FMO DATABASE

FMODB ID: 3MMML

Calculation Name: 2PK5-A-Xray547

Preferred Name: Gag-Pol polyprotein

Target Type: SINGLE PROTEIN

Ligand Name: (4r)-n-[(1s,2r)-2-hydroxy-2,3-dihydro-1h-inden-1-yl]-3-[(2s,3s)-2-hydroxy-3-({n-[(isoquinolin-5-yloxy)acetyl]-3-(methyl sulfonyl)-l-alanyl}amino)-4-phenylbutanoyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide

Ligand 3-letter code: 075

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2PK5

Chain ID: A

ChEMBL ID: CHEMBL3638326

UniProt ID: P03367

Base Structure: X-ray

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	99
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-685678.790266
FMO2-HF: Nuclear repulsion	647949.939573
FMO2-HF: Total energy	-37728.850693
FMO2-MP2: Total energy	-37838.436028

3D Structure Molmil

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:1:PRO)

Summations of interaction energy for fragment #1(A:1:PRO)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-6.738	-3.921	0.067	-1.137	-1.747	-0.004

Interaction energy analysis for fragmet #1(A:1:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.877 / q_NPA : 0.914

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	3	ILE	0	0.001	-0.003	3.278	-0.492	1.788	0.053	-0.935	-1.398	-0.003
4	A	4	THR	0	0.003	0.002	5.162	3.567	3.581	-0.001	-0.003	-0.009	0.000
67	A	67	CYS	0	-0.006	-0.005	4.042	-2.092	-1.926	0.000	-0.020	-0.146	0.000
69	A	69	HIS	0	-0.043	-0.014	3.322	-1.698	-1.341	0.015	-0.179	-0.194	-0.001
5	A	5	LEU	0	0.037	0.005	8.795	0.025	0.025	0.000	0.000	0.000	0.000
6	A	6	TRP	0	0.007	0.013	11.797	1.803	1.803	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.952	0.982	10.693	24.487	24.487	0.000	0.000	0.000	0.000
8	A	8	ARG	1	1.002	0.997	12.500	14.862	14.862	0.000	0.000	0.000	0.000
9	A	9	PRO	0	0.034	0.028	8.937	-0.493	-0.493	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.037	-0.016	9.984	-0.205	-0.205	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.010	-0.012	5.995	-2.735	-2.735	0.000	0.000	0.000	0.000
12	A	12	THR	0	0.003	0.002	8.973	2.056	2.056	0.000	0.000	0.000	0.000
13	A	13	ILE	0	-0.006	-0.006	9.567	-2.282	-2.282	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.941	0.971	12.200	18.232	18.232	0.000	0.000	0.000	0.000
15	A	15	ILE	0	0.070	0.027	15.005	-0.339	-0.339	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.035	0.019	18.071	0.527	0.527	0.000	0.000	0.000	0.000
17	A	17	GLY	0	-0.047	-0.020	20.350	0.557	0.557	0.000	0.000	0.000	0.000
18	A	18	GLN	0	-0.004	-0.004	20.047	-0.305	-0.305	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.001	-0.006	14.120	-0.774	-0.774	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.829	0.904	15.349	15.292	15.292	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.898	-0.942	13.107	-20.328	-20.328	0.000	0.000	0.000	0.000
22	A	22	ALA	0	-0.006	-0.015	12.533	1.334	1.334	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.003	-0.001	11.579	-1.711	-1.711	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.026	-0.014	5.991	0.003	0.003	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.844	-0.930	10.664	-17.759	-17.759	0.000	0.000	0.000	0.000
26	A	26	THR	0	0.001	-0.019	12.235	0.375	0.375	0.000	0.000	0.000	0.000
27	A	27	GLY	0	-0.008	0.003	14.865	0.729	0.729	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.018	0.006	17.313	0.953	0.953	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.825	-0.895	17.663	-15.382	-15.382	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.847	-0.931	18.896	-13.990	-13.990	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.010	-0.011	16.126	-0.778	-0.778	0.000	0.000	0.000	0.000
32	A	32	VAL	0	-0.034	-0.016	18.004	0.929	0.929	0.000	0.000	0.000	0.000
33	A	33	ILE	0	-0.030	-0.011	16.579	-0.753	-0.753	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.733	-0.851	20.364	-13.523	-13.523	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.825	-0.903	22.976	-10.847	-10.847	0.000	0.000	0.000	0.000
36	A	36	MET	0	-0.019	0.002	21.395	-0.277	-0.277	0.000	0.000	0.000	0.000
37	A	37	SER	0	-0.012	-0.008	25.835	0.353	0.353	0.000	0.000	0.000	0.000
38	A	38	LEU	0	0.002	-0.002	22.008	-0.475	-0.475	0.000	0.000	0.000	0.000
39	A	39	PRO	0	0.003	0.003	24.628	0.491	0.491	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.036	0.018	27.281	-0.216	-0.216	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.932	0.957	29.700	9.578	9.578	0.000	0.000	0.000	0.000
42	A	42	TRP	0	0.020	0.014	29.229	-0.346	-0.346	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.889	0.956	29.069	11.101	11.101	0.000	0.000	0.000	0.000
44	A	44	PRO	0	-0.019	-0.009	30.504	-0.329	-0.329	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.863	0.936	25.265	12.189	12.189	0.000	0.000	0.000	0.000
46	A	46	MET	0	-0.014	0.003	30.292	0.048	0.048	0.000	0.000	0.000	0.000
47	A	47	ILE	0	0.012	0.000	23.794	-0.174	-0.174	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.041	0.005	26.800	0.345	0.345	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.015	0.016	25.761	-0.473	-0.473	0.000	0.000	0.000	0.000
50	A	50	ILE	0	0.003	0.002	24.519	0.497	0.497	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.003	0.007	27.552	-0.151	-0.151	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.015	0.010	29.995	0.345	0.345	0.000	0.000	0.000	0.000
53	A	53	PHE	0	0.005	-0.016	29.447	-0.383	-0.383	0.000	0.000	0.000	0.000
54	A	54	ILE	0	0.002	0.013	25.535	0.265	0.265	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.975	0.975	29.577	8.790	8.790	0.000	0.000	0.000	0.000
56	A	56	VAL	0	-0.018	-0.008	25.578	-0.106	-0.106	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.801	0.868	27.964	11.045	11.045	0.000	0.000	0.000	0.000
58	A	58	GLN	0	-0.011	-0.035	25.707	-0.216	-0.216	0.000	0.000	0.000	0.000
59	A	59	TYR	0	0.042	0.026	24.462	0.546	0.546	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.798	-0.885	24.155	-12.345	-12.345	0.000	0.000	0.000	0.000
61	A	61	GLN	0	-0.032	-0.023	22.156	0.331	0.331	0.000	0.000	0.000	0.000
62	A	62	ILE	0	0.032	0.030	19.517	0.089	0.089	0.000	0.000	0.000	0.000
63	A	63	ILE	0	-0.008	-0.006	16.301	-0.584	-0.584	0.000	0.000	0.000	0.000
64	A	64	ILE	0	-0.024	-0.012	13.180	0.617	0.617	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.960	-0.975	10.910	-23.023	-23.023	0.000	0.000	0.000	0.000
66	A	66	ILE	0	0.054	0.014	7.257	0.996	0.996	0.000	0.000	0.000	0.000
68	A	68	GLY	0	0.014	0.019	5.588	-4.417	-4.417	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.922	0.961	7.928	20.670	20.670	0.000	0.000	0.000	0.000
71	A	71	ALA	0	0.052	0.034	11.695	-0.247	-0.247	0.000	0.000	0.000	0.000
72	A	72	ILE	0	-0.017	-0.020	13.422	0.899	0.899	0.000	0.000	0.000	0.000
73	A	73	GLY	0	0.029	0.010	17.207	-0.218	-0.218	0.000	0.000	0.000	0.000
74	A	74	THR	0	-0.071	-0.043	19.452	0.333	0.333	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.014	-0.001	18.537	-0.826	-0.826	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.035	-0.008	21.126	0.885	0.885	0.000	0.000	0.000	0.000
77	A	77	VAL	0	-0.020	-0.003	22.245	-0.488	-0.488	0.000	0.000	0.000	0.000
78	A	78	GLY	0	0.029	0.017	24.677	0.545	0.545	0.000	0.000	0.000	0.000
79	A	79	PRO	0	-0.014	0.005	25.555	-0.363	-0.363	0.000	0.000	0.000	0.000
80	A	80	THR	0	-0.005	-0.017	21.069	0.282	0.282	0.000	0.000	0.000	0.000
81	A	81	PRO	0	-0.022	-0.009	22.974	0.031	0.031	0.000	0.000	0.000	0.000
82	A	82	VAL	0	-0.004	-0.011	17.164	-0.236	-0.236	0.000	0.000	0.000	0.000
83	A	83	ASN	0	-0.040	0.002	16.594	0.682	0.682	0.000	0.000	0.000	0.000
84	A	84	ILE	0	0.013	-0.001	15.286	-1.092	-1.092	0.000	0.000	0.000	0.000
85	A	85	ILE	0	-0.001	-0.004	10.890	0.613	0.613	0.000	0.000	0.000	0.000
86	A	86	GLY	0	0.099	0.049	13.322	-0.828	-0.828	0.000	0.000	0.000	0.000
87	A	87	ARG	1	0.879	0.903	14.482	15.169	15.169	0.000	0.000	0.000	0.000
88	A	88	ASN	0	-0.028	-0.013	15.093	-1.345	-1.345	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.009	-0.003	13.322	0.158	0.158	0.000	0.000	0.000	0.000
90	A	90	LEU	0	-0.011	-0.006	9.355	-2.027	-2.027	0.000	0.000	0.000	0.000
91	A	91	THR	0	-0.010	-0.007	10.004	-2.201	-2.201	0.000	0.000	0.000	0.000
92	A	92	GLN	0	-0.059	-0.018	11.804	-0.448	-0.448	0.000	0.000	0.000	0.000
93	A	93	ILE	0	-0.042	-0.017	6.541	-0.042	-0.042	0.000	0.000	0.000	0.000
94	A	94	GLY	0	-0.001	0.009	6.681	-5.110	-5.110	0.000	0.000	0.000	0.000
95	A	95	CYS	0	-0.087	-0.035	6.254	-4.491	-4.491	0.000	0.000	0.000	0.000
96	A	96	THR	0	-0.009	-0.016	7.047	3.746	3.746	0.000	0.000	0.000	0.000
97	A	97	LEU	0	-0.041	-0.017	8.402	-1.989	-1.989	0.000	0.000	0.000	0.000
98	A	98	ASN	0	-0.035	-0.025	8.988	-1.633	-1.633	0.000	0.000	0.000	0.000
99	A	99	PHE	-1	-0.898	-0.927	11.544	-20.523	-20.523	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:PRO)