FMO DATABASE

FMODB ID: 39QVL

Calculation Name: 3N7C-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3N7C

Chain ID: A

ChEMBL ID:

UniProt ID: Q75DJ0

Base Structure: X-ray

Registration Date: 2023-06-21

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	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	113
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-898076.19747
FMO2-HF: Nuclear repulsion	853736.637159
FMO2-HF: Total energy	-44339.560311
FMO2-MP2: Total energy	-44468.818813

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:503:GLU)

Summations of interaction energy for fragment #1(A:503:GLU)

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.
-319.26	-310.606	33.064	-20.084	-21.633	0.171

Interaction energy analysis for fragmet #1(A:503:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.810 / q_NPA : -0.902

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	505	VAL	0	-0.018	-0.027	3.804	3.204	4.957	-0.008	-0.871	-0.875	0.002
4	A	506	LEU	0	-0.015	0.000	5.768	-3.169	-3.169	0.000	0.000	0.000	0.000
5	A	507	PHE	0	0.023	-0.005	8.430	-2.570	-2.570	0.000	0.000	0.000	0.000
6	A	508	CYS	0	-0.023	-0.037	9.258	3.393	3.393	0.000	0.000	0.000	0.000
7	A	509	GLU	-1	-0.823	-0.877	11.584	15.202	15.202	0.000	0.000	0.000	0.000
8	A	510	LYS	1	0.830	0.915	14.825	-15.936	-15.936	0.000	0.000	0.000	0.000
9	A	511	ALA	0	-0.036	-0.028	16.562	-0.541	-0.541	0.000	0.000	0.000	0.000
10	A	512	LYS	1	0.931	0.968	18.311	-13.016	-13.016	0.000	0.000	0.000	0.000
11	A	513	LEU	0	0.000	0.024	16.269	0.143	0.143	0.000	0.000	0.000	0.000
12	A	514	LEU	0	-0.056	-0.027	19.433	-0.676	-0.676	0.000	0.000	0.000	0.000
13	A	515	ILE	0	0.025	0.007	19.315	0.475	0.475	0.000	0.000	0.000	0.000
14	A	516	PHE	0	0.004	-0.001	23.068	-0.469	-0.469	0.000	0.000	0.000	0.000
15	A	517	ASP	-1	-0.940	-0.974	26.407	11.020	11.020	0.000	0.000	0.000	0.000
16	A	518	SER	0	0.019	0.011	28.915	-0.154	-0.154	0.000	0.000	0.000	0.000
17	A	519	ASP	-1	-0.816	-0.909	32.183	9.261	9.261	0.000	0.000	0.000	0.000
18	A	520	THR	0	-0.034	-0.019	34.138	-0.266	-0.266	0.000	0.000	0.000	0.000
19	A	521	LYS	1	0.805	0.903	32.694	-9.064	-9.064	0.000	0.000	0.000	0.000
20	A	522	GLY	0	0.057	0.035	31.411	-0.226	-0.226	0.000	0.000	0.000	0.000
21	A	523	TYR	0	-0.055	-0.012	23.887	0.113	0.113	0.000	0.000	0.000	0.000
22	A	524	THR	0	0.050	0.022	26.568	-0.016	-0.016	0.000	0.000	0.000	0.000
23	A	525	SER	0	-0.007	-0.031	23.924	0.682	0.682	0.000	0.000	0.000	0.000
24	A	526	ARG	1	0.941	0.970	20.572	-13.763	-13.763	0.000	0.000	0.000	0.000
25	A	527	GLY	0	0.032	0.013	19.964	0.264	0.264	0.000	0.000	0.000	0.000
26	A	528	VAL	0	-0.075	-0.043	19.477	0.036	0.036	0.000	0.000	0.000	0.000
27	A	529	GLY	0	0.056	0.013	15.622	-0.022	-0.022	0.000	0.000	0.000	0.000
28	A	530	GLU	-1	-0.858	-0.902	12.507	18.489	18.489	0.000	0.000	0.000	0.000
29	A	531	LEU	0	-0.030	-0.028	11.165	2.254	2.254	0.000	0.000	0.000	0.000
30	A	532	LYS	1	0.972	0.968	6.900	-35.187	-35.187	0.000	0.000	0.000	0.000
31	A	533	LEU	0	-0.001	0.015	7.757	2.274	2.274	0.000	0.000	0.000	0.000
32	A	534	LEU	0	-0.056	-0.028	2.438	-7.669	-4.086	2.038	-2.152	-3.469	0.025
33	A	535	ARG	1	0.941	0.998	3.584	-29.011	-27.815	0.011	-0.279	-0.928	0.000
34	A	536	LYS	1	0.901	0.947	2.192	-37.632	-37.072	9.298	-5.223	-4.634	-0.031
35	A	537	LYS	1	0.941	0.959	2.687	-45.169	-44.771	1.756	0.337	-2.491	0.012
36	A	538	ASP	-1	-0.825	-0.899	4.429	32.607	32.724	0.000	-0.025	-0.092	0.000
37	A	539	ASP	-1	-0.924	-0.963	6.324	26.737	26.737	0.000	0.000	0.000	0.000
38	A	540	LYS	1	0.899	0.926	6.138	-26.562	-26.562	0.000	0.000	0.000	0.000
39	A	541	GLY	0	0.064	0.032	8.651	-0.097	-0.097	0.000	0.000	0.000	0.000
40	A	542	LYS	1	0.876	0.959	4.443	-42.484	-42.353	-0.001	-0.013	-0.117	0.000
41	A	543	VAL	0	0.036	0.002	4.949	7.362	7.457	-0.001	-0.004	-0.089	0.000
42	A	544	ARG	1	0.769	0.858	1.782	-138.750	-137.929	19.971	-11.854	-8.938	0.163
43	A	545	VAL	0	0.025	0.022	5.951	1.146	1.146	0.000	0.000	0.000	0.000
44	A	546	LEU	0	-0.050	-0.030	5.618	0.378	0.378	0.000	0.000	0.000	0.000
45	A	547	CYS	0	-0.017	0.003	8.356	-1.950	-1.950	0.000	0.000	0.000	0.000
46	A	548	ARG	1	0.931	0.972	7.902	-32.042	-32.042	0.000	0.000	0.000	0.000
47	A	549	SER	0	0.087	0.036	12.525	-0.384	-0.384	0.000	0.000	0.000	0.000
48	A	550	GLU	-1	-0.932	-0.955	16.228	16.111	16.111	0.000	0.000	0.000	0.000
49	A	551	GLY	0	0.048	0.025	18.316	-0.840	-0.840	0.000	0.000	0.000	0.000
50	A	552	MET	0	0.019	0.020	18.920	-0.595	-0.595	0.000	0.000	0.000	0.000
51	A	553	GLY	0	-0.056	-0.028	14.578	0.652	0.652	0.000	0.000	0.000	0.000
52	A	554	HIS	0	0.043	0.022	13.950	1.935	1.935	0.000	0.000	0.000	0.000
53	A	555	VAL	0	-0.016	-0.015	10.436	1.241	1.241	0.000	0.000	0.000	0.000
54	A	556	LEU	0	-0.030	0.000	12.973	-1.209	-1.209	0.000	0.000	0.000	0.000
55	A	557	LEU	0	0.003	-0.001	11.968	-0.859	-0.859	0.000	0.000	0.000	0.000
56	A	558	ASN	0	0.041	0.006	7.160	7.303	7.303	0.000	0.000	0.000	0.000
57	A	559	THR	0	0.011	0.018	8.865	-1.105	-1.105	0.000	0.000	0.000	0.000
58	A	560	SER	0	0.007	0.005	8.000	4.584	4.584	0.000	0.000	0.000	0.000
59	A	561	VAL	0	0.010	0.006	8.794	-2.568	-2.568	0.000	0.000	0.000	0.000
60	A	562	VAL	0	0.002	0.007	10.810	0.482	0.482	0.000	0.000	0.000	0.000
61	A	563	LYS	1	0.907	0.920	13.925	-18.648	-18.648	0.000	0.000	0.000	0.000
62	A	564	SER	0	0.004	-0.003	15.994	-0.564	-0.564	0.000	0.000	0.000	0.000
63	A	565	PHE	0	-0.018	0.009	16.552	-0.890	-0.890	0.000	0.000	0.000	0.000
64	A	566	LYS	1	0.984	0.993	18.037	-12.319	-12.319	0.000	0.000	0.000	0.000
65	A	567	TYR	0	0.055	0.049	14.201	-0.018	-0.018	0.000	0.000	0.000	0.000
66	A	568	GLN	0	-0.033	-0.028	18.430	0.025	0.025	0.000	0.000	0.000	0.000
67	A	569	PRO	0	0.045	0.022	21.427	0.265	0.265	0.000	0.000	0.000	0.000
68	A	570	ILE	0	-0.042	-0.027	23.691	-0.134	-0.134	0.000	0.000	0.000	0.000
69	A	571	ASP	-1	-0.790	-0.900	26.212	10.343	10.343	0.000	0.000	0.000	0.000
70	A	572	ALA	0	0.003	0.000	28.136	0.311	0.311	0.000	0.000	0.000	0.000
71	A	573	ASP	-1	-0.841	-0.916	30.109	9.568	9.568	0.000	0.000	0.000	0.000
72	A	574	ASN	0	-0.105	-0.054	27.401	0.023	0.023	0.000	0.000	0.000	0.000
73	A	575	GLU	-1	-0.808	-0.920	23.959	12.494	12.494	0.000	0.000	0.000	0.000
74	A	576	ASN	0	-0.005	-0.014	22.864	0.393	0.393	0.000	0.000	0.000	0.000
75	A	577	LEU	0	-0.047	-0.016	22.686	0.464	0.464	0.000	0.000	0.000	0.000
76	A	578	ILE	0	-0.023	0.005	17.862	-0.375	-0.375	0.000	0.000	0.000	0.000
77	A	579	LYS	1	0.962	0.989	20.218	-12.506	-12.506	0.000	0.000	0.000	0.000
78	A	580	TRP	0	0.015	-0.016	11.567	0.293	0.293	0.000	0.000	0.000	0.000
79	A	581	PRO	0	0.008	0.006	17.795	-0.113	-0.113	0.000	0.000	0.000	0.000
80	A	582	ILE	0	-0.053	-0.029	14.085	1.762	1.762	0.000	0.000	0.000	0.000
81	A	583	ILE	0	0.001	0.013	16.845	-1.062	-1.062	0.000	0.000	0.000	0.000
82	A	584	THR	0	0.024	-0.010	17.553	1.334	1.334	0.000	0.000	0.000	0.000
83	A	585	ASP	-1	-0.859	-0.912	20.006	13.564	13.564	0.000	0.000	0.000	0.000
84	A	586	GLY	0	-0.004	-0.012	21.398	-0.604	-0.604	0.000	0.000	0.000	0.000
85	A	587	LYS	1	0.852	0.918	23.038	-13.777	-13.777	0.000	0.000	0.000	0.000
86	A	588	LEU	0	-0.038	-0.017	20.594	0.735	0.735	0.000	0.000	0.000	0.000
87	A	589	GLU	-1	-0.817	-0.892	20.466	14.253	14.253	0.000	0.000	0.000	0.000
88	A	590	THR	0	-0.043	-0.027	20.607	0.617	0.617	0.000	0.000	0.000	0.000
89	A	591	PHE	0	0.019	0.017	16.621	-0.212	-0.212	0.000	0.000	0.000	0.000
90	A	592	ILE	0	-0.003	-0.009	20.081	-0.104	-0.104	0.000	0.000	0.000	0.000
91	A	593	ILE	0	0.003	0.007	14.953	0.349	0.349	0.000	0.000	0.000	0.000
92	A	594	LYS	1	0.947	0.983	19.053	-12.582	-12.582	0.000	0.000	0.000	0.000
93	A	595	VAL	0	0.041	0.025	17.880	0.507	0.507	0.000	0.000	0.000	0.000
94	A	596	LYS	1	0.784	0.883	19.531	-15.979	-15.979	0.000	0.000	0.000	0.000
95	A	597	GLN	0	0.031	0.014	22.740	-0.638	-0.638	0.000	0.000	0.000	0.000
96	A	598	LYS	1	0.880	0.942	22.826	-10.301	-10.301	0.000	0.000	0.000	0.000
97	A	599	ALA	0	-0.003	-0.001	23.188	0.167	0.167	0.000	0.000	0.000	0.000
98	A	600	ASP	-1	-0.797	-0.912	18.949	15.227	15.227	0.000	0.000	0.000	0.000
99	A	601	GLY	0	-0.004	0.003	18.326	0.936	0.936	0.000	0.000	0.000	0.000
100	A	602	ARG	1	0.868	0.923	19.601	-11.651	-11.651	0.000	0.000	0.000	0.000
101	A	603	ARG	1	0.970	0.989	15.927	-15.007	-15.007	0.000	0.000	0.000	0.000
102	A	604	LEU	0	-0.015	0.017	13.407	0.804	0.804	0.000	0.000	0.000	0.000
103	A	605	VAL	0	0.031	0.002	15.301	0.925	0.925	0.000	0.000	0.000	0.000
104	A	606	GLY	0	-0.007	-0.002	17.460	0.207	0.207	0.000	0.000	0.000	0.000
105	A	607	ALA	0	0.002	-0.002	12.228	0.325	0.325	0.000	0.000	0.000	0.000
106	A	608	VAL	0	-0.016	-0.014	12.215	1.261	1.261	0.000	0.000	0.000	0.000
107	A	609	ALA	0	0.022	0.017	13.880	0.394	0.394	0.000	0.000	0.000	0.000
108	A	610	ASP	-1	-0.946	-0.963	13.432	19.731	19.731	0.000	0.000	0.000	0.000
109	A	611	ALA	0	0.003	-0.009	10.069	0.474	0.474	0.000	0.000	0.000	0.000
110	A	612	GLN	0	-0.061	-0.049	12.003	-0.097	-0.097	0.000	0.000	0.000	0.000
111	A	613	GLN	0	-0.068	-0.039	14.254	-1.241	-1.241	0.000	0.000	0.000	0.000
112	A	614	ALA	0	0.008	0.015	12.306	-0.412	-0.412	0.000	0.000	0.000	0.000
113	A	615	MET	0	-0.065	0.003	10.550	-1.124	-1.124	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:503:GLU)