FMO DATABASE

FMODB ID: ZV6QN

Calculation Name: 3JV0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3JV0

Chain ID: A

ChEMBL ID:

UniProt ID: Q04863

Base Structure: X-ray

Registration Date: 2023-09-21

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	101
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-608809.586683
FMO2-HF: Nuclear repulsion	568122.908917
FMO2-HF: Total energy	-40686.677766
FMO2-MP2: Total energy	-40803.662184

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:278:THR)

Summations of interaction energy for fragment #1(A:278:THR)

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.
-4.291	-0.618	0.023	-1.664	-2.032	0.004

Interaction energy analysis for fragmet #1(A:278:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.048 / q_NPA : 0.015

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	280	GLU	-1	-0.913	-0.944	3.243	-4.419	-0.983	0.024	-1.639	-1.821	0.004
4	A	281	LEU	0	0.010	0.020	4.479	0.814	1.051	-0.001	-0.025	-0.211	0.000
5	A	282	ARG	1	0.824	0.878	6.418	0.529	0.529	0.000	0.000	0.000	0.000
6	A	283	ILE	0	0.017	0.002	8.791	0.174	0.174	0.000	0.000	0.000	0.000
7	A	284	CYS	0	-0.068	-0.036	12.170	0.084	0.084	0.000	0.000	0.000	0.000
8	A	285	ARG	1	0.908	0.946	14.965	0.254	0.254	0.000	0.000	0.000	0.000
9	A	286	ILE	0	0.030	0.014	16.509	-0.052	-0.052	0.000	0.000	0.000	0.000
10	A	287	ASP	-1	-0.787	-0.902	19.688	-0.203	-0.203	0.000	0.000	0.000	0.000
11	A	288	LYS	1	0.824	0.917	22.909	0.213	0.213	0.000	0.000	0.000	0.000
12	A	289	GLU	-1	-0.953	-0.975	22.424	-0.183	-0.183	0.000	0.000	0.000	0.000
13	A	290	SER	0	-0.099	-0.052	23.738	0.005	0.005	0.000	0.000	0.000	0.000
14	A	291	GLY	0	0.111	0.058	25.955	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	292	PRO	0	-0.052	-0.002	27.932	0.006	0.006	0.000	0.000	0.000	0.000
16	A	293	CYS	0	0.007	-0.020	28.310	-0.008	-0.008	0.000	0.000	0.000	0.000
17	A	294	THR	0	-0.051	-0.026	29.014	0.000	0.000	0.000	0.000	0.000	0.000
18	A	295	GLY	0	-0.008	0.011	26.709	-0.007	-0.007	0.000	0.000	0.000	0.000
19	A	296	GLY	0	-0.007	-0.018	26.709	0.014	0.014	0.000	0.000	0.000	0.000
20	A	297	GLU	-1	-0.878	-0.933	27.090	-0.169	-0.169	0.000	0.000	0.000	0.000
21	A	298	GLU	-1	-0.946	-0.961	25.969	-0.198	-0.198	0.000	0.000	0.000	0.000
22	A	299	LEU	0	-0.036	-0.028	22.291	0.008	0.008	0.000	0.000	0.000	0.000
23	A	300	TYR	0	-0.038	-0.016	21.025	-0.014	-0.014	0.000	0.000	0.000	0.000
24	A	301	LEU	0	-0.006	-0.005	14.668	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	302	LEU	0	-0.026	-0.004	17.216	0.016	0.016	0.000	0.000	0.000	0.000
26	A	303	CYS	0	-0.023	-0.022	11.824	-0.033	-0.033	0.000	0.000	0.000	0.000
27	A	304	ASP	-1	-0.778	-0.838	10.132	-0.294	-0.294	0.000	0.000	0.000	0.000
28	A	305	LYS	1	0.847	0.912	10.500	0.203	0.203	0.000	0.000	0.000	0.000
29	A	306	VAL	0	0.082	0.048	9.562	-0.137	-0.137	0.000	0.000	0.000	0.000
30	A	307	GLN	0	-0.045	-0.028	9.627	0.282	0.282	0.000	0.000	0.000	0.000
31	A	308	LYS	1	0.895	0.932	11.762	0.209	0.209	0.000	0.000	0.000	0.000
32	A	309	GLU	-1	-0.865	-0.923	13.680	-0.340	-0.340	0.000	0.000	0.000	0.000
33	A	310	ASP	-1	-0.974	-0.985	8.360	-1.039	-1.039	0.000	0.000	0.000	0.000
34	A	311	ILE	0	0.018	0.015	9.820	-0.199	-0.199	0.000	0.000	0.000	0.000
35	A	312	SER	0	-0.067	-0.034	11.684	0.160	0.160	0.000	0.000	0.000	0.000
36	A	313	VAL	0	0.057	0.033	12.250	-0.123	-0.123	0.000	0.000	0.000	0.000
37	A	314	ARG	1	0.861	0.918	11.556	0.677	0.677	0.000	0.000	0.000	0.000
38	A	315	PHE	0	0.038	0.023	14.579	-0.015	-0.015	0.000	0.000	0.000	0.000
39	A	316	SER	0	-0.028	-0.030	15.539	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	317	THR	0	0.015	0.004	17.861	0.015	0.015	0.000	0.000	0.000	0.000
41	A	318	ALA	0	0.012	-0.003	18.495	-0.015	-0.015	0.000	0.000	0.000	0.000
42	A	319	SER	0	-0.032	-0.013	19.781	0.011	0.011	0.000	0.000	0.000	0.000
43	A	320	TRP	0	-0.015	-0.001	20.558	0.004	0.004	0.000	0.000	0.000	0.000
44	A	321	GLU	-1	-0.842	-0.916	15.324	-0.506	-0.506	0.000	0.000	0.000	0.000
45	A	322	GLY	0	0.008	0.016	18.527	0.035	0.035	0.000	0.000	0.000	0.000
46	A	323	ARG	1	0.928	0.954	15.505	0.462	0.462	0.000	0.000	0.000	0.000
47	A	324	GLY	0	0.004	0.016	17.930	0.043	0.043	0.000	0.000	0.000	0.000
48	A	325	ASP	-1	-0.960	-0.983	19.271	-0.303	-0.303	0.000	0.000	0.000	0.000
49	A	326	PHE	0	-0.020	-0.004	15.590	-0.009	-0.009	0.000	0.000	0.000	0.000
50	A	327	SER	0	-0.031	-0.036	20.917	-0.011	-0.011	0.000	0.000	0.000	0.000
51	A	328	GLN	0	0.037	-0.010	18.290	0.002	0.002	0.000	0.000	0.000	0.000
52	A	329	ALA	0	-0.036	-0.015	19.882	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	330	ASP	-1	-0.791	-0.859	21.417	-0.236	-0.236	0.000	0.000	0.000	0.000
54	A	331	VAL	0	-0.064	-0.022	15.434	-0.023	-0.023	0.000	0.000	0.000	0.000
55	A	332	HIS	0	-0.002	0.006	18.720	0.026	0.026	0.000	0.000	0.000	0.000
56	A	333	ARG	1	0.913	0.951	18.222	0.110	0.110	0.000	0.000	0.000	0.000
57	A	334	GLN	0	0.030	0.014	20.192	0.027	0.027	0.000	0.000	0.000	0.000
58	A	335	PHE	0	0.001	0.005	21.322	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	336	ALA	0	0.009	-0.001	21.933	-0.010	-0.010	0.000	0.000	0.000	0.000
60	A	337	ILE	0	0.006	0.000	23.931	0.014	0.014	0.000	0.000	0.000	0.000
61	A	338	VAL	0	-0.010	0.001	22.797	-0.009	-0.009	0.000	0.000	0.000	0.000
62	A	339	PHE	0	-0.013	-0.008	26.122	0.013	0.013	0.000	0.000	0.000	0.000
63	A	340	LYS	1	0.942	0.965	29.658	0.018	0.018	0.000	0.000	0.000	0.000
64	A	341	THR	0	0.036	0.026	32.352	0.002	0.002	0.000	0.000	0.000	0.000
65	A	342	PRO	0	0.016	0.017	35.329	0.003	0.003	0.000	0.000	0.000	0.000
66	A	343	PRO	0	-0.001	0.001	38.595	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	344	TYR	0	-0.016	-0.027	41.472	0.000	0.000	0.000	0.000	0.000	0.000
68	A	345	GLU	-1	-0.927	-0.947	44.026	-0.021	-0.021	0.000	0.000	0.000	0.000
69	A	346	ASP	-1	-0.858	-0.929	47.544	-0.020	-0.020	0.000	0.000	0.000	0.000
70	A	347	LEU	0	-0.059	-0.036	44.247	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	348	GLU	-1	-0.878	-0.929	47.314	-0.020	-0.020	0.000	0.000	0.000	0.000
72	A	349	ILE	0	-0.031	0.004	45.080	0.000	0.000	0.000	0.000	0.000	0.000
73	A	350	SER	0	-0.010	-0.039	48.897	0.000	0.000	0.000	0.000	0.000	0.000
74	A	351	GLU	-1	-0.902	-0.927	48.725	-0.033	-0.033	0.000	0.000	0.000	0.000
75	A	352	PRO	0	-0.031	-0.033	43.624	0.000	0.000	0.000	0.000	0.000	0.000
76	A	353	VAL	0	-0.003	0.015	44.327	0.001	0.001	0.000	0.000	0.000	0.000
77	A	354	THR	0	-0.006	-0.014	42.281	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	355	VAL	0	-0.043	-0.014	40.268	0.003	0.003	0.000	0.000	0.000	0.000
79	A	356	ASN	0	0.003	-0.002	40.441	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	357	VAL	0	-0.018	-0.005	34.219	0.003	0.003	0.000	0.000	0.000	0.000
81	A	358	GLN	0	0.011	-0.011	36.189	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	359	LEU	0	-0.024	-0.004	31.159	0.004	0.004	0.000	0.000	0.000	0.000
83	A	360	GLN	0	0.046	0.006	35.290	0.003	0.003	0.000	0.000	0.000	0.000
84	A	361	ARG	1	0.701	0.812	36.206	0.029	0.029	0.000	0.000	0.000	0.000
85	A	362	LEU	0	0.003	-0.016	35.678	0.002	0.002	0.000	0.000	0.000	0.000
86	A	363	THR	0	-0.054	-0.041	38.391	0.002	0.002	0.000	0.000	0.000	0.000
87	A	364	ASP	-1	-0.830	-0.883	40.497	-0.019	-0.019	0.000	0.000	0.000	0.000
88	A	365	GLY	0	0.031	0.028	41.669	0.000	0.000	0.000	0.000	0.000	0.000
89	A	366	GLU	-1	-0.834	-0.871	39.487	-0.036	-0.036	0.000	0.000	0.000	0.000
90	A	367	CYS	0	-0.052	-0.037	39.034	0.000	0.000	0.000	0.000	0.000	0.000
91	A	368	SER	0	-0.045	-0.020	35.647	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	369	GLU	-1	-0.862	-0.940	37.733	-0.051	-0.051	0.000	0.000	0.000	0.000
93	A	370	PRO	0	-0.073	-0.010	37.579	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	371	LEU	0	0.021	0.008	32.804	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	372	PRO	0	-0.011	-0.003	36.788	0.005	0.005	0.000	0.000	0.000	0.000
96	A	373	PHE	0	0.002	-0.003	34.849	-0.006	-0.006	0.000	0.000	0.000	0.000
97	A	374	THR	0	-0.018	-0.018	37.824	0.003	0.003	0.000	0.000	0.000	0.000
98	A	375	TYR	0	-0.021	-0.005	39.194	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	376	LEU	0	-0.010	-0.020	39.159	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	377	PRO	0	0.028	0.031	42.724	0.002	0.002	0.000	0.000	0.000	0.000
101	A	378	ARG	1	0.785	0.883	43.870	0.019	0.019	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:278:THR)