FMO DATABASE

FMODB ID: 72ZGK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-804679.295042
FMO2-HF: Nuclear repulsion	762747.716165
FMO2-HF: Total energy	-41931.578877
FMO2-MP2: Total energy	-42054.485275

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.
-209.642	-207.917	27.86	-15.551	-14.03	-0.158

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 : 0.853 / q_NPA : 0.908

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	0.033	0.022	3.876	-2.636	-0.094	-0.018	-1.366	-1.157	0.005
4	A	452	PRO	0	-0.017	0.002	6.382	1.862	1.862	0.000	0.000	0.000	0.000
5	A	453	ALA	0	0.001	0.010	9.659	1.003	1.003	0.000	0.000	0.000	0.000
6	A	454	VAL	0	-0.018	-0.021	12.789	-0.055	-0.055	0.000	0.000	0.000	0.000
7	A	455	TYR	0	-0.029	-0.016	15.482	0.366	0.366	0.000	0.000	0.000	0.000
8	A	456	LEU	0	-0.011	0.001	19.191	-0.225	-0.225	0.000	0.000	0.000	0.000
9	A	457	LEU	0	-0.028	-0.011	22.127	0.351	0.351	0.000	0.000	0.000	0.000
10	A	458	PRO	0	0.041	0.019	25.500	-0.081	-0.081	0.000	0.000	0.000	0.000
11	A	459	PRO	0	0.009	0.013	28.926	-0.053	-0.053	0.000	0.000	0.000	0.000
12	A	460	ALA	0	0.019	0.018	31.449	0.138	0.138	0.000	0.000	0.000	0.000
13	A	461	ARG	1	0.896	0.927	32.989	7.924	7.924	0.000	0.000	0.000	0.000
14	A	462	GLU	-1	-0.848	-0.926	35.910	-8.102	-8.102	0.000	0.000	0.000	0.000
15	A	463	GLN	0	0.018	0.007	33.278	-0.023	-0.023	0.000	0.000	0.000	0.000
16	A	464	LEU	0	0.041	0.016	34.809	0.180	0.180	0.000	0.000	0.000	0.000
17	A	465	ASN	0	-0.050	-0.037	38.272	0.202	0.202	0.000	0.000	0.000	0.000
18	A	466	LEU	0	-0.036	-0.013	39.113	0.214	0.214	0.000	0.000	0.000	0.000
19	A	467	ARG	1	0.759	0.871	41.572	7.356	7.356	0.000	0.000	0.000	0.000
20	A	468	GLU	-1	-0.850	-0.888	40.052	-7.767	-7.767	0.000	0.000	0.000	0.000
21	A	469	SER	0	-0.032	-0.041	36.086	-0.148	-0.148	0.000	0.000	0.000	0.000
22	A	470	ALA	0	-0.045	-0.024	33.748	0.078	0.078	0.000	0.000	0.000	0.000
23	A	471	THR	0	0.003	0.003	28.475	-0.030	-0.030	0.000	0.000	0.000	0.000
24	A	472	VAL	0	0.025	0.037	25.960	-0.035	-0.035	0.000	0.000	0.000	0.000
25	A	473	THR	0	0.003	-0.002	23.320	-0.212	-0.212	0.000	0.000	0.000	0.000
26	A	474	CYS	0	-0.073	-0.010	19.126	-0.502	-0.502	0.000	0.000	0.000	0.000
27	A	475	LEU	0	-0.015	-0.009	18.466	-0.178	-0.178	0.000	0.000	0.000	0.000
28	A	476	VAL	0	0.017	0.010	12.372	-0.269	-0.269	0.000	0.000	0.000	0.000
29	A	477	LYS	1	0.879	0.905	12.627	17.043	17.043	0.000	0.000	0.000	0.000
30	A	478	GLY	0	0.053	0.029	9.753	-0.805	-0.805	0.000	0.000	0.000	0.000
31	A	479	PHE	0	-0.018	0.024	6.551	-1.227	-1.227	0.000	0.000	0.000	0.000
32	A	480	SER	0	-0.005	-0.029	3.100	0.843	1.264	0.050	-0.119	-0.352	0.000
33	A	481	PRO	0	0.029	0.016	2.275	-7.335	-4.612	2.598	-2.212	-3.108	-0.022
34	A	482	ALA	0	0.013	-0.011	5.104	1.238	1.243	-0.001	-0.003	0.000	0.000
35	A	483	ASP	-1	-0.929	-0.951	6.981	-30.597	-30.597	0.000	0.000	0.000	0.000
36	A	484	ILE	0	-0.045	-0.025	7.997	-2.962	-2.962	0.000	0.000	0.000	0.000
37	A	485	SER	0	-0.025	0.007	10.549	2.300	2.300	0.000	0.000	0.000	0.000
38	A	486	VAL	0	0.013	-0.011	13.636	-0.378	-0.378	0.000	0.000	0.000	0.000
39	A	487	GLN	0	0.023	0.034	16.572	1.087	1.087	0.000	0.000	0.000	0.000
40	A	488	TRP	0	0.032	0.003	19.799	0.132	0.132	0.000	0.000	0.000	0.000
41	A	489	LEU	0	-0.030	-0.005	22.853	0.015	0.015	0.000	0.000	0.000	0.000
42	A	490	GLN	0	-0.027	-0.037	24.837	-0.092	-0.092	0.000	0.000	0.000	0.000
43	A	491	ARG	1	0.818	0.863	28.508	9.055	9.055	0.000	0.000	0.000	0.000
44	A	492	GLY	0	0.019	0.022	27.873	0.182	0.182	0.000	0.000	0.000	0.000
45	A	493	GLN	0	-0.035	-0.010	26.591	-0.063	-0.063	0.000	0.000	0.000	0.000
46	A	494	LEU	0	0.006	-0.002	20.427	0.003	0.003	0.000	0.000	0.000	0.000
47	A	495	LEU	0	-0.016	-0.012	24.306	0.496	0.496	0.000	0.000	0.000	0.000
48	A	496	PRO	0	-0.007	0.006	24.375	-0.580	-0.580	0.000	0.000	0.000	0.000
49	A	497	GLN	0	0.031	-0.008	20.694	0.369	0.369	0.000	0.000	0.000	0.000
50	A	498	GLU	-1	-0.896	-0.944	24.945	-11.157	-11.157	0.000	0.000	0.000	0.000
51	A	499	LYS	1	0.891	0.942	27.714	10.668	10.668	0.000	0.000	0.000	0.000
52	A	500	TYR	0	-0.053	-0.019	20.912	-0.163	-0.163	0.000	0.000	0.000	0.000
53	A	501	VAL	0	0.017	0.015	24.400	0.041	0.041	0.000	0.000	0.000	0.000
54	A	502	THR	0	-0.008	-0.013	18.097	0.159	0.159	0.000	0.000	0.000	0.000
55	A	503	SER	0	-0.028	0.000	19.169	0.336	0.336	0.000	0.000	0.000	0.000
56	A	504	ALA	0	0.022	0.013	17.434	-0.918	-0.918	0.000	0.000	0.000	0.000
57	A	505	PRO	0	-0.010	-0.009	12.091	0.590	0.590	0.000	0.000	0.000	0.000
58	A	506	MET	0	-0.030	0.004	14.084	1.004	1.004	0.000	0.000	0.000	0.000
59	A	507	PRO	0	0.013	-0.005	12.388	-0.959	-0.959	0.000	0.000	0.000	0.000
60	A	508	GLU	-1	-0.784	-0.888	11.863	-16.982	-16.982	0.000	0.000	0.000	0.000
61	A	509	PRO	0	-0.027	-0.013	13.566	0.043	0.043	0.000	0.000	0.000	0.000
62	A	510	GLY	0	-0.014	0.000	15.764	0.664	0.664	0.000	0.000	0.000	0.000
63	A	511	ALA	0	-0.053	-0.023	10.777	0.109	0.109	0.000	0.000	0.000	0.000
64	A	512	PRO	0	0.039	0.017	10.990	-1.224	-1.224	0.000	0.000	0.000	0.000
65	A	513	GLY	0	0.019	0.009	8.001	-0.163	-0.163	0.000	0.000	0.000	0.000
66	A	514	PHE	0	-0.052	-0.011	5.684	-3.546	-3.546	0.000	0.000	0.000	0.000
67	A	515	TYR	0	-0.035	-0.014	7.409	1.543	1.543	0.000	0.000	0.000	0.000
68	A	516	PHE	0	-0.030	-0.022	10.253	-0.249	-0.249	0.000	0.000	0.000	0.000
69	A	517	THR	0	0.005	-0.014	13.060	0.250	0.250	0.000	0.000	0.000	0.000
70	A	518	HIS	0	0.013	0.010	15.833	0.044	0.044	0.000	0.000	0.000	0.000
71	A	519	SER	0	0.032	0.010	19.056	0.011	0.011	0.000	0.000	0.000	0.000
72	A	520	ILE	0	-0.022	-0.012	21.440	0.229	0.229	0.000	0.000	0.000	0.000
73	A	521	LEU	0	0.042	0.026	25.058	-0.139	-0.139	0.000	0.000	0.000	0.000
74	A	522	THR	0	-0.056	-0.032	27.535	0.099	0.099	0.000	0.000	0.000	0.000
75	A	523	VAL	0	-0.015	0.009	31.219	-0.014	-0.014	0.000	0.000	0.000	0.000
76	A	524	THR	0	0.018	0.005	33.876	0.205	0.205	0.000	0.000	0.000	0.000
77	A	525	GLU	-1	-0.878	-0.942	36.456	-8.002	-8.002	0.000	0.000	0.000	0.000
78	A	526	GLU	-1	-0.758	-0.879	38.199	-7.397	-7.397	0.000	0.000	0.000	0.000
79	A	527	GLU	-1	-0.843	-0.895	33.893	-9.331	-9.331	0.000	0.000	0.000	0.000
80	A	528	TRP	0	0.081	0.043	29.648	-0.158	-0.158	0.000	0.000	0.000	0.000
81	A	529	ASN	0	-0.046	-0.023	35.368	-0.051	-0.051	0.000	0.000	0.000	0.000
82	A	530	SER	0	-0.109	-0.075	37.774	0.110	0.110	0.000	0.000	0.000	0.000
83	A	531	GLY	0	-0.006	0.001	35.659	0.097	0.097	0.000	0.000	0.000	0.000
84	A	532	GLU	-1	-0.800	-0.832	32.239	-9.582	-9.582	0.000	0.000	0.000	0.000
85	A	533	THR	0	-0.051	-0.025	29.043	-0.122	-0.122	0.000	0.000	0.000	0.000
86	A	534	TYR	0	-0.041	-0.054	27.118	-0.091	-0.091	0.000	0.000	0.000	0.000
87	A	535	THR	0	0.030	0.017	21.596	0.067	0.067	0.000	0.000	0.000	0.000
88	A	537	VAL	0	0.001	-0.008	17.281	-0.314	-0.314	0.000	0.000	0.000	0.000
89	A	538	VAL	0	0.011	-0.011	11.855	-0.148	-0.148	0.000	0.000	0.000	0.000
90	A	539	GLY	0	0.029	0.025	11.944	-0.193	-0.193	0.000	0.000	0.000	0.000
91	A	540	HIS	0	0.013	-0.023	4.060	-0.313	-0.171	-0.001	-0.010	-0.131	0.000
92	A	541	GLU	-1	-0.778	-0.876	1.793	-144.010	-148.834	24.489	-11.438	-8.228	-0.139
93	A	542	ALA	0	-0.019	0.002	2.346	-5.757	-5.146	0.742	-0.369	-0.983	-0.002
94	A	543	LEU	0	-0.051	-0.015	4.116	5.217	5.322	0.001	-0.034	-0.071	0.000
95	A	544	PRO	0	-0.019	-0.017	7.906	-0.619	-0.619	0.000	0.000	0.000	0.000
96	A	545	HIS	0	0.010	0.009	9.878	0.174	0.174	0.000	0.000	0.000	0.000
97	A	546	LEU	0	-0.012	0.010	8.312	1.457	1.457	0.000	0.000	0.000	0.000
98	A	547	VAL	0	0.012	-0.017	10.459	-0.812	-0.812	0.000	0.000	0.000	0.000
99	A	548	THR	0	-0.056	-0.015	12.725	1.012	1.012	0.000	0.000	0.000	0.000
100	A	549	GLU	-1	-0.839	-0.926	14.640	-15.319	-15.319	0.000	0.000	0.000	0.000
101	A	550	ARG	1	0.801	0.896	14.459	17.526	17.526	0.000	0.000	0.000	0.000
102	A	551	THR	0	0.028	-0.006	20.423	-0.116	-0.116	0.000	0.000	0.000	0.000
103	A	552	VAL	0	-0.054	-0.024	24.215	0.081	0.081	0.000	0.000	0.000	0.000
104	A	553	ASP	-1	-0.743	-0.853	27.237	-9.616	-9.616	0.000	0.000	0.000	0.000
105	A	554	LYS	1	0.849	0.931	30.984	7.884	7.884	0.000	0.000	0.000	0.000
106	A	555	SER	0	-0.061	-0.047	32.719	0.266	0.266	0.000	0.000	0.000	0.000
107	A	556	THR	0	-0.075	-0.033	27.495	-0.145	-0.145	0.000	0.000	0.000	0.000

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