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      "distance": 2.908,
      "atom1_id": "///C/107/O",
      "atom2_id": "///C/111/N",
      "atom_pair": "O:N",
      "residue_pair": "aa:aa"
    },
    {
      "index": 371,
      "atom1_serNum": 3261,
      "atom2_serNum": 3287,
      "donAcc_type": "standard",
      "distance": 3.438,
      "atom1_id": "///C/108/O",
      "atom2_id": "///C/112/N",
      "atom_pair": "O:N",
      "residue_pair": "aa:aa"
    },
    {
      "index": 372,
      "atom1_serNum": 3269,
      "atom2_serNum": 3295,
      "donAcc_type": "standard",
      "distance": 3.031,
      "atom1_id": "///C/109/O",
      "atom2_id": "///C/113/N",
      "atom_pair": "O:N",
      "residue_pair": "aa:aa"
    },
    {
      "index": 373,
      "atom1_serNum": 3278,
      "atom2_serNum": 3295,
      "donAcc_type": "standard",
      "distance": 3.114,
      "atom1_id": "///C/110/O",
      "atom2_id": "///C/113/N",
      "atom_pair": "O:N",
      "residue_pair": "aa:aa"
    },
    {
      "index": 374,
      "atom1_serNum": 3278,
      "atom2_serNum": 3323,
      "donAcc_type": "standard",
      "distance": 2.625,
      "atom1_id": "///C/110/O",
      "atom2_id": "///C/116/ND2",
      "atom_pair": "O:N",
      "residue_pair": "aa:aa"
    },
    {
      "index": 375,
      "atom1_serNum": 3298,
      "atom2_serNum": 3316,
      "donAcc_type": "standard",
      "distance": 3.119,
      "atom1_id": "///C/113/O",
      "atom2_id": "///C/116/N",
      "atom_pair": "O:N",
      "residue_pair": "aa:aa"
    },
    {
      "index": 376,
      "atom1_serNum": 3319,
      "atom2_serNum": 3346,
      "donAcc_type": "standard",
      "distance": 3.100,
      "atom1_id": "///C/116/O",
      "atom2_id": "///C/120/N",
      "atom_pair": "O:N",
      "residue_pair": "aa:aa"
    },
    {
      "index": 377,
      "atom1_serNum": 3319,
      "atom2_serNum": 3351,
      "donAcc_type": "acceptable",
      "distance": 2.588,
      "atom1_id": "///C/116/O",
      "atom2_id": "///C/120/OG",
      "atom_pair": "O:O",
      "residue_pair": "aa:aa"
    },
    {
      "index": 378,
      "atom1_serNum": 3327,
      "atom2_serNum": 3352,
      "donAcc_type": "standard",
      "distance": 2.897,
      "atom1_id": "///C/117/O",
      "atom2_id": "///C/121/N",
      "atom_pair": "O:N",
      "residue_pair": "aa:aa"
    },
    {
      "index": 379,
      "atom1_serNum": 3334,
      "atom2_serNum": 3357,
      "donAcc_type": "standard",
      "distance": 3.058,
      "atom1_id": "///C/118/O",
      "atom2_id": "///C/122/N",
      "atom_pair": "O:N",
      "residue_pair": "aa:aa"
    },
    {
      "index": 380,
      "atom1_serNum": 3342,
      "atom2_serNum": 3365,
      "donAcc_type": "standard",
      "distance": 2.920,
      "atom1_id": "///C/119/O",
      "atom2_id": "///C/123/N",
      "atom_pair": "O:N",
      "residue_pair": "aa:aa"
    },
    {
      "index": 381,
      "atom1_serNum": 3355,
      "atom2_serNum": 3370,
      "donAcc_type": "standard",
      "distance": 3.000,
      "atom1_id": "///C/121/O",
      "atom2_id": "///C/124/N",
      "atom_pair": "O:N",
      "residue_pair": "aa:aa"
    },
    {
      "index": 382,
      "atom1_serNum": 3355,
      "atom2_serNum": 3383,
      "donAcc_type": "standard",
      "distance": 2.823,
      "atom1_id": "///C/121/O",
      "atom2_id": "///C/126/N",
      "atom_pair": "O:N",
      "residue_pair": "aa:aa"
    },
    {
      "index": 383,
      "atom1_serNum": 3360,
      "atom2_serNum": 3375,
      "donAcc_type": "standard",
      "distance": 3.168,
      "atom1_id": "///C/122/O",
      "atom2_id": "///C/125/N",
      "atom_pair": "O:N",
      "residue_pair": "aa:aa"
    },
    {
      "index": 384,
      "atom1_serNum": 3373,
      "atom2_serNum": 3388,
      "donAcc_type": "acceptable",
      "distance": 2.746,
      "atom1_id": "///C/124/O",
      "atom2_id": "///C/126/OG",
      "atom_pair": "O:O",
      "residue_pair": "aa:aa"
    }
  ],
  "refCoords": {
    "purine": [
      "   12 ATOMS,    12 BONDS",
      "    1 N      -2.2500   5.0000   0.4000",
      "    2 N      -2.2500  -0.5000   0.4000",
      "    3 N      -2.2500  -0.5000  -0.4000",
      "    4 N      -2.2500   5.0000  -0.4000",
      "    5 C       1.2500   5.0000   0.4000",
      "    6 C       1.2500  -0.5000   0.4000",
      "    7 C       1.2500  -0.5000  -0.4000",
      "    8 C       1.2500   5.0000  -0.4000",
      "    9 C      -2.2500   5.0000   0.4000",
      "   10 C      -2.2500  -0.5000   0.4000",
      "   11 C      -2.2500  -0.5000  -0.4000",
      "   12 C      -2.2500   5.0000  -0.4000",
      "    1     1     2",
      "    2     2     3",
      "    3     3     4",
      "    4     4     1",
      "    5     5     6",
      "    6     6     7",
      "    7     7     8",
      "    8     5     8",
      "    9     9     5",
      "   10    10     6",
      "   11    11     7",
      "   12    12     8"
    ],
    "pyrimidine": [
      "   12 ATOMS,    12 BONDS",
      "    1 N      -2.2500   5.0000   0.4000",
      "    2 N      -2.2500   1.0000   0.4000",
      "    3 N      -2.2500   1.0000  -0.4000",
      "    4 N      -2.2500   5.0000  -0.4000",
      "    5 C       1.2500   5.0000   0.4000",
      "    6 C       1.2500   1.0000   0.4000",
      "    7 C       1.2500   1.0000  -0.4000",
      "    8 C       1.2500   5.0000  -0.4000",
      "    9 C      -2.2500   5.0000   0.4000",
      "   10 C      -2.2500   1.0000   0.4000",
      "   11 C      -2.2500   1.0000  -0.4000",
      "   12 C      -2.2500   5.0000  -0.4000",
      "    1     1     2",
      "    2     2     3",
      "    3     3     4",
      "    4     4     1",
      "    5     5     6",
      "    6     6     7",
      "    7     7     8",
      "    8     5     8",
      "    9     9     5",
      "   10    10     6",
      "   11    11     7",
      "   12    12     8"
    ],
    "wc_pair": [
      "   12 ATOMS,    12 BONDS",
      "    1 N      -2.2500   5.0000   0.4000",
      "    2 N      -2.2500  -5.0000   0.4000",
      "    3 N      -2.2500  -5.0000  -0.4000",
      "    4 N      -2.2500   5.0000  -0.4000",
      "    5 C       2.2500   5.0000   0.4000",
      "    6 C       2.2500  -5.0000   0.4000",
      "    7 C       2.2500  -5.0000  -0.4000",
      "    8 C       2.2500   5.0000  -0.4000",
      "    9 C      -2.2500   5.0000   0.4000",
      "   10 C      -2.2500  -5.0000   0.4000",
      "   11 C      -2.2500  -5.0000  -0.4000",
      "   12 C      -2.2500   5.0000  -0.4000",
      "    1     1     2",
      "    2     2     3",
      "    3     3     4",
      "    4     4     1",
      "    5     5     6",
      "    6     6     7",
      "    7     7     8",
      "    8     5     8",
      "    9     9     5",
      "   10    10     6",
      "   11    11     7",
      "   12    12     8"
    ]
  },
  "metadata": {
    "license": "http://innovation.columbia.edu/technologies/CU20391",
    "url": "http://x3dna.org/",
    "url_alt": "http://home.x3dna.org/",
    "forum": "http://forum.x3dna.org/",
    "citation": "Lu et al. (2015). 'DSSR: an integrated software tool for dissecting the spatial structure of RNA.' Nucleic Acids Res., 43(21):e142 [doi:10.1093/nar/gkv716].",
    "str_id": "6msf",
    "num_aaChains": 3,
    "aaChains": "A=129,B=129,C=129",
    "num_naChains": 2,
    "naChains": "R=14,S=10",
    "num_atoms": 3486,
    "num_waters": 86,
    "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": 15,
    "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-hairpins.pdb",
        "desc": "an ensemble of hairpin loops"
      },
      {
        "index": 5,
        "name": "dssr-bulges.pdb",
        "desc": "an ensemble of bulges"
      },
      {
        "index": 6,
        "name": "dssr-2ndstrs.bpseq",
        "desc": "secondary structure in bpseq format"
      },
      {
        "index": 7,
        "name": "dssr-2ndstrs.ct",
        "desc": "secondary structure in connectivity table format"
      },
      {
        "index": 8,
        "name": "dssr-2ndstrs.dbn",
        "desc": "secondary structure in dot-bracket notation"
      },
      {
        "index": 9,
        "name": "dssr-torsions.txt",
        "desc": "backbone torsion angles and suite names"
      },
      {
        "index": 10,
        "name": "dssr-splays.pdb",
        "desc": "an ensemble of splayed-apart units"
      },
      {
        "index": 11,
        "name": "dssr-stacks.pdb",
        "desc": "an ensemble of base stacks"
      },
      {
        "index": 12,
        "name": "dssr-rotmat.txt",
        "desc": "position vector and rotation matrix"
      },
      {
        "index": 13,
        "name": "dssr-viewV.pdb",
        "desc": "vertical view of the principal moment of inertia"
      },
      {
        "index": 14,
        "name": "dssr-viewH.pdb",
        "desc": "horizontal view of the principal moment of inertia"
      },
      {
        "index": 15,
        "name": "dssr-viewT.pdb",
        "desc": "top view of the principal moment of inertia"
      }
    ],
    "time_used": "999"
  }
}