FMO DATABASE

FMODB ID: 6YNJZ

Calculation Name: 3LOF-A-Xray372

Preferred Name: Heat shock 70 kDa protein 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3LOF

Chain ID: A

ChEMBL ID: CHEMBL5460

UniProt ID: P0DMV8

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	84
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-539719.189883
FMO2-HF: Nuclear repulsion	506563.008878
FMO2-HF: Total energy	-33156.181005
FMO2-MP2: Total energy	-33252.150655

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:530:ASN)

Summations of interaction energy for fragment #1(A:530:ASN)

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.
-26.979	-20.038	6.946	-6.068	-7.816	-0.005

Interaction energy analysis for fragmet #1(A:530:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / 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

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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	532	ALA	0	0.021	0.019	2.422	-7.631	-4.210	1.689	-2.115	-2.994	0.019
4	A	533	ALA	0	-0.001	-0.006	2.562	-6.485	-4.309	0.692	-1.072	-1.796	0.009
5	A	534	GLU	-1	-0.906	-0.967	2.106	-15.230	-13.886	4.565	-2.881	-3.026	-0.033
6	A	535	ARG	1	0.836	0.913	5.524	-0.520	-0.520	0.000	0.000	0.000	0.000
7	A	536	VAL	0	0.002	0.004	7.578	-0.164	-0.164	0.000	0.000	0.000	0.000
8	A	537	SER	0	-0.025	-0.005	7.742	0.073	0.073	0.000	0.000	0.000	0.000
9	A	538	ALA	0	0.002	0.000	9.535	0.124	0.124	0.000	0.000	0.000	0.000
10	A	539	LYS	1	0.854	0.926	11.600	0.217	0.217	0.000	0.000	0.000	0.000
11	A	540	ASN	0	0.042	0.007	12.412	0.128	0.128	0.000	0.000	0.000	0.000
12	A	541	ALA	0	-0.002	0.017	13.491	0.029	0.029	0.000	0.000	0.000	0.000
13	A	542	LEU	0	-0.016	0.002	15.248	0.044	0.044	0.000	0.000	0.000	0.000
14	A	543	GLU	-1	-0.844	-0.914	17.355	-0.169	-0.169	0.000	0.000	0.000	0.000
15	A	544	SER	0	-0.035	-0.027	17.060	0.017	0.017	0.000	0.000	0.000	0.000
16	A	545	TYR	0	0.017	0.000	19.364	0.033	0.033	0.000	0.000	0.000	0.000
17	A	546	ALA	0	0.033	0.012	21.224	0.023	0.023	0.000	0.000	0.000	0.000
18	A	547	PHE	0	0.015	-0.002	22.001	0.019	0.019	0.000	0.000	0.000	0.000
19	A	548	ASN	0	-0.065	-0.037	22.174	0.017	0.017	0.000	0.000	0.000	0.000
20	A	549	MET	0	0.007	0.009	24.924	0.010	0.010	0.000	0.000	0.000	0.000
21	A	550	LYS	1	0.807	0.890	27.060	0.127	0.127	0.000	0.000	0.000	0.000
22	A	551	SER	0	0.030	0.006	28.423	0.008	0.008	0.000	0.000	0.000	0.000
23	A	552	ALA	0	-0.036	-0.009	29.058	0.006	0.006	0.000	0.000	0.000	0.000
24	A	553	VAL	0	-0.024	-0.016	30.910	0.009	0.009	0.000	0.000	0.000	0.000
25	A	554	GLU	-1	-0.840	-0.916	31.857	-0.100	-0.100	0.000	0.000	0.000	0.000
26	A	555	ASP	-1	-0.854	-0.908	34.050	-0.122	-0.122	0.000	0.000	0.000	0.000
27	A	556	GLU	-1	-0.845	-0.913	35.780	-0.080	-0.080	0.000	0.000	0.000	0.000
28	A	557	GLY	0	0.007	0.006	38.260	0.005	0.005	0.000	0.000	0.000	0.000
29	A	558	LEU	0	-0.026	-0.027	33.643	0.001	0.001	0.000	0.000	0.000	0.000
30	A	559	LYS	1	0.808	0.891	38.332	0.086	0.086	0.000	0.000	0.000	0.000
31	A	560	GLY	0	-0.028	-0.009	41.909	0.000	0.000	0.000	0.000	0.000	0.000
32	A	561	LYS	1	0.900	0.959	38.350	0.106	0.106	0.000	0.000	0.000	0.000
33	A	562	ILE	0	0.005	0.012	34.483	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	563	SER	0	-0.025	-0.029	38.538	0.006	0.006	0.000	0.000	0.000	0.000
35	A	564	GLU	-1	-0.808	-0.939	38.883	-0.076	-0.076	0.000	0.000	0.000	0.000
36	A	565	ALA	0	0.001	0.007	39.107	0.000	0.000	0.000	0.000	0.000	0.000
37	A	566	ASP	-1	-0.844	-0.882	35.472	-0.081	-0.081	0.000	0.000	0.000	0.000
38	A	567	LYS	1	0.916	0.968	34.520	0.085	0.085	0.000	0.000	0.000	0.000
39	A	568	LYS	1	0.856	0.907	34.529	0.047	0.047	0.000	0.000	0.000	0.000
40	A	569	LYS	1	0.842	0.903	32.819	0.078	0.078	0.000	0.000	0.000	0.000
41	A	570	VAL	0	0.028	0.006	29.132	0.000	0.000	0.000	0.000	0.000	0.000
42	A	571	LEU	0	-0.001	0.010	29.985	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	572	ASP	-1	-0.809	-0.884	30.990	-0.053	-0.053	0.000	0.000	0.000	0.000
44	A	573	LYS	1	0.772	0.867	26.680	0.063	0.063	0.000	0.000	0.000	0.000
45	A	574	CYS	0	-0.020	-0.014	26.279	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	575	GLN	0	0.013	-0.001	26.572	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	576	GLU	-1	-0.817	-0.883	27.052	-0.032	-0.032	0.000	0.000	0.000	0.000
48	A	577	VAL	0	0.013	0.006	22.050	0.012	0.012	0.000	0.000	0.000	0.000
49	A	578	ILE	0	-0.008	-0.003	23.224	0.009	0.009	0.000	0.000	0.000	0.000
50	A	579	SER	0	-0.020	-0.013	23.957	0.013	0.013	0.000	0.000	0.000	0.000
51	A	580	TRP	0	-0.014	-0.004	17.817	0.005	0.005	0.000	0.000	0.000	0.000
52	A	581	LEU	0	0.001	-0.008	17.400	0.026	0.026	0.000	0.000	0.000	0.000
53	A	582	ASP	-1	-0.948	-0.971	19.806	0.052	0.052	0.000	0.000	0.000	0.000
54	A	583	ALA	0	-0.004	0.001	21.360	0.028	0.028	0.000	0.000	0.000	0.000
55	A	584	ASN	0	-0.064	-0.034	18.881	0.059	0.059	0.000	0.000	0.000	0.000
56	A	585	THR	0	0.015	0.011	15.665	0.014	0.014	0.000	0.000	0.000	0.000
57	A	586	LEU	0	-0.087	-0.061	13.199	0.053	0.053	0.000	0.000	0.000	0.000
58	A	587	ALA	0	0.037	0.047	14.297	0.103	0.103	0.000	0.000	0.000	0.000
59	A	588	GLU	-1	-0.821	-0.927	10.544	1.192	1.192	0.000	0.000	0.000	0.000
60	A	589	LYS	1	0.837	0.915	6.810	0.982	0.982	0.000	0.000	0.000	0.000
61	A	590	ASP	-1	-0.921	-0.965	11.098	-0.025	-0.025	0.000	0.000	0.000	0.000
62	A	591	GLU	-1	-0.813	-0.893	13.451	0.216	0.216	0.000	0.000	0.000	0.000
63	A	592	PHE	0	0.002	-0.006	12.494	-0.062	-0.062	0.000	0.000	0.000	0.000
64	A	593	GLU	-1	-0.870	-0.931	11.103	-0.700	-0.700	0.000	0.000	0.000	0.000
65	A	594	HIS	0	-0.030	-0.010	15.222	-0.034	-0.034	0.000	0.000	0.000	0.000
66	A	595	LYS	1	0.845	0.910	18.477	0.027	0.027	0.000	0.000	0.000	0.000
67	A	596	ARG	1	0.855	0.909	14.190	0.435	0.435	0.000	0.000	0.000	0.000
68	A	597	LYS	1	0.907	0.939	14.596	0.327	0.327	0.000	0.000	0.000	0.000
69	A	598	GLU	-1	-0.842	-0.875	20.537	-0.035	-0.035	0.000	0.000	0.000	0.000
70	A	599	LEU	0	0.007	0.003	22.467	0.009	0.009	0.000	0.000	0.000	0.000
71	A	600	GLU	-1	-0.838	-0.910	19.021	-0.327	-0.327	0.000	0.000	0.000	0.000
72	A	601	GLN	0	-0.075	-0.045	23.628	0.017	0.017	0.000	0.000	0.000	0.000
73	A	602	VAL	0	-0.033	-0.007	26.406	0.009	0.009	0.000	0.000	0.000	0.000
74	A	603	CYS	0	-0.023	-0.001	25.894	0.006	0.006	0.000	0.000	0.000	0.000
75	A	604	ASN	0	0.055	0.019	23.143	-0.006	-0.006	0.000	0.000	0.000	0.000
76	A	605	PRO	0	-0.002	0.010	27.423	0.000	0.000	0.000	0.000	0.000	0.000
77	A	606	ILE	0	0.014	0.013	30.975	0.004	0.004	0.000	0.000	0.000	0.000
78	A	607	ILE	0	0.004	0.004	25.761	0.001	0.001	0.000	0.000	0.000	0.000
79	A	608	SER	0	-0.027	-0.028	29.582	-0.003	-0.003	0.000	0.000	0.000	0.000
80	A	609	GLY	0	-0.019	-0.008	31.406	0.004	0.004	0.000	0.000	0.000	0.000
81	A	610	LEU	0	-0.021	-0.016	32.081	0.004	0.004	0.000	0.000	0.000	0.000
82	A	611	TYR	0	-0.031	-0.021	28.008	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	612	GLN	0	-0.067	-0.020	33.368	0.005	0.005	0.000	0.000	0.000	0.000
84	A	613	GLY	0	-0.064	-0.015	36.257	0.009	0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:530:ASN)