diff --git a/science/py-rmsd/Makefile b/science/py-rmsd/Makefile
index 462ac446a02e..1a3748a45b95 100644
--- a/science/py-rmsd/Makefile
+++ b/science/py-rmsd/Makefile
@@ -1,26 +1,27 @@
 PORTNAME=	rmsd
 DISTVERSIONPREFIX=	${PORTNAME}-
-DISTVERSION=	1.6.3
-PORTREVISION=	3
+DISTVERSION=	1.6.5
 CATEGORIES=	science
 #MASTER_SITES=	PYPI # missing test files, see https://github.com/charnley/rmsd/issues/123
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Calculate root-mean-square deviation (RMSD) between coordinate sets
 WWW=		https://github.com/charnley/rmsd
 
 LICENSE=	BSD2CLAUSE
 
+BUILD_DEPENDS=	${PY_SETUPTOOLS} \
+		${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR}
 RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}numpy>=1.16:math/py-numpy@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR}
 
 USES=		python
-USE_PYTHON=	distutils autoplist concurrent pytest
+USE_PYTHON=	pep517 autoplist concurrent pytest
 
 USE_GITHUB=	yes
 GH_ACCOUNT=	charnley
 
-# tests as of 1.6.3: 1 failed, 51 passed, 1 skipped in 8.53s, failure due to the missing science/py-qmllib that fails to build
+# tests as of 1.6.5: 52 passed, 1 skipped in 0.84s
 
 .include <bsd.port.mk>
diff --git a/science/py-rmsd/distinfo b/science/py-rmsd/distinfo
index 0e598d8c8e2e..210240fced7d 100644
--- a/science/py-rmsd/distinfo
+++ b/science/py-rmsd/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1736672385
-SHA256 (charnley-rmsd-rmsd-1.6.3_GH0.tar.gz) = 4bba161f0312e6e775261a3a4364670190b7be0c51fafc9b4e53351d1ae7ed0b
-SIZE (charnley-rmsd-rmsd-1.6.3_GH0.tar.gz) = 248837
+TIMESTAMP = 1785096722
+SHA256 (charnley-rmsd-rmsd-1.6.5_GH0.tar.gz) = 587a463be35b437228a8141d096214fb237420a99848f3d55898a83ee87673a5
+SIZE (charnley-rmsd-rmsd-1.6.5_GH0.tar.gz) = 248676
diff --git a/science/py-rmsd/files/patch-pyproject.toml b/science/py-rmsd/files/patch-pyproject.toml
new file mode 100644
index 000000000000..71027caaa68e
--- /dev/null
+++ b/science/py-rmsd/files/patch-pyproject.toml
@@ -0,0 +1,10 @@
+--- pyproject.toml.orig	2026-07-26 20:26:36 UTC
++++ pyproject.toml
+@@ -7,7 +7,6 @@ requires-python = ">=3.10"
+ dynamic = ["version"]
+ authors = []
+ requires-python = ">=3.10"
+-license-files = ["LICENSE"]
+ readme="README.rst"
+ description="Calculate Root-mean-square deviation (RMSD) of two molecules, using rotation, in xyz or pdb format "
+ classifiers = [