FMO DATABASE

FMODB ID: 5234Z

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:

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	84
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-638766.171986
FMO2-HF: Nuclear repulsion	603545.944465
FMO2-HF: Total energy	-35220.227521
FMO2-MP2: Total energy	-35323.198611

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.
-23.478	-23.477	35.952	-14.536	-21.414	-0.057

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 : -0.009 / q_NPA : -0.031

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	1381	PHE	0	0.009	0.022	1.856	-3.226	-1.767	4.864	-2.435	-3.888	0.002
4	A	1382	VAL	0	0.022	-0.004	3.185	-0.511	0.513	0.057	-0.101	-0.979	-0.001
5	A	1383	ASP	-1	-0.839	-0.896	5.444	2.916	2.916	0.000	0.000	0.000	0.000
6	A	1384	GLN	0	-0.042	-0.020	6.520	0.113	0.113	0.000	0.000	0.000	0.000
7	A	1385	TYR	0	-0.011	-0.017	6.333	0.047	0.047	0.000	0.000	0.000	0.000
8	A	1386	ARG	1	0.889	0.953	9.300	-0.223	-0.223	0.000	0.000	0.000	0.000
9	A	1387	GLU	-1	-0.755	-0.882	10.608	0.022	0.022	0.000	0.000	0.000	0.000
10	A	1388	GLN	0	0.009	0.011	12.390	0.001	0.001	0.000	0.000	0.000	0.000
11	A	1389	LEU	0	0.040	0.017	7.682	-0.026	-0.026	0.000	0.000	0.000	0.000
12	A	1390	ILE	0	-0.061	-0.015	12.320	0.016	0.016	0.000	0.000	0.000	0.000
13	A	1391	ALA	0	0.004	0.000	15.092	0.008	0.008	0.000	0.000	0.000	0.000
14	A	1392	ARG	1	0.772	0.861	14.706	0.269	0.269	0.000	0.000	0.000	0.000
15	A	1393	VAL	0	0.008	0.010	12.074	-0.011	-0.011	0.000	0.000	0.000	0.000
16	A	1394	THR	0	0.024	0.016	15.116	0.037	0.037	0.000	0.000	0.000	0.000
17	A	1395	SER	0	0.035	0.013	17.408	0.041	0.041	0.000	0.000	0.000	0.000
18	A	1396	VAL	0	-0.012	-0.017	15.831	-0.041	-0.041	0.000	0.000	0.000	0.000
19	A	1397	GLU	-1	-0.872	-0.930	16.878	-0.248	-0.248	0.000	0.000	0.000	0.000
20	A	1398	VAL	0	0.043	0.023	17.069	-0.018	-0.018	0.000	0.000	0.000	0.000
21	A	1399	VAL	0	-0.067	-0.037	11.789	-0.057	-0.057	0.000	0.000	0.000	0.000
22	A	1400	LEU	0	0.000	-0.005	13.523	-0.065	-0.065	0.000	0.000	0.000	0.000
23	A	1401	ASP	-1	-0.814	-0.893	15.440	-0.298	-0.298	0.000	0.000	0.000	0.000
24	A	1402	LYS	1	0.767	0.873	13.283	0.622	0.622	0.000	0.000	0.000	0.000
25	A	1403	LEU	0	-0.045	-0.016	9.544	-0.111	-0.111	0.000	0.000	0.000	0.000
26	A	1404	HIS	0	-0.015	-0.019	13.057	0.021	0.021	0.000	0.000	0.000	0.000
27	A	1405	GLY	0	0.035	0.033	16.078	0.040	0.040	0.000	0.000	0.000	0.000
28	A	1406	GLN	0	-0.094	-0.062	11.347	0.102	0.102	0.000	0.000	0.000	0.000
29	A	1407	VAL	0	-0.080	-0.037	8.579	-0.019	-0.019	0.000	0.000	0.000	0.000
30	A	1408	LEU	0	-0.038	-0.004	11.453	0.105	0.105	0.000	0.000	0.000	0.000
31	A	1409	SER	0	0.036	0.017	14.065	-0.026	-0.026	0.000	0.000	0.000	0.000
32	A	1410	GLN	0	0.040	0.010	17.856	-0.028	-0.028	0.000	0.000	0.000	0.000
33	A	1411	GLU	-1	-0.812	-0.897	20.883	-0.007	-0.007	0.000	0.000	0.000	0.000
34	A	1412	GLN	0	-0.013	-0.016	15.532	-0.022	-0.022	0.000	0.000	0.000	0.000
35	A	1413	TYR	0	0.010	-0.018	17.433	0.009	0.009	0.000	0.000	0.000	0.000
36	A	1414	GLU	-1	-0.847	-0.909	18.499	-0.095	-0.095	0.000	0.000	0.000	0.000
37	A	1415	ARG	1	0.820	0.902	19.948	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	1416	VAL	0	-0.082	-0.032	16.018	0.015	0.015	0.000	0.000	0.000	0.000
39	A	1417	LEU	0	0.049	0.009	19.132	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	1418	ALA	0	-0.008	0.009	21.318	0.005	0.005	0.000	0.000	0.000	0.000
41	A	1419	GLU	-1	-0.910	-0.935	20.238	-0.046	-0.046	0.000	0.000	0.000	0.000
42	A	1420	ASN	0	-0.011	-0.006	23.113	-0.015	-0.015	0.000	0.000	0.000	0.000
43	A	1421	THR	0	0.005	-0.011	23.352	-0.010	-0.010	0.000	0.000	0.000	0.000
44	A	1422	ARG	1	0.877	0.941	17.923	0.245	0.245	0.000	0.000	0.000	0.000
45	A	1423	PRO	0	0.003	-0.005	18.512	-0.019	-0.019	0.000	0.000	0.000	0.000
46	A	1424	SER	0	0.014	0.014	18.508	0.006	0.006	0.000	0.000	0.000	0.000
47	A	1425	GLN	0	0.062	0.026	18.281	-0.014	-0.014	0.000	0.000	0.000	0.000
48	A	1426	MET	0	0.027	0.031	10.935	0.008	0.008	0.000	0.000	0.000	0.000
49	A	1427	ARG	1	0.861	0.903	13.899	0.009	0.009	0.000	0.000	0.000	0.000
50	A	1428	LYS	1	0.839	0.921	15.356	0.088	0.088	0.000	0.000	0.000	0.000
51	A	1429	LEU	0	0.038	0.013	11.130	0.034	0.034	0.000	0.000	0.000	0.000
52	A	1430	PHE	0	-0.011	-0.019	7.427	0.035	0.035	0.000	0.000	0.000	0.000
53	A	1431	SER	0	-0.051	-0.017	11.622	0.134	0.134	0.000	0.000	0.000	0.000
54	A	1432	LEU	0	-0.013	0.002	12.434	0.054	0.054	0.000	0.000	0.000	0.000
55	A	1433	SER	0	-0.049	-0.051	8.077	0.004	0.004	0.000	0.000	0.000	0.000
56	A	1434	GLN	0	-0.049	-0.023	9.291	0.329	0.329	0.000	0.000	0.000	0.000
57	A	1435	SER	0	0.014	0.013	11.367	0.027	0.027	0.000	0.000	0.000	0.000
58	A	1436	TRP	0	-0.005	0.008	6.200	-0.043	-0.043	0.000	0.000	0.000	0.000
59	A	1437	ASP	-1	-0.680	-0.845	6.177	1.071	1.071	0.000	0.000	0.000	0.000
60	A	1438	ARG	1	0.833	0.899	1.851	-2.959	-2.095	3.688	-1.563	-2.988	0.003
61	A	1439	LYS	1	0.857	0.917	4.172	-1.350	-1.248	-0.001	-0.003	-0.097	0.000
62	A	1440	CYS	0	-0.005	0.009	6.146	-0.458	-0.458	0.000	0.000	0.000	0.000
63	A	1441	LYS	1	0.859	0.911	2.021	-3.071	-5.056	6.589	-2.305	-2.298	0.004
64	A	1442	ASP	-1	-0.807	-0.881	1.734	-17.489	-21.312	17.973	-7.317	-6.833	-0.056
65	A	1443	GLY	0	0.044	0.027	3.300	0.998	0.973	0.064	0.239	-0.278	0.000
66	A	1444	LEU	0	0.017	0.014	5.325	0.179	0.179	0.000	0.000	0.000	0.000
67	A	1445	TYR	0	0.010	-0.009	2.787	-2.031	-0.270	2.670	-0.943	-3.488	-0.009
68	A	1446	GLN	0	-0.035	-0.029	5.041	0.244	0.332	-0.001	-0.004	-0.084	0.000
69	A	1447	ALA	0	0.064	0.031	6.852	0.310	0.310	0.000	0.000	0.000	0.000
70	A	1448	LEU	0	0.007	-0.001	7.165	0.237	0.237	0.000	0.000	0.000	0.000
71	A	1449	LYS	1	0.866	0.941	5.431	1.990	1.990	0.000	0.000	0.000	0.000
72	A	1450	GLU	-1	-0.837	-0.896	9.085	-0.695	-0.695	0.000	0.000	0.000	0.000
73	A	1451	THR	0	-0.042	-0.023	12.165	0.141	0.141	0.000	0.000	0.000	0.000
74	A	1452	HIS	0	-0.037	-0.029	11.991	0.153	0.153	0.000	0.000	0.000	0.000
75	A	1453	PRO	0	0.038	0.031	10.952	-0.050	-0.050	0.000	0.000	0.000	0.000
76	A	1454	HIS	0	0.051	0.006	11.427	-0.059	-0.059	0.000	0.000	0.000	0.000
77	A	1455	LEU	0	-0.003	0.024	11.179	0.037	0.037	0.000	0.000	0.000	0.000
78	A	1456	ILE	0	0.001	-0.018	6.434	0.001	0.001	0.000	0.000	0.000	0.000
79	A	1457	MET	0	-0.039	-0.003	8.753	-0.009	-0.009	0.000	0.000	0.000	0.000
80	A	1458	GLU	-1	-0.758	-0.841	11.143	-0.219	-0.219	0.000	0.000	0.000	0.000
81	A	1459	LEU	0	-0.048	-0.039	9.028	0.058	0.058	0.000	0.000	0.000	0.000
82	A	1460	TRP	0	-0.023	-0.016	3.136	-0.673	-0.137	0.049	-0.104	-0.481	0.000
83	A	1461	GLU	-1	-0.914	-0.935	9.716	-0.200	-0.200	0.000	0.000	0.000	0.000
84	A	1462	LYS	1	0.819	0.912	11.811	0.191	0.191	0.000	0.000	0.000	0.000

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