FAIRMol

OHD_Leishmania_136

Pose ID 5433 Compound 636 Pose 15

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
T09
L. major DHFR-TS L. major
Ligand OHD_Leishmania_136

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
46.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.81, Jaccard 0.71, H-bond role recall 0.67
Burial
88%
Hydrophobic fit
80%
Reason: strain 46.6 kcal/mol
strain ΔE 46.6 kcal/mol 2 protein-contact clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.949 kcal/mol/HA) ✓ Good fit quality (FQ -9.15) ✓ Strong H-bond network (11 bonds) ✓ Deep burial (88% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ Extreme strain energy (46.6 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-28.474
kcal/mol
LE
-0.949
kcal/mol/HA
Fit Quality
-9.15
FQ (Leeson)
HAC
30
heavy atoms
MW
400
Da
LogP
2.26
cLogP
Strain ΔE
46.6 kcal/mol
SASA buried
88%
Lipo contact
80% BSA apolar/total
SASA unbound
685 Ų
Apolar buried
480 Ų

Interaction summary

HB 11 HY 24 PI 1 CLASH 2
Final rank3.995Score-28.474
Inter norm-1.077Intra norm0.128
Top1000noExcludedno
Contacts20H-bonds11
Artifact reasongeometry warning; 13 clashes; 2 protein clashes; high strain Δ 46.6
Residues
NDP301 ALA32 ARG48 ASP52 GLY157 ILE45 LEU94 MET53 PHE55 PHE56 SER44 SER86 THR180 THR83 TRP47 TYR162 VAL156 VAL30 VAL31 VAL87

Protein summary

511 residues
Protein targetT09Atoms8170
Residues511Chains2
Residue summaryLEU:1064; ARG:840; LYS:572; GLU:570; VAL:528; PHE:460; ILE:456; ALA:440; PRO:420; THR:406; TYR:357; ASP:312; GLN:289; ASN:238; SER:231; GLY:224

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.
Name3CL9Contacts21
PoseOpen native poseHB0
IFP residues
NDP301 ALA32 ARG97 ASP52 GLY157 ILE45 LEU94 LYS57 MET53 PHE55 PHE56 PHE91 PRO88 SER86 THR180 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap17Native recall0.81
Jaccard0.71RMSD-
HB strict4Strict recall0.57
HB same residue+role4HB role recall0.67
HB same residue4HB residue recall0.67

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
59 1.8077656603314811 -1.33737 -41.1817 8 18 0 0.00 0.00 - no Open
21 1.8167442151259838 -1.3248 -40.6867 9 18 0 0.00 0.00 - no Open
69 2.0383590711769224 -1.31566 -36.354 9 18 0 0.00 0.00 - no Open
18 2.07494107366931 -1.35194 -41.1881 8 18 0 0.00 0.00 - no Open
51 2.4756796252970026 -0.987142 -25.1715 6 16 0 0.00 0.00 - no Open
17 2.659480533179131 -0.988025 -29.206 7 15 0 0.00 0.00 - no Open
72 2.6888440031633536 -0.750575 -21.7979 3 14 0 0.00 0.00 - no Open
17 3.58601093162473 -0.977028 -29.0743 11 20 1 0.05 0.00 - no Open
44 3.8186271411229127 -0.825732 -21.4312 7 17 0 0.00 0.00 - no Open
69 3.822991328266453 -0.994304 -25.3242 10 18 1 0.05 0.00 - no Open
15 3.9945811977562276 -1.07747 -28.4735 11 20 17 0.81 0.67 - no Current
6 4.1125363457515824 -0.789709 -22.5077 7 16 0 0.00 0.00 - no Open
59 4.174917693331722 -0.958177 -28.341 9 18 1 0.05 0.00 - no Open
51 4.210198956266459 -1.07569 -27.4595 10 20 17 0.81 0.67 - no Open
18 4.247291649628563 -0.861737 -21.7221 4 20 0 0.00 0.00 - no Open
77 4.253748462384305 -0.861034 -20.9423 10 20 0 0.00 0.00 - no Open
15 4.305552679508108 -0.796609 -24.1605 4 14 0 0.00 0.00 - no Open
14 4.938291489005273 -0.642126 -17.5617 5 14 0 0.00 0.00 - no Open
67 5.1022653534044835 -0.644701 -19.1146 6 14 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 -28.474kcal/mol
Ligand efficiency (LE) -0.9491kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.155
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 400.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.26
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 46.62kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 26.61kcal/mol
Minimised FF energy -20.01kcal/mol

SASA & burial

✓ computed
SASA (unbound) 684.9Ų
Total solvent-accessible surface area of free ligand
BSA total 599.2Ų
Buried surface area upon binding
BSA apolar 480.1Ų
Hydrophobic contacts buried
BSA polar 119.1Ų
Polar contacts buried
Fraction buried 87.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 80.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3307.0Ų
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 4428.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1683.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)