Ring mis-typed as aromatic

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-5.15.0-56-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.6.dev202301180300 (2023-01-18 03:00:03 UTC)
Description
AddH seems to be getting it wrong on C13 and C14 of the ligand O6O (https://www.rcsb.org/ligand/O6O - should be tetrahedral single-bonded carbons, being treated as double-bonded). Geometry is perhaps a little on the flat side, but still looks closer to tetrahedral than planar. If I add the ligand from the ideal coordinates in the CCD templates, delete the hydrogens and add them back, I get the same result.

Log:
> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.6.dev202301180300 (2023-01-18)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7usi

7usi title:  
BRD2-BD1 in complex with MDP5 [more info...]  
  
Chain information for 7usi #1  
---  
Chain | Description | UniProt  
A B C D E F | Bromodomain-containing protein 2 | BRD2_HUMAN 73-183  
  
Non-standard residues in 7usi #1  
---  
CL — chloride ion  
DMS — dimethyl sulfoxide  
EDO — 1,2-ethanediol (ethylene glycol)  
NA — sodium ion  
O6O —
(8M)-8-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-(morpholin-4-yl)-4H-1-benzopyran-4-one  
PEG — di(hydroxyethyl)ether  
PGE — triethylene glycol  
  
7usi mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
3| author_defined_assembly  
4| author_defined_assembly  
5| author_defined_assembly  
6| author_defined_assembly  
  

> view /A:O6O

> addh

Summary of feedback from adding hydrogens to 7usi #1  
---  
warnings | Not adding hydrogens to /A GLU 183 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /C GLU 183 CA because it is missing heavy-atom bond
partners  
Not adding hydrogens to /E GLU 183 CA because it is missing heavy-atom bond
partners  
Not adding hydrogens to /F GLU 183 CA because it is missing heavy-atom bond
partners  
notes | Termini for 7usi (#1) chain A determined from SEQRES records  
Termini for 7usi (#1) chain B determined from SEQRES records  
Termini for 7usi (#1) chain C determined from SEQRES records  
Termini for 7usi (#1) chain D determined from SEQRES records  
Termini for 7usi (#1) chain E determined from SEQRES records  
1 messages similar to the above omitted  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A GLY 73, /B GLY 73, /C
GLY 73, /D GLY 73, /E GLY 73, /F GLY 73  
Chain-final residues that are actual C termini: /A GLU 183, /B GLU 183, /C GLU
183, /D GLU 183, /E GLU 183, /F GLU 183  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue /A GLU 183  
Missing OXT added to C-terminal residue /B GLU 183  
Missing OXT added to C-terminal residue /C GLU 183  
Missing OXT added to C-terminal residue /D GLU 183  
Missing OXT added to C-terminal residue /E GLU 183  
1 messages similar to the above omitted  
877 hydrogen bonds  
Adding 'H' to /A GLY 73  
Adding 'H' to /B GLY 73  
Adding 'H' to /C GLY 73  
Adding 'H' to /D GLY 73  
Adding 'H' to /E GLY 73  
1 messages similar to the above omitted  
6086 hydrogens added  
  

> color byhetero

> view /B:O6O

> view /C:O6O

> view /D:O6O




OpenGL version: 3.3.0 NVIDIA 515.86.01
OpenGL renderer: NVIDIA GeForce RTX 3070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_GB.UTF-8
Qt version: PyQt6 6.4.0, Qt 6.4.0
Qt runtime version: 6.4.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: XPS 8950
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700
Cache Size: 25600 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            31Gi        20Gi       454Mi       1.4Gi        10Gi       8.8Gi
	Swap:          2.0Gi       1.3Gi       678Mi

Graphics:
	0000:01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA104 [GeForce RTX 3070 Lite Hash Rate] [10de:2488] (rev a1)	
	Subsystem: Dell GA104 [GeForce RTX 3070 Lite Hash Rate] [1028:c903]	
	Kernel driver in use: nvidia

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[Eric Pettersen]

Aromaticity isn't judged from ring planarity. There are plenty of non-aromatic rings that are completely flat. Aromaticity is judged by bond lengths around the ring. The problem is that the aromaticity-judging algorithm only had parameters for C-C and C-N bonds, and the ring in question has two oxygens, leaving only two C-C bonds to work with, one of which is also part of the fused aromatic ring! The algorithm comes from a journal article, and that article does have C-O parameters so I added them. I'm guessing they were omitted originally due to poor results with the lower resolution structures of the era.

fix: ​https://github.com/RBVI/ChimeraX/commit/d145706f81a6186254228d4beb0614b7ea3acf9f