FMO DATABASE

FMODB ID: 942G2

Calculation Name: 4JVW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4JVW

Chain ID: A

ChEMBL ID:

UniProt ID: P01872

Base Structure: X-ray

Registration Date: 2023-06-26

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	107
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-804388.857256
FMO2-HF: Nuclear repulsion	762457.782921
FMO2-HF: Total energy	-41931.074334
FMO2-MP2: Total energy	-42053.934114

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:449:LYS)

Summations of interaction energy for fragment #1(A:449:LYS)

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.
-170.606	-155.311	6.081	-9.91	-11.468	-0.104

Interaction energy analysis for fragmet #1(A:449:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.874 / q_NPA : 0.925

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	451	PRO	0	0.031	0.022	3.781	-1.658	0.363	-0.032	-0.932	-1.057	-0.001
4	A	452	PRO	0	-0.015	0.008	6.254	2.127	2.127	0.000	0.000	0.000	0.000
5	A	453	ALA	0	-0.004	0.000	9.337	0.700	0.700	0.000	0.000	0.000	0.000
6	A	454	VAL	0	-0.004	-0.013	12.654	0.122	0.122	0.000	0.000	0.000	0.000
7	A	455	TYR	0	-0.037	-0.026	15.455	0.370	0.370	0.000	0.000	0.000	0.000
8	A	456	LEU	0	-0.012	0.004	19.062	-0.134	-0.134	0.000	0.000	0.000	0.000
9	A	457	LEU	0	-0.033	-0.025	21.779	0.371	0.371	0.000	0.000	0.000	0.000
10	A	458	PRO	0	0.038	0.017	24.997	-0.037	-0.037	0.000	0.000	0.000	0.000
11	A	459	PRO	0	0.025	0.021	28.361	-0.022	-0.022	0.000	0.000	0.000	0.000
12	A	460	ALA	0	0.016	0.021	30.992	0.129	0.129	0.000	0.000	0.000	0.000
13	A	461	ARG	1	0.988	0.976	32.756	7.944	7.944	0.000	0.000	0.000	0.000
14	A	462	GLU	-1	-0.934	-0.975	35.465	-8.186	-8.186	0.000	0.000	0.000	0.000
15	A	463	GLN	0	0.025	0.018	33.128	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	464	LEU	0	0.026	0.010	34.201	0.185	0.185	0.000	0.000	0.000	0.000
17	A	465	ASN	0	-0.030	-0.027	37.761	0.157	0.157	0.000	0.000	0.000	0.000
18	A	466	LEU	0	-0.053	-0.024	39.437	0.208	0.208	0.000	0.000	0.000	0.000
19	A	467	ARG	1	0.805	0.909	41.135	7.226	7.226	0.000	0.000	0.000	0.000
20	A	468	GLU	-1	-0.894	-0.934	39.358	-7.482	-7.482	0.000	0.000	0.000	0.000
21	A	469	SER	0	-0.044	-0.025	35.114	-0.123	-0.123	0.000	0.000	0.000	0.000
22	A	470	ALA	0	-0.024	-0.014	32.890	0.101	0.101	0.000	0.000	0.000	0.000
23	A	471	THR	0	-0.030	-0.018	28.169	-0.033	-0.033	0.000	0.000	0.000	0.000
24	A	472	VAL	0	-0.001	0.013	25.203	0.020	0.020	0.000	0.000	0.000	0.000
25	A	473	THR	0	0.010	-0.003	22.432	-0.198	-0.198	0.000	0.000	0.000	0.000
26	A	474	CYS	0	-0.093	-0.023	18.461	-0.555	-0.555	0.000	0.000	0.000	0.000
27	A	475	LEU	0	-0.015	-0.009	18.082	-0.298	-0.298	0.000	0.000	0.000	0.000
28	A	476	VAL	0	0.012	0.006	11.959	-0.218	-0.218	0.000	0.000	0.000	0.000
29	A	477	LYS	1	0.897	0.930	12.403	16.083	16.083	0.000	0.000	0.000	0.000
30	A	478	GLY	0	0.080	0.053	9.521	-0.822	-0.822	0.000	0.000	0.000	0.000
31	A	479	PHE	0	-0.035	0.001	6.203	-1.033	-1.033	0.000	0.000	0.000	0.000
32	A	480	SER	0	-0.004	-0.001	3.195	-0.379	0.725	0.069	-0.538	-0.636	-0.002
33	A	481	PRO	0	0.040	0.014	2.489	-9.224	-6.402	3.096	-2.359	-3.559	-0.024
34	A	482	ALA	0	0.023	-0.005	5.101	1.475	1.471	-0.001	-0.004	0.009	0.000
35	A	483	ASP	-1	-0.925	-0.953	7.438	-28.652	-28.652	0.000	0.000	0.000	0.000
36	A	484	ILE	0	-0.027	-0.013	7.873	-2.459	-2.459	0.000	0.000	0.000	0.000
37	A	485	SER	0	-0.017	0.015	10.501	1.801	1.801	0.000	0.000	0.000	0.000
38	A	486	VAL	0	0.024	-0.004	13.752	-0.360	-0.360	0.000	0.000	0.000	0.000
39	A	487	GLN	0	0.002	0.015	16.283	1.402	1.402	0.000	0.000	0.000	0.000
40	A	488	TRP	0	0.032	0.015	19.532	0.004	0.004	0.000	0.000	0.000	0.000
41	A	489	LEU	0	-0.017	0.012	22.570	0.095	0.095	0.000	0.000	0.000	0.000
42	A	490	GLN	0	-0.027	-0.039	24.449	-0.138	-0.138	0.000	0.000	0.000	0.000
43	A	491	ARG	1	0.819	0.874	28.050	9.081	9.081	0.000	0.000	0.000	0.000
44	A	492	GLY	0	-0.006	0.003	27.359	0.117	0.117	0.000	0.000	0.000	0.000
45	A	493	GLN	0	-0.009	-0.002	26.779	-0.083	-0.083	0.000	0.000	0.000	0.000
46	A	494	LEU	0	-0.005	-0.002	20.624	0.066	0.066	0.000	0.000	0.000	0.000
47	A	495	LEU	0	-0.024	-0.014	24.406	0.430	0.430	0.000	0.000	0.000	0.000
48	A	496	PRO	0	0.029	0.013	24.687	-0.500	-0.500	0.000	0.000	0.000	0.000
49	A	497	GLN	0	0.009	-0.017	21.674	0.061	0.061	0.000	0.000	0.000	0.000
50	A	498	GLU	-1	-0.910	-0.950	25.025	-11.023	-11.023	0.000	0.000	0.000	0.000
51	A	499	LYS	1	0.884	0.940	27.676	10.314	10.314	0.000	0.000	0.000	0.000
52	A	500	TYR	0	-0.037	-0.004	21.026	-0.181	-0.181	0.000	0.000	0.000	0.000
53	A	501	VAL	0	0.021	0.020	24.305	-0.031	-0.031	0.000	0.000	0.000	0.000
54	A	502	THR	0	0.014	0.013	17.820	0.203	0.203	0.000	0.000	0.000	0.000
55	A	503	SER	0	-0.027	0.015	18.919	0.358	0.358	0.000	0.000	0.000	0.000
56	A	504	ALA	0	0.020	0.015	16.896	-0.885	-0.885	0.000	0.000	0.000	0.000
57	A	505	PRO	0	-0.001	-0.009	12.022	0.670	0.670	0.000	0.000	0.000	0.000
58	A	506	MET	0	-0.050	-0.012	14.079	0.861	0.861	0.000	0.000	0.000	0.000
59	A	507	PRO	0	0.020	0.003	12.445	-0.886	-0.886	0.000	0.000	0.000	0.000
60	A	508	GLU	-1	-0.803	-0.923	11.445	-17.963	-17.963	0.000	0.000	0.000	0.000
61	A	509	PRO	0	-0.037	-0.016	13.727	0.098	0.098	0.000	0.000	0.000	0.000
62	A	510	GLY	0	-0.019	-0.011	16.197	0.293	0.293	0.000	0.000	0.000	0.000
63	A	511	ALA	0	-0.034	-0.004	11.045	0.150	0.150	0.000	0.000	0.000	0.000
64	A	512	PRO	0	0.048	0.011	11.142	-1.038	-1.038	0.000	0.000	0.000	0.000
65	A	513	GLY	0	-0.009	-0.001	8.478	-0.357	-0.357	0.000	0.000	0.000	0.000
66	A	514	PHE	0	-0.041	-0.012	5.369	-2.570	-2.570	0.000	0.000	0.000	0.000
67	A	515	TYR	0	-0.031	-0.010	7.640	1.297	1.297	0.000	0.000	0.000	0.000
68	A	516	PHE	0	-0.047	-0.022	10.200	-0.169	-0.169	0.000	0.000	0.000	0.000
69	A	517	THR	0	0.009	-0.016	12.860	0.521	0.521	0.000	0.000	0.000	0.000
70	A	518	HIS	0	0.016	0.001	15.613	0.085	0.085	0.000	0.000	0.000	0.000
71	A	519	SER	0	0.015	-0.004	18.774	0.098	0.098	0.000	0.000	0.000	0.000
72	A	520	ILE	0	-0.022	-0.013	21.031	0.189	0.189	0.000	0.000	0.000	0.000
73	A	521	LEU	0	0.047	0.031	24.600	-0.068	-0.068	0.000	0.000	0.000	0.000
74	A	522	THR	0	-0.022	-0.013	27.063	0.209	0.209	0.000	0.000	0.000	0.000
75	A	523	VAL	0	0.011	0.027	30.778	0.047	0.047	0.000	0.000	0.000	0.000
76	A	524	THR	0	0.038	0.009	33.370	0.093	0.093	0.000	0.000	0.000	0.000
77	A	525	GLU	-1	-0.918	-0.980	36.087	-7.934	-7.934	0.000	0.000	0.000	0.000
78	A	526	GLU	-1	-0.809	-0.900	37.625	-7.297	-7.297	0.000	0.000	0.000	0.000
79	A	527	GLU	-1	-0.839	-0.880	33.330	-9.299	-9.299	0.000	0.000	0.000	0.000
80	A	528	TRP	0	0.054	0.039	29.352	-0.171	-0.171	0.000	0.000	0.000	0.000
81	A	529	ASN	0	0.038	0.027	34.875	-0.113	-0.113	0.000	0.000	0.000	0.000
82	A	530	SER	0	-0.131	-0.079	37.156	0.099	0.099	0.000	0.000	0.000	0.000
83	A	531	GLY	0	-0.013	-0.007	35.281	0.091	0.091	0.000	0.000	0.000	0.000
84	A	532	GLU	-1	-0.802	-0.853	31.864	-9.467	-9.467	0.000	0.000	0.000	0.000
85	A	533	THR	0	-0.040	-0.017	28.324	-0.118	-0.118	0.000	0.000	0.000	0.000
86	A	534	TYR	0	-0.044	-0.057	26.517	-0.038	-0.038	0.000	0.000	0.000	0.000
87	A	535	THR	0	0.019	-0.001	21.179	0.037	0.037	0.000	0.000	0.000	0.000
88	A	537	VAL	0	0.010	-0.014	16.855	-0.387	-0.387	0.000	0.000	0.000	0.000
89	A	538	VAL	0	0.001	-0.021	11.470	-0.117	-0.117	0.000	0.000	0.000	0.000
90	A	539	GLY	0	0.011	0.012	11.741	-0.313	-0.313	0.000	0.000	0.000	0.000
91	A	540	HIS	0	0.030	-0.017	3.618	-0.722	-0.515	0.001	-0.030	-0.179	0.000
92	A	541	GLU	-1	-0.832	-0.922	2.282	-103.789	-95.330	2.347	-5.729	-5.077	-0.076
93	A	542	ALA	0	-0.042	-0.013	2.376	-5.371	-4.781	0.600	-0.287	-0.903	-0.001
94	A	543	LEU	0	-0.047	-0.020	4.126	4.558	4.654	0.001	-0.031	-0.066	0.000
95	A	544	PRO	0	-0.010	-0.004	7.890	-0.394	-0.394	0.000	0.000	0.000	0.000
96	A	545	HIS	0	0.003	-0.008	9.779	0.266	0.266	0.000	0.000	0.000	0.000
97	A	546	LEU	0	-0.015	0.018	8.819	1.447	1.447	0.000	0.000	0.000	0.000
98	A	547	VAL	0	0.024	-0.007	10.833	-0.773	-0.773	0.000	0.000	0.000	0.000
99	A	548	THR	0	-0.065	-0.016	12.560	1.083	1.083	0.000	0.000	0.000	0.000
100	A	549	GLU	-1	-0.864	-0.944	14.420	-15.235	-15.235	0.000	0.000	0.000	0.000
101	A	550	ARG	1	0.819	0.913	14.692	17.127	17.127	0.000	0.000	0.000	0.000
102	A	551	THR	0	0.048	0.023	20.211	-0.039	-0.039	0.000	0.000	0.000	0.000
103	A	552	VAL	0	-0.059	-0.015	23.927	0.042	0.042	0.000	0.000	0.000	0.000
104	A	553	ASP	-1	-0.772	-0.907	26.701	-9.727	-9.727	0.000	0.000	0.000	0.000
105	A	554	LYS	1	0.842	0.900	30.437	7.872	7.872	0.000	0.000	0.000	0.000
106	A	555	SER	0	-0.031	-0.004	32.817	0.261	0.261	0.000	0.000	0.000	0.000
107	A	556	THR	0	-0.057	-0.016	27.126	-0.177	-0.177	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:449:LYS)