![\tdplotsetmaincoords{-15}{0}\begin{tikzpicture}[scale=1,tdplot_main_coords,rotate=0,declare function = {opc=0.9;Cvdw=1.70 cm; Nvdw=1.55 cm; Ovdw=1.52 cm; Hvdw=1.20 cm; Bvdw=1.92 cm; Clvdw=1.75 cm; Fvdw=1.47 cm; Svdw=1.80 cm; Pvdw=1.80cm; Brvdw=1.85 cm; Ivdw=1.98 cm; Ptvdw=1.75 cm; Mgvdw=0.86 cm;vdw=1/5; lw=3;_cell.entry_id = Cadaverine_132872;_cell.length_a = 17.709;_cell.length_b = 6.228;_cell.length_c = 5.857;_cell.angle_alpha = 90.00;_cell.angle_beta = 90.00;_cell.angle_gamma = 90.00;_symmetry.space_group_name_H-M = Cmc21;x0=8.854375; y0=1.570667; z0=1.125833;}]\coordinate (N) at (5.037-x0,1.846-y0,1.320-z0);\coordinate (C1) at (6.316-x0,1.315-y0,0.834-z0);\coordinate (C2) at (7.574-x0,1.851-y0,1.515-z0);\coordinate (C3) at (8.854-x0,1.291-y0,0.897-z0);\coordinate (H1) at (5.010-x0,2.722-y0,1.208-z0);\coordinate (H2) at (4.897-x0,1.673-y0,2.164-z0);\coordinate (H1A) at (6.301-x0,0.351-y0,0.867-z0);\coordinate (H1B) at (6.368-x0,1.503-y0,-0.101-z0);\coordinate (H2A) at (7.544-x0,1.649-y0,2.509-z0);\coordinate (H2B) at (7.567-x0,2.836-y0,1.436-z0);\coordinate (H3A) at (8.854-x0,0.310-y0,0.930-z0);\coordinate (H3B) at (8.854-x0,1.501-y0,-0.069-z0);\coordinate (NX) at (12.672-x0,1.846-y0,1.320-z0);\coordinate (C1X) at (11.393-x0,1.315-y0,0.834-z0);\coordinate (C2X) at (10.135-x0,1.851-y0,1.515-z0);\coordinate (C3X) at (8.854-x0,1.291-y0,0.897-z0);\coordinate (H1X) at (12.699-x0,2.722-y0,1.208-z0);\coordinate (H2X) at (12.812-x0,1.673-y0,2.164-z0);\coordinate (H1AX) at (11.408-x0,0.351-y0,0.867-z0);\coordinate (H1BX) at (11.341-x0,1.503-y0,-0.101-z0);\coordinate (H2AX) at (10.165-x0,1.649-y0,2.509-z0);\coordinate (H2BX) at (10.142-x0,2.836-y0,1.436-z0);\coordinate (H3AX) at (8.854-x0,0.310-y0,0.930-z0);\coordinate (H3BX) at (8.854-x0,1.501-y0,-0.069-z0);\foreach \labelx /\labely in {N/H1, N/H2, C1/H1A, C1/H1B, C2/H2A, C2/H2B, C3/H3A, C3/H3B, NX/H1X, NX/H2X, C1X/H1AX, C1X/H1BX, C2X/H2AX, C2X/H2BX} \draw[line width = lw, Pink1] (\labelx) -- (\labely);\draw[line width = lw, gray] (N) -- (C1) -- (C2) -- (C3) -- (C2X) -- (C1X) -- (NX);\foreach \label in {H1, H2, H1A, H2A, H2B, H3A, H1X, H2X, H1AX, H2AX, H2BX} \shade[ball color = white, opacity=opc] (\label) circle (vdw*Hvdw);\foreach \label in {C1, C2, C3, C1X, C2X} \shade[ball color = black, opacity=opc] (\label) circle (vdw*Cvdw);\foreach \label in {N, NX} \shade[ball color = blue, opacity=opc] (\label) circle (vdw*Nvdw);\foreach \label in {H1B, H3B, H1BX} \shade[ball color = white, opacity=opc] (\label) circle (vdw*Hvdw);\end{tikzpicture}](https://gaia-sb.iwate-med.ac.jp/pharm/filter/tex/pix.php/7f990df5b25d2e42f97f6b51a8ff746b.svg "\tdplotsetmaincoords{-15}{0}\begin{tikzpicture}[scale=1,tdplot_main_coords,rotate=0,declare function = {opc=0.9;Cvdw=1.70 cm; Nvdw=1.55 cm; Ovdw=1.52 cm; Hvdw=1.20 cm; Bvdw=1.92 cm; Clvdw=1.75 cm; Fvdw=1.47 cm; Svdw=1.80 cm; Pvdw=1.80cm; Brvdw=1.85 cm; Ivdw=1.98 cm; Ptvdw=1.75 cm; Mgvdw=0.86 cm;vdw=1/5; lw=3;_cell.entry_id = Cadaverine_132872;_cell.length_a = 17.709;_cell.length_b = 6.228;_cell.length_c = 5.857;_cell.angle_alpha = 90.00;_cell.angle_beta = 90.00;_cell.angle_gamma = 90.00;_symmetry.space_group_name_H-M = Cmc21;x0=8.854375; y0=1.570667; z0=1.125833;}]\coordinate (N) at (5.037-x0,1.846-y0,1.320-z0);\coordinate (C1) at (6.316-x0,1.315-y0,0.834-z0);\coordinate (C2) at (7.574-x0,1.851-y0,1.515-z0);\coordinate (C3) at (8.854-x0,1.291-y0,0.897-z0);\coordinate (H1) at (5.010-x0,2.722-y0,1.208-z0);\coordinate (H2) at (4.897-x0,1.673-y0,2.164-z0);\coordinate (H1A) at (6.301-x0,0.351-y0,0.867-z0);\coordinate (H1B) at (6.368-x0,1.503-y0,-0.101-z0);\coordinate (H2A) at (7.544-x0,1.649-y0,2.509-z0);\coordinate (H2B) at (7.567-x0,2.836-y0,1.436-z0);\coordinate (H3A) at (8.854-x0,0.310-y0,0.930-z0);\coordinate (H3B) at (8.854-x0,1.501-y0,-0.069-z0);\coordinate (NX) at (12.672-x0,1.846-y0,1.320-z0);\coordinate (C1X) at (11.393-x0,1.315-y0,0.834-z0);\coordinate (C2X) at (10.135-x0,1.851-y0,1.515-z0);\coordinate (C3X) at (8.854-x0,1.291-y0,0.897-z0);\coordinate (H1X) at (12.699-x0,2.722-y0,1.208-z0);\coordinate (H2X) at (12.812-x0,1.673-y0,2.164-z0);\coordinate (H1AX) at (11.408-x0,0.351-y0,0.867-z0);\coordinate (H1BX) at (11.341-x0,1.503-y0,-0.101-z0);\coordinate (H2AX) at (10.165-x0,1.649-y0,2.509-z0);\coordinate (H2BX) at (10.142-x0,2.836-y0,1.436-z0);\coordinate (H3AX) at (8.854-x0,0.310-y0,0.930-z0);\coordinate (H3BX) at (8.854-x0,1.501-y0,-0.069-z0);\foreach \labelx /\labely in {N/H1, N/H2, C1/H1A, C1/H1B, C2/H2A, C2/H2B, C3/H3A, C3/H3B, NX/H1X, NX/H2X, C1X/H1AX, C1X/H1BX, C2X/H2AX, C2X/H2BX} \draw[line width = lw, Pink1] (\labelx) -- (\labely);\draw[line width = lw, gray] (N) -- (C1) -- (C2) -- (C3) -- (C2X) -- (C1X) -- (NX);\foreach \label in {H1, H2, H1A, H2A, H2B, H3A, H1X, H2X, H1AX, H2AX, H2BX} \shade[ball color = white, opacity=opc] (\label) circle (vdw*Hvdw);\foreach \label in {C1, C2, C3, C1X, C2X} \shade[ball color = black, opacity=opc] (\label) circle (vdw*Cvdw);\foreach \label in {N, NX} \shade[ball color = blue, opacity=opc] (\label) circle (vdw*Nvdw);\foreach \label in {H1B, H3B, H1BX} \shade[ball color = white, opacity=opc] (\label) circle (vdw*Hvdw);\end{tikzpicture}")
\tdplotsetmaincoords{-15}{0}
\begin{tikzpicture}[scale=1,tdplot_main_coords,rotate=0,
declare function = {
opc=0.9;
Cvdw=1.70 cm; Nvdw=1.55 cm; Ovdw=1.52 cm; Hvdw=1.20 cm; Bvdw=1.92 cm; Clvdw=1.75 cm; Fvdw=1.47 cm; Svdw=1.80 cm; Pvdw=1.80cm; Brvdw=1.85 cm; Ivdw=1.98 cm; Ptvdw=1.75 cm; Mgvdw=0.86 cm;
vdw=1/5; lw=3;
_cell.entry_id = Cadaverine_132872;
_cell.length_a = 17.709;
_cell.length_b = 6.228;
_cell.length_c = 5.857;
_cell.angle_alpha = 90.00;
_cell.angle_beta = 90.00;
_cell.angle_gamma = 90.00;
_symmetry.space_group_name_H-M = Cmc21;
x0=8.854375; y0=1.570667; z0=1.125833;
}]
\coordinate (N) at (5.037-x0,1.846-y0,1.320-z0);
\coordinate (C1) at (6.316-x0,1.315-y0,0.834-z0);
\coordinate (C2) at (7.574-x0,1.851-y0,1.515-z0);
\coordinate (C3) at (8.854-x0,1.291-y0,0.897-z0);
\coordinate (H1) at (5.010-x0,2.722-y0,1.208-z0);
\coordinate (H2) at (4.897-x0,1.673-y0,2.164-z0);
\coordinate (H1A) at (6.301-x0,0.351-y0,0.867-z0);
\coordinate (H1B) at (6.368-x0,1.503-y0,-0.101-z0);
\coordinate (H2A) at (7.544-x0,1.649-y0,2.509-z0);
\coordinate (H2B) at (7.567-x0,2.836-y0,1.436-z0);
\coordinate (H3A) at (8.854-x0,0.310-y0,0.930-z0);
\coordinate (H3B) at (8.854-x0,1.501-y0,-0.069-z0);
\coordinate (NX) at (12.672-x0,1.846-y0,1.320-z0);
\coordinate (C1X) at (11.393-x0,1.315-y0,0.834-z0);
\coordinate (C2X) at (10.135-x0,1.851-y0,1.515-z0);
\coordinate (C3X) at (8.854-x0,1.291-y0,0.897-z0);
\coordinate (H1X) at (12.699-x0,2.722-y0,1.208-z0);
\coordinate (H2X) at (12.812-x0,1.673-y0,2.164-z0);
\coordinate (H1AX) at (11.408-x0,0.351-y0,0.867-z0);
\coordinate (H1BX) at (11.341-x0,1.503-y0,-0.101-z0);
\coordinate (H2AX) at (10.165-x0,1.649-y0,2.509-z0);
\coordinate (H2BX) at (10.142-x0,2.836-y0,1.436-z0);
\coordinate (H3AX) at (8.854-x0,0.310-y0,0.930-z0);
\coordinate (H3BX) at (8.854-x0,1.501-y0,-0.069-z0);
\foreach \labelx /\labely in {N/H1, N/H2, C1/H1A, C1/H1B, C2/H2A, C2/H2B, C3/H3A, C3/H3B, NX/H1X, NX/H2X, C1X/H1AX, C1X/H1BX, C2X/H2AX, C2X/H2BX}
\draw[line width = lw, Pink1] (\labelx) -- (\labely);
\draw[line width = lw, gray] (N) -- (C1) -- (C2) -- (C3) -- (C2X) -- (C1X) -- (NX);
\foreach \label in {H1, H2, H1A, H2A, H2B, H3A, H1X, H2X, H1AX, H2AX, H2BX}
\shade[ball color = white, opacity=opc] (\label) circle (vdw*Hvdw);
\foreach \label in {C1, C2, C3, C1X, C2X}
\shade[ball color = black, opacity=opc] (\label) circle (vdw*Cvdw);
\foreach \label in {N, NX}
\shade[ball color = blue, opacity=opc] (\label) circle (vdw*Nvdw);
\foreach \label in {H1B, H3B, H1BX}
\shade[ball color = white, opacity=opc] (\label) circle (vdw*Hvdw);
\end{tikzpicture}