Table 2.

The HADDOCK docking predictions for all bromelain-derived peptide with RBD variants complexes, along with additional parameters such as cluster size, Van der Waals energy, electrostatic energy, and Z-score. The KD and MM/GBSA free binding energy (kcal/mol) are also included in the table.

Parameters	WT	SA	BR	UK	CA	SG	SN	SC	IN	NG
HADDOCK Score (a.u.)	−69.3 ± 3.2	−78.6 ± 0.7	−72.7 ± 3.3	−70.7 ± 5.3	−71.0 ± 2.2	−70.3 ± 1.5	−70.5 ± 2.3	−75.6 ± 0.4	−68.6 ± 2.3	−82.1 ± 6.0
MM/GBSA (kcal/mol)	−42.69	−42.74	−38.91	−19.03	−37.99	−26.66	26.84	−29.27	−29.54	−46.87
Cluster Size	9	16	15	15	13	60	66	66	7	8
RMSD (Å)	2.2 ± 0.1	0.3 ± 0.0	0.4 ± 0.3	3.0 ± 0.0	1.9 ± 0.1	2.2 ± 0.1	0.9 ± 0.5	0.8 ± 0.5	4.1 ± 0.0	0.2 ± 0.1
Intermolecular Van der Waals Energy (kcal/mol)	−36.7 ± 2.6	−32.2 ± 2.2	−33.0 ± 0.3	−37.3 ± 3.1	−45.0 ± 6.5	−40.3 ± 2.4	−36.2 ± 2.3	−39.6 ± 1.8	−36.7 ± 2.0	−37.4 ± 1.3
Intermolecular electrostatic Energy (kcal/mol)	−156.9 ± 5.0	−205.6 ± 12.8	−179.2 ± 38.8	−117.2 ± 22.2	−122.9 ± 40.7	−86.8 ± 8.0	−134.7 ± 35.2	−132.8 ± 22.1	−128.8 ± 22.9	−220.1 ± 10.1
Desolvation Energy (kcal/mol)	−4.2 ± 1.3	−9.5 ± 2.0	−10.0 ± 5.1	−15.3 ± 4.5	−5.6 ± 2.8	−15.8 ± 1.8	−10.8 ± 4.2	−11.9 ± 2.5	−11.5 ± 2.9	−3.0 ± 2.0
Restraint Violation Energy (kcal/mol)	29.4 ± 15.1	42.3 ± 17.2	60.8 ± 12.3	53.4 ± 31.6	41.9 ± 2.1	32.8 ± 32.2	34.1 ± 19.5	24.8 ± 18.9	53.7 ± 19.3	22.5 ± 11.3
Buried Surface Area (Å)	1079.4 ± 65.4	1122.3 ± 27.5	1083.8 ± 28.1	1090.8 ± 51.4	1107.7 ± 35.2	1029.4 ± 22.3	1022.8 ± 58.6	1102.2 ± 52.0	1098.0 ± 47.5	1094.2 ± 30.7
Z-Score	−1.6	−2.2	−1.8	−1.4	−1.6	−1.4	−1.7	−2.0	−1.2	−2.4
Prodigy ΔG (kcal/mol)	−9.2	−8.8	−8.6	−9.4	−9.6	−9.2	−9.0	−9.3	−8.9	−9.9
KD (M) at 37.0 °C	3.3 × 10−7	6.6 × 10−7	9.0 × 10−7	2.4 × 10−7	1.8 × 10−7	3.5 × 10−7	4.7 × 10−7	2.7 × 10−7	5.1 × 10−7	9 × 10−8