Chemical bonds and atom position with chemfig

Question

I have been working in the cylindrospermopsin structure using chemfig. The structure is:

I draw it with te following code:

\documentclass[12pt, border={10pt 10pt 10pt 10pt}]{standalone}
\pagestyle{empty}
\usepackage{standalone} 
\usepackage[utf8]{inputenc}%Para copiar caracteres especiais como ç, á, à
\usepackage[T1]{fontenc}%Para copiar caracteres especiais como ç, á, à
\usepackage{amsmath}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{makeidx}
\usepackage{graphicx,graphics}
\usepackage[brazil]{babel}
\usepackage{chemfig}
\begin{document}
\chemfig{%
*6(-(-[:-72]?[a])(<[:-150]H)-N*6(-^{+}(-[:-108]NH2?[a])-NH1-(<[:90]H)(-[:30](<[:90]OH)-[:-30]*6(-M-(=[:-90]O)-NH-(=[:30]O)-=\phantom{L}))-?[b])-?[b](<[:90]H)--(<[:150]^{-}O_{3}SO)-)(<[:-150]H_3C)
}
\end{document}

The result is:

My questions:

1. How can I put the positive charge out the structure, like the example?
2. How can I draw the double bonds with one dashed line between N, NH1 and NH2?
3. How can I link the NH2 atom correctly with the hydrogen outside?
4. How can I put HN instead of M? I've been trying, but the bounds link in the H atom

Any help, indication, suggestion?

Answer 1

\documentclass[12pt, border=3mm,tikz]{standalone}
\usepackage[utf8]{inputenc}%Para copiar caracteres especiais como ç, á, à
\usepackage[T1]{fontenc}%Para copiar caracteres especiais como ç, á, à
\usepackage{chemfig}
\usetikzlibrary{decorations.markings} % You need this for q2

% From package documentation, pg 29, change ‘ to ` (2 instances)
\catcode`\@=11
\tikzset{
    ddbond/.style args={#1}{
        draw=none,
        decoration={%
            markings,
            mark=at position 0 with {
                \coordinate (CF@startdeloc) at (0,\dimexpr#1\CF@double@sep/2)
                coordinate (CF@startaxis) at (0,\dimexpr-#1\CF@double@sep/2);
            },
            mark=at position 1 with {
                \coordinate (CF@enddeloc) at (0,\dimexpr#1\CF@double@sep/2)
                coordinate (CF@endaxis) at (0,\dimexpr-#1\CF@double@sep/2);
                \draw[dash pattern=on 2pt off 1.5pt] (CF@startdeloc)--(CF@enddeloc);
                \draw (CF@startaxis)--(CF@endaxis);
            }
        },
        postaction={decorate}
    }
}
\catcode`\@=12

\begin{document}
\chemfig{%
    *6(-(-[:-72]?[a])(<[:-150]H)
    -N*6(-[,,,,ddbond={+}](-[7,0.2,,,draw=none]{\scriptstyle+})
    (-[:-108,,,1,ddbond={-}]N?[a]H2)
    -[,,,,ddbond={+}]NH1-(<[:90]H)(-[:30](<[:90]OH)
    -[:-30]*6(-[,,,2]HN-(=[:-90]O)-NH-(=[:30]O)-
    =\phantom{L}))-?[b])-?[b](<[:90]H)--(<[:150]^{-}O_{3}SO)-)(<[:-150]H_3C)
}

\end{document}

Just some small notes on each question. The very well-written package documentation goes into more details, I'll just point you to what's relevant.

1. with -[7,0.2,,,draw=none]{\scriptstyle+}: This draws a + at the end of an invisible bond, drawn -45deg from the C atom (that's what the 7 means), 0.2*bond length away.

2. with -[,,,,ddbond={+/-}]: this is taken from the chemfig documentation, pg 29. You need to use \usetikzlibrary{decorations.markings} in the preamble for this to work, and add the relevant part in the preamble. Then just add the ddbond={+} or ddbond={-} option to the relevant bonds (after 4 commas in the optional argument).

3. with -[:-108,,,1]N?[a]H2: This bond is drawn from the + to the NH2, so set its arrival atom to 1 explicitly, which is the N atom. (Try removing the 1 in the argument, note what you get).

4. with -[,,,2]HN instead of -M Similar with question 3, set the arrival atom to the second atom (the N), by passing 2 to the fourth optional argument.

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