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BIOVIA Chemical Representation Guide

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BIOVIA Chemical Representation Guide CHEMICAL REPRESENTATION GUIDE 2017 Copyright Notice ©2016 Dassault Systèmes. All rights reserved. 3DEXPERIENCE, the Compass icon and the 3DS logo, CATIA, SOLIDWORKS, ENOVIA, DELMIA, SIMULIA, GEOVIA, EXALEAD, 3D VIA, BIOVIA and NETVIBES are commercial trademarks or registered trademarks of Dassault Systèmes or its subsidiaries in the U.S. and/or other countries. All other trademarks are owned by their respective owners. Use of any Dassault Systèmes or its subsidiaries trademarks is subject to their express written approval. Acknowledgments and References To print photographs or files of computational results (figures and/or data) obtained using BIOVIA software, acknowledge the source in an appropriate format. BIOVIA may grant permission to republish or reprint its copyrighted materials. Requests should be submitted to BIOVIA Support, either through electronic mail to [email protected] , or in writing to: BIOVIA Support 5005 Wateridge Vista Drive, San Diego, CA 92121 USA (Sgroups) Contents Data Sgroups 29 Abbreviated Structures 29 Overview 1 Multiple Groups 29 Audience for this Guide 1 Other Chemical Sgroups 30 Prerequisite Knowledge 1 Structural Uncertainty 30 Related BIOVIA Documentation 1 Star Atoms (*) 30 Molecule Representation 3 No-Structures 31 Substances, Structures and Fragments 3 Reaction Representation 32 The BIOVIA Periodic Table 3 Introduction 32 Atom Properties 3 Reaction Mapping 32 Charges, Radicals and Isotopes 3 Mapping Reactions Automatically 33 Valences and Implicit Hydrogens 4 Mapping Reactions Manually 34 Default Valences 4 Stereoconfiguration Atom Properties in Explicit Valence 5 Mapped Reactions 35 Rules for Calculation of Valence and Implicit Properties of Bonds in Mapped Reactions 35 Hydrogen 5 Simple Bond Properties 35 Bond Types 5 Combined Bond Properties 36 Aromaticity 7 Example: Ambiguity in the Fate of Reacting Tautomers 8 Atoms and Bonds 36 Salts 8 Example: Multiple Fates of Bonds in Tetrahedral Stereochemistry 9 Products 37 Stereogroup Information in Reactants and Grouping Related Stereogenic Centers 9 Products 37 Structures with One Stereogenic Center 10 Markush (Rgroup) Structures 39 Structures with Multiple Stereogenic Centers 11 Library Representation 39 Chiral Labels 13 The Root Structure 40 Rules for Unambiguous Representation of Tetrahedral Stereochemistry 15 Rgroups and Rgroup Members 41 Stereochemistry of Sulfur 16 Nested Rgroups 41 Original Accelrys Representation of One Attachment Point 43 Tetrahedral Stereochemistry 16 Two Attachment Points 43 Examples of Stereogroups 17 Unconnected Rgroup Atom 44 Example 1: Racemic Mixture 17 Null Members 45 Example 2: Acquiring Increasing Amounts of Markush Structures Differ From Markush Information on the Stereochemistry of a Queries 46 Sample 18 Enumeration of Markush Structures 46 Example 3: A Mixture of Epimers in a Scaffold-based Enumeration 46 Reaction Product 21 Reaction-based Enumeration 47 Stereochemistry of Allenes and Biaryls 24 Rgroup Decomposition 47 Higher Order Stereochemistry 25 Homology Groups 50 Square Planar 25 About Homology Groups 50 Trigonal Bipyramidal 25 Creating Substructure Search (SSS) Queries 50 Octahedral 26 Limitations 51 Limitations and Restrictions 27 Biopoloymer Representation 52 Use in Queries 27 Configuring Databases for Biopolymer Cis and Trans Stereochemistry 27 Registration and Searching 52 Meso Compounds 27 Condensed Representation of Biopolymers 52 Spiro Compounds 28 Hybrid Representation 52 Chemical and Data Substance Groups 28 *Atoms Alone 52 Implementing Subsequence Search for Full Pseudoatoms Alone 53 Structure Representations 68 *Atoms and Pseudoatoms 54 Related Documentation for BIOVIA Draw 68 Summary of Biopolymer Structure Mixture Representation 69 Conventions 54 Ordered and Unordered Mixtures 69 Compatibility of Sequences Created in Using * atoms for Unspecified Structures in ISIS/Draw 55 Mixtures 69 ISIS/Draw Sequences Use the Full Structure Examples of Mixtures 70 Convention 55 Unordered Mixtures 70 ISIS/Draw Residue Templates Lack Explicit Reaction Product 70 Attachment Atoms 55 Mixture of Stereoisomers 70 Stereochemistry of ISIS/Draw Residue Template 55 Aspirin Tablet 71 Compatibility of Condensed and Full Ordered Mixture 72 Structure Conventions 56 Polymer Representation 73 Required Sgroup Fields for Biopolymer Introduction to Polymer Representation 73 Representation 56 Structure-based and Source-based Sgroup Field for Identifying Attachment Representation 73 Atoms 56 Polymer Bracket Types 74 Sgroup Field for *Atom Representation 57 Structural Repeating Unit (SRU) Brackets 74 Structures Used in Biopolymer Representation 57 Monomer Brackets (mon) 74 Biopolymer Residues 58 Mer Brackets (mer) 74 Single-attachment Groups 58 Copolymer Brackets (co) 74 Protecting Groups 58 Additional Polymer Brackets 75 PEG Molecules 58 Cyclization and Phase Shifting 75 Special Features of Abbreviated Structures 58 Polymer Repeat Pattern 76 Template Format for Biopolymer Residues 59 Polymers with Two Crossing Bonds 76 Abbreviation Class 59 Ladder-type Polymers 77 Terminal Leaving Groups 60 Polymers with Three or More Brackets 79 Order and Bond Matching Attributes of Attachment Atoms 61 Polymer End Groups 80 Why Are Representation Conventions Attachment Atoms on Reactive Chains 61 Important? 80 Explicit Hydrogen Leaving Groups on Guidelines for Graphical Representation of Attachment Atoms of Reactive Chains 62 Polymers 81 Explicit Hydrogen Leaving Groups on Structure-based and Source-based Histidine 64 Representation 81 Molfile Features in Biopolymer Templates 65 Stereoregularity in Polymers 82 Abbreviation Class (SCL) 65 Using Attached Data in Polymer Sgroup Subscript (SMT) 65 Representation 82 Abbreviation Attachment Atom (SAP) 65 Required Attached Data for Polymer Creating and Enforcing Conventions for Representation 82 Biopolymer Representation 66 Polymer or Copolymer Type 82 Choose One Convention for Each Chemical Stereoregularity 82 Entity 66 Guidelines for Defining Additional Attached Use Standard Abbreviations 66 Data 83 Subsequence Searching in Isentris Applications 67 Examples of Structure-Based Representation 84 Subsequence Search Differs from Regular Homopolymers 84 Substructure Search 67 Simple Homopolymers 84 BIOVIA Draw Programming Interface (API) for subsequence search 68 Stereoregularity 85 Ladder-type Polymers 85 Irregular Homopolymers 85 Radicals (RAD) 107 Alternating and Periodic Polymers 86 Valence (VAL) 107 Statistical, Random, and Unspecified Substance Groups (Sgroups) 107 Copolymers 87 Attached Data (DAT) 107 Unspecified Copolymers 87 Polymer End Groups (end) 107 Random Copolymers 88 Mixtures (MIX) 108 Statistical Copolymers 89 Monomer/SRU Uniqueness (MSU) 108 Regular Block Copolymers 89 Polymers (POL) 109 Ordered Diblock 89 Polymer Type (TYP) 109 Block Copolymer with Junction Unit 90 Dependencies Between Switches 109 Segmented Block Copolymers 90 Examples of the Interactivity of Flexmatch Star Block Copolymers 92 Switches 109 Irregular Block Copolymers 92 Sulfones 109 Chemically Modified Polymers 93 Sulfoxides 110 Graft Polymers and Copolymers 94 Thiocarboxylic Acid Salts 110 Single Graft at a Known Site 95 Organometallic Complexes 110 Mixed Graft at a Known Site 95 Flexmatch Search of Structures with Cross-linked Polymers 95 Tetrahedral Stereochemistry 112 Examples of Source-based Representation 97 Absolute Configuration 114 Guidelines for Source-based Representation 97 Relative Stereoconfigurations (OR groups) 114 Homopolymers 98 Example 1 115 Alternating and Other Periodic Polymers 98 Example 2 115 Copolymers from Monomers that Do Not Example 3 116 Homopolymerize 99 Example 4 118 Statistical, Random, and Unspecified Example 5 118 Copolymers 99 Example 6 120 Unspecified Copolymers 99 Mixtures of Relative Stereoconfigurations Random Copolymers 100 (AND groups) 120 Statistical Copolymers 101 Flexmatch Search of Polymers 122 Block Copolymer 101 Useful Combinations of Flexmatch Switches 124 Exact Search (Flexmatch) 103 Exact Match/As Drawn 124 Flexmatch Switches 103 Exact Match/As Drawn plus Tautomers 125 How to Specify Switches 103 Tetrahedral Stereochemistry 125 Description of Switches 104 Cis/Trans Geometric Stereochemistry 125 Isotopes (MAS) 104 Exact Match/As Drawn plus Stereoisomers 126 Bonds (BON, STE, TAU) 104 Tetrahedral Stereochemistry 126 Bond (BON) 104 Cis and Trans Stereochemistry 127 Stereochemistry (STE) 104 Original Tautomer Search 127 Tautomer Bonds (TAU) 105 Exact Match/As Drawn plus Salts 127 Salts and Parent Compounds (CHA, ION, The Least Restrictive Flexmatch Switches 129 FRA, SAL) 105 Exact Match/As Drawn Polymer Search 129 Charge (CHA and ION) 105 Sourced-based and Structure-based Fragments (FRA) 106 Polymer Search 129 Hydrogen Count (HYD) 106 Copolymer Search 130 Salts (SAL) 106 Substructure Search 131 Alternative Structure Representations (MET, Definition of Substructure Search 131 RAD, VAL, IgnoreChargesInPiSystems) 106 Query Features on Atoms and Bonds 132 Metal Bonds (MET) 106 Allowing or Excluding Specific Atoms 133 Atom Query Feature: Any Atom (A) 133 Bond Query Feature: Single/Aromatic Atom Query Feature: Heteroatoms (Q) 133 Bond 144 Atom Query Feature: Metal Atom (M) 133 Bond Query Feature: Double/Aromatic Bond 144 Atom Query Feature: Any Atom Including Hydrogen (R) 133 Bond Topology 145 Atom Query Feature: Halogen Atom (X) 134 Bond Query Feature: Ch 145 Atom Query Feature: List 134 Bond Query Feature: Rn 145 Atom Query Feature: Not List 134 Bond Query Feature: Cis/Trans Geometric Double Bonds as Drawn 145 Atom Query Feature: H0 135 How Compounds are Perceived
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