When I choose Check Structure or Analyze Structure, it says there is an invalid valence in a phosphate group.
Because of its many resonance forms, there are many plausible ways to draw a phosphate group. Several of the most popular ways are shown below, along with a discussion of how ChemDraw will interpret them.
|Neutral Structure||Ionic Structure||Analyze Structure||Discussion|
|Succeeds||This diagram minimizes the number of formal charges at the expense of violating the octet rule. However, unlike nitrogen, phosphorus can use its d orbitals for bonding, and it is not a big deal for phosphorus to violate the octet rule. These particular diagrams have been drawn to emphasize the tetrahedral nature of the phosphate group, but they could have just as easily been drawn with 90-degree angles between the bonds.|
|Succeeds||These diagrams leave the phosphate group as an atom label. ChemDraw recognizes this structure as identical to those above, and these diagrams will be analyzed without problems. When writing files (such as MDL Molfiles) that require chemical meaning, these atom labels will automatically be expanded into the form above, so they will also be recognized by most online and desktop databases.|
|Succeeds||This diagram emphasizes the symmetry of the phosphate group (particularly in ionic state), at the expense of introducing formal charges. Unlike the first structures above, these diagrams do observe the octet rule. These particular diagrams have been drawn to emphasize the tetrahedral nature of the phosphate group, but they could have just as easily been drawn with 90-degree angles between the bonds.|
Conclusion: The Analyze Structure and Check Structure commands in ChemDraw are designed to assist in finding errors in chemical diagrams. ChemDraw will mark anything that looks questionable. There is nothing wrong with drawing something that ChemDraw does not understand. Live human beings are a lot smarter than computers, and will probably stay that way for a long time. As long as your drawing is clear to you and to the other people who look at it, ChemDraw's opinion doesn't mean much. You should always feel free to override any recommendations it makes.