FMO DATABASE

FMODB ID: 9RRG2

Calculation Name: 2O4L-A-Xray547

Preferred Name: Gag-Pol polyprotein

Target Type: SINGLE PROTEIN

Ligand Name: n-(3-{(1r)-1-[(6r)-4-hydroxy-2-oxo-6-phenethyl-6-propyl-5,6-dihydro-2h-pyran-3-yl]propyl}phenyl)-5-(trifluoromethyl)-2-pyridinesulfonamide

Ligand 3-letter code: TPV

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2O4L

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	-685005.813539
FMO2-HF: Nuclear repulsion	647315.916508
FMO2-HF: Total energy	-37689.897031
FMO2-MP2: Total energy	-37799.349656

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.
-13.006	-9.053	0.99	-1.653	-3.288	-0.01

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 : 0.875 / q_NPA : 0.915

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	-0.008	-0.006	2.625	-0.806	2.008	0.373	-1.131	-2.056	-0.005
4	A	4	THR	0	0.005	0.003	4.737	4.162	4.192	-0.001	-0.009	-0.020	0.000
67	A	67	CYS	0	0.003	-0.005	3.367	-7.232	-6.712	0.579	-0.291	-0.807	-0.003
68	A	68	GLY	0	0.012	0.015	4.770	-6.318	-6.195	-0.001	-0.004	-0.118	0.000
69	A	69	HIS	0	-0.058	-0.020	3.256	-1.418	-0.952	0.040	-0.218	-0.287	-0.002
5	A	5	LEU	0	0.036	0.003	8.327	-0.183	-0.183	0.000	0.000	0.000	0.000
6	A	6	TRP	0	0.009	0.013	11.264	1.853	1.853	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.954	0.985	10.105	25.741	25.741	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.999	0.994	12.178	15.212	15.212	0.000	0.000	0.000	0.000
9	A	9	PRO	0	0.038	0.029	8.171	-0.433	-0.433	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.034	-0.021	9.320	0.009	0.009	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.025	-0.017	5.062	-2.947	-2.947	0.000	0.000	0.000	0.000
12	A	12	THR	0	0.012	-0.009	8.386	1.489	1.489	0.000	0.000	0.000	0.000
13	A	13	ILE	0	-0.052	-0.026	9.066	-2.652	-2.652	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.825	0.905	11.807	22.267	22.267	0.000	0.000	0.000	0.000
15	A	15	ILE	0	0.053	0.014	14.432	-0.237	-0.237	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.025	0.019	17.328	0.478	0.478	0.000	0.000	0.000	0.000
17	A	17	GLY	0	-0.035	-0.018	20.200	0.535	0.535	0.000	0.000	0.000	0.000
18	A	18	GLN	0	-0.030	-0.008	19.507	0.132	0.132	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.017	0.001	13.578	-0.854	-0.854	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.914	0.951	14.781	15.773	15.773	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.803	-0.874	11.375	-24.858	-24.858	0.000	0.000	0.000	0.000
22	A	22	ALA	0	-0.029	-0.022	11.943	1.609	1.609	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.016	-0.006	10.936	-1.964	-1.964	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.019	-0.011	5.561	0.112	0.112	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.847	-0.926	10.084	-18.426	-18.426	0.000	0.000	0.000	0.000
26	A	26	THR	0	0.009	-0.016	11.473	0.408	0.408	0.000	0.000	0.000	0.000
27	A	27	GLY	0	-0.011	0.002	14.100	0.753	0.753	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.019	-0.001	16.809	0.974	0.974	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.820	-0.891	17.181	-15.690	-15.690	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.837	-0.924	18.521	-14.288	-14.288	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.011	-0.010	15.657	-0.877	-0.877	0.000	0.000	0.000	0.000
32	A	32	VAL	0	-0.027	-0.013	17.528	0.977	0.977	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.003	-0.001	16.285	-0.735	-0.735	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.841	-0.940	19.936	-13.641	-13.641	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.847	-0.914	22.385	-11.280	-11.280	0.000	0.000	0.000	0.000
36	A	36	MET	0	-0.018	0.005	20.317	-0.422	-0.422	0.000	0.000	0.000	0.000
37	A	37	SER	0	-0.012	-0.001	25.134	0.252	0.252	0.000	0.000	0.000	0.000
38	A	38	LEU	0	0.028	0.004	21.090	-0.597	-0.597	0.000	0.000	0.000	0.000
39	A	39	PRO	0	0.002	0.006	23.810	0.524	0.524	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.033	0.014	26.491	-0.214	-0.214	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.919	0.952	28.958	9.324	9.324	0.000	0.000	0.000	0.000
42	A	42	TRP	0	0.026	0.015	28.378	-0.360	-0.360	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.901	0.963	28.660	11.229	11.229	0.000	0.000	0.000	0.000
44	A	44	PRO	0	-0.019	-0.011	29.953	-0.344	-0.344	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.845	0.924	24.502	12.703	12.703	0.000	0.000	0.000	0.000
46	A	46	MET	0	-0.019	-0.001	29.915	0.046	0.046	0.000	0.000	0.000	0.000
47	A	47	ILE	0	0.025	0.006	23.450	-0.115	-0.115	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.036	0.006	26.539	0.340	0.340	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.015	0.013	24.854	-0.474	-0.474	0.000	0.000	0.000	0.000
50	A	50	VAL	0	0.002	0.001	24.236	0.516	0.516	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.003	0.007	26.325	-0.166	-0.166	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.013	0.009	28.926	0.375	0.375	0.000	0.000	0.000	0.000
53	A	53	PHE	0	0.004	-0.017	28.632	-0.389	-0.389	0.000	0.000	0.000	0.000
54	A	54	ILE	0	0.001	0.013	24.877	0.255	0.255	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.971	0.975	29.133	8.921	8.921	0.000	0.000	0.000	0.000
56	A	56	VAL	0	-0.019	-0.006	25.170	-0.101	-0.101	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.803	0.872	27.481	11.350	11.350	0.000	0.000	0.000	0.000
58	A	58	GLN	0	-0.013	-0.038	25.144	-0.269	-0.269	0.000	0.000	0.000	0.000
59	A	59	TYR	0	0.038	0.026	23.689	0.576	0.576	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.793	-0.882	23.389	-12.580	-12.580	0.000	0.000	0.000	0.000
61	A	61	GLN	0	-0.031	-0.024	21.883	0.360	0.360	0.000	0.000	0.000	0.000
62	A	62	ILE	0	0.031	0.028	19.051	0.140	0.140	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.003	-0.004	17.424	-0.695	-0.695	0.000	0.000	0.000	0.000
64	A	64	ILE	0	-0.018	-0.009	12.749	0.493	0.493	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.847	-0.917	9.906	-23.621	-23.621	0.000	0.000	0.000	0.000
66	A	66	ILE	0	0.054	0.021	7.069	1.106	1.106	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.923	0.959	7.419	21.741	21.741	0.000	0.000	0.000	0.000
71	A	71	ALA	0	0.041	0.027	11.203	-0.514	-0.514	0.000	0.000	0.000	0.000
72	A	72	ILE	0	-0.015	-0.016	13.254	0.920	0.920	0.000	0.000	0.000	0.000
73	A	73	GLY	0	0.026	0.013	16.935	-0.309	-0.309	0.000	0.000	0.000	0.000
74	A	74	THR	0	-0.069	-0.039	18.812	0.370	0.370	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.014	0.000	17.877	-0.854	-0.854	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.033	-0.005	20.472	0.925	0.925	0.000	0.000	0.000	0.000
77	A	77	VAL	0	-0.023	-0.003	21.743	-0.542	-0.542	0.000	0.000	0.000	0.000
78	A	78	GLY	0	0.034	0.018	24.161	0.590	0.590	0.000	0.000	0.000	0.000
79	A	79	PRO	0	-0.016	0.005	24.915	-0.387	-0.387	0.000	0.000	0.000	0.000
80	A	80	THR	0	-0.003	-0.015	20.348	0.277	0.277	0.000	0.000	0.000	0.000
81	A	81	PRO	0	-0.025	-0.017	21.869	0.072	0.072	0.000	0.000	0.000	0.000
82	A	82	VAL	0	0.000	-0.002	16.536	-0.178	-0.178	0.000	0.000	0.000	0.000
83	A	83	ASN	0	-0.033	0.016	16.027	0.558	0.558	0.000	0.000	0.000	0.000
84	A	84	ILE	0	0.017	0.005	14.771	-1.122	-1.122	0.000	0.000	0.000	0.000
85	A	85	ILE	0	-0.020	-0.014	10.660	0.626	0.626	0.000	0.000	0.000	0.000
86	A	86	GLY	0	0.104	0.053	12.871	-0.905	-0.905	0.000	0.000	0.000	0.000
87	A	87	ARG	1	0.881	0.904	14.133	15.358	15.358	0.000	0.000	0.000	0.000
88	A	88	ASN	0	-0.027	-0.015	14.799	-1.383	-1.383	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.011	-0.003	12.437	0.227	0.227	0.000	0.000	0.000	0.000
90	A	90	LEU	0	-0.006	-0.005	8.883	-2.110	-2.110	0.000	0.000	0.000	0.000
91	A	91	THR	0	-0.010	-0.004	9.743	-2.134	-2.134	0.000	0.000	0.000	0.000
92	A	92	GLN	0	-0.062	-0.021	11.723	-0.236	-0.236	0.000	0.000	0.000	0.000
93	A	93	ILE	0	-0.045	-0.020	5.972	-0.080	-0.080	0.000	0.000	0.000	0.000
94	A	94	GLY	0	0.001	0.010	6.710	-5.186	-5.186	0.000	0.000	0.000	0.000
95	A	95	CYS	0	-0.088	-0.036	6.097	-4.407	-4.407	0.000	0.000	0.000	0.000
96	A	96	THR	0	-0.008	-0.016	6.985	4.012	4.012	0.000	0.000	0.000	0.000
97	A	97	LEU	0	-0.041	-0.017	8.311	-2.161	-2.161	0.000	0.000	0.000	0.000
98	A	98	ASN	0	-0.034	-0.024	9.050	-1.607	-1.607	0.000	0.000	0.000	0.000
99	A	99	PHE	-1	-0.898	-0.928	11.593	-20.375	-20.375	0.000	0.000	0.000	0.000

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