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 880

• Job completed successfully
• Versions GRADE 1.2.7 <February 19 2014> , MOGUL 1.6(RC5), CSD as535be, with quantum mechanics RM1
• 880 PDB chemical component details from RCSB Ligand Expo , RCSB ligand summary , EBI PDBeChem
• 880.grade_PDB_ligand.cif - cif restraint dictionary
• 880.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.
880.gradeserver_all.tgz - gzipped tar ball containing all results
• recognise-compound thinks:
  

  Input is known PDB chemical component "cyclohexyl-{4-[5-(3,4-dichlorophenyl)-2-piperidin-4-yl-3-propyl-3h-imidazol-4-yl]-pyrimidin-2-yl}amine" with three-letter code 880

• 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 880.grade_PDB_ligand.cif:
  

   Number of restraints found:
   Bond lengths
       lengths/sigmas set by mogul                38
       bonds to hydrogen set to neutron values    34
       bonds lengths set by partial QM             1
   Bond Angles
       angles/sigmas set by mogul                 41
       non-H angles set by partial QM             13
       H bond angles set by partial QM            81
   Trigonal planes (atoms bonded to 3 others that are held flat)
       trigonal atoms from 3 mogul bond angles     5
       atoms NOT trigonal from 3 mogul angles      0
       trigonal atoms from partial QM             10
       atoms not trigonal from partial QM          1
   Torsions and 1-4 planes                                      
       bonds where mogul states cis/trans          1
       bonds mogul indicates flat                  0
       bonds mogul indicates 3-fold staggered      1
       bonds mogul indicates not flat              0
       in flat 5/6 membered rings after PQM       17
       other flat bonds after partial QM           0
       sp3-sp3 set 3-fold staggered by QM         11
       All other torsions (unrestrained)           7
  

• Job queued for 2 secs and grade ran for 130 wallclock secs ( 0.01 usr 0.01 sys + 120.86 cusr 5.61 csys = 126.49 CPU)
• Run completed Wed May 28 20:08:38 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.