FMO DATABASE

FMODB ID: 8N1MY

Calculation Name: 3KAT-A-Xray540

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

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3KAT

Chain ID: A

ChEMBL ID: CHEMBL1741214

UniProt ID: Q9C000

Base Structure: X-ray

Registration Date: 2025-07-11

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	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	164
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-638748.422471
FMO2-HF: Nuclear repulsion	603545.944465
FMO2-HF: Total energy	-35202.478007
FMO2-MP2: Total energy	-35304.988596

3D Structure Molmil

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.
-2.342	-16.675	27.521	-3.379	-9.814	-0.039

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 : 0.156 / q_NPA : 0.028

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].
4	A	1380	HIS	0	-0.067	0.090	4.406	0.311	0.632	0.001	-0.189	-0.134	0.000
5	A	1381	PHE	0	0.108	-0.083	3.572	-0.562	1.113	0.005	-0.994	-0.686	0.004
6	A	1381	PHE	0	-0.094	0.094	3.894	-0.487	-0.429	-0.001	0.011	-0.069	0.000
7	A	1382	VAL	0	0.021	-0.122	4.226	0.666	0.948	-0.002	-0.139	-0.142	0.000
8	A	1382	VAL	0	-0.051	0.104	3.493	-0.247	0.011	0.006	-0.075	-0.190	0.000
9	A	1383	ASP	0	0.098	-0.096	5.670	0.304	0.304	0.000	0.000	0.000	0.000
10	A	1383	ASP	-1	-0.913	-0.801	5.497	3.774	3.774	0.000	0.000	0.000	0.000
11	A	1384	GLN	0	0.085	-0.098	7.308	0.125	0.125	0.000	0.000	0.000	0.000
12	A	1384	GLN	0	-0.114	0.098	8.252	0.154	0.154	0.000	0.000	0.000	0.000
13	A	1385	TYR	0	0.042	-0.102	8.781	0.219	0.219	0.000	0.000	0.000	0.000
14	A	1385	TYR	0	-0.095	0.089	8.349	0.018	0.018	0.000	0.000	0.000	0.000
15	A	1386	ARG	0	0.174	-0.068	10.048	-0.093	-0.093	0.000	0.000	0.000	0.000
16	A	1386	ARG	1	0.752	1.017	9.813	-0.154	-0.154	0.000	0.000	0.000	0.000
17	A	1387	GLU	0	0.064	-0.115	10.784	-0.055	-0.055	0.000	0.000	0.000	0.000
18	A	1387	GLU	-1	-0.837	-0.753	15.089	0.064	0.064	0.000	0.000	0.000	0.000
19	A	1388	GLN	0	0.071	-0.134	13.880	0.060	0.060	0.000	0.000	0.000	0.000
20	A	1388	GLN	0	-0.022	0.123	13.831	-0.060	-0.060	0.000	0.000	0.000	0.000
21	A	1389	LEU	0	0.087	-0.088	11.661	0.037	0.037	0.000	0.000	0.000	0.000
22	A	1389	LEU	0	-0.077	0.107	8.740	-0.022	-0.022	0.000	0.000	0.000	0.000
23	A	1390	ILE	0	0.078	-0.091	13.168	-0.007	-0.007	0.000	0.000	0.000	0.000
24	A	1390	ILE	0	-0.139	0.083	13.490	0.015	0.015	0.000	0.000	0.000	0.000
25	A	1391	ALA	0	0.129	-0.104	15.374	0.022	0.022	0.000	0.000	0.000	0.000
26	A	1391	ALA	0	-0.085	0.118	18.101	0.005	0.005	0.000	0.000	0.000	0.000
27	A	1392	ARG	0	-0.073	-0.153	16.550	0.056	0.056	0.000	0.000	0.000	0.000
28	A	1392	ARG	1	0.781	0.975	16.047	0.445	0.445	0.000	0.000	0.000	0.000
29	A	1393	VAL	0	0.141	-0.075	14.849	0.001	0.001	0.000	0.000	0.000	0.000
30	A	1393	VAL	0	-0.093	0.115	12.724	-0.020	-0.020	0.000	0.000	0.000	0.000
31	A	1394	THR	0	0.012	-0.062	16.020	0.075	0.075	0.000	0.000	0.000	0.000
32	A	1394	THR	0	-0.037	0.062	19.555	-0.016	-0.016	0.000	0.000	0.000	0.000
33	A	1395	SER	0	0.047	-0.038	18.633	0.057	0.057	0.000	0.000	0.000	0.000
34	A	1395	SER	0	-0.025	0.052	18.376	0.006	0.006	0.000	0.000	0.000	0.000
35	A	1396	VAL	0	0.129	-0.098	16.328	-0.053	-0.053	0.000	0.000	0.000	0.000
36	A	1396	VAL	0	-0.075	0.101	15.831	0.000	0.000	0.000	0.000	0.000	0.000
37	A	1397	GLU	0	0.118	-0.100	16.878	-0.014	-0.014	0.000	0.000	0.000	0.000
38	A	1397	GLU	-1	-0.992	-0.843	21.027	-0.214	-0.214	0.000	0.000	0.000	0.000
39	A	1398	VAL	0	0.144	-0.049	18.357	0.014	0.014	0.000	0.000	0.000	0.000
40	A	1398	VAL	0	-0.086	0.093	17.628	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	1399	VAL	0	0.025	-0.105	13.954	-0.017	-0.017	0.000	0.000	0.000	0.000
42	A	1399	VAL	0	-0.121	0.073	11.985	-0.024	-0.024	0.000	0.000	0.000	0.000
43	A	1400	LEU	0	0.085	-0.115	13.523	-0.066	-0.066	0.000	0.000	0.000	0.000
44	A	1400	LEU	0	-0.088	0.100	13.959	0.009	0.009	0.000	0.000	0.000	0.000
45	A	1401	ASP	0	0.125	-0.117	15.440	0.034	0.034	0.000	0.000	0.000	0.000
46	A	1401	ASP	-1	-0.921	-0.793	18.430	-0.242	-0.242	0.000	0.000	0.000	0.000
47	A	1402	LYS	0	0.017	-0.096	14.289	0.064	0.064	0.000	0.000	0.000	0.000
48	A	1402	LYS	1	0.758	0.987	13.515	0.623	0.623	0.000	0.000	0.000	0.000
49	A	1403	LEU	0	0.054	-0.083	12.229	-0.071	-0.071	0.000	0.000	0.000	0.000
50	A	1403	LEU	0	-0.115	0.071	9.544	-0.010	-0.010	0.000	0.000	0.000	0.000
51	A	1404	HIS	0	0.128	-0.098	13.057	0.083	0.083	0.000	0.000	0.000	0.000
52	A	1404	HIS	0	-0.117	0.071	17.640	-0.012	-0.012	0.000	0.000	0.000	0.000
53	A	1405	GLY	0	0.009	-0.082	16.078	0.043	0.043	0.000	0.000	0.000	0.000
54	A	1406	GLN	0	-0.004	-0.009	13.730	0.044	0.044	0.000	0.000	0.000	0.000
55	A	1406	GLN	0	-0.118	0.053	11.347	0.038	0.038	0.000	0.000	0.000	0.000
56	A	1407	VAL	0	0.001	-0.106	10.073	0.063	0.063	0.000	0.000	0.000	0.000
57	A	1407	VAL	0	-0.090	0.078	8.579	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	1408	LEU	0	0.121	-0.068	11.453	0.157	0.157	0.000	0.000	0.000	0.000
59	A	1408	LEU	0	-0.135	0.072	11.928	0.002	0.002	0.000	0.000	0.000	0.000
60	A	1409	SER	0	0.105	-0.034	14.065	-0.055	-0.055	0.000	0.000	0.000	0.000
61	A	1409	SER	0	-0.046	0.038	18.117	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	1410	GLN	0	0.169	-0.041	17.856	-0.017	-0.017	0.000	0.000	0.000	0.000
63	A	1410	GLN	0	-0.119	0.072	22.072	-0.012	-0.012	0.000	0.000	0.000	0.000
64	A	1411	GLU	0	0.176	-0.091	20.883	-0.023	-0.023	0.000	0.000	0.000	0.000
65	A	1411	GLU	-1	-0.963	-0.822	21.463	0.157	0.157	0.000	0.000	0.000	0.000
66	A	1412	GLN	0	0.014	-0.115	17.156	-0.011	-0.011	0.000	0.000	0.000	0.000
67	A	1412	GLN	0	-0.037	0.100	15.532	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	1413	TYR	0	0.139	-0.085	17.613	0.002	0.002	0.000	0.000	0.000	0.000
69	A	1413	TYR	0	-0.138	0.067	17.433	0.014	0.014	0.000	0.000	0.000	0.000
70	A	1414	GLU	0	0.092	-0.097	18.499	-0.024	-0.024	0.000	0.000	0.000	0.000
71	A	1414	GLU	-1	-0.939	-0.802	22.730	0.010	0.010	0.000	0.000	0.000	0.000
72	A	1415	ARG	0	0.051	-0.120	20.893	-0.017	-0.017	0.000	0.000	0.000	0.000
73	A	1415	ARG	1	0.744	0.998	19.948	-0.167	-0.167	0.000	0.000	0.000	0.000
74	A	1416	VAL	0	0.022	-0.099	17.597	0.022	0.022	0.000	0.000	0.000	0.000
75	A	1416	VAL	0	-0.109	0.092	16.018	0.000	0.000	0.000	0.000	0.000	0.000
76	A	1417	LEU	0	0.128	-0.123	19.132	-0.018	-0.018	0.000	0.000	0.000	0.000
77	A	1417	LEU	0	-0.089	0.123	19.924	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	1418	ALA	0	0.103	-0.089	21.318	-0.016	-0.016	0.000	0.000	0.000	0.000
79	A	1418	ALA	0	-0.076	0.102	23.896	0.005	0.005	0.000	0.000	0.000	0.000
80	A	1419	GLU	0	0.021	-0.119	21.741	0.009	0.009	0.000	0.000	0.000	0.000
81	A	1419	GLU	-1	-0.926	-0.829	20.238	0.011	0.011	0.000	0.000	0.000	0.000
82	A	1420	ASN	0	0.119	-0.057	23.113	-0.021	-0.021	0.000	0.000	0.000	0.000
83	A	1420	ASN	0	-0.133	0.062	26.777	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	1421	THR	0	0.005	-0.101	24.058	-0.018	-0.018	0.000	0.000	0.000	0.000
85	A	1421	THR	0	-0.057	0.055	23.352	0.002	0.002	0.000	0.000	0.000	0.000
86	A	1422	ARG	0	0.213	-0.025	20.644	0.015	0.015	0.000	0.000	0.000	0.000
87	A	1422	ARG	1	0.724	0.993	18.553	0.315	0.315	0.000	0.000	0.000	0.000
88	A	1423	PRO	0	-0.031	-0.125	18.559	-0.015	-0.015	0.000	0.000	0.000	0.000
89	A	1424	SER	0	-0.004	-0.004	18.508	0.012	0.012	0.000	0.000	0.000	0.000
90	A	1424	SER	0	-0.003	0.105	21.968	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	1425	GLN	0	0.156	-0.060	18.608	0.048	0.048	0.000	0.000	0.000	0.000
92	A	1425	GLN	0	-0.053	0.110	18.281	-0.041	-0.041	0.000	0.000	0.000	0.000
93	A	1426	MET	0	0.162	-0.069	14.720	0.043	0.043	0.000	0.000	0.000	0.000
94	A	1426	MET	0	-0.136	0.114	10.942	0.000	0.000	0.000	0.000	0.000	0.000
95	A	1427	ARG	0	0.070	-0.100	13.899	0.014	0.014	0.000	0.000	0.000	0.000
96	A	1427	ARG	1	0.789	1.001	16.393	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	1428	LYS	0	0.089	-0.105	15.356	0.079	0.079	0.000	0.000	0.000	0.000
98	A	1428	LYS	1	0.760	1.021	17.911	-0.065	-0.065	0.000	0.000	0.000	0.000
99	A	1429	LEU	0	0.139	-0.095	13.265	0.095	0.095	0.000	0.000	0.000	0.000
100	A	1429	LEU	0	-0.079	0.090	11.130	-0.017	-0.017	0.000	0.000	0.000	0.000
101	A	1430	PHE	0	0.002	-0.114	10.623	0.106	0.106	0.000	0.000	0.000	0.000
102	A	1430	PHE	0	-0.121	0.086	7.427	-0.035	-0.035	0.000	0.000	0.000	0.000
103	A	1431	SER	0	0.085	-0.058	11.622	0.204	0.204	0.000	0.000	0.000	0.000
104	A	1431	SER	0	-0.055	0.061	15.793	-0.013	-0.013	0.000	0.000	0.000	0.000
105	A	1432	LEU	0	-0.011	-0.117	13.051	0.057	0.057	0.000	0.000	0.000	0.000
106	A	1432	LEU	0	-0.044	0.111	12.434	-0.008	-0.008	0.000	0.000	0.000	0.000
107	A	1433	SER	0	0.004	-0.112	9.041	0.062	0.062	0.000	0.000	0.000	0.000
108	A	1433	SER	0	-0.077	0.039	8.077	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	1434	GLN	0	0.054	-0.103	9.291	0.502	0.502	0.000	0.000	0.000	0.000
110	A	1434	GLN	0	-0.085	0.095	13.103	0.020	0.020	0.000	0.000	0.000	0.000
111	A	1435	SER	0	0.024	-0.066	11.367	0.080	0.080	0.000	0.000	0.000	0.000
112	A	1435	SER	0	-0.022	0.078	12.157	-0.099	-0.099	0.000	0.000	0.000	0.000
113	A	1436	TRP	0	0.032	-0.121	7.118	-0.232	-0.232	0.000	0.000	0.000	0.000
114	A	1436	TRP	0	-0.068	0.104	6.200	0.119	0.119	0.000	0.000	0.000	0.000
115	A	1437	ASP	0	0.110	-0.061	6.177	0.908	0.908	0.000	0.000	0.000	0.000
116	A	1437	ASP	-1	-0.752	-0.767	7.275	1.470	1.470	0.000	0.000	0.000	0.000
117	A	1438	ARG	0	0.105	-0.060	3.111	1.123	1.530	0.031	-0.170	-0.268	0.000
118	A	1438	ARG	1	0.772	1.001	2.636	-1.701	-1.156	0.893	-0.378	-1.059	-0.002
119	A	1439	LYS	0	0.046	-0.122	4.172	-1.482	-1.440	-0.002	-0.003	-0.037	0.000
120	A	1439	LYS	1	0.786	1.007	7.357	-0.907	-0.907	0.000	0.000	0.000	0.000
121	A	1440	CYS	0	0.140	-0.101	6.146	-0.780	-0.780	0.000	0.000	0.000	0.000
122	A	1440	CYS	0	-0.124	0.100	6.788	-0.005	-0.005	0.000	0.000	0.000	0.000
123	A	1441	LYS	0	0.082	-0.102	2.514	4.870	-2.788	0.015	8.146	-0.503	-0.005
124	A	1441	LYS	1	0.757	1.003	2.021	-2.245	-5.067	8.906	-4.424	-1.660	0.010
125	A	1442	ASP	0	0.070	-0.105	2.790	-4.378	-4.259	1.319	-0.189	-1.249	-0.003
126	A	1442	ASP	-1	-0.843	-0.768	1.734	-7.263	-15.172	16.305	-4.927	-3.469	-0.043
127	A	1443	GLY	0	0.026	-0.081	3.562	0.064	0.139	0.036	0.006	-0.118	0.000
128	A	1444	LEU	0	0.124	0.026	5.870	-0.065	-0.065	0.000	0.000	0.000	0.000
129	A	1444	LEU	0	-0.094	0.099	5.325	0.055	0.055	0.000	0.000	0.000	0.000
130	A	1445	TYR	0	0.085	-0.090	4.428	0.957	1.019	0.001	-0.012	-0.051	0.000
131	A	1445	TYR	0	-0.110	0.072	3.988	-0.902	-0.744	0.010	-0.042	-0.127	0.000
132	A	1446	GLN	0	0.102	-0.101	5.895	0.312	0.366	-0.002	0.000	-0.052	0.000
133	A	1446	GLN	0	-0.106	0.078	7.798	-0.287	-0.287	0.000	0.000	0.000	0.000
134	A	1447	ALA	0	0.145	-0.100	8.295	0.204	0.204	0.000	0.000	0.000	0.000
135	A	1447	ALA	0	-0.056	0.123	10.141	0.043	0.043	0.000	0.000	0.000	0.000
136	A	1448	LEU	0	0.072	-0.091	9.563	0.313	0.313	0.000	0.000	0.000	0.000
137	A	1448	LEU	0	-0.088	0.088	7.886	0.016	0.016	0.000	0.000	0.000	0.000
138	A	1449	LYS	0	0.104	-0.074	9.636	0.262	0.262	0.000	0.000	0.000	0.000
139	A	1449	LYS	1	0.781	1.028	7.982	2.224	2.224	0.000	0.000	0.000	0.000
140	A	1450	GLU	0	0.028	-0.133	10.989	0.124	0.124	0.000	0.000	0.000	0.000
141	A	1450	GLU	-1	-0.891	-0.770	12.757	-0.896	-0.896	0.000	0.000	0.000	0.000
142	A	1451	THR	0	0.019	-0.084	13.617	0.124	0.124	0.000	0.000	0.000	0.000
143	A	1451	THR	0	-0.076	0.042	14.146	0.055	0.055	0.000	0.000	0.000	0.000
144	A	1452	HIS	0	0.032	-0.101	14.320	0.112	0.112	0.000	0.000	0.000	0.000
145	A	1452	HIS	0	-0.114	0.078	13.522	0.103	0.103	0.000	0.000	0.000	0.000
146	A	1453	PRO	0	0.049	-0.076	13.272	-0.086	-0.086	0.000	0.000	0.000	0.000
147	A	1454	HIS	0	0.109	0.010	13.918	-0.109	-0.109	0.000	0.000	0.000	0.000
148	A	1454	HIS	0	-0.053	0.090	18.016	-0.035	-0.035	0.000	0.000	0.000	0.000
149	A	1455	LEU	0	0.172	-0.055	14.566	0.042	0.042	0.000	0.000	0.000	0.000
150	A	1455	LEU	0	-0.127	0.105	12.987	0.012	0.012	0.000	0.000	0.000	0.000
151	A	1456	ILE	0	0.057	-0.120	10.187	0.099	0.099	0.000	0.000	0.000	0.000
152	A	1456	ILE	0	-0.082	0.100	8.882	-0.081	-0.081	0.000	0.000	0.000	0.000
153	A	1457	MET	0	0.127	-0.079	11.264	-0.163	-0.163	0.000	0.000	0.000	0.000
154	A	1457	MET	0	-0.128	0.092	14.602	0.007	0.007	0.000	0.000	0.000	0.000
155	A	1458	GLU	0	0.152	-0.070	13.775	0.010	0.010	0.000	0.000	0.000	0.000
156	A	1458	GLU	-1	-0.887	-0.783	15.831	-0.497	-0.497	0.000	0.000	0.000	0.000
157	A	1459	LEU	0	-0.011	-0.116	11.808	0.144	0.144	0.000	0.000	0.000	0.000
158	A	1459	LEU	0	-0.123	0.075	10.664	-0.022	-0.022	0.000	0.000	0.000	0.000
159	A	1460	TRP	0	0.092	-0.078	11.483	0.027	0.027	0.000	0.000	0.000	0.000
160	A	1460	TRP	0	-0.118	0.060	6.246	-0.346	-0.346	0.000	0.000	0.000	0.000
161	A	1461	GLU	0	0.109	-0.113	12.042	0.062	0.062	0.000	0.000	0.000	0.000
162	A	1461	GLU	-1	-0.986	-0.824	16.059	-0.553	-0.553	0.000	0.000	0.000	0.000
163	A	1462	LYS	0	-0.126	-0.158	14.397	0.093	0.093	0.000	0.000	0.000	0.000
164	A	1462	LYS	1	0.923	0.972	14.583	0.430	0.430	0.000	0.000	0.000	0.000

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