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      "num_nts": 5,
      "nts_short": "UCGUA",
      "nts_long": "///V/94,///V/95,///V/137,///V/138,///V/139",
      "num_stems": 2,
      "bridges": [
        {
          "index": 1,
          "num_nts": 0,
          "nts_short": "",
          "nts_long": ""
        },
        {
          "index": 2,
          "num_nts": 1,
          "nts_short": "U",
          "nts_long": "///V/138"
        }
      ]
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    {
      "index": 1,
      "type": "symmetric internal loop",
      "bridging_nts": [
        1,
        1
      ],
      "stem_indices": [
        1,
        2
      ],
      "summary": "[2] 1 1 [V.11 W.70 V.13 W.68] 11 5",
      "num_nts": 6,
      "nts_short": "ACGCCU",
      "nts_long": "///V/11,///V/12,///V/13,///W/68,///W/69,///W/70",
      "num_stems": 2,
      "bridges": [
        {
          "index": 1,
          "num_nts": 1,
          "nts_short": "C",
          "nts_long": "///V/12"
        },
        {
          "index": 2,
          "num_nts": 1,
          "nts_short": "C",
          "nts_long": "///W/69"
        }
      ]
    },
    {
      "index": 2,
      "type": "symmetric internal loop",
      "bridging_nts": [
        1,
        1
      ],
      "stem_indices": [
        8,
        9
      ],
      "summary": "[2] 1 1 [V.97 V.135 V.99 V.133] 3 3",
      "num_nts": 6,
      "nts_short": "UGGCUA",
      "nts_long": "///V/97,///V/98,///V/99,///V/133,///V/134,///V/135",
      "num_stems": 2,
      "bridges": [
        {
          "index": 1,
          "num_nts": 1,
          "nts_short": "G",
          "nts_long": "///V/98"
        },
        {
          "index": 2,
          "num_nts": 1,
          "nts_short": "U",
          "nts_long": "///V/134"
        }
      ]
    },
    {
      "index": 3,
      "type": "asymmetric internal loop",
      "bridging_nts": [
        2,
        1
      ],
      "stem_indices": [
        13,
        14
      ],
      "summary": "[2] 2 1 [U.31 U.122 U.34 U.120] 4 7",
      "num_nts": 7,
      "nts_short": "GGUCGUC",
      "nts_long": "///U/31,///U/32,///U/33,///U/34,///U/120,///U/121,///U/122",
      "num_stems": 2,
      "bridges": [
        {
          "index": 1,
          "num_nts": 2,
          "nts_short": "GU",
          "nts_long": "///U/32,///U/33"
        },
        {
          "index": 2,
          "num_nts": 1,
          "nts_short": "U",
          "nts_long": "///U/121"
        }
      ]
    },
    {
      "index": 4,
      "type": "asymmetric internal loop",
      "bridging_nts": [
        1,
        3
      ],
      "stem_indices": [
        -1,
        11
      ],
      "summary": "[2] 1 3 [W.33 W.50 W.35 W.46] 1 3",
      "num_nts": 8,
      "nts_short": "CAAUACAG",
      "nts_long": "///W/33,///W/34,///W/35,///W/46,///W/47,///W/48,///W/49,///W/50",
      "num_stems": 2,
      "bridges": [
        {
          "index": 1,
          "num_nts": 1,
          "nts_short": "A",
          "nts_long": "///W/34"
        },
        {
          "index": 2,
          "num_nts": 3,
          "nts_short": "ACA",
          "nts_long": "///W/47,///W/48,///W/49"
        }
      ]
    },
    {
      "index": 5,
      "type": "symmetric internal loop",
      "bridging_nts": [
        2,
        2
      ],
      "stem_indices": [
        15,
        16
      ],
      "summary": "[2] 2 2 [U.43 U.72 U.46 U.69] 3 8",
      "num_nts": 8,
      "nts_short": "GAACGAAC",
      "nts_long": "///U/43,///U/44,///U/45,///U/46,///U/69,///U/70,///U/71,///U/72",
      "num_stems": 2,
      "bridges": [
        {
          "index": 1,
          "num_nts": 2,
          "nts_short": "AA",
          "nts_long": "///U/44,///U/45"
        },
        {
          "index": 2,
          "num_nts": 2,
          "nts_short": "AA",
          "nts_long": "///U/70,///U/71"
        }
      ]
    },
    {
      "index": 6,
      "type": "asymmetric internal loop",
      "bridging_nts": [
        3,
        1
      ],
      "stem_indices": [
        -3,
        17
      ],
      "summary": "[2] 3 1 [U.80 U.112 U.84 U.110] 1 8",
      "num_nts": 8,
      "nts_short": "GAACAUCC",
      "nts_long": "///U/80,///U/81,///U/82,///U/83,///U/84,///U/110,///U/111,///U/112",
      "num_stems": 2,
      "bridges": [
        {
          "index": 1,
          "num_nts": 3,
          "nts_short": "AAC",
          "nts_long": "///U/81,///U/82,///U/83"
        },
        {
          "index": 2,
          "num_nts": 1,
          "nts_short": "C",
          "nts_long": "///U/111"
        }
      ]
    },
    {
      "index": 7,
      "type": "asymmetric internal loop",
      "bridging_nts": [
        5,
        2
      ],
      "stem_indices": [
        4,
        5
      ],
      "summary": "[2] 5 2 [V.28 V.46 V.34 V.43] 3 3 k-turn:normal",
      "num_nts": 11,
      "nts_short": "CAGUGAGCGAG",
      "nts_long": "///V/28,///V/29,///V/30,///V/31,///V/32,///V/33,///V/34,///V/43,///V/44,///V/45,///V/46",
      "num_stems": 2,
      "bridges": [
        {
          "index": 1,
          "num_nts": 5,
          "nts_short": "AGUGA",
          "nts_long": "///V/29,///V/30,///V/31,///V/32,///V/33"
        },
        {
          "index": 2,
          "num_nts": 2,
          "nts_short": "GA",
          "nts_long": "///V/44,///V/45"
        }
      ]
    },
    {
      "index": 8,
      "type": "asymmetric internal loop",
      "bridging_nts": [
        7,
        3
      ],
      "stem_indices": [
        12,
        -2
      ],
      "summary": "[2] 7 3 [U.12 U.136 U.20 U.132] 9 1",
      "num_nts": 14,
      "nts_short": "CAGAUCAAUACAGG",
      "nts_long": "///U/12,///U/13,///U/14,///U/15,///U/16,///U/17,///U/18,///U/19,///U/20,///U/132,///U/133,///U/134,///U/135,///U/136",
      "num_stems": 2,
      "bridges": [
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          "index": 1,
          "num_nts": 7,
          "nts_short": "AGAUCAA",
          "nts_long": "///U/13,///U/14,///U/15,///U/16,///U/17,///U/18,///U/19"
        },
        {
          "index": 2,
          "num_nts": 3,
          "nts_short": "CAG",
          "nts_long": "///U/133,///U/134,///U/135"
        }
      ]
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      "index": 9,
      "type": "asymmetric internal loop",
      "bridging_nts": [
        7,
        6
      ],
      "stem_indices": [
        -2,
        13
      ],
      "summary": "[2] 7 6 [U.20 U.132 U.28 U.125] 1 4",
      "num_nts": 17,
      "nts_short": "UGGCGGAGGCAUAGAAA",
      "nts_long": "///U/20,///U/21,///U/22,///U/23,///U/24,///U/25,///U/26,///U/27,///U/28,///U/125,///U/126,///U/127,///U/128,///U/129,///U/130,///U/131,///U/132",
      "num_stems": 2,
      "bridges": [
        {
          "index": 1,
          "num_nts": 7,
          "nts_short": "GGCGGAG",
          "nts_long": "///U/21,///U/22,///U/23,///U/24,///U/25,///U/26,///U/27"
        },
        {
          "index": 2,
          "num_nts": 6,
          "nts_short": "AUAGAA",
          "nts_long": "///U/126,///U/127,///U/128,///U/129,///U/130,///U/131"
        }
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      "type": "3-way junction",
      "bridging_nts": [
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        3,
        6
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      "num_nts": 12,
      "nts_short": "AAUAUUUUUAGU",
      "nts_long": "///V/17,///V/18,///V/19,///V/20,///V/53,///V/54,///V/55,///V/56,///V/57,///W/62,///W/63,///W/64",
      "num_stems": 3,
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        },
        {
          "index": 2,
          "num_nts": 3,
          "nts_short": "UUU",
          "nts_long": "///V/54,///V/55,///V/56"
        },
        {
          "index": 3,
          "num_nts": 1,
          "nts_short": "G",
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      "index": 2,
      "type": "3-way junction",
      "bridging_nts": [
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        1
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        15,
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      "summary": "[3] 0 5 1 [U.40 U.114 U.41 U.74 U.80 U.112] 7 3 1",
      "num_nts": 12,
      "nts_short": "CAUAUAACGCGG",
      "nts_long": "///U/40,///U/41,///U/74,///U/75,///U/76,///U/77,///U/78,///U/79,///U/80,///U/112,///U/113,///U/114",
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          "nts_short": "",
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        },
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          "index": 2,
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          "nts_short": "AUAAC",
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        },
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      "is_broken": true,
      "num_nts": 23,
      "nts_short": "GAAAUUAUAAACCAGACCGUCUC",
      "nts_long": "///V/65,///V/66,///V/67,///V/73,///V/74,///V/75,///V/76,///V/77,///V/78,///V/79,///V/80,///V/81,///V/82,///V/83,///V/84,///V/85,///V/86,///V/87,///V/88,///V/89,///V/90,///V/91,///V/92"
    },
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      "index": 2,
      "is_broken": true,
      "num_nts": 6,
      "nts_short": "AAUCAA",
      "nts_long": "///V/102,///V/103,///V/104,///V/128,///V/129,///V/130"
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      "nts_short": "GGAAUUUUUGGA",
      "nts_long": "///V/141,///V/142,///V/143,///V/144,///V/145,///V/146,///V/147,///V/148,///V/149,///V/150,///V/151,///V/152"
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      "nts_short": "GAACCGUUGUUUU",
      "nts_long": "///W/81,///W/82,///W/83,///W/84,///W/85,///W/86,///W/87,///W/88,///W/108,///W/109,///W/110,///W/111,///W/112"
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  "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].",
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    "num_naChains": 3,
    "naChains": "U=141,V=124,W=80",
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    "num_notes": 52,
    "notes": [
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        "Aminors": "A-minor interactions (including types I and II)"
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      {
        "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": 20,
    "auxfiles": [
      {
        "index": 1,
        "name": "dssr-pairs.pdb",
        "desc": "an ensemble of base pairs"
      },
      {
        "index": 2,
        "name": "dssr-multiplets.pdb",
        "desc": "an ensemble of multiplets"
      },
      {
        "index": 3,
        "name": "dssr-stems.pdb",
        "desc": "an ensemble of stems"
      },
      {
        "index": 4,
        "name": "dssr-helices.pdb",
        "desc": "an ensemble of helices (coaxial stacking)"
      },
      {
        "index": 5,
        "name": "dssr-hairpins.pdb",
        "desc": "an ensemble of hairpin loops"
      },
      {
        "index": 6,
        "name": "dssr-bulges.pdb",
        "desc": "an ensemble of bulges"
      },
      {
        "index": 7,
        "name": "dssr-iloops.pdb",
        "desc": "an ensemble of internal loops"
      },
      {
        "index": 8,
        "name": "dssr-junctions.pdb",
        "desc": "an ensemble of junctions (multi-branch)"
      },
      {
        "index": 9,
        "name": "dssr-2ndstrs.bpseq",
        "desc": "secondary structure in bpseq format"
      },
      {
        "index": 10,
        "name": "dssr-2ndstrs.ct",
        "desc": "secondary structure in connectivity table format"
      },
      {
        "index": 11,
        "name": "dssr-2ndstrs.dbn",
        "desc": "secondary structure in dot-bracket notation"
      },
      {
        "index": 12,
        "name": "dssr-torsions.txt",
        "desc": "backbone torsion angles and suite names"
      },
      {
        "index": 13,
        "name": "dssr-splays.pdb",
        "desc": "an ensemble of splayed-apart units"
      },
      {
        "index": 14,
        "name": "dssr-Kturns.pdb",
        "desc": "an ensemble of kink-turn motifs"
      },
      {
        "index": 15,
        "name": "dssr-stacks.pdb",
        "desc": "an ensemble of base stacks"
      },
      {
        "index": 16,
        "name": "dssr-atom2bases.pdb",
        "desc": "an ensemble of atom-base stacking interactions"
      },
      {
        "index": 17,
        "name": "dssr-rotmat.txt",
        "desc": "position vector and rotation matrix"
      },
      {
        "index": 18,
        "name": "dssr-viewV.pdb",
        "desc": "vertical view of the principal moment of inertia"
      },
      {
        "index": 19,
        "name": "dssr-viewH.pdb",
        "desc": "horizontal view of the principal moment of inertia"
      },
      {
        "index": 20,
        "name": "dssr-viewT.pdb",
        "desc": "top view of the principal moment of inertia"
      }
    ],
    "time_used": "999"
  }
}