FMO DATABASE

FMODB ID: 4Q4QN

Calculation Name: 2F3K-A-Xray547

Preferred Name: Gag-Pol polyprotein

Target Type: SINGLE PROTEIN

Ligand Name: (3s,4as,8as)-n-(tert-butyl)-2-[(3s)-3-({3-(methylsulfonyl)-n-[(pyridin-3-yloxy)acetyl]-l-valyl}amino)-2-oxo-4-phenylbutyl]decahydroisoquinoline-3-carboxamide | phosphate ion

Ligand 3-letter code: RO1 | PO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2F3K

Chain ID: A

ChEMBL ID: CHEMBL3638331

UniProt ID: P03369

Base Structure: X-ray

Registration Date: 2025-10-04

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	-686486.371402
FMO2-HF: Nuclear repulsion	648704.706148
FMO2-HF: Total energy	-37781.665255
FMO2-MP2: Total energy	-37891.424871

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.
-22.214	-18.328	2.123	-2.168	-3.837	-0.017

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 : 0.869 / q_NPA : 0.912

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	-0.006	2.773	-2.396	0.458	0.313	-1.219	-1.947	-0.007
4	A	4	THR	0	0.004	0.004	4.934	2.822	2.838	-0.001	-0.006	-0.008	0.000
67	A	67	CYS	0	0.020	0.006	3.032	-7.719	-7.615	1.639	-0.541	-1.202	-0.006
68	A	68	GLY	0	0.012	0.014	4.592	-6.828	-6.685	-0.001	-0.007	-0.134	0.000
69	A	69	HIS	0	-0.052	-0.014	3.037	-2.076	-1.307	0.173	-0.395	-0.546	-0.004
5	A	5	LEU	0	0.054	0.013	8.634	-0.058	-0.058	0.000	0.000	0.000	0.000
6	A	6	TRP	0	0.004	0.011	11.724	0.872	0.872	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.932	0.964	11.573	21.221	21.221	0.000	0.000	0.000	0.000
8	A	8	ARG	1	1.006	1.002	12.103	15.656	15.656	0.000	0.000	0.000	0.000
9	A	9	PRO	0	0.053	0.041	8.114	-0.417	-0.417	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.040	-0.025	9.099	-0.041	-0.041	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.021	-0.013	4.816	-3.181	-3.181	0.000	0.000	0.000	0.000
12	A	12	THR	0	0.010	-0.010	8.020	1.527	1.527	0.000	0.000	0.000	0.000
13	A	13	ILE	0	-0.059	-0.030	8.634	-2.824	-2.824	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.826	0.890	11.283	22.389	22.389	0.000	0.000	0.000	0.000
15	A	15	ILE	0	0.034	0.016	14.223	-0.412	-0.412	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.021	0.009	17.051	0.626	0.626	0.000	0.000	0.000	0.000
17	A	17	GLY	0	-0.038	-0.012	18.812	0.644	0.644	0.000	0.000	0.000	0.000
18	A	18	GLN	0	0.017	0.009	19.096	-0.322	-0.322	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.004	-0.006	13.453	-0.868	-0.868	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.888	0.940	14.431	16.347	16.347	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.802	-0.868	11.286	-24.845	-24.845	0.000	0.000	0.000	0.000
22	A	22	ALA	0	-0.030	-0.026	11.618	1.585	1.585	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.025	-0.005	10.602	-1.958	-1.958	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.014	-0.014	5.326	0.150	0.150	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.850	-0.933	9.733	-19.214	-19.214	0.000	0.000	0.000	0.000
26	A	26	THR	0	-0.010	-0.018	11.446	0.337	0.337	0.000	0.000	0.000	0.000
27	A	27	GLY	0	-0.012	-0.001	14.015	0.857	0.857	0.000	0.000	0.000	0.000
28	A	28	ALA	0	0.003	0.011	16.378	0.917	0.917	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.815	-0.885	16.824	-15.931	-15.931	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.852	-0.939	18.273	-14.431	-14.431	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.004	-0.012	15.567	-0.893	-0.893	0.000	0.000	0.000	0.000
32	A	32	VAL	0	-0.034	-0.015	17.365	1.028	1.028	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.005	-0.002	16.135	-0.633	-0.633	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.794	-0.909	19.298	-14.531	-14.531	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.848	-0.907	21.992	-11.229	-11.229	0.000	0.000	0.000	0.000
36	A	36	MET	0	0.001	0.016	20.478	-0.361	-0.361	0.000	0.000	0.000	0.000
37	A	37	ASN	0	-0.006	-0.002	24.977	0.342	0.342	0.000	0.000	0.000	0.000
38	A	38	LEU	0	0.018	0.005	20.980	-0.546	-0.546	0.000	0.000	0.000	0.000
39	A	39	PRO	0	0.004	-0.007	23.995	0.486	0.486	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.029	0.024	26.427	-0.234	-0.234	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.938	0.966	28.981	9.288	9.288	0.000	0.000	0.000	0.000
42	A	42	TRP	0	0.015	0.014	28.113	-0.325	-0.325	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.828	0.901	27.672	11.451	11.451	0.000	0.000	0.000	0.000
44	A	44	PRO	0	0.005	-0.003	29.748	-0.334	-0.334	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.873	0.958	24.251	12.738	12.738	0.000	0.000	0.000	0.000
46	A	46	MET	0	-0.041	-0.023	29.537	0.196	0.196	0.000	0.000	0.000	0.000
47	A	47	ILE	0	0.015	0.006	23.456	-0.166	-0.166	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.024	0.017	26.579	0.378	0.378	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.025	0.005	25.186	-0.589	-0.589	0.000	0.000	0.000	0.000
50	A	50	ILE	0	0.011	0.002	24.514	0.515	0.515	0.000	0.000	0.000	0.000
51	A	51	GLY	0	-0.001	0.005	27.158	-0.145	-0.145	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.016	0.005	29.465	0.369	0.369	0.000	0.000	0.000	0.000
53	A	53	PHE	0	0.000	-0.011	29.021	-0.385	-0.385	0.000	0.000	0.000	0.000
54	A	54	ILE	0	0.013	0.021	24.974	0.304	0.304	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.933	0.955	29.514	8.931	8.931	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.009	0.005	24.857	-0.146	-0.146	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.798	0.871	27.135	11.409	11.409	0.000	0.000	0.000	0.000
58	A	58	GLN	0	-0.029	-0.042	24.809	-0.277	-0.277	0.000	0.000	0.000	0.000
59	A	59	TYR	0	0.042	0.021	23.325	0.582	0.582	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.743	-0.852	22.964	-12.796	-12.796	0.000	0.000	0.000	0.000
61	A	61	GLN	0	-0.019	-0.011	20.893	0.366	0.366	0.000	0.000	0.000	0.000
62	A	62	ILE	0	0.048	0.031	18.743	0.129	0.129	0.000	0.000	0.000	0.000
63	A	63	PRO	0	-0.029	-0.023	16.641	-0.817	-0.817	0.000	0.000	0.000	0.000
64	A	64	ILE	0	-0.014	-0.004	12.244	0.552	0.552	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.857	-0.891	9.608	-24.025	-24.025	0.000	0.000	0.000	0.000
66	A	66	ILE	0	0.068	0.023	7.136	1.212	1.212	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.836	0.902	6.937	24.212	24.212	0.000	0.000	0.000	0.000
71	A	71	ALA	0	0.068	0.040	10.615	-0.679	-0.679	0.000	0.000	0.000	0.000
72	A	72	ILE	0	-0.023	-0.024	12.646	1.011	1.011	0.000	0.000	0.000	0.000
73	A	73	GLY	0	0.025	0.018	16.502	0.122	0.122	0.000	0.000	0.000	0.000
74	A	74	THR	0	-0.060	-0.035	18.716	0.282	0.282	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.003	0.006	17.747	-0.847	-0.847	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.021	-0.002	20.281	0.942	0.942	0.000	0.000	0.000	0.000
77	A	77	VAL	0	-0.022	0.000	21.512	-0.546	-0.546	0.000	0.000	0.000	0.000
78	A	78	GLY	0	0.024	0.013	23.849	0.594	0.594	0.000	0.000	0.000	0.000
79	A	79	PRO	0	-0.014	-0.005	24.721	-0.324	-0.324	0.000	0.000	0.000	0.000
80	A	80	THR	0	0.017	0.001	20.092	0.156	0.156	0.000	0.000	0.000	0.000
81	A	81	PRO	0	-0.041	-0.020	21.634	0.092	0.092	0.000	0.000	0.000	0.000
82	A	82	VAL	0	-0.003	-0.005	16.038	-0.304	-0.304	0.000	0.000	0.000	0.000
83	A	83	ASN	0	-0.055	-0.013	15.699	0.634	0.634	0.000	0.000	0.000	0.000
84	A	84	ILE	0	0.024	0.011	14.487	-1.226	-1.226	0.000	0.000	0.000	0.000
85	A	85	ILE	0	-0.014	-0.013	10.467	0.744	0.744	0.000	0.000	0.000	0.000
86	A	86	GLY	0	0.097	0.050	12.662	-0.790	-0.790	0.000	0.000	0.000	0.000
87	A	87	ARG	1	0.878	0.901	13.839	15.656	15.656	0.000	0.000	0.000	0.000
88	A	88	ASN	0	-0.019	0.003	14.603	-1.435	-1.435	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.030	-0.008	12.542	0.241	0.241	0.000	0.000	0.000	0.000
90	A	90	LEU	0	0.001	-0.004	8.560	-2.145	-2.145	0.000	0.000	0.000	0.000
91	A	91	THR	0	-0.026	-0.025	9.570	-2.236	-2.236	0.000	0.000	0.000	0.000
92	A	92	GLN	0	-0.020	-0.008	11.654	-0.857	-0.857	0.000	0.000	0.000	0.000
93	A	93	ILE	0	-0.050	-0.023	5.783	-0.067	-0.067	0.000	0.000	0.000	0.000
94	A	94	GLY	0	0.002	0.011	6.474	-5.419	-5.419	0.000	0.000	0.000	0.000
95	A	95	CYS	0	-0.082	-0.032	6.067	-4.080	-4.080	0.000	0.000	0.000	0.000
96	A	96	THR	0	-0.007	-0.013	6.952	3.973	3.973	0.000	0.000	0.000	0.000
97	A	97	LEU	0	-0.043	-0.018	8.259	-2.241	-2.241	0.000	0.000	0.000	0.000
98	A	98	ASN	0	-0.034	-0.024	9.099	-1.388	-1.388	0.000	0.000	0.000	0.000
99	A	99	PHE	-1	-0.900	-0.929	11.545	-20.562	-20.562	0.000	0.000	0.000	0.000

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