Add OFF 2.0.0 RBFE summary

summaries/dec_09_2025/README.md

@@ -0,0 +1,15 @@
+# Summary Dec 09 2025
+- Number of Datasets: 19
+- Number of Ligands: 476
+- Number of Edges: 843
+- Total Wallclock Time: 109.24 Hours
+- Average Time Per Edge: 0.13 Hours
+- TMD Sha: [c1f675e11c1e05722eb072dcd5938757baab1a6b](https://github.com/tmd-industries/tmd/tree/c1f675e11c1e05722eb072dcd5938757baab1a6b)
+
+![Retrospective dG performance](dg_plot.png)
+
+## Notes:
+- Adds an aggregate plot to the summary. Don't read into these plots, the per target performance is what matters
+- Adds comparison plots for each set against the the results of the Dec 08 2025 run, which used OpenFF 2.2.1.
+- Repeat of December 8th summary, but with OpenFF 2.0.0 and run on a machine with a RTX 5090 and RTX 5080
+- Hif2a Ligand 35 still has an incorrect experimental [label](https://chemrxiv.org/engage/chemrxiv/article-details/65281c688bab5d205536cc7b).

summaries/dec_09_2025/jacs/cdk2/README.md

@@ -0,0 +1,38 @@
+# Cdk2 Map
+
+![Retrospective dG performance](dg_plot.png)
+
+## Statistics Summary
+- MUE: 0.70
+- RMSE: 0.89
+- R²: 0.70
+- Kendall 𝜏: 0.60
+- Spearman ρ: 0.83
+
+## System Details
+- Ligands: 16
+- Host Atoms: 4825
+- Map Details:
+  - Edges: 29
+  - Min Dummy Atoms: 0
+  - Max Dummy Atoms: 11
+  - Mean Dummy Atoms: 4.5
+  - Median Dummy Atoms: 4.0
+
+## Simulation Details
+- TMD Sha: [c1f675e11c1e05722eb072dcd5938757baab1a6b](https://github.com/tmd-industries/tmd/tree/c1f675e11c1e05722eb072dcd5938757baab1a6b)
+- GPU: RTX 5090, RTX 5080
+- MPS Processes: 12
+- Total Wallclock Time: 3.47 Hours
+- Total Nanoseconds Simulated: 3549.00
+- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py
+- Ligand Charges: Amber AM1BCC ELF10
+- Simulation Details:
+  - Seed: 912
+  - 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

summaries/dec_09_2025/jacs/cdk2/ddg_results.csv

@@ -0,0 +1,30 @@
+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),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol)
+17,1oiu,-61.46467892453873,0.04831895359814959,-58.24215208748517,0.04632132936372358,-3.2225268370535667,0.0669356917559137,-2.04
+17,20,-5.141454756239709,0.06815680504505664,-4.6236440294885774,0.0669081505346736,-0.5178107267511314,0.09550942718873567,-1.6800000000000006
+17,21,3.1299027741380305,0.06692047726080952,2.4274547634027055,0.06574192901958172,0.7024480107353248,0.09381018872185604,-0.7899999999999991
+17,26,2.051862466154019,0.0665680462743112,2.355117589713989,0.0664003037919182,-0.30325512355997025,0.0940228968307075,-1.3900000000000001
+1h1r,1h1q,2.6614117771770855,0.055295277744575294,1.3691512277780933,0.05432230281242264,1.2922605493989923,0.07751438784957451,-0.5099999999999998
+1h1r,1oi9,-7.478462282302443,0.05865800782597856,-6.714702493807048,0.05836095691797328,-0.7637597884953955,0.08274517009768059,-2.070000000000001
+1h1r,1oiu,-60.01620453378869,0.04710599232597582,-57.942787360185605,0.047049331329375506,-2.0734171736030813,0.06657787989682645,-1.4100000000000013
+1h1r,20,-3.962142490125225,0.06444778813963181,-4.321980298699953,0.06329786500299135,0.35983780857472775,0.09033347723866154,-1.0500000000000016
+1h1r,21,3.9863454874322293,0.06372098907659432,2.866853055215251,0.06209637244744842,1.1194924322169784,0.08897372600960175,-0.16000000000000036
+1h1r,26,3.174085267939755,0.06298864715936456,2.711955340734717,0.06098310254031643,0.4621299272050383,0.08767273502298005,-0.7600000000000013
+1h1s,1oi9,43.90453904939905,0.07219608007344822,42.11359438280252,0.07050622835408392,1.790944666596533,0.10091284464670479,1.5099999999999991
+1h1s,1oiy,36.355661508549595,0.06495032689496233,35.37792208290524,0.06424959484457617,0.9777394256443468,0.09135948446359937,1.4600000000000002
+1h1s,29,50.10026488403073,0.05990315448534542,47.51985202027057,0.060233776270748565,2.5804128637601615,0.08494996010081317,1.369999999999999
+1h1s,31,41.93603214008069,0.05589219806241611,40.458105815023785,0.05374566069164238,1.477926325056909,0.07754053035303217,1.71
+1h1s,32,11.377666163077583,0.053841414463502824,7.9897523185012504,0.049990431540099946,3.387913844576332,0.07347068229570289,1.4999999999999991
+1oiu,1h1q,63.02487465267697,0.06659864744797775,59.47380700170865,0.06591275095888197,3.551067650968319,0.09370096360693218,0.9000000000000015
+1oiy,31,1.2751900264620126,0.0677348184473766,0.21301254546037782,0.06877706397113786,1.0621774810016347,0.09653129108526964,0.24999999999999983
+21,20,-7.2989226660725155,0.052754348062902155,-6.440710582476848,0.0519485933065714,-0.8582120835956668,0.0740383521296455,-0.8900000000000013
+22,1h1q,-1.187380820704362,0.06316506361402169,0.23763057238884966,0.06050999882209375,-1.4250113930932116,0.0874716252210578,-0.31999999999999906
+22,1h1r,-4.018685036105246,0.07228776121532574,-1.2685340042442899,0.06830071170178663,-2.750151031860956,0.09945103136968728,0.19000000000000075
+22,32,-55.027377342828835,0.07287377524456015,-51.217658116775574,0.07194166679879824,-3.809719226053267,0.10240210222541321,-1.8900000000000008
+26,1oi9,-9.549530102175414,0.058584846292244,-9.088561729462642,0.05712628666420647,-0.4609683727127716,0.08182662673682052,-1.31
+28,1h1s,-22.77485518294535,0.0590302765830656,-23.506567530526187,0.05698429919258725,0.7317123475808389,0.08204744912514662,-0.14000000000000012
+28,1oiy,11.869174829429705,0.06832011505609249,11.307651601682814,0.06640733220360454,0.5615232277468918,0.0952762923904872,1.32
+28,30,17.12078305663577,0.055889729997829124,15.881026462045071,0.056237063568714905,1.2397565945906992,0.07928599648148418,1.2999999999999998
+29,1oi9,-5.621412278290615,0.07559849437467307,-6.247314158362024,0.07250713239417442,0.6259018800714092,0.10474930357641436,0.14000000000000012
+30,29,14.015953054091776,0.062142728651729956,13.876926992099778,0.06024872330393724,0.13902606199199813,0.08655418755922172,-0.07000000000000091
+30,31,3.9397406041848986,0.04841736252366757,2.66051305574073,0.04677807429768206,1.2792275484441682,0.06732331861062489,0.2700000000000001
+30,32,-30.80166514691511,0.05789829385374023,-30.566832781709973,0.058290330605524146,-0.23483236520513592,0.08215823192641962,0.05999999999999908

summaries/dec_09_2025/jacs/cdk2/dg_results.csv

@@ -0,0 +1,17 @@
+mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol)
+17,Brc1cccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)c1,-7.836119457012859,0.058638610140029516,-7.04
+1oiu,NS(=O)(=O)c1cccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)c1,-10.86340191746214,0.061177090634747223,-9.08
+20,OCc1cccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)c1,-8.267680359658707,0.06579982200104406,-8.72
+21,COc1cccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)c1,-7.362557079839101,0.05730179348009877,-7.829999999999999
+26,COc1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-8.378274726392972,0.05591517173297361,-8.43
+1h1r,Clc1cccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)c1,-8.620196288471277,0.043907200366213574,-7.669999999999999
+1h1q,c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-7.266036172571557,0.05708041023111441,-8.18
+1oi9,Oc1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-9.212004760008341,0.04689814968614398,-9.74
+1h1s,NS(=O)(=O)c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-11.588628165644918,0.05137621338902752,-11.25
+1oiy,NC(=O)c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-10.721205747685305,0.06418524889905178,-9.79
+29,CN(C)S(=O)(=O)c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-9.542148831190099,0.06508490624149531,-9.88
+31,C[S@](=O)c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-9.40716138780068,0.05989605471499196,-9.54
+32,COc1cc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)ccc1S(N)(=O)=O,-9.211132100475796,0.049684591211010834,-9.75
+22,CSc1cccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)c1,-5.7218541544611305,0.062411757414341115,-7.86
+28,CNS(=O)(=O)c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-11.648068311141179,0.06438563755269504,-11.11
+30,CS(=O)(=O)c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-10.033530540183927,0.055517229256799826,-9.81

summaries/dec_09_2025/jacs/mcl1/README.md

@@ -0,0 +1,38 @@
+# Mcl1 Map
+
+![Retrospective dG performance](dg_plot.png)
+
+## Statistics Summary
+- MUE: 1.48
+- RMSE: 1.81
+- R²: 0.17
+- Kendall 𝜏: 0.27
+- Spearman ρ: 0.39
+
+## System Details
+- Ligands: 69
+- Host Atoms: 2536
+- Map Details:
+  - Edges: 129
+  - Min Dummy Atoms: 0
+  - Max Dummy Atoms: 12
+  - Mean Dummy Atoms: 3.3
+  - Median Dummy Atoms: 3.0
+
+## Simulation Details
+- TMD Sha: [c1f675e11c1e05722eb072dcd5938757baab1a6b](https://github.com/tmd-industries/tmd/tree/c1f675e11c1e05722eb072dcd5938757baab1a6b)
+- GPU: RTX 5090, RTX 5080
+- MPS Processes: 12
+- Total Wallclock Time: 15.37 Hours
+- Total Nanoseconds Simulated: 17045.40
+- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py
+- Ligand Charges: Amber AM1BCC ELF10
+- Simulation Details:
+  - Seed: 912
+  - 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