FMO DATABASE

FMODB ID: VY5L1

Calculation Name: 1VFJ-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1VFJ

Chain ID: A

ChEMBL ID:

UniProt ID: P83820

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	116
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-851867.576978
FMO2-HF: Nuclear repulsion	807339.971622
FMO2-HF: Total energy	-44527.605356
FMO2-MP2: Total energy	-44659.275782

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:MET)

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

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.
-186.509	-179.276	29.271	-12.68	-23.82	-0.172

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.767 / q_NPA : 0.904

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

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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	LEU	0	0.019	0.024	3.573	-0.233	1.521	-0.002	-0.838	-0.913	-0.001
65	A	65	VAL	0	0.005	0.002	3.898	2.991	3.284	-0.001	-0.068	-0.224	0.000
66	A	66	SER	0	0.121	0.044	2.483	-21.288	-18.259	2.371	-2.779	-2.622	-0.029
67	A	67	GLU	-1	-0.787	-0.890	1.766	-101.571	-105.042	13.277	-5.621	-4.185	-0.080
68	A	68	PRO	0	-0.005	-0.003	4.914	4.711	4.748	-0.001	-0.006	-0.029	0.000
96	A	96	VAL	0	-0.019	-0.019	2.321	3.388	4.535	1.402	-0.516	-2.032	-0.002
97	A	97	GLU	-1	-0.957	-0.964	2.860	-46.185	-43.987	0.321	-1.332	-1.187	-0.014
98	A	98	LYS	1	0.831	0.888	2.648	28.579	30.288	1.174	-1.055	-1.827	-0.010
99	A	99	VAL	0	-0.062	-0.031	2.355	-0.487	0.443	1.965	-0.292	-2.603	-0.007
100	A	100	TYR	0	0.073	0.036	4.076	1.266	1.413	-0.001	-0.003	-0.144	0.000
108	A	108	ASP	-1	-0.801	-0.924	2.349	-48.713	-49.652	6.605	-1.562	-4.103	-0.014
109	A	109	GLU	-1	-0.903	-0.971	3.053	-46.316	-46.838	1.423	1.642	-2.542	-0.012
110	A	110	ALA	0	-0.005	0.028	3.845	1.940	1.985	0.010	0.053	-0.108	0.000
111	A	111	ALA	0	-0.033	-0.010	4.624	2.295	2.352	-0.001	-0.004	-0.052	0.000
112	A	112	VAL	0	-0.058	-0.034	2.467	0.946	1.765	0.729	-0.299	-1.249	-0.003
4	A	4	ILE	0	-0.015	-0.009	5.977	2.784	2.784	0.000	0.000	0.000	0.000
5	A	5	VAL	0	0.016	0.011	8.993	1.632	1.632	0.000	0.000	0.000	0.000
6	A	6	ALA	0	-0.020	-0.012	12.195	0.417	0.417	0.000	0.000	0.000	0.000
7	A	7	ILE	0	-0.025	-0.001	15.345	0.605	0.605	0.000	0.000	0.000	0.000
8	A	8	VAL	0	0.022	0.004	18.703	0.160	0.160	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.896	0.928	21.397	11.218	11.218	0.000	0.000	0.000	0.000
10	A	10	PRO	0	0.008	0.007	24.392	-0.302	-0.302	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.887	-0.946	25.793	-10.757	-10.757	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.823	0.922	23.957	11.674	11.674	0.000	0.000	0.000	0.000
13	A	13	LEU	0	0.010	0.017	19.926	-0.426	-0.426	0.000	0.000	0.000	0.000
14	A	14	ASN	0	-0.004	-0.018	21.968	-0.646	-0.646	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.873	-0.930	23.916	-11.598	-11.598	0.000	0.000	0.000	0.000
16	A	16	VAL	0	0.006	-0.003	17.907	-0.408	-0.408	0.000	0.000	0.000	0.000
17	A	17	LEU	0	0.008	0.005	17.584	-0.721	-0.721	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.941	0.977	19.002	11.119	11.119	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.004	0.010	19.349	-0.055	-0.055	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.001	-0.003	13.331	-0.574	-0.574	0.000	0.000	0.000	0.000
21	A	21	PHE	0	-0.038	-0.027	15.655	-0.367	-0.367	0.000	0.000	0.000	0.000
22	A	22	GLN	0	-0.039	-0.015	17.898	0.111	0.111	0.000	0.000	0.000	0.000
23	A	23	ALA	0	-0.026	-0.006	14.625	0.208	0.208	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.893	-0.951	13.569	-20.812	-20.812	0.000	0.000	0.000	0.000
25	A	25	VAL	0	0.000	0.003	10.394	-1.110	-1.110	0.000	0.000	0.000	0.000
26	A	26	ARG	1	0.829	0.912	12.771	17.919	17.919	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.002	0.008	11.111	1.067	1.067	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.027	-0.011	10.365	-1.860	-1.860	0.000	0.000	0.000	0.000
29	A	29	THR	0	-0.012	0.004	12.513	1.427	1.427	0.000	0.000	0.000	0.000
30	A	30	LEU	0	0.000	-0.014	14.669	-0.339	-0.339	0.000	0.000	0.000	0.000
31	A	31	SER	0	-0.006	0.005	17.462	0.610	0.610	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.952	0.979	20.216	11.974	11.974	0.000	0.000	0.000	0.000
33	A	33	VAL	0	0.007	0.005	20.663	-0.106	-0.106	0.000	0.000	0.000	0.000
34	A	34	GLN	0	0.028	0.014	23.684	0.342	0.342	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.001	-0.006	25.001	-0.328	-0.328	0.000	0.000	0.000	0.000
36	A	36	HIS	1	0.852	0.922	25.997	10.781	10.781	0.000	0.000	0.000	0.000
37	A	37	GLY	0	-0.012	-0.012	25.690	-0.547	-0.547	0.000	0.000	0.000	0.000
38	A	38	GLY	0	-0.004	-0.004	26.034	0.417	0.417	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.946	-0.966	27.084	-11.931	-11.931	0.000	0.000	0.000	0.000
40	A	40	THR	0	-0.028	-0.019	29.968	0.390	0.390	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.882	-0.941	32.581	-9.731	-9.731	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.849	0.913	35.215	8.088	8.088	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.056	0.016	38.658	-0.047	-0.047	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.822	-0.909	41.418	-7.376	-7.376	0.000	0.000	0.000	0.000
45	A	45	THR	0	-0.055	-0.056	35.118	0.140	0.140	0.000	0.000	0.000	0.000
46	A	46	TYR	0	0.063	0.044	36.162	0.105	0.105	0.000	0.000	0.000	0.000
47	A	47	ARG	1	0.871	0.944	38.388	7.021	7.021	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.047	0.026	38.792	0.162	0.162	0.000	0.000	0.000	0.000
49	A	49	THR	0	-0.075	-0.032	39.859	0.139	0.139	0.000	0.000	0.000	0.000
50	A	50	THR	0	-0.043	-0.039	39.673	0.184	0.184	0.000	0.000	0.000	0.000
51	A	51	VAL	0	0.043	0.021	33.664	-0.144	-0.144	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.897	0.954	36.441	7.433	7.433	0.000	0.000	0.000	0.000
53	A	53	MET	0	0.019	0.023	35.742	-0.174	-0.174	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.796	-0.871	33.043	-9.294	-9.294	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.031	-0.009	28.360	-0.409	-0.409	0.000	0.000	0.000	0.000
56	A	56	HIS	0	-0.017	-0.013	29.008	0.264	0.264	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.882	-0.944	26.479	-11.389	-11.389	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.853	0.917	22.624	11.691	11.691	0.000	0.000	0.000	0.000
59	A	59	VAL	0	0.003	0.001	19.453	0.071	0.071	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.827	0.886	13.335	19.263	19.263	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.002	-0.015	14.632	0.247	0.247	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.816	-0.879	10.435	-22.971	-22.971	0.000	0.000	0.000	0.000
63	A	63	ILE	0	0.034	0.010	8.565	1.048	1.048	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.024	0.027	4.988	-2.352	-2.352	0.000	0.000	0.000	0.000
69	A	69	PHE	0	0.073	0.034	6.889	2.577	2.577	0.000	0.000	0.000	0.000
70	A	70	VAL	0	-0.026	0.014	5.223	2.580	2.580	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.978	0.983	7.815	23.334	23.334	0.000	0.000	0.000	0.000
72	A	72	PRO	0	0.043	0.021	10.478	1.471	1.471	0.000	0.000	0.000	0.000
73	A	73	THR	0	0.035	0.003	9.559	1.732	1.732	0.000	0.000	0.000	0.000
74	A	74	VAL	0	-0.039	-0.024	11.075	1.434	1.434	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.930	-0.959	13.465	-14.992	-14.992	0.000	0.000	0.000	0.000
76	A	76	ALA	0	-0.006	-0.003	15.375	1.223	1.223	0.000	0.000	0.000	0.000
77	A	77	ILE	0	-0.011	-0.014	13.558	1.108	1.108	0.000	0.000	0.000	0.000
78	A	78	LEU	0	-0.018	-0.009	17.161	1.056	1.056	0.000	0.000	0.000	0.000
79	A	79	LYS	1	0.943	0.984	19.416	14.150	14.150	0.000	0.000	0.000	0.000
80	A	80	ALA	0	-0.045	-0.024	20.760	0.724	0.724	0.000	0.000	0.000	0.000
81	A	81	ALA	0	0.007	-0.015	20.763	0.582	0.582	0.000	0.000	0.000	0.000
82	A	82	ARG	1	0.907	0.977	22.766	11.658	11.658	0.000	0.000	0.000	0.000
83	A	83	THR	0	-0.050	-0.069	25.130	0.395	0.395	0.000	0.000	0.000	0.000
84	A	84	GLY	0	-0.082	-0.062	28.177	0.295	0.295	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.883	-0.917	29.575	-9.182	-9.182	0.000	0.000	0.000	0.000
86	A	86	VAL	0	0.017	-0.009	29.117	-0.498	-0.498	0.000	0.000	0.000	0.000
87	A	87	GLY	0	-0.008	-0.002	27.019	0.138	0.138	0.000	0.000	0.000	0.000
88	A	88	ASP	-1	-0.687	-0.785	24.682	-11.704	-11.704	0.000	0.000	0.000	0.000
89	A	89	GLY	0	0.017	-0.002	21.645	-0.227	-0.227	0.000	0.000	0.000	0.000
90	A	90	LYS	1	0.871	0.943	17.921	15.455	15.455	0.000	0.000	0.000	0.000
91	A	91	ILE	0	0.028	0.021	13.041	-0.192	-0.192	0.000	0.000	0.000	0.000
92	A	92	PHE	0	-0.009	-0.005	13.213	0.735	0.735	0.000	0.000	0.000	0.000
93	A	93	VAL	0	0.017	0.004	7.943	-1.102	-1.102	0.000	0.000	0.000	0.000
94	A	94	LEU	0	0.017	0.015	8.237	0.186	0.186	0.000	0.000	0.000	0.000
95	A	95	PRO	0	0.001	-0.007	5.799	-6.639	-6.639	0.000	0.000	0.000	0.000
101	A	101	ARG	1	0.826	0.927	7.499	26.163	26.163	0.000	0.000	0.000	0.000
102	A	102	ILE	0	0.022	-0.002	9.845	1.333	1.333	0.000	0.000	0.000	0.000
103	A	103	ARG	1	0.920	0.967	13.339	17.465	17.465	0.000	0.000	0.000	0.000
104	A	104	THR	0	-0.067	-0.080	12.187	0.830	0.830	0.000	0.000	0.000	0.000
105	A	105	GLY	0	0.027	0.030	11.848	0.611	0.611	0.000	0.000	0.000	0.000
106	A	106	GLU	-1	-0.849	-0.891	9.123	-22.304	-22.304	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.825	-0.911	5.792	-28.281	-28.281	0.000	0.000	0.000	0.000
113	A	113	THR	0	-0.027	-0.018	5.568	0.839	0.839	0.000	0.000	0.000	0.000
114	A	114	PRO	0	-0.030	-0.014	7.579	1.530	1.530	0.000	0.000	0.000	0.000
115	A	115	VAL	0	-0.053	-0.035	10.999	0.432	0.432	0.000	0.000	0.000	0.000
116	A	116	GLN	-1	-0.879	-0.923	13.692	-16.684	-16.684	0.000	0.000	0.000	0.000

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