FMO DATABASE

FMODB ID: Y16J2

Calculation Name: 2O4N-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: 2O4N

Chain ID: A

ChEMBL ID: CHEMBL3638326

UniProt ID: P03367

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	-686444.145431
FMO2-HF: Nuclear repulsion	648658.412075
FMO2-HF: Total energy	-37785.733356
FMO2-MP2: Total energy	-37895.524184

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.
-29.785	-26.198	0.251	-1.347	-2.491	-0.006

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 : 0.878 / q_NPA : 0.916

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	0.002	-0.002	2.785	-1.307	1.487	0.229	-1.148	-1.876	-0.005
4	A	4	THR	0	0.000	0.002	4.899	4.128	4.151	-0.001	-0.006	-0.016	0.000
67	A	67	CYS	0	-0.010	-0.006	3.704	-5.273	-4.873	0.018	-0.092	-0.326	0.000
68	A	68	GLY	0	0.018	0.021	4.894	-5.076	-4.978	-0.001	-0.003	-0.094	0.000
69	A	69	HIS	0	-0.055	-0.022	3.814	-0.867	-0.595	0.006	-0.098	-0.179	-0.001
5	A	5	LEU	0	0.046	0.010	8.521	-0.105	-0.105	0.000	0.000	0.000	0.000
6	A	6	TRP	0	0.008	0.013	11.584	1.989	1.989	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.930	0.963	12.340	19.458	19.458	0.000	0.000	0.000	0.000
8	A	8	ARG	1	1.005	1.002	12.249	15.526	15.526	0.000	0.000	0.000	0.000
9	A	9	PRO	0	0.043	0.035	8.065	-0.434	-0.434	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.033	-0.011	9.257	-0.139	-0.139	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.007	-0.010	5.015	-2.817	-2.817	0.000	0.000	0.000	0.000
12	A	12	THR	0	0.006	0.001	8.201	2.298	2.298	0.000	0.000	0.000	0.000
13	A	13	VAL	0	-0.021	-0.010	8.725	-2.711	-2.711	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.947	0.982	11.369	20.550	20.550	0.000	0.000	0.000	0.000
15	A	15	ILE	0	0.044	0.009	13.910	-0.279	-0.279	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.047	0.027	16.763	0.587	0.587	0.000	0.000	0.000	0.000
17	A	17	GLY	0	-0.059	-0.028	19.525	0.580	0.580	0.000	0.000	0.000	0.000
18	A	18	GLN	0	-0.025	-0.006	19.125	0.068	0.068	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.016	0.005	13.283	-0.903	-0.903	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.881	0.933	14.488	16.070	16.070	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.889	-0.938	12.370	-21.124	-21.124	0.000	0.000	0.000	0.000
22	A	22	ALA	0	-0.004	-0.008	11.830	1.497	1.497	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.005	0.002	10.826	-2.012	-2.012	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.032	-0.016	5.640	-0.097	-0.097	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.842	-0.928	10.087	-18.664	-18.664	0.000	0.000	0.000	0.000
26	A	26	THR	0	0.005	-0.017	11.555	0.471	0.471	0.000	0.000	0.000	0.000
27	A	27	GLY	0	-0.014	-0.001	14.101	0.764	0.764	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.015	0.004	16.628	0.982	0.982	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.820	-0.887	17.221	-15.690	-15.690	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.888	-0.960	18.427	-15.428	-15.428	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.033	-0.018	15.496	-0.775	-0.775	0.000	0.000	0.000	0.000
32	A	32	ILE	0	-0.023	-0.008	17.485	1.036	1.036	0.000	0.000	0.000	0.000
33	A	33	PHE	0	0.001	-0.016	14.606	-0.927	-0.927	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.848	-0.937	19.931	-13.384	-13.384	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.842	-0.909	22.461	-11.224	-11.224	0.000	0.000	0.000	0.000
36	A	36	MET	0	-0.022	0.003	20.038	-0.377	-0.377	0.000	0.000	0.000	0.000
37	A	37	SER	0	-0.023	-0.007	24.910	0.270	0.270	0.000	0.000	0.000	0.000
38	A	38	LEU	0	0.026	0.003	20.683	-0.627	-0.627	0.000	0.000	0.000	0.000
39	A	39	PRO	0	-0.009	0.002	23.355	0.532	0.532	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.034	0.016	26.030	-0.227	-0.227	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.923	0.951	28.477	9.287	9.287	0.000	0.000	0.000	0.000
42	A	42	TRP	0	0.034	0.023	28.292	-0.323	-0.323	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.942	0.982	28.825	11.146	11.146	0.000	0.000	0.000	0.000
44	A	44	PRO	0	-0.038	-0.014	29.996	-0.345	-0.345	0.000	0.000	0.000	0.000
45	A	45	ILE	0	0.002	0.002	26.258	0.222	0.222	0.000	0.000	0.000	0.000
46	A	46	MET	0	-0.029	-0.008	30.383	0.030	0.030	0.000	0.000	0.000	0.000
47	A	47	ILE	0	0.032	0.017	23.651	-0.105	-0.105	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.034	0.002	26.643	0.336	0.336	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.016	0.015	24.779	-0.503	-0.503	0.000	0.000	0.000	0.000
50	A	50	ILE	0	0.001	-0.001	23.351	0.526	0.526	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.000	0.005	26.330	-0.143	-0.143	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.019	0.005	28.948	0.383	0.383	0.000	0.000	0.000	0.000
53	A	53	PHE	0	0.003	-0.016	28.724	-0.384	-0.384	0.000	0.000	0.000	0.000
54	A	54	ILE	0	0.000	0.011	25.008	0.279	0.279	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.967	0.974	29.347	9.004	9.004	0.000	0.000	0.000	0.000
56	A	56	VAL	0	-0.011	-0.002	25.119	-0.124	-0.124	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.793	0.861	27.453	11.397	11.397	0.000	0.000	0.000	0.000
58	A	58	GLN	0	0.004	-0.027	25.026	-0.160	-0.160	0.000	0.000	0.000	0.000
59	A	59	TYR	0	0.028	0.015	23.463	0.609	0.609	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.812	-0.883	23.119	-12.821	-12.821	0.000	0.000	0.000	0.000
61	A	61	GLN	0	-0.043	-0.030	21.429	0.385	0.385	0.000	0.000	0.000	0.000
62	A	62	ILE	0	0.031	0.028	18.382	0.083	0.083	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.040	-0.020	15.585	-0.638	-0.638	0.000	0.000	0.000	0.000
64	A	64	ILE	0	-0.007	-0.003	11.968	0.439	0.439	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.913	-0.967	9.883	-24.070	-24.070	0.000	0.000	0.000	0.000
66	A	66	ILE	0	0.046	0.023	5.915	0.840	0.840	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.944	0.973	7.466	19.263	19.263	0.000	0.000	0.000	0.000
71	A	71	ALA	0	0.031	0.019	11.187	-0.367	-0.367	0.000	0.000	0.000	0.000
72	A	72	ILE	0	-0.040	-0.034	12.920	0.908	0.908	0.000	0.000	0.000	0.000
73	A	73	GLY	0	0.029	0.015	16.581	-0.238	-0.238	0.000	0.000	0.000	0.000
74	A	74	THR	0	-0.042	-0.024	18.522	0.415	0.415	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.014	-0.005	17.739	-0.882	-0.882	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.002	0.009	20.363	0.924	0.924	0.000	0.000	0.000	0.000
77	A	77	VAL	0	-0.031	-0.009	21.851	-0.515	-0.515	0.000	0.000	0.000	0.000
78	A	78	GLY	0	0.038	0.019	24.215	0.596	0.596	0.000	0.000	0.000	0.000
79	A	79	PRO	0	-0.028	0.000	24.980	-0.371	-0.371	0.000	0.000	0.000	0.000
80	A	80	THR	0	-0.006	-0.017	20.403	0.254	0.254	0.000	0.000	0.000	0.000
81	A	81	PRO	0	-0.028	-0.023	21.756	0.087	0.087	0.000	0.000	0.000	0.000
82	A	82	LEU	0	0.013	0.015	16.204	-0.156	-0.156	0.000	0.000	0.000	0.000
83	A	83	ASN	0	-0.005	0.013	15.807	0.760	0.760	0.000	0.000	0.000	0.000
84	A	84	VAL	0	-0.003	0.000	14.530	-1.058	-1.058	0.000	0.000	0.000	0.000
85	A	85	ILE	0	-0.013	-0.012	10.803	0.641	0.641	0.000	0.000	0.000	0.000
86	A	86	GLY	0	0.097	0.050	12.957	-0.828	-0.828	0.000	0.000	0.000	0.000
87	A	87	ARG	1	0.865	0.896	14.088	15.317	15.317	0.000	0.000	0.000	0.000
88	A	88	ASN	0	-0.041	-0.018	14.740	-1.794	-1.794	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.020	-0.008	12.585	0.075	0.075	0.000	0.000	0.000	0.000
90	A	90	LEU	0	-0.009	-0.008	8.977	-2.292	-2.292	0.000	0.000	0.000	0.000
91	A	91	THR	0	-0.016	-0.013	9.670	-2.230	-2.230	0.000	0.000	0.000	0.000
92	A	92	GLN	0	-0.064	-0.021	11.655	-0.307	-0.307	0.000	0.000	0.000	0.000
93	A	93	ILE	0	-0.049	-0.020	5.730	-0.038	-0.038	0.000	0.000	0.000	0.000
94	A	94	GLY	0	-0.004	0.007	6.745	-5.214	-5.214	0.000	0.000	0.000	0.000
95	A	95	CYS	0	-0.085	-0.035	6.097	-4.346	-4.346	0.000	0.000	0.000	0.000
96	A	96	THR	0	-0.004	-0.013	6.985	3.843	3.843	0.000	0.000	0.000	0.000
97	A	97	LEU	0	-0.039	-0.015	8.292	-2.180	-2.180	0.000	0.000	0.000	0.000
98	A	98	ASN	0	-0.036	-0.025	9.385	-1.297	-1.297	0.000	0.000	0.000	0.000
99	A	99	PHE	-1	-0.905	-0.932	11.666	-20.444	-20.444	0.000	0.000	0.000	0.000

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