FMO DATABASE

FMODB ID: YYQV2

Calculation Name: 4JE3-B-Xray322

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4JE3

Chain ID: B

ChEMBL ID:

UniProt ID: P38265

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

Apendix: None

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	79
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-452632.413049
FMO2-HF: Nuclear repulsion	422538.064987
FMO2-HF: Total energy	-30094.348062
FMO2-MP2: Total energy	-30182.556587

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(B:373:ACE )

Summations of interaction energy for fragment #1(B:373:ACE )

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.
0.935	1.533	-0.007	-0.275	-0.316	0.001

Interaction energy analysis for fragmet #1(B:373:ACE )

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 : -0.001

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	B	375	ARG	1	0.904	0.944	3.802	1.252	1.850	-0.007	-0.275	-0.316	0.001
4	B	376	TYR	0	-0.085	-0.150	7.137	0.241	0.241	0.000	0.000	0.000	0.000
5	B	377	SER	0	-0.049	0.017	8.245	0.116	0.116	0.000	0.000	0.000	0.000
6	B	378	SER	0	0.037	0.010	9.916	0.123	0.123	0.000	0.000	0.000	0.000
7	B	379	LEU	0	-0.036	-0.021	13.516	-0.017	-0.017	0.000	0.000	0.000	0.000
8	B	380	VAL	0	-0.012	-0.016	15.519	0.012	0.012	0.000	0.000	0.000	0.000
9	B	381	PRO	0	-0.005	0.012	13.570	0.028	0.028	0.000	0.000	0.000	0.000
10	B	382	ILE	0	0.001	0.016	16.119	0.048	0.048	0.000	0.000	0.000	0.000
11	B	383	GLU	-1	-0.890	-0.938	17.260	-0.281	-0.281	0.000	0.000	0.000	0.000
12	B	384	LYS	1	0.932	0.941	19.322	0.152	0.152	0.000	0.000	0.000	0.000
13	B	385	VAL	0	0.005	0.024	22.606	0.004	0.004	0.000	0.000	0.000	0.000
14	B	386	GLY	0	-0.042	-0.035	24.772	0.004	0.004	0.000	0.000	0.000	0.000
15	B	387	PHE	0	0.069	0.033	24.779	0.004	0.004	0.000	0.000	0.000	0.000
16	B	388	THR	0	-0.060	-0.027	29.983	0.006	0.006	0.000	0.000	0.000	0.000
17	B	389	LEU	0	0.013	0.018	32.864	0.000	0.000	0.000	0.000	0.000	0.000
18	B	390	LYS	1	0.921	0.947	34.655	0.062	0.062	0.000	0.000	0.000	0.000
19	B	391	ASN	0	0.053	0.026	36.489	-0.001	-0.001	0.000	0.000	0.000	0.000
20	B	392	GLU	-1	-0.891	-0.944	40.221	-0.040	-0.040	0.000	0.000	0.000	0.000
21	B	393	ILE	0	-0.026	-0.024	40.713	0.000	0.000	0.000	0.000	0.000	0.000
22	B	394	ASN	0	-0.024	-0.014	45.060	0.001	0.001	0.000	0.000	0.000	0.000
23	B	395	SER	0	0.025	0.019	48.292	0.002	0.002	0.000	0.000	0.000	0.000
24	B	396	ARG	1	0.951	0.987	45.847	0.037	0.037	0.000	0.000	0.000	0.000
25	B	397	ILE	0	0.012	0.010	42.380	-0.002	-0.002	0.000	0.000	0.000	0.000
26	B	398	ILE	0	-0.031	-0.008	39.109	0.001	0.001	0.000	0.000	0.000	0.000
27	B	399	THR	0	-0.012	-0.023	37.401	-0.003	-0.003	0.000	0.000	0.000	0.000
28	B	400	ILE	0	0.016	0.017	32.419	0.002	0.002	0.000	0.000	0.000	0.000
29	B	401	LYS	1	0.915	0.946	32.601	0.070	0.070	0.000	0.000	0.000	0.000
30	B	402	LEU	0	0.023	0.023	27.237	0.002	0.002	0.000	0.000	0.000	0.000
31	B	403	LYS	1	0.924	0.951	26.701	0.094	0.094	0.000	0.000	0.000	0.000
32	B	404	PHE	0	0.026	0.024	21.141	0.003	0.003	0.000	0.000	0.000	0.000
33	B	405	ASN	0	-0.016	-0.029	21.040	0.004	0.004	0.000	0.000	0.000	0.000
34	B	406	GLY	0	0.002	0.001	16.932	0.000	0.000	0.000	0.000	0.000	0.000
35	B	407	ASN	0	0.039	0.021	12.381	0.052	0.052	0.000	0.000	0.000	0.000
36	B	408	ASP	-1	-0.789	-0.902	12.524	-0.620	-0.620	0.000	0.000	0.000	0.000
37	B	409	ILE	0	-0.044	-0.011	14.507	-0.015	-0.015	0.000	0.000	0.000	0.000
38	B	410	PHE	0	0.003	-0.001	16.901	0.012	0.012	0.000	0.000	0.000	0.000
39	B	411	GLY	0	0.103	0.072	12.883	0.015	0.015	0.000	0.000	0.000	0.000
40	B	412	GLY	0	-0.005	-0.006	13.281	-0.003	-0.003	0.000	0.000	0.000	0.000
41	B	413	LEU	0	-0.038	-0.036	14.363	0.040	0.040	0.000	0.000	0.000	0.000
42	B	414	HIS	0	0.002	0.020	13.917	-0.012	-0.012	0.000	0.000	0.000	0.000
43	B	415	GLU	-1	-0.857	-0.936	10.845	-0.366	-0.366	0.000	0.000	0.000	0.000
44	B	416	LEU	0	-0.081	-0.045	13.778	0.059	0.059	0.000	0.000	0.000	0.000
45	B	417	CYS	0	-0.053	-0.025	17.094	0.038	0.038	0.000	0.000	0.000	0.000
46	B	418	ASP	-1	-0.738	-0.754	14.177	-0.216	-0.216	0.000	0.000	0.000	0.000
47	B	419	LYS	1	0.821	0.909	12.509	0.191	0.191	0.000	0.000	0.000	0.000
48	B	420	ASN	0	-0.026	-0.012	17.225	0.022	0.022	0.000	0.000	0.000	0.000
49	B	421	LEU	0	-0.041	-0.010	18.192	0.010	0.010	0.000	0.000	0.000	0.000
50	B	422	ILE	0	-0.027	-0.014	20.921	0.005	0.005	0.000	0.000	0.000	0.000
51	B	423	ASN	0	0.020	-0.003	22.441	-0.004	-0.004	0.000	0.000	0.000	0.000
52	B	424	ILE	0	0.065	0.020	21.055	0.000	0.000	0.000	0.000	0.000	0.000
53	B	425	ASP	-1	-0.865	-0.920	24.118	-0.078	-0.078	0.000	0.000	0.000	0.000
54	B	426	LYS	1	0.827	0.901	27.377	0.066	0.066	0.000	0.000	0.000	0.000
55	B	427	VAL	0	-0.042	-0.006	23.401	0.001	0.001	0.000	0.000	0.000	0.000
56	B	428	PRO	0	-0.026	0.004	26.635	0.000	0.000	0.000	0.000	0.000	0.000
57	B	429	GLY	0	0.112	0.038	26.870	-0.010	-0.010	0.000	0.000	0.000	0.000
58	B	430	TRP	0	0.036	-0.005	26.291	-0.012	-0.012	0.000	0.000	0.000	0.000
59	B	431	LEU	0	-0.053	-0.015	23.871	-0.007	-0.007	0.000	0.000	0.000	0.000
60	B	432	ALA	0	0.012	0.001	22.253	-0.016	-0.016	0.000	0.000	0.000	0.000
61	B	433	GLY	0	0.029	0.005	21.721	-0.019	-0.019	0.000	0.000	0.000	0.000
62	B	434	GLU	-1	-0.950	-0.961	23.129	-0.108	-0.108	0.000	0.000	0.000	0.000
63	B	435	ASN	0	-0.079	-0.034	25.238	0.007	0.007	0.000	0.000	0.000	0.000
64	B	436	GLY	0	0.089	0.029	22.802	-0.002	-0.002	0.000	0.000	0.000	0.000
65	B	437	SER	0	-0.083	-0.045	23.061	0.004	0.004	0.000	0.000	0.000	0.000
66	B	438	PHE	0	-0.025	-0.012	23.867	0.010	0.010	0.000	0.000	0.000	0.000
67	B	439	SER	0	0.037	0.015	27.353	-0.005	-0.005	0.000	0.000	0.000	0.000
68	B	440	GLY	0	0.028	0.012	28.784	0.005	0.005	0.000	0.000	0.000	0.000
69	B	441	THR	0	-0.069	-0.024	31.979	-0.001	-0.001	0.000	0.000	0.000	0.000
70	B	442	ILE	0	0.014	0.014	30.719	0.000	0.000	0.000	0.000	0.000	0.000
71	B	443	MET	0	-0.008	-0.015	35.053	0.004	0.004	0.000	0.000	0.000	0.000
72	B	444	ASN	0	0.019	0.007	38.761	0.000	0.000	0.000	0.000	0.000	0.000
73	B	445	GLY	0	-0.024	-0.016	35.825	0.001	0.001	0.000	0.000	0.000	0.000
74	B	446	ASP	-1	-0.915	-0.939	35.845	-0.071	-0.071	0.000	0.000	0.000	0.000
75	B	447	PHE	0	-0.002	-0.010	29.831	-0.001	-0.001	0.000	0.000	0.000	0.000
76	B	448	GLN	0	0.016	0.008	34.249	0.003	0.003	0.000	0.000	0.000	0.000
77	B	449	ARG	1	0.904	0.947	29.391	0.112	0.112	0.000	0.000	0.000	0.000
78	B	450	GLU	-1	-0.911	-0.946	32.429	-0.078	-0.078	0.000	0.000	0.000	0.000
79	B	451	NME	0	-0.068	-0.028	33.576	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:373:ACE )