Molecular coordination topology
Derived normalized geometry · coordinate-blind external transfer
- Client problem
- Can a frozen local-topology operator transfer across newly opened rubredoxin structures without target-specific fitting?
- Public capability
- From connectivity alone, LINUR derives the regular four-coordinate topology and transfers it across newly opened rubredoxin structures.
- Public result
- All 16 eligible external Zn–S₄ structures passed the frozen angular and normalized-topology panel limits.
- Headline metrics
- 16 / 16external structures passed4.97°median angular MAE0target-specific fits< 1 sforward evaluation on the local Mac
- Evidence boundary
- Local coordination topology only—not a complete protein fold, absolute bond length or X-ray electron-density reconstruction.

Conditional Fe–S₄ Molecular Reconstruction
CALIBRATED CONDITIONAL RECONSTRUCTION / REGRESSION COMPARISON
Given Fe–S₄ connectivity, the sealed tetrahedral topology and one independently published ferric-tetrathiolate scale, LINUR reconstructed the dominant local geometry with zero target-specific fits. Across two regression structures, Fe–S bond-length MAE was 0.0218–0.0330 Å. The stricter complete-coordinate gate did not yet pass, identifying the protein-environment physics still required.
Connectivity-only sealed tetrahedral topology · 109.4712206° · zero target-specific fits.
One independent ferric-tetrathiolate scale · 2.284 ± 0.002 Å · frozen before scoring.
9TA4 0.1684 Å · 9TA6 0.1661 Å aligned local RMSD · frozen gate 0.15 Å.
Numerical certificate. 1.13 × 10⁻¹⁶ relative build-bond residual. This is a coordinate numerical certificate, not a physical-accuracy claim.
Evidence boundary. The scale is calibrated, and 9TA4/9TA6 are previously opened regression structures—not new blind targets. This does not establish measurement-free absolute scale, exact complete structures, a full protein fold or replacement of X-ray crystallography.
Technical evidence boundary
Expanded local-topology evidence
- Frozen ideal angle: 109.4712206°. Sixteen of sixteen external Zn–S₄ structures were eligible and passed.
- Median angular MAE: 4.9680°; range 4.4316° to 5.3013°.
- Median normalized topology energy: 0.04808 against a frozen 0.15 panel limit.
- Earlier Fe–S₄ comparisons remain preserved: 5.8312° MAE for 9TA4 and 5.6825° for 9TA6.
Reduced Fe–S scale · separate result
A general UFF radial adapter estimated the Fe–S bond scale with 0.0195 Å MAE in the earlier comparison. This is a reduced empirical result, not yet an Engine-derived absolute length.
Reduced interpretable resultWhole-fold and dose-response boundary
The earlier whole-fold model did not pass its conjunction gate. A single-drive elastic network improved the 8 Å dose-response RMS by only 1.52%; the 7 Å and 9 Å variants were worse than zero response. These remain negative or weak technical results, not success metrics.
Negative result30OH / 30OR continuation
The 0.43 Å rubredoxin study identifies Fe–S₄ electronic structure as an unresolved modelling problem. LINUR’s frozen, coordinate-blind 30OH/30OR comparison remains pending because deposited coordinates were not publicly retrievable at freeze. No Max Planck electron-density result is claimed.
Extension in progress


