## fullatom protein phosphorylation patch for serine ## By Andy M. Chen, June 2009, achen39@jhu.edu NAME phosphorylated TYPES PHOSPHORYLATION ## general requirements for this patch BEGIN_SELECTOR PROPERTY PROTEIN NAME3 SER DSE HAS_ATOMS HG OG NOT VARIANT_TYPE PHOSPHORYLATION ## Don't phosphorylate a residue twice END_SELECTOR ## now we search for a case that matches the residue, take the first one ## so put generic case last BEGIN_CASE ### THE GENERAL CASE ########################################## SET_IO_STRING SPF S SET_INTERCHANGEABILITY_GROUP SPF ## these are the operations involved ADD_ATOM P Phos P 1.50 ## Best guess from the small molecule ligand params file generator molfile_to_params.py ADD_ATOM O1P OOC ON3 -0.78 ## The charge is taken from the free oxygen atoms of the phosphate backbone in DNA residues ADD_ATOM O2P OOC ON2 -0.78 ADD_ATOM O3P OOC ON3 -0.78 ADD_ATOM C1 CH2 CT2 -0.17 ADD_ATOM C2 CH1 CT1 -0.08 ADD_ATOM C3 CH3 CT3 -0.26 ADD_ATOM H09 Hapo HA 0.10 ADD_ATOM H10 Hapo HA 0.10 ADD_ATOM H11 Hapo HA 0.10 ADD_ATOM C4 CH3 CT3 -0.26 ADD_ATOM H06 Hapo HA 0.10 ADD_ATOM H07 Hapo HA 0.10 ADD_ATOM H08 Hapo HA 0.10 ADD_ATOM C5 CH1 CT1 -0.08 ADD_ATOM O5 OH OH1 -0.65 ADD_ATOM HO5 Hpol H 0.44 ADD_ATOM C6 COO CC 0.63 ADD_ATOM N1 Ntrp NY -0.60 ADD_ATOM C7 CH2 CT2 -0.17 ADD_ATOM C8 CH2 CT2 -0.17 ADD_ATOM C9 COO CC 0.63 ADD_ATOM N2 Ntrp NY -0.60 ADD_ATOM C10 CH2 CT2 -0.17 ADD_ATOM C11 CH2 CT2 -0.17 ADD_ATOM S S S -0.15 ADD_ATOM C12 COO CC 0.63 ADD_ATOM O12 OOC OC -0.75 ADD_ATOM C13 CH2 CT2 -0.17 ADD_ATOM C14 CH2 CT2 -0.17 ADD_ATOM C15 CH2 CT2 -0.17 ADD_ATOM C16 CH2 CT2 -0.17 ADD_ATOM C17 CH2 CT2 -0.17 ADD_ATOM C18 CH2 CT2 -0.17 ADD_ATOM C19 CH2 CT2 -0.17 ADD_ATOM C20 CH2 CT2 -0.17 ADD_ATOM C21 CH2 CT2 -0.17 ADD_ATOM C22 CH2 CT2 -0.17 ADD_ATOM C23 CH2 CT2 -0.17 ADD_ATOM C24 CH2 CT2 -0.17 ADD_ATOM C25 CH3 CT3 -0.26 ADD_ATOM H03 Hapo HA 0.10 ADD_ATOM H04 Hapo HA 0.10 ADD_ATOM H05 Hapo HA 0.10 ADD_ATOM H24A Hapo HA 0.10 ADD_ATOM H24B Hapo HA 0.10 ADD_ATOM H23A Hapo HA 0.10 ADD_ATOM H23B Hapo HA 0.10 ADD_ATOM H22A Hapo HA 0.10 ADD_ATOM H22B Hapo HA 0.10 ADD_ATOM H21A Hapo HA 0.10 ADD_ATOM H21B Hapo HA 0.10 ADD_ATOM H20A Hapo HA 0.10 ADD_ATOM H20B Hapo HA 0.10 ADD_ATOM H19A Hapo HA 0.10 ADD_ATOM H19B Hapo HA 0.10 ADD_ATOM H18A Hapo HA 0.10 ADD_ATOM H18B Hapo HA 0.10 ADD_ATOM H17A Hapo HA 0.10 ADD_ATOM H17B Hapo HA 0.10 ADD_ATOM H16A Hapo HA 0.10 ADD_ATOM H16B Hapo HA 0.10 ADD_ATOM H15A Hapo HA 0.10 ADD_ATOM H15B Hapo HA 0.10 ADD_ATOM H14A Hapo HA 0.10 ADD_ATOM H14B Hapo HA 0.10 ADD_ATOM H13A Hapo HA 0.10 ADD_ATOM H13B Hapo HA 0.10 ADD_ATOM H11A Hapo HA 0.10 ADD_ATOM H11B Hapo HA 0.10 ADD_ATOM H10A Hapo HA 0.10 ADD_ATOM H10B Hapo HA 0.10 ADD_ATOM HN2 Hpol H 0.44 ADD_ATOM O9 ONH2 O -0.54 ADD_ATOM H8A Hapo HA 0.10 ADD_ATOM H8B Hapo HA 0.10 ADD_ATOM H7A Hapo HA 0.10 ADD_ATOM H7B Hapo HA 0.10 ADD_ATOM HN1 Hpol H 0.44 ADD_ATOM O6 ONH2 O -0.54 ADD_ATOM H5A Hapo HA 0.10 ADD_ATOM H01 Hapo HA 0.10 ADD_ATOM H02 Hapo HA 0.10 ADD_BOND OG P ADD_BOND P O1P ADD_BOND P O2P ADD_BOND P O3P ADD_BOND O2P C1 ADD_BOND O3P H15 ADD_BOND C1 C2 ADD_BOND C1 H01 ADD_BOND C1 H02 ADD_BOND N1 C6 ADD_BOND N1 C7 ADD_BOND N1 HN1 ADD_BOND C2 C3 ADD_BOND C2 C4 ADD_BOND C2 C5 ADD_BOND N2 C9 ADD_BOND N2 C10 ADD_BOND N2 HN2 ADD_BOND C3 H09 ADD_BOND C3 H10 ADD_BOND C3 H11 ADD_BOND C4 H06 ADD_BOND C4 H07 ADD_BOND C4 H08 ADD_BOND C5 O5 ADD_BOND C5 C6 ADD_BOND C5 H5A ADD_BOND O5 HO5 ADD_BOND C6 O6 ADD_BOND C7 C8 ADD_BOND C7 H7A ADD_BOND C7 H7B ADD_BOND C8 C9 ADD_BOND C8 H8A ADD_BOND C8 H8B ADD_BOND C9 O9 ADD_BOND C10 C11 ADD_BOND C10 H10A ADD_BOND C10 H10B ADD_BOND C11 S ADD_BOND C11 H11A ADD_BOND C11 H11B ADD_BOND C12 O12 ADD_BOND C12 C13 ADD_BOND C12 S ADD_BOND C13 C14 ADD_BOND C13 H13A ADD_BOND C13 H13B ADD_BOND C14 C15 ADD_BOND C14 H14A ADD_BOND C14 H14B ADD_BOND C15 C16 ADD_BOND C15 H15A ADD_BOND C15 H15B ADD_BOND C16 C17 ADD_BOND C16 H16A ADD_BOND C16 H16B ADD_BOND C17 C18 ADD_BOND C17 H17A ADD_BOND C17 H17B ADD_BOND C18 C19 ADD_BOND C18 H18A ADD_BOND C18 H18B ADD_BOND C19 C20 ADD_BOND C19 H19A ADD_BOND C19 H19B ADD_BOND C20 C21 ADD_BOND C20 H20A ADD_BOND C20 H20B ADD_BOND C21 C22 ADD_BOND C21 H21A ADD_BOND C21 H21B ADD_BOND C22 C23 ADD_BOND C22 H22A ADD_BOND C22 H22B ADD_BOND C23 C24 ADD_BOND C23 H23A ADD_BOND C23 H23B ADD_BOND C24 C25 ADD_BOND C24 H24A ADD_BOND C24 H24B ADD_BOND C25 H03 ADD_BOND C25 H04 ADD_BOND C25 H05 SET_MM_ATOM_TYPE OG ON2 ## The information for the following was calculated by taking the arithmetic mean ## of data taken from 155 samples of RCSB's PDB files (with the NMR structures and homologues with >70% similarity excluded): ## OG-P bond length, P-O1P/O2P/O3P bond length, CB-OG-P bond angle, OG-P-O1P/O2P/O3P bond angle ## For dihedral angles, O1P is given the anti conformation (180 degrees), ## while O2P and O3P are placed in their ideal positions for a tetrahedral configuration. ## ## The dihedral angle for placing P was taken from the mean value of the rotamer bin ## with the highest probability. ## SET_ICOOR P -179.16 66.09 1.615 OG CB CA SET_ICOOR O1P 180.00 72.49 1.597 P OG CB SET_ICOOR O2P -120.00 72.49 1.597 P OG O1P SET_ICOOR O3P -120.00 72.49 1.597 P OG O2P SET_ICOOR C1 85.547046 56.650141 1.141854 O2P P OG SET_ICOOR C2 165.158563 51.422411 1.401481 C1 O2P P SET_ICOOR C3 137.001567 74.980730 1.407970 C2 C1 O2P SET_ICOOR H09 -110.479509 70.562367 1.090318 C3 C2 C1 SET_ICOOR H10 119.938383 70.475978 1.090024 C3 C2 H09 SET_ICOOR H11 120.076297 70.485810 1.090369 C3 C2 H10 SET_ICOOR C4 112.835988 73.297721 1.391680 C2 C1 C3 SET_ICOOR H06 82.577008 70.535929 1.090054 C4 C2 C1 SET_ICOOR H07 119.940504 70.511874 1.090471 C4 C2 H06 SET_ICOOR H08 120.090755 70.483925 1.090110 C4 C2 H07 SET_ICOOR C5 120.868785 69.194064 1.461515 C2 C1 C4 SET_ICOOR O5 52.137203 70.876410 1.353523 C5 C2 C1 SET_ICOOR HO5 -42.725494 76.817602 0.880880 O5 C5 C2 SET_ICOOR C6 130.722580 61.156653 1.491244 C5 C2 O5 SET_ICOOR N1 -46.076010 59.305057 1.380338 C6 C5 C2 SET_ICOOR C7 -71.945286 69.239110 1.385335 N1 C6 C5 SET_ICOOR C8 -88.237243 65.878194 1.413427 C7 N1 C6 SET_ICOOR C9 -88.751576 67.698540 1.439285 C8 C7 N1 SET_ICOOR N2 66.507804 64.924253 1.376318 C9 C8 C7 SET_ICOOR C10 143.006648 72.014046 1.408154 N2 C9 C8 SET_ICOOR C11 73.970708 63.994594 1.457704 C10 N2 C9 SET_ICOOR S -179.379740 68.849104 1.722704 C11 C10 N2 SET_ICOOR C12 96.388234 81.772977 1.729886 S C11 C10 SET_ICOOR O12 -136.538918 69.609874 1.356313 C12 S C11 SET_ICOOR C13 -125.198986 70.034152 1.462438 C12 S O12 SET_ICOOR C14 167.264626 66.739826 1.450141 C13 C12 S SET_ICOOR C15 170.936344 68.279365 1.460914 C14 C13 C12 SET_ICOOR C16 94.265381 65.839204 1.431320 C15 C14 C13 SET_ICOOR C17 -166.115042 70.393919 1.453423 C16 C15 C14 SET_ICOOR C18 -176.855220 67.760013 1.429269 C17 C16 C15 SET_ICOOR C19 -175.886955 67.705822 1.432823 C18 C17 C16 SET_ICOOR C20 175.907953 67.471954 1.425696 C19 C18 C17 SET_ICOOR C21 163.108331 66.405458 1.448260 C20 C19 C18 SET_ICOOR C22 62.966997 67.243766 1.413135 C21 C20 C19 SET_ICOOR C23 -173.787758 68.392051 1.437399 C22 C21 C20 SET_ICOOR C24 95.229237 63.078919 1.306951 C23 C22 C21 SET_ICOOR C25 -170.130144 61.436809 1.410629 C24 C23 C22 SET_ICOOR H03 13.283130 70.537903 1.089814 C25 C24 C23 SET_ICOOR H04 119.972680 70.468471 1.089894 C25 C24 H03 SET_ICOOR H05 120.072485 70.510606 1.090140 C25 C24 H04 SET_ICOOR H24A 125.108252 73.845492 0.872948 C24 C23 C25 SET_ICOOR H24B 111.879127 74.419309 0.873827 C24 C23 H24A SET_ICOOR H23A -121.286804 68.283337 0.901384 C23 C22 C24 SET_ICOOR H23B -115.892024 69.723950 0.896532 C23 C22 H23A SET_ICOOR H22A 120.586128 70.862993 1.007576 C22 C21 C23 SET_ICOOR H22B 118.200350 70.620323 0.994422 C22 C21 H22A SET_ICOOR H21A 121.465023 70.122063 1.019770 C21 C20 C22 SET_ICOOR H21B 116.672723 71.345213 1.013379 C21 C20 H21A SET_ICOOR H20A 122.754826 71.589451 1.012993 C20 C19 C21 SET_ICOOR H20B 116.600089 72.098466 1.014249 C20 C19 H20A SET_ICOOR H19A -122.031750 71.325595 0.998885 C19 C18 C20 SET_ICOOR H19B -116.038146 70.878003 1.000541 C19 C18 H19A SET_ICOOR H18A -120.145466 71.918173 0.989830 C18 C17 C19 SET_ICOOR H18B -117.149461 70.960690 0.992207 C18 C17 H18A SET_ICOOR H17A -121.866798 70.283033 1.018095 C17 C16 C18 SET_ICOOR H17B -115.975911 69.756684 1.012539 C17 C16 H17A SET_ICOOR H16A -120.508063 70.890027 1.026631 C16 C15 C17 SET_ICOOR H16B -118.079723 68.745035 1.029101 C16 C15 H16A SET_ICOOR H15A -122.073318 70.089437 1.026330 C15 C14 C16 SET_ICOOR H15B -116.553672 71.775516 1.031742 C15 C14 H15A SET_ICOOR H14A -121.422393 72.890725 1.034430 C14 C13 C15 SET_ICOOR H14B -115.818183 69.554440 1.025949 C14 C13 H14A SET_ICOOR H13A -122.448021 69.598586 1.031844 C13 C12 C14 SET_ICOOR H13B -116.621115 71.521613 1.029826 C13 C12 H13A SET_ICOOR H11A -121.579310 71.954820 1.016808 C11 C10 S SET_ICOOR H11B -117.074533 68.211393 1.025070 C11 C10 H11A SET_ICOOR H10A -124.036459 70.962781 1.020511 C10 N2 C11 SET_ICOOR H10B -114.827146 74.024211 1.022644 C10 N2 H10A SET_ICOOR HN2 -116.261490 75.112522 0.974189 N2 C9 C10 SET_ICOOR O9 -122.089907 69.080862 1.336350 C9 C8 N2 SET_ICOOR H8A 124.231902 68.097173 1.033347 C8 C7 C9 SET_ICOOR H8B 118.578749 71.925839 1.028036 C8 C7 H8A SET_ICOOR H7A 122.507971 68.337577 1.001610 C7 N1 C8 SET_ICOOR H7B 116.112116 71.206338 1.018665 C7 N1 H7A SET_ICOOR HN1 117.958206 73.144337 0.950802 N1 C6 C7 SET_ICOOR O6 125.622829 69.490957 1.346231 C6 C5 N1 SET_ICOOR H5A 117.791728 74.289364 1.043738 C5 C2 C6 SET_ICOOR H01 107.745373 81.669705 1.089838 C1 O2P C2 SET_ICOOR H02 129.675395 75.461878 1.089760 C1 O2P H01 ADD_PROPERTY CHARGED ## For the phosphate group ## Chi 2 was a proton chi in SER.params. Since the hydrogen atom isn't there anymore, ## redefine the fourth atom of chi2 to the added P and then remove the hydrogen. REDEFINE_CHI 2 CA CB OG P DELETE_ATOM HG ## Manually define rotamer bins for chi 2 using data from the 155 samples. ## Note: The rotamers are listed in the order of decreasing frequency. ## The percentages may not add up to 100% due to rounding or exclusion of outliers. ADD_CHI_ROTAMER 2 -179.16 10.17 #32.9% (+/- 180 bin) ADD_CHI_ROTAMER 2 152.48 4.57 #19.4% ADD_CHI_ROTAMER 2 117.55 15.89 #16.1% ADD_CHI_ROTAMER 2 -106.20 15.99 #15.5% ADD_CHI_ROTAMER 2 153.19 7.19 #14.8% DELETE_PROPERTY CANONICAL_AA DELETE_PROPERTY CANONICAL_NUCLEIC END_CASE