REM ================================================
REM DNA Dictionary for SHELXL
REM Revised 11/7/99 by Chad C. Sines
REM Lit:
REM Sugar/Base Restraints:
REM L. Clowney et al., Geometric Parameters in Nucleic
REM Acids: Nitrogenous Bases,
REM J. Am. Chem. Soc. (1996) 118, 509-518
REM
REM A. Gelbin et al., Geometric Parameters in Nucleic
REM Acids: Sugar and Phosphate Constituents,
REM J. Am. Chem. Soc. (1996) 118, 519-529
REM
REM G. Parkinson et al., New Parameters for the Refinement
REM of Nucleic Acid-Containing Structures,
REM Acta Cryst. (1996) D52, 57-64
REM http://ndbserver.rutgers.edu:80/
REM
REM Spermine Restraints:
REM Y. Iitaka et al., Acta Cryst. (1965) 18, 110-121.
REM
REM ================================================
REM Similar chiral volume restraints on deoxyriboses
REM ================================================
CHIV_* C1' 2.44 0.03
CHIV_* C3' -2.54 0.03
CHIV_* C4' -2.49 0.03

REM ================================================
REM Planarity restraints for bases (REM if not needed here)
REM ================================================

FLAT_C C1' O2 N4 N1 C2 N3 C4 C5 C6
FLAT_T C1' O2 O4 N1 C2 N3 C4 C5 C6 C5M
FLAT_A C1' C2 N6 N1 N3 C4 C5 C6 N7 C8 N9
FLAT_G C1' N2 O6 N1 C2 N3 C4 C5 C6 N7 C8 N9

REM ================================================
REM Adding Hydrogens
REM Remove REM to generate hydrogen atoms. Note OH for first O5' and
REM last O3' - the latter residue number will have to be changed for
REM other structures. All hydrogens have been included although using
REM all may not be justified
REM ================================================
!SUGAR TERMINAL HYDROXYLS
REM HFIX_1 87 O5'
REM HFIX_13 87 O5'
REM HFIX_12 87 O3'
REM HFIX_24 87 O3'
!SUGAR HYDROGENS
REM HFIX_* 13 C1' C3' C4' !safe hydrogen
REM HFIX_* 23 C2' C5' !safe hydrogen
!BASE HYDROGENS
REM HFIX_C 43 C5 C6 !safe hydrogen
REM HFIX_C 93 N4

REM HFIX_T 43 N3 C6 !safe hydrogen
REM HFIX_T 33 C5M

REM HFIX_A 43 C2 C8 !safe hydrogen
REM HFIX_A 93 N6

REM HFIX_G 43 N1 C8 !safe hydrogen
REM HFIX_G 93 N2
REM
REM @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
REM @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
REM Both C2' and C3' Endo sugar restraints have been included.
REM You may REM out all the restraints for the conformation that
REM is not applicable or you may "mix-and-match" conformations by
REM specifying residue numbers. Certain phosphate restraints are
REM conformation dependent and have been marked
REM @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
REM @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
REM
REM ================================================
REM Sugar Restraints-
REM C3' ENDO.
REM ================================================
REM DFIX_* 1.519 C1' C2'
REM DFIX_* 1.518 C2' C3'
REM DFIX_* 1.521 C3' C4'
REM DFIX_* 1.449 C4' O4'
REM DFIX_* 1.418 O4' C1'
REM DFIX_* 1.419 C3' O3'
REM DFIX_* 1.509 C5' C4'
REM DFIX_G 1.488 C1' N9
REM DFIX_A 1.488 C1' N9
REM DFIX_C 1.488 C1' N1
REM DFIX_T 1.488 C1' N1
REM DFIX_* 1.423 O5' C5'
REM DANG_* 2.367 C1' C3'
REM DANG_* 2.365 C2' C4'
REM DANG_* 2.349 C3' O4'
REM DANG_* 2.353 C4' C1'
REM DANG_* 2.359 O4' C2'
REM DANG_* 2.444 C2' O3'
REM DANG_* 2.442 C4' O3'
REM DANG_* 2.565 C5' C3'
REM DANG_* 2.420 C5' O4'
REM DANG_A 2.356 O4' N9
REM DANG_G 2.356 O4' N9
REM DANG_C 2.356 O4' N1
REM DANG_T 2.356 O4' N1
REM DANG_A 2.502 C2' N9
REM DANG_G 2.502 C2' N9
REM DANG_C 2.502 C2' N1
REM DANG_T 2.502 C2' N1
REM DANG_* 2.417 O5' C4'
REM DANG_A 2.526 C1' C4
REM DANG_G 2.527 C1' C4
REM DANG_C 2.467 C1' C2
REM DANG_T 2.449 C1' C2
REM ================================================
REM Phosphate Restraints for C3' endo(first P is in residue 2).
REM Note P-O-C angles more flexible than other angles.
REM ================================================
REM DFIX_* 1.485 O1P P O2P P
REM DFIX_* 1.607 O3' P_+
REM DFIX_* 1.593 O5' P
REM DFIX_* 1.440 O5' C5'
REM DFIX_* 1.433 O3' C3'
REM DANG_* 2.567 O1P O2P
REM DANG_* 2.454 O5' O1P O5' O2P ! SMALL
REM DANG_* 2.533 O5' O1P O5' O2P ! LARGE
REM DANG_* 2.522 O3' O5'_+
REM DANG_* 2.640 P C5'
REM DANG_* 2.630 C3' P_+
REM DANG_* 2.457 O3' O1P_+ O3' O2P_+ ! SMALL
REM DANG_* 2.541 O3' O1P_+ O3' O2P_+ ! LARGE
REM DANG_* 2.407 O5' C4' !conformation dependent
REM DANG_* 2.410 O3' C4' !conformation dependent

REM @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
REM ================================================
REM Sugar Restraints-
REM C2' ENDO.
REM ================================================
DFIX_* 1.518 C1' C2'
DFIX_* 1.516 C2' C3'
DFIX_* 1.529 C3' C4'
DFIX_* 1.446 C4' O4'
DFIX_* 1.420 O4' C1'
DFIX_* 1.435 C3' O3'
DFIX_* 1.512 C5' C4'
DFIX_G 1.468 C1' N9
DFIX_A 1.468 C1' N9
DFIX_C 1.468 C1' N1
DFIX_T 1.468 C1' N1
DFIX_* 1.424 O5' C5'
DANG_* 2.366 C1' C3'
DANG_* 2.385 C2' C4'
DANG_* 2.376 C3' O4'
DANG_* 2.349 C4' C1'
DANG_* 2.346 O4' C2'
DANG_* 2.409 C2' O3'
DANG_* 2.424 C4' O3'
DANG_* 2.552 C5' C3'
DANG_* 2.413 C5' O4'
DANG_A 2.337 O4' N9
DANG_G 2.337 O4' N9
DANG_C 2.337 O4' N1
DANG_T 2.337 O4' N1
DANG_A 2.509 C2' N9
DANG_G 2.509 C2' N9
DANG_C 2.509 C2' N1
DANG_T 2.509 C2' N1
DANG_* 2.414 O5' C4'
DANG_A 2.536 C1' C4
DANG_G 2.537 C1' C4
DANG_C 2.453 C1' C2
DANG_T 2.436 C1' C2
REM ================================================
REM Phosphate Restraints for C2' endo(first P is in residue 2).
REM Note P-O-C angles more flexible than other angles.
REM ================================================
DFIX_* 1.485 O1P P O2P P
DFIX_* 1.607 O3' P_+
DFIX_* 1.593 O5' P
DFIX_* 1.440 O5' C5'
DFIX_* 1.433 O3' C3'
DANG_* 2.567 O1P O2P
DANG_* 2.454 O5' O1P O5' O2P ! SMALL
DANG_* 2.533 O5' O1P O5' O2P ! LARGE
DANG_* 2.522 O3' O5'_+
DANG_* 2.640 P C5'
DANG_* 2.630 C3' P_+
DANG_* 2.457 O3' O1P_+ O3' O2P_+ ! SMALL
DANG_* 2.541 O3' O1P_+ O3' O2P_+ ! LARGE
DANG_* 2.410 O5' C4' !conformation dependent
DANG_* 2.416 O3' C4' !conformation dependent

REM ================================================
REM Cytosine
REM =================
REM 1-2 Distances
DFIX_C 1.397 N1 C2
DFIX_C 1.367 N1 C6
DFIX_C 1.353 C2 N3
DFIX_C 1.240 C2 O2
DFIX_C 1.335 N3 C4
DFIX_C 1.425 C4 C5
DFIX_C 1.335 C4 N4
DFIX_C 1.339 C5 C6
REM -----------------------
REM 1-3 Distances
REM -----------------------
DANG_C 2.397 C6 C2
DANG_C 2.372 N1 N3
DANG_C 2.329 C2 C4
DANG_C 2.413 N3 C5
DANG_C 2.362 C4 C6
DANG_C 2.355 C5 N1
DANG_C 2.272 N1 O2
DANG_C 2.267 N3 O2
DANG_C 2.289 N3 N4
DANG_C 2.393 C5 N4
DANG_C 2.467 C6 C1'
DANG_C 2.468 C2 C1'
REM ================================================
REM Thymine
REM ================
REM 1-2 Distances
DFIX_T 1.376 N1 C2
DFIX_T 1.378 N1 C6
DFIX_T 1.373 C2 N3
DFIX_T 1.220 C2 O2
DFIX_T 1.382 N3 C4
DFIX_T 1.445 C4 C5
DFIX_T 1.228 C4 O4
DFIX_T 1.339 C5 C6
DFIX_T 1.496 C5 C5M
REM -----------------------
REM 1-3 Distances
REM -----------------------
DANG_T 2.401 C2 C6
DANG_T 2.313 N1 N3
DANG_T 2.468 C2 C4
DANG_T 2.387 N3 C5
DANG_T 2.387 C4 C6
DANG_T 2.396 N1 C5
DANG_T 2.284 N1 O2
DANG_T 2.272 N3 O2
DANG_T 2.261 N3 O4
DANG_T 2.372 O4 C5
DANG_T 2.534 C4 C5M
DANG_T 2.491 C6 C5M
DANG_T 2.474 C6 C1'
DANG_T 2.445 C2 C1'
REM ================================================
REM Adenine
REM ================

REM 1-2 Distances
DFIX_A 1.339 N1 C2
DFIX_A 1.351 N1 C6
DFIX_A 1.331 C2 N3
DFIX_A 1.344 N3 C4
DFIX_A 1.383 C4 C5
DFIX_A 1.406 C5 C6
DFIX_A 1.335 N6 C6
DFIX_A 1.374 C4 N9
DFIX_A 1.373 C8 N9
DFIX_A 1.311 N7 C8
DFIX_A 1.388 N7 C5
REM -----------------------
REM 1-3 Distances
REM -----------------------
DANG_A 2.313 C6 C2
DANG_A 2.413 N1 N3
DANG_A 2.199 C2 C4
DANG_A 2.438 N3 C5
DANG_A 2.378 C4 C6
DANG_A 2.360 C5 N1
DANG_A 2.280 C4 N7
DANG_A 2.126 C5 C8
DANG_A 2.249 N7 N9
DANG_A 2.191 C8 C4
DANG_A 2.199 N9 C5
DANG_A 2.437 N3 N9
DANG_A 2.555 C6 N7
DANG_A 2.310 N1 N6
DANG_A 2.417 C5 N6
DANG_A 2.545 C8 C1'
DANG_A 2.531 C4 C1'
REM ================================================
REM Guanine
REM ================
REM 1-2 Distances
DFIX_G 1.373 N1 C2
DFIX_G 1.391 N1 C6
DFIX_G 1.341 C2 N2
DFIX_G 1.323 C2 N3
DFIX_G 1.350 N3 C4
DFIX_G 1.379 C4 C5
DFIX_G 1.375 C4 N9
DFIX_G 1.419 C5 C6
DFIX_G 1.388 C5 N7
DFIX_G 1.237 C6 O6
DFIX_G 1.305 N7 C8
DFIX_G 1.374 C8 N9
REM -----------------------
REM 1-3 Distances
REM -----------------------
DANG_G 2.453 C6 C2
DANG_G 2.379 N1 N3
DANG_G 2.215 C2 C4
DANG_G 2.459 N3 C5
DANG_G 2.408 C4 C6
DANG_G 2.323 C5 N1
DANG_G 2.278 C4 N7
DANG_G 2.127 C5 C8
DANG_G 2.236 N7 N9
DANG_G 2.201 C8 C4
DANG_G 2.191 N9 C5
DANG_G 2.428 N3 N9
DANG_G 2.548 C6 N7
DANG_G 2.304 N1 N2
DANG_G 2.306 N3 N2
DANG_G 2.276 N1 O6
DANG_G 2.395 C5 O6
DANG_G 2.563 C8 C1'
DANG_G 2.531 C4 C1'

REM ================================================
REM ====== ADDITIONAL RESIDUES ======
REM ================================================
REM @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
REM Spermine restraints
REM ================
REM 1-2 Distances
REM ----------------------
REM DFIX_SPM 1.500 N1 C2
REM DFIX_SPM 1.510 C2 C3
REM DFIX_SPM 1.520 C3 C4
REM DFIX_SPM 1.510 C6 C7
REM DFIX_SPM 1.540 C7 C8
REM DFIX_SPM 1.510 C4 N5
REM DFIX_SPM 1.490 N5 C6
REM DFIX_SPM 1.540 C7 C8
REM DFIX_SPM 1.490 C9 N10
REM DFIX_SPM 1.51 N10 C11
REM DFIX_SPM 1.52 C11 C12
REM DFIX_SPM 1.51 C12 C13
REM DFIX_SPM 1.50 C13 N14
REM -----------------------
REM 1-3 Distances
REM ----------------------
REM DANG_SPM 2.495 N1 C3
REM DANG_SPM 2.467 C2 C4
REM DANG_SPM 2.512 C3 N5
REM DANG_SPM 2.472 C4 C6
REM DANG_SPM 2.487 N5 C7
REM DANG_SPM 2.514 C6 C8
REM DANG_SPM 2.514 C6 C8
REM DANG_SPM 2.487 C8 N10
REM DANG_SPM 2.472 C9 C11
REM DANG_SPM 2.512 N10 C12
REM DANG_SPM 2.467 C11 C13
REM DANG_SPM 2.495 C12 N14

REM ================================================
REM Hydrated Magnessium
REM ====================
REM 1-2 Distances
DFIX_ION 2.125 MG O1 MG O2 MG O3 MG O4 MG O5 MG O6
REM ======================
REM 1-3 Distances
REM ----------------
DANG_ION 4.250 O1 O3 O5 O6 O2 O4
DANG_ION 3.005 O1 O6 O1 O4 O1 O5 O1 O2 O4 O5 O4 O6
DANG_ION 3.005 O3 O4 O3 O6 O3 O2 O3 O5 O2 O6 O2 O5
REM Dictionary END
REM @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@