FMO DATABASE

FMODB ID: R8V98

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

Total energy (hartree)

FMO2-HF: Electronic energy	-805014.209656
FMO2-HF: Nuclear repulsion	763814.495378
FMO2-HF: Total energy	-41199.714278
FMO2-MP2: Total energy	-41320.827048

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.
-4.721	-13.447	22.465	-8.536	-5.201	-0.052

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 : 0.057 / q_NPA : 0.013

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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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	-0.029	-0.034	3.809	-0.505	0.717	-0.005	-0.575	-0.642	0.003
4	A	549	GLY	0	0.040	0.055	3.199	1.246	1.732	0.014	-0.214	-0.286	0.000
5	A	550	SER	0	0.041	0.000	4.205	0.852	0.925	-0.001	-0.013	-0.059	0.000
6	A	551	GLU	-1	-0.920	-0.962	5.854	-0.023	-0.023	0.000	0.000	0.000	0.000
7	A	552	GLU	-1	-0.826	-0.911	1.718	-11.272	-21.995	22.454	-7.629	-4.102	-0.055
8	A	553	ILE	0	0.006	0.003	5.144	0.839	0.894	-0.001	-0.004	-0.049	0.000
9	A	554	LYS	1	0.898	0.947	7.570	1.668	1.668	0.000	0.000	0.000	0.000
10	A	555	ASN	0	-0.016	-0.007	7.875	0.431	0.431	0.000	0.000	0.000	0.000
11	A	556	ILE	0	-0.033	-0.010	6.880	0.269	0.269	0.000	0.000	0.000	0.000
12	A	557	ASP	-1	-0.775	-0.869	10.371	-0.831	-0.831	0.000	0.000	0.000	0.000
13	A	558	ALA	0	-0.039	-0.022	12.863	0.128	0.128	0.000	0.000	0.000	0.000
14	A	559	LYS	1	0.882	0.955	13.233	0.233	0.233	0.000	0.000	0.000	0.000
15	A	560	ILE	0	0.034	0.011	13.687	0.074	0.074	0.000	0.000	0.000	0.000
16	A	561	ARG	1	0.972	1.015	15.205	0.542	0.542	0.000	0.000	0.000	0.000
17	A	562	LYS	1	0.949	0.979	17.560	0.172	0.172	0.000	0.000	0.000	0.000
18	A	563	TRP	0	-0.074	-0.052	18.808	0.019	0.019	0.000	0.000	0.000	0.000
19	A	564	SER	0	0.025	-0.008	20.201	0.024	0.024	0.000	0.000	0.000	0.000
20	A	565	SER	0	0.012	0.015	22.326	0.011	0.011	0.000	0.000	0.000	0.000
21	A	566	GLY	0	0.019	0.009	24.498	0.015	0.015	0.000	0.000	0.000	0.000
22	A	567	LYS	1	0.772	0.884	23.145	0.141	0.141	0.000	0.000	0.000	0.000
23	A	568	SER	0	0.012	0.007	25.508	0.001	0.001	0.000	0.000	0.000	0.000
24	A	569	GLY	0	0.057	0.038	26.901	0.012	0.012	0.000	0.000	0.000	0.000
25	A	570	ASN	0	-0.002	0.001	29.018	0.014	0.014	0.000	0.000	0.000	0.000
26	A	571	ILE	0	0.020	0.002	27.858	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	572	ARG	1	0.893	0.919	28.984	0.069	0.069	0.000	0.000	0.000	0.000
28	A	573	SER	0	0.019	0.035	28.545	0.006	0.006	0.000	0.000	0.000	0.000
29	A	574	LEU	0	0.007	0.022	23.486	0.002	0.002	0.000	0.000	0.000	0.000
30	A	575	LEU	0	0.014	-0.006	24.995	0.003	0.003	0.000	0.000	0.000	0.000
31	A	576	SER	0	-0.022	-0.025	26.653	0.009	0.009	0.000	0.000	0.000	0.000
32	A	577	THR	0	-0.043	-0.027	24.356	0.007	0.007	0.000	0.000	0.000	0.000
33	A	578	LEU	0	0.071	0.040	20.858	-0.007	-0.007	0.000	0.000	0.000	0.000
34	A	579	GLN	0	0.014	0.003	20.395	-0.017	-0.017	0.000	0.000	0.000	0.000
35	A	580	TYR	0	-0.041	-0.016	20.256	0.017	0.017	0.000	0.000	0.000	0.000
36	A	581	ILE	0	-0.059	-0.028	15.350	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	582	LEU	0	-0.014	-0.010	15.488	-0.033	-0.033	0.000	0.000	0.000	0.000
38	A	583	TRP	0	0.020	0.016	12.914	0.029	0.029	0.000	0.000	0.000	0.000
39	A	584	SER	0	0.026	-0.005	14.948	-0.027	-0.027	0.000	0.000	0.000	0.000
40	A	585	GLY	0	0.025	0.012	16.781	0.006	0.006	0.000	0.000	0.000	0.000
41	A	586	SER	0	-0.011	0.001	17.465	-0.010	-0.010	0.000	0.000	0.000	0.000
42	A	587	GLY	0	0.019	0.003	18.890	-0.014	-0.014	0.000	0.000	0.000	0.000
43	A	588	TRP	0	-0.036	-0.017	21.766	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	589	LYS	1	0.931	0.967	23.566	0.002	0.002	0.000	0.000	0.000	0.000
45	A	590	PRO	0	0.020	0.011	25.904	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	591	VAL	0	0.006	0.006	27.521	0.005	0.005	0.000	0.000	0.000	0.000
47	A	592	PRO	0	0.027	0.029	30.221	-0.008	-0.008	0.000	0.000	0.000	0.000
48	A	593	LEU	0	0.066	-0.005	32.126	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	594	MET	0	-0.011	-0.012	34.310	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	595	ASP	-1	-0.882	-0.926	34.436	-0.018	-0.018	0.000	0.000	0.000	0.000
51	A	596	MET	0	-0.096	-0.037	29.784	-0.007	-0.007	0.000	0.000	0.000	0.000
52	A	597	ILE	0	0.046	0.042	35.452	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	598	GLU	-1	-0.790	-0.890	38.738	-0.047	-0.047	0.000	0.000	0.000	0.000
54	A	599	GLY	0	0.062	0.015	38.529	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	600	ASN	0	-0.047	-0.047	37.603	-0.006	-0.006	0.000	0.000	0.000	0.000
56	A	601	ALA	0	0.040	0.049	36.536	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	602	VAL	0	-0.031	-0.004	32.954	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	603	ARG	1	0.899	0.938	32.663	0.072	0.072	0.000	0.000	0.000	0.000
59	A	604	LYS	1	0.946	0.986	32.910	0.036	0.036	0.000	0.000	0.000	0.000
60	A	605	SER	0	-0.009	-0.014	30.007	0.001	0.001	0.000	0.000	0.000	0.000
61	A	606	TYR	0	0.060	0.021	27.217	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	607	GLN	0	-0.005	0.004	27.947	-0.005	-0.005	0.000	0.000	0.000	0.000
63	A	608	ARG	1	0.939	0.957	27.542	0.036	0.036	0.000	0.000	0.000	0.000
64	A	609	ALA	0	0.045	0.029	24.195	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	610	LEU	0	0.018	0.006	23.352	-0.018	-0.018	0.000	0.000	0.000	0.000
66	A	611	LEU	0	-0.055	-0.024	23.976	-0.014	-0.014	0.000	0.000	0.000	0.000
67	A	612	ILE	0	-0.073	-0.029	19.712	0.006	0.006	0.000	0.000	0.000	0.000
68	A	613	LEU	0	0.001	-0.013	17.844	-0.018	-0.018	0.000	0.000	0.000	0.000
69	A	614	HIS	0	0.051	0.045	19.657	-0.048	-0.048	0.000	0.000	0.000	0.000
70	A	615	PRO	0	0.053	0.022	18.711	0.007	0.007	0.000	0.000	0.000	0.000
71	A	616	ASP	-1	-0.811	-0.911	19.416	-0.169	-0.169	0.000	0.000	0.000	0.000
72	A	617	LYS	1	0.787	0.887	21.630	0.149	0.149	0.000	0.000	0.000	0.000
73	A	618	LEU	0	0.009	0.005	15.820	0.015	0.015	0.000	0.000	0.000	0.000
74	A	619	GLN	0	-0.005	0.007	16.478	-0.038	-0.038	0.000	0.000	0.000	0.000
75	A	620	GLN	0	-0.021	-0.020	17.976	0.043	0.043	0.000	0.000	0.000	0.000
76	A	621	LYS	1	0.904	0.971	18.340	0.097	0.097	0.000	0.000	0.000	0.000
77	A	622	GLY	0	0.011	0.020	15.868	0.037	0.037	0.000	0.000	0.000	0.000
78	A	623	ALA	0	-0.042	-0.008	13.351	0.029	0.029	0.000	0.000	0.000	0.000
79	A	624	SER	0	0.032	-0.019	7.682	-0.155	-0.155	0.000	0.000	0.000	0.000
80	A	625	ALA	0	0.026	-0.004	7.340	0.001	0.001	0.000	0.000	0.000	0.000
81	A	626	ASN	0	0.064	0.042	3.187	0.612	0.773	0.004	-0.101	-0.063	0.000
82	A	627	GLN	0	0.030	0.042	7.663	0.215	0.215	0.000	0.000	0.000	0.000
83	A	628	LYS	1	0.909	0.958	10.782	0.560	0.560	0.000	0.000	0.000	0.000
84	A	629	TYR	0	0.003	-0.015	9.657	0.040	0.040	0.000	0.000	0.000	0.000
85	A	630	MET	0	-0.040	-0.015	10.840	0.133	0.133	0.000	0.000	0.000	0.000
86	A	631	ALA	0	-0.017	-0.029	12.507	0.096	0.096	0.000	0.000	0.000	0.000
87	A	632	GLU	-1	-0.858	-0.896	15.029	-0.608	-0.608	0.000	0.000	0.000	0.000
88	A	633	LYS	1	0.819	0.883	14.559	0.663	0.663	0.000	0.000	0.000	0.000
89	A	634	VAL	0	-0.017	-0.010	16.393	0.059	0.059	0.000	0.000	0.000	0.000
90	A	635	PHE	0	-0.034	-0.026	18.765	0.055	0.055	0.000	0.000	0.000	0.000
91	A	636	GLU	-1	-0.820	-0.904	19.582	-0.429	-0.429	0.000	0.000	0.000	0.000
92	A	637	LEU	0	-0.006	0.001	20.017	0.033	0.033	0.000	0.000	0.000	0.000
93	A	638	LEU	0	-0.016	-0.014	22.434	0.030	0.030	0.000	0.000	0.000	0.000
94	A	639	GLN	0	-0.063	-0.037	24.603	0.014	0.014	0.000	0.000	0.000	0.000
95	A	640	GLU	-1	-0.850	-0.910	26.216	-0.192	-0.192	0.000	0.000	0.000	0.000
96	A	641	ALA	0	0.009	-0.004	27.444	0.016	0.016	0.000	0.000	0.000	0.000
97	A	642	TRP	0	-0.034	-0.034	28.991	0.022	0.022	0.000	0.000	0.000	0.000
98	A	643	ASP	-1	-0.919	-0.949	30.804	-0.124	-0.124	0.000	0.000	0.000	0.000
99	A	644	HIS	0	0.060	0.044	32.279	0.004	0.004	0.000	0.000	0.000	0.000
100	A	645	PHE	0	-0.074	-0.049	33.353	0.013	0.013	0.000	0.000	0.000	0.000
101	A	646	ASN	0	-0.088	-0.050	34.132	0.016	0.016	0.000	0.000	0.000	0.000
102	A	647	THR	0	0.001	0.007	36.786	0.004	0.004	0.000	0.000	0.000	0.000
103	A	648	LEU	0	0.015	0.016	37.135	0.006	0.006	0.000	0.000	0.000	0.000
104	A	649	GLY	0	-0.030	0.002	37.062	0.006	0.006	0.000	0.000	0.000	0.000
105	A	650	PRO	0	-0.019	-0.018	35.661	-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)