ID Instance Status Selection Details Score

LIG A505 LIGAND CODE MATCHED XYZ

XYP A503 CLOSE MATCH

XYP A504 NO MATCH

MAN A500 PASSED

GLC A501 PASSED

NAG A502 PASSED

2010/09/01 JY1

Batch Search SummaryQuery type: Default

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Instance Search

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Rerun BatchInput new parameters here

When you change parameters, those will be displayed here

Input your notes here

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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?

XX

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

0AI 98

1NA 97

5AX 96

A2G 96

Model CC

Input new parameters here

Input your notes here

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Show Hydrogens

Show Lables

Create new ligand

Select Extracted Ligands: XYP LIG

XYP_B_287 ID Instance StatusSelection for force

match, edit or create new

XYP A503 CLOSE MATCH

XYP A504 NO MATCH

More XYP ligands to be displayed on this page with scroll bar

Selected Ligand instances Selected Ligand instances

Search results for 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

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Ligand Module:Level 2 – Instance Search UI --> Drilldown to Detailed Report I

COMPARE

3

Search Result SummaryResult 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

ID Formula Name Score (%)

Selection for compariaon

0AI C9 H15 N O7 methyl 2-(acetylamino)-2-deoxy-alpha-D-galactopyranosiduronic acid 98

1NA C9 H17 N O6 N-ACETYL-O-METHYL-D-GLUCOSAMINE 97

5AX C8 H15 N O5 2-(ACETYLAMINO)-1,5-ANHYDRO-2-DEOXY-D-GLUCITOL 96

A2G C8 H15 N O6 N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE 96

BGN C10 H19 N O6 N-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

APC C5 N ABG C6 NAPC C4 R ABG C5 RAPC O4 N ABG O3 NAPC C3 S ABG C4 SAPC O3 N ABG O4 NAPC C2 R ABG C2 RAPC O2 N ABG O2 NAPC C1 S ABG C1 R

3/22 MZ GS CS

Formula: C11 H19 N1 O9

Name: Adenosyl …Formula: C11 H19 N1 O9

Name: Diphospho…

Author’s 2D & 3D viewAuthor’s 2D & 3D view

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Ligand Module:Level 3 – Edit UI – Structure Edit

Model CCView 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 UndoModify 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?

Version Date Annotator SIte Modify type Modify details

1 1997-03-01 CS RCSB Linking type

2 2003-04-01 MZ RCSB parent

Ligand Module:Level 3 – Edit UI – Text Edit (collapsed)

Model CCView 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

Version Date Annotator SIte Modify type Modify details

1 1997-03-01 CS RCSB Linking type

2 2003-04-01 MZ RCSB parent

Modify exist ligand

Ligand Module:Level 3 – Edit UI – Text Edit (expanded)

Model CCView 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 UndoInput 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 #9 1.65 0.229 -3.721

Add 2D and 3D view with mouse over functions

Version Date Annotator SIte Modify type Modify details1 1997-03-01 CS RCSB Linking type

2 2003-04-01 MZ RCSB parent

ID NAGName N-ACETYL-D-GLUCOSAMINE Type D-SACCHARIDE

PDBx type ATOMS Formula C8 H15 N O6Parent

SynonymsFormal charge

Ambiguous flagCreation dateID replaced by

ID replacesOne letter code

Subcomponent list

Atom name Element type Charge Aromatic flag Leaving atom flag chiral center flag Subcomponent residue name Linking atom flag

C1 C 0 Pull down Y/N Pull down Y/N Pull down R,S,N Pull down N-terminal, C-terminal, central

C2 C 0 Pull down Y/N Pull down Y/N Pull down R,S,N Pull down N-terminal, C-terminal, central

C3 C 0 Pull down Y/N Pull down Y/N Pull down R,S,N Pull down N-terminal, C-terminal, central

Atom 1 Atom 2 Bond order Aromatic flag

C1 C2 Pull down SING/DOUB Pull down Y/N

C1 O1 Pull down SING/DOUB Pull down Y/N

C2 C3 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 codeLigand match XXX: Exact match for all atom types, number of atoms and connectivity except the 3 letter codeClose match: exact match for all atom types and connectivity, but not the number of atoms (query could have less atoms) nor the chiralityNo 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 nomenclatureModified nucleic acids should follow standard nucleic acid nomenclatureAll sugars should follow standard sugars nomenclatureOthers 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.