$$\int\limits_{0}^{\infty}\frac{\log\left(x\right)\arctan\left(x\right)}{e^{\pi x}-1}\,dx$$
$$\sum_{k=0}^{\infty}\frac{\left(-1\right)^k}{2k+1}\int\limits_{0}^{\infty}\frac{x^{2k+1}\log\left(x\right)}{e^{\pi x}-1}\,dx$$
From my notes on the Zeta function:
$$ \int\limits_{0}^{\infty} \frac{x^{s-1}}{e^{ax^b}-1}\,dx=\frac{\zeta\left(\frac{s}{b}\right)\Gamma\left(\frac{s}{b}\right)}{ba^{\frac{s}{b}}}$$
$$s=2k+2,\quad b=1, \quad a=\pi$$
$$\frac{d}{dk}\left[\frac{\zeta\left(2k+2\right)\Gamma\left(2k+2\right)}{\pi^{2k+2}}\right]=2\int\limits_{0}^{\infty}\frac{x^{2k+2}\log\left(x\right)}{e^{\pi x}-1}\,dx$$
$$\int\limits_{0}^{\infty}\frac{x^{2k+1}\log\left(x\right)}{e^{\pi x}-1}\,dx =\frac{1}{2}\frac{d}{dk}\left[\frac{\zeta\left(2k+2\right)\Gamma\left(2k+2\right)}{\pi^{2k+2}}\right]=\zeta'\left(2k+2\right)\Gamma\left(2k+2\right)\pi^{-2k-2}+\zeta\left(2k+2\right)\Gamma\left(2k+2\right)\psi^{\left(0\right)}\left(2k+2\right)\pi^{-2k-2}-\log\left(\pi\right)\zeta\left(2k+2\right)\Gamma\left(2k+2\right)$$
$$\frac{1}{\pi^2}\left(\sum_{k=0}^{\infty}\frac{\left(-1\right)^k\zeta'\left(2k+2\right)\Gamma\left(2k+2\right)}{\pi^{2k}\left(2k+1\right)}+\sum_{k=0}^{\infty}\frac{\left(-1\right)^k\zeta\left(2k+2\right)\Gamma\left(2k+2\right)\psi^{\left(0\right)}\left(2k+2\right)}{\pi^{2k}\left(2k+1\right)} - \log\left(\pi\right)\sum_{k=0}^{\infty}\frac{\left(-1\right)^k\zeta\left(2k+2\right)\Gamma\left(2k+2\right)}{\pi^{2k}\left(2k+1\right)}\right)$$
$$\boxed{\int\limits_{0}^{\infty}\frac{\log\left(x\right)\arctan\left(x\right)}{e^{\pi x}-1}\,dx = \frac{1}{2\pi^2}\sum_{k=0}^{\infty}\frac{\left(-1\right)^k}{2k+1}\left(\frac{d}{dk}\left[\frac{\zeta\left(2k+2\right)\Gamma\left(2k+2\right)}{\pi^{2k}}\right]\right)}$$
$$\int\limits_{0}^{\infty}\frac{\log\left(x\right)\arctan\left(x\right)}{e^{\pi x}-1}\,dx = -\gamma\frac{1}{6}-\log\left(\pi\right)\frac{1}{6}+\frac{\zeta\left(2,1\right)}{\pi^2}-\left(-\gamma+1\right)\frac{1}{18}+\log\left(\pi\right)\frac{1}{18}+\dots$$