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One file seems to be in common between openbabel and openbox: /usr/bin/obprop. I doubt they provide the same functionality.
:: Synchronizing package databases...
community-testing is up to date
testing is up to date
core is up to date
extra is up to date
community is up to date
:: Starting full system upgrade...
resolving dependencies...
looking for inter-conflicts...
Targets (16): consolekit-0.4.1-2 devicekit-power-013-1 eog-2.28.2-1
gtksourceview2-2.8.2-1 gedit-2.28.3-1
gnome2-user-docs-2.28.2-1 hal-info-0.20091130-1 hal-0.5.14-1
kernel26-firmware-2.6.32.2-1 kernel26-2.6.32.2-1
xcb-proto-1.6-1 libxcb-1.5-1 mono-2.6.1-1 openbox-3.4.9-1
tint2-0.8-1 xorg-xkb-utils-7.5-2
Total Download Size: 0.00 MB
Total Installed Size: 288.12 MB
Proceed with installation? [Y/n] Y
checking package integrity...
(16/16) checking for file conflicts [#####################] 100%
error: failed to commit transaction (conflicting files)
openbox: /usr/bin/obprop exists in filesystem
Errors occurred, no packages were upgraded.Offline
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