FMO DATABASE

FMODB ID: 2NKJR

Calculation Name: 3F1I-S-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3F1I

Chain ID: S

ChEMBL ID:
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UniProt ID: O14964

Base Structure: X-ray

Registration Date: 2023-09-20

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	77
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-396140.397401
FMO2-HF: Nuclear repulsion	363242.484398
FMO2-HF: Total energy	-32897.913003
FMO2-MP2: Total energy	-32988.571471

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(S:301:PHE)

Summations of interaction energy for fragment #1(S:301:PHE)

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.
-14.114	-5.269	6.673	-3.871	-11.645	-0.008

Interaction energy analysis for fragmet #1(S:301:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.031 / q_NPA : -0.037

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	S	303	ASP	-1	-0.848	-0.932	3.866	-2.086	-0.514	-0.001	-0.507	-1.064	0.001
4	S	304	GLU	-1	-0.874	-0.953	5.670	-0.353	-0.353	0.000	0.000	0.000	0.000
5	S	305	ASP	-1	-0.903	-0.945	9.252	-0.584	-0.584	0.000	0.000	0.000	0.000
6	S	306	LYS	1	0.819	0.888	6.072	1.063	1.063	0.000	0.000	0.000	0.000
7	S	307	MET	0	-0.002	-0.007	6.535	0.131	0.131	0.000	0.000	0.000	0.000
8	S	308	ASP	-1	-0.909	-0.943	10.130	-0.378	-0.378	0.000	0.000	0.000	0.000
9	S	309	GLN	0	-0.073	-0.040	12.221	0.028	0.028	0.000	0.000	0.000	0.000
10	S	310	LEU	0	-0.001	-0.004	9.327	0.061	0.061	0.000	0.000	0.000	0.000
11	S	311	LEU	0	-0.010	0.004	12.755	0.076	0.076	0.000	0.000	0.000	0.000
12	S	312	GLN	0	0.013	-0.010	15.156	0.055	0.055	0.000	0.000	0.000	0.000
13	S	313	MET	0	-0.014	0.021	15.430	0.030	0.030	0.000	0.000	0.000	0.000
14	S	314	LEU	0	0.002	0.010	13.893	0.043	0.043	0.000	0.000	0.000	0.000
15	S	315	GLN	0	-0.074	-0.042	17.917	0.042	0.042	0.000	0.000	0.000	0.000
16	S	316	SER	0	-0.103	-0.063	20.685	0.035	0.035	0.000	0.000	0.000	0.000
17	S	317	THR	0	-0.024	-0.007	20.077	0.021	0.021	0.000	0.000	0.000	0.000
18	S	318	ASP	-1	-0.845	-0.907	22.613	-0.170	-0.170	0.000	0.000	0.000	0.000
19	S	319	PRO	0	-0.056	-0.025	24.974	-0.001	-0.001	0.000	0.000	0.000	0.000
20	S	320	SER	0	-0.091	-0.074	26.056	0.010	0.010	0.000	0.000	0.000	0.000
21	S	321	ASP	-1	-0.882	-0.936	25.878	-0.180	-0.180	0.000	0.000	0.000	0.000
22	S	322	ASP	-1	-0.973	-0.977	27.868	-0.129	-0.129	0.000	0.000	0.000	0.000
23	S	323	GLN	0	-0.131	-0.065	24.333	0.009	0.009	0.000	0.000	0.000	0.000
24	S	324	PRO	0	-0.065	-0.026	20.954	-0.009	-0.009	0.000	0.000	0.000	0.000
25	S	325	ASP	-1	-0.857	-0.934	16.597	-0.333	-0.333	0.000	0.000	0.000	0.000
26	S	326	LEU	0	-0.001	-0.003	17.070	0.015	0.015	0.000	0.000	0.000	0.000
27	S	327	PRO	0	-0.017	-0.030	14.661	-0.038	-0.038	0.000	0.000	0.000	0.000
28	S	328	GLU	-1	-0.903	-0.950	12.620	-0.393	-0.393	0.000	0.000	0.000	0.000
29	S	329	LEU	0	0.065	0.036	11.570	-0.076	-0.076	0.000	0.000	0.000	0.000
30	S	330	LEU	0	0.046	0.021	11.461	-0.099	-0.099	0.000	0.000	0.000	0.000
31	S	331	HIS	0	-0.050	-0.023	6.749	-0.169	-0.169	0.000	0.000	0.000	0.000
32	S	332	LEU	0	-0.025	-0.017	6.888	-0.210	-0.210	0.000	0.000	0.000	0.000
33	S	333	GLU	-1	-0.894	-0.936	7.406	-1.035	-1.035	0.000	0.000	0.000	0.000
34	S	334	ALA	0	-0.024	-0.013	6.592	-0.302	-0.302	0.000	0.000	0.000	0.000
35	S	335	MET	0	-0.068	-0.038	2.588	-2.628	-1.070	1.774	-0.746	-2.585	0.005
36	S	336	CYS	0	0.005	-0.012	2.747	-5.101	-3.391	0.449	-0.832	-1.327	-0.011
37	S	337	HIS	0	-0.011	0.001	5.219	-0.314	-0.227	-0.001	-0.006	-0.080	0.000
38	S	338	GLN	0	-0.023	-0.020	2.433	-0.350	0.543	1.213	-0.522	-1.583	0.001
39	S	339	MET	0	-0.060	0.010	2.340	-2.159	-0.231	2.054	-0.887	-3.095	-0.004
40	S	340	GLY	0	0.037	0.036	3.521	1.350	1.476	0.026	0.042	-0.194	-0.001
41	S	341	PRO	0	0.049	0.015	6.150	0.358	0.358	0.000	0.000	0.000	0.000
42	S	342	LEU	0	-0.038	-0.013	2.478	-0.531	0.440	1.159	-0.413	-1.717	0.001
43	S	343	ILE	0	0.012	0.002	6.222	0.522	0.522	0.000	0.000	0.000	0.000
44	S	344	ASP	-1	-0.888	-0.949	8.169	-0.229	-0.229	0.000	0.000	0.000	0.000
45	S	345	GLU	-1	-0.902	-0.928	8.727	1.215	1.215	0.000	0.000	0.000	0.000
46	S	346	LYS	1	0.799	0.875	7.203	-1.400	-1.400	0.000	0.000	0.000	0.000
47	S	347	LEU	0	0.011	0.011	11.525	-0.015	-0.015	0.000	0.000	0.000	0.000
48	S	348	GLU	-1	-0.874	-0.915	14.261	0.230	0.230	0.000	0.000	0.000	0.000
49	S	349	ASP	-1	-0.773	-0.868	14.194	0.418	0.418	0.000	0.000	0.000	0.000
50	S	350	ILE	0	-0.036	-0.019	13.708	-0.012	-0.012	0.000	0.000	0.000	0.000
51	S	351	ASP	-1	-0.878	-0.940	17.200	0.005	0.005	0.000	0.000	0.000	0.000
52	S	352	ARG	1	0.738	0.870	17.327	-0.267	-0.267	0.000	0.000	0.000	0.000
53	S	353	LYS	1	0.856	0.914	16.234	-0.402	-0.402	0.000	0.000	0.000	0.000
54	S	354	HIS	0	-0.021	-0.001	21.313	-0.013	-0.013	0.000	0.000	0.000	0.000
55	S	355	SER	0	-0.042	-0.041	23.185	-0.012	-0.012	0.000	0.000	0.000	0.000
56	S	356	GLU	-1	-0.893	-0.955	22.638	0.182	0.182	0.000	0.000	0.000	0.000
57	S	357	LEU	0	-0.027	-0.023	23.845	-0.008	-0.008	0.000	0.000	0.000	0.000
58	S	358	SER	0	-0.012	0.003	27.078	-0.013	-0.013	0.000	0.000	0.000	0.000
59	S	359	GLU	-1	-0.840	-0.925	28.933	0.042	0.042	0.000	0.000	0.000	0.000
60	S	360	LEU	0	-0.014	-0.003	30.070	-0.005	-0.005	0.000	0.000	0.000	0.000
61	S	361	ASN	0	-0.003	-0.011	31.023	-0.004	-0.004	0.000	0.000	0.000	0.000
62	S	362	VAL	0	0.005	0.002	32.856	-0.006	-0.006	0.000	0.000	0.000	0.000
63	S	363	LYS	1	0.797	0.911	34.918	-0.049	-0.049	0.000	0.000	0.000	0.000
64	S	364	VAL	0	-0.005	0.005	35.001	-0.003	-0.003	0.000	0.000	0.000	0.000
65	S	365	MET	0	-0.005	-0.004	36.391	-0.004	-0.004	0.000	0.000	0.000	0.000
66	S	366	GLU	-1	-0.855	-0.925	38.999	0.033	0.033	0.000	0.000	0.000	0.000
67	S	367	ALA	0	0.000	0.003	40.534	-0.003	-0.003	0.000	0.000	0.000	0.000
68	S	368	LEU	0	0.002	-0.001	39.561	-0.002	-0.002	0.000	0.000	0.000	0.000
69	S	369	SER	0	-0.031	-0.018	42.719	-0.004	-0.004	0.000	0.000	0.000	0.000
70	S	370	LEU	0	-0.048	-0.024	44.950	-0.002	-0.002	0.000	0.000	0.000	0.000
71	S	371	TYR	0	0.006	-0.001	46.081	-0.001	-0.001	0.000	0.000	0.000	0.000
72	S	372	THR	0	-0.019	-0.029	46.471	-0.002	-0.002	0.000	0.000	0.000	0.000
73	S	373	LYS	1	0.908	0.952	47.517	-0.020	-0.020	0.000	0.000	0.000	0.000
74	S	374	LEU	0	0.025	0.018	49.646	-0.001	-0.001	0.000	0.000	0.000	0.000
75	S	375	MET	0	-0.058	-0.026	51.155	-0.001	-0.001	0.000	0.000	0.000	0.000
76	S	376	ASN	0	-0.040	-0.003	53.616	-0.001	-0.001	0.000	0.000	0.000	0.000
77	S	377	GLU	-1	-1.045	-1.014	54.943	0.019	0.019	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(S:301:PHE)