FMO DATABASE

FMODB ID: 3J86L

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

Total energy (hartree)

FMO2-HF: Electronic energy	-413515.988875
FMO2-HF: Nuclear repulsion	384148.022758
FMO2-HF: Total energy	-29367.966117
FMO2-MP2: Total energy	-29450.528226

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.
-5.544	-3.787	0.002	-0.705	-1.054	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 : -0.013 / 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	-0.900	-0.955	3.720	-6.574	-4.817	0.002	-0.705	-1.054	0.001
4	A	309	PHE	0	-0.087	-0.042	5.192	0.727	0.727	0.000	0.000	0.000	0.000
5	A	310	GLU	-1	-0.845	-0.916	8.428	-0.854	-0.854	0.000	0.000	0.000	0.000
6	A	311	PRO	0	-0.079	-0.027	10.887	0.014	0.014	0.000	0.000	0.000	0.000
7	A	312	SER	0	0.057	0.025	12.102	-0.011	-0.011	0.000	0.000	0.000	0.000
8	A	313	ASP	-1	-0.788	-0.904	13.498	-0.443	-0.443	0.000	0.000	0.000	0.000
9	A	314	LYS	1	0.901	0.945	14.741	0.296	0.296	0.000	0.000	0.000	0.000
10	A	315	HIS	0	0.015	0.015	16.023	0.039	0.039	0.000	0.000	0.000	0.000
11	A	316	ILE	0	0.031	0.013	17.193	0.046	0.046	0.000	0.000	0.000	0.000
12	A	317	LYS	1	0.928	0.960	19.425	0.310	0.310	0.000	0.000	0.000	0.000
13	A	318	GLU	-1	-0.907	-0.939	19.739	-0.209	-0.209	0.000	0.000	0.000	0.000
14	A	319	TYR	0	-0.062	-0.043	22.047	0.030	0.030	0.000	0.000	0.000	0.000
15	A	320	LEU	0	0.013	-0.004	23.469	0.018	0.018	0.000	0.000	0.000	0.000
16	A	321	ASN	0	0.004	0.005	25.656	0.024	0.024	0.000	0.000	0.000	0.000
17	A	322	LYS	1	0.948	0.984	26.699	0.183	0.183	0.000	0.000	0.000	0.000
18	A	323	ILE	0	-0.024	-0.013	27.431	0.013	0.013	0.000	0.000	0.000	0.000
19	A	324	GLN	0	-0.021	-0.018	30.070	0.010	0.010	0.000	0.000	0.000	0.000
20	A	325	ASN	0	-0.020	-0.020	31.515	0.006	0.006	0.000	0.000	0.000	0.000
21	A	326	SER	0	-0.059	-0.011	32.662	0.004	0.004	0.000	0.000	0.000	0.000
22	A	327	LEU	0	-0.039	-0.003	28.942	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	328	SER	0	0.064	0.029	32.350	0.010	0.010	0.000	0.000	0.000	0.000
24	A	329	THR	0	0.028	0.015	32.255	-0.009	-0.009	0.000	0.000	0.000	0.000
25	A	330	GLU	-1	-0.943	-0.960	33.076	-0.141	-0.141	0.000	0.000	0.000	0.000
26	A	331	TRP	0	-0.095	-0.052	24.992	-0.009	-0.009	0.000	0.000	0.000	0.000
27	A	332	SER	0	0.042	0.027	26.984	0.004	0.004	0.000	0.000	0.000	0.000
28	A	333	PRO	0	0.053	0.021	28.489	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	334	CYS	0	-0.087	-0.001	19.160	0.015	0.015	0.000	0.000	0.000	0.000
30	A	335	SER	0	0.009	0.010	21.242	0.006	0.006	0.000	0.000	0.000	0.000
31	A	336	VAL	0	-0.029	-0.005	20.001	0.012	0.012	0.000	0.000	0.000	0.000
32	A	337	THR	0	0.012	-0.011	23.361	0.002	0.002	0.000	0.000	0.000	0.000
33	A	338	CYS	0	-0.004	-0.005	20.482	0.020	0.020	0.000	0.000	0.000	0.000
34	A	339	GLY	0	0.015	0.011	18.874	-0.018	-0.018	0.000	0.000	0.000	0.000
35	A	340	ASN	0	0.001	-0.016	14.669	0.068	0.068	0.000	0.000	0.000	0.000
36	A	341	GLY	0	0.010	0.007	17.773	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	342	ILE	0	-0.019	-0.018	18.113	-0.037	-0.037	0.000	0.000	0.000	0.000
38	A	343	GLN	0	-0.034	-0.027	20.795	0.023	0.023	0.000	0.000	0.000	0.000
39	A	344	VAL	0	0.018	-0.013	23.299	-0.026	-0.026	0.000	0.000	0.000	0.000
40	A	345	ARG	1	0.906	0.962	25.598	0.207	0.207	0.000	0.000	0.000	0.000
41	A	346	ILE	0	0.024	0.014	28.128	-0.015	-0.015	0.000	0.000	0.000	0.000
42	A	347	LYS	1	0.893	0.946	25.890	0.226	0.226	0.000	0.000	0.000	0.000
43	A	348	PRO	0	0.080	0.029	31.072	0.009	0.009	0.000	0.000	0.000	0.000
44	A	349	GLY	0	-0.033	-0.010	33.963	0.008	0.008	0.000	0.000	0.000	0.000
45	A	350	SER	0	-0.067	-0.081	31.721	0.005	0.005	0.000	0.000	0.000	0.000
46	A	351	ALA	0	-0.025	-0.013	34.356	0.002	0.002	0.000	0.000	0.000	0.000
47	A	352	ASN	0	-0.024	-0.010	36.691	0.005	0.005	0.000	0.000	0.000	0.000
48	A	353	LYS	1	0.851	0.937	32.291	0.134	0.134	0.000	0.000	0.000	0.000
49	A	354	PRO	0	0.071	0.052	36.615	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	355	LYS	1	0.975	0.961	33.055	0.100	0.100	0.000	0.000	0.000	0.000
51	A	356	ASP	-1	-1.002	-1.005	32.691	-0.095	-0.095	0.000	0.000	0.000	0.000
52	A	357	GLU	-1	-0.930	-0.952	32.803	-0.088	-0.088	0.000	0.000	0.000	0.000
53	A	358	LEU	0	-0.063	-0.022	29.545	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	359	ASP	-1	-0.821	-0.925	25.949	-0.200	-0.200	0.000	0.000	0.000	0.000
55	A	360	TYR	0	-0.044	-0.056	18.144	0.008	0.008	0.000	0.000	0.000	0.000
56	A	361	ALA	0	-0.007	0.000	21.858	-0.024	-0.024	0.000	0.000	0.000	0.000
57	A	362	ASN	0	-0.042	-0.028	23.032	-0.022	-0.022	0.000	0.000	0.000	0.000
58	A	363	ASP	-1	-0.720	-0.804	26.462	-0.146	-0.146	0.000	0.000	0.000	0.000
59	A	364	ILE	0	-0.021	0.008	24.606	0.005	0.005	0.000	0.000	0.000	0.000
60	A	365	GLU	-1	-0.896	-0.958	24.648	-0.237	-0.237	0.000	0.000	0.000	0.000
61	A	366	LYS	1	0.860	0.904	20.400	0.333	0.333	0.000	0.000	0.000	0.000
62	A	367	LYS	1	0.911	0.975	20.567	0.237	0.237	0.000	0.000	0.000	0.000
63	A	368	ILE	0	0.057	0.034	14.822	0.028	0.028	0.000	0.000	0.000	0.000
64	A	370	LYS	1	0.942	0.961	16.428	0.438	0.438	0.000	0.000	0.000	0.000
65	A	371	MET	0	-0.018	0.015	20.824	0.027	0.027	0.000	0.000	0.000	0.000
66	A	372	GLU	-1	-0.918	-0.950	22.071	-0.168	-0.168	0.000	0.000	0.000	0.000
67	A	373	LYS	1	0.973	0.969	21.084	0.148	0.148	0.000	0.000	0.000	0.000
68	A	375	PRO	0	0.013	0.015	22.326	0.003	0.003	0.000	0.000	0.000	0.000
69	A	376	HIS	0	0.009	0.006	21.427	0.007	0.007	0.000	0.000	0.000	0.000

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