FMO DATABASE

FMODB ID: M349Z

Calculation Name: 3F1I-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3F1I

Chain ID: H

ChEMBL ID:

UniProt ID: O14964

Base Structure: X-ray

Registration Date: 2023-06-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
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	98
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-554881.512845
FMO2-HF: Nuclear repulsion	514940.358014
FMO2-HF: Total energy	-39941.154831
FMO2-MP2: Total energy	-40057.564865

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(H:404:SER)

Summations of interaction energy for fragment #1(H:404:SER)

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.
-18.151	-14.061	7.358	-4.855	-6.593	0.032

Interaction energy analysis for fragmet #1(H:404:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : 0.005

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	H	406	GLU	-1	-0.847	-0.912	2.459	0.445	2.906	1.558	-1.471	-2.548	0.011
4	H	407	GLN	0	-0.058	-0.023	2.136	-9.800	-9.171	5.779	-2.872	-3.536	0.018
5	H	408	PHE	0	0.026	-0.003	3.420	-2.700	-1.700	0.021	-0.512	-0.509	0.003
6	H	409	LEU	0	0.041	0.018	5.433	-0.590	-0.590	0.000	0.000	0.000	0.000
7	H	410	LYS	1	0.875	0.933	5.641	-3.608	-3.608	0.000	0.000	0.000	0.000
8	H	411	ALA	0	-0.010	0.009	7.821	-0.437	-0.437	0.000	0.000	0.000	0.000
9	H	412	LEU	0	0.062	0.025	9.422	-0.298	-0.298	0.000	0.000	0.000	0.000
10	H	413	GLN	0	0.008	-0.001	11.406	-0.112	-0.112	0.000	0.000	0.000	0.000
11	H	414	ASN	0	0.010	-0.002	11.576	-0.240	-0.240	0.000	0.000	0.000	0.000
12	H	415	ALA	0	0.017	0.028	13.545	-0.136	-0.136	0.000	0.000	0.000	0.000
13	H	416	VAL	0	0.040	0.017	15.410	-0.104	-0.104	0.000	0.000	0.000	0.000
14	H	417	THR	0	-0.029	-0.019	16.993	-0.089	-0.089	0.000	0.000	0.000	0.000
15	H	418	THR	0	-0.041	-0.038	17.403	-0.072	-0.072	0.000	0.000	0.000	0.000
16	H	419	PHE	0	-0.003	-0.001	19.388	-0.053	-0.053	0.000	0.000	0.000	0.000
17	H	420	VAL	0	0.039	0.014	21.205	-0.045	-0.045	0.000	0.000	0.000	0.000
18	H	421	ASN	0	-0.016	-0.015	22.751	-0.049	-0.049	0.000	0.000	0.000	0.000
19	H	422	ARG	1	0.883	0.921	23.800	-0.288	-0.288	0.000	0.000	0.000	0.000
20	H	423	MET	0	-0.015	0.000	24.080	-0.033	-0.033	0.000	0.000	0.000	0.000
21	H	424	LYS	1	0.968	0.993	26.247	-0.283	-0.283	0.000	0.000	0.000	0.000
22	H	425	SER	0	0.037	0.021	28.314	-0.020	-0.020	0.000	0.000	0.000	0.000
23	H	426	ASN	0	-0.079	-0.070	28.450	-0.027	-0.027	0.000	0.000	0.000	0.000
24	H	427	HIS	0	0.077	0.050	31.518	-0.008	-0.008	0.000	0.000	0.000	0.000
25	H	428	MET	0	-0.042	-0.030	32.749	-0.005	-0.005	0.000	0.000	0.000	0.000
26	H	429	ARG	1	0.865	0.949	29.917	-0.189	-0.189	0.000	0.000	0.000	0.000
27	H	430	GLY	0	0.015	0.028	36.008	-0.008	-0.008	0.000	0.000	0.000	0.000
28	H	431	ARG	1	0.847	0.915	31.256	-0.169	-0.169	0.000	0.000	0.000	0.000
29	H	432	SER	0	0.049	0.025	34.416	0.010	0.010	0.000	0.000	0.000	0.000
30	H	433	ILE	0	0.043	-0.007	28.347	0.003	0.003	0.000	0.000	0.000	0.000
31	H	434	THR	0	0.009	0.014	29.717	0.010	0.010	0.000	0.000	0.000	0.000
32	H	435	ASN	0	-0.020	-0.008	31.734	-0.005	-0.005	0.000	0.000	0.000	0.000
33	H	436	ASP	-1	-0.848	-0.895	27.194	0.226	0.226	0.000	0.000	0.000	0.000
34	H	437	SER	0	0.056	0.030	26.956	0.014	0.014	0.000	0.000	0.000	0.000
35	H	438	ALA	0	0.029	0.006	22.930	0.012	0.012	0.000	0.000	0.000	0.000
36	H	439	VAL	0	-0.021	-0.007	22.354	0.031	0.031	0.000	0.000	0.000	0.000
37	H	440	LEU	0	0.038	0.026	23.161	0.021	0.021	0.000	0.000	0.000	0.000
38	H	441	SER	0	0.019	0.018	20.412	0.022	0.022	0.000	0.000	0.000	0.000
39	H	442	LEU	0	0.020	0.003	17.302	0.030	0.030	0.000	0.000	0.000	0.000
40	H	443	PHE	0	0.008	0.002	18.692	0.038	0.038	0.000	0.000	0.000	0.000
41	H	444	GLN	0	0.008	0.011	19.792	0.007	0.007	0.000	0.000	0.000	0.000
42	H	445	SER	0	-0.024	-0.021	14.867	0.018	0.018	0.000	0.000	0.000	0.000
43	H	446	ILE	0	-0.019	-0.006	14.975	0.068	0.068	0.000	0.000	0.000	0.000
44	H	447	ASN	0	-0.050	-0.037	16.087	0.017	0.017	0.000	0.000	0.000	0.000
45	H	448	GLY	0	-0.010	0.008	15.851	-0.019	-0.019	0.000	0.000	0.000	0.000
46	H	449	MET	0	-0.026	-0.022	10.914	0.086	0.086	0.000	0.000	0.000	0.000
47	H	450	HIS	0	0.005	0.009	12.741	0.090	0.090	0.000	0.000	0.000	0.000
48	H	451	PRO	0	0.051	0.019	14.624	0.004	0.004	0.000	0.000	0.000	0.000
49	H	452	GLN	0	0.061	0.045	5.869	-0.095	-0.095	0.000	0.000	0.000	0.000
50	H	453	LEU	0	-0.038	-0.026	11.155	0.031	0.031	0.000	0.000	0.000	0.000
51	H	454	LEU	0	-0.025	-0.014	12.477	-0.051	-0.051	0.000	0.000	0.000	0.000
52	H	455	GLU	-1	-0.889	-0.940	11.740	0.295	0.295	0.000	0.000	0.000	0.000
53	H	456	LEU	0	-0.054	-0.033	7.603	-0.075	-0.075	0.000	0.000	0.000	0.000
54	H	457	LEU	0	-0.031	-0.015	11.680	-0.061	-0.061	0.000	0.000	0.000	0.000
55	H	458	ASN	0	0.019	0.012	14.974	-0.035	-0.035	0.000	0.000	0.000	0.000
56	H	459	GLN	0	-0.028	-0.007	11.512	-0.127	-0.127	0.000	0.000	0.000	0.000
57	H	460	LEU	0	-0.019	-0.016	11.841	-0.057	-0.057	0.000	0.000	0.000	0.000
58	H	461	ASP	-1	-0.803	-0.884	15.018	0.104	0.104	0.000	0.000	0.000	0.000
59	H	462	GLU	-1	-0.866	-0.929	16.515	-0.072	-0.072	0.000	0.000	0.000	0.000
60	H	463	ARG	1	0.811	0.899	12.574	0.185	0.185	0.000	0.000	0.000	0.000
61	H	464	ARG	1	0.777	0.870	17.432	-0.086	-0.086	0.000	0.000	0.000	0.000
62	H	465	LEU	0	0.033	0.017	20.027	-0.008	-0.008	0.000	0.000	0.000	0.000
63	H	466	TYR	0	-0.060	-0.025	20.026	-0.010	-0.010	0.000	0.000	0.000	0.000
64	H	467	TYR	0	0.008	-0.015	17.536	-0.014	-0.014	0.000	0.000	0.000	0.000
65	H	468	GLU	-1	-0.832	-0.894	22.853	0.038	0.038	0.000	0.000	0.000	0.000
66	H	469	GLY	0	0.063	0.038	25.385	0.001	0.001	0.000	0.000	0.000	0.000
67	H	470	LEU	0	-0.058	-0.031	23.579	-0.002	-0.002	0.000	0.000	0.000	0.000
68	H	471	GLN	0	-0.017	-0.024	26.983	0.002	0.002	0.000	0.000	0.000	0.000
69	H	472	ASP	-1	-0.865	-0.927	28.707	-0.004	-0.004	0.000	0.000	0.000	0.000
70	H	473	LYS	1	0.895	0.947	30.288	0.062	0.062	0.000	0.000	0.000	0.000
71	H	474	LEU	0	-0.015	-0.013	29.162	0.000	0.000	0.000	0.000	0.000	0.000
72	H	475	ALA	0	-0.012	0.010	32.884	0.002	0.002	0.000	0.000	0.000	0.000
73	H	476	GLN	0	0.044	0.014	34.931	-0.003	-0.003	0.000	0.000	0.000	0.000
74	H	477	ILE	0	-0.014	-0.001	33.895	0.000	0.000	0.000	0.000	0.000	0.000
75	H	478	ARG	1	0.928	0.967	36.214	0.008	0.008	0.000	0.000	0.000	0.000
76	H	479	ASP	-1	-0.877	-0.943	38.681	-0.010	-0.010	0.000	0.000	0.000	0.000
77	H	480	ALA	0	-0.011	0.003	40.684	0.001	0.001	0.000	0.000	0.000	0.000
78	H	481	ARG	1	0.904	0.950	41.384	0.033	0.033	0.000	0.000	0.000	0.000
79	H	482	GLY	0	0.037	0.011	42.843	0.001	0.001	0.000	0.000	0.000	0.000
80	H	483	ALA	0	0.021	0.013	44.716	0.001	0.001	0.000	0.000	0.000	0.000
81	H	484	LEU	0	0.003	0.003	46.254	0.000	0.000	0.000	0.000	0.000	0.000
82	H	485	SER	0	-0.074	-0.057	46.382	0.000	0.000	0.000	0.000	0.000	0.000
83	H	486	ALA	0	0.006	0.012	48.910	0.001	0.001	0.000	0.000	0.000	0.000
84	H	487	LEU	0	0.053	0.035	49.940	0.000	0.000	0.000	0.000	0.000	0.000
85	H	488	ARG	1	0.893	0.945	48.774	0.027	0.027	0.000	0.000	0.000	0.000
86	H	489	GLU	-1	-0.762	-0.846	53.167	-0.012	-0.012	0.000	0.000	0.000	0.000
87	H	490	GLU	-1	-0.822	-0.901	54.938	-0.010	-0.010	0.000	0.000	0.000	0.000
88	H	491	HIS	0	-0.022	-0.018	56.478	0.001	0.001	0.000	0.000	0.000	0.000
89	H	492	ARG	1	0.874	0.904	52.925	0.016	0.016	0.000	0.000	0.000	0.000
90	H	493	GLU	-1	-0.967	-0.971	58.627	-0.007	-0.007	0.000	0.000	0.000	0.000
91	H	494	LYS	1	0.839	0.909	59.151	0.011	0.011	0.000	0.000	0.000	0.000
92	H	495	LEU	0	-0.028	-0.012	60.955	0.000	0.000	0.000	0.000	0.000	0.000
93	H	496	ARG	1	0.836	0.904	58.936	0.010	0.010	0.000	0.000	0.000	0.000
94	H	497	ARG	1	1.003	1.005	63.871	0.007	0.007	0.000	0.000	0.000	0.000
95	H	498	ALA	0	-0.043	-0.023	67.054	0.000	0.000	0.000	0.000	0.000	0.000
96	H	499	ALA	0	-0.038	-0.013	68.422	0.000	0.000	0.000	0.000	0.000	0.000
97	H	500	GLU	-1	-0.982	-0.996	67.871	-0.007	-0.007	0.000	0.000	0.000	0.000
98	H	501	GLU	-1	-1.014	-0.983	71.770	-0.007	-0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(H:404:SER)