FMO DATABASE

FMODB ID: K93J3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-640245.449889
FMO2-HF: Nuclear repulsion	605026.932539
FMO2-HF: Total energy	-35218.517349
FMO2-MP2: Total energy	-35321.643012

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.
-25.573	-37.64	53.457	-16.532	-24.857	-0.086

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 : 0.000 / q_NPA : -0.025

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	0.047	0.033	1.835	-1.704	-3.474	12.056	-4.102	-6.184	0.009
4	A	1382	VAL	0	0.015	0.005	2.948	1.112	0.586	0.152	1.528	-1.153	-0.002
5	A	1383	ASP	-1	-0.845	-0.928	5.017	2.836	2.836	0.000	0.000	0.000	0.000
6	A	1384	GLN	0	-0.016	0.002	6.022	0.178	0.178	0.000	0.000	0.000	0.000
7	A	1385	TYR	0	-0.098	-0.036	6.196	0.072	0.072	0.000	0.000	0.000	0.000
8	A	1386	ARG	1	1.042	1.012	8.931	-0.287	-0.287	0.000	0.000	0.000	0.000
9	A	1387	GLU	-1	-0.996	-1.007	10.315	-0.055	-0.055	0.000	0.000	0.000	0.000
10	A	1388	GLN	0	0.026	0.002	11.902	-0.005	-0.005	0.000	0.000	0.000	0.000
11	A	1389	LEU	0	0.007	0.008	7.676	-0.042	-0.042	0.000	0.000	0.000	0.000
12	A	1390	ILE	0	-0.035	-0.016	12.369	0.023	0.023	0.000	0.000	0.000	0.000
13	A	1391	ALA	0	-0.021	-0.018	14.685	0.020	0.020	0.000	0.000	0.000	0.000
14	A	1392	ARG	1	0.902	0.947	14.877	0.328	0.328	0.000	0.000	0.000	0.000
15	A	1393	VAL	0	0.013	0.021	12.082	-0.021	-0.021	0.000	0.000	0.000	0.000
16	A	1394	THR	0	0.027	-0.010	15.038	0.053	0.053	0.000	0.000	0.000	0.000
17	A	1395	SER	0	-0.013	0.006	17.522	0.053	0.053	0.000	0.000	0.000	0.000
18	A	1396	VAL	0	0.013	-0.013	15.623	-0.049	-0.049	0.000	0.000	0.000	0.000
19	A	1397	GLU	-1	-0.858	-0.937	16.267	-0.263	-0.263	0.000	0.000	0.000	0.000
20	A	1398	VAL	0	0.043	0.027	17.030	-0.014	-0.014	0.000	0.000	0.000	0.000
21	A	1399	VAL	0	-0.074	-0.028	11.606	-0.068	-0.068	0.000	0.000	0.000	0.000
22	A	1400	LEU	0	-0.036	-0.032	12.944	-0.086	-0.086	0.000	0.000	0.000	0.000
23	A	1401	ASP	-1	-0.850	-0.916	14.793	-0.319	-0.319	0.000	0.000	0.000	0.000
24	A	1402	LYS	1	0.867	0.940	13.128	0.692	0.692	0.000	0.000	0.000	0.000
25	A	1403	LEU	0	-0.053	-0.019	8.692	-0.046	-0.046	0.000	0.000	0.000	0.000
26	A	1404	HIS	0	0.001	-0.012	12.566	0.062	0.062	0.000	0.000	0.000	0.000
27	A	1405	GLY	0	0.027	0.026	15.991	0.048	0.048	0.000	0.000	0.000	0.000
28	A	1406	GLN	0	-0.065	-0.033	11.095	0.080	0.080	0.000	0.000	0.000	0.000
29	A	1407	VAL	0	-0.053	-0.021	8.318	0.061	0.061	0.000	0.000	0.000	0.000
30	A	1408	LEU	0	-0.043	0.000	11.090	0.142	0.142	0.000	0.000	0.000	0.000
31	A	1409	SER	0	0.024	0.013	13.773	-0.033	-0.033	0.000	0.000	0.000	0.000
32	A	1410	GLN	0	0.109	0.055	17.460	-0.039	-0.039	0.000	0.000	0.000	0.000
33	A	1411	GLU	-1	-0.921	-0.968	20.470	0.017	0.017	0.000	0.000	0.000	0.000
34	A	1412	GLN	0	-0.056	-0.051	14.715	0.006	0.006	0.000	0.000	0.000	0.000
35	A	1413	TYR	0	0.009	-0.006	16.861	0.006	0.006	0.000	0.000	0.000	0.000
36	A	1414	GLU	-1	-0.804	-0.918	18.164	-0.086	-0.086	0.000	0.000	0.000	0.000
37	A	1415	ARG	1	0.871	0.954	19.169	-0.066	-0.066	0.000	0.000	0.000	0.000
38	A	1416	VAL	0	-0.087	-0.049	15.171	0.008	0.008	0.000	0.000	0.000	0.000
39	A	1417	LEU	0	0.010	-0.003	18.354	-0.019	-0.019	0.000	0.000	0.000	0.000
40	A	1418	ALA	0	-0.020	0.008	20.490	0.000	0.000	0.000	0.000	0.000	0.000
41	A	1419	GLU	-1	-0.983	-0.973	19.821	-0.039	-0.039	0.000	0.000	0.000	0.000
42	A	1420	ASN	0	0.049	0.010	22.643	-0.026	-0.026	0.000	0.000	0.000	0.000
43	A	1421	THR	0	-0.039	-0.044	22.692	-0.014	-0.014	0.000	0.000	0.000	0.000
44	A	1422	ARG	1	0.969	1.010	18.381	0.287	0.287	0.000	0.000	0.000	0.000
45	A	1423	PRO	0	0.012	-0.001	17.763	-0.018	-0.018	0.000	0.000	0.000	0.000
46	A	1424	SER	0	-0.004	0.017	17.916	0.010	0.010	0.000	0.000	0.000	0.000
47	A	1425	GLN	0	0.104	0.055	17.961	-0.017	-0.017	0.000	0.000	0.000	0.000
48	A	1426	MET	0	-0.005	0.007	10.150	0.017	0.017	0.000	0.000	0.000	0.000
49	A	1427	ARG	1	0.928	0.947	13.408	0.026	0.026	0.000	0.000	0.000	0.000
50	A	1428	LYS	1	0.959	1.003	14.950	0.029	0.029	0.000	0.000	0.000	0.000
51	A	1429	LEU	0	0.059	0.022	10.319	0.056	0.056	0.000	0.000	0.000	0.000
52	A	1430	PHE	0	-0.010	-0.008	7.140	0.082	0.082	0.000	0.000	0.000	0.000
53	A	1431	SER	0	-0.103	-0.040	11.315	0.142	0.142	0.000	0.000	0.000	0.000
54	A	1432	LEU	0	-0.030	-0.026	12.359	0.066	0.066	0.000	0.000	0.000	0.000
55	A	1433	SER	0	0.003	-0.007	8.061	0.011	0.011	0.000	0.000	0.000	0.000
56	A	1434	GLN	0	-0.049	-0.014	9.406	0.376	0.376	0.000	0.000	0.000	0.000
57	A	1435	SER	0	-0.005	-0.005	11.281	0.003	0.003	0.000	0.000	0.000	0.000
58	A	1436	TRP	0	-0.018	0.002	5.996	0.067	0.067	0.000	0.000	0.000	0.000
59	A	1437	ASP	-1	-0.758	-0.892	6.691	1.697	1.697	0.000	0.000	0.000	0.000
60	A	1438	ARG	1	0.889	0.934	2.018	-4.779	-6.006	7.541	-2.718	-3.596	0.001
61	A	1439	LYS	1	0.950	0.983	4.066	-2.724	-2.517	-0.001	-0.049	-0.158	0.000
62	A	1440	CYS	0	0.019	0.036	5.925	-0.775	-0.775	0.000	0.000	0.000	0.000
63	A	1441	LYS	1	0.863	0.929	2.078	-1.043	-6.468	10.649	-2.482	-2.742	0.006
64	A	1442	ASP	-1	-0.829	-0.914	1.848	-23.620	-28.452	22.785	-8.810	-9.142	-0.097
65	A	1443	GLY	0	0.028	0.021	2.980	1.490	1.010	0.124	0.600	-0.243	0.000
66	A	1444	LEU	0	0.023	0.010	4.967	0.074	0.074	0.000	0.000	0.000	0.000
67	A	1445	TYR	0	-0.075	-0.040	3.290	-1.310	0.346	0.146	-0.447	-1.355	-0.003
68	A	1446	GLN	0	-0.052	-0.030	5.400	0.404	0.404	0.000	0.000	0.000	0.000
69	A	1447	ALA	0	0.060	0.025	7.466	0.375	0.375	0.000	0.000	0.000	0.000
70	A	1448	LEU	0	-0.038	-0.013	7.039	0.264	0.264	0.000	0.000	0.000	0.000
71	A	1449	LYS	1	0.910	0.959	6.224	2.209	2.209	0.000	0.000	0.000	0.000
72	A	1450	GLU	-1	-0.901	-0.960	9.410	-0.816	-0.816	0.000	0.000	0.000	0.000
73	A	1451	THR	0	-0.067	-0.032	12.688	0.172	0.172	0.000	0.000	0.000	0.000
74	A	1452	HIS	0	-0.032	-0.016	12.695	0.166	0.166	0.000	0.000	0.000	0.000
75	A	1453	PRO	0	0.052	0.031	11.478	-0.072	-0.072	0.000	0.000	0.000	0.000
76	A	1454	HIS	0	0.052	-0.003	12.024	-0.055	-0.055	0.000	0.000	0.000	0.000
77	A	1455	LEU	0	0.003	0.033	12.036	0.036	0.036	0.000	0.000	0.000	0.000
78	A	1456	ILE	0	0.040	-0.010	6.464	0.000	0.000	0.000	0.000	0.000	0.000
79	A	1457	MET	0	-0.076	-0.016	8.972	-0.045	-0.045	0.000	0.000	0.000	0.000
80	A	1458	GLU	-1	-0.898	-0.942	11.263	-0.337	-0.337	0.000	0.000	0.000	0.000
81	A	1459	LEU	0	-0.082	-0.061	8.464	0.065	0.065	0.000	0.000	0.000	0.000
82	A	1460	TRP	0	0.007	0.006	3.704	-0.538	-0.208	0.005	-0.052	-0.284	0.000
83	A	1461	GLU	-1	-0.922	-0.952	9.899	-0.334	-0.334	0.000	0.000	0.000	0.000
84	A	1462	LYS	1	0.890	0.963	12.282	0.270	0.270	0.000	0.000	0.000	0.000

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