Author: Dave Case Date: 07/01/03 Programs: protonate Description: doesn't work well with the alternate "PROTON_INFO.Brook" file Fix: apply the following patch to amber7/src/protonate/protonate.f and to amber7/dat/PROTON_INFO.Brook ------------------------------------------------------------------------------ *** protonate.f 2002/03/28 20:58:20 7.4 --- protonate.f 2003/07/01 15:42:51 *************** *** 43,51 **** character*(NLINSZ) inline, line character*3 cdresnam(NR), cpro, creslast character*4 cmnatm(3), ctemp character*4 camide, camidet(3) logical first, header, aminot, nterm(MAXAT), lhyd ! integer minres, maxres, ksave, . iat, icout, ic, iar, nscat, i, j, k, l, m, n, . nrs, nhyd, lres c --- 43,52 ---- character*(NLINSZ) inline, line character*3 cdresnam(NR), cpro, creslast character*4 cmnatm(3), ctemp + character*1 ctemp1 character*4 camide, camidet(3) logical first, header, aminot, nterm(MAXAT), lhyd ! integer minres, maxres, ksave, lname, . iat, icout, ic, iar, nscat, i, j, k, l, m, n, . nrs, nhyd, lres c *************** *** 87,92 **** --- 88,116 ---- 35 format( A6, 6X, A4, 1X, A3, 1X, A1, I4, A1, 3X, 3F8.3 ) if ( cresnam(iat) .eq. 'HIS' ) cresnam(iat) = 'HID' c + c -- convert Brookhaven-style names in to Amber style names: + c + if( cnamat(iat)(1:1).eq.' ') then + cnamat(iat)(1:1) = cnamat(iat)(2:2) + cnamat(iat)(2:2) = cnamat(iat)(3:3) + cnamat(iat)(3:3) = cnamat(iat)(4:4) + cnamat(iat)(4:4) = ' ' + end if + c + lname = 3 + if( cnamat(iat)(3:3).eq.' ' ) lname = 2 + if( cnamat(iat)(2:2).eq.' ' ) lname = 1 + c + if( cnamat(iat)(1:1).eq.'1' .or. cnamat(iat)(1:1).eq.'2' .or. + . cnamat(iat)(1:1).eq.'3' ) then + ctemp1 = cnamat(iat)(1:1) + do i=1,lname + cnamat(iat)(i:i) = cnamat(iat)(i+1:i+1) + end do + cnamat(iat)(lname+1:lname+1) = ctemp1 + end if + if( cnamat(iat)(3:3).eq.'*' ) cnamat(iat)(3:3) = '''' + c c -- remember positions of protons in input file for later checking: c if ( lhyd( cnamat(iat) ) ) then *************** *** 872,878 **** end if end if end do ! if ( imatch .eq. 0 ) go to 5000 c c -- check if closest proton is bonded to same atom as proton c currently being considered. Bonded (heavy) atom is in --- 896,902 ---- end if end if end do ! if ( imatch .eq. 0 ) go to 3000 c c -- check if closest proton is bonded to same atom as proton c currently being considered. Bonded (heavy) atom is in *************** *** 907,913 **** c long! In that case, wrap around the final character into c column 13. c ! printa = ' ' printa(2:4) = atomname(1:3) if (printa(4:4) .ne. ' ') printa(1:1) = atomname(4:4) c --- 931,937 ---- c long! In that case, wrap around the final character into c column 13. c ! 3000 printa = ' ' printa(2:4) = atomname(1:3) if (printa(4:4) .ne. ' ') printa(1:1) = atomname(4:4) c *************** *** 928,938 **** --- 952,964 ---- printa(1:1) = printa(4:4) printa(4:4) = ' ' end if + write(6,*) 'converted |',atomname,'| to |',printa,'|' c c ---Finally, convert nucleic acid primed names into asterisk: these c are always in the fourth column of the atom name: c if (printa(4:4).eq.'''') printa(4:4) = '*' + if( imatch .eq. 0 ) go to 5000 c c -- check for matches, but add special code so that atom "H" in c residue 1 can never be matched: *** PROTON_INFO.Brook 1999/03/10 15:17:28 1.1 --- PROTON_INFO.Brook 2003/07/01 15:43:52 *************** *** 1,158 **** ! amide backbone: H : H1 : H2 : H3 : ALA 5 ! CA N C O CB 2 ! 12 1 2 3 5 HA ! 5 5 1 2 1HB 2HB 3HB ARG 11 CA N C O CB CG CD NE CZ NH1 NH2 7 ! 12 1 2 3 5 HA ! 2 5 1 6 2HB 1HB ! 2 6 5 7 2HG 1HG ! 2 7 6 8 2HD 1HD ! 8 8 7 9 HE ! 9 10 9 8 11 1HH1 2HH1 ! 9 11 9 8 10 1HH2 2HH2 ASN 8 CA N C O CB CG OD1 ND2 3 ! 12 1 2 3 5 HA ! 2 5 1 6 2HB 1HB ! 9 8 6 5 7 2HD2 1HD2 ASP 8 CA N C O CB CG OD1 OD2 2 ! 12 1 2 3 5 HA ! 2 5 1 6 2HB 1HB ! CYH 9 ! CA N C O CB SG SG2 CB2 CA2 ! 4 ! 12 1 2 3 5 HA ! 2 5 1 6 2HB 1HB ! 2 8 7 9 ? ? ! 5 9 8 7 ? ? CYS 6 CA N C O CB SG 2 ! 12 1 2 3 5 HA ! 2 5 1 6 2HB 1HB GLN 9 CA N C O CB CG CD OE1 NE2 4 ! 12 1 2 3 5 HA ! 2 5 1 6 2HB 1HB ! 2 6 5 7 2HG 1HG ! 9 9 7 6 8 2HE2 1HE2 GLU 9 CA N C O CB CG CD OE1 OE2 3 ! 12 1 2 3 5 HA ! 2 5 1 6 2HB 1HB ! 2 6 5 7 2HG 1HG GLY 4 CA N C O 1 ! 11 1 2 3 2HA 1HA HEM 44 ! CHA C1A C2A CAA CBA CGA C3A CMA C4A CHB C1B C2B CMB C3B CAB CBB C4B CHC C1C C2C CMC C3C CAC CBC C4C CHD C1D C2D CMD C3D CAD CBD CGD C4D CA N C O CB CG ND1 CE1 NE2 CD2 21 ! 1 1 2 34 HGM ! 2 4 3 5 1HP7 2HP7 ! 2 5 4 6 3HP7 4HP7 ! 6 8 7 3 9 1HM8 2HM8 3HM8 ! 1 10 9 11 HDM ! 6 13 12 11 14 1HM1 2HM1 3HM1 ! 1 15 14 16 AHV2 ! 4 16 15 14 12 CHV2 THV2 ! 1 18 17 19 HAM ! 6 21 20 19 22 1HM3 2HM3 3HM3 ! 1 23 22 24 AHV4 ! 4 24 23 22 20 CHV4 THV4 ! 1 26 25 27 HBM ! 6 29 28 27 30 1HM5 2HM5 3HM5 ! 2 31 30 32 1HP6 2HP6 ! 2 32 31 33 3HP6 4HP6 ! 12 35 36 37 42 HA ! 2 39 35 40 2HB 1HB ! 8 41 40 42 HD1 ! 1 42 41 43 HE1 ! 1 44 43 40 HD2 HID 10 CA N C O CB CG ND1 CE1 NE2 CD2 5 ! 12 1 2 3 5 HA ! 2 5 1 6 2HB 1HB ! 8 7 6 8 HD1 ! 1 8 7 9 HE1 ! 1 10 9 6 HD2 HIE 10 CA N C O CB CG ND1 CE1 NE2 CD2 5 ! 12 1 2 3 5 HA ! 2 5 1 6 2HB 1HB ! 1 8 7 9 HE1 ! 8 9 8 10 HE2 ! 1 10 9 6 HD2 HIP 10 CA N C O CB CG ND1 CE1 NE2 CD2 6 ! 12 1 2 3 5 HA ! 2 5 1 6 2HB 1HB ! 8 7 6 8 HD1 ! 1 8 7 9 HE1 ! 8 9 8 10 HE2 ! 1 10 9 6 HD2 HIC 11 CA N C O CB CG ND1 CU CE1 NE2 CD2 5 ! 12 1 2 3 5 HA ! 2 5 1 6 2HB 1HB 1 9 7 10 ? 8 10 9 11 ? 1 11 10 6 ? HIS 10 CA N C O CB CG ND1 CE1 NE2 CD2 5 ! 12 1 2 3 5 HA ! 2 5 1 6 2HB 1HB ! 8 7 6 8 HD1 ! 1 8 7 9 HE1 ! 1 10 9 6 HD2 ILE 8 CA N C O CB CG2 CG1 CD1 5 ! 12 1 2 3 5 HA ! 3 5 1 6 7 HB ! 5 6 5 1 1HG2 2HG2 3HG2 ! 2 7 5 8 2HG1 1HG1 ! 5 8 7 5 1HD1 2HD1 3HD1 LEU 8 CA N C O CB CG CD1 CD2 5 ! 12 1 2 3 5 HA ! 2 5 1 6 2HB 1HB ! 3 6 5 7 8 HG ! 5 7 6 5 1HD1 2HD1 3HD1 ! 5 8 6 5 1HD2 2HD2 3HD2 LYS 9 CA N C O CB CG CD CE NZ 6 ! 12 1 2 3 5 HA ! 2 5 1 6 2HB 1HB ! 2 6 5 7 2HG 1HG ! 2 7 6 8 2HD 1HD ! 2 8 7 9 2HE 1HE ! 10 9 8 7 1HZ 2HZ 3HZ MET 8 CA N C O CB CG SD CE 4 ! 12 1 2 3 5 HA ! 2 5 1 6 2HB 1HB ! 2 6 5 7 2HG 1HG ! 5 8 7 6 1HE 2HE 3HE MTX 33 CA N CT O1 O2 CB CG CD OE1 OE2 C O C11 C12 C13 C14 C15 C16 N10 CM C9 C6 N5 C4A C4 NA4 N3 C2 NA2 N1 C8A N8 C7 --- 1,178 ---- ! amide backbone:H :H1 :H2 :H3 : ! ACE 3 ! CH3 C O ! 1 ! 5 1 2 3 HT1 HT2 HT3 ! AME 3 ! N H CT ! 1 ! 5 3 2 1 HT1 HT2 HT3 ALA 5 ! CA N C O CB 2 ! 12 1 2 3 5 HA ! 5 5 1 2 HB1 HB2 HB3 ARG 11 CA N C O CB CG CD NE CZ NH1 NH2 7 ! 12 1 2 3 5 HA ! 2 5 1 6 HB2 HB1 ! 2 6 5 7 HG2 HG1 ! 2 7 6 8 HD2 HD1 ! 8 8 7 9 HE ! 9 10 9 8 11 HH11 HH12 ! 9 11 9 8 10 HH21 HH22 ASN 8 CA N C O CB CG OD1 ND2 3 ! 12 1 2 3 5 HA ! 2 5 1 6 HB2 HB1 ! 9 8 6 5 7 HD22 HD21 ASP 8 CA N C O CB CG OD1 OD2 2 ! 12 1 2 3 5 HA ! 2 5 1 6 HB2 HB1 ! ASH 8 ! CA N C O CB CG OD1 OD2 ! 3 ! 12 1 2 3 5 HA ! 2 5 1 6 HB2 HB1 ! 7 8 6 5 HD2 CYS 6 CA N C O CB SG + 3 + 12 1 2 3 5 HA + 2 5 1 6 HB2 HB1 + 13 6 5 1 HG + CYX 6 + CA N C O CB SG 2 ! 12 1 2 3 5 HA ! 2 5 1 6 HB2 HB1 GLN 9 CA N C O CB CG CD OE1 NE2 4 ! 12 1 2 3 5 HA ! 2 5 1 6 HB2 HB1 ! 2 6 5 7 HG2 HG1 ! 9 9 7 6 8 HE22 HE21 GLU 9 CA N C O CB CG CD OE1 OE2 3 ! 12 1 2 3 5 HA ! 2 5 1 6 HB2 HB1 ! 2 6 5 7 HG2 HG1 ! GLH 9 ! CA N C O CB CG CD OE1 OE2 ! 4 ! 12 1 2 3 5 HA ! 2 5 1 6 HB2 HB1 ! 2 6 5 7 HG2 HG1 ! 7 9 7 6 HE2 GLY 4 CA N C O 1 ! 11 1 2 3 HA2 HA1 HEM 44 ! CHA C1A C2A CAA CBA CGA C3A CMA C4A CHB C1B C2B CMB C3B CAB CBB C4B CHC C1C C2C CMC C3C CAC CBC C4C CHD C1D C2D CMD C3D CAD CBD CGD C4D CA N C O CB CG ND1 CE1 NE2 CD2 21 ! 1 1 2 34 HGM ! 2 4 3 5 HP72 HP71 ! 2 5 4 6 HP73 HP74 ! 6 8 7 3 9 HM81 HM83 HM82 ! 1 10 9 11 HDM ! 6 13 12 11 14 HM11 HM13 HM12 ! 1 15 14 16 HV2A ! 4 16 15 14 12 HV2T HV2C ! 1 18 17 19 HAM ! 6 21 20 19 22 HM31 HM33 HM32 ! 1 23 22 24 HV4A ! 4 24 23 22 20 HV4T HV4C ! 1 26 25 27 HBM ! 6 29 28 27 30 HM51 HM53 HM52 ! 2 31 30 32 HP62 HP61 ! 2 32 31 33 HP64 HP63 ! 12 35 36 37 39 HA ! 2 39 35 40 HB3 HB2 ! 8 41 40 42 HD1 ! 1 42 41 43 HE1 ! 1 44 43 40 HD2 HID 10 CA N C O CB CG ND1 CE1 NE2 CD2 5 ! 12 1 2 3 5 HA ! 2 5 1 6 HB2 HB1 ! 8 7 6 8 HD1 ! 1 8 7 9 HE1 ! 1 10 9 6 HD2 HIE 10 CA N C O CB CG ND1 CE1 NE2 CD2 5 ! 12 1 2 3 5 HA ! 2 5 1 6 HB2 HB1 ! 1 8 7 9 HE1 ! 8 9 8 10 HE2 ! 1 10 9 6 HD2 HIP 10 CA N C O CB CG ND1 CE1 NE2 CD2 6 ! 12 1 2 3 5 HA ! 2 5 1 6 HB2 HB1 ! 8 7 6 8 HD1 ! 1 8 7 9 HE1 ! 8 9 8 10 HE2 ! 1 10 9 6 HD2 HIC 11 CA N C O CB CG ND1 CU CE1 NE2 CD2 5 ! 12 1 2 3 5 HA ! 2 5 1 6 HB2 HB1 1 9 7 10 ? 8 10 9 11 ? 1 11 10 6 ? HIS 10 CA N C O CB CG ND1 CE1 NE2 CD2 5 ! 12 1 2 3 5 HA ! 2 5 1 6 HB2 HB1 ! 8 7 6 8 HD1 ! 1 8 7 9 HE1 ! 1 10 9 6 HD2 ILE 8 CA N C O CB CG2 CG1 CD1 5 ! 12 1 2 3 5 HA ! 3 5 1 6 7 HB ! 5 6 5 1 HG21 HG22 HG23 ! 2 7 5 8 HG12 HG11 ! 5 8 7 5 HD11 HD12 HD13 LEU 8 CA N C O CB CG CD1 CD2 5 ! 12 1 2 3 5 HA ! 2 5 1 6 HB2 HB1 ! 3 6 5 7 8 HG ! 5 7 6 5 HD11 HD12 HD13 ! 5 8 6 5 HD21 HD22 HD23 LYS 9 CA N C O CB CG CD CE NZ 6 ! 12 1 2 3 5 HA ! 2 5 1 6 HB2 HB1 ! 2 6 5 7 HG2 HG1 ! 2 7 6 8 HD2 HD1 ! 2 8 7 9 HE2 HE1 ! 10 9 8 7 HZ1 HZ2 HZ3 MET 8 CA N C O CB CG SD CE 4 ! 12 1 2 3 5 HA ! 2 5 1 6 HB2 HB1 ! 2 6 5 7 HG2 HG1 ! 5 8 7 6 HE1 HE2 HE3 MTX 33 CA N CT O1 O2 CB CG CD OE1 OE2 C O C11 C12 C13 C14 C15 C16 N10 CM C9 C6 N5 C4A C4 NA4 N3 C2 NA2 N1 C8A N8 C7 *************** *** 173,322 **** PHE 11 CA N C O CB CG CD1 CE1 CZ CE2 CD2 7 ! 12 1 2 3 5 HA ! 2 5 1 6 2HB 1HB ! 1 7 6 8 HD1 ! 1 8 7 9 HE1 ! 1 9 8 10 HZ ! 1 10 9 11 HE2 ! 1 11 10 6 HD2 PRO 7 CA N C O CB CG CD 4 ! 12 1 2 3 5 HA ! 2 5 1 6 2HB 1HB ! 2 6 5 7 2HG 1HG ! 2 7 6 2 2HD 1HD SER 6 CA N C O CB OG 3 ! 12 1 2 3 5 HA ! 2 5 1 6 2HB 1HB ! 7 6 5 1 HG THR 7 CA N C O CB CG2 OG1 4 ! 12 1 2 3 5 HA ! 3 5 1 6 7 HB ! 5 6 5 1 1HG2 2HG2 3HG2 ! 7 7 5 1 HG1 TRP 14 CA N C O CB CG CD1 NE1 CE2 CZ2 CH2 CZ3 CE3 CD2 8 ! 12 1 2 3 5 HA ! 2 5 1 6 2HB 1HB ! 1 7 6 8 HD1 ! 8 8 7 9 HE1 ! 1 10 9 11 HZ2 ! 1 11 10 12 HH2 ! 1 12 11 13 HZ3 ! 1 13 12 14 HE3 TYR 12 CA N C O CB CG CD1 CE1 CZ CE2 CD2 OH 7 ! 12 1 2 3 5 HA ! 2 5 1 6 2HB 1HB ! 1 7 6 8 HD1 ! 1 8 7 9 HE1 ! 1 10 9 11 HE2 ! 1 11 10 6 HD2 ! 7 12 9 8 HH VAL 7 CA N C O CB CG1 CG2 4 ! 12 1 2 3 5 HA ! 3 5 1 6 7 HB ! 5 6 5 1 1HG1 2HG1 3HG1 ! 5 7 5 1 1HG2 2HG2 3HG2 GUA 22 ! P O1P O2P O3* O5* C1* C2* C3* C4* C5* O4* N2 O6 C6 C5 N7 C8 N9 C4 N3 C2 N1 8 ! 12 9 10 8 11 H4* ! 2 10 9 5 2H5* 1H5* ! 12 8 7 9 4 H3* ! 2 7 6 8 1H2* 2H2* ! 12 6 7 11 18 H1* ! 1 17 16 18 H8 ! 8 22 21 14 H1 ! 9 12 21 22 20 1H2 2H2 ADE 21 ! P O1P O2P O3* O5* C1* C2* C3* C4* C5* O4* N6 C6 C5 N7 C8 N9 C4 N3 C2 N1 - 8 - 12 9 10 8 11 H4* - 2 10 9 5 2H5* 1H5* - 12 8 7 9 4 H3* - 2 7 6 8 1H2* 2H2* - 12 6 7 11 17 H1* - 1 16 15 17 H8 - 1 20 19 21 H2 - 9 12 13 21 14 1H6 2H6 - CYT 19 - P O1P O2P O3* O5* C1* C2* C3* C4* C5* O4* N4 C4 N3 C2 O2 N1 C6 C5 - 8 - 12 9 10 8 11 H4* - 2 10 9 5 2H5* 1H5* - 12 8 7 9 4 H3* - 2 7 6 8 1H2* 2H2* - 12 6 7 11 17 H1* - 1 18 17 19 H6 - 1 19 18 13 H5 - 9 12 13 14 19 1H4 2H4 - THY 20 - P O1P O2P O3* O5* C1* C2* C3* C4* C5* O4* O4 C4 N3 C2 O2 N1 C6 C5 C5M 8 ! 12 9 10 8 11 H4* ! 2 10 9 5 2H5* 1H5* ! 12 8 7 9 4 H3* ! 2 7 6 8 1H2* 2H2* ! 12 6 7 11 17 H1* ! 1 18 17 19 H6 ! 8 14 15 13 H3 ! 6 20 19 18 13 1H5M 2H5M 3H5M ! G 22 ! P O1P O2P O3* O5* C1* C2* C3* C4* C5* O4* N2 O6 C6 C5 N7 C8 N9 C4 N3 ! C2 N1 8 ! 12 9 10 8 11 H4* ! 2 10 9 5 2H5* 1H5* ! 12 8 7 9 4 H3* ! 2 7 6 8 1H2* 2H2* ! 12 6 7 11 18 H1* ! 1 17 16 18 H8 ! 8 22 21 14 H1 ! 9 12 21 22 20 1H2 2H2 ! A 21 ! P O1P O2P O3* O5* C1* C2* C3* C4* C5* O4* N6 C6 C5 N7 C8 N9 C4 N3 C2 N1 8 ! 12 9 10 8 11 H4* ! 2 10 9 5 2H5* 1H5* ! 12 8 7 9 4 H3* ! 2 7 6 8 1H2* 2H2* ! 12 6 7 11 17 H1* ! 1 16 15 17 H8 ! 1 20 19 21 H2 ! 9 12 13 21 14 1H6 2H6 ! C 19 ! P O1P O2P O3* O5* C1* C2* C3* C4* C5* O4* N4 C4 N3 C2 O2 N1 C6 C5 8 ! 12 9 10 8 11 H4* ! 2 10 9 5 2H5* 1H5* ! 12 8 7 9 4 H3* ! 2 7 6 8 1H2* 2H2* ! 12 6 7 11 17 H1* ! 1 18 17 19 H6 ! 1 19 18 13 H5 ! 9 12 13 14 19 1H4 2H4 ! T 20 ! P O1P O2P O3* O5* C1* C2* C3* C4* C5* O4* O4 C4 N3 C2 O2 N1 C6 C5 C5M 8 ! 12 9 10 8 11 H4* ! 2 10 9 5 2H5* 1H5* ! 12 8 7 9 4 H3* ! 2 7 6 8 1H2* 2H2* ! 12 6 7 11 17 H1* ! 1 18 17 19 H6 ! 8 14 15 13 H3 ! 6 20 19 18 13 1H5M 2H5M 3H5M --- 193,596 ---- PHE 11 CA N C O CB CG CD1 CE1 CZ CE2 CD2 7 ! 12 1 2 3 5 HA ! 2 5 1 6 HB2 HB1 ! 1 7 6 8 HD1 ! 1 8 7 9 HE1 ! 1 9 8 10 HZ ! 1 10 9 11 HE2 ! 1 11 10 6 HD2 PRO 7 CA N C O CB CG CD 4 ! 12 1 2 3 5 HA ! 2 5 1 6 HB2 HB1 ! 2 6 5 7 HG2 HG1 ! 2 7 6 2 HD2 HD1 SER 6 CA N C O CB OG 3 ! 12 1 2 3 5 HA ! 2 5 1 6 HB2 HB1 ! 7 6 5 1 HG THR 7 CA N C O CB CG2 OG1 4 ! 12 1 2 3 5 HA ! 3 5 1 6 7 HB ! 5 6 5 1 HG21 HG22 HG23 ! 7 7 5 1 HG1 TRP 14 CA N C O CB CG CD1 NE1 CE2 CZ2 CH2 CZ3 CE3 CD2 8 ! 12 1 2 3 5 HA ! 2 5 1 6 HB2 HB1 ! 1 7 6 8 HD1 ! 8 8 7 9 HE1 ! 1 10 9 11 HZ2 ! 1 11 10 12 HH2 ! 1 12 11 13 HZ3 ! 1 13 12 14 HE3 TYR 12 CA N C O CB CG CD1 CE1 CZ CE2 CD2 OH 7 ! 12 1 2 3 5 HA ! 2 5 1 6 HB2 HB1 ! 1 7 6 8 HD1 ! 1 8 7 9 HE1 ! 1 10 9 11 HE2 ! 1 11 10 6 HD2 ! 7 12 9 8 HH VAL 7 CA N C O CB CG1 CG2 4 ! 12 1 2 3 5 HA ! 3 5 1 6 7 HB ! 5 6 5 1 HG11 HG12 HG13 ! 5 7 5 1 HG21 HG22 HG23 GUA 22 ! P O1P O2P O3' O5' C1' C2' C3' C4' C5' O4' N2 O6 C6 C5 N7 C8 N9 C4 N3 ! C2 N1 ! 8 ! 12 9 10 8 11 H4' ! 2 10 9 5 H5'2 H5'1 ! 12 8 7 9 4 H3' ! 2 7 6 8 H2'1 H2'2 ! 12 6 7 11 18 H1' ! 1 17 16 18 H8 ! 8 22 21 14 H1 ! 9 12 21 22 20 H21 H22 ! DG 22 ! P O1P O2P O3' O5' C1' C2' C3' C4' C5' O4' N2 O6 C6 C5 N7 C8 N9 C4 N3 C2 N1 8 ! 12 9 10 8 11 H4' ! 2 10 9 5 H5'2 H5'1 ! 12 8 7 9 4 H3' ! 2 7 6 8 H2'1 H2'2 ! 12 6 7 11 18 H1' ! 1 17 16 18 H8 ! 8 22 21 14 H1 ! 9 12 21 22 20 H21 H22 ! DG3 22 ! P O1P O2P O3' O5' C1' C2' C3' C4' C5' O4' N2 O6 C6 C5 N7 C8 N9 C4 N3 ! C2 N1 ! 9 ! 7 4 8 9 H3T ! 12 9 10 8 11 H4' ! 2 10 9 5 H5'2 H5'1 ! 12 8 7 9 4 H3' ! 2 7 6 8 H2'1 H2'2 ! 12 6 7 11 18 H1' ! 1 17 16 18 H8 ! 8 22 21 14 H1 ! 9 12 21 22 20 H21 H22 ! DG5 19 ! O3' O5' C1' C2' C3' C4' C5' O4' N2 O6 C6 C5 N7 C8 N9 C4 N3 C2 N1 ! 9 ! 7 2 7 6 H5T ! 12 6 7 5 8 H4' ! 2 7 6 2 H5'2 H5'1 ! 12 5 4 6 1 H3' ! 2 4 3 5 H2'1 H2'2 ! 12 3 4 7 15 H1' ! 1 14 13 15 H8 ! 8 19 18 11 H1 ! 9 9 18 19 17 H21 H22 ! RG 23 ! P O1P O2P O3' O5' C1' C2' C3' C4' C5' O4' N2 O6 C6 C5 N7 C8 N9 C4 N3 ! C2 N1 O2' ! 9 ! 12 9 10 8 11 H4' ! 2 10 9 5 H5'2 H5'1 ! 12 8 7 9 4 H3' ! 12 7 6 8 23 H2' ! 12 6 7 11 18 H1' ! 1 17 16 18 H8 ! 8 22 21 14 H1 ! 9 12 21 22 20 H21 H22 ! 7 23 7 6 HO'2 ! RG3 23 ! P O1P O2P O3' O5' C1' C2' C3' C4' C5' O4' N2 O6 C6 C5 N7 C8 N9 C4 N3 ! C2 N1 O2' ! 10 ! 7 4 8 9 H3T ! 12 9 10 8 11 H4' ! 2 10 9 5 H5'2 H5'1 ! 12 8 7 9 4 H3' ! 12 7 6 8 23 H2' ! 12 6 7 11 18 H1' ! 1 17 16 18 H8 ! 8 22 21 14 H1 ! 9 12 21 22 20 H21 H22 ! 7 23 7 6 HO'2 ! RG5 20 ! O3' O5' C1' C2' C3' C4' C5' O4' N2 O6 C6 C5 N7 C8 N9 C4 N3 C2 N1 O2' ! 10 ! 7 2 7 6 H5T ! 12 6 7 5 8 H4' ! 2 7 6 2 H5'2 H5'1 ! 12 5 4 6 1 H3' ! 12 4 3 5 20 H2' ! 12 3 4 7 15 H1' ! 1 14 13 15 H8 ! 8 19 18 11 H1 ! 9 9 18 19 17 H21 H22 ! 7 20 4 3 HO'2 ADE 21 ! P O1P O2P O3' O5' C1' C2' C3' C4' C5' O4' N6 C6 C5 N7 C8 N9 C4 N3 C2 N1 8 ! 12 9 10 8 11 H4' ! 2 10 9 5 H5'2 H5'1 ! 12 8 7 9 4 H3' ! 2 7 6 8 H2'1 H2'2 ! 12 6 7 11 17 H1' ! 1 16 15 17 H8 ! 1 20 19 21 H2 ! 9 12 13 21 14 H61 H62 ! DA 21 ! P O1P O2P O3' O5' C1' C2' C3' C4' C5' O4' N6 C6 C5 N7 C8 N9 C4 N3 C2 ! N1 8 ! 12 9 10 8 11 H4' ! 2 10 9 5 H5'2 H5'1 ! 12 8 7 9 4 H3' ! 2 7 6 8 H2'1 H2'2 ! 12 6 7 11 17 H1' ! 1 16 15 17 H8 ! 1 20 19 21 H2 ! 9 12 13 21 14 H61 H62 ! DA3 21 ! P O1P O2P O3' O5' C1' C2' C3' C4' C5' O4' N6 C6 C5 N7 C8 N9 C4 N3 C2 N1 + 9 + 7 4 8 9 H3T + 12 9 10 8 11 H4' + 2 10 9 5 H5'2 H5'1 + 12 8 7 9 4 H3' + 2 7 6 8 H2'1 H2'2 + 12 6 7 11 17 H1' + 1 16 15 17 H8 + 1 20 19 21 H2 + 9 12 13 21 14 H61 H62 + DA5 18 + O3' O5' C1' C2' C3' C4' C5' O4' N6 C6 C5 N7 C8 N9 C4 N3 C2 N1 + 9 + 7 2 7 6 H5T + 12 6 7 5 8 H4' + 2 7 6 2 H5'2 H5'1 + 12 5 4 6 1 H3' + 2 4 3 5 H2'1 H2'2 + 12 3 4 8 14 H1' + 1 13 12 14 H8 + 1 17 16 18 H2 + 9 9 10 18 11 H61 H62 + RA 22 + P O1P O2P O3' O5' C1' C2' C3' C4' C5' O4' N6 C6 C5 N7 C8 N9 C4 N3 C2 + N1 O2' + 9 + 12 9 10 8 11 H4' + 2 10 9 5 H5'2 H5'1 + 12 8 7 9 4 H3' + 12 7 6 8 22 H2' + 12 6 7 11 17 H1' + 1 16 15 17 H8 + 1 20 19 21 H2 + 9 12 13 21 14 H61 H62 + 7 22 7 6 HO'2 + RA3 22 + P O1P O2P O3' O5' C1' C2' C3' C4' C5' O4' N6 C6 C5 N7 C8 N9 C4 N3 C2 + N1 O2' + 10 + 7 4 8 9 H3T + 12 9 10 8 11 H4' + 2 10 9 5 H5'2 H5'1 + 12 8 7 9 4 H3' + 12 7 6 8 22 H2' + 12 6 7 11 17 H1' + 1 16 15 17 H8 + 1 20 19 21 H2 + 9 12 13 21 14 H61 H62 + 7 22 7 6 HO'2 + RA5 19 + O3' O5' C1' C2' C3' C4' C5' O4' N6 C6 C5 N7 C8 N9 C4 N3 C2 N1 O2' + 10 + 7 2 7 6 H5T + 12 6 7 5 8 H4' + 2 7 6 2 H5'2 H5'1 + 12 5 4 6 1 H3' + 12 4 3 5 19 H2' + 12 3 4 8 14 H1' + 1 13 12 14 H8 + 1 17 16 18 H2 + 9 9 10 18 11 H61 H62 + 7 19 4 3 HO'2 + CYT 19 + P O1P O2P O3' O5' C1' C2' C3' C4' C5' O4' N4 C4 N3 C2 O2 N1 C6 C5 8 ! 12 9 10 8 11 H4' ! 2 10 9 5 H5'2 H5'1 ! 12 8 7 9 4 H3' ! 2 7 6 8 H2'1 H2'2 ! 12 6 7 11 17 H1' ! 1 18 17 19 H6 ! 1 19 18 13 H5 ! 9 12 13 14 19 H41 H42 ! DC 19 ! P O1P O2P O3' O5' C1' C2' C3' C4' C5' O4' N4 C4 N3 C2 O2 N1 C6 C5 ! 8 ! 12 9 10 8 11 H4' ! 2 10 9 5 H5'2 H5'1 ! 12 8 7 9 4 H3' ! 2 7 6 8 H2'1 H2'2 ! 12 6 7 11 17 H1' ! 1 18 17 19 H6 ! 1 19 18 13 H5 ! 9 12 13 14 19 H41 H42 ! DC3 19 ! P O1P O2P O3' O5' C1' C2' C3' C4' C5' O4' N4 C4 N3 C2 O2 N1 C6 C5 ! 9 ! 7 4 8 9 H3T ! 12 9 10 8 11 H4' ! 2 10 9 5 H5'2 H5'1 ! 12 8 7 9 4 H3' ! 2 7 6 8 H2'1 H2'2 ! 12 6 7 11 17 H1' ! 1 18 17 19 H6 ! 1 19 18 13 H5 ! 9 12 13 14 19 H41 H42 ! DC5 16 ! O3' O5' C1' C2' C3' C4' C5' O4' N4 C4 N3 C2 O2 N1 C6 C5 ! 9 ! 7 2 7 6 H5T ! 12 6 7 5 8 H4' ! 2 7 6 2 H5'2 H5'1 ! 12 5 4 6 1 H3' ! 2 4 3 5 H2'1 H2'2 ! 12 3 4 8 14 H1' ! 1 15 14 16 H6 ! 1 16 15 10 H5 ! 9 9 10 11 16 H41 H42 ! RC 20 ! P O1P O2P O3' O5' C1' C2' C3' C4' C5' O4' N4 C4 N3 C2 O2 N1 C6 C5 O2' ! 9 ! 12 9 10 8 11 H4' ! 2 10 9 5 H5'2 H5'1 ! 12 8 7 9 4 H3' ! 12 7 6 8 20 H2' ! 12 6 7 11 17 H1' ! 1 18 17 19 H6 ! 1 19 18 13 H5 ! 9 12 13 14 19 H41 H42 ! 7 20 7 6 HO'2 ! RC3 20 ! P O1P O2P O3' O5' C1' C2' C3' C4' C5' O4' N4 C4 N3 C2 O2 N1 C6 C5 O2' ! 10 ! 7 4 8 9 H3T ! 12 9 10 8 11 H4' ! 2 10 9 5 H5'2 H5'1 ! 12 8 7 9 4 H3' ! 12 7 6 8 20 H2' ! 12 6 7 11 17 H1' ! 1 18 17 19 H6 ! 1 19 18 13 H5 ! 9 12 13 14 19 H41 H42 ! 7 20 7 6 HO'2 ! RC5 17 ! O3' O5' C1' C2' C3' C4' C5' O4' N4 C4 N3 C2 O2 N1 C6 C5 O2' ! 10 ! 7 2 7 6 H5T ! 12 6 7 5 8 H4' ! 2 7 6 2 H5'2 H5'1 ! 12 5 4 6 1 H3' ! 12 4 3 5 17 H2' ! 12 3 4 8 14 H1' ! 1 15 14 16 H6 ! 1 16 15 10 H5 ! 9 9 10 11 16 H41 H42 ! 7 17 4 3 HO'2 ! THY 20 ! P O1P O2P O3' O5' C1' C2' C3' C4' C5' O4' O4 C4 N3 C2 O2 N1 C6 C5 C7 8 ! 12 9 10 8 11 H4' ! 2 10 9 5 H5'2 H5'1 ! 12 8 7 9 4 H3' ! 2 7 6 8 H2'1 H2'2 ! 12 6 7 11 17 H1' ! 1 18 17 19 H6 ! 8 14 15 13 H3 ! 6 20 19 18 13 H71 H72 H73 ! DT 20 ! P O1P O2P O3' O5' C1' C2' C3' C4' C5' O4' O4 C4 N3 C2 O2 N1 C6 C5 C7 8 ! 12 9 10 8 11 H4' ! 2 10 9 5 H5'2 H5'1 ! 12 8 7 9 4 H3' ! 2 7 6 8 H2'1 H2'2 ! 12 6 7 11 17 H1' ! 1 18 17 19 H6 ! 8 14 15 13 H3 ! 6 20 19 18 13 H71 H72 H73 ! DT3 20 ! P O1P O2P O3' O5' C1' C2' C3' C4' C5' O4' O4 C4 N3 C2 O2 N1 C6 C5 C7 ! 9 ! 7 4 8 9 H3T ! 12 9 10 8 11 H4' ! 2 10 9 5 H5'2 H5'1 ! 12 8 7 9 4 H3' ! 2 7 6 8 H2'1 H2'2 ! 12 6 7 11 17 H1' ! 1 18 17 19 H6 ! 8 14 15 13 H3 ! 6 20 19 18 13 H71 H72 H73 ! DT5 17 ! O3' O5' C1' C2' C3' C4' C5' O4' O4 C4 N3 C2 O2 N1 C6 C5 C7 ! 9 ! 7 2 7 6 H5T ! 12 6 7 5 8 H4' ! 2 7 6 2 H5'2 H5'1 ! 12 5 4 6 1 H3' ! 2 4 3 5 H2'1 H2'2 ! 12 3 4 8 14 H1' ! 1 15 47 16 H6 ! 8 11 12 10 H3 ! 6 17 16 15 10 H71 H72 H73 ! RU 20 ! P O1P O2P O3' O5' C1' C2' C3' C4' C5' O4' O4 C4 N3 C2 O2 N1 C6 C5 O2' ! 9 ! 12 9 10 8 11 H4' ! 2 10 9 5 H5'2 H5'1 ! 12 8 7 9 4 H3' ! 12 7 6 8 21 H2' ! 12 6 7 11 17 H1' ! 1 18 17 19 H6 ! 8 14 15 13 H3 ! 1 19 18 13 H5 ! 7 20 7 6 HO'2 ! RU3 20 ! P O1P O2P O3' O5' C1' C2' C3' C4' C5' O4' O4 C4 N3 C2 O2 N1 C6 C5 O2' ! 10 ! 7 4 8 9 H3T ! 12 9 10 8 11 H4' ! 2 10 9 5 H5'2 H5'1 ! 12 8 7 9 4 H3' ! 12 7 6 8 21 H2' ! 12 6 7 11 17 H1' ! 1 18 17 19 H6 ! 8 14 15 13 H3 ! 1 19 18 13 H5 ! 7 20 7 6 HO'2 ! RU5 17 ! O3' O5' C1' C2' C3' C4' C5' O4' O4 C4 N3 C2 O2 N1 C6 C5 O2' ! 10 ! 7 2 7 6 H5T ! 12 6 7 5 8 H4' ! 2 7 6 2 H5'2 H5'1 ! 12 5 4 6 1 H3' ! 12 4 3 5 18 H2' ! 12 3 4 8 14 H1' ! 1 15 47 16 H6 ! 8 11 12 10 H3 ! 1 16 15 10 H5 ! 7 17 4 3 HO'2 ------------------------------------------------------------------------------ Temporary workarounds: none