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      "atom_pair": "N:N",
      "residue_pair": "nt:nt"
    },
    {
      "index": 61,
      "atom1_serNum": 508,
      "atom2_serNum": 899,
      "donAcc_type": "standard",
      "distance": 2.666,
      "atom1_id": "///B/16/O6",
      "atom2_id": "///B/28/N1",
      "atom_pair": "O:N",
      "residue_pair": "nt:nt"
    },
    {
      "index": 62,
      "atom1_serNum": 509,
      "atom2_serNum": 609,
      "donAcc_type": "standard",
      "distance": 2.940,
      "atom1_id": "///B/16/N1",
      "atom2_id": "///B/19/O6",
      "atom_pair": "N:O",
      "residue_pair": "nt:nt"
    },
    {
      "index": 63,
      "atom1_serNum": 511,
      "atom2_serNum": 606,
      "donAcc_type": "standard",
      "distance": 2.699,
      "atom1_id": "///B/16/N2",
      "atom2_id": "///B/19/N7",
      "atom_pair": "N:N",
      "residue_pair": "nt:nt"
    },
    {
      "index": 64,
      "atom1_serNum": 576,
      "atom2_serNum": 760,
      "donAcc_type": "standard",
      "distance": 2.947,
      "atom1_id": "///B/18/N1",
      "atom2_id": "///B/24/N7",
      "atom_pair": "N:N",
      "residue_pair": "nt:nt"
    },
    {
      "index": 65,
      "atom1_serNum": 576,
      "atom2_serNum": 763,
      "donAcc_type": "standard",
      "distance": 2.858,
      "atom1_id": "///B/18/N1",
      "atom2_id": "///B/24/O6",
      "atom_pair": "N:O",
      "residue_pair": "nt:nt"
    },
    {
      "index": 66,
      "atom1_serNum": 578,
      "atom2_serNum": 760,
      "donAcc_type": "standard",
      "distance": 2.570,
      "atom1_id": "///B/18/N2",
      "atom2_id": "///B/24/N7",
      "atom_pair": "N:N",
      "residue_pair": "nt:nt"
    },
    {
      "index": 67,
      "atom1_serNum": 602,
      "atom2_serNum": 629,
      "donAcc_type": "acceptable",
      "distance": 2.265,
      "atom1_id": "///B/19/O2'",
      "atom2_id": "///B/20/O5'",
      "atom_pair": "O:O",
      "residue_pair": "nt:nt"
    },
    {
      "index": 68,
      "atom1_serNum": 602,
      "atom2_serNum": 632,
      "donAcc_type": "acceptable",
      "distance": 2.271,
      "atom1_id": "///B/19/O2'",
      "atom2_id": "///B/20/O4'",
      "atom_pair": "O:O",
      "residue_pair": "nt:nt"
    },
    {
      "index": 69,
      "atom1_serNum": 609,
      "atom2_serNum": 797,
      "donAcc_type": "questionable",
      "distance": 2.478,
      "atom1_id": "///B/19/O6",
      "atom2_id": "///B/25/O6",
      "atom_pair": "O:O",
      "residue_pair": "nt:nt"
    },
    {
      "index": 70,
      "atom1_serNum": 610,
      "atom2_serNum": 794,
      "donAcc_type": "standard",
      "distance": 3.366,
      "atom1_id": "///B/19/N1",
      "atom2_id": "///B/25/N7",
      "atom_pair": "N:N",
      "residue_pair": "nt:nt"
    },
    {
      "index": 71,
      "atom1_serNum": 610,
      "atom2_serNum": 797,
      "donAcc_type": "standard",
      "distance": 2.827,
      "atom1_id": "///B/19/N1",
      "atom2_id": "///B/25/O6",
      "atom_pair": "N:O",
      "residue_pair": "nt:nt"
    },
    {
      "index": 72,
      "atom1_serNum": 612,
      "atom2_serNum": 756,
      "donAcc_type": "acceptable",
      "distance": 3.878,
      "atom1_id": "///B/19/N2",
      "atom2_id": "///B/24/O2'",
      "atom_pair": "N:O",
      "residue_pair": "nt:nt"
    },
    {
      "index": 73,
      "atom1_serNum": 612,
      "atom2_serNum": 794,
      "donAcc_type": "standard",
      "distance": 2.989,
      "atom1_id": "///B/19/N2",
      "atom2_id": "///B/25/N7",
      "atom_pair": "N:N",
      "residue_pair": "nt:nt"
    },
    {
      "index": 74,
      "atom1_serNum": 636,
      "atom2_serNum": 640,
      "donAcc_type": "acceptable",
      "distance": 3.157,
      "atom1_id": "///B/20/O2'",
      "atom2_id": "///B/20/O2",
      "atom_pair": "O:O",
      "residue_pair": "nt:nt"
    },
    {
      "index": 75,
      "atom1_serNum": 726,
      "atom2_serNum": 747,
      "donAcc_type": "acceptable",
      "distance": 2.567,
      "atom1_id": "///B/23/O2'",
      "atom2_id": "///B/24/OP1",
      "atom_pair": "O:O",
      "residue_pair": "nt:nt"
    },
    {
      "index": 76,
      "atom1_serNum": 756,
      "atom2_serNum": 782,
      "donAcc_type": "acceptable",
      "distance": 2.565,
      "atom1_id": "///B/24/O2'",
      "atom2_id": "///B/25/OP2",
      "atom_pair": "O:O",
      "residue_pair": "nt:nt"
    },
    {
      "index": 77,
      "atom1_serNum": 756,
      "atom2_serNum": 783,
      "donAcc_type": "acceptable",
      "distance": 3.000,
      "atom1_id": "///B/24/O2'",
      "atom2_id": "///B/25/O5'",
      "atom_pair": "O:O",
      "residue_pair": "nt:nt"
    },
    {
      "index": 78,
      "atom1_serNum": 764,
      "atom2_serNum": 864,
      "donAcc_type": "standard",
      "distance": 2.885,
      "atom1_id": "///B/24/N1",
      "atom2_id": "///B/27/O6",
      "atom_pair": "N:O",
      "residue_pair": "nt:nt"
    },
    {
      "index": 79,
      "atom1_serNum": 766,
      "atom2_serNum": 828,
      "donAcc_type": "standard",
      "distance": 3.102,
      "atom1_id": "///B/24/N2",
      "atom2_id": "///B/26/N7",
      "atom_pair": "N:N",
      "residue_pair": "nt:nt"
    },
    {
      "index": 80,
      "atom1_serNum": 766,
      "atom2_serNum": 861,
      "donAcc_type": "standard",
      "distance": 2.514,
      "atom1_id": "///B/24/N2",
      "atom2_id": "///B/27/N7",
      "atom_pair": "N:N",
      "residue_pair": "nt:nt"
    },
    {
      "index": 81,
      "atom1_serNum": 767,
      "atom2_serNum": 831,
      "donAcc_type": "standard",
      "distance": 2.924,
      "atom1_id": "///B/24/N3",
      "atom2_id": "///B/26/N6",
      "atom_pair": "N:N",
      "residue_pair": "nt:nt"
    },
    {
      "index": 82,
      "atom1_serNum": 798,
      "atom2_serNum": 898,
      "donAcc_type": "standard",
      "distance": 3.182,
      "atom1_id": "///B/25/N1",
      "atom2_id": "///B/28/O6",
      "atom_pair": "N:O",
      "residue_pair": "nt:nt"
    },
    {
      "index": 83,
      "atom1_serNum": 800,
      "atom2_serNum": 895,
      "donAcc_type": "standard",
      "distance": 2.788,
      "atom1_id": "///B/25/N2",
      "atom2_id": "///B/28/N7",
      "atom_pair": "N:N",
      "residue_pair": "nt:nt"
    },
    {
      "index": 84,
      "atom1_serNum": 857,
      "atom2_serNum": 868,
      "donAcc_type": "acceptable",
      "distance": 2.887,
      "atom1_id": "///B/27/O2'",
      "atom2_id": "///B/27/N3",
      "atom_pair": "O:N",
      "residue_pair": "nt:nt"
    },
    {
      "index": 85,
      "atom1_serNum": 857,
      "atom2_serNum": 887,
      "donAcc_type": "acceptable",
      "distance": 2.303,
      "atom1_id": "///B/27/O2'",
      "atom2_id": "///B/28/O4'",
      "atom_pair": "O:O",
      "residue_pair": "nt:nt"
    }
  ],
  "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": "1my9",
    "num_naChains": 2,
    "naChains": "A=14,B=14",
    "num_atoms": 914,
    "num_waters": 0,
    "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": 14,
    "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-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"
      },
      {
        "index": 8,
        "name": "dssr-splays.pdb",
        "desc": "an ensemble of splayed-apart units"
      },
      {
        "index": 9,
        "name": "dssr-stacks.pdb",
        "desc": "an ensemble of base stacks"
      },
      {
        "index": 10,
        "name": "dssr-atom2bases.pdb",
        "desc": "an ensemble of atom-base stacking interactions"
      },
      {
        "index": 11,
        "name": "dssr-rotmat.txt",
        "desc": "position vector and rotation matrix"
      },
      {
        "index": 12,
        "name": "dssr-viewV.pdb",
        "desc": "vertical view of the principal moment of inertia"
      },
      {
        "index": 13,
        "name": "dssr-viewH.pdb",
        "desc": "horizontal view of the principal moment of inertia"
      },
      {
        "index": 14,
        "name": "dssr-viewT.pdb",
        "desc": "top view of the principal moment of inertia"
      }
    ],
    "time_used": "999"
  }
}