Needs["MolecularGraphics`"]

\(\(atoms =  (*atomic\ positions\ in\ atomic\ units*) {
{6, 1.3799039209, 0.0000291166, 
            0.1789567798}, {7, \(-1.2486079261\), 
            0.0000390842, \(-0.200347113\)}, {1, 2.3378337605, 
            1.7328860028, \(-0.2857713814\)}, {1, 
            2.3378174666, \(-1.7328426279\), \(-0.2857495652\)}, {1, \(-2.1074204095\), 1.5470997308, 
            0.450187402}, {1, \(-2.1074349559\), \(-1.5470052969\), 
            0.4502068786000001}};\)

 (*Alternative\ \(form : 
\(\(===\)\(===\)\(===\)\(===\)\(===\)\(===\)\(\(==\)\(atoms\)\)\)\) = {{"C", 1.3799039209, 0.0000291166, 
            0.1789567798}, {"N", \(-1.2486079261\), 
            0.0000390842, \(-0.200347113\)}, {"H", 2.3378337605, 
            1.7328860028, \(-0.2857713814\)}, {"H", 
            2.3378174666, \(-1.7328426279\), \(-0.2857495652\)}, {"H", \(-2.1074204095\), 1.5470997308, 
            0.450187402}, {"H", \(-2.1074349559\), \(-1.5470052969\), 
            0.4502068786000001}}*) 
\)
displacementvectors = {{1. *10^-6, 
            0.123878, -(1. *10^-6)}, {1. *10^-6, 
            0.150602, -(1. *10^-6)}, {0.096767, -0.04820800000000001, -0.459905}, {-0.096768, -0.048202, 
            0.459906}, {-0.065477, -0.089032, 
            0.495552}, {0.065476, -0.089039, -0.4955510000000001}};

nuclei = 
        DrawNuclei[atoms, CoordinateUnit -> AtomicUnit, 
          PlotLabel -> "DrawNuclei[Coordinates]"];

bonds = 
        DrawBonds[atoms, CoordinateUnit -> AtomicUnit, 
          PlotLabel -> "DrawBonds[Coordinates]"];

molecule = 
        DrawMolecule[atoms, CoordinateUnit -> AtomicUnit, 
          PlotLabel -> "DrawMolecule[Coordinates]"];

vectors = 
        DrawVectors[2.5*displacementvectors, atoms, 
          CoordinateUnit -> AtomicUnit, 
          PlotLabel -> "DrawVectors[Vectors,Coordinates]"];

normalcoordinate = 
        DrawDistortion[atoms, 2.5*displacementvectors, 
          CoordinateUnit -> AtomicUnit, 
          PlotLabel -> "DrawDistortion[Coordinates,Vectors]"];

\(\(\( (*\(Draw\ the\ normal\ coordinate\ without\ the\ \(nuclei : 
\(\(===\)\(===\)\(===\)\(===\)\(===\)\(===\)\(===\)\(===\)\(===\)\(===\)\(===\)\(===\)\(===\)\(===\)\(===\)\(===\)\)\)\)\(=\)*) \)\(
\)\(Show[{bonds, vectors}, 
        PlotLabel -> "bonds & vectors together"];\)\)\)

\(\(\( (*Draw\ the\ atoms\ as\ spheres . 
            This\ takes\ longer\ \(time!\) ===  ===  ===  ===  ===  ===  ===  ===  ===  ===  ===  ===  ===  ===  ===  ===  ===  === *) \)\(
\)\(DrawDistortion[atoms, 2.5*displacementvectors, 
        AtomicShape -> Sphere, CoordinateUnit -> AtomicUnit, 
        PlotLabel -> "DrawDistortion[Coords,Vecs,AtomicShape -> Sphere]"];\)\)\)