diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index f6223fecd56d..6038260a25f3 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -332,7 +332,7 @@ let
     Cairo = with pkgs; [ libtiff libjpeg cairo.dev xorg.libXt.dev fontconfig.lib ];
     Cardinal = [ pkgs.which ];
     chebpol = [ pkgs.fftw.dev ];
-    ChemmineOB = with pkgs; [ openbabel pkg-config ];
+    ChemmineOB = [ pkgs.pkg-config ];
     curl = [ pkgs.curl.dev ];
     CytoML = [ pkgs.libxml2.dev ];
     data_table = with pkgs; [ pkg-config zlib.dev ] ++ lib.optional stdenv.isDarwin pkgs.llvmPackages.openmp;
@@ -706,6 +706,7 @@ let
     ragg = with pkgs; [ freetype.dev libpng.dev libtiff.dev zlib.dev libjpeg.dev bzip2.dev ] ++ lib.optional stdenv.isDarwin lerc.dev;
     qqconf = [ pkgs.fftw.dev ];
     vapour = with pkgs; [ proj.dev gdal ];
+    ChemmineOB = [ pkgs.eigen ];
   };
 
   packagesRequiringX = [
@@ -1370,6 +1371,31 @@ let
       PKGCONFIG_LIBS = "-Wl,-rpath,${lib.getLib pkgs.openssl}/lib -L${lib.getLib pkgs.openssl}/lib -L${pkgs.cyrus_sasl.out}/lib -L${pkgs.zlib.out}/lib -lssl -lcrypto -lsasl2 -lz";
     });
 
+    ChemmineOB = let
+      # R package doesn't compile with the latest (unstable) version.
+      # Override from nixpkgs-23.11
+      openbabel3 = pkgs.openbabel.overrideAttrs (attrs: {
+        version = "3.1.1";
+        src = pkgs.fetchFromGitHub {
+          owner = "openbabel";
+          repo = "openbabel";
+          rev = "openbabel-${lib.replaceStrings ["."] ["-"] attrs.version}";
+          sha256 = "sha256-wQpgdfCyBAoh4pmj9j7wPTlMtraJ62w/EShxi/olVMY=";
+        };
+      });
+    in
+    old.ChemmineOB.overrideAttrs (attrs: {
+      # pkg-config knows openbabel-3 without the .0
+      # Eigen3 is also looked for in the wrong location
+      postPatch = ''
+        substituteInPlace configure \
+          --replace-fail openbabel-3.0 openbabel-3
+        substituteInPlace src/Makevars.in \
+          --replace-fail "-I/usr/include/eigen3" "-I${pkgs.eigen}/include/eigen3"
+      '';
+      buildInputs = attrs.buildInputs ++ [openbabel3];
+    });
+
     ps = old.ps.overrideAttrs (attrs: {
       preConfigure = "patchShebangs configure";
     });