Hannah Baumann

I opened a new issue here: https://github.com/choderalab/pymbar/issues/419 and provided some input files! Let me know if you need more information!

Update: If I load in the .sdf ``` file = "cofactor.sdf" off_cft = Molecule.from_file(file) off_cft.assign_partial_charges('am1bccelf10') ``` Running this I'm getting following warning: `Warning: 3L9H: Failed due to unspecified stereochemistry` This...

### **Things changed in the PR** ### Thrombin: - Problem 1 - Lig_7d deposited 3x (3 different stereoisomers) - Action - Removed ligand lig_7d - Rationale - unspecified absolute configuration...

### SYK - Problem - ligands lig_CHEMBL3265030_n and lig_CHEMBL3265035 have both two copies of the ligand in the .sdf, those are two "stereoisomers" (around a tetravalent nitrogen, so not a...

### P38 - Problem - Lig_p38a_2ff was deposited twice with two orientations of the cyclohexyl ring - Action - Removed one configuration - Rationale - kept the configuration that was...

### Eg5 - Problem - ligand lig_CHEMBL1084935 was present twice, with two different “stereocenters” (around a tertiary charged amine) - Action - Kept the same isomer as was used in...

### Tnks2 - Problem - lig_7 was negatively charged even though all other ligands in the series have the same core, but different protonation state of the core - Rationale...

### PFKFB3 - Problem - Cofactors were not readable by rdkit - Action - Fix cofactors - Note: for POP, we used the protonation state as suggested by openeye, but...

### PDE2 - Problem - Sidechain for two of the ligands (49932129 and 50107616) pointing towards a different orientation compared to other ligands and towards the ions, leading to samping...

### Networks Generated new networks - Kartograf mapper, Lomap scorer - MST, radial, Lomap networks - Allow element changes - Not allowing element changes - Lomap mapper, Lomap scorer -...