FMO DATABASE

FMODB ID: 4935N

Calculation Name: 3KAT-A-Xray372

Preferred Name: NACHT, LRR and PYD domains-containing protein 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3KAT

Chain ID: A

ChEMBL ID: CHEMBL1741214

UniProt ID: Q9C000

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:

Apendix: None

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	84
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-639536.24358
FMO2-HF: Nuclear repulsion	604316.547869
FMO2-HF: Total energy	-35219.695711
FMO2-MP2: Total energy	-35322.724135

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:1379:LEU)

Summations of interaction energy for fragment #1(A:1379:LEU)

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.
-26.221	-33.589	51.806	-18.24	-26.196	-0.082

Interaction energy analysis for fragmet #1(A:1379:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / q_NPA : -0.026

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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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	1381	PHE	0	0.017	0.012	2.096	-4.799	-1.243	5.546	-3.402	-5.700	0.001
4	A	1382	VAL	0	0.024	0.004	3.182	-0.176	0.949	0.090	-0.079	-1.136	-0.001
5	A	1383	ASP	-1	-0.824	-0.897	5.036	3.171	3.171	0.000	0.000	0.000	0.000
6	A	1384	GLN	0	-0.018	-0.008	6.178	0.198	0.198	0.000	0.000	0.000	0.000
7	A	1385	TYR	0	-0.062	-0.022	6.618	0.125	0.125	0.000	0.000	0.000	0.000
8	A	1386	ARG	1	0.940	0.956	9.331	-0.174	-0.174	0.000	0.000	0.000	0.000
9	A	1387	GLU	-1	-0.894	-0.950	10.269	-0.027	-0.027	0.000	0.000	0.000	0.000
10	A	1388	GLN	0	-0.003	-0.006	12.237	-0.017	-0.017	0.000	0.000	0.000	0.000
11	A	1389	LEU	0	0.023	0.011	7.615	-0.028	-0.028	0.000	0.000	0.000	0.000
12	A	1390	ILE	0	-0.032	-0.012	12.245	0.029	0.029	0.000	0.000	0.000	0.000
13	A	1391	ALA	0	0.004	-0.003	14.699	0.023	0.023	0.000	0.000	0.000	0.000
14	A	1392	ARG	1	0.812	0.884	14.608	0.352	0.352	0.000	0.000	0.000	0.000
15	A	1393	VAL	0	0.001	0.014	11.868	-0.018	-0.018	0.000	0.000	0.000	0.000
16	A	1394	THR	0	0.031	0.008	14.930	0.050	0.050	0.000	0.000	0.000	0.000
17	A	1395	SER	0	0.001	0.016	17.440	0.044	0.044	0.000	0.000	0.000	0.000
18	A	1396	VAL	0	0.015	-0.016	15.517	-0.042	-0.042	0.000	0.000	0.000	0.000
19	A	1397	GLU	-1	-0.866	-0.930	16.263	-0.245	-0.245	0.000	0.000	0.000	0.000
20	A	1398	VAL	0	0.041	0.022	17.307	-0.014	-0.014	0.000	0.000	0.000	0.000
21	A	1399	VAL	0	-0.079	-0.037	11.535	-0.061	-0.061	0.000	0.000	0.000	0.000
22	A	1400	LEU	0	-0.022	-0.024	12.934	-0.081	-0.081	0.000	0.000	0.000	0.000
23	A	1401	ASP	-1	-0.845	-0.905	14.785	-0.274	-0.274	0.000	0.000	0.000	0.000
24	A	1402	LYS	1	0.812	0.903	13.202	0.657	0.657	0.000	0.000	0.000	0.000
25	A	1403	LEU	0	-0.054	-0.024	8.994	-0.052	-0.052	0.000	0.000	0.000	0.000
26	A	1404	HIS	0	-0.008	-0.014	12.551	0.053	0.053	0.000	0.000	0.000	0.000
27	A	1405	GLY	0	0.032	0.030	15.977	0.043	0.043	0.000	0.000	0.000	0.000
28	A	1406	GLN	0	-0.079	-0.050	11.177	0.075	0.075	0.000	0.000	0.000	0.000
29	A	1407	VAL	0	-0.068	-0.023	8.048	0.054	0.054	0.000	0.000	0.000	0.000
30	A	1408	LEU	0	-0.035	-0.002	11.074	0.129	0.129	0.000	0.000	0.000	0.000
31	A	1409	SER	0	0.024	0.012	13.764	-0.033	-0.033	0.000	0.000	0.000	0.000
32	A	1410	GLN	0	0.058	0.022	17.451	-0.034	-0.034	0.000	0.000	0.000	0.000
33	A	1411	GLU	-1	-0.830	-0.921	20.461	0.038	0.038	0.000	0.000	0.000	0.000
34	A	1412	GLN	0	-0.022	-0.018	15.154	-0.009	-0.009	0.000	0.000	0.000	0.000
35	A	1413	TYR	0	-0.007	-0.022	16.955	0.006	0.006	0.000	0.000	0.000	0.000
36	A	1414	GLU	-1	-0.821	-0.911	18.159	-0.078	-0.078	0.000	0.000	0.000	0.000
37	A	1415	ARG	1	0.819	0.911	19.570	-0.055	-0.055	0.000	0.000	0.000	0.000
38	A	1416	VAL	0	-0.075	-0.044	15.060	0.005	0.005	0.000	0.000	0.000	0.000
39	A	1417	LEU	0	0.018	0.004	18.356	-0.018	-0.018	0.000	0.000	0.000	0.000
40	A	1418	ALA	0	-0.026	0.004	20.489	0.000	0.000	0.000	0.000	0.000	0.000
41	A	1419	GLU	-1	-0.923	-0.934	19.832	-0.036	-0.036	0.000	0.000	0.000	0.000
42	A	1420	ASN	0	0.025	0.002	22.649	-0.022	-0.022	0.000	0.000	0.000	0.000
43	A	1421	THR	0	-0.007	-0.006	22.824	-0.011	-0.011	0.000	0.000	0.000	0.000
44	A	1422	ARG	1	0.947	0.987	17.899	0.281	0.281	0.000	0.000	0.000	0.000
45	A	1423	PRO	0	0.012	-0.002	17.770	-0.016	-0.016	0.000	0.000	0.000	0.000
46	A	1424	SER	0	-0.017	-0.011	17.928	0.009	0.009	0.000	0.000	0.000	0.000
47	A	1425	GLN	0	0.083	0.043	17.860	-0.009	-0.009	0.000	0.000	0.000	0.000
48	A	1426	MET	0	-0.017	0.002	10.286	0.016	0.016	0.000	0.000	0.000	0.000
49	A	1427	ARG	1	0.940	0.951	13.429	0.044	0.044	0.000	0.000	0.000	0.000
50	A	1428	LYS	1	0.878	0.941	14.964	0.054	0.054	0.000	0.000	0.000	0.000
51	A	1429	LEU	0	0.051	0.025	10.416	0.049	0.049	0.000	0.000	0.000	0.000
52	A	1430	PHE	0	-0.011	-0.016	7.080	0.062	0.062	0.000	0.000	0.000	0.000
53	A	1431	SER	0	-0.080	-0.025	11.328	0.131	0.131	0.000	0.000	0.000	0.000
54	A	1432	LEU	0	-0.013	-0.013	12.416	0.058	0.058	0.000	0.000	0.000	0.000
55	A	1433	SER	0	-0.032	-0.026	8.029	0.038	0.038	0.000	0.000	0.000	0.000
56	A	1434	GLN	0	-0.024	-0.001	9.417	0.354	0.354	0.000	0.000	0.000	0.000
57	A	1435	SER	0	0.032	0.018	11.416	0.008	0.008	0.000	0.000	0.000	0.000
58	A	1436	TRP	0	-0.056	-0.028	6.103	0.035	0.035	0.000	0.000	0.000	0.000
59	A	1437	ASP	-1	-0.673	-0.842	6.617	1.428	1.428	0.000	0.000	0.000	0.000
60	A	1438	ARG	1	0.835	0.916	1.812	-3.632	-5.793	9.444	-3.056	-4.227	0.008
61	A	1439	LYS	1	0.894	0.939	4.029	-2.622	-2.411	-0.001	-0.062	-0.148	0.000
62	A	1440	CYS	0	-0.019	0.014	5.892	-0.670	-0.670	0.000	0.000	0.000	0.000
63	A	1441	LYS	1	0.841	0.903	2.075	-1.379	-5.612	8.850	-2.028	-2.589	0.006
64	A	1442	ASP	-1	-0.790	-0.886	1.751	-20.268	-28.362	26.709	-9.389	-9.226	-0.088
65	A	1443	GLY	0	0.022	0.022	3.010	1.446	0.950	0.119	0.635	-0.257	0.000
66	A	1444	LEU	0	0.020	0.009	5.029	0.051	0.051	0.000	0.000	0.000	0.000
67	A	1445	TYR	0	0.013	-0.008	2.969	-2.145	0.028	1.008	-0.766	-2.415	-0.008
68	A	1446	GLN	0	-0.028	-0.029	5.349	0.301	0.387	-0.001	-0.002	-0.083	0.000
69	A	1447	ALA	0	0.051	0.017	7.088	0.351	0.351	0.000	0.000	0.000	0.000
70	A	1448	LEU	0	-0.016	-0.011	7.176	0.249	0.249	0.000	0.000	0.000	0.000
71	A	1449	LYS	1	0.883	0.949	5.563	2.179	2.179	0.000	0.000	0.000	0.000
72	A	1450	GLU	-1	-0.852	-0.899	9.255	-0.704	-0.704	0.000	0.000	0.000	0.000
73	A	1451	THR	0	-0.071	-0.030	12.331	0.158	0.158	0.000	0.000	0.000	0.000
74	A	1452	HIS	0	-0.020	-0.013	12.443	0.151	0.151	0.000	0.000	0.000	0.000
75	A	1453	PRO	0	0.057	0.028	11.478	-0.065	-0.065	0.000	0.000	0.000	0.000
76	A	1454	HIS	0	0.048	0.002	11.912	-0.059	-0.059	0.000	0.000	0.000	0.000
77	A	1455	LEU	0	0.008	0.032	11.335	0.032	0.032	0.000	0.000	0.000	0.000
78	A	1456	ILE	0	0.021	-0.010	6.769	0.003	0.003	0.000	0.000	0.000	0.000
79	A	1457	MET	0	-0.029	-0.003	8.656	-0.040	-0.040	0.000	0.000	0.000	0.000
80	A	1458	GLU	-1	-0.826	-0.886	11.037	-0.316	-0.316	0.000	0.000	0.000	0.000
81	A	1459	LEU	0	-0.071	-0.062	8.572	0.061	0.061	0.000	0.000	0.000	0.000
82	A	1460	TRP	0	-0.035	-0.009	3.257	-0.622	-0.157	0.042	-0.091	-0.415	0.000
83	A	1461	GLU	-1	-0.923	-0.945	9.498	-0.277	-0.277	0.000	0.000	0.000	0.000
84	A	1462	LYS	1	0.880	0.953	12.450	0.306	0.306	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1379:LEU)