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Robin Taylor - One of the best experts on this subject based on the ideXlab platform.
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knowledge based conformer generation using the cambridge Structural Database
Journal of Chemical Information and Modeling, 2018Co-Authors: Jason C Cole, Patrick Mccabe, Oliver Korb, Murray G Read, Robin TaylorAbstract:Fast generation of plausible molecular conformations is central to molecular modeling. This paper presents an approach to conformer generation that makes extensive use of the information available in the Cambridge Structural Database. By using geometric distributions derived from the Cambridge Structural Database, it is possible to create biologically relevant conformations in the majority of cases analyzed. The paper compares the performance of the approach with previously published evaluations, and presents some cases where the method fails. The method appears to show significantly improved performance in reproduction of the conformations of structures observed in the Cambridge Structural Database and the Protein Data Bank as compared to other published methods of a similar speed.
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research applications of the cambridge Structural Database csd
ChemInform, 2005Co-Authors: Frank H. Allen, Robin TaylorAbstract:Crystal structure data are of fundamental importance in a wide spectrum of scientific activities. This tutorial review summarises the principal application areas, so far, for the data from more than 300,000 crystal structures of small organic and metal-organic compounds that are stored in the Cambridge Structural Database (CSD). Direct use of the accumulated data is valuable in establishing standard molecular dimensions, determining conformational preferences and in the study of intermolecular interactions, all of which are crucial in Structural chemistry and rational drug design. More recently, information derived from the CSD has been used to construct two dynamic libraries of Structural knowledge: Mogul, which stores intramolecular information, and IsoStar, which stores information about intermolecular interactions. These electronic libraries provide information "at the touch of a button". In their turn, the libraries also serve as sources of Structural knowledge for applications software that address specific problems in small-molecule and biological chemistry.
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new software for searching the cambridge Structural Database and visualizing crystal structures
Acta Crystallographica Section B-structural Science, 2002Co-Authors: Ian J Bruno, Jason C Cole, Paul R Edgington, Magnus Kessler, Clare F Macrae, Patrick Mccabe, Jonathan Pearson, Robin TaylorAbstract:Two new programs have been developed for searching the Cambridge Structural Database (CSD) and visualizing Database entries: ConQuest and Mercury. The former is a new search interface to the CSD, the latter is a high-performance crystal-structure visualizer with extensive facilities for exploring networks of intermolecular contacts. Particular emphasis has been placed on making the programs as intuitive as possible. Both ConQuest and Mercury run under Windows and various types of Unix, including Linux.
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life science applications of the cambridge Structural Database
Acta Crystallographica Section B-structural Science, 2002Co-Authors: Robin TaylorAbstract:Several studies show that the molecular geometries and intermolecular interactions observed in small-molecule crystal structures are relevant to the modelling of in vivo situations, although the influence of crystal packing is sometimes important and should always be borne in mind. Torsional distributions derived from the Cambridge Structural Database (CSD) can be used to map out potential-energy surfaces and thereby help identify experimentally validated conformational minima of molecules with several rotatable bonds. The use of crystallographic data in this way is complementary to in vacuo theoretical calculations since it gives insights into conformational preferences in condensed-phase situations. Crystallographic data also underpin many molecular-fragment libraries and programs for generating three-dimensional models from two-dimensional chemical structures. The modelling of ligand binding to metalloenzymes is assisted by information in the CSD on preferred coordination numbers and geometries. CSD data on intermolecular interactions are useful in structure-based inhibitor design both in indicating how probable a protein-ligand interaction is and what its geometry is likely to be. They can also be used to guide searches for bioisosteric replacements. Crystallographically derived information has contributed to many life-science software applications, including programs for locating binding 'hot spots' on proteins, docking ligands into enzyme active sites, de novo ligand design, molecular superposition and three-dimensional QSAR. Overall, crystallographic data in general, and the CSD in particular, are very significant tools for the rational design of biologically active molecules.
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organic fluorine hardly ever accepts hydrogen bonds
Chemistry: A European Journal, 1997Co-Authors: J D Dunitz, Robin TaylorAbstract:Statistical analysis of Structural data and detailed inspection of individual crystal structures culled from the Cambridge Structural Database and the Brookhaven Protein Data Bank show that covalently bound fluorine (in contrast to anionic fluoride) hardly ever acts as a hydrogen-bond acceptor. The weakness of covalently bound fluorine as hydrogen-bond acceptor is backed by results of new molecular orbital calculations on model systems using ab initio intermolecular perturbation theory (IMPT), and is in accord with results of other physicochemical studies and with the physical properties of fluorinated organic compounds. Factors influencing the strength of hydrogen bonding in extended systems are discussed.
Frank H. Allen - One of the best experts on this subject based on the ideXlab platform.
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die cambridge Structural Database ruckblick und vorausschau
Angewandte Chemie, 2014Co-Authors: Colin R Groom, Frank H. AllenAbstract:Das Cambridge Crystallographic Data Centre (CCDC) wurde 1965 gegrundet. Das Ziel war die Einrichtung einer Institution, die numerische, chemische und bibliographische Daten von organischen und metallorganischen Kristallstrukturen archiviert. In der Cambridge Structural Database (CSD) sind heute nahezu 700 000 Strukturen hinterlegt, und sie ist ein historisch luckenloses Archiv der niedermolekularen Kristallographie. Fast 40 000 Neueintrage werden jedes Jahr verzeichnet. Da die Rontgenkristallographie ihr einhundertstes Jubilaum feiert – und das CCDC bald sein funfzigstes –, wollen wir in diesem Kurzaufsatz die Anfange des CCDC als eine offentlich geforderte Institution und seine weitere Entwicklung in eine gemeinnutzige Einrichtung nachverfolgen. Wir beschreiben die Entwicklung der CSD und ihres Softwaresystems und betrachten ihre Auswirkungen auf die Forschung in der Strukturchemie, den Materialwissenschaften sowie der Biologie und Medizin. Auserdem diskutieren wir das Finanzierungsmodell des CCDC vor dem Hintergrund der Open-Access- und Open-Data-Debatte.
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the cambridge Structural Database in retrospect and prospect
Angewandte Chemie, 2014Co-Authors: Colin R Groom, Frank H. AllenAbstract:The Cambridge Crystallographic Data Centre (CCDC) was established in 1965 to record numerical, chemical and bibliographic data relating to published organic and metal–organic crystal structures. The Cambridge Structural Database (CSD) now stores data for nearly 700 000 structures and is a comprehensive and fully retrospective historical archive of small-molecule crystallography. Nearly 40 000 new structures are added each year. As X-ray crystallography celebrates its centenary as a subject, and the CCDC approaches its own 50th year, this article traces the origins of the CCDC as a publicly funded organization and its onward development into a self-financing charitable institution. Principally, however, we describe the growth of the CSD and its extensive associated software system, and summarize its impact and value as a basis for research in Structural chemistry, materials science and the life sciences, including drug discovery and drug development. Finally, the article considers the CCDC’s funding model in relation to open access and open data paradigms.
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hydrogen bond landscapes geometry and energetics of squaric acid and its mono and dianions a cambridge Structural Database isostar and computational study
Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry, 2013Co-Authors: Frank H. Allen, Peter A Wood, Aurora J Cruzcabeza, David A BardwellAbstract:As part of a programme of work to extend central-group coverage in the Cambridge Crystallographic Data Centre's (CCDC) IsoStar knowledge base of intermolecular interactions, we have studied the hydrogen-bonding abilities of squaric acid (H(2)SQ) and its mono-and dianions (HSQ(-) and SQ(2-)) using the Cambridge Structural Database (CSD) along with dispersion-corrected density functional theory (DFT-D) calculations for a range of hydrogen-bonded dimers. The -OH and -C=O groups of H(2)SQ, HSQ(-) and SQ(2-) are potent donors and acceptors, as indicated by their hydrogenbond geometries in available crystal structures in the CSD, and by the attractive energies calculated for their dimers with acetone and methanol, which were used as model acceptors and donors. The two anions have sufficient examples in the CSD for their addition as new central groups in IsoStar. It is also shown that charge-and resonance-assisted hydrogen bonds involving H(2)SQ and HSQ(-) are similar in strength to those made by carboxylate COO- acceptors, while hydrogen bonds made by the dianion SQ(2-) are somewhat stronger. The study reinforces the value of squaric acid and its anions as cocrystal formers and their actual and potential importance as isosteric replacements for carboxylic acid and carboxylate functions.
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learning about intermolecular interactions from the cambridge Structural Database
Journal of Chemical Education, 2012Co-Authors: Gary M Battle, Frank H. AllenAbstract:A clear understanding and appreciation of noncovalent interactions, especially hydrogen bonding, are vitally important to students of chemistry and the life sciences, including biochemistry, molecular biology, pharmacology, and medicine. The opportunities afforded by the IsoStar knowledge base of intermolecular interactions to enhance the educational experience of students are summarized. Derived from experimentally determined crystal structures in the Cambridge Structural Database and Protein Data Bank, IsoStar contains geometrical and spatial information on nearly 30,000 different types of interactions in small molecules and proteins.
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new software for statistical analysis of cambridge Structural Database data
Journal of Applied Crystallography, 2011Co-Authors: Richard Sykes, Ian J Bruno, Patrick Mccabe, Frank H. Allen, Gary M Battle, Peter A WoodAbstract:A collection of new software tools is presented for the analysis of geometrical, chemical and crystallographic data from the Cambridge Structural Database (CSD). This software supersedes the program Vista. The new functionality is integrated into the program Mercury in order to provide statistical, charting and plotting options alongside three-dimensional Structural visualization and analysis. The integration also permits immediate access to other information about specific CSD entries through the Mercury framework, a common requirement in CSD data analyses. In addition, the new software includes a range of more advanced features focused towards Structural analysis such as principal components analysis, cone-angle correction in hydrogen-bond analyses and the ability to deal with topological symmetry that may be exhibited in molecular search fragments.
Antonio Frontera - One of the best experts on this subject based on the ideXlab platform.
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gallic acid dimer as a double π hole donor evidence from x ray theoretical calculations and generalization from the cambridge Structural Database
Crystal Growth & Design, 2019Co-Authors: Rafel Prohens, Dafne De Sande, Merce Fontbardia, Antonio Franconetti, Jose F Gonzalez, Antonio FronteraAbstract:In this work, we demonstrate that the centrosymmetric eight-membered supramolecular ring R22(8) that is formed upon dimerization of benzoic acids has a marked tendency to establish π–hole interactions with electron-rich atoms. We have used the Cambridge Structural Database to demonstrate the preference of carboxylic acid dimers to form donor–acceptor interactions involving π–holes located at the C atoms above and below the molecular plane. Moreover, we have carried out DFT calculations (PBE0-D3/def2-TZVP) to investigate the geometric and energetic features of these interactions and how they are affected by the substituents of the aromatic ring. Finally, as an example we report the synthesis and X-ray characterization of a solvate of gallic acid with dioxane, where two molecules of dioxane are located above and below the eight-membered supramolecular ring, forming two symmetrically equivalent O···C π–hole interactions.
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a combined theoretical and cambridge Structural Database study of π hole pnicogen bonding complexes between electron rich molecules and both nitro compounds and inorganic bromides yo2br y n p and as
Journal of Physical Chemistry A, 2014Co-Authors: Antonio Bauza, Rafael Ramis, Antonio FronteraAbstract:Quantum calculations at the DFT-D3/def2-TZVPD level of theory have been used to examine complexes between O2YBr (Y═N, P, and As) molecules and several Lewis bases, that is, NH3, H2O, and HF. The interactions of the lone pair of the ammonia, water, and hydrogen fluoride with the σ-hole and π-hole of O2YBr molecules have been considered. In general, the complexes where the Lewis base lone pair interacts with the π-hole are more favorable than those with σ-hole. The nature of the interactions has been characterized with the Bader theory of atoms in molecules (AIM). We have also studied the ability of trifluoronitromethane and nitromethane to interact with anions using their π-hole along with an analysis the Cambridge Structural Database. We have found a large number of hits that provide strong experimental support for ability of the nitryl (−NO2) group to interact with anions and Lewis bases. In some X-ray structures, the π-hole interaction is crucial in the crystal packing and has a strong influence in the ...
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halogen bonding versus chalcogen and pnicogen bonding a combined cambridge Structural Database and theoretical study
CrystEngComm, 2013Co-Authors: Antonio Bauza, David Quinonero, Pere M Deya, Antonio FronteraAbstract:In this manuscript we analyze the Cambridge Structural Database (CSD) to compare the relative importance of halogen, chalcogen and pnicogen bonding. The three interactions can be explained in terms of electrostatic effects, considering the halogen, chalcogen or pnicogen as a Lewis acid due to the presence of a sigma hole (σ-hole). We have studied the behaviour of the three interactions considering two types of Lewis bases: amines and arenes. Combining the CSD search and a comprehensive theoretical study (DFT-D3) we conclude that the halogen bonding interaction is the energetically most favourable when the electron donor is an amine. In contrast, the pnicogen bond is the most favourable if the Lewis base is benzene (pnicogen–π interaction).
Jason C Cole - One of the best experts on this subject based on the ideXlab platform.
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new insights and innovation from a million crystal structures in the cambridge Structural Database
Structural Dynamics, 2019Co-Authors: Jason C Cole, Seth B Wiggin, Francesca StanzioneAbstract:The Cambridge Structural Database (CSD) is the world's largest and most comprehensive collection of organic, organometallic, and metal-organic crystal structure information. Analyses using the data have wide impact across the chemical sciences in allowing understanding of Structural preferences. In this short review, we illustrate the more common methods by which CSD data influence molecular design. We show how more data could lead to more refined insights into the future using a simple example of trifluoromethylphenyl fragments, highlighting how with sufficient data one can build a reasonable model of geometric change in a chemical fragment with torsional rotation, and show some recent examples where the CSD has been used in conjunction with other methods to provide design ideas and more computationally tractable workflows for derivation of useful insights into Structural design.
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improved crystal structure solution from powder diffraction data by the use of conformational information
Acta Crystallographica Section A, 2018Co-Authors: Elena A Kabova, Jason C Cole, Oliver Korb, Adrian C Williams, Kenneth ShanklandAbstract:The effect of introducing conformational information to the DASH implementation of crystal structure determination from powder diffraction data is investigated using 51 crystal structures, with the aim of allowing increasingly complex crystal structures to be solved more easily. The findings confirm that conformational information derived from the Cambridge Structural Database is indeed of value, considerably increasing the chances of obtaining a successful structure determination. Its routine use is therefore encouraged.
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knowledge based conformer generation using the cambridge Structural Database
Journal of Chemical Information and Modeling, 2018Co-Authors: Jason C Cole, Patrick Mccabe, Oliver Korb, Murray G Read, Robin TaylorAbstract:Fast generation of plausible molecular conformations is central to molecular modeling. This paper presents an approach to conformer generation that makes extensive use of the information available in the Cambridge Structural Database. By using geometric distributions derived from the Cambridge Structural Database, it is possible to create biologically relevant conformations in the majority of cases analyzed. The paper compares the performance of the approach with previously published evaluations, and presents some cases where the method fails. The method appears to show significantly improved performance in reproduction of the conformations of structures observed in the Cambridge Structural Database and the Protein Data Bank as compared to other published methods of a similar speed.
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mining the cambridge Structural Database for matched molecular crystal structures a systematic exploration of isoStructurality
Crystal Growth & Design, 2017Co-Authors: Ilenia Giangreco, Jason C Cole, Elizabeth ThomasAbstract:The Cambridge Structural Database (CSD) is the world leading collection of small-molecule crystal structures and represents an invaluable resource for crystal engineers. It enables structures to be readily compared and new insights to be gained from the comparison. In order to search the Database for pairs of structures that are related by the same chemical transformation, and to systematically investigate the effect of this transformation on crystal packing, a repository of matched molecular crystal structures has been derived from the CSD. This makes it easy to find all pairs of structures differing by the same chemical change or, alternatively, all available chemical modifications to a given CSD entry. Our analysis shows one of the many possible applications of these data. An extensive, yet not exhaustive, exploration of isoStructurality across the entire CSD has been carried out with the aim of identifying packing features within crystals that maintain isoStructurality. With particular focus on termin...
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webcsd the online portal to the cambridge Structural Database
Journal of Applied Crystallography, 2010Co-Authors: Ian R Thomas, Ian J Bruno, Jason C Cole, Clare F Macrae, Elna Pidcock, Peter A WoodAbstract:WebCSD, a new web-based application developed by the Cambridge Crystallographic Data Centre, offers fast searching of the Cambridge Structural Database using only a standard internet browser. Search facilities include two-dimensional substructure, molecular similarity, text/numeric and reduced cell searching. Text, chemical diagrams and three-dimensional Structural information can all be studied in the results browser using the efficient entry summaries and embedded three-dimensional viewer.
Peter A Wood - One of the best experts on this subject based on the ideXlab platform.
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targeted classification of metal organic frameworks in the cambridge Structural Database csd
Chemical Science, 2020Co-Authors: Peyman Z Moghadam, Peter A Wood, Seth B Wiggin, Rocio Buenoperez, Xiaowei Liu, Shudong Wang, David FairenjimenezAbstract:Large-scale targeted exploration of metal–organic frameworks (MOFs) with characteristics such as specific surface chemistry or metal-cluster family has not been investigated so far. These definitions are particularly important because they can define the way MOFs interact with specific molecules (e.g. their hydrophilic/phobic character) or their physicochemical stability. We report here the development of algorithms to break down the overarching family of MOFs into a number of subgroups according to some of their key chemical and physical features. Available within the Cambridge Crystallographic Data Centre's (CCDC) software, we introduce new approaches to allow researchers to browse and efficiently look for targeted MOF families based on some of the most well-known secondary building units. We then classify them in terms of their crystalline properties: metal-cluster, network and pore dimensionality, surface chemistry (i.e. functional groups) and chirality. This dynamic Database and family of algorithms allow experimentalists and computational users to benefit from the developed criteria to look for specific classes of MOFs but also enable users – and encourage them – to develop additional MOF queries based on desired chemistries. These tools are backed-up by an interactive web-based data explorer containing all the data obtained. We also demonstrate the usefulness of these tools with a high-throughput screening for hydrogen storage at room temperature. This toolbox, integrated in the CCDC software, will guide future exploration of MOFs and similar materials, as well as their design and development for an ever-increasing range of potential applications.
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automated oxidation state assignment for metal sites in coordination complexes in the cambridge Structural Database
Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry, 2019Co-Authors: Matthew Reeves, Peter A Wood, Simon ParsonsAbstract:The Cambridge Structural Database (CSD) currently contains over 400 000 transition-metal-containing entries, however many entries still lack curated oxidation-state assignments. Surveying and editing the remaining entries would be far too resource- and time-intensive to be carried out manually. Here, a highly reliable automated workflow for oxidation-state assignment in transition-metal coordination complexes via CSD Python API (application programming interface) scripts is presented. The strengths and limitations of the bond-valence sum (BVS) method are discussed and the use of complementary methods for improved assignment confidence is explored. In total, four complementary techniques have been implemented in this study. The resulting workflow overcomes the limitations of the BVS approach, widening the applicability of an automated procedure to more CSD entries. Assignments are successful for 99% of the cases where a high consensus between different methodologies is observed. Out of a total number of 54 999 unique metal atoms in a test dataset, the procedure yielded the correct oxidation state in 47 072 (86%) of cases.
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development of a cambridge Structural Database subset a collection of metal organic frameworks for past present and future
Chemistry of Materials, 2017Co-Authors: Peyman Z Moghadam, Suzanna C Ward, Peter A Wood, Seth B Wiggin, Andi Tao, Andrew G P Maloney, David FairenjimenezAbstract:We report the generation and characterization of the most complete collection of metal–organic frameworks (MOFs) maintained and updated, for the first time, by the Cambridge Crystallographic Data Centre (CCDC). To set up this subset, we asked the question “what is a MOF?” and implemented a number of “look-for-MOF” criteria embedded within a bespoke Cambridge Structural Database (CSD) Python API workflow to identify and extract information on 69 666 MOF materials. The CSD MOF subset is updated regularly with subsequent MOF additions to the CSD, bringing a unique record for all researchers working in the area of porous materials around the world, whether to perform high-throughput computational screening for materials discovery or to have a global view over the existing structures in a single resource. Using this resource, we then developed and used an array of computational tools to remove residual solvent molecules from the framework pores of all the MOFs identified and went on to analyze geometrical and ...
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hydrogen bond landscapes geometry and energetics of squaric acid and its mono and dianions a cambridge Structural Database isostar and computational study
Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry, 2013Co-Authors: Frank H. Allen, Peter A Wood, Aurora J Cruzcabeza, David A BardwellAbstract:As part of a programme of work to extend central-group coverage in the Cambridge Crystallographic Data Centre's (CCDC) IsoStar knowledge base of intermolecular interactions, we have studied the hydrogen-bonding abilities of squaric acid (H(2)SQ) and its mono-and dianions (HSQ(-) and SQ(2-)) using the Cambridge Structural Database (CSD) along with dispersion-corrected density functional theory (DFT-D) calculations for a range of hydrogen-bonded dimers. The -OH and -C=O groups of H(2)SQ, HSQ(-) and SQ(2-) are potent donors and acceptors, as indicated by their hydrogenbond geometries in available crystal structures in the CSD, and by the attractive energies calculated for their dimers with acetone and methanol, which were used as model acceptors and donors. The two anions have sufficient examples in the CSD for their addition as new central groups in IsoStar. It is also shown that charge-and resonance-assisted hydrogen bonds involving H(2)SQ and HSQ(-) are similar in strength to those made by carboxylate COO- acceptors, while hydrogen bonds made by the dianion SQ(2-) are somewhat stronger. The study reinforces the value of squaric acid and its anions as cocrystal formers and their actual and potential importance as isosteric replacements for carboxylic acid and carboxylate functions.
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new software for statistical analysis of cambridge Structural Database data
Journal of Applied Crystallography, 2011Co-Authors: Richard Sykes, Ian J Bruno, Patrick Mccabe, Frank H. Allen, Gary M Battle, Peter A WoodAbstract:A collection of new software tools is presented for the analysis of geometrical, chemical and crystallographic data from the Cambridge Structural Database (CSD). This software supersedes the program Vista. The new functionality is integrated into the program Mercury in order to provide statistical, charting and plotting options alongside three-dimensional Structural visualization and analysis. The integration also permits immediate access to other information about specific CSD entries through the Mercury framework, a common requirement in CSD data analyses. In addition, the new software includes a range of more advanced features focused towards Structural analysis such as principal components analysis, cone-angle correction in hydrogen-bond analyses and the ability to deal with topological symmetry that may be exhibited in molecular search fragments.