How the 2D/3D flag in Mol blocks is used

documentation

technical

Specifications meet the real world

Published

August 22, 2025

[This is an expanded version of a section which will be added to the RDKit documentation to clarify an important detail about the way Mol and SD files are parsed.]

Background

Mol blocks, Mol files, and SD files can describe 2D or 3D molecules and include a flag (called “dimensional code” in the spec) to indicate whether the coordinates are 2D or 3D. The flag shows up in the second line of the Mol block, and is present in both V2000:

nitrogen
     RDKit          2D

  2  1  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -1.5000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  0
M  END

and V3000 mol blocks:

nitrogen
     RDKit          2D

  0  0  0  0  0  0  0  0  0  0999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 2 1 0 0 0
M  V30 BEGIN ATOM
M  V30 1 N 0.000000 0.000000 0.000000 0
M  V30 2 N -0.000000 -1.500000 0.000000 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 3 1 2
M  V30 END BOND
M  V30 END CTAB
M  END

The CTFile specification says the following about this flag: > The “dimensional code” is maintained explicitly. Thus “3D” really means 3D, > although “2D” will be interpreted as 3D if any non-zero Z-coordinates are > found

That’s simple (and logical) enough, but of course in the real world things are more complicated. Files found “in the wild” include every possible combination of 2D/3D flag and 2D/3D coordinates, so we need to decide how to interpret these combinations. Things are made more complicated by the possible presence of wedged bonds in the Mol block. Wedged bonds are typically a signal that something is known about the stereochemistry of the molecule; how do we combine this information with the coordinates?

Aside on 2D vs 3D coordinates: in Mol blocks X, Y, and Z coordinates are always provided (if any of them are missing, they are set to zero). It’s also possible to have 3D coordinates for planar molecules. For the purposes of this discussion, “2D” coordinates means that all Z coordinates are zero, and a “2D” RDKit molecule is one where the (default) conformer is marked as being 2D (i.e. the conformer’s Is3D() method returns False).

What the RDKit does

The following table describes how the RDKit interprets all possible combinations of dimensionality flag, coordinate dimensionality, and the presence or absence of wedged bonds:

flag	coords	wedging	result	notes
2D	2D	no	2D	no chirality
3D	2D	no	3D	no chirality
3D	3D	no	3D	chirality from coords
2D	3D	no	3D	chirality from coords
2D	2D	yes	2D	chirality from wedging
3D	2D	yes	2D	chirality from wedging
3D	3D	yes	3D	chirality from coords
2D	3D	yes	3D	chirality from coords

This is consistent with what the specification says except for the case where the 3D flag is set for 2D coordinates and a wedge is present, in which case we ignore the 3D flag, mark the conformer as 2D, and set the stereochemistry based on the wedging.

In cases where no 2D/3D flag is provided, the default value of the flag is 2D.

In a 2D structure, wedging is interpreted as a signal to indicate that stereochemistry is present and to indicate what the stereochemistry is (i.e. the stereochemistry is determined based on the 2D coordinates and the direction of the wedge).

When 3D coordinates are provided, stereochemistry is perceived from the coordinates themselves. If wedging is also present it will be ignored; the 3D signal is “stronger” than the wedging signal. The exception to this rule is atropisomeric bonds, where the wedged bond indicates that atropisomerism should be perceived, but the direction of the wedge is ignored.