FMO DATABASE

FMODB ID: VQ251

Calculation Name: 3F89-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3F89

Chain ID: A

ChEMBL ID:

UniProt ID: O88522

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	83
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-397877.658082
FMO2-HF: Nuclear repulsion	363550.02907
FMO2-HF: Total energy	-34327.629012
FMO2-MP2: Total energy	-34429.268172

3D Structure

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:254:GLU)

Summations of interaction energy for fragment #1(A:254:GLU)

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.
-23.313	-18.796	0.489	-1.611	-3.395	0.011

Interaction energy analysis for fragmet #1(A:254:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.970 / q_NPA : -0.991

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	256	LEU	0	0.002	-0.001	2.715	-11.570	-8.362	0.440	-1.228	-2.421	0.009
4	A	257	ARG	1	0.958	0.984	3.460	-40.831	-39.755	0.050	-0.332	-0.793	0.002
5	A	258	GLN	0	-0.143	-0.060	4.851	-7.007	-6.774	-0.001	-0.051	-0.181	0.000
6	A	259	GLN	0	0.120	0.062	6.456	-2.504	-2.504	0.000	0.000	0.000	0.000
7	A	260	LEU	0	-0.051	-0.025	8.828	-1.567	-1.567	0.000	0.000	0.000	0.000
8	A	261	GLN	0	-0.016	-0.003	9.487	-2.262	-2.262	0.000	0.000	0.000	0.000
9	A	262	GLN	0	0.041	0.035	11.937	0.326	0.326	0.000	0.000	0.000	0.000
10	A	263	ALA	0	-0.034	-0.009	13.701	-1.192	-1.192	0.000	0.000	0.000	0.000
11	A	264	GLU	-1	-0.886	-0.968	13.942	17.503	17.503	0.000	0.000	0.000	0.000
12	A	265	GLU	-1	-0.950	-0.961	16.519	15.516	15.516	0.000	0.000	0.000	0.000
13	A	266	ALA	0	-0.047	-0.032	18.380	-0.781	-0.781	0.000	0.000	0.000	0.000
14	A	267	LEU	0	-0.072	-0.062	18.236	-0.713	-0.713	0.000	0.000	0.000	0.000
15	A	268	VAL	0	0.050	0.056	20.902	-0.582	-0.582	0.000	0.000	0.000	0.000
16	A	269	ALA	0	0.048	0.026	22.819	-0.551	-0.551	0.000	0.000	0.000	0.000
17	A	270	LYS	1	0.867	0.913	23.916	-12.511	-12.511	0.000	0.000	0.000	0.000
18	A	271	GLN	0	0.050	0.000	25.855	0.032	0.032	0.000	0.000	0.000	0.000
19	A	272	GLU	-1	-0.912	-0.927	27.145	10.697	10.697	0.000	0.000	0.000	0.000
20	A	273	LEU	0	-0.079	-0.055	29.035	-0.380	-0.380	0.000	0.000	0.000	0.000
21	A	274	ILE	0	-0.057	-0.019	28.571	-0.324	-0.324	0.000	0.000	0.000	0.000
22	A	275	ASP	-1	-0.804	-0.895	31.073	9.316	9.316	0.000	0.000	0.000	0.000
23	A	276	LYS	1	0.870	0.959	33.349	-8.977	-8.977	0.000	0.000	0.000	0.000
24	A	277	LEU	0	-0.030	-0.021	33.621	-0.191	-0.191	0.000	0.000	0.000	0.000
25	A	278	LYS	1	0.917	0.958	33.793	-9.051	-9.051	0.000	0.000	0.000	0.000
26	A	279	GLU	-1	-0.857	-0.941	36.033	8.251	8.251	0.000	0.000	0.000	0.000
27	A	280	GLU	-1	-0.955	-0.969	38.674	7.715	7.715	0.000	0.000	0.000	0.000
28	A	281	ALA	0	0.008	-0.017	39.936	-0.231	-0.231	0.000	0.000	0.000	0.000
29	A	282	GLU	-1	-0.938	-0.967	41.625	6.928	6.928	0.000	0.000	0.000	0.000
30	A	283	GLN	0	0.013	-0.001	43.466	-0.210	-0.210	0.000	0.000	0.000	0.000
31	A	284	HIS	0	-0.079	-0.031	41.345	-0.160	-0.160	0.000	0.000	0.000	0.000
32	A	285	ASN	0	-0.079	-0.067	44.677	-0.234	-0.234	0.000	0.000	0.000	0.000
33	A	286	ILE	0	0.050	0.047	47.120	-0.132	-0.132	0.000	0.000	0.000	0.000
34	A	287	VAL	0	-0.010	-0.002	49.399	-0.161	-0.161	0.000	0.000	0.000	0.000
35	A	288	MET	0	-0.035	-0.003	49.605	-0.148	-0.148	0.000	0.000	0.000	0.000
36	A	289	GLU	-1	-0.868	-0.945	51.502	5.913	5.913	0.000	0.000	0.000	0.000
37	A	290	THR	0	-0.048	-0.029	54.030	-0.152	-0.152	0.000	0.000	0.000	0.000
38	A	291	VAL	0	-0.006	-0.016	54.354	-0.115	-0.115	0.000	0.000	0.000	0.000
39	A	292	PRO	0	-0.020	-0.001	55.585	-0.117	-0.117	0.000	0.000	0.000	0.000
40	A	293	VAL	0	0.023	0.024	58.773	-0.121	-0.121	0.000	0.000	0.000	0.000
41	A	294	LEU	0	0.045	0.026	59.187	-0.104	-0.104	0.000	0.000	0.000	0.000
42	A	295	LYS	1	0.869	0.946	60.009	-5.204	-5.204	0.000	0.000	0.000	0.000
43	A	296	ALA	0	0.009	0.008	62.597	-0.081	-0.081	0.000	0.000	0.000	0.000
44	A	297	GLN	0	0.014	-0.006	64.346	-0.057	-0.057	0.000	0.000	0.000	0.000
45	A	298	ALA	0	-0.015	0.001	65.700	-0.088	-0.088	0.000	0.000	0.000	0.000
46	A	299	ASP	-1	-0.937	-0.993	66.165	4.757	4.757	0.000	0.000	0.000	0.000
47	A	300	ILE	0	0.016	0.016	68.290	-0.082	-0.082	0.000	0.000	0.000	0.000
48	A	301	TYR	0	0.046	0.019	68.461	-0.051	-0.051	0.000	0.000	0.000	0.000
49	A	302	LYS	1	0.911	0.975	71.478	-4.514	-4.514	0.000	0.000	0.000	0.000
50	A	303	ALA	0	-0.040	-0.026	72.967	-0.078	-0.078	0.000	0.000	0.000	0.000
51	A	304	ASP	-1	-0.839	-0.924	74.195	4.240	4.240	0.000	0.000	0.000	0.000
52	A	305	PHE	0	-0.035	-0.007	75.915	-0.083	-0.083	0.000	0.000	0.000	0.000
53	A	306	GLN	0	-0.086	-0.056	76.118	-0.042	-0.042	0.000	0.000	0.000	0.000
54	A	307	ALA	0	0.027	0.018	79.029	-0.064	-0.064	0.000	0.000	0.000	0.000
55	A	308	GLU	-1	-0.885	-0.947	80.323	3.878	3.878	0.000	0.000	0.000	0.000
56	A	309	ARG	1	0.891	0.946	79.776	-4.044	-4.044	0.000	0.000	0.000	0.000
57	A	310	HIS	0	-0.020	-0.016	83.395	-0.075	-0.075	0.000	0.000	0.000	0.000
58	A	311	ALA	0	0.060	0.035	84.982	-0.053	-0.053	0.000	0.000	0.000	0.000
59	A	312	ARG	1	0.911	0.953	85.041	-3.794	-3.794	0.000	0.000	0.000	0.000
60	A	313	GLU	-1	-0.933	-0.972	87.604	3.529	3.529	0.000	0.000	0.000	0.000
61	A	314	LYS	1	0.975	0.985	89.481	-3.595	-3.595	0.000	0.000	0.000	0.000
62	A	315	LEU	0	-0.026	-0.013	89.404	-0.053	-0.053	0.000	0.000	0.000	0.000
63	A	316	VAL	0	-0.050	-0.023	91.530	-0.042	-0.042	0.000	0.000	0.000	0.000
64	A	317	GLU	-1	-0.844	-0.907	93.611	3.398	3.398	0.000	0.000	0.000	0.000
65	A	318	LYS	1	0.915	0.960	95.597	-3.309	-3.309	0.000	0.000	0.000	0.000
66	A	319	LYS	1	0.904	0.948	96.085	-3.387	-3.387	0.000	0.000	0.000	0.000
67	A	320	GLU	-1	-0.915	-0.972	97.458	3.302	3.302	0.000	0.000	0.000	0.000
68	A	321	TYR	0	0.001	-0.011	99.804	-0.036	-0.036	0.000	0.000	0.000	0.000
69	A	322	LEU	0	-0.043	-0.025	100.068	-0.033	-0.033	0.000	0.000	0.000	0.000
70	A	323	GLN	0	-0.022	-0.007	100.288	0.011	0.011	0.000	0.000	0.000	0.000
71	A	324	GLU	-1	-0.881	-0.932	103.838	3.043	3.043	0.000	0.000	0.000	0.000
72	A	325	GLN	0	-0.101	-0.047	104.778	-0.057	-0.057	0.000	0.000	0.000	0.000
73	A	326	LEU	0	0.001	-0.009	104.948	-0.030	-0.030	0.000	0.000	0.000	0.000
74	A	327	GLU	-1	-0.946	-0.958	106.260	3.020	3.020	0.000	0.000	0.000	0.000
75	A	328	GLN	0	-0.053	-0.057	109.947	-0.034	-0.034	0.000	0.000	0.000	0.000
76	A	329	LEU	0	0.104	0.076	111.707	-0.027	-0.027	0.000	0.000	0.000	0.000
77	A	330	GLN	0	0.004	-0.018	110.863	-0.047	-0.047	0.000	0.000	0.000	0.000
78	A	331	ARG	1	0.877	0.955	111.444	-2.899	-2.899	0.000	0.000	0.000	0.000
79	A	332	GLU	-1	-0.957	-0.972	116.098	2.750	2.750	0.000	0.000	0.000	0.000
80	A	333	PHE	0	-0.004	-0.004	116.680	-0.029	-0.029	0.000	0.000	0.000	0.000
81	A	334	ASN	0	-0.009	-0.010	115.582	-0.027	-0.027	0.000	0.000	0.000	0.000
82	A	335	LYS	1	0.882	0.972	119.439	-2.610	-2.610	0.000	0.000	0.000	0.000
83	A	336	LEU	0	-0.051	-0.020	121.194	-0.034	-0.034	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:254:GLU)