FMO DATABASE

FMODB ID: K3163

Calculation Name: 3A4C-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3A4C

Chain ID: A

ChEMBL ID:

UniProt ID: Q8R4E9

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	106
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-829720.407481
FMO2-HF: Nuclear repulsion	786805.513983
FMO2-HF: Total energy	-42914.893498
FMO2-MP2: Total energy	-43037.922388

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:452:ARG)

Summations of interaction energy for fragment #1(A:452:ARG)

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.
-148.652	-149.387	35.425	-12.756	-21.933	-0.111

Interaction energy analysis for fragmet #1(A:452:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.909 / q_NPA : 0.949

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	454	PRO	0	0.080	0.025	2.858	-9.252	-6.398	0.250	-1.409	-1.696	-0.004
4	A	455	GLU	-1	-0.911	-0.952	5.375	-26.278	-26.151	-0.001	-0.005	-0.120	0.000
5	A	456	GLN	0	0.041	0.003	2.286	-9.779	-7.919	3.443	-1.788	-3.515	-0.025
6	A	457	GLU	-1	-0.866	-0.941	2.185	-102.632	-95.372	4.191	-5.158	-6.293	-0.071
7	A	458	LEU	0	-0.034	-0.009	3.400	4.622	4.615	0.029	0.188	-0.209	0.000
8	A	459	ARG	1	0.789	0.853	6.259	29.419	29.419	0.000	0.000	0.000	0.000
9	A	460	LEU	0	0.037	0.018	2.739	1.650	1.965	1.904	-0.408	-1.810	-0.001
10	A	461	GLN	0	0.032	0.010	5.683	7.604	7.604	0.000	0.000	0.000	0.000
11	A	462	ARG	1	0.886	0.941	7.927	27.037	27.037	0.000	0.000	0.000	0.000
12	A	463	LEU	0	-0.014	-0.015	8.069	2.576	2.576	0.000	0.000	0.000	0.000
13	A	464	GLU	-1	-0.925	-0.957	6.156	-38.901	-38.901	0.000	0.000	0.000	0.000
14	A	465	ARG	1	0.896	0.951	10.439	25.969	25.969	0.000	0.000	0.000	0.000
15	A	466	LEU	0	-0.027	-0.003	13.577	1.941	1.941	0.000	0.000	0.000	0.000
16	A	467	PRO	0	0.013	0.010	14.287	1.636	1.636	0.000	0.000	0.000	0.000
17	A	468	GLU	-1	-0.929	-0.965	16.792	-16.064	-16.064	0.000	0.000	0.000	0.000
18	A	469	LEU	0	0.013	-0.009	16.703	1.069	1.069	0.000	0.000	0.000	0.000
19	A	470	ALA	0	0.019	0.020	19.502	0.946	0.946	0.000	0.000	0.000	0.000
20	A	471	ARG	1	0.955	0.977	21.452	14.286	14.286	0.000	0.000	0.000	0.000
21	A	472	VAL	0	-0.003	0.006	22.406	0.768	0.768	0.000	0.000	0.000	0.000
22	A	473	LEU	0	0.018	0.009	23.269	0.666	0.666	0.000	0.000	0.000	0.000
23	A	474	ARG	1	0.891	0.933	25.318	11.803	11.803	0.000	0.000	0.000	0.000
24	A	475	ASN	0	0.028	-0.001	27.253	0.482	0.482	0.000	0.000	0.000	0.000
25	A	476	VAL	0	0.030	0.030	27.891	0.486	0.486	0.000	0.000	0.000	0.000
26	A	477	PHE	0	0.001	-0.017	28.259	0.431	0.431	0.000	0.000	0.000	0.000
27	A	478	VAL	0	-0.112	-0.044	31.533	0.368	0.368	0.000	0.000	0.000	0.000
28	A	479	SER	0	-0.015	-0.008	33.248	0.329	0.329	0.000	0.000	0.000	0.000
29	A	480	GLU	-1	-0.822	-0.879	34.238	-8.409	-8.409	0.000	0.000	0.000	0.000
30	A	481	ARG	1	0.963	0.979	36.020	7.502	7.502	0.000	0.000	0.000	0.000
31	A	482	LYS	1	0.855	0.923	37.085	8.489	8.489	0.000	0.000	0.000	0.000
32	A	483	PRO	0	0.041	0.014	35.704	-0.201	-0.201	0.000	0.000	0.000	0.000
33	A	484	ALA	0	-0.017	-0.012	32.897	-0.266	-0.266	0.000	0.000	0.000	0.000
34	A	485	LEU	0	-0.045	-0.010	31.071	0.314	0.314	0.000	0.000	0.000	0.000
35	A	486	THR	0	0.053	0.032	30.934	-0.298	-0.298	0.000	0.000	0.000	0.000
36	A	487	MET	0	0.055	0.012	22.434	-0.058	-0.058	0.000	0.000	0.000	0.000
37	A	488	GLU	-1	-0.900	-0.926	27.120	-10.206	-10.206	0.000	0.000	0.000	0.000
38	A	489	VAL	0	-0.021	-0.014	28.904	-0.065	-0.065	0.000	0.000	0.000	0.000
39	A	490	VAL	0	-0.030	-0.017	25.660	-0.071	-0.071	0.000	0.000	0.000	0.000
40	A	491	CYS	0	-0.013	0.004	24.010	-0.442	-0.442	0.000	0.000	0.000	0.000
41	A	492	ALA	0	0.036	0.022	25.586	-0.272	-0.272	0.000	0.000	0.000	0.000
42	A	493	ARG	1	0.910	0.941	28.279	9.540	9.540	0.000	0.000	0.000	0.000
43	A	494	MET	0	-0.034	-0.010	21.684	0.002	0.002	0.000	0.000	0.000	0.000
44	A	495	VAL	0	-0.051	-0.031	22.602	-0.341	-0.341	0.000	0.000	0.000	0.000
45	A	496	ASP	-1	-0.879	-0.928	24.737	-10.821	-10.821	0.000	0.000	0.000	0.000
46	A	497	SER	0	-0.112	-0.058	26.682	0.386	0.386	0.000	0.000	0.000	0.000
47	A	498	CYS	0	-0.099	-0.041	22.541	-0.340	-0.340	0.000	0.000	0.000	0.000
48	A	499	GLN	0	0.004	-0.001	22.634	0.056	0.056	0.000	0.000	0.000	0.000
49	A	500	THR	0	0.016	0.012	19.188	-0.819	-0.819	0.000	0.000	0.000	0.000
50	A	501	ALA	0	0.007	0.004	16.858	0.487	0.487	0.000	0.000	0.000	0.000
51	A	502	LEU	0	-0.064	-0.024	15.411	-0.221	-0.221	0.000	0.000	0.000	0.000
52	A	503	SER	0	0.041	0.021	19.327	0.950	0.950	0.000	0.000	0.000	0.000
53	A	504	PRO	0	0.070	0.014	21.228	-0.490	-0.490	0.000	0.000	0.000	0.000
54	A	505	GLY	0	0.056	0.031	21.977	-0.101	-0.101	0.000	0.000	0.000	0.000
55	A	506	GLU	-1	-0.902	-0.957	16.927	-17.571	-17.571	0.000	0.000	0.000	0.000
56	A	507	MET	0	0.005	0.025	17.586	-1.144	-1.144	0.000	0.000	0.000	0.000
57	A	508	GLU	-1	-0.868	-0.959	19.674	-13.150	-13.150	0.000	0.000	0.000	0.000
58	A	509	LYS	1	0.904	0.948	15.648	16.451	16.451	0.000	0.000	0.000	0.000
59	A	510	HIS	0	0.019	-0.001	13.892	-2.018	-2.018	0.000	0.000	0.000	0.000
60	A	511	LEU	0	-0.002	-0.017	16.604	-0.095	-0.095	0.000	0.000	0.000	0.000
61	A	512	VAL	0	-0.015	0.000	18.137	0.336	0.336	0.000	0.000	0.000	0.000
62	A	513	LEU	0	-0.002	0.008	12.167	-0.340	-0.340	0.000	0.000	0.000	0.000
63	A	514	LEU	0	0.002	-0.003	16.210	-0.026	-0.026	0.000	0.000	0.000	0.000
64	A	515	ALA	0	-0.036	-0.021	18.416	0.392	0.392	0.000	0.000	0.000	0.000
65	A	516	GLU	-1	-0.944	-0.972	16.493	-16.917	-16.917	0.000	0.000	0.000	0.000
66	A	517	LEU	0	-0.028	-0.017	13.611	-0.016	-0.016	0.000	0.000	0.000	0.000
67	A	518	LEU	0	-0.084	-0.045	17.922	0.388	0.388	0.000	0.000	0.000	0.000
68	A	519	PRO	0	0.057	0.039	21.264	0.568	0.568	0.000	0.000	0.000	0.000
69	A	520	ASP	-1	-0.929	-0.961	23.903	-11.318	-11.318	0.000	0.000	0.000	0.000
70	A	521	TRP	0	-0.117	-0.044	22.176	0.251	0.251	0.000	0.000	0.000	0.000
71	A	522	LEU	0	-0.015	-0.013	21.978	0.532	0.532	0.000	0.000	0.000	0.000
72	A	523	SER	0	0.038	0.021	25.032	-0.085	-0.085	0.000	0.000	0.000	0.000
73	A	524	LEU	0	0.009	-0.009	23.088	0.127	0.127	0.000	0.000	0.000	0.000
74	A	525	HIS	0	-0.006	-0.007	27.631	-0.042	-0.042	0.000	0.000	0.000	0.000
75	A	526	ARG	1	0.966	0.992	26.195	11.082	11.082	0.000	0.000	0.000	0.000
76	A	527	ILE	0	-0.014	-0.006	32.000	0.282	0.282	0.000	0.000	0.000	0.000
77	A	528	ARG	1	0.943	0.967	35.564	7.528	7.528	0.000	0.000	0.000	0.000
78	A	529	THR	0	0.030	0.005	33.772	-0.070	-0.070	0.000	0.000	0.000	0.000
79	A	530	ASP	-1	-0.907	-0.913	32.483	-9.151	-9.151	0.000	0.000	0.000	0.000
80	A	531	THR	0	0.005	-0.020	27.082	-0.041	-0.041	0.000	0.000	0.000	0.000
81	A	532	TYR	0	-0.059	-0.034	29.973	-0.097	-0.097	0.000	0.000	0.000	0.000
82	A	533	VAL	0	0.045	0.024	26.415	-0.190	-0.190	0.000	0.000	0.000	0.000
83	A	534	LYS	1	0.950	0.961	28.919	9.611	9.611	0.000	0.000	0.000	0.000
84	A	535	LEU	0	0.016	0.007	26.190	-0.294	-0.294	0.000	0.000	0.000	0.000
85	A	536	ASP	-1	-0.849	-0.910	29.242	-9.516	-9.516	0.000	0.000	0.000	0.000
86	A	537	LYS	1	0.889	0.909	30.552	9.200	9.200	0.000	0.000	0.000	0.000
87	A	538	ALA	0	-0.029	0.008	32.727	0.143	0.143	0.000	0.000	0.000	0.000
88	A	539	VAL	0	-0.035	-0.005	27.749	-0.115	-0.115	0.000	0.000	0.000	0.000
89	A	540	ASP	-1	-0.819	-0.925	29.009	-11.026	-11.026	0.000	0.000	0.000	0.000
90	A	541	LEU	0	-0.015	-0.017	23.485	-0.328	-0.328	0.000	0.000	0.000	0.000
91	A	542	ALA	0	-0.014	0.019	24.133	-0.712	-0.712	0.000	0.000	0.000	0.000
92	A	543	GLY	0	0.032	0.007	24.048	-0.444	-0.444	0.000	0.000	0.000	0.000
93	A	544	LEU	0	-0.011	-0.019	23.048	-0.487	-0.487	0.000	0.000	0.000	0.000
94	A	545	THR	0	-0.025	-0.017	19.303	-0.854	-0.854	0.000	0.000	0.000	0.000
95	A	546	ALA	0	-0.001	0.007	19.088	-0.910	-0.910	0.000	0.000	0.000	0.000
96	A	547	ARG	1	0.947	0.972	19.010	12.317	12.317	0.000	0.000	0.000	0.000
97	A	548	LEU	0	0.011	0.016	15.733	-0.546	-0.546	0.000	0.000	0.000	0.000
98	A	549	ALA	0	0.014	0.004	14.721	-1.309	-1.309	0.000	0.000	0.000	0.000
99	A	550	HIS	0	-0.036	-0.014	14.087	-1.281	-1.281	0.000	0.000	0.000	0.000
100	A	551	HIS	0	0.014	0.001	14.790	-1.100	-1.100	0.000	0.000	0.000	0.000
101	A	552	VAL	0	0.022	0.007	10.201	-1.040	-1.040	0.000	0.000	0.000	0.000
102	A	553	HIS	0	-0.029	-0.014	10.271	-3.472	-3.472	0.000	0.000	0.000	0.000
103	A	554	ALA	0	-0.024	-0.018	10.376	-1.379	-1.379	0.000	0.000	0.000	0.000
104	A	555	GLU	-1	-0.832	-0.874	9.523	-27.455	-27.455	0.000	0.000	0.000	0.000
105	A	556	GLY	0	-0.023	0.009	7.631	-1.054	-1.054	0.000	0.000	0.000	0.000
106	A	557	LEU	0	-0.070	-0.027	1.646	-7.754	-20.898	25.609	-4.176	-8.290	-0.010

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Interactive mode: IFIE and PIEDA for fragment #1(A:452:ARG)