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The Fortran90 source code associated with the paper by Li et al. [1] gives the following information about an amino acid glycine:

ConnectionTypes
================
atomConType = 
    {"CT1","CT2","CT3","C","CC","CPH1","CPH2","CPT","N",
        "NH1","NH2","NH3","NC2","CY","NR2","NY","H","HA",
        "HB","HC","HS","HR1","CA","HR3","HP","O","OC","OH1",
        "S","CP1","CP2","CP3","NP"};

    AcidInfo 
================
name = "GLY";
heavyAtoms = 4;
totalAtoms = 7;
atomNames = {" N  ", " CA ", " C  ", " O  ", " H  ", "1HA ", "2HA "};
atomConnections = {10, 2, 4, 26, 17, 19, 19};
bdc = {{ 1, 4, 0, 0},
       { 4,-1, 1, 5},
       {-1, 0, 1, 0},
       {-1, 0, 0, 0},
       {-4, 0, 0, 0},
       {-4, 0, 0, 0},
       {-5, 0, 0, 0},
       {-3, 0, 0, 0}};

What do the values atomConType , atomConnections, and bdc (bond distance count?) represent in the case of glycine?

Reference

  1. Li, Y.; Roy, A.; Zhang, Y. HAAD: A Quick Algorithm for Accurate Prediction of Hydrogen Atoms in Protein Structures. PLOS One 2009, 4 (8), e6701. DOI: 10.1371/journal.pone.0006701. (Open Access, PDF)
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