FMO DATABASE

FMODB ID: 2NJ1R

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

Total energy (hartree)

FMO2-HF: Electronic energy	-610986.144201
FMO2-HF: Nuclear repulsion	570300.855535
FMO2-HF: Total energy	-40685.288666
FMO2-MP2: Total energy	-40802.430763

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.
-6.273	-2.222	0.102	-1.576	-2.578	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 : 0.054 / q_NPA : 0.016

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	-0.921	-0.956	2.925	-6.333	-2.585	0.103	-1.533	-2.318	0.004
4	A	281	LEU	0	0.011	0.038	4.171	0.987	1.290	-0.001	-0.043	-0.260	0.000
5	A	282	ARG	1	0.933	0.946	6.106	0.760	0.760	0.000	0.000	0.000	0.000
6	A	283	ILE	0	0.034	0.021	8.994	0.163	0.163	0.000	0.000	0.000	0.000
7	A	284	CYS	0	-0.116	-0.055	12.420	0.051	0.051	0.000	0.000	0.000	0.000
8	A	285	ARG	1	0.928	0.957	15.085	0.305	0.305	0.000	0.000	0.000	0.000
9	A	286	ILE	0	0.044	0.021	16.619	-0.048	-0.048	0.000	0.000	0.000	0.000
10	A	287	ASP	-1	-0.827	-0.909	19.969	-0.232	-0.232	0.000	0.000	0.000	0.000
11	A	288	LYS	1	0.917	0.967	23.421	0.209	0.209	0.000	0.000	0.000	0.000
12	A	289	GLU	-1	-0.941	-0.979	22.528	-0.218	-0.218	0.000	0.000	0.000	0.000
13	A	290	SER	0	-0.101	-0.059	23.978	0.009	0.009	0.000	0.000	0.000	0.000
14	A	291	GLY	0	0.103	0.062	26.347	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	292	PRO	0	-0.082	-0.022	28.227	0.005	0.005	0.000	0.000	0.000	0.000
16	A	293	CYS	0	0.000	-0.011	28.095	-0.009	-0.009	0.000	0.000	0.000	0.000
17	A	294	THR	0	-0.014	-0.016	28.867	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	295	GLY	0	-0.023	0.000	26.811	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	296	GLY	0	-0.019	-0.024	26.540	0.012	0.012	0.000	0.000	0.000	0.000
20	A	297	GLU	-1	-0.906	-0.956	26.764	-0.186	-0.186	0.000	0.000	0.000	0.000
21	A	298	GLU	-1	-0.943	-0.961	25.353	-0.222	-0.222	0.000	0.000	0.000	0.000
22	A	299	LEU	0	-0.045	-0.022	21.810	0.007	0.007	0.000	0.000	0.000	0.000
23	A	300	TYR	0	-0.012	-0.005	20.702	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	301	LEU	0	0.004	0.000	14.203	0.004	0.004	0.000	0.000	0.000	0.000
25	A	302	LEU	0	-0.058	-0.019	17.190	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	303	CYS	0	0.007	-0.015	11.832	-0.037	-0.037	0.000	0.000	0.000	0.000
27	A	304	ASP	-1	-0.866	-0.917	10.016	-0.564	-0.564	0.000	0.000	0.000	0.000
28	A	305	LYS	1	0.907	0.941	10.680	0.249	0.249	0.000	0.000	0.000	0.000
29	A	306	VAL	0	0.054	0.026	9.367	-0.231	-0.231	0.000	0.000	0.000	0.000
30	A	307	GLN	0	-0.006	0.005	9.010	0.227	0.227	0.000	0.000	0.000	0.000
31	A	308	LYS	1	0.977	1.004	11.435	0.249	0.249	0.000	0.000	0.000	0.000
32	A	309	GLU	-1	-0.979	-1.002	13.272	-0.385	-0.385	0.000	0.000	0.000	0.000
33	A	310	ASP	-1	-1.015	-1.021	8.627	-0.958	-0.958	0.000	0.000	0.000	0.000
34	A	311	ILE	0	0.024	0.019	9.432	-0.228	-0.228	0.000	0.000	0.000	0.000
35	A	312	SER	0	-0.060	-0.024	11.540	0.195	0.195	0.000	0.000	0.000	0.000
36	A	313	VAL	0	0.078	0.038	12.071	-0.132	-0.132	0.000	0.000	0.000	0.000
37	A	314	ARG	1	0.848	0.901	11.978	0.568	0.568	0.000	0.000	0.000	0.000
38	A	315	PHE	0	0.010	0.007	14.534	-0.013	-0.013	0.000	0.000	0.000	0.000
39	A	316	SER	0	-0.047	-0.036	15.766	0.008	0.008	0.000	0.000	0.000	0.000
40	A	317	THR	0	0.028	0.015	18.026	0.007	0.007	0.000	0.000	0.000	0.000
41	A	318	ALA	0	0.006	-0.004	18.946	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	319	SER	0	-0.026	-0.016	19.975	0.004	0.004	0.000	0.000	0.000	0.000
43	A	320	TRP	0	0.006	0.018	21.078	0.003	0.003	0.000	0.000	0.000	0.000
44	A	321	GLU	-1	-0.831	-0.914	15.238	-0.406	-0.406	0.000	0.000	0.000	0.000
45	A	322	GLY	0	-0.002	0.007	18.473	0.029	0.029	0.000	0.000	0.000	0.000
46	A	323	ARG	1	0.940	0.964	15.806	0.408	0.408	0.000	0.000	0.000	0.000
47	A	324	GLY	0	-0.012	0.015	17.698	0.038	0.038	0.000	0.000	0.000	0.000
48	A	325	ASP	-1	-0.953	-0.982	19.106	-0.290	-0.290	0.000	0.000	0.000	0.000
49	A	326	PHE	0	-0.017	0.000	15.184	-0.017	-0.017	0.000	0.000	0.000	0.000
50	A	327	SER	0	-0.050	-0.045	20.498	-0.011	-0.011	0.000	0.000	0.000	0.000
51	A	328	GLN	0	0.013	-0.030	17.692	0.009	0.009	0.000	0.000	0.000	0.000
52	A	329	ALA	0	-0.020	-0.009	19.740	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	330	ASP	-1	-0.822	-0.867	21.200	-0.256	-0.256	0.000	0.000	0.000	0.000
54	A	331	VAL	0	-0.045	-0.008	15.774	-0.033	-0.033	0.000	0.000	0.000	0.000
55	A	332	HIS	0	0.029	0.014	19.030	0.036	0.036	0.000	0.000	0.000	0.000
56	A	333	ARG	1	0.903	0.948	18.059	0.150	0.150	0.000	0.000	0.000	0.000
57	A	334	GLN	0	0.015	0.003	20.007	0.030	0.030	0.000	0.000	0.000	0.000
58	A	335	PHE	0	-0.001	0.007	21.132	-0.008	-0.008	0.000	0.000	0.000	0.000
59	A	336	ALA	0	0.008	-0.007	21.845	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	337	ILE	0	0.010	0.005	23.834	0.010	0.010	0.000	0.000	0.000	0.000
61	A	338	VAL	0	-0.004	0.005	22.876	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	339	PHE	0	-0.019	-0.016	26.108	0.013	0.013	0.000	0.000	0.000	0.000
63	A	340	LYS	1	0.954	0.975	29.611	0.045	0.045	0.000	0.000	0.000	0.000
64	A	341	THR	0	0.024	0.015	32.202	0.002	0.002	0.000	0.000	0.000	0.000
65	A	342	PRO	0	0.007	0.018	35.143	0.003	0.003	0.000	0.000	0.000	0.000
66	A	343	PRO	0	0.000	0.008	38.470	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	344	TYR	0	0.049	0.015	41.153	0.001	0.001	0.000	0.000	0.000	0.000
68	A	345	GLU	-1	-0.970	-0.982	43.758	-0.030	-0.030	0.000	0.000	0.000	0.000
69	A	346	ASP	-1	-0.850	-0.906	47.274	-0.030	-0.030	0.000	0.000	0.000	0.000
70	A	347	LEU	0	-0.049	-0.049	44.006	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	348	GLU	-1	-0.925	-0.974	47.258	-0.030	-0.030	0.000	0.000	0.000	0.000
72	A	349	ILE	0	-0.054	-0.002	45.169	0.000	0.000	0.000	0.000	0.000	0.000
73	A	350	SER	0	0.021	-0.010	48.727	0.000	0.000	0.000	0.000	0.000	0.000
74	A	351	GLU	-1	-0.935	-0.975	48.904	-0.044	-0.044	0.000	0.000	0.000	0.000
75	A	352	PRO	0	-0.017	-0.017	43.808	0.000	0.000	0.000	0.000	0.000	0.000
76	A	353	VAL	0	0.012	0.017	44.404	0.001	0.001	0.000	0.000	0.000	0.000
77	A	354	THR	0	-0.056	-0.044	42.200	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	355	VAL	0	0.000	0.012	40.498	0.003	0.003	0.000	0.000	0.000	0.000
79	A	356	ASN	0	0.031	0.004	40.461	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	357	VAL	0	-0.039	-0.013	34.535	0.003	0.003	0.000	0.000	0.000	0.000
81	A	358	GLN	0	-0.017	-0.020	36.126	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	359	LEU	0	-0.029	-0.007	31.162	0.003	0.003	0.000	0.000	0.000	0.000
83	A	360	GLN	0	0.049	0.008	35.318	0.003	0.003	0.000	0.000	0.000	0.000
84	A	361	ARG	1	0.781	0.887	35.922	0.044	0.044	0.000	0.000	0.000	0.000
85	A	362	LEU	0	-0.007	-0.012	35.612	0.002	0.002	0.000	0.000	0.000	0.000
86	A	363	THR	0	-0.021	-0.025	37.982	0.001	0.001	0.000	0.000	0.000	0.000
87	A	364	ASP	-1	-0.803	-0.886	40.469	-0.034	-0.034	0.000	0.000	0.000	0.000
88	A	365	GLY	0	0.016	0.022	41.351	0.000	0.000	0.000	0.000	0.000	0.000
89	A	366	GLU	-1	-0.946	-0.959	39.589	-0.044	-0.044	0.000	0.000	0.000	0.000
90	A	367	CYS	0	-0.042	-0.026	39.223	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	368	SER	0	-0.026	-0.003	35.785	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	369	GLU	-1	-0.904	-0.962	37.569	-0.064	-0.064	0.000	0.000	0.000	0.000
93	A	370	PRO	0	-0.057	-0.019	37.501	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	371	LEU	0	0.021	0.004	33.012	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	372	PRO	0	0.016	0.009	37.109	0.004	0.004	0.000	0.000	0.000	0.000
96	A	373	PHE	0	0.004	0.000	34.363	-0.007	-0.007	0.000	0.000	0.000	0.000
97	A	374	THR	0	-0.018	-0.006	37.840	0.005	0.005	0.000	0.000	0.000	0.000
98	A	375	TYR	0	-0.056	-0.028	39.270	-0.004	-0.004	0.000	0.000	0.000	0.000
99	A	376	LEU	0	-0.002	-0.012	38.836	0.001	0.001	0.000	0.000	0.000	0.000
100	A	377	PRO	0	0.004	0.024	42.547	0.001	0.001	0.000	0.000	0.000	0.000
101	A	378	ARG	1	0.843	0.931	43.613	0.032	0.032	0.000	0.000	0.000	0.000

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