REMARK To keep xtal waters intact, add hydrogens using VMD. The parts end REMARK up having resname TIP3 and atomnames OH2, HI, and H2. As DOWSER REMARK has a silly way of reading in the resname, this residue appears REMARK as TIP in the dictionary. Note that retaining oxygens (xtal waters REMARK without hydrogens) would be much more tricky! REMARK REMARK Ribonucleotides adapted from GROMOS FF (ffgmx.rtp). REMARK Hence, all hydrogens are not explicitly represented. REMARK Assumes input PDB contains all RNA heavy atoms, except REMARK for the phosphate group in the 5' terminal end. REMARK REMARK Modified from Cameron Mura's DNA extension. Note REMARK that we need to REMARK - add uracil, REMARK - add O2* to all residues, and REMARK - pay attention to the charges (not same in, eg, REMARK DGUA and GUA). REMARK See below for other modifications. REMARK REMARK Note that as far as LJ parameters are concerned for REMARK the atom types: REMARK O = OM = OS, CS2 = CH2, CS1 = CH1, REMARK NR5* = NR5 = NR6* = NR6 = N, REMARK CR51 and CR61 correspond to CHR, and CB corresponds to CR. REMARK Therefore the atom types need not be the same as in REMARK ffgmx.rtp. REMARK REMARK Cameron Mura had set OS = OA, which does not seem to be REMARK the case. Why? Probably does not matter much. REMARK Will make them Os instead. This is the case for REMARK O5*, O4*, O3*. REMARK REMARK Mura has, in the 5' termini, whose force fields are very REMARK hard to find, hydrogenated the terminal oxygen such REMARK that the hydrogen and oxygen have charges that take out each REMARK other. More important, I'd rather keep the phosphate in the REMARK 5' terminal end, as does patch 5PHO (as opposed 5TER). REMARK Further, there is a no hydrogen in the O3' of the 3' terminus. REMARK REMARK As force field parameters for termini were few and far between, REMARK I made some educated guesses, that are good enough. REMARK My educated guesses are based on CHARMM, adapted to the GROMOS FF REMARK used here. They also are more or less in line with OPLS. REMARK The procedure is a as follows. REMARK REMARK 1. In 5' end, CHARMM's 5PHO makes O1P, O2P, and O5' about 5% more REMARK negative than in the non-terminal residues. Hence, I chose REMARK values -0.67 for O1P and O2P, and -0.38 for O5'. REMARK 2. In the CHARMM 5PHO, O5T is slightly more negative than O5'. I REMARK decided to give it a charge of -0.42. REMARK 3. In the CHARMM 5PHO, H5T is half of the absolute value of REMARK O5T. I therefore assigned H5T a charge of 0.21. REMARK 4. The total charge of the 5' terminal resisue is now -1.3. As REMARK the total charge of the two terminal residues must be -2.0, REMARK we know that the charge of the 3' terminus must be 0.7. REMARK 5. In the CHARMM 3TER, O3' is about the same as O5T, a tiny REMARK bit lower. As we assigned a charge of -0.42 to O5T, we will REMARK give a charge -0.38 to O3'. REMARK 6. Again in the CHARMM 3TER, H3T has a charge that is REMARK approximately 2/3 of the absolute value of O3T. We therefore REMARK give it a value 0.25. REMARK 7. In the CHARMM 3TER, charge of C3' changes from 0.01 to REMARK 0.14 when a non-terminal residue becomes a terminal one. REMARK So, C3' has to become somewhat more positive. As the whole REMARK residue needs to have charge 0.7, we can figure out that REMARK it has to be given a charge of 0.07. REMARK REMARK Added MO6, MO5, MO4, MO3, MO2. Doing this with DOWSER needs tricks REMARK to the actual reformatPDB.c file. The orientations of the REMARK of the waters (hydrogens) here are not perhaps wonderful, REMARK probably decent enough. Oh, and MO1 is not doable, REMARK but needs to be done as an MG residue and a TIP water. :( REMARK REMARK ---------- GUANINE ---------------------------------------- RESIDUE G ATOM G P NOT NOT 0.000 0.000 0.0 0.990 P ATOM G O1P NOT NOT 0.000 0.000 0.0 -0.635 O ATOM G O2P NOT NOT 0.000 0.000 0.0 -0.635 O ATOM G O5* NOT NOT 0.000 0.000 0.0 -0.360 O ATOM G C5* NOT NOT 0.000 0.000 0.0 0.000 CH2 ATOM G C4* NOT NOT 0.000 0.000 0.0 0.160 CH1 ATOM G O4* NOT NOT 0.000 0.000 0.0 -0.360 O ATOM G C1* NOT NOT 0.000 0.000 0.0 0.200 CH1 ATOM G N9 NOT NOT 0.000 0.000 0.0 -0.200 N ATOM G C4 NOT NOT 0.000 0.000 0.0 0.200 CR ATOM G N3 NOT NOT 0.000 0.000 0.0 -0.360 N ATOM G C2 N3 N2 0.000 0.000 0.0 0.360 CR ATOM G N2 C2 H22 0.000 0.000 0.0 -0.830 N ATOM G H21 N2 NOT 1.000 120.000 180.0 0.415 H ATOM G H22 N2 NOT 1.000 120.000 0.0 0.415 H ATOM G N1 C2 H1 0.000 0.000 0.0 -0.280 N ATOM G H1 N1 NOT 1.000 120.000 180.0 0.280 H ATOM G C6 NOT NOT 0.000 0.000 0.0 0.380 CR ATOM G O6 NOT NOT 0.000 0.000 0.0 -0.380 O ATOM G C5 NOT NOT 0.000 0.000 0.0 0.000 CR ATOM G N7 NOT NOT 0.000 0.000 0.0 -0.360 N ATOM G C8 NOT NOT 0.000 0.000 0.0 0.360 CHR ATOM G C3* NOT NOT 0.000 0.000 0.0 0.000 CH1 ATOM G C2* C3* O2* 0.000 0.000 0.0 0.150 CH1 ATOM G O2* C2* H2* 0.000 0.000 0.0 -0.548 OA ATOM G H2* O2* NOT 1.000 115.000 148.6 0.398 H ATOM G O3* NOT NOT 0.000 0.000 0.0 -0.360 O REMARK NOTE: had to slightly reorder the terminal sugar atoms so REMARK that defined ones lie ahead in the list of undefined REMARK ones ("defined" = coordinated provided in input PDB). RESIDUE G5 ATOM G5 C4* NOT NOT 0.000 0.000 0.0 0.160 CH1 ATOM G5 O4* NOT NOT 0.000 0.000 0.0 -0.360 O ATOM G5 C1* NOT NOT 0.000 0.000 0.0 0.200 CH1 ATOM G5 C5* C4* O5* 0.000 0.000 0.0 0.000 CH2 ATOM G5 O5* C5* H5T 0.000 0.000 0.0 -0.398 OA ATOM G5 H5T O5* NOT 1.000 109.500 180.0 0.398 H ATOM G5 N9 NOT NOT 0.000 0.000 0.0 -0.200 N ATOM G5 C4 NOT NOT 0.000 0.000 0.0 0.200 CR ATOM G5 N3 NOT NOT 0.000 0.000 0.0 -0.360 N ATOM G5 C2 N3 N2 0.000 0.000 0.0 0.360 CR ATOM G5 N2 C2 H22 0.000 0.000 0.0 -0.830 N ATOM G5 H21 N2 NOT 1.000 120.000 180.0 0.415 H ATOM G5 H22 N2 NOT 1.000 120.000 0.0 0.415 H ATOM G5 N1 C2 H1 0.000 0.000 0.0 -0.280 N ATOM G5 H1 N1 NOT 1.000 120.000 180.0 0.280 H ATOM G5 C6 NOT NOT 0.000 0.000 0.0 0.380 CR ATOM G5 O6 NOT NOT 0.000 0.000 0.0 -0.380 O ATOM G5 C5 NOT NOT 0.000 0.000 0.0 0.000 CR ATOM G5 N7 NOT NOT 0.000 0.000 0.0 -0.360 N ATOM G5 C8 NOT NOT 0.000 0.000 0.0 0.360 CHR ATOM G5 C3* NOT NOT 0.000 0.000 0.0 0.000 CH1 ATOM G5 C2* C3* O2* 0.000 0.000 0.0 0.150 CH1 ATOM G5 O2* C2* H2* 0.000 0.000 0.0 -0.548 OA ATOM G5 H2* O2* NOT 1.000 115.000 148.6 0.398 H ATOM G5 O3* NOT NOT 0.000 0.000 0.0 -0.360 O RESIDUE G3 ATOM G3 P NOT NOT 0.000 0.000 0.0 0.990 P ATOM G3 O1P NOT NOT 0.000 0.000 0.0 -0.635 O ATOM G3 O2P NOT NOT 0.000 0.000 0.0 -0.635 O ATOM G3 O5* NOT NOT 0.000 0.000 0.0 -0.360 O ATOM G3 C5* NOT NOT 0.000 0.000 0.0 0.000 CH2 ATOM G3 C4* NOT NOT 0.000 0.000 0.0 0.160 CH1 ATOM G3 O4* NOT NOT 0.000 0.000 0.0 -0.360 O ATOM G3 C1* NOT NOT 0.000 0.000 0.0 0.200 CH1 ATOM G3 N9 NOT NOT 0.000 0.000 0.0 -0.200 N ATOM G3 C4 NOT NOT 0.000 0.000 0.0 0.200 CR ATOM G3 N3 NOT NOT 0.000 0.000 0.0 -0.360 N ATOM G3 C2 N3 N2 0.000 0.000 0.0 0.360 CR ATOM G3 N2 C2 H22 0.000 0.000 0.0 -0.830 N ATOM G3 H21 N2 NOT 1.000 120.000 180.0 0.415 H ATOM G3 H22 N2 NOT 1.000 120.000 0.0 0.415 H ATOM G3 N1 C2 H1 0.000 0.000 0.0 -0.280 N ATOM G3 H1 N1 NOT 1.000 120.000 180.0 0.280 H ATOM G3 C6 NOT NOT 0.000 0.000 0.0 0.380 CR ATOM G3 O6 NOT NOT 0.000 0.000 0.0 -0.380 O ATOM G3 C5 NOT NOT 0.000 0.000 0.0 0.000 CR ATOM G3 N7 NOT NOT 0.000 0.000 0.0 -0.360 N ATOM G3 C8 NOT NOT 0.000 0.000 0.0 0.360 CHR ATOM G3 C3* C4* NOT 0.000 0.000 0.0 0.070 CH1 ATOM G3 C2* C3* O2* 0.000 0.000 0.0 0.150 CH1 ATOM G3 O2* C2* H2* 0.000 0.000 0.0 -0.548 OA ATOM G3 H2* O2* NOT 1.000 115.000 148.6 0.398 H ATOM G3 O3* C3* NOT 0.000 0.000 0.0 -0.380 OA ATOM G3 H3T O3* NOT 1.000 115.000 148.6 0.250 H REMARK ---------- URACIL ---------------------------------------- RESIDUE U ATOM U P NOT NOT 0.000 0.000 0.0 0.990 P ATOM U O1P NOT NOT 0.000 0.000 0.0 -0.635 O ATOM U O2P NOT NOT 0.000 0.000 0.0 -0.635 O ATOM U O5* NOT NOT 0.000 0.000 0.0 -0.360 O ATOM U C5* NOT NOT 0.000 0.000 0.0 0.000 CH2 ATOM U C4* NOT NOT 0.000 0.000 0.0 0.160 CH1 ATOM U O4* NOT NOT 0.000 0.000 0.0 -0.360 O ATOM U C1* NOT NOT 0.000 0.000 0.0 0.200 CH1 ATOM U N1 NOT NOT 0.000 0.000 0.0 -0.200 N ATOM U C6 NOT NOT 0.000 0.000 0.0 0.200 CHR ATOM U C2 N1 N3 0.000 0.000 0.0 0.380 CR ATOM U O2 NOT NOT 0.000 0.000 0.0 -0.380 O ATOM U N3 C2 C4 0.000 0.000 0.0 -0.280 N ATOM U H3 N3 NOT 1.000 120.000 180.0 0.280 H ATOM U C4 NOT NOT 0.000 0.000 0.0 0.380 CR ATOM U O4 NOT NOT 0.000 0.000 0.0 -0.380 O ATOM U C5 NOT NOT 0.000 0.000 0.0 0.000 CHR ATOM U C3* NOT NOT 0.000 0.000 0.0 0.000 CH1 ATOM U C2* C3* O2* 0.000 0.000 0.0 0.150 CH1 ATOM U O2* C2* H2* 0.000 0.000 0.0 -0.548 OA ATOM U H2* O2* NOT 1.000 115.000 148.6 0.398 H ATOM U O3* NOT NOT 0.000 0.000 0.0 -0.360 O RESIDUE U5 ATOM U5 C4* NOT NOT 0.000 0.000 0.0 0.160 CH1 ATOM U5 O4* NOT NOT 0.000 0.000 0.0 -0.360 O ATOM U5 C1* NOT NOT 0.000 0.000 0.0 0.200 CH1 ATOM U5 C5* C4* O5* 0.000 0.000 0.0 0.000 CH2 ATOM U5 O5* C5* H5T 0.000 0.000 0.0 -0.398 OA ATOM U5 H5T O5* NOT 1.000 109.500 180.0 0.398 H ATOM U5 N1 NOT NOT 0.000 0.000 0.0 -0.200 N ATOM U5 C6 NOT NOT 0.000 0.000 0.0 0.200 CHR ATOM U5 C2 N1 N3 0.000 0.000 0.0 0.380 CR ATOM U5 O2 NOT NOT 0.000 0.000 0.0 -0.380 O ATOM U5 N3 C2 C4 0.000 0.000 0.0 -0.280 N ATOM U5 H3 N3 NOT 1.000 120.000 180.0 0.280 H ATOM U5 C4 NOT NOT 0.000 0.000 0.0 0.380 CR ATOM U5 O4 NOT NOT 0.000 0.000 0.0 -0.380 O ATOM U5 C5 NOT NOT 0.000 0.000 0.0 0.000 CHR ATOM U5 C3* NOT NOT 0.000 0.000 0.0 0.000 CH1 ATOM U5 C2* C3* O2* 0.000 0.000 0.0 0.150 CH1 ATOM U5 O2* C2* H2* 0.000 0.000 0.0 -0.548 OA ATOM U5 H2* O2* NOT 1.000 115.000 148.6 0.398 H ATOM U5 O3* NOT NOT 0.000 0.000 0.0 -0.360 O RESIDUE U3 ATOM U3 P NOT NOT 0.000 0.000 0.0 0.990 P ATOM U3 O1P NOT NOT 0.000 0.000 0.0 -0.635 O ATOM U3 O2P NOT NOT 0.000 0.000 0.0 -0.635 O ATOM U3 O5* NOT NOT 0.000 0.000 0.0 -0.360 O ATOM U3 C5* NOT NOT 0.000 0.000 0.0 0.000 CH2 ATOM U3 C4* NOT NOT 0.000 0.000 0.0 0.160 CH1 ATOM U3 O4* NOT NOT 0.000 0.000 0.0 -0.360 O ATOM U3 C1* NOT NOT 0.000 0.000 0.0 0.200 CH1 ATOM U3 N1 NOT NOT 0.000 0.000 0.0 -0.200 N ATOM U3 C6 NOT NOT 0.000 0.000 0.0 0.200 CHR ATOM U3 C2 N1 N3 0.000 0.000 0.0 0.380 CR ATOM U3 O2 NOT NOT 0.000 0.000 0.0 -0.380 O ATOM U3 N3 C2 C4 0.000 0.000 0.0 -0.280 N ATOM U3 H3 N3 NOT 1.000 120.000 180.0 0.280 H ATOM U3 C4 NOT NOT 0.000 0.000 0.0 0.380 CR ATOM U3 O4 NOT NOT 0.000 0.000 0.0 -0.380 O ATOM U3 C5 NOT NOT 0.000 0.000 0.0 0.000 CHR ATOM U3 C3* C4* NOT 0.000 0.000 0.0 0.070 CH1 ATOM U3 C2* C3* O2* 0.000 0.000 0.0 0.150 CH1 ATOM U3 O2* C2* H2* 0.000 0.000 0.0 -0.548 OA ATOM U3 H2* O2* NOT 1.000 115.000 148.6 0.398 H ATOM U3 O3* C3* NOT 0.000 0.000 0.0 -0.380 OA ATOM U3 H3T O3* NOT 1.000 115.000 148.6 0.250 H REMARK ---------- CYTOSINE --------------------------------------- RESIDUE C ATOM C P NOT NOT 0.000 0.000 0.0 0.990 P ATOM C O1P NOT NOT 0.000 0.000 0.0 -0.635 O ATOM C O2P NOT NOT 0.000 0.000 0.0 -0.635 O ATOM C O5* NOT NOT 0.000 0.000 0.0 -0.360 O ATOM C C5* NOT NOT 0.000 0.000 0.0 0.000 CH2 ATOM C C4* NOT NOT 0.000 0.000 0.0 0.160 CH1 ATOM C O4* NOT NOT 0.000 0.000 0.0 -0.360 O ATOM C C1* NOT NOT 0.000 0.000 0.0 0.200 CH1 ATOM C N1 NOT NOT 0.000 0.000 0.0 -0.200 N ATOM C C6 NOT NOT 0.000 0.000 0.0 0.200 CHR ATOM C C2 NOT NOT 0.000 0.000 0.0 0.380 CR ATOM C O2 NOT NOT 0.000 0.000 0.0 -0.380 O ATOM C N3 NOT NOT 0.000 0.000 0.0 -0.360 N ATOM C C4 N3 C5 0.000 0.000 0.0 0.360 CR ATOM C N4 C4 H42 0.000 0.000 0.0 -0.830 N ATOM C H41 N4 NOT 1.000 120.000 180.0 0.415 H ATOM C H42 N4 NOT 1.000 120.000 0.0 0.415 H ATOM C C5 NOT NOT 0.000 0.000 0.0 0.000 CHR ATOM C C3* NOT NOT 0.000 0.000 0.0 0.000 CH1 ATOM C C2* C3* O2* 0.000 0.000 0.0 0.150 CH1 ATOM C O2* C2* H2* 0.000 0.000 0.0 -0.548 OA ATOM C H2* O2* NOT 1.000 115.000 148.6 0.398 H ATOM C O3* NOT NOT 0.000 0.000 0.0 -0.360 O RESIDUE C5 ATOM C5 C4* NOT NOT 0.000 0.000 0.0 0.160 CH1 ATOM C5 O4* NOT NOT 0.000 0.000 0.0 -0.360 O ATOM C5 C1* NOT NOT 0.000 0.000 0.0 0.200 CH1 ATOM C5 C5* C4* O5* 0.000 0.000 0.0 0.000 CH2 ATOM C5 O5* C5* H5T 0.000 0.000 0.0 -0.398 OA ATOM C5 H5T O5* NOT 1.000 109.500 180.0 0.398 H ATOM C5 N1 NOT NOT 0.000 0.000 0.0 -0.200 N ATOM C5 C6 NOT NOT 0.000 0.000 0.0 0.200 CHR ATOM C5 C2 NOT NOT 0.000 0.000 0.0 0.380 CR ATOM C5 O2 NOT NOT 0.000 0.000 0.0 -0.380 O ATOM C5 N3 NOT NOT 0.000 0.000 0.0 -0.360 N ATOM C5 C4 N3 C5 0.000 0.000 0.0 0.360 CR ATOM C5 N4 C4 H42 0.000 0.000 0.0 -0.830 N ATOM C5 H41 N4 NOT 1.000 120.000 180.0 0.415 H ATOM C5 H42 N4 NOT 1.000 120.000 0.0 0.415 H ATOM C5 C5 NOT NOT 0.000 0.000 0.0 0.000 CHR ATOM C5 C3* NOT NOT 0.000 0.000 0.0 0.000 CH1 ATOM C5 C2* C3* O2* 0.000 0.000 0.0 0.150 CH1 ATOM C5 O2* C2* H2* 0.000 0.000 0.0 -0.548 OA ATOM C5 H2* O2* NOT 1.000 115.000 148.6 0.398 H ATOM C5 O3* NOT NOT 0.000 0.000 0.0 -0.360 O RESIDUE C3 ATOM C3 P NOT NOT 0.000 0.000 0.0 0.990 P ATOM C3 O1P NOT NOT 0.000 0.000 0.0 -0.635 O ATOM C3 O2P NOT NOT 0.000 0.000 0.0 -0.635 O ATOM C3 O5* NOT NOT 0.000 0.000 0.0 -0.360 O ATOM C3 C5* NOT NOT 0.000 0.000 0.0 0.000 CH2 ATOM C3 C4* NOT NOT 0.000 0.000 0.0 0.160 CH1 ATOM C3 O4* NOT NOT 0.000 0.000 0.0 -0.360 O ATOM C3 C1* NOT NOT 0.000 0.000 0.0 0.200 CH1 ATOM C3 N1 NOT NOT 0.000 0.000 0.0 -0.200 N ATOM C3 C6 NOT NOT 0.000 0.000 0.0 0.200 CHR ATOM C3 C2 NOT NOT 0.000 0.000 0.0 0.380 CR ATOM C3 O2 NOT NOT 0.000 0.000 0.0 -0.380 O ATOM C3 N3 NOT NOT 0.000 0.000 0.0 -0.360 N ATOM C3 C4 N3 C5 0.000 0.000 0.0 0.360 CR ATOM C3 N4 C4 H42 0.000 0.000 0.0 -0.830 N ATOM C3 H41 N4 NOT 1.000 120.000 180.0 0.415 H ATOM C3 H42 N4 NOT 1.000 120.000 0.0 0.415 H ATOM C3 C5 NOT NOT 0.000 0.000 0.0 0.000 CHR ATOM C3 C3* C4* NOT 0.000 0.000 0.0 0.070 CH1 ATOM C3 C2* C3* O2* 0.000 0.000 0.0 0.150 CH1 ATOM C3 O2* C2* H2* 0.000 0.000 0.0 -0.548 OA ATOM C3 H2* O2* NOT 1.000 115.000 148.6 0.398 H ATOM C3 O3* C3* NOT 0.000 0.000 0.0 -0.380 OA ATOM C3 H3T O3* NOT 1.000 115.000 148.6 0.250 H REMARK ---------- ADENINE ---------------------------------------- RESIDUE A ATOM A P NOT NOT 0.000 0.000 0.0 0.990 P ATOM A O1P NOT NOT 0.000 0.000 0.0 -0.635 O ATOM A O2P NOT NOT 0.000 0.000 0.0 -0.635 O ATOM A O5* NOT NOT 0.000 0.000 0.0 -0.360 O ATOM A C5* NOT NOT 0.000 0.000 0.0 0.000 CH2 ATOM A C4* NOT NOT 0.000 0.000 0.0 0.160 CH1 ATOM A O4* NOT NOT 0.000 0.000 0.0 -0.360 O ATOM A C1* NOT NOT 0.000 0.000 0.0 0.200 CH1 ATOM A N9 NOT NOT 0.000 0.000 0.0 -0.200 N ATOM A C4 NOT NOT 0.000 0.000 0.0 0.200 CR ATOM A N3 NOT NOT 0.000 0.000 0.0 -0.360 N ATOM A C2 NOT NOT 0.000 0.000 0.0 0.360 CHR ATOM A N1 NOT NOT 0.000 0.000 0.0 -0.360 N ATOM A C6 N1 C5 0.000 0.000 0.0 0.360 CR ATOM A N6 C6 H62 0.000 0.000 0.0 -0.830 N ATOM A H61 N6 NOT 1.000 120.000 180.0 0.415 H ATOM A H62 N6 NOT 1.000 120.000 0.0 0.415 H ATOM A C5 NOT NOT 0.000 0.000 0.0 0.000 CR ATOM A N7 NOT NOT 0.000 0.000 0.0 -0.360 N ATOM A C8 NOT NOT 0.000 0.000 0.0 0.360 CHR ATOM A C3* NOT NOT 0.000 0.000 0.0 0.000 CH1 ATOM A C2* C3* O2* 0.000 0.000 0.0 0.150 CH1 ATOM A O2* C2* H2* 0.000 0.000 0.0 -0.548 OA ATOM A H2* O2* NOT 1.000 115.000 148.6 0.398 H ATOM A O3* NOT NOT 0.000 0.000 0.0 -0.360 O RESIDUE A5 ATOM A5 C4* NOT NOT 0.000 0.000 0.0 0.160 CH1 ATOM A5 O4* NOT NOT 0.000 0.000 0.0 -0.360 O ATOM A5 C1* NOT NOT 0.000 0.000 0.0 0.200 CH1 ATOM A5 C5* C4* O5* 0.000 0.000 0.0 0.000 CH2 ATOM A5 O5* C5* H5T 0.000 0.000 0.0 -0.398 OA ATOM A5 H5T O5* NOT 1.000 109.500 180.0 0.398 H ATOM A5 N9 NOT NOT 0.000 0.000 0.0 -0.200 N ATOM A5 C4 NOT NOT 0.000 0.000 0.0 0.200 CR ATOM A5 N3 NOT NOT 0.000 0.000 0.0 -0.360 N ATOM A5 C2 NOT NOT 0.000 0.000 0.0 0.360 CHR ATOM A5 N1 NOT NOT 0.000 0.000 0.0 -0.360 N ATOM A5 C6 N1 C5 0.000 0.000 0.0 0.360 CR ATOM A5 N6 C6 H62 0.000 0.000 0.0 -0.830 N ATOM A5 H61 N6 NOT 1.000 120.000 180.0 0.415 H ATOM A5 H62 N6 NOT 1.000 120.000 0.0 0.415 H ATOM A5 C5 NOT NOT 0.000 0.000 0.0 0.000 CR ATOM A5 N7 NOT NOT 0.000 0.000 0.0 -0.360 N ATOM A5 C8 NOT NOT 0.000 0.000 0.0 0.360 CHR ATOM A5 C3* NOT NOT 0.000 0.000 0.0 0.000 CH1 ATOM A5 C2* C3* O2* 0.000 0.000 0.0 0.150 CH1 ATOM A5 O2* C2* H2* 0.000 0.000 0.0 -0.548 OA ATOM A5 H2* O2* NOT 1.000 115.000 148.6 0.398 H ATOM A5 O3* NOT NOT 0.000 0.000 0.0 -0.360 O RESIDUE A3 ATOM A3 P NOT NOT 0.000 0.000 0.0 0.990 P ATOM A3 O1P NOT NOT 0.000 0.000 0.0 -0.635 O ATOM A3 O2P NOT NOT 0.000 0.000 0.0 -0.635 O ATOM A3 O5* NOT NOT 0.000 0.000 0.0 -0.360 O ATOM A3 C5* NOT NOT 0.000 0.000 0.0 0.000 CH2 ATOM A3 C4* NOT NOT 0.000 0.000 0.0 0.160 CH1 ATOM A3 O4* NOT NOT 0.000 0.000 0.0 -0.360 O ATOM A3 C1* NOT NOT 0.000 0.000 0.0 0.200 CH1 ATOM A3 N9 NOT NOT 0.000 0.000 0.0 -0.200 N ATOM A3 C4 NOT NOT 0.000 0.000 0.0 0.200 CR ATOM A3 N3 NOT NOT 0.000 0.000 0.0 -0.360 N ATOM A3 C2 NOT NOT 0.000 0.000 0.0 0.360 CHR ATOM A3 N1 NOT NOT 0.000 0.000 0.0 -0.360 N ATOM A3 C6 N1 C5 0.000 0.000 0.0 0.360 CR ATOM A3 N6 C6 H62 0.000 0.000 0.0 -0.830 N ATOM A3 H61 N6 NOT 1.000 120.000 180.0 0.415 H ATOM A3 H62 N6 NOT 1.000 120.000 0.0 0.415 H ATOM A3 C5 NOT NOT 0.000 0.000 0.0 0.000 CR ATOM A3 N7 NOT NOT 0.000 0.000 0.0 -0.360 N ATOM A3 C8 NOT NOT 0.000 0.000 0.0 0.360 CHR ATOM A3 C3* C4* NOT 0.000 0.000 0.0 0.070 CH1 ATOM A3 C2* C3* O2* 0.000 0.000 0.0 0.150 CH1 ATOM A3 O2* C2* H2* 0.000 0.000 0.0 -0.548 OA ATOM A3 H2* O2* NOT 1.000 115.000 148.6 0.398 H ATOM A3 O3* C3* NOT 0.000 0.000 0.0 -0.380 OA ATOM A3 H3T O3* NOT 1.000 115.000 148.6 0.250 H REMARK ---------- MAGNESIUMS ---------------------------------------- RESIDUE MO6 ATOM MO6 O1 NOT MG 0.000 0.0 0.0 -0.820 OW ATOM MO6 MG O1 O6 0.000 0.0 0.0 2.000 MG ATOM MO6 O2 MG H22 0.000 0.0 0.0 -0.820 OW ATOM MO6 H21 O2 NOT 1.000 125.3 90.0 0.410 H ATOM MO6 H22 O2 NOT 1.000 125.3 -90.0 0.410 H ATOM MO6 O3 MG H32 0.000 0.0 0.0 -0.820 OW ATOM MO6 H31 O3 NOT 1.000 125.3 180.0 0.410 H ATOM MO6 H32 O3 NOT 1.000 125.3 0.0 0.410 H ATOM MO6 O4 MG H42 0.000 0.0 0.0 -0.820 OW ATOM MO6 H41 O4 NOT 1.000 125.3 180.0 0.410 H ATOM MO6 H42 O4 NOT 1.000 125.3 0.0 0.410 H ATOM MO6 O5 MG H52 0.000 0.0 0.0 -0.820 OW ATOM MO6 H51 O5 NOT 1.000 125.3 90.0 0.410 H ATOM MO6 H52 O5 NOT 1.000 125.3 -90.0 0.410 H ATOM MO6 O6 MG H62 0.000 0.0 0.0 -0.820 OW ATOM MO6 H61 O6 NOT 1.000 125.3 90.0 0.410 H ATOM MO6 H62 O6 NOT 1.000 125.3 -90.0 0.410 H ATOM MO6 H11 O1 NOT 1.000 125.3 180.0 0.410 H ATOM MO6 H12 O1 NOT 1.000 125.3 0.0 0.410 H RESIDUE MO5 ATOM MO5 O1 NOT MG 0.000 0.0 0.0 -0.820 OW ATOM MO5 MG O1 O5 0.000 0.0 0.0 2.000 MG ATOM MO5 O2 MG H22 0.000 0.0 0.0 -0.820 OW ATOM MO5 H21 O2 NOT 1.000 125.3 90.0 0.410 H ATOM MO5 H22 O2 NOT 1.000 125.3 -90.0 0.410 H ATOM MO5 O3 MG H32 0.000 0.0 0.0 -0.820 OW ATOM MO5 H31 O3 NOT 1.000 125.3 180.0 0.410 H ATOM MO5 H32 O3 NOT 1.000 125.3 0.0 0.410 H ATOM MO5 O4 MG H42 0.000 0.0 0.0 -0.820 OW ATOM MO5 H41 O4 NOT 1.000 125.3 180.0 0.410 H ATOM MO5 H42 O4 NOT 1.000 125.3 0.0 0.410 H ATOM MO5 O5 MG H52 0.000 0.0 0.0 -0.820 OW ATOM MO5 H51 O5 NOT 1.000 125.3 90.0 0.410 H ATOM MO5 H52 O5 NOT 1.000 125.3 -90.0 0.410 H ATOM MO5 H11 O1 NOT 1.000 125.3 180.0 0.410 H ATOM MO5 H12 O1 NOT 1.000 125.3 0.0 0.410 H RESIDUE MO4 ATOM MO4 O1 NOT MG 0.000 0.0 0.0 -0.820 OW ATOM MO4 MG O1 O4 0.000 0.0 0.0 2.000 MG ATOM MO4 O2 MG H22 0.000 0.0 0.0 -0.820 OW ATOM MO4 H21 O2 NOT 1.000 125.3 90.0 0.410 H ATOM MO4 H22 O2 NOT 1.000 125.3 -90.0 0.410 H ATOM MO4 O3 MG H32 0.000 0.0 0.0 -0.820 OW ATOM MO4 H31 O3 NOT 1.000 125.3 180.0 0.410 H ATOM MO4 H32 O3 NOT 1.000 125.3 0.0 0.410 H ATOM MO4 O4 MG H42 0.000 0.0 0.0 -0.820 OW ATOM MO4 H41 O4 NOT 1.000 125.3 180.0 0.410 H ATOM MO4 H42 O4 NOT 1.000 125.3 0.0 0.410 H ATOM MO4 H11 O1 NOT 1.000 125.3 180.0 0.410 H ATOM MO4 H12 O1 NOT 1.000 125.3 0.0 0.410 H RESIDUE MO3 ATOM MO3 O1 NOT MG 0.000 0.0 0.0 -0.820 OW ATOM MO3 MG O1 O3 0.000 0.0 0.0 2.000 MG ATOM MO3 O2 MG H22 0.000 0.0 0.0 -0.820 OW ATOM MO3 H21 O2 NOT 1.000 125.3 90.0 0.410 H ATOM MO3 H22 O2 NOT 1.000 125.3 -90.0 0.410 H ATOM MO3 O3 MG H32 0.000 0.0 0.0 -0.820 OW ATOM MO3 H31 O3 NOT 1.000 125.3 180.0 0.410 H ATOM MO3 H32 O3 NOT 1.000 125.3 0.0 0.410 H ATOM MO3 H11 O1 NOT 1.000 125.3 180.0 0.410 H ATOM MO3 H12 O1 NOT 1.000 125.3 0.0 0.410 H RESIDUE MO2 ATOM MO2 O1 NOT MG 0.000 0.0 0.0 -0.820 OW ATOM MO2 MG O1 O2 0.000 0.0 0.0 2.000 MG ATOM MO2 O2 MG H22 0.000 0.0 0.0 -0.820 OW ATOM MO2 H21 O2 NOT 1.000 125.3 90.0 0.410 H ATOM MO2 H22 O2 NOT 1.000 125.3 -90.0 0.410 H ATOM MO2 H11 O1 NOT 1.000 125.3 180.0 0.410 H ATOM MO2 H12 O1 NOT 1.000 125.3 0.0 0.410 H RESIDUE MG ATOM MG MG NOT NOT 0.000 0.0 0.0 2.000 MG RESIDUE TIP ATOM TIP OH2 NOT H2 0.000 0.0 0.0 -0.820 OW ATOM TIP H1 OH2 NOT 1.000 0.0 0.0 0.410 H ATOM TIP H2 OH2 NOT 1.000 0.0 0.0 0.410 H