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CVE-2026-2705

Open Babel MOL2 File atom.h SetFormalCharge out-of-bounds

5.3 MediumFix available

A vulnerability was detected in Open Babel up to 3.1.1. The impacted element is the function OBAtom::SetFormalCharge in the library include/openbabel/atom.h of the component MOL2 File Handler. The manipulation results in out-of-bounds read. It is possible to launch the attack remotely. The exploit is now public and may be used. The patch is identified as e23a224b8fd9d7c2a7cde9ef4ec6afb4c05aa08a. A patch should be applied to remediate this issue. The project was informed of the problem early through an issue report but has not responded yet.

Attack profile

How easy it is to exploit

Attack vector
Network
Complexity
Low
Privileges needed
None
User interaction
Passive

What an attacker can affect

Confidentiality
None
Integrity
None
Availability
Low

Exploit likelihood

0.84%Up 0.8 points since Feb 19, 2026
90%50%10%1%

What each source reports

CVE List Score used 5.3

Open Babel MOL2 File atom.h SetFormalCharge out-of-bounds

A vulnerability was detected in Open Babel up to 3.1.1. The impacted element is the function OBAtom::SetFormalCharge in the library include/openbabel/atom.h of the component MOL2 File Handler. The manipulation results in out-of-bounds read. It is possible to launch the attack remotely. The exploit is now public and may be used. The patch is identified as e23a224b8fd9d7c2a7cde9ef4ec6afb4c05aa08a. A patch should be applied to remediate this issue. The project was informed of the problem early through an issue report but has not responded yet.

Record
CVE-2026-2705
CVSS 4.0
5.3 MediumCVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:P/VC:N/VI:N/VA:L/SC:N/SI:N/SA:N/E:P
CVSS 3.1
4.3 MediumCVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:N/I:N/A:L/E:P/RL:O/RC:C
CVSS 3.0
4.3 MediumCVSS:3.0/AV:N/AC:L/PR:N/UI:R/S:U/C:N/I:N/A:L/E:P/RL:O/RC:C
CVSS 2.0
5.0 AV:N/AC:L/Au:N/C:N/I:N/A:P/E:POC/RL:OF/RC:C
Weakness
CWE-125, CWE-119
Updated
2026-11-02
EUVDEUVD-2026-7561 5.3

A vulnerability was detected in Open Babel up to 3.1.1. The impacted element is the function OBAtom::SetFormalCharge in the library include/openbabel/atom.h of the component MOL2 File Handler. The manipulation results in out-of-bounds read. It is possible to launch the attack remotely. The exploit is now public and may be used. The patch is identified as e23a224b8fd9d7c2a7cde9ef4ec6afb4c05aa08a. A patch should be applied to remediate this issue. The project was informed of the problem early through an issue report but has not responded yet.

Record
EUVD-2026-7561
CVSS 4.0
5.3 MediumCVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:P/VC:N/VI:N/VA:L/SC:N/SI:N/SA:N/E:P
Updated
2026-11-02
GitHub AdvisoriesGHSA-3f56-w4g2-mx64 2.1

Duplicate Advisory: Open Babel has NULL pointer dereference in MOL2 OBAtom::SetFormalCharge

Duplicate Advisory

This advisory has been withdrawn because it is a duplicate of GHSA-4w5w-4fhm-q483. This link is maintained to preserve external references.

Original Description

A vulnerability was detected in Open Babel up to 3.1.1. The impacted element is the function OBAtom::SetFormalCharge in the library include/openbabel/atom.h of the component MOL2 File Handler. The manipulation results in out-of-bounds read. It is possible to launch the attack remotely. The exploit is now public and may be used. The project was informed of the problem early through an issue report but has not responded yet.

Record
GHSA-3f56-w4g2-mx64
CVSS 4.0
2.1 LowCVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:P/VC:N/VI:N/VA:L/SC:N/SI:N/SA:N/E:P/CR:X/IR:X/AR:X/MAV:X/MAC:X/MAT:X/MPR:X/MUI:X/MVC:X/MVI:X/MVA:X/MSC:X/MSI:X/MSA:X/S:X/AU:X/R:X/V:X/RE:X/U:X
CVSS 3.1
4.3 MediumCVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:N/I:N/A:L
Weakness
CWE-119
Updated
2026-11-02
GitHub AdvisoriesGHSA-4w5w-4fhm-q483 2.1

Open Babel has NULL pointer dereference in MOL2 OBAtom::SetFormalCharge

Summary

A memory-safety vulnerability in Open Babel's MOL2 file format parser caused a NULL pointer dereference when reading a crafted input file.

Details

The flaw was in OBAtom::SetFormalCharge as called from the MOL2 parser. A malformed atom record caused the parser to call the method on a NULL atom pointer.

Impact

Open Babel is a C++ library and CLI used to read and write chemistry file formats; it is shipped by Linux distributions and embedded in services that may parse untrusted input. Triggering this vulnerability requires the victim to open a malicious MOL2 file with the obabel tool, the OBConversion API, or any of the language bindings (Python, Ruby, Java, R, Perl, C#, PHP).

Affected versions

All releases up to and including 3.1.1.

Patched version

3.2.0 (released 2026-05-26).

Patch

Fix commit: https://github.com/openbabel/openbabel/commit/e23a224b Tracked in #2862.

A minimized reproducer for this CVE is checked in under test/files/fuzz_regress/ and is exercised on every CI build under ASAN+UBSAN by the fuzzregresstest harness.

Credit

Reported by Vedant Madane (@VedantMadane) via VulDB.

Record
GHSA-4w5w-4fhm-q483
CVSS 4.0
2.1 LowCVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:P/VC:N/VI:N/VA:L/SC:N/SI:N/SA:N/E:P
CVSS 3.1
5.5 MediumCVSS:3.1/AV:L/AC:L/PR:N/UI:R/S:U/C:N/I:N/A:H
Weakness
CWE-119, CWE-476
Updated
2026-11-02
NVD 2.1

A vulnerability was detected in Open Babel up to 3.1.1. The impacted element is the function OBAtom::SetFormalCharge in the library include/openbabel/atom.h of the component MOL2 File Handler. The manipulation results in out-of-bounds read. It is possible to launch the attack remotely. The exploit is now public and may be used. The patch is identified as e23a224b8fd9d7c2a7cde9ef4ec6afb4c05aa08a. A patch should be applied to remediate this issue. The project was informed of the problem early through an issue report but has not responded yet.

Record
CVE-2026-2705
CVSS 4.0
2.1 LowCVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:P/VC:N/VI:N/VA:L/SC:N/SI:N/SA:N/E:P/CR:X/IR:X/AR:X/MAV:X/MAC:X/MAT:X/MPR:X/MUI:X/MVC:X/MVI:X/MVA:X/MSC:X/MSI:X/MSA:X/S:X/AU:X/R:X/V:X/RE:X/U:X
CVSS 3.1
4.3 MediumCVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:N/I:N/A:L
CVSS 3.1
8.1 HighCVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:H/I:N/A:H
CVSS 2.0
5.0 MediumAV:N/AC:L/Au:N/C:N/I:N/A:P
Weakness
CWE-119, CWE-125
Updated
2026-11-02
OSV 2.1

Open Babel MOL2 File atom.h SetFormalCharge out-of-bounds

A vulnerability was detected in Open Babel up to 3.1.1. The impacted element is the function OBAtom::SetFormalCharge in the library include/openbabel/atom.h of the component MOL2 File Handler. The manipulation results in out-of-bounds read. It is possible to launch the attack remotely. The exploit is now public and may be used. The patch is identified as e23a224b8fd9d7c2a7cde9ef4ec6afb4c05aa08a. A patch should be applied to remediate this issue. The project was informed of the problem early through an issue report but has not responded yet.

Record
CVE-2026-2705
CVSS 4.0
2.1 LowCVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:P/VC:N/VI:N/VA:L/SC:N/SI:N/SA:N/E:P
Weakness
CWE-119, CWE-125
Updated
2026-11-02
Show 7 moreShow less
OSVDEBIAN-CVE-2026-2705 8.1

A vulnerability was detected in Open Babel up to 3.1.1. The impacted element is the function OBAtom::SetFormalCharge in the library include/openbabel/atom.h of the component MOL2 File Handler. The manipulation results in out-of-bounds read. It is possible to launch the attack remotely. The exploit is now public and may be used. The patch is identified as e23a224b8fd9d7c2a7cde9ef4ec6afb4c05aa08a. A patch should be applied to remediate this issue. The project was informed of the problem early through an issue report but has not responded yet.

Record
DEBIAN-CVE-2026-2705
CVSS 3.1
8.1 HighCVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:H/I:N/A:H
Updated
2026-11-07
OSVGHSA-3f56-w4g2-mx64 2.1

Duplicate Advisory: Open Babel has NULL pointer dereference in MOL2 OBAtom::SetFormalCharge

Duplicate Advisory

This advisory has been withdrawn because it is a duplicate of GHSA-4w5w-4fhm-q483. This link is maintained to preserve external references.

Original Description

A vulnerability was detected in Open Babel up to 3.1.1. The impacted element is the function OBAtom::SetFormalCharge in the library include/openbabel/atom.h of the component MOL2 File Handler. The manipulation results in out-of-bounds read. It is possible to launch the attack remotely. The exploit is now public and may be used. The project was informed of the problem early through an issue report but has not responded yet.

Record
GHSA-3f56-w4g2-mx64
CVSS 4.0
2.1 LowCVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:P/VC:N/VI:N/VA:L/SC:N/SI:N/SA:N/E:P/CR:X/IR:X/AR:X/MAV:X/MAC:X/MAT:X/MPR:X/MUI:X/MVC:X/MVI:X/MVA:X/MSC:X/MSI:X/MSA:X/S:X/AU:X/R:X/V:X/RE:X/U:X
CVSS 3.1
4.3 MediumCVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:N/I:N/A:L
Weakness
CWE-119
Updated
2026-11-02
OSVGHSA-4w5w-4fhm-q483 2.1

Open Babel has NULL pointer dereference in MOL2 OBAtom::SetFormalCharge

Summary

A memory-safety vulnerability in Open Babel's MOL2 file format parser caused a NULL pointer dereference when reading a crafted input file.

Details

The flaw was in OBAtom::SetFormalCharge as called from the MOL2 parser. A malformed atom record caused the parser to call the method on a NULL atom pointer.

Impact

Open Babel is a C++ library and CLI used to read and write chemistry file formats; it is shipped by Linux distributions and embedded in services that may parse untrusted input. Triggering this vulnerability requires the victim to open a malicious MOL2 file with the obabel tool, the OBConversion API, or any of the language bindings (Python, Ruby, Java, R, Perl, C#, PHP).

Affected versions

All releases up to and including 3.1.1.

Patched version

3.2.0 (released 2026-05-26).

Patch

Fix commit: https://github.com/openbabel/openbabel/commit/e23a224b Tracked in #2862.

A minimized reproducer for this CVE is checked in under test/files/fuzz_regress/ and is exercised on every CI build under ASAN+UBSAN by the fuzzregresstest harness.

Credit

Reported by Vedant Madane (@VedantMadane) via VulDB.

Record
GHSA-4w5w-4fhm-q483
CVSS 4.0
2.1 LowCVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:P/VC:N/VI:N/VA:L/SC:N/SI:N/SA:N/E:P
CVSS 3.1
5.5 MediumCVSS:3.1/AV:L/AC:L/PR:N/UI:R/S:U/C:N/I:N/A:H
Weakness
CWE-119, CWE-476
Updated
2026-11-02
OSVPYSEC-2026-2770 2.1

Open Babel has NULL pointer dereference in MOL2 OBAtom::SetFormalCharge

Summary

A memory-safety vulnerability in Open Babel's MOL2 file format parser caused a NULL pointer dereference when reading a crafted input file.

Details

The flaw was in OBAtom::SetFormalCharge as called from the MOL2 parser. A malformed atom record caused the parser to call the method on a NULL atom pointer.

Impact

Open Babel is a C++ library and CLI used to read and write chemistry file formats; it is shipped by Linux distributions and embedded in services that may parse untrusted input. Triggering this vulnerability requires the victim to open a malicious MOL2 file with the obabel tool, the OBConversion API, or any of the language bindings (Python, Ruby, Java, R, Perl, C#, PHP).

Affected versions

All releases up to and including 3.1.1.

Patched version

3.2.0 (released 2026-05-26).

Patch

Fix commit: https://github.com/openbabel/openbabel/commit/e23a224b Tracked in #2862.

A minimized reproducer for this CVE is checked in under test/files/fuzz_regress/ and is exercised on every CI build under ASAN+UBSAN by the fuzzregresstest harness.

Credit

Reported by Vedant Madane (@VedantMadane) via VulDB.

Record
PYSEC-2026-2770
CVSS 4.0
2.1 LowCVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:P/VC:N/VI:N/VA:L/SC:N/SI:N/SA:N/E:P
CVSS 3.1
5.5 MediumCVSS:3.1/AV:L/AC:L/PR:N/UI:R/S:U/C:N/I:N/A:H
Updated
2026-11-02
OSVUBUNTU-CVE-2026-2705 2.1

A vulnerability was detected in Open Babel up to 3.1.1. The impacted element is the function OBAtom::SetFormalCharge in the library include/openbabel/atom.h of the component MOL2 File Handler. The manipulation results in out-of-bounds read. It is possible to launch the attack remotely. The exploit is now public and may be used. The patch is identified as e23a224b8fd9d7c2a7cde9ef4ec6afb4c05aa08a. A patch should be applied to remediate this issue. The project was informed of the problem early through an issue report but has not responded yet.

Record
UBUNTU-CVE-2026-2705
CVSS 4.0
2.1 LowCVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:P/VC:N/VI:N/VA:L/SC:N/SI:N/SA:N/E:P
CVSS 3.1
8.1 HighCVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:H/I:N/A:H
CVSS 3.1
4.3 MediumCVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:N/I:N/A:L
Updated
2026-11-02
OSVopenSUSE-SU-2026:10936-1 No score

libopenbabel8-3.2.0-1.1 on GA media

These are all security issues fixed in the libopenbabel8-3.2.0-1.1 package on the GA media of openSUSE Tumbleweed.

Record
openSUSE-SU-2026:10936-1
Updated
2026-11-02
OSVopenSUSE-SU-2026:21190-1 No score

Security update for openbabel

This update for openbabel fixes the following issues:

Changes in openbabel:

  • Update to version 3.2.0:
    • Add an L-BFGS optimizer, used by default for gen3d and conformer searches
    • New macrocycle ring builder (Dale codes) for better initial 3D geometry of large rings
    • Add KET (Ketcher JSON) and ChemicalJSON (.cjson) format support
    • Drop Python 2 support; Python 3.13 supported
    • Faster, vectorized distance-geometry implementation
    • Full CMake 4 compatibility and modernized build
    • Backwards compatible with 3.0 and 3.1
    • Fix many crash and memory-safety bugs found via OSS-Fuzz and TALOS, including the following security issues: CVE-2022-37331 (boo#1217676), CVE-2022-41793, CVE-2022-42885, CVE-2022-43467, CVE-2022-43607, CVE-2022-44451, CVE-2022-46280, CVE-2022-46289, CVE-2022-46290, CVE-2022-46291, CVE-2022-46292, CVE-2022-46294, CVE-2022-46295, CVE-2025-10994, CVE-2025-10995, CVE-2025-10996, CVE-2025-10997, CVE-2025-10998, CVE-2025-10999, CVE-2025-11000, CVE-2026-2704 (boo#1258501), CVE-2026-2705 (boo#1258507) and CVE-2026-3408 (boo#1259041)
Record
openSUSE-SU-2026:21190-1
Updated
2026-11-02

Affected products

Affected packages

Affected packages
PackageAffectedFixed
openbabel
PyPI
 before 3.2.0
3.2.0
openbabel
Debian:12
 All versions, plus listed versions
3.1.1+dfsg-103.1.1+dfsg-113.1.1+dfsg-123.1.1+dfsg-133.1.1+dfsg-14
Show 5 moreShow less
3.1.1+dfsg-15~exp3.1.1+dfsg-93.2.0+dfsg-13.2.0+dfsg-1~exp3.2.0+dfsg-2
 None known
openbabel
Debian:13
 All versions, plus listed versions
3.1.1+dfsg-123.1.1+dfsg-133.1.1+dfsg-143.1.1+dfsg-15~exp3.2.0+dfsg-13.2.0+dfsg-1~exp3.2.0+dfsg-2
 None known
openbabel
Debian:14
 before 3.2.0+dfsg-1, plus listed versions
3.1.1+dfsg-123.1.1+dfsg-133.1.1+dfsg-143.1.1+dfsg-15~exp3.2.0+dfsg-1~exp
3.2.0+dfsg-1
openbabel
PyPI
 before 3.2.0, plus listed versions
1.81.8.11.8.21.8.31.8.4
Show 6 moreShow less
2.4.02.4.13.0.03.0.0a13.1.13.1.1.1
3.2.0
openbabel
Ubuntu:16.04:LTS
 All versions, plus listed versions
2.3.2+dfsg-2.22.3.2+dfsg-2.2build1
 None known
openbabel
Ubuntu:18.04:LTS
 All versions, plus listed versions
2.3.2+dfsg-3build1
 None known
openbabel
Ubuntu:20.04:LTS
 All versions, plus listed versions
2.4.1+dfsg-32.4.1+dfsg-3build12.4.1+dfsg-5.12.4.1+dfsg-63.0.0+dfsg-33.0.0+dfsg-3ubuntu3
 None known
openbabel
Ubuntu:22.04:LTS
 All versions, plus listed versions
3.1.1+dfsg-6ubuntu13.1.1+dfsg-6ubuntu5
 None known
openbabel
Ubuntu:24.04:LTS
 All versions, plus listed versions
3.1.1+dfsg-9build23.1.1+dfsg-9ubuntu13.1.1+dfsg-9ubuntu23.1.1+dfsg-9ubuntu43.1.1+dfsg-9ubuntu5
 None known
Show 5 moreShow less
Affected packages
PackageAffectedFixed
openbabel
Ubuntu:25.10
 All versions, plus listed versions
3.1.1+dfsg-11ubuntu33.1.1+dfsg-11ubuntu4
 None known
openbabel
Ubuntu:26.10
 All versions, plus listed versions
3.1.1+dfsg-11ubuntu53.1.1+dfsg-14ubuntu2
 None known
openbabel
Ubuntu:26.04:LTS
 All versions, plus listed versions
3.1.1+dfsg-11ubuntu43.1.1+dfsg-11ubuntu5
 None known
openbabel
openSUSE:Tumbleweed
From an advisory covering 8 CVEs
 before 3.2.0-1.1
3.2.0-1.1
openbabel
openSUSE:Leap 16.0
From an advisory covering 23 CVEs
 before 3.2.0-bp160.1.1
3.2.0-bp160.1.1

History

History
RecordedChangedSources
affectedOSV
affected, facts
affected
first indexedCVE List, EUVD, GitHub Advisories, NVD, OSV

Dates are when Every CVE recorded each change. Upstream dates may differ.

In short

CVE-2026-2705 is a medium vulnerability (CVSS 5.3) in Openbabel Open Babel, published February 19, 2026. No source lists public exploit code. EPSS puts the chance of exploitation in the next 30 days at 0.84%, the 58th percentile. Fixed in openbabel 3.2.0.

References

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