FAIRMol

GemmaOHDUnisi_41

Pose ID 1739 Compound 1416 Pose 384

DB SELECTIONDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T03
L. major DHFR L. major
Ligand GemmaOHDUnisi_41

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry high Native strong SASA done
Strain ΔE
20.0 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.55, Jaccard 0.44, H-bond role recall 0.20
Burial
87%
Hydrophobic fit
82%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.746 kcal/mol/HA) ✓ Good fit quality (FQ -7.52) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (87% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ Moderate strain (20.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (14)
Score
-26.102
kcal/mol
LE
-0.746
kcal/mol/HA
Fit Quality
-7.52
FQ (Leeson)
HAC
35
heavy atoms
MW
462
Da
LogP
6.37
cLogP
Strain ΔE
20.0 kcal/mol
SASA buried
87%
Lipo contact
82% BSA apolar/total
SASA unbound
765 Ų
Apolar buried
547 Ų

Interaction summary

HB 8 HY 24 PI 2 CLASH 1
Final rank3.636Score-26.102
Inter norm-0.841Intra norm0.096
Top1000noExcludedno
Contacts16H-bonds8
Artifact reasongeometry warning; 14 clashes; 2 protein clashes
Residues
ARG92 ARG97 ASP52 ILE45 LEU94 LYS57 LYS90 LYS95 MET53 PHE56 PHE91 PRO88 PRO93 SER44 SER86 VAL87

Protein summary

225 residues
Protein targetT03Atoms3428
Residues225Chains2
Residue summaryLEU:380; ARG:360; VAL:272; LYS:264; ALA:240; GLU:240; PRO:224; PHE:180; THR:154; ILE:152; SER:132; TYR:126; GLN:119; ASN:98; GLY:84; NDP:74

Receptor context

1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1 Excluded HETATM 0
Kept cofactors / ions
A:NDP301

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name3CL9Contacts20
PoseOpen native poseHB0
IFP residues
ALA32 ARG97 ASP52 ILE45 LEU94 LYS57 MET53 NDP301 PHE56 PHE91 PRO88 SER86 THR180 THR54 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap11Native recall0.55
Jaccard0.44RMSD-
HB strict1Strict recall0.14
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
360 1.9858794448475394 -0.60587 -22.5384 8 15 0 0.00 0.00 - no Open
310 2.215876786266132 -0.810312 -26.2423 7 20 0 0.00 0.00 - no Open
296 2.3735761215630813 -0.974129 -31.9318 5 22 0 0.00 0.00 - no Open
304 2.4109016880892273 -0.837854 -29.8668 7 13 0 0.00 0.00 - no Open
350 2.5106836985505296 -0.819328 -29.6374 5 17 1 0.05 0.00 - no Open
350 2.9414702362290113 -0.751309 -27.9819 5 17 0 0.00 0.00 - no Open
358 3.175808622050242 -0.595751 -15.5491 3 17 0 0.00 0.00 - no Open
421 3.3117905327030788 -0.65678 -23.4933 3 16 0 0.00 0.00 - no Open
340 3.408980607340969 -0.695149 -24.1764 7 10 0 0.00 0.00 - no Open
387 3.5593066442778185 -0.749818 -29.818 7 21 0 0.00 0.00 - no Open
384 3.6360066859245648 -0.841444 -26.102 8 16 11 0.55 0.20 - no Current
458 3.684952783737684 -0.836742 -25.2904 4 18 0 0.00 0.00 - no Open
341 4.458291848249892 -0.632747 -19.3542 9 19 0 0.00 0.00 - no Open
340 4.6006376252543095 -0.940685 -33.7094 11 24 0 0.00 0.00 - no Open
312 5.204738389636102 -0.790161 -23.6613 11 20 0 0.00 0.00 - no Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -26.102kcal/mol
Ligand efficiency (LE) -0.7458kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.522
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 35HA

Physicochemical properties
Molecular weight 461.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 6.37
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 19.97kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 109.59kcal/mol
Minimised FF energy 89.62kcal/mol

SASA & burial

✓ computed
SASA (unbound) 765.0Ų
Total solvent-accessible surface area of free ligand
BSA total 666.6Ų
Buried surface area upon binding
BSA apolar 546.5Ų
Hydrophobic contacts buried
BSA polar 120.0Ų
Polar contacts buried
Fraction buried 87.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 82.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1636.8Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 1820.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 819.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)