! Topology definitions for retinal with protonated Schiff-base link ! to lysine (LYR). ! Use at your own risk! ! Compiled by: ! Jan Saam ! Humboldt-University Berlin ! Medizinische Fakultät (Charité) ! Institute for Biochemisty ! Monbijoustr. 2 ! 10117 Berlin ! Germany ! phone: +49 30 450 528 449 ! email: saam@charite.de ! Atoms defined for Retinal and Schiff base in Bacteriorhodospin ! and Rhodopsin (Mafalda Nina) MASS 64 HPL 1.00800 H ! Mafalda polyene Schiff base MASS 65 HPL1 1.00800 H ! Mafalda polyene Schiff base MASS 66 HAR 1.00800 H ! nonpolar H (idem HA for me SBH+ Mafalda ) MASS 67 HCR 1.00800 H ! Mafalda polyene Schiff base MASS 68 CTR 12.01100 C ! tetrahedral C (idem CT for SBH+ Mafalda) MASS 69 NCH1 14.00700 N ! protonated nitrogen Schiff base MASS 70 CR5 12.01100 C ! Aliphatic carbon SP2 MASS 71 CR6 12.01100 C ! Aliphatic carbon SP2 MASS 72 CR7 12.01100 C ! Aliphatic carbon SP2 MASS 73 CR8 12.01100 C ! Aliphatic carbon SP2 MASS 74 CR9 12.01100 C ! Aliphatic carbon SP2 MASS 75 CR10 12.01100 C ! Aliphatic carbon SP2 MASS 76 CR11 12.01100 C ! Aliphatic carbon SP2 MASS 77 CR12 12.01100 C ! Aliphatic carbon SP2 MASS 78 CR13 12.01100 C ! Aliphatic carbon SP2 MASS 79 CR14 12.01100 C ! Aliphatic carbon SP2 MASS 80 CR15 12.01100 C ! Aliphatic carbon SP2 RESI LYR 1.00 ! PROTONATED SCHIFF BASE ! ! Charges taken from: ! ------------------- ! Hayashi, S. and I. Ohmine. 2000. Proton transfer in ! bacteriorhodopsin: Structure, excitation and IR spectra, ! and potential energy surface analyses by an ab initio ! QM/MM method. J. Phys. Chem. B 104:10678 10691. ! ! Hayashi, S., E. Tajkhorshid, E. Pebay-Peyroula, A. Royant, ! E. M. Landau, J. Navarro, and K. Schulten. 2001. ! Structural determinants of spectral tuning in retinal proteins ! bacteriorhodopsin vs sensory rhodopsin II. J. Phys. Chem. B ! 105:10124 10131. ! GROUP ATOM N NH1 -0.47000 ! ALLOW PEP | ATOM HN H 0.31000 ! ALLOW PEP HN-N ATOM CA CT1 0.07000 ! ALLOW PEP | ATOM HA HB 0.09000 ! ALLOW PEP | GROUP ! HA-CA-----| ATOM C C 0.51000 ! ALLOW PEP | | ATOM O O -0.51000 ! ALLOW PEP | | GROUP ! O=C | ATOM CB CT2 -0.18000 ! ALLOW ALI | | ATOM HB1 HA 0.09000 ! ALLOW ALI HB2-CB-HB1 ATOM HB2 HA 0.09000 ! ALLOW ALI | GROUP ATOM CG CT2 -0.18000 ! ALLOW ALI | ATOM HG1 HA 0.09000 ! ALLOW ALI HG2-CG-HG1 ATOM HG2 HA 0.09000 ! ALLOW ALI | GROUP ATOM CD CT2 -0.18000 ! ALLOW ALI | ATOM HD1 HA 0.09000 ! ALLOW ALI HD2-CD-HD1 ATOM HD2 HA 0.09000 ! ALLOW ALI | GROUP ATOM CE CT2 0.340 ! 0.01 ! | ATOM HE1 HA 0.050 ! 0.20 ! HE2-CE-HE1 ATOM HE2 HA 0.050 ! 0.20 ! | ATOM N16 NCH1 -0.727 ! -0.65 ! H16-N16+ ATOM H16 HCR 0.505 ! 0.45 ! \\ ATOM C15 CR15 0.362 ! 0.25 ! C15-H15 ATOM H15 HPL1 0.189 ! 0.29 ! | ATOM C14 CR14 -0.180 ! -0.18 ! H20B C14-H14 ATOM H14 HPL 0.180 ! 0.20 ! | // ATOM C13 CR13 0.131 ! 0.13 ! H20A-C20 -- C13 ATOM C20 CT3 -0.170 ! -0.17 ! | | ATOM H20A HA 0.090 ! 0.09 ! H20C C12-H12 ATOM H20B HA 0.090 ! 0.09 ! \\ ATOM H20C HA 0.090 ! 0.09 ! H11-C11 ATOM C12 CR12 -0.110 ! -0.10 ! | ATOM H12 HPL 0.110 ! 0.10 ! H19B C10-H10 ATOM C11 CR11 -0.090 ! -0.10 ! | // ATOM H11 HPL 0.090 ! 0.10 ! H19A-C19 -- C9 ! | | GROUP ! H19C C8-H8 ATOM C10 CR10 -0.100 ! -0.10 ! // ATOM H10 HPL 0.100 ! 0.10 ! H7-C7 ! | GROUP ! C6 ATOM C9 CR9 0.00 ! | ATOM C19 CT3 -0.27 ! | ATOM H19A HA 0.09 ! ATOM H19B HA 0.09 ! | ATOM H19C HA 0.09 ! | GROUP ATOM C8 CR8 -0.10 ! | ATOM H8 HPL 0.10 ! | ATOM C7 CR7 -0.10 ! | ATOM H7 HPL 0.10 ! \ ! H17A H17B GROUP ! C6 \ / ATOM C6 CR6 0.00 ! // \ C17-H17C ! H18B // \ / H16B GROUP ! | // \/ | ATOM C5 CR5 0.00 ! H18A-C18 -- C5 C1 -- C16-H16A ATOM C18 CT3 -0.27 ! | | | | ATOM H18A HA 0.09 ! H18C | | H16C ATOM H18B HA 0.09 ! H4A-C4 C2-H2A ATOM H18C HA 0.09 ! / \ / \ ! H4B \ / H2B GROUP ! \ / ATOM C4 CT2 -0.20 ! C3-H3A ATOM H4A HA 0.10 ! \ ATOM H4B HA 0.10 ! H3B GROUP ATOM C3 CT2 -0.20 ATOM H3A HA 0.10 ATOM H3B HA 0.10 GROUP ATOM C2 CT2 -0.20 ATOM H2A HA 0.10 ATOM H2B HA 0.10 GROUP ATOM C1 CT3 0.00 ATOM C16 CT3 -0.27 ATOM H16A HA 0.09 ATOM H16B HA 0.09 ATOM H16C HA 0.09 GROUP ATOM C17 CT3 -0.27 ATOM H17A HA 0.09 ATOM H17B HA 0.09 ATOM H17C HA 0.09 BOND CB CA CG CB CD CG CE CD N16 CE BOND N HN N CA O C C CA BOND C +N CA HA CB HB1 CB HB2 CG HG1 BOND CG HG2 CD HD1 CD HD2 CE HE1 CE HE2 BOND C1 C2 C1 C6 C1 C16 C1 C17 BOND C2 C3 C2 H2A C2 H2B BOND C3 C4 C3 H3A C3 H3B BOND C4 C5 C4 H4A C4 H4B BOND C5 C6 C5 C18 BOND C6 C7 BOND C7 C8 C7 H7 BOND C8 C9 C8 H8 BOND C9 C10 C9 C19 BOND C10 C11 C10 H10 BOND C11 C12 C11 H11 BOND C12 C13 C12 H12 BOND C13 C14 C13 C20 BOND C14 C15 C14 H14 BOND C15 N16 C15 H15 N16 H16 BOND C16 H16A C16 H16B C16 H16C BOND C17 H17A C17 H17B C17 H17C BOND C18 H18A C18 H18B C18 H18C BOND C19 H19A C19 H19B C19 H19C BOND C20 H20A C20 H20B C20 H20C IMPR N -C CA HN C CA +N O IMPR C5 C6 C4 C18 IMPR C6 C1 C5 C7 IMPR C7 C8 C6 H7 IMPR C8 C7 C9 H8 IMPR C9 C10 C8 C19 IMPR C10 C9 C11 H10 IMPR C11 C12 C10 H11 IMPR C12 C11 C13 H12 IMPR C13 C14 C12 C20 IMPR C14 C13 C15 H14 IMPR C15 N16 C14 H15 IMPR N16 CE C15 H16 DONOR HN N DONOR H16 N16 ACCEPTOR O C IC -C CA *N HN 1.3482 123.5700 180.0000 115.1100 0.9988 IC -C N CA C 1.3482 123.5700 180.0000 107.2900 1.5187 IC N CA C +N 1.4504 107.2900 180.0000 117.2700 1.3478 IC +N CA *C O 1.3478 117.2700 180.0000 120.7900 1.2277 IC CA C +N +CA 1.5187 117.2700 180.0000 124.9100 1.4487 IC N C *CA CB 1.4504 107.2900 122.2300 111.3600 1.5568 IC N C *CA HA 1.4504 107.2900 -116.8800 107.3600 1.0833 IC N CA CB CG 1.4504 111.4700 180.0000 115.7600 1.5435 IC CG CA *CB HB1 1.5435 115.7600 120.9000 107.1100 1.1146 IC CG CA *CB HB2 1.5435 115.7600 -124.4800 108.9900 1.1131 IC CA CB CG CD 1.5568 115.7600 180.0000 113.2800 1.5397 IC CD CB *CG HG1 1.5397 113.2800 120.7400 109.1000 1.1138 IC CD CB *CG HG2 1.5397 113.2800 -122.3400 108.9900 1.1143 IC CB CG CD CE 1.5435 113.2800 180.0000 112.3300 1.5350 IC CE CG *CD HD1 1.5350 112.3300 122.2500 108.4100 1.1141 IC CE CG *CD HD2 1.5350 112.3300 -121.5900 108.1300 1.1146 IC CG CD CE N16 1.5397 112.3300 180.0000 110.4600 1.4604 IC N16 CD *CE HE1 1.4604 110.4600 119.9100 110.5100 1.1128 IC N16 CD *CE HE2 1.4604 110.4600 -120.0200 110.5700 1.1123 IC CD CE N16 H16 1.53 109 103.66 120 1.10 IC CD CE N16 C15 1.53 109 -76.44 120 1.35 IC CE N16 C15 C14 1.46 120 180.00 120 1.10 IC CE N16 C15 H15 1.46 120 0.00 120 1.10 IC C1 C2 C3 C4 1.58 0.00 0.00 0.00 1.58 IC C2 C3 C4 C5 1.58 0.00 0.00 0.00 0.0000 IC C2 C1 C6 C5 1.58 0.00 0.00 0.00 0.0000 IC C3 C4 C5 C6 1.58 0.00 0.00 0.00 0.0000 IC C3 C4 C5 C18 1.58 0.00 0.00 0.00 0.0000 IC C3 C2 C1 C6 1.58 0.00 0.00 0.00 0.0000 IC C3 C2 C1 C16 1.58 0.00 0.00 0.00 0.0000 IC C3 C2 C1 C17 1.58 0.00 0.00 0.00 0.0000 IC C4 C5 C6 C1 1.58 0.00 0.00 0.00 0.0000 IC C5 C6 C1 C2 1.58 0.00 0.00 0.00 0.0000 IC C5 C6 C1 C17 1.58 0.00 0.00 0.00 0.0000 IC C5 C6 C1 C16 1.58 0.00 0.00 0.00 0.0000 IC C7 C6 C1 C17 1.58 0.00 0.00 0.00 0.0000 IC C7 C6 C1 C16 1.58 0.00 0.00 0.00 0.0000 IC C2 C1 C6 C7 1.58 0.00 0.00 0.00 0.0000 IC C4 C5 C6 C7 1.58 0.00 0.00 0.00 0.0000 IC C1 C6 C7 C8 1.58 0.00 0.00 0.00 0.0000 IC C5 C6 C7 C8 1.58 0.00 0.00 120 1.58 IC C6 C7 C8 C9 1.58 120 180 120 1.58 IC C7 C8 C9 C10 1.58 120 180 120 1.58 IC C8 C9 C10 C11 1.58 120 180 120 1.58 IC C9 C10 C11 C12 1.58 120 180 120 1.58 IC C10 C11 C12 C13 1.58 120 0.00 120 1.58 ! cis IC C11 C12 C13 C14 1.58 120 180 120 1.58 IC C12 C13 C14 C15 1.58 120 180 120 1.58 IC C13 C14 C15 N16 1.58 120 180 120 1.35 IC C7 C8 C9 C19 1.58 120 0.00 120 1.58 IC C19 C9 C10 C11 1.58 120 0.00 120 1.58 IC C19 C9 C8 C7 1.58 120 0.00 120 1.58 IC C20 C13 C12 C11 1.58 120 0.00 120 1.58 IC C20 C13 C14 C15 1.58 120 0.00 120 1.58 ! all hydrogen atoms !IC H14 C14 C15 N16 1.10 120 0.00 120 1.35 IC C15 CE *N16 H16 1.58 120 180.00 120 1.10 !IC H14 C14 C15 H15 1.10 120 180.00 120 1.10 !IC C14 N16 *C15 H15 1.58 120 180.00 120 1.10 ! let psfgen guess this one IC H14 C14 C13 C20 1.10 120 180.00 120 1.58 !IC H14 C14 C13 C12 1.10 120 0.00 120 1.58 IC C15 C13 *C14 H14 1.58 120 180.00 120 1.10 IC C14 C13 C20 H20A 1.58 120 180.00 109 1.10 IC C14 C13 C20 H20B 1.58 120 60.00 109 1.10 IC C14 C13 C20 H20C 1.58 120 -60.00 109 1.10 !IC C20 C13 C12 H12 1.58 120 180.00 109 1.10 !IC H12 C12 C11 C10 1.10 120 180.00 120 1.58 IC C13 C11 *C12 H12 1.58 120 180.00 120 1.10 !IC H11 C11 C10 C9 1.10 120 0.00 120 1.58 !IC H11 *C11 C12 C10 1.10 120 180.00 120 1.58 IC C10 C12 *C11 H11 1.58 120 180.00 120 1.10 !IC H10 C10 C9 C19 1.10 120 180.00 120 1.58 !IC H10 C10 C9 C8 1.10 120 0.00 120 1.58 IC C9 C11 *C10 H10 1.58 120 180.00 120 1.10 IC C10 C9 C19 H19A 1.58 120 180.00 109 1.10 IC C10 C9 C19 H19B 1.58 120 60.00 109 1.10 IC C10 C9 C19 H19C 1.58 120 -60.00 109 1.10 !IC C10 C9 C8 H8 1.58 120 0.00 120 1.10 !IC H8 C8 C7 C6 1.10 120 0.00 120 1.58 IC C7 C9 *C8 H8 1.58 120 180.00 120 1.10 !IC H7 C7 C6 C1 1.10 120 0.00 120 1.58 !IC H7 C7 C6 C5 1.10 120 180.00 120 1.58 !IC H7 C7 C8 C9 1.10 120 0.00 120 1.58 IC C6 C8 *C7 H7 1.58 120 180.00 120 1.10 IC C6 C1 C17 H17A 1.58 125 180.00 109 1.10 IC C6 C1 C17 H17B 1.58 0.00 60.00 109 1.10 IC C6 C1 C17 H17C 1.58 0.00 -60.00 109 1.10 IC C6 C1 C16 H16A 1.58 0.00 180.00 109 1.10 IC C6 C1 C16 H16B 1.58 0.00 60.00 109 1.10 IC C6 C1 C16 H16C 1.58 111.68 -60.00 109 1.10 IC C17 C1 C2 H2A 1.58 100.40 -60.00 109 1.10 IC C17 C1 C2 H2B 1.58 100.40 60.00 109 1.10 IC C1 C2 C3 H3A 1.58 113.17 -60.00 109 1.10 IC C1 C2 C3 H3B 1.58 113.17 180.00 109 1.10 IC H4A C4 C5 C18 1.10 109 -20.00 112.17 1.58 IC H4B C4 C5 C18 1.10 109 100.00 112.17 1.58 IC C4 C5 C18 H18A 1.58 112.17 180.00 109 1.10 IC C4 C5 C18 H18B 1.58 112.17 -60.00 109 1.10 IC C4 C5 C18 H18C 1.58 112.17 60.00 109 1.10 ! ! PATCH FIRST NONE LAST NONE