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badisa merged 2 commits into from
Jun 17, 2026
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Evaluate change to REST region #21

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5d197d7
Evaluate change to REST region
badisa Jun 17, 2026
48672aa
Fix linting
badisa Jun 17, 2026
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79 changes: 79 additions & 0 deletions summaries/2026_june_08/README.md
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# Summary 2026 June 08
- Number of Datasets: 61
- Number of Ligands: 961
- Number of Edges: 1624
- Total Wallclock Time: 207.50 Hours
- Average Time Per Edge: 0.13 Hours
- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398)


## Description
Evalutes changing the REST region to only include rings that are connected to dummy atoms (https://github.com/tmd-industries/tmd/pull/133)


![Retrospective dG performance](dg_plot.png)

## Dataset Metrics
| set | dataset | N | Kendall 𝜏 | MUE | RMSE | R² | Spearman ρ |
| :--- | :--- | :--- | :--- | :--- | :--- | :--- | :--- |
| jacs_set | Thrombin | 11 | 0.60 | 0.62 | 0.72 | 0.85 | 0.78 |
| jacs_set | Bace | 36 | 0.31 | 1.21 | 1.51 | 0.20 | 0.44 |
| jacs_set | Mcl1 | 42 | 0.48 | 1.45 | 1.90 | 0.44 | 0.66 |
| jacs_set | Jnk1 | 21 | 0.57 | 1.29 | 1.47 | 0.51 | 0.71 |
| jacs_set | Ptp1B | 23 | 0.53 | 1.29 | 2.14 | 0.32 | 0.65 |
| jacs_set | Tyk2 | 16 | 0.67 | 0.40 | 0.50 | 0.84 | 0.84 |
| jacs_set | Cdk2 | 16 | 0.58 | 0.66 | 0.76 | 0.67 | 0.79 |
| jacs_set | P38 | 34 | 0.48 | 1.05 | 1.36 | 0.49 | 0.65 |
| miscellaneous_set | Hiv1 Protease | 13 | -0.09 | 1.36 | 1.64 | 0.09 | -0.12 |
| miscellaneous_set | Faah | 24 | 0.40 | 1.58 | 1.80 | 0.57 | 0.51 |
| miscellaneous_set | Btk | 6 | 0.60 | 1.80 | 2.19 | 0.71 | 0.71 |
| miscellaneous_set | Cdk8 | 10 | 0.11 | 1.55 | 1.82 | 0.01 | 0.14 |
| miscellaneous_set | Malt1 | 16 | 0.47 | 1.58 | 1.78 | 0.52 | 0.59 |
| miscellaneous_set | Galectin | 26 | 0.50 | 0.90 | 1.24 | 0.60 | 0.70 |
| janssen_bace | Keranen P2 | 12 | 0.08 | 0.61 | 0.71 | 0.08 | 0.11 |
| janssen_bace | Bace Ciordia Prospective | 9 | 0.78 | 1.28 | 1.76 | 0.48 | 0.88 |
| janssen_bace | Bace P3 Arg368 In | 21 | 0.22 | 1.62 | 1.84 | 0.16 | 0.32 |
| janssen_bace | Ciordia Retro | 32 | 0.59 | 1.01 | 1.31 | 0.62 | 0.79 |
| water_set | Chk1 | 13 | -0.43 | 2.29 | 2.97 | 0.03 | -0.45 |
| water_set | Thrombin | 21 | 0.35 | 0.93 | 1.14 | 0.29 | 0.50 |
| water_set | Scyt Dehyd | 7 | 0.52 | 2.10 | 2.63 | 0.64 | 0.71 |
| water_set | Urokinase | 4 | 0.67 | 0.69 | 0.73 | 0.59 | 0.80 |
| water_set | Hsp90 Woodhead | 4 | 0.33 | 1.30 | 1.41 | 0.51 | 0.60 |
| water_set | Hsp90 Kung | 11 | 0.60 | 2.04 | 2.61 | 0.53 | 0.78 |
| water_set | Taf12 | 8 | 0.29 | 0.63 | 0.78 | 0.14 | 0.29 |
| water_set | Brd4 | 8 | 0.14 | 1.35 | 1.69 | 0.02 | -0.02 |
| gpcrs | A2A | 25 | 0.55 | 1.72 | 2.34 | 0.57 | 0.72 |
| gpcrs | P2Y1 Ortho Sub | 12 | 0.75 | 1.19 | 1.46 | 0.92 | 0.88 |
| gpcrs | P2Y1 Meta Sub | 20 | 0.38 | 1.05 | 1.47 | 0.40 | 0.54 |
| merck | Shp2 | 26 | 0.16 | 1.66 | 2.09 | 0.11 | 0.23 |
| merck | Cdk8 | 32 | 0.68 | 1.89 | 2.16 | 0.73 | 0.86 |
| merck | Pfkfb3 | 40 | 0.43 | 0.93 | 1.19 | 0.38 | 0.62 |
| merck | Cmet Charge 1 | 12 | 0.58 | 1.31 | 1.74 | 0.38 | 0.67 |
| merck | Cmet Charge 0 | 12 | 0.66 | 1.15 | 1.46 | 0.82 | 0.78 |
| merck | Hif2A Jmc2023 | 38 | 0.59 | 1.63 | 1.84 | 0.58 | 0.78 |
| merck | Tnks2 Charge 0 | 21 | 0.55 | 0.57 | 0.80 | 0.60 | 0.73 |
| merck | Tnks2 Charge 1 | 6 | 0.47 | 0.60 | 0.68 | 0.45 | 0.66 |
| merck | Syk Charge 0 | 40 | 0.03 | 1.19 | 1.45 | 0.03 | 0.01 |
| merck | Syk Charge -1 | 6 | 0.07 | 0.85 | 1.18 | 0.71 | 0.09 |
| merck | Hif2A | 41 | 0.17 | 1.63 | 1.94 | 0.11 | 0.26 |
| merck | Eg5 Charge 0 | 9 | 0.54 | 0.88 | 1.09 | 0.72 | 0.74 |
| merck | Eg5 Charge 1 | 19 | 0.33 | 0.87 | 1.02 | 0.22 | 0.44 |
| mcs_docking_set | Renin | 29 | 0.38 | 1.41 | 1.86 | 0.26 | 0.51 |
| mcs_docking_set | Hne Charge -1 | 2 | 1.00 | 0.17 | 0.17 | 1.00 | 1.00 |
| mcs_docking_set | Hne Charge 0 | 14 | 0.76 | 0.69 | 0.84 | 0.82 | 0.88 |
| schrodinger_macrocycles | Mht1 | 3 | 1.00 | 1.06 | 1.18 | 0.87 | 1.00 |
| schrodinger_macrocycles | 2Ep9 | 4 | 0.67 | 0.92 | 1.11 | 0.06 | 0.80 |
| schrodinger_macrocycles | 3Rkz | 7 | 0.62 | 1.31 | 1.40 | 0.60 | 0.71 |
| schrodinger_macrocycles | Hsp90 | 10 | 0.56 | 0.83 | 1.01 | 0.70 | 0.73 |
| scaffold_hopping_set | Bace1 | 3 | 1.00 | 1.77 | 1.92 | 0.71 | 1.00 |
| bayer_macrocycles | Ftase | 5 | 0.40 | 0.94 | 0.98 | 0.22 | 0.50 |
| bayer_macrocycles | Brd4 | 3 | 1.00 | 0.55 | 0.66 | 0.89 | 1.00 |
| fragments | Hsp90 Single Ring | 7 | 0.49 | 0.77 | 0.94 | 0.39 | 0.63 |
| fragments | Mup1 | 6 | 1.00 | 0.82 | 0.96 | 0.97 | 1.00 |
| fragments | Hsp90 2Rings | 6 | 0.73 | 1.33 | 1.47 | 0.43 | 0.83 |
| fragments | Mcl1 | 12 | 0.18 | 0.76 | 0.93 | 0.21 | 0.24 |
| fragments | Jak2 Set1 | 10 | 0.64 | 0.54 | 0.72 | 0.76 | 0.77 |
| fragments | P38 | 6 | 0.60 | 1.10 | 1.37 | 0.83 | 0.77 |
| fragments | T4 Lysozyme | 12 | 0.55 | 0.79 | 0.96 | 0.62 | 0.72 |
| fragments | Jak2 Set2 | 8 | 0.57 | 1.96 | 2.38 | 0.51 | 0.76 |
| fragments | Liga | 11 | 0.78 | 1.64 | 2.09 | 0.94 | 0.90 |
40 changes: 40 additions & 0 deletions summaries/2026_june_08/bayer_macrocycles/brd4/README.md
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# Brd4 Map

![Retrospective dG performance](dg_plot.png)

## Statistics Summary
- MUE: 0.55
- RMSE: 0.66
- R²: 0.89
- Kendall 𝜏: 1.00
- Spearman ρ: 1.00

## System Details
- Ligands: 3
- Host Atoms: 2055
- Map Details:
- Edges: 3
- Min Dummy Atoms: 8
- Max Dummy Atoms: 47
- Mean Dummy Atoms: 29.3
- Median Dummy Atoms: 33.0

## Simulation Details
- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398)
- GPU: RTX 5090, RTX 5080
- MPS Processes: 2
- Batch Mode: True
- Total Wallclock Time: 0.50 Hours
- Average Time Per Edge: 0.17 Hours
- Total Nanoseconds Simulated: 605.20
- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py
- Ligand Charges: Amber AM1BCC ELF10
- Simulation Details:
- Seed: 608
- Equilibration Steps: 200000
- Steps Per Frame: 400
- Production Ns: 2
- Target Overlap: 0.667
- Water Sampling: True
- REST: Temperature Scale 3.0
- Local MD: Steps 390, Radius 1.2
4 changes: 4 additions & 0 deletions summaries/2026_june_08/bayer_macrocycles/brd4/ddg_results.csv
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mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol)
25e,11,65.09205567169391,0.08711500029188558,62.68960798053202,0.08959048103771447,3.1000000000000014,2.4024476911618935,0.12496190446861917,2.3544710628364527,0.0753072568388216
61a,11,51.771121043854265,0.09420017741519852,47.15837820149695,0.0974022725883792,3.8000000000000007,4.612742842357308,0.13550231042471492,4.669154369060836,0.07254069942294414
61a,25e,-22.06860334475711,0.062288834535805894,-24.408178977041924,0.06497752310512511,0.6999999999999993,2.3395756322848142,0.09001098497797963,2.3146833062243832,0.06756915264354413
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4 changes: 4 additions & 0 deletions summaries/2026_june_08/bayer_macrocycles/brd4/dg_results.csv
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mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol)
25e,CCOc1cc(=O)n(C)cc1-c1cc(NS(=O)(=O)CC)ccc1Oc1ccc(F)cc1F,-10.513262585537356,0.04987293980098266,-11.3
11,COc1cc(=O)n(C)nc1-c1ccccc1Oc1ccccc1,-8.158791522700904,0.05642581685891488,-8.2
61a,CCS(=O)(=O)Nc1ccc2c(c1)-c1cn(C)c(=O)cc1OCCCCc1cc(F)cc(F)c1O2,-12.82794589176174,0.04558815925845357,-12.0
40 changes: 40 additions & 0 deletions summaries/2026_june_08/bayer_macrocycles/ftase/README.md
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# Ftase Map

![Retrospective dG performance](dg_plot.png)

## Statistics Summary
- MUE: 0.94
- RMSE: 0.98
- R²: 0.22
- Kendall 𝜏: 0.40
- Spearman ρ: 0.50

## System Details
- Ligands: 5
- Host Atoms: 13188
- Map Details:
- Edges: 8
- Min Dummy Atoms: 5
- Max Dummy Atoms: 58
- Mean Dummy Atoms: 36.6
- Median Dummy Atoms: 39.5

## Simulation Details
- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398)
- GPU: RTX 5090, RTX 5080
- MPS Processes: 1
- Batch Mode: True
- Total Wallclock Time: 3.54 Hours
- Average Time Per Edge: 0.44 Hours
- Total Nanoseconds Simulated: 1513.60
- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py
- Ligand Charges: Amber AM1BCC ELF10
- Simulation Details:
- Seed: 608
- Equilibration Steps: 200000
- Steps Per Frame: 400
- Production Ns: 2
- Target Overlap: 0.667
- Water Sampling: True
- REST: Temperature Scale 3.0
- Local MD: Steps 390, Radius 1.2
9 changes: 9 additions & 0 deletions summaries/2026_june_08/bayer_macrocycles/ftase/ddg_results.csv
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mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol)
"lig 2, deprot",lig 49 stereo,5.764328191077008,0.09245334168085052,1.7150371462211504,0.0908721070478824,0.8100000000000005,4.049291044855857,0.1296354898447099,3.190374661813207,0.07516319565388352
"lig 2, deprot",lig 51 stereo,17.595533057282708,0.09431687345924944,16.76307911905845,0.09264269860252268,1.0099999999999998,0.8324539382242587,0.1322056815098577,1.1852365001458285,0.07380027240098457
"lig 2, deprot","lig 66, deprot",16.69637950398279,0.09142193866146102,15.099012721902232,0.09190342274791857,0.120000000000001,1.597366782080556,0.1296310533066926,2.1170484881886704,0.07692507158109016
lig 51 stereo,lig 49 stereo,-11.23778266156757,0.04902303942583153,-13.063222152747365,0.05273488459738261,-0.1999999999999993,1.8254394911797946,0.0720015725387015,2.0051381616673787,0.056845032061041315
"lig 66, deprot",lig 49 stereo,-7.681505018005634,0.08441806943911394,-8.050834529334457,0.08200152409017783,0.6899999999999995,0.369329511328823,0.11768882870068458,1.0733261736245368,0.060846890646253524
"lig 66, deprot","lig 68, deprot",9.860684925274699,0.054232776464812255,11.05889442945298,0.052402509143906345,0.17999999999999972,-1.198209504178281,0.07541363940070445,-1.3113963562738693,0.06334077033588915
"lig 68, deprot",lig 49 stereo,-15.930017216756259,0.0863682721081385,-18.821141824516467,0.08526329918998542,0.5099999999999998,2.8911246077602084,0.12136436303835826,2.384722529898406,0.0611889902669752
"lig 68, deprot",lig 51 stereo,-4.1950457500431755,0.08834943914564383,-4.352412937233825,0.08684671986978922,0.7099999999999991,0.15736718719064965,0.12388694906846105,0.37958436823102737,0.05950686309533998
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6 changes: 6 additions & 0 deletions summaries/2026_june_08/bayer_macrocycles/ftase/dg_results.csv
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mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol)
"lig 2, deprot",N#Cc1ccc(Cn2cncc2CN2CCN(c3cccc(Cl)c3)C(=O)C2)cc1,-13.421662356412503,0.06270816740003922,-12.41
lig 49 stereo,N#Cc1ccc2cc1Oc1ccc3cccc(c3c1)N1CC[C@H](NCc3cncn3C2)C1=O,-10.231287694599295,0.04143901208079932,-11.6
lig 51 stereo,CN1Cc2cncn2Cc2ccc(C#N)c(c2)Oc2ccc3cccc(c3c2)N2CC[C@H]1C2=O,-12.236425856266674,0.03891228530667638,-11.4
"lig 66, deprot",N#Cc1ccc2cc1Oc1ccc3cccc(c3c1)N1CC[C@H](NCCc3cncn3C2)C1=O,-11.304613868223832,0.044555048861879866,-12.29
"lig 68, deprot",CN1CCc2cncn2Cc2ccc(C#N)c(c2)Oc2ccc3cccc(c3c2)N2CC[C@H]1C2=O,-12.616010224497701,0.04502111513122874,-12.11
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40 changes: 40 additions & 0 deletions summaries/2026_june_08/fragments/hsp90_2rings/README.md
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# Hsp90 2Rings Map

![Retrospective dG performance](dg_plot.png)

## Statistics Summary
- MUE: 1.33
- RMSE: 1.47
- R²: 0.43
- Kendall 𝜏: 0.73
- Spearman ρ: 0.83

## System Details
- Ligands: 6
- Host Atoms: 3795
- Map Details:
- Edges: 9
- Min Dummy Atoms: 1
- Max Dummy Atoms: 6
- Mean Dummy Atoms: 3.3
- Median Dummy Atoms: 3.0

## Simulation Details
- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398)
- GPU: RTX 5090, RTX 5080
- MPS Processes: 2
- Batch Mode: True
- Total Wallclock Time: 0.61 Hours
- Average Time Per Edge: 0.07 Hours
- Total Nanoseconds Simulated: 720.00
- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py
- Ligand Charges: Amber AM1BCC ELF10
- Simulation Details:
- Seed: 608
- Equilibration Steps: 200000
- Steps Per Frame: 400
- Production Ns: 2
- Target Overlap: 0.667
- Water Sampling: True
- REST: Temperature Scale 3.0
- Local MD: Steps 390, Radius 1.2
10 changes: 10 additions & 0 deletions summaries/2026_june_08/fragments/hsp90_2rings/ddg_results.csv
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mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol)
15,14,-4.619227091875192,0.047225818131352876,-5.8375915326680845,0.0473894790814662,1.1600000000000001,1.2183644407928915,0.06690321835149891,1.1039049417424307,0.04936632966725383
14,16,-9.206210689290423,0.051304991717911926,-10.639848619008786,0.05490562775500082,0.6000000000000014,1.4336379297183635,0.07514539330089189,1.341694979595271,0.04987448562479691
17,16,-3.0107321499110355,0.03980674529514113,-5.868847202808255,0.043335319747861506,1.8000000000000007,2.8581150528972197,0.05884324012698175,2.836278841263268,0.04661676708194859
17,14,6.2045095449023675,0.05296663066332629,4.763707868984378,0.05462767890031872,1.1999999999999993,1.4408016759179896,0.07608973167163585,1.494583861667997,0.047673280390838915
17,19,-2.7877867733421944,0.040404330917765706,-0.41732724923729614,0.03903745972767,-0.33999999999999986,-2.3704595241048985,0.05618214323877094,-2.3798749549516955,0.04109900162350875
18,15,3.952112975143815,0.04026252259289224,1.296587698246239,0.041687157253171965,-0.9199999999999999,2.6555252768975763,0.057955929855312005,2.5152570784210653,0.04508247303656
18,19,-10.186637502893635,0.03786606923307111,-9.87560753116087,0.03838263542810388,-1.299999999999999,-0.31102997173276453,0.0539172134069489,-0.2552967964561965,0.03998579932789611
18,16,-10.580400715877087,0.04382662325041237,-15.444947949312692,0.04840310161655989,0.8400000000000016,4.864547233435605,0.0652965018330738,4.960856999758767,0.04563835214613087
19,15,13.700873976471343,0.04630547518007192,11.002671345206002,0.04821876328573498,0.379999999999999,2.6982026312653407,0.06685242078233218,2.770553874877262,0.04305137368356105
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7 changes: 7 additions & 0 deletions summaries/2026_june_08/fragments/hsp90_2rings/dg_results.csv
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mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol)
15,Cc1nc(N)nc2c1/C(=N/O)C[C@@H](c1ccccc1-c1ccccc1)C2,-8.955502498309372,0.03381557335934877,-9.88
14,Nc1ncc2c(n1)C[C@H](c1ccccc1-c1ccccc1)C/C2=N\O,-7.851597556566941,0.035965838002116494,-8.72
16,Cc1nc(N)nc2c1/C(=N/O)C[C@@H](c1ccccc1-c1ccncc1)C2,-6.50990257697167,0.03455318817625353,-8.12
17,Cc1nc(N)nc2c1/C(=N/O)C[C@@H](c1ccccc1-c1cccnc1)C2,-9.346181418234938,0.03129217410198689,-9.92
19,Cc1nc(N)nc2c1/C(=N/O)C[C@@H](c1ccc(F)cc1-c1cccnc1)C2,-11.726056373186633,0.026644469865623435,-10.26
18,Cc1nc(N)nc2c1/C(=N/O)C[C@@H](c1ccc(F)cc1-c1ccccc1)C2,-11.470759576730437,0.02981503603000777,-8.96
40 changes: 40 additions & 0 deletions summaries/2026_june_08/fragments/hsp90_single_ring/README.md
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# Hsp90 Single Ring Map

![Retrospective dG performance](dg_plot.png)

## Statistics Summary
- MUE: 0.77
- RMSE: 0.94
- R²: 0.39
- Kendall 𝜏: 0.49
- Spearman ρ: 0.63

## System Details
- Ligands: 7
- Host Atoms: 3795
- Map Details:
- Edges: 11
- Min Dummy Atoms: 2
- Max Dummy Atoms: 5
- Mean Dummy Atoms: 3.4
- Median Dummy Atoms: 4.0

## Simulation Details
- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398)
- GPU: RTX 5090, RTX 5080
- MPS Processes: 2
- Batch Mode: True
- Total Wallclock Time: 0.73 Hours
- Average Time Per Edge: 0.07 Hours
- Total Nanoseconds Simulated: 907.60
- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py
- Ligand Charges: Amber AM1BCC ELF10
- Simulation Details:
- Seed: 608
- Equilibration Steps: 200000
- Steps Per Frame: 400
- Production Ns: 2
- Target Overlap: 0.667
- Water Sampling: True
- REST: Temperature Scale 3.0
- Local MD: Steps 390, Radius 1.2
12 changes: 12 additions & 0 deletions summaries/2026_june_08/fragments/hsp90_single_ring/ddg_results.csv
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mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol)
10,3,2.582839202470162,0.04061238664650558,0.8526933114418969,0.040277819024084636,0.0,1.7301458910282648,0.057198502204709685,1.4451143462194356,0.048446410940078406
10,12,10.468213692552125,0.048804607070191575,10.405369753483459,0.045823733181244254,-0.27999999999999936,0.06284393906866584,0.06694553154573991,0.2716762591259023,0.04722512583705337
10,9,-2.9059662710123426,0.04542655105217846,-4.095928024353846,0.04788865921956056,0.9500000000000002,1.189961753341503,0.06600678163903599,1.366522845445317,0.05191571811057148
11,12,4.732467127405716,0.04996666010838553,5.872716744594642,0.04805418966991159,-0.47000000000000064,-1.1402496171889271,0.06932439878728675,-1.2474077841196536,0.04300431949313861
11,2,-6.789091690051441,0.0527059253048489,-7.929850704085222,0.051680847544599555,1.1899999999999995,1.1407590140337813,0.07381615382264545,1.6145854775699258,0.0469125121349964
3,12,8.57102358259717,0.05095337852951381,9.615304684868953,0.052144130443886876,-0.27999999999999936,-1.0442811022717815,0.07290580994215076,-1.1734380870935333,0.04504628671288877
3,2,-2.2651346155533445,0.04994542960126793,-4.249342957446693,0.04702838291720601,1.3800000000000008,1.9842083418933483,0.068601856664835,1.688555174596046,0.04879119025365155
8,11,-2.69454578939336,0.03800899527218823,-0.8376928651745156,0.03937559960337026,-0.08999999999999986,-1.8568529242188447,0.05472770382289174,-1.7728150543884054,0.04531339562480224
8,2,-8.763778887425387,0.047676586262556456,-8.705477551849743,0.043207594569655276,1.0999999999999996,-0.05830133557564453,0.06434246736135234,-0.1582295768184796,0.049675651497494255
9,11,8.570453304585097,0.046078104666291274,8.568458463268831,0.044611836878211845,-0.7599999999999989,0.0019948413162671945,0.06413585361781564,0.1525611978002388,0.04810821937755269
9,8,11.244966148659904,0.052831853074926445,9.340797383471443,0.0511651696539534,-0.669999999999999,1.9041687651884598,0.07354644304824298,1.9253762521886442,0.050806370944627165
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8 changes: 8 additions & 0 deletions summaries/2026_june_08/fragments/hsp90_single_ring/dg_results.csv
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mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol)
10,Cc1nc(N)nc2c1C(=O)C[C@@H](c1ccc(F)cc1)C2,-9.525423730355092,0.035693832076989826,-8.31
3,Cc1nc(N)nc2c1C(=O)C[C@@H](c1ccccc1)C2,-8.080309384135656,0.03275675632040818,-8.31
12,Cc1nc(N)nc2c1/C(=N/O)C[C@@H](c1ccc(F)cc1)C2,-9.25374747122919,0.030921883221841102,-8.59
9,Nc1ncc2c(n1)C[C@H](c1ccc(F)cc1)CC2=O,-8.158900884909775,0.03769870208105277,-7.36
11,Nc1ncc2c(n1)C[C@H](c1ccc(F)cc1)C/C2=N\O,-8.006339687109536,0.029886596211056948,-8.12
2,Nc1ncc2c(n1)C[C@H](c1ccccc1)CC2=O,-6.39175420953961,0.03616040876059645,-6.93
8,Nc1ncc2c(n1)C[C@H](c1ccccc1)C/C2=N\O,-6.233524632721131,0.0340601701400196,-8.03
40 changes: 40 additions & 0 deletions summaries/2026_june_08/fragments/jak2_set1/README.md
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# Jak2 Set1 Map

![Retrospective dG performance](dg_plot.png)

## Statistics Summary
- MUE: 0.54
- RMSE: 0.72
- R²: 0.76
- Kendall 𝜏: 0.64
- Spearman ρ: 0.77

## System Details
- Ligands: 10
- Host Atoms: 5622
- Map Details:
- Edges: 17
- Min Dummy Atoms: 1
- Max Dummy Atoms: 12
- Mean Dummy Atoms: 7.0
- Median Dummy Atoms: 8.0

## Simulation Details
- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398)
- GPU: RTX 5090, RTX 5080
- MPS Processes: 2
- Batch Mode: True
- Total Wallclock Time: 1.70 Hours
- Average Time Per Edge: 0.10 Hours
- Total Nanoseconds Simulated: 1927.20
- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py
- Ligand Charges: Amber AM1BCC ELF10
- Simulation Details:
- Seed: 608
- Equilibration Steps: 200000
- Steps Per Frame: 400
- Production Ns: 2
- Target Overlap: 0.667
- Water Sampling: True
- REST: Temperature Scale 3.0
- Local MD: Steps 390, Radius 1.2
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