FMO DATABASE

FMODB ID: QMK3Y

Calculation Name: 3VBZ-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3VBZ

Chain ID: A

ChEMBL ID:

UniProt ID: P0CG57

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	111
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-971661.838008
FMO2-HF: Nuclear repulsion	921156.458998
FMO2-HF: Total energy	-50505.37901
FMO2-MP2: Total energy	-50639.605178

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:ASN)

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

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.
-216.431	-208.335	47.882	-25.509	-30.468	-0.162

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.755 / q_NPA : 0.875

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	VAL	0	0.006	0.016	2.200	1.606	3.783	3.833	-2.489	-3.520	0.022
4	A	4	GLN	0	-0.013	-0.012	1.943	-38.923	-39.618	15.996	-6.785	-8.516	-0.018
5	A	5	PHE	0	0.049	0.033	3.841	5.122	5.763	0.017	-0.277	-0.381	0.001
51	A	52	TYR	0	-0.020	-0.065	4.579	-1.961	-1.890	-0.001	-0.004	-0.065	0.000
62	A	63	SER	0	0.041	0.013	2.987	-17.299	-15.365	0.130	-0.917	-1.148	-0.009
63	A	64	LEU	0	0.019	-0.001	2.541	-15.992	-12.880	1.669	-2.343	-2.438	-0.028
64	A	65	THR	0	-0.037	-0.019	3.343	-1.664	-0.011	0.116	-0.774	-0.995	-0.005
65	A	66	THR	0	-0.014	0.005	1.810	-56.989	-59.910	19.403	-8.116	-8.366	-0.090
66	A	67	TYR	0	-0.041	-0.042	2.214	8.498	8.761	6.651	-2.742	-4.172	-0.024
67	A	68	GLN	0	-0.053	-0.023	4.989	1.845	1.858	-0.001	-0.001	-0.011	0.000
85	A	88	VAL	0	0.017	0.005	3.737	0.663	0.815	0.001	-0.037	-0.115	0.000
87	A	92	ASP	-1	-0.736	-0.808	2.890	-72.683	-70.987	0.068	-1.024	-0.741	-0.011
6	A	6	GLY	0	0.049	0.022	5.414	5.333	5.333	0.000	0.000	0.000	0.000
7	A	7	PHE	0	0.020	-0.003	5.850	2.152	2.152	0.000	0.000	0.000	0.000
8	A	8	MET	0	-0.075	-0.026	6.044	2.906	2.906	0.000	0.000	0.000	0.000
9	A	9	ILE	0	0.047	0.030	9.130	2.687	2.687	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.862	-0.921	11.428	-19.829	-19.829	0.000	0.000	0.000	0.000
11	A	11	CYS	0	-0.136	-0.051	11.929	2.179	2.179	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.021	-0.008	13.205	1.525	1.525	0.000	0.000	0.000	0.000
13	A	13	ILE	0	-0.047	-0.008	14.904	1.424	1.424	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.901	0.927	15.983	18.240	18.240	0.000	0.000	0.000	0.000
15	A	15	ASN	0	-0.010	-0.020	15.608	0.086	0.086	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.918	0.978	17.518	15.092	15.092	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.878	0.946	17.671	15.147	15.147	0.000	0.000	0.000	0.000
18	A	18	PRO	0	0.019	0.028	14.878	-0.782	-0.782	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.035	-0.006	10.407	0.134	0.134	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.023	-0.014	12.434	-0.311	-0.311	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.859	-0.928	14.172	-14.627	-14.627	0.000	0.000	0.000	0.000
22	A	22	PHE	0	-0.010	-0.014	13.661	0.904	0.904	0.000	0.000	0.000	0.000
23	A	23	MET	0	-0.041	-0.017	10.925	-1.498	-1.498	0.000	0.000	0.000	0.000
24	A	24	ASN	0	-0.012	-0.019	14.691	0.449	0.449	0.000	0.000	0.000	0.000
25	A	25	TYR	0	-0.026	-0.034	18.220	0.853	0.853	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.024	0.005	19.181	-0.488	-0.488	0.000	0.000	0.000	0.000
27	A	27	CYS	0	-0.116	-0.010	21.081	0.324	0.324	0.000	0.000	0.000	0.000
28	A	28	TYR	0	-0.023	-0.037	16.336	-0.241	-0.241	0.000	0.000	0.000	0.000
29	A	29	CYS	0	-0.097	-0.010	13.366	-3.386	-3.386	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.013	0.000	13.748	0.450	0.450	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.067	-0.036	14.662	0.338	0.338	0.000	0.000	0.000	0.000
32	A	32	VAL	0	-0.054	-0.031	17.264	-0.308	-0.308	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.020	0.025	17.205	0.060	0.060	0.000	0.000	0.000	0.000
34	A	34	ARG	1	0.855	0.923	17.805	13.006	13.006	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.085	0.051	21.442	0.143	0.143	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.034	-0.013	23.710	-0.388	-0.388	0.000	0.000	0.000	0.000
37	A	37	PRO	0	-0.016	-0.002	21.288	0.126	0.126	0.000	0.000	0.000	0.000
38	A	38	VAL	0	-0.065	-0.030	23.125	0.550	0.550	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.780	-0.861	22.219	-12.986	-12.986	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.825	-0.929	21.949	-13.148	-13.148	0.000	0.000	0.000	0.000
41	A	41	LEU	0	0.012	0.009	17.658	-0.902	-0.902	0.000	0.000	0.000	0.000
42	A	42	ASP	-1	-0.711	-0.879	17.561	-16.227	-16.227	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.924	0.975	17.935	12.624	12.624	0.000	0.000	0.000	0.000
44	A	44	CYS	0	-0.018	0.020	14.174	1.019	1.019	0.000	0.000	0.000	0.000
45	A	46	GLN	0	0.028	0.019	13.989	-0.668	-0.668	0.000	0.000	0.000	0.000
46	A	47	VAL	0	0.019	0.002	14.485	-0.629	-0.629	0.000	0.000	0.000	0.000
47	A	48	HIS	1	0.797	0.896	6.510	34.226	34.226	0.000	0.000	0.000	0.000
48	A	49	ASP	-1	-0.864	-0.933	10.869	-25.056	-25.056	0.000	0.000	0.000	0.000
49	A	50	GLU	-1	-0.892	-0.944	12.543	-16.994	-16.994	0.000	0.000	0.000	0.000
50	A	51	CYS	0	-0.070	-0.017	7.263	2.504	2.504	0.000	0.000	0.000	0.000
52	A	53	ALA	0	0.060	0.032	9.991	0.075	0.075	0.000	0.000	0.000	0.000
53	A	54	THR	0	-0.080	-0.040	13.205	2.022	2.022	0.000	0.000	0.000	0.000
54	A	55	ALA	0	0.011	-0.008	9.387	0.421	0.421	0.000	0.000	0.000	0.000
55	A	56	GLU	-1	-0.929	-0.968	10.404	-25.152	-25.152	0.000	0.000	0.000	0.000
56	A	57	LYS	1	0.815	0.911	12.358	19.673	19.673	0.000	0.000	0.000	0.000
57	A	58	HIS	0	-0.035	-0.007	12.735	1.686	1.686	0.000	0.000	0.000	0.000
58	A	59	GLY	0	0.001	0.011	14.073	0.209	0.209	0.000	0.000	0.000	0.000
59	A	60	CYS	0	-0.035	-0.011	8.092	-0.450	-0.450	0.000	0.000	0.000	0.000
60	A	61	TYR	0	0.093	0.035	7.931	1.165	1.165	0.000	0.000	0.000	0.000
61	A	62	PRO	0	0.006	0.024	5.282	-7.364	-7.364	0.000	0.000	0.000	0.000
68	A	69	TRP	0	0.040	0.002	5.873	0.628	0.628	0.000	0.000	0.000	0.000
69	A	70	GLU	-1	-0.887	-0.929	8.830	-18.293	-18.293	0.000	0.000	0.000	0.000
70	A	72	ARG	1	0.914	0.954	13.414	19.465	19.465	0.000	0.000	0.000	0.000
71	A	73	GLN	0	-0.009	-0.017	16.997	-0.110	-0.110	0.000	0.000	0.000	0.000
72	A	74	VAL	0	-0.018	-0.017	19.654	0.401	0.401	0.000	0.000	0.000	0.000
73	A	75	GLY	0	0.004	0.014	16.616	0.139	0.139	0.000	0.000	0.000	0.000
74	A	76	ASN	0	0.008	-0.006	10.504	1.184	1.184	0.000	0.000	0.000	0.000
75	A	77	GLU	-1	-0.875	-0.924	12.030	-18.667	-18.667	0.000	0.000	0.000	0.000
76	A	78	CYS	0	-0.038	0.009	5.051	-4.737	-4.737	0.000	0.000	0.000	0.000
77	A	79	ASN	0	0.031	0.009	10.482	0.018	0.018	0.000	0.000	0.000	0.000
78	A	80	SER	0	0.002	-0.007	7.915	-2.112	-2.112	0.000	0.000	0.000	0.000
79	A	81	LYS	1	0.949	0.983	10.012	23.112	23.112	0.000	0.000	0.000	0.000
80	A	82	THR	0	-0.046	-0.050	9.395	2.019	2.019	0.000	0.000	0.000	0.000
81	A	83	GLN	0	0.032	0.004	10.418	-1.780	-1.780	0.000	0.000	0.000	0.000
82	A	85	GLU	-1	-0.825	-0.894	5.751	-38.082	-38.082	0.000	0.000	0.000	0.000
83	A	86	VAL	0	0.006	-0.005	6.670	-2.946	-2.946	0.000	0.000	0.000	0.000
84	A	87	PHE	0	0.019	0.012	9.383	-0.014	-0.014	0.000	0.000	0.000	0.000
86	A	90	ALA	0	0.022	0.004	5.938	2.811	2.811	0.000	0.000	0.000	0.000
88	A	93	LEU	0	0.026	0.001	6.488	3.771	3.771	0.000	0.000	0.000	0.000
89	A	94	ALA	0	-0.041	-0.019	9.198	2.690	2.690	0.000	0.000	0.000	0.000
90	A	95	ALA	0	0.029	0.016	9.507	1.803	1.803	0.000	0.000	0.000	0.000
91	A	96	ALA	0	0.001	-0.002	9.130	1.643	1.643	0.000	0.000	0.000	0.000
92	A	97	LYS	1	0.910	0.957	11.110	20.707	20.707	0.000	0.000	0.000	0.000
93	A	99	LEU	0	0.014	-0.013	11.869	0.914	0.914	0.000	0.000	0.000	0.000
94	A	100	ALA	0	-0.053	-0.034	15.317	0.846	0.846	0.000	0.000	0.000	0.000
95	A	101	GLN	0	-0.100	-0.055	16.924	0.274	0.274	0.000	0.000	0.000	0.000
96	A	102	GLU	-1	-0.901	-0.941	19.239	-13.274	-13.274	0.000	0.000	0.000	0.000
97	A	103	ASP	-1	-0.924	-0.958	21.163	-11.793	-11.793	0.000	0.000	0.000	0.000
98	A	104	TYR	0	-0.093	-0.067	18.772	0.228	0.228	0.000	0.000	0.000	0.000
99	A	105	ASN	0	0.042	0.015	22.674	0.700	0.700	0.000	0.000	0.000	0.000
100	A	106	PRO	0	0.009	-0.013	24.803	-0.255	-0.255	0.000	0.000	0.000	0.000
101	A	107	ALA	0	-0.036	-0.011	26.304	-0.080	-0.080	0.000	0.000	0.000	0.000
102	A	108	HIS	0	-0.042	-0.041	23.786	0.658	0.658	0.000	0.000	0.000	0.000
103	A	109	PHE	0	0.028	0.027	19.122	-0.483	-0.483	0.000	0.000	0.000	0.000
104	A	110	ASN	0	-0.050	-0.010	22.249	0.262	0.262	0.000	0.000	0.000	0.000
105	A	111	ILE	0	-0.005	0.013	23.883	0.676	0.676	0.000	0.000	0.000	0.000
106	A	112	ASN	0	0.024	0.007	25.592	-0.461	-0.461	0.000	0.000	0.000	0.000
107	A	113	THR	0	0.071	0.013	22.279	0.382	0.382	0.000	0.000	0.000	0.000
108	A	114	GLY	0	-0.010	0.010	25.639	-0.014	-0.014	0.000	0.000	0.000	0.000
109	A	115	GLU	-1	-1.001	-1.011	28.323	-8.936	-8.936	0.000	0.000	0.000	0.000
110	A	116	ARG	1	0.885	0.923	27.395	11.087	11.087	0.000	0.000	0.000	0.000
111	A	118	LYS	0	0.010	0.011	25.286	-1.333	-1.333	0.000	0.000	0.000	0.000

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