FMO DATABASE

FMODB ID: ZV16N

Calculation Name: 3AG7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3AG7

Chain ID: A

ChEMBL ID:

UniProt ID: Q9C9Q4

Base Structure: X-ray

Registration Date: 2023-09-23

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	105
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-803891.717167
FMO2-HF: Nuclear repulsion	762692.780213
FMO2-HF: Total energy	-41198.936954
FMO2-MP2: Total energy	-41320.064153

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:546:GLY)

Summations of interaction energy for fragment #1(A:546:GLY)

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.
37.887	-88.737	181.932	-44.469	-10.84	-0.069

Interaction energy analysis for fragmet #1(A:546:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : 0.006

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	548	LEU	0	-0.014	-0.022	3.809	-0.478	0.607	-0.005	-0.487	-0.593	0.003
4	A	549	GLY	0	0.052	0.060	3.324	1.145	1.750	0.019	-0.285	-0.339	0.001
5	A	550	SER	0	0.016	-0.017	4.226	0.835	0.895	-0.001	-0.008	-0.052	0.000
6	A	551	GLU	-1	-0.919	-0.952	6.091	-0.262	-0.262	0.000	0.000	0.000	0.000
7	A	552	GLU	-1	-0.804	-0.919	1.551	32.783	-95.855	181.916	-43.560	-9.718	-0.073
8	A	553	ILE	0	-0.002	0.005	5.091	0.684	0.736	-0.001	-0.004	-0.047	0.000
9	A	554	LYS	1	0.972	0.987	7.464	1.523	1.523	0.000	0.000	0.000	0.000
10	A	555	ASN	0	0.015	0.008	7.856	0.245	0.245	0.000	0.000	0.000	0.000
11	A	556	ILE	0	-0.039	-0.013	6.954	0.228	0.228	0.000	0.000	0.000	0.000
12	A	557	ASP	-1	-0.807	-0.881	10.418	-0.652	-0.652	0.000	0.000	0.000	0.000
13	A	558	ALA	0	-0.055	-0.035	12.855	0.106	0.106	0.000	0.000	0.000	0.000
14	A	559	LYS	1	0.933	0.967	13.398	0.038	0.038	0.000	0.000	0.000	0.000
15	A	560	ILE	0	0.039	0.012	13.563	0.061	0.061	0.000	0.000	0.000	0.000
16	A	561	ARG	1	0.983	1.005	15.513	0.420	0.420	0.000	0.000	0.000	0.000
17	A	562	LYS	1	0.919	0.964	17.453	0.109	0.109	0.000	0.000	0.000	0.000
18	A	563	TRP	0	-0.085	-0.057	18.886	0.015	0.015	0.000	0.000	0.000	0.000
19	A	564	SER	0	0.029	0.012	20.481	0.017	0.017	0.000	0.000	0.000	0.000
20	A	565	SER	0	0.025	0.021	22.399	0.005	0.005	0.000	0.000	0.000	0.000
21	A	566	GLY	0	0.016	0.006	24.547	0.014	0.014	0.000	0.000	0.000	0.000
22	A	567	LYS	1	0.788	0.895	23.400	0.081	0.081	0.000	0.000	0.000	0.000
23	A	568	SER	0	0.014	0.005	25.717	0.004	0.004	0.000	0.000	0.000	0.000
24	A	569	GLY	0	0.095	0.053	26.942	0.008	0.008	0.000	0.000	0.000	0.000
25	A	570	ASN	0	0.015	0.019	29.105	0.012	0.012	0.000	0.000	0.000	0.000
26	A	571	ILE	0	0.036	0.004	27.989	0.002	0.002	0.000	0.000	0.000	0.000
27	A	572	ARG	1	0.891	0.924	29.113	0.044	0.044	0.000	0.000	0.000	0.000
28	A	573	SER	0	0.007	0.017	28.575	0.008	0.008	0.000	0.000	0.000	0.000
29	A	574	LEU	0	0.007	0.022	23.540	0.005	0.005	0.000	0.000	0.000	0.000
30	A	575	LEU	0	0.000	-0.012	25.151	0.007	0.007	0.000	0.000	0.000	0.000
31	A	576	SER	0	-0.039	-0.029	26.840	0.010	0.010	0.000	0.000	0.000	0.000
32	A	577	THR	0	-0.037	-0.018	24.403	0.006	0.006	0.000	0.000	0.000	0.000
33	A	578	LEU	0	0.070	0.034	21.002	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	579	GLN	0	0.030	0.015	20.604	-0.008	-0.008	0.000	0.000	0.000	0.000
35	A	580	TYR	0	-0.046	-0.019	20.489	0.020	0.020	0.000	0.000	0.000	0.000
36	A	581	ILE	0	-0.079	-0.033	15.563	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	582	LEU	0	-0.027	-0.009	15.690	-0.010	-0.010	0.000	0.000	0.000	0.000
38	A	583	TRP	0	0.026	0.013	13.166	0.036	0.036	0.000	0.000	0.000	0.000
39	A	584	SER	0	0.041	-0.009	15.216	-0.041	-0.041	0.000	0.000	0.000	0.000
40	A	585	GLY	0	-0.011	0.001	16.864	0.014	0.014	0.000	0.000	0.000	0.000
41	A	586	SER	0	0.008	0.016	17.777	-0.014	-0.014	0.000	0.000	0.000	0.000
42	A	587	GLY	0	0.018	0.002	19.145	-0.017	-0.017	0.000	0.000	0.000	0.000
43	A	588	TRP	0	-0.041	-0.018	22.008	-0.011	-0.011	0.000	0.000	0.000	0.000
44	A	589	LYS	1	0.928	0.964	23.809	-0.038	-0.038	0.000	0.000	0.000	0.000
45	A	590	PRO	0	0.017	0.008	26.023	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	591	VAL	0	0.004	0.007	27.765	0.002	0.002	0.000	0.000	0.000	0.000
47	A	592	PRO	0	0.036	0.031	30.430	-0.006	-0.006	0.000	0.000	0.000	0.000
48	A	593	LEU	0	0.068	-0.008	32.496	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	594	MET	0	-0.012	-0.014	34.498	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	595	ASP	-1	-0.877	-0.913	34.706	0.007	0.007	0.000	0.000	0.000	0.000
51	A	596	MET	0	-0.115	-0.049	30.028	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	597	ILE	0	0.050	0.044	35.632	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	598	GLU	-1	-0.846	-0.920	38.906	-0.021	-0.021	0.000	0.000	0.000	0.000
54	A	599	GLY	0	0.062	0.010	38.686	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	600	ASN	0	-0.007	-0.024	37.746	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	601	ALA	0	0.035	0.045	36.715	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	602	VAL	0	-0.019	-0.002	33.031	0.000	0.000	0.000	0.000	0.000	0.000
58	A	603	ARG	1	0.918	0.943	32.814	0.046	0.046	0.000	0.000	0.000	0.000
59	A	604	LYS	1	0.940	0.981	33.060	0.006	0.006	0.000	0.000	0.000	0.000
60	A	605	SER	0	0.007	-0.011	30.153	0.003	0.003	0.000	0.000	0.000	0.000
61	A	606	TYR	0	0.057	0.026	27.399	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	607	GLN	0	-0.002	0.005	28.092	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	608	ARG	1	0.927	0.952	27.835	0.002	0.002	0.000	0.000	0.000	0.000
64	A	609	ALA	0	0.055	0.039	24.263	0.003	0.003	0.000	0.000	0.000	0.000
65	A	610	LEU	0	0.028	0.008	23.505	-0.011	-0.011	0.000	0.000	0.000	0.000
66	A	611	LEU	0	-0.075	-0.034	24.109	-0.009	-0.009	0.000	0.000	0.000	0.000
67	A	612	ILE	0	-0.063	-0.024	19.806	0.008	0.008	0.000	0.000	0.000	0.000
68	A	613	LEU	0	-0.002	-0.018	18.165	-0.007	-0.007	0.000	0.000	0.000	0.000
69	A	614	HIS	0	0.049	0.049	19.757	-0.039	-0.039	0.000	0.000	0.000	0.000
70	A	615	PRO	0	0.045	0.021	18.753	0.009	0.009	0.000	0.000	0.000	0.000
71	A	616	ASP	-1	-0.852	-0.944	19.444	-0.119	-0.119	0.000	0.000	0.000	0.000
72	A	617	LYS	1	0.928	0.965	21.657	0.066	0.066	0.000	0.000	0.000	0.000
73	A	618	LEU	0	-0.010	-0.003	15.847	0.020	0.020	0.000	0.000	0.000	0.000
74	A	619	GLN	0	-0.025	-0.001	16.967	-0.028	-0.028	0.000	0.000	0.000	0.000
75	A	620	GLN	0	-0.084	-0.053	18.001	0.042	0.042	0.000	0.000	0.000	0.000
76	A	621	LYS	1	0.887	0.957	18.410	0.019	0.019	0.000	0.000	0.000	0.000
77	A	622	GLY	0	0.010	0.020	15.889	0.039	0.039	0.000	0.000	0.000	0.000
78	A	623	ALA	0	-0.016	0.003	13.374	0.044	0.044	0.000	0.000	0.000	0.000
79	A	624	SER	0	0.035	0.010	7.766	-0.177	-0.177	0.000	0.000	0.000	0.000
80	A	625	ALA	0	0.035	-0.002	7.304	-0.012	-0.012	0.000	0.000	0.000	0.000
81	A	626	ASN	0	0.064	0.033	3.197	0.567	0.779	0.004	-0.125	-0.091	0.000
82	A	627	GLN	0	0.005	0.010	7.750	0.157	0.157	0.000	0.000	0.000	0.000
83	A	628	LYS	1	0.933	0.973	10.939	0.426	0.426	0.000	0.000	0.000	0.000
84	A	629	TYR	0	0.003	-0.023	9.661	0.013	0.013	0.000	0.000	0.000	0.000
85	A	630	MET	0	-0.046	-0.024	11.030	0.109	0.109	0.000	0.000	0.000	0.000
86	A	631	ALA	0	-0.023	-0.026	12.587	0.070	0.070	0.000	0.000	0.000	0.000
87	A	632	GLU	-1	-0.917	-0.942	15.083	-0.493	-0.493	0.000	0.000	0.000	0.000
88	A	633	LYS	1	0.968	0.985	14.519	0.596	0.596	0.000	0.000	0.000	0.000
89	A	634	VAL	0	-0.020	-0.013	16.484	0.047	0.047	0.000	0.000	0.000	0.000
90	A	635	PHE	0	-0.042	-0.030	18.841	0.044	0.044	0.000	0.000	0.000	0.000
91	A	636	GLU	-1	-0.898	-0.947	20.018	-0.326	-0.326	0.000	0.000	0.000	0.000
92	A	637	LEU	0	-0.015	-0.004	20.044	0.027	0.027	0.000	0.000	0.000	0.000
93	A	638	LEU	0	-0.044	-0.027	22.796	0.024	0.024	0.000	0.000	0.000	0.000
94	A	639	GLN	0	-0.035	-0.021	24.702	0.007	0.007	0.000	0.000	0.000	0.000
95	A	640	GLU	-1	-0.893	-0.932	26.242	-0.151	-0.151	0.000	0.000	0.000	0.000
96	A	641	ALA	0	-0.010	-0.009	27.494	0.013	0.013	0.000	0.000	0.000	0.000
97	A	642	TRP	0	-0.052	-0.043	29.056	0.018	0.018	0.000	0.000	0.000	0.000
98	A	643	ASP	-1	-0.930	-0.965	30.847	-0.094	-0.094	0.000	0.000	0.000	0.000
99	A	644	HIS	0	0.066	0.043	32.319	0.003	0.003	0.000	0.000	0.000	0.000
100	A	645	PHE	0	-0.084	-0.052	33.419	0.010	0.010	0.000	0.000	0.000	0.000
101	A	646	ASN	0	-0.074	-0.034	34.402	0.013	0.013	0.000	0.000	0.000	0.000
102	A	647	THR	0	0.000	0.014	36.891	0.003	0.003	0.000	0.000	0.000	0.000
103	A	648	LEU	0	0.015	0.016	37.212	0.005	0.005	0.000	0.000	0.000	0.000
104	A	649	GLY	0	-0.028	0.002	37.141	0.005	0.005	0.000	0.000	0.000	0.000
105	A	650	PRO	0	-0.023	-0.019	35.633	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:546:GLY)