Grade Web Server http://grade.globalphasing.org

• Grade Web Server version Release v1.101 Feb 19 2014
• Grade Web Server conditions of use
• Run by: Oliver Smart osmart@globalphasing.com 87.114.133.240
• Command run by server:
  

  grade_PDB_ligand 468

• Job completed successfully
• Versions GRADE 1.2.7 <February 19 2014> , MOGUL 1.6(RC5), CSD as535be, with quantum mechanics RM1
• 468 PDB chemical component details from RCSB Ligand Expo , RCSB ligand summary , EBI PDBeChem
• 468.grade_PDB_ligand.cif - cif restraint dictionary
• 468.grade_PDB_ligand.pdb - ideal coordinates in PDB format
• grade_log.txt - grade log file
• obprop.txt - Open Babel obprop results for output pdb file.
• 468.gradeserver_all.tgz - gzipped tar ball containing all results
• recognise-compound thinks:
  

  Input is known PDB chemical component "(3s)-n-(3-chloro-2-methylphenyl)-1-cyclohexyl-5-oxopyrrolidine-3-carboxamide" with three-letter code 468

• Open Babel 2D diagram:
  
• PyMOL pictures with atom labels:
noH-view1 noH-view2 noH-view3 withH-view1 withH-view2 withH-view3


• Useful information from comments at top of 468.grade_PDB_ligand.cif:
  

   Number of restraints found:
   Bond lengths
       lengths/sigmas set by mogul                25
       bonds to hydrogen set to neutron values    23
       bonds lengths set by partial QM             0
   Bond Angles
       angles/sigmas set by mogul                 29
       non-H angles set by partial QM              6
       H bond angles set by partial QM            55
   Trigonal planes (atoms bonded to 3 others that are held flat)
       trigonal atoms from 3 mogul bond angles     4
       atoms NOT trigonal from 3 mogul angles      0
       trigonal atoms from partial QM              6
       atoms not trigonal from partial QM          0
   Torsions and 1-4 planes                                      
       bonds where mogul states cis/trans          1
       bonds mogul indicates flat                  2
       bonds mogul indicates 3-fold staggered      0
       bonds mogul indicates not flat              0
       in flat 5/6 membered rings after PQM        6
       other flat bonds after partial QM           1
       sp3-sp3 set 3-fold staggered by QM          6
       All other torsions (unrestrained)           8
  

• Job queued for 1 secs and grade ran for 57 wallclock secs ( 0.00 usr 0.01 sys + 49.17 cusr 5.13 csys = 54.31 CPU)
• Run completed Thu May 29 19:28:23 2014

For help and further details see grade section on the BUSTER wiki.

Please email buster-develop@globalphasing.com with any problems, queries or suggestions.