FMO DATABASE

FMODB ID: 98K32

Calculation Name: 3VDJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VDJ

Chain ID: A

ChEMBL ID:

UniProt ID: Q7K740

Base Structure: X-ray

Registration Date: 2023-09-23

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	OptAll
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	69
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-414638.99484
FMO2-HF: Nuclear repulsion	385270.62822
FMO2-HF: Total energy	-29368.36662
FMO2-MP2: Total energy	-29450.932456

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:306:TYR)

Summations of interaction energy for fragment #1(A:306:TYR)

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.
-4.462	-2.571	0.011	-0.738	-1.164	0

Interaction energy analysis for fragmet #1(A:306:TYR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.021

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].
3	A	308	GLU	-1	-0.862	-0.935	3.626	-5.922	-4.031	0.011	-0.738	-1.164
4	A	309	PHE	0	-0.077	-0.044	5.020	0.774	0.774	0.000	0.000	0.000
5	A	310	GLU	-1	-0.890	-0.937	8.127	-0.476	-0.476	0.000	0.000	0.000
6	A	311	PRO	0	-0.071	-0.026	10.781	-0.025	-0.025	0.000	0.000	0.000
7	A	312	SER	0	0.028	0.007	12.046	0.020	0.020	0.000	0.000	0.000
8	A	313	ASP	-1	-0.759	-0.871	13.397	-0.281	-0.281	0.000	0.000	0.000
9	A	314	LYS	1	0.934	0.973	14.362	0.267	0.267	0.000	0.000	0.000
10	A	315	HIS	0	0.008	0.001	16.306	0.030	0.030	0.000	0.000	0.000
11	A	316	ILE	0	0.023	0.013	16.633	0.038	0.038	0.000	0.000	0.000
12	A	317	LYS	1	0.854	0.926	19.072	0.298	0.298	0.000	0.000	0.000
13	A	318	GLU	-1	-0.864	-0.928	18.794	-0.181	-0.181	0.000	0.000	0.000
14	A	319	TYR	0	-0.053	-0.045	21.987	0.027	0.027	0.000	0.000	0.000
15	A	320	LEU	0	0.010	-0.009	23.520	0.016	0.016	0.000	0.000	0.000
16	A	321	ASN	0	-0.001	-0.002	25.587	0.020	0.020	0.000	0.000	0.000
17	A	322	LYS	1	0.916	0.973	25.837	0.155	0.155	0.000	0.000	0.000
18	A	323	ILE	0	-0.009	0.002	27.304	0.009	0.009	0.000	0.000	0.000
19	A	324	GLN	0	0.031	0.021	30.019	0.008	0.008	0.000	0.000	0.000
20	A	325	ASN	0	-0.031	-0.019	31.559	0.003	0.003	0.000	0.000	0.000
21	A	326	SER	0	-0.060	-0.031	32.393	0.005	0.005	0.000	0.000	0.000
22	A	327	LEU	0	-0.038	0.001	28.740	-0.005	-0.005	0.000	0.000	0.000
23	A	328	SER	0	0.048	0.023	32.116	0.008	0.008	0.000	0.000	0.000
24	A	329	THR	0	0.027	-0.006	32.179	-0.007	-0.007	0.000	0.000	0.000
25	A	330	GLU	-1	-0.883	-0.907	32.687	-0.121	-0.121	0.000	0.000	0.000
26	A	331	TRP	0	-0.053	-0.041	24.719	-0.008	-0.008	0.000	0.000	0.000
27	A	332	SER	0	0.051	0.029	26.565	0.003	0.003	0.000	0.000	0.000
28	A	333	PRO	0	0.069	0.031	28.201	-0.007	-0.007	0.000	0.000	0.000
29	A	334	CYS	0	-0.072	0.021	18.884	0.013	0.013	0.000	0.000	0.000
30	A	335	SER	0	-0.007	0.001	20.398	0.009	0.009	0.000	0.000	0.000
31	A	336	VAL	0	-0.013	-0.004	19.867	0.017	0.017	0.000	0.000	0.000
32	A	337	THR	0	0.028	-0.002	23.140	-0.001	-0.001	0.000	0.000	0.000
33	A	338	CYS	0	0.007	-0.003	20.853	0.016	0.016	0.000	0.000	0.000
34	A	339	GLY	0	0.035	0.019	18.678	-0.011	-0.011	0.000	0.000	0.000
35	A	340	ASN	0	-0.021	-0.024	13.455	0.057	0.057	0.000	0.000	0.000
36	A	341	GLY	0	0.026	0.016	17.279	0.003	0.003	0.000	0.000	0.000
37	A	342	ILE	0	-0.024	-0.019	17.833	-0.028	-0.028	0.000	0.000	0.000
38	A	343	GLN	0	-0.036	-0.037	20.466	0.023	0.023	0.000	0.000	0.000
39	A	344	VAL	0	0.012	-0.016	22.882	-0.021	-0.021	0.000	0.000	0.000
40	A	345	ARG	1	0.816	0.879	25.320	0.167	0.167	0.000	0.000	0.000
41	A	346	ILE	0	0.023	0.017	27.909	-0.013	-0.013	0.000	0.000	0.000
42	A	347	LYS	1	0.875	0.929	26.044	0.186	0.186	0.000	0.000	0.000
43	A	348	PRO	0	0.029	-0.005	31.057	0.007	0.007	0.000	0.000	0.000
44	A	349	GLY	0	-0.026	0.000	34.079	0.006	0.006	0.000	0.000	0.000
45	A	350	SER	0	-0.018	-0.048	31.931	0.005	0.005	0.000	0.000	0.000
46	A	351	ALA	0	-0.028	-0.016	34.271	0.002	0.002	0.000	0.000	0.000
47	A	352	ASN	0	-0.048	-0.015	36.389	0.007	0.007	0.000	0.000	0.000
48	A	353	LYS	1	0.816	0.907	32.174	0.115	0.115	0.000	0.000	0.000
49	A	354	PRO	0	0.034	0.033	37.249	-0.001	-0.001	0.000	0.000	0.000
50	A	355	LYS	1	0.893	0.914	32.955	0.084	0.084	0.000	0.000	0.000
51	A	356	ASP	-1	-0.930	-0.969	32.907	-0.080	-0.080	0.000	0.000	0.000
52	A	357	GLU	-1	-0.893	-0.941	33.288	-0.075	-0.075	0.000	0.000	0.000
53	A	358	LEU	0	-0.072	-0.027	30.111	-0.006	-0.006	0.000	0.000	0.000
54	A	359	ASP	-1	-0.753	-0.870	25.854	-0.180	-0.180	0.000	0.000	0.000
55	A	360	TYR	0	-0.024	-0.044	18.441	0.005	0.005	0.000	0.000	0.000
56	A	361	ALA	0	-0.028	-0.014	22.501	-0.022	-0.022	0.000	0.000	0.000
57	A	362	ASN	0	-0.058	-0.045	23.449	-0.013	-0.013	0.000	0.000	0.000
58	A	363	ASP	-1	-0.724	-0.806	26.603	-0.123	-0.123	0.000	0.000	0.000
59	A	364	ILE	0	-0.022	0.006	24.592	0.005	0.005	0.000	0.000	0.000
60	A	365	GLU	-1	-0.835	-0.895	24.641	-0.192	-0.192	0.000	0.000	0.000
61	A	366	LYS	1	0.827	0.878	20.275	0.273	0.273	0.000	0.000	0.000
62	A	367	LYS	1	0.879	0.973	20.364	0.193	0.193	0.000	0.000	0.000
63	A	368	ILE	0	0.038	0.022	15.105	0.021	0.021	0.000	0.000	0.000
64	A	370	LYS	1	0.949	0.962	14.907	0.414	0.414	0.000	0.000	0.000
65	A	371	MET	0	-0.011	0.026	20.344	0.020	0.020	0.000	0.000	0.000
66	A	372	GLU	-1	-0.910	-0.952	21.742	-0.140	-0.140	0.000	0.000	0.000
67	A	373	LYS	1	0.939	0.957	20.768	0.134	0.134	0.000	0.000	0.000
68	A	375	PRO	0	0.019	0.023	22.681	0.001	0.001	0.000	0.000	0.000
69	A	376	HIS	0	-0.003	0.000	21.170	0.013	0.013	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:306:TYR)