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Nucleic Acids Res., 43(21):e142 [doi:10.1093/nar/gkv716].","command":"x3dna-dssr -i=1BNA.pdb --json --more -o=1bna_native_v2.6.json","input_file":"1BNA.pdb","str_id":"1BNA","num_naChains":2,"naChains":"A=12,B=12","num_atoms":566,"num_waters":80,"num_notes":52,"notes":[{"Aminors":"A-minor interactions (including types I and II)"},{"Cstem_index":"stem index of the 'Canonical' helix in k-turn"},{"Cstem_pair":"Cstem bp delineating the k-turn internal loop"},{"Dp":"perpendicular distance of the 3' P atom to the glycosidic bond"},{"GA_pair":"sheared G-A pair in k-turn"},{"HtypePknot":"H-type pseudoknot"},{"Kturn":"kink-turn (k-turn)"},{"LW":"Leontis-Westhof"},{"NCstem_index":"stem index of the 'Non-Canonical' helix in k-turn"},{"NCstem_pair":"NCstem bp delineating the k-turn internal loop"},{"Uturn":"U-turn of the UNR- or GNRA-type"},{"aa":"amino acid"},{"atom_pair":"symbols of the two atoms involved in an H-bond"},{"auxfiles":"auxiliary files"},{"glyco_bond":"conformation of base related to sugar (syn or anti)"},{"bb_type":"backbone conformation, BI or BII"},{"bending_angle":"angle between two helical axes"},{"bp":"base pair"},{"bseq":"base sequence in one-letter code"},{"bulge":"bulge loop"},{"coaxStacks":"coaxial stacking of stems within a helix"},{"dbn":"dot bracket notation"},{"desc":"description"},{"donAcc_type":"donor/acceptor type of the atom pair in an H-bond"},{"epsilon_zeta":"difference between epsilon and zeta torsion angles"},{"hairpin":"hairpin loop"},{"hbond":"hydrogen bond (H-bond)"},{"helix":"defined by base-stacking interactions, regardless of bp type and backbone connectivity"},{"id":"identifier"},{"iloop":"internal loop"},{"index":"serial number"},{"isoCanonPairs":"isolated canonical pairs"},{"junction":"(multi-branched) junction loop"},{"kissingLoop":"kissing loop"},{"multiplet":"3+ bases in a coplanar geometry"},{"na":"nucleic acid"},{"nonPair":"two nts not forming a pair, but with H-bonding/stacking interactions"},{"nonStack":"nucleotide not involved in stacking interactions"},{"nt":"nucleotide"},{"num":"number"},{"oArea":"overlap areas between two bases, including exocyclic atoms"},{"oArea_ring":"overlap areas between two bases, including only ring atoms"},{"phosContacts":"H-bonding and atom-capping interactions involving a phosphate"},{"residue_pair":"types of the two residues involved in an H-bond"},{"rmsd":"root-mean-squares deviation"},{"serNum":"serial number"},{"ssSegments":"single-stranded segments not involved in loops"},{"ssZp":"Z-coordinate of the 3' phosphorus atom with reference to the 5' base plane"},{"sstr":"secondary structure in dbn"},{"stem":"helix consisting of only canonical pairs, with a continuous backbone"},{"str_id":"structure identifier, derived from inpfile with extension removed"},{"vert_dist":"vertical distance from an atom to a base plane"}],"num_auxfiles":7,"auxfiles":[{"index":1,"name":"dssr-pairs.pdb","desc":"an ensemble of base pairs"},{"index":2,"name":"dssr-stems.pdb","desc":"an ensemble of stems"},{"index":3,"name":"dssr-helices.pdb","desc":"an ensemble of helices (coaxial stacking)"},{"index":4,"name":"dssr-2ndstrs.bpseq","desc":"secondary structure in bpseq format"},{"index":5,"name":"dssr-2ndstrs.ct","desc":"secondary structure in connectivity table format"},{"index":6,"name":"dssr-2ndstrs.dbn","desc":"secondary structure in dot-bracket notation"},{"index":7,"name":"dssr-torsions.txt","desc":"backbone torsion angles and suite names"}],"start_at":"2026-06-05 10:29:42","finish_at":"2026-06-05 10:29:42","time_used":"00:00:00:00"}}