IDInstanceStatusSelectionDetailsScore LIGA505 LIGAND CODE MATCHED XYZ XYPA503CLOSE MATCH XYPA504NO MATCH MANA500PASSED GLC A501 PASSED NAG A502 PASSED 2010/09/01 JY1 Batch Search Summary Query type: Default Show Details Instance Search Save Rerun Batch Input new parameters here When you change parameters, those will be displayed here Input your notes here Show Details New window will pop-up with log file; Details are to be discussed. Ligand Module: Level 1- Batch Search Report (pre-searched) Help Table is sorted by status (order: no match, close match, ligand code matched XXX, passed), then by 3 letter code Passed: Exact match for all atom types, number of atoms, connectivity and 3 letter code Ligand match XXX: Exact match for all atom types, number of atoms and connectivity except the 3 letter code Close match: exact match for all atom types and connectivity, but not the number of atoms (query could have less atoms) nor the chirality No match: none of above, treat as a new ligand. Capture processing details in proc cycle Finish Save and come back later Save and complete ligand module Rerun Batch Create new ligand Upon closing window browser from the top right corner, tool should pop up a window and provide 3 options before closing window: Save? Cancel? No save? X X Batch Search: Automatically search all ligand instances in an entry against CCD/PRD and report the results before annotators begin annotation. Instance search: Annotators review and select instances that are failed from batch search (not passed) and perform search with different parameters or force to pass (force match)

2 Level 2- Instance Search UI Run Global Split/Merge Group all the ligands that have the same 3 letter Force Match ID Score (%) Selection for comparison 0AI98 1NA 97 5AX96 A2G 96 Model CC Input new parameters here Input your notes here COMPARE Show Hydrogens Show Lables Create new ligand Select Extracted Ligands: XYP LIG XYP_B_287 IDInstanceStatus Selection for force match, edit or create new XYPA503 CLOSE MATCH XYPA504NO MATCH More XYP ligands to be displayed on this page with scroll bar Selected Ligand instances Search results for Ligand instances XYP_B _287 Note: Using the above table, you can select more than one instances for force match. Run Instance search Note: Have drop down options for table or sketch Save Undo

Ligand Module: Level 2 – Instance Search UI --> Drilldown to Detailed Report I COMPARE 3 Search Result Summary Result count: 23, top 5 shown Query file: NAG L 741 Query type: Close (formula bounded) Target name: 2-(acetylamino)-1,5-anhydro-2-deoxy-D-glucitol Target formula: C8 H15 N O5 Authors Name: 1,5-anhydro-2-(acetylamino)-2-deoxy-D-glucitol Authors Formula: C8 H15 N O5 IDFormulaName Score (%) Selection for compariaon 0AIC9 H15 N O7 methyl 2-(acetylamino)-2-deoxy-alpha-D-galactopyranosiduronic acid 98 1NAC9 H17 N O6N-ACETYL-O-METHYL-D-GLUCOSAMINE 97 5AXC8 H15 N O52-(ACETYLAMINO)-1,5-ANHYDRO-2-DEOXY-D-GLUCITOL96 A2GC8 H15 N O6N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE 96 BGNC10 H19 N O6N-BUTANOYL-2-AMINO-2-DEOXY-GLUCOPYRANOSIDE 95 dictionary link to subject link to comparative report Scoring algorithm to be discussed SEE ALL Force Match XYP_B _287 Save Undo

Ligand Module: Level 2 – Instance Search UI --> Drilldown to Detailed Report II: Comparative output 4 Interactive atom-level mapping including stereo- chemistry. Clicking on the atom in the table will highlight the atom in the 3D graph and vice versa (on all instances). 2D and 3D side- by-side comparison Author Query Subject (deposited info)(model coordinates)(ideal coordinates) FORCE MATCH CREATE NEW LIGAND APCC5 NABGC6 N APCC4 RABGC5 R APCO4 NABGO3 N APCC3 SABGC4 S APCO3 NABGO4 N APCC2 RABGC2 R APCO2 NABGO2 N APCC1 SABGC1 R 3/22 MZ GS CS Formula: C11 H19 N1 O9 Name: Adenosyl … Formula: C11 H19 N1 O9 Name: Diphospho… Author’s 2D & 3D view Save Undo

Ligand Module: Level 3 – Edit UI – Structure Edit Model CC View report or Chemical mmCIF file View report View CC file Add to CVS Note: automatically validate and check for duplicated ligands before adding to CVS Save Undo Modify exist ligand Input ligand 3 letter code Reconcile and check for duplicate ligands, the newly created ligand must be available for search immediately The tool should check for 3 letter code. If the code is unique to the dictionary, it will retain the 3 letter code. If the code already exists in the dictionary, the tool will automatically assign a unique 3 letter code. Should there be a hard coded black list for bad ligand codes? VersionDateAnnotatorSIteModify typeModify details CSRCSBLinking type MZ RCSB parent

Ligand Module: Level 3 – Edit UI – Text Edit (collapsed) Model CC View report or Chemical mmCIF file View report View CC file Add to CVS Note: automatically validate and check for duplicated ligands before adding to CVS Save Undo Input ligand 3 letter code Note: model database code should be automatically generated Note: Type and NDB type should be updated automatically if parent info is provided VersionDateAnnotatorSIteModify typeModify details CSRCSBLinking type MZ RCSB parent Modify exist ligand

Ligand Module: Level 3 – Edit UI – Text Edit (expanded) Model CC View report or Chemical mmCIF file View report View CC file Add to CVS Note: automatically validate and check for duplicated ligands before adding to CVS Save Undo Input ligand 3 letter code Note: when save button clicked, check parent and linking type, then automatically update atom names again Allow add/delete rows Mouse over function [SIA]1:A.C2 # Add 2D and 3D view with mouse over functions VersionDateAnnotatorSIteModify typeModify details CSRCSBLinking type MZRCSBparent IDNAG NameN-ACETYL-D-GLUCOSAMINE TypeD-SACCHARIDE PDBx typeATOMS FormulaC8 H15 N O6 Parent Synonyms Formal charge Ambiguous flag Creation date ID replaced by ID replaces One letter code Subcomponent list Atom nameElement typeChargeAromatic flagLeaving atom flagchiral center flagSubcomponent residue nameLinking atom flag C1C0Pull down Y/N Pull down R,S,NPull down N-terminal, C-terminal, central C2C0Pull down Y/N Pull down R,S,NPull down N-terminal, C-terminal, central C3C0Pull down Y/N Pull down R,S,N Pull down N-terminal, C-terminal, central Atom 1Atom 2Bond orderAromatic flag C1C2 Pull down SING/DOUB Pull down Y/N C1O1 Pull down SING/DOUB Pull down Y/N C2C3 Pull down SING/DOUB Pull down Y/N Modify exist ligand

1. At deposition- validate atom name against element type to resolve the shifted column issue, for example chlorine vs carbon, carbon vs calcium 2. Instance search UI will provide command line for parameter change, no graph edit tool required. 3. Close match is defined as exact match for all atom types and connectivity, but not the number of atoms (query could have less atoms) nor the chirality. Chirality is relaxed so that it can find all the possible stereochemistry and rank the order (scoring) by the best match of stereochemistry. Definition of status is defined as below: Passed: Exact match for all atom types, number of atoms, connectivity and 3 letter code Ligand match XXX: Exact match for all atom types, number of atoms and connectivity except the 3 letter code Close match: exact match for all atom types and connectivity, but not the number of atoms (query could have less atoms) nor the chirality No match: none of above, treat as a new ligand. 4. Score: it should be based on the # of missing atoms and # of matched chiral centers. Annotators suggest software team to consult with Kim/Terry on this. In the mean time Guarav will look for someone to consult with CCDC.

5. Atom nomenclature: Jasmine discussed w/ Jawahar after Kim’s visit at RCSB that the atom nomenclature should be standardized as below when creating new ligands: Modified amino acids should follow standard amino acid nomenclature Modified nucleic acids should follow standard nucleic acid nomenclature All sugars should follow standard sugars nomenclature Others should begin with atom type followed by number, for example, C1, C2, CL1, etc instead of CAA, CAB, CLA, etc. The system can recognize the first 3 by looking for parent residue or linking type (whether it is peptide linking or nucleotide linking or saccharide linking). 6. Relax chiral center for close match: It is recommended to search based on 3 letter code first, if no match found, then look for possible stereo isomers. This is based on the work practice that most of the sugars have wrong chirality in the coordinates. If 3 letter code match, however one or more of the chiral centers is (are) flat, it should report as close match and state the discrepancy, for example, planar found at C1 center. 7. Please note that request of new cif tokens are added to the CCD to identify N- terminal, or C-terminal or central heavy atom. This is for calculate the distance on neighboring residues when there is a break in the coordinates where C or N atoms may not be observed.