## fullatom protein N(4)-methylation patch for histidine ## By Andy M. Chen, July 2009, achen39@jhu.edu ## Note: This patch does work for regular HIS. However, it will result in a "failed patch" ## error message for HIS_D due to the shifted locations of the hydrogens. ## a possible way to fix this issue is to make HIS_D a TAUTOMER variant of HIS ## so that two patches could be created, one for HIS and one for HIS_D ## (with the selector using the TAUTOMER variant to control which patch goes where). ## But as things now stand, there's no way to patch only HIS without affecting HIS_D. ## Hence, the patch is currently commented out (as of 7/31/2009). NAME phosphorylated TYPES PHOSPHORYLATION ## general requirements for this patch BEGIN_SELECTOR PROPERTY PROTEIN NAME3 HIS DHI AA HIS NOT VARIANT_TYPE PHOSPHORYLATION #NOT VARIANT_TYPE PROTONATED #NOT VARIANT_TYPE DEPROTONATED END_SELECTOR ## now we search for a case that matches the residue, take the first one ## so put generic case last BEGIN_CASE #### HIS_D ########################################## BEGIN_SELECTOR PROPERTY TAUTOMER #only on HIS_D END_SELECTOR SET_IO_STRING NEP H SET_INTERCHANGEABILITY_GROUP NEP ## these are the operations involved DELETE_ATOM HD1 ADD_ATOM P Phos X 1.50 ## Best guess from the small molecule ligand params file generator molfile_to_params.py ADD_ATOM O1P OOC OC -0.78 ## The charge is taken from the free oxygen atoms of the phosphate backbone in DNA residues ADD_ATOM O2P OOC OC -0.78 ADD_ATOM O3P OOC OC -0.78 ADD_BOND NE2 P ADD_BOND P O1P ADD_BOND P O2P ADD_BOND P O3P ## SET_ICOOR P -179.16 66.09 1.615 NE2 CE1 ND1 SET_ICOOR O1P -88.30 72.49 1.597 P NE2 CD2 SET_ICOOR O2P 33.10 72.49 1.597 P NE2 CD2 SET_ICOOR O3P 151.70 72.49 1.597 P NE2 CD2 ADD_PROPERTY CHARGED ## For the phosphate group END_CASE BEGIN_CASE ### THE GENERAL CASE ########################################## SET_IO_STRING NEP H SET_INTERCHANGEABILITY_GROUP NEP ## these are the operations involved DELETE_ATOM HE2 ADD_ATOM P Phos X 1.50 ## Best guess from the small molecule ligand params file generator molfile_to_params.py ADD_ATOM O1P OOC OC -0.78 ## The charge is taken from the free oxygen atoms of the phosphate backbone in DNA residues ADD_ATOM O2P OOC OC -0.78 ADD_ATOM O3P OOC OC -0.78 ADD_BOND NE2 P ADD_BOND P O1P ADD_BOND P O2P ADD_BOND P O3P ## SET_ICOOR P -179.16 66.09 1.615 NE2 CE1 ND1 SET_ICOOR O1P -88.30 72.49 1.597 P NE2 CD2 SET_ICOOR O2P 33.10 72.49 1.597 P NE2 CD2 SET_ICOOR O3P 151.70 72.49 1.597 P NE2 CD2 ADD_PROPERTY CHARGED ## For the phosphate group END_CASE