FMO DATABASE

FMODB ID: LN919

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	OptHSide
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	-414011.04205
FMO2-HF: Nuclear repulsion	384642.788326
FMO2-HF: Total energy	-29368.253724
FMO2-MP2: Total energy	-29450.8323

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.
-5.22	-3.46	0.003	-0.711	-1.053	0.001

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 : -0.018 / q_NPA : -0.025

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	308	GLU	-1	-0.887	-0.946	3.714	-6.308	-4.548	0.003	-0.711	-1.053	0.001
4	A	309	PHE	0	-0.096	-0.052	4.903	0.694	0.694	0.000	0.000	0.000	0.000
5	A	310	GLU	-1	-0.840	-0.918	8.423	-0.683	-0.683	0.000	0.000	0.000	0.000
6	A	311	PRO	0	-0.069	-0.016	10.860	0.030	0.030	0.000	0.000	0.000	0.000
7	A	312	SER	0	0.050	0.017	12.128	-0.005	-0.005	0.000	0.000	0.000	0.000
8	A	313	ASP	-1	-0.735	-0.862	13.568	-0.281	-0.281	0.000	0.000	0.000	0.000
9	A	314	LYS	1	0.924	0.959	14.654	0.159	0.159	0.000	0.000	0.000	0.000
10	A	315	HIS	0	-0.012	-0.010	16.200	0.019	0.019	0.000	0.000	0.000	0.000
11	A	316	ILE	0	0.018	0.009	17.049	0.033	0.033	0.000	0.000	0.000	0.000
12	A	317	LYS	1	0.841	0.905	18.799	0.262	0.262	0.000	0.000	0.000	0.000
13	A	318	GLU	-1	-0.864	-0.910	19.405	-0.145	-0.145	0.000	0.000	0.000	0.000
14	A	319	TYR	0	-0.067	-0.050	22.134	0.024	0.024	0.000	0.000	0.000	0.000
15	A	320	LEU	0	0.012	-0.002	23.675	0.013	0.013	0.000	0.000	0.000	0.000
16	A	321	ASN	0	0.007	0.005	25.745	0.018	0.018	0.000	0.000	0.000	0.000
17	A	322	LYS	1	0.937	0.985	26.581	0.146	0.146	0.000	0.000	0.000	0.000
18	A	323	ILE	0	-0.019	-0.014	27.472	0.009	0.009	0.000	0.000	0.000	0.000
19	A	324	GLN	0	0.006	-0.001	30.149	0.006	0.006	0.000	0.000	0.000	0.000
20	A	325	ASN	0	-0.022	-0.022	31.592	0.004	0.004	0.000	0.000	0.000	0.000
21	A	326	SER	0	-0.005	0.008	32.583	0.004	0.004	0.000	0.000	0.000	0.000
22	A	327	LEU	0	-0.070	-0.017	28.980	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	328	SER	0	0.057	0.024	32.374	0.008	0.008	0.000	0.000	0.000	0.000
24	A	329	THR	0	0.017	0.007	32.223	-0.008	-0.008	0.000	0.000	0.000	0.000
25	A	330	GLU	-1	-0.897	-0.932	33.045	-0.121	-0.121	0.000	0.000	0.000	0.000
26	A	331	TRP	0	-0.064	-0.046	24.792	-0.008	-0.008	0.000	0.000	0.000	0.000
27	A	332	SER	0	0.041	0.029	26.951	0.003	0.003	0.000	0.000	0.000	0.000
28	A	333	PRO	0	0.059	0.027	28.462	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	334	CYS	0	-0.093	0.002	19.135	0.013	0.013	0.000	0.000	0.000	0.000
30	A	335	SER	0	-0.002	0.004	21.087	0.007	0.007	0.000	0.000	0.000	0.000
31	A	336	VAL	0	-0.011	0.002	20.009	0.014	0.014	0.000	0.000	0.000	0.000
32	A	337	THR	0	0.018	-0.007	23.363	0.000	0.000	0.000	0.000	0.000	0.000
33	A	338	CYS	0	-0.003	-0.005	20.459	0.018	0.018	0.000	0.000	0.000	0.000
34	A	339	GLY	0	0.018	0.013	18.882	-0.013	-0.013	0.000	0.000	0.000	0.000
35	A	340	ASN	0	-0.012	-0.023	14.256	0.057	0.057	0.000	0.000	0.000	0.000
36	A	341	GLY	0	0.026	0.017	17.774	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	342	ILE	0	-0.035	-0.027	18.029	-0.033	-0.033	0.000	0.000	0.000	0.000
38	A	343	GLN	0	-0.037	-0.036	20.768	0.022	0.022	0.000	0.000	0.000	0.000
39	A	344	VAL	0	0.017	-0.016	23.243	-0.022	-0.022	0.000	0.000	0.000	0.000
40	A	345	ARG	1	0.850	0.911	25.566	0.173	0.173	0.000	0.000	0.000	0.000
41	A	346	ILE	0	0.021	0.012	28.101	-0.012	-0.012	0.000	0.000	0.000	0.000
42	A	347	LYS	1	0.881	0.935	26.288	0.181	0.181	0.000	0.000	0.000	0.000
43	A	348	PRO	0	0.066	0.024	31.037	0.008	0.008	0.000	0.000	0.000	0.000
44	A	349	GLY	0	-0.037	-0.012	33.921	0.007	0.007	0.000	0.000	0.000	0.000
45	A	350	SER	0	-0.047	-0.063	31.772	0.004	0.004	0.000	0.000	0.000	0.000
46	A	351	ALA	0	-0.025	-0.014	34.375	0.002	0.002	0.000	0.000	0.000	0.000
47	A	352	ASN	0	-0.039	-0.019	36.718	0.004	0.004	0.000	0.000	0.000	0.000
48	A	353	LYS	1	0.834	0.923	32.152	0.107	0.107	0.000	0.000	0.000	0.000
49	A	354	PRO	0	0.049	0.042	36.867	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	355	LYS	1	0.926	0.938	32.897	0.074	0.074	0.000	0.000	0.000	0.000
51	A	356	ASP	-1	-0.974	-0.992	32.754	-0.067	-0.067	0.000	0.000	0.000	0.000
52	A	357	GLU	-1	-0.935	-0.960	32.873	-0.063	-0.063	0.000	0.000	0.000	0.000
53	A	358	LEU	0	-0.056	-0.019	29.668	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	359	ASP	-1	-0.769	-0.895	25.881	-0.159	-0.159	0.000	0.000	0.000	0.000
55	A	360	TYR	0	-0.028	-0.045	18.203	0.004	0.004	0.000	0.000	0.000	0.000
56	A	361	ALA	0	-0.010	0.000	21.896	-0.022	-0.022	0.000	0.000	0.000	0.000
57	A	362	ASN	0	-0.070	-0.049	23.051	-0.016	-0.016	0.000	0.000	0.000	0.000
58	A	363	ASP	-1	-0.711	-0.797	26.472	-0.115	-0.115	0.000	0.000	0.000	0.000
59	A	364	ILE	0	-0.013	0.012	24.702	0.003	0.003	0.000	0.000	0.000	0.000
60	A	365	GLU	-1	-0.845	-0.897	24.649	-0.199	-0.199	0.000	0.000	0.000	0.000
61	A	366	LYS	1	0.832	0.878	20.315	0.273	0.273	0.000	0.000	0.000	0.000
62	A	367	LYS	1	0.897	0.976	20.526	0.198	0.198	0.000	0.000	0.000	0.000
63	A	368	ILE	0	0.043	0.028	15.007	0.028	0.028	0.000	0.000	0.000	0.000
64	A	370	LYS	1	0.950	0.965	15.870	0.422	0.422	0.000	0.000	0.000	0.000
65	A	371	MET	0	-0.014	0.016	20.820	0.023	0.023	0.000	0.000	0.000	0.000
66	A	372	GLU	-1	-0.918	-0.949	22.074	-0.151	-0.151	0.000	0.000	0.000	0.000
67	A	373	LYS	1	0.958	0.963	20.721	0.150	0.150	0.000	0.000	0.000	0.000
68	A	375	PRO	0	0.017	0.017	22.340	0.000	0.000	0.000	0.000	0.000	0.000
69	A	376	HIS	0	0.007	0.006	21.173	0.012	0.012	0.000	0.000	0.000	0.000

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