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      "atom1_serNum": 5840,
      "atom2_serNum": 5897,
      "donAcc_type": "acceptable",
      "distance": 3.572,
      "atom1_id": "///B/47/O2'",
      "atom2_id": "///B/50/OP1",
      "atom_pair": "O:O",
      "residue_pair": "nt:nt"
    },
    {
      "index": 657,
      "atom1_serNum": 5851,
      "atom2_serNum": 5898,
      "donAcc_type": "questionable",
      "distance": 3.036,
      "atom1_id": "///B/48/OP1",
      "atom2_id": "///B/50/OP2",
      "atom_pair": "O:O",
      "residue_pair": "nt:nt"
    },
    {
      "index": 658,
      "atom1_serNum": 5860,
      "atom2_serNum": 5874,
      "donAcc_type": "acceptable",
      "distance": 3.042,
      "atom1_id": "///B/48/O2'",
      "atom2_id": "///B/49/OP1",
      "atom_pair": "O:O",
      "residue_pair": "nt:nt"
    },
    {
      "index": 659,
      "atom1_serNum": 5890,
      "atom2_serNum": 6229,
      "donAcc_type": "standard",
      "distance": 2.756,
      "atom1_id": "///B/49/O6",
      "atom2_id": "///B/65/N4",
      "atom_pair": "O:N",
      "residue_pair": "nt:nt"
    },
    {
      "index": 660,
      "atom1_serNum": 5891,
      "atom2_serNum": 6227,
      "donAcc_type": "standard",
      "distance": 2.899,
      "atom1_id": "///B/49/N1",
      "atom2_id": "///B/65/N3",
      "atom_pair": "N:N",
      "residue_pair": "nt:nt"
    },
    {
      "index": 661,
      "atom1_serNum": 5893,
      "atom2_serNum": 6226,
      "donAcc_type": "standard",
      "distance": 2.980,
      "atom1_id": "///B/49/N2",
      "atom2_id": "///B/65/O2",
      "atom_pair": "N:O",
      "residue_pair": "nt:nt"
    },
    {
      "index": 662,
      "atom1_serNum": 5913,
      "atom2_serNum": 6209,
      "donAcc_type": "standard",
      "distance": 3.227,
      "atom1_id": "///B/50/N6",
      "atom2_id": "///B/64/O4",
      "atom_pair": "N:O",
      "residue_pair": "nt:nt"
    },
    {
      "index": 663,
      "atom1_serNum": 5914,
      "atom2_serNum": 6207,
      "donAcc_type": "standard",
      "distance": 2.821,
      "atom1_id": "///B/50/N1",
      "atom2_id": "///B/64/N3",
      "atom_pair": "N:N",
      "residue_pair": "nt:nt"
    },
    {
      "index": 664,
      "atom1_serNum": 5935,
      "atom2_serNum": 6189,
      "donAcc_type": "standard",
      "distance": 3.044,
      "atom1_id": "///B/51/O6",
      "atom2_id": "///B/63/N4",
      "atom_pair": "O:N",
      "residue_pair": "nt:nt"
    },
    {
      "index": 665,
      "atom1_serNum": 5936,
      "atom2_serNum": 6187,
      "donAcc_type": "standard",
      "distance": 3.071,
      "atom1_id": "///B/51/N1",
      "atom2_id": "///B/63/N3",
      "atom_pair": "N:N",
      "residue_pair": "nt:nt"
    },
    {
      "index": 666,
      "atom1_serNum": 5938,
      "atom2_serNum": 6186,
      "donAcc_type": "standard",
      "distance": 2.986,
      "atom1_id": "///B/51/N2",
      "atom2_id": "///B/63/O2",
      "atom_pair": "N:O",
      "residue_pair": "nt:nt"
    },
    {
      "index": 667,
      "atom1_serNum": 5938,
      "atom2_serNum": 6187,
      "donAcc_type": "standard",
      "distance": 3.160,
      "atom1_id": "///B/51/N2",
      "atom2_id": "///B/63/N3",
      "atom_pair": "N:N",
      "residue_pair": "nt:nt"
    },
    {
      "index": 668,
      "atom1_serNum": 5958,
      "atom2_serNum": 6169,
      "donAcc_type": "standard",
      "distance": 3.558,
      "atom1_id": "///B/52/O6",
      "atom2_id": "///B/62/N4",
      "atom_pair": "O:N",
      "residue_pair": "nt:nt"
    },
    {
      "index": 669,
      "atom1_serNum": 5959,
      "atom2_serNum": 6167,
      "donAcc_type": "standard",
      "distance": 3.347,
      "atom1_id": "///B/52/N1",
      "atom2_id": "///B/62/N3",
      "atom_pair": "N:N",
      "residue_pair": "nt:nt"
    },
    {
      "index": 670,
      "atom1_serNum": 5961,
      "atom2_serNum": 6166,
      "donAcc_type": "standard",
      "distance": 2.980,
      "atom1_id": "///B/52/N2",
      "atom2_id": "///B/62/O2",
      "atom_pair": "N:O",
      "residue_pair": "nt:nt"
    },
    {
      "index": 671,
      "atom1_serNum": 5981,
      "atom2_serNum": 6149,
      "donAcc_type": "standard",
      "distance": 3.129,
      "atom1_id": "///B/53/O6",
      "atom2_id": "///B/61/N4",
      "atom_pair": "O:N",
      "residue_pair": "nt:nt"
    },
    {
      "index": 672,
      "atom1_serNum": 5982,
      "atom2_serNum": 6147,
      "donAcc_type": "standard",
      "distance": 2.979,
      "atom1_id": "///B/53/N1",
      "atom2_id": "///B/61/N3",
      "atom_pair": "N:N",
      "residue_pair": "nt:nt"
    },
    {
      "index": 673,
      "atom1_serNum": 5984,
      "atom2_serNum": 6146,
      "donAcc_type": "standard",
      "distance": 2.743,
      "atom1_id": "///B/53/N2",
      "atom2_id": "///B/61/O2",
      "atom_pair": "N:O",
      "residue_pair": "nt:nt"
    },
    {
      "index": 674,
      "atom1_serNum": 6001,
      "atom2_serNum": 6087,
      "donAcc_type": "standard",
      "distance": 3.269,
      "atom1_id": "///B/54/O2",
      "atom2_id": "///B/58/N6",
      "atom_pair": "O:N",
      "residue_pair": "nt:nt"
    },
    {
      "index": 675,
      "atom1_serNum": 6002,
      "atom2_serNum": 6084,
      "donAcc_type": "standard",
      "distance": 2.766,
      "atom1_id": "///B/54/N3",
      "atom2_id": "///B/58/N7",
      "atom_pair": "N:N",
      "residue_pair": "nt:nt"
    },
    {
      "index": 676,
      "atom1_serNum": 6017,
      "atom2_serNum": 6061,
      "donAcc_type": "acceptable",
      "distance": 2.686,
      "atom1_id": "///B/55/O2'",
      "atom2_id": "///B/57/N7",
      "atom_pair": "O:N",
      "residue_pair": "nt:nt"
    },
    {
      "index": 677,
      "atom1_serNum": 6022,
      "atom2_serNum": 6072,
      "donAcc_type": "standard",
      "distance": 2.339,
      "atom1_id": "///B/55/N3",
      "atom2_id": "///B/58/OP2",
      "atom_pair": "N:O",
      "residue_pair": "nt:nt"
    },
    {
      "index": 678,
      "atom1_serNum": 6080,
      "atom2_serNum": 6114,
      "donAcc_type": "acceptable",
      "distance": 2.552,
      "atom1_id": "///B/58/O2'",
      "atom2_id": "///B/60/OP2",
      "atom_pair": "O:O",
      "residue_pair": "nt:nt"
    },
    {
      "index": 679,
      "atom1_serNum": 6080,
      "atom2_serNum": 6149,
      "donAcc_type": "acceptable",
      "distance": 3.172,
      "atom1_id": "///B/58/O2'",
      "atom2_id": "///B/61/N4",
      "atom_pair": "O:N",
      "residue_pair": "nt:nt"
    },
    {
      "index": 680,
      "atom1_serNum": 6114,
      "atom2_serNum": 6149,
      "donAcc_type": "standard",
      "distance": 3.099,
      "atom1_id": "///B/60/OP2",
      "atom2_id": "///B/61/N4",
      "atom_pair": "O:N",
      "residue_pair": "nt:nt"
    },
    {
      "index": 681,
      "atom1_serNum": 6142,
      "atom2_serNum": 6158,
      "donAcc_type": "acceptable",
      "distance": 3.269,
      "atom1_id": "///B/61/O2'",
      "atom2_id": "///B/62/O4'",
      "atom_pair": "O:O",
      "residue_pair": "nt:nt"
    },
    {
      "index": 682,
      "atom1_serNum": 6262,
      "atom2_serNum": 6278,
      "donAcc_type": "acceptable",
      "distance": 2.990,
      "atom1_id": "///B/67/O2'",
      "atom2_id": "///B/67/O4'",
      "atom_pair": "O:O",
      "residue_pair": "nt:nt"
    },
    {
      "index": 683,
      "atom1_serNum": 6460,
      "atom2_serNum": 6462,
      "donAcc_type": "acceptable",
      "distance": 2.892,
      "atom1_id": "///A/2002/OG",
      "atom2_id": "///A/2002/O9",
      "atom_pair": "O:O",
      "residue_pair": "ligand:ligand"
    }
  ],
  "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": "3w3s",
    "num_aaChains": 1,
    "aaChains": "A=528",
    "num_naChains": 1,
    "naChains": "B=98",
    "num_atoms": 6536,
    "num_waters": 0,
    "num_metals": 14,
    "metals_desc": "Zn=1,Pt=13",
    "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": 19,
    "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-stacks.pdb",
        "desc": "an ensemble of base stacks"
      },
      {
        "index": 15,
        "name": "dssr-atom2bases.pdb",
        "desc": "an ensemble of atom-base stacking interactions"
      },
      {
        "index": 16,
        "name": "dssr-rotmat.txt",
        "desc": "position vector and rotation matrix"
      },
      {
        "index": 17,
        "name": "dssr-viewV.pdb",
        "desc": "vertical view of the principal moment of inertia"
      },
      {
        "index": 18,
        "name": "dssr-viewH.pdb",
        "desc": "horizontal view of the principal moment of inertia"
      },
      {
        "index": 19,
        "name": "dssr-viewT.pdb",
        "desc": "top view of the principal moment of inertia"
      }
    ],
    "time_used": "999"
  }
}