca2+ cation. Therefore, the coefficients up to order 6 of the Gram-Charlier expansion [15] were refined for the calcium cation in the scolecite. 

According to [98,99], the compound Tc2O3[C5(CH3)5 n has a polymeric structure with R(Tc-Tc) = 1.867(4) A. However, these authors do not report the details of the X-ray diffraction experiment and the atomic coordinates. Therefore, these data seem doubtful. 

With this structure model, the refinement readily converged to very good discrepancy factors RF2 = 5.4%, Rwp = 7.3%, Rp = 5.3%. More details concerning data collection and refinement are given in Table 1, whereas the atomic coordinate, occupancies and displacement parameters of ECS-2 are reported in Table 2. 

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