FMO DATABASE

FMODB ID: 393ZL

Calculation Name: 3TNU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3TNU

Chain ID: A

ChEMBL ID:

UniProt ID: P02533

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	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	90
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-440287.12322
FMO2-HF: Nuclear repulsion	401605.240631
FMO2-HF: Total energy	-38681.882589
FMO2-MP2: Total energy	-38789.815811

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:332:SER)

Summations of interaction energy for fragment #1(A:332:SER)

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.
-20.037	-15.096	5.897	-4.76	-6.079	0.03

Interaction energy analysis for fragmet #1(A:332:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / q_NPA : -0.002

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	334	LEU	0	0.033	0.026	3.076	-1.853	0.795	0.061	-1.203	-1.506	0.003
4	A	335	ARG	1	0.982	0.981	2.580	-4.367	-2.446	0.859	-1.041	-1.740	-0.003
5	A	336	ARG	1	0.932	0.973	2.007	-13.890	-13.518	4.977	-2.516	-2.833	0.030
6	A	337	THR	0	0.011	0.000	5.567	-0.255	-0.255	0.000	0.000	0.000	0.000
7	A	338	MET	0	0.005	0.009	7.334	-0.143	-0.143	0.000	0.000	0.000	0.000
8	A	339	GLN	0	0.026	0.012	6.526	0.053	0.053	0.000	0.000	0.000	0.000
9	A	340	ASN	0	-0.009	-0.013	9.454	-0.135	-0.135	0.000	0.000	0.000	0.000
10	A	341	LEU	0	-0.004	0.010	11.495	-0.139	-0.139	0.000	0.000	0.000	0.000
11	A	342	GLU	-1	-0.896	-0.944	11.177	0.808	0.808	0.000	0.000	0.000	0.000
12	A	343	ILE	0	-0.024	-0.019	12.677	-0.089	-0.089	0.000	0.000	0.000	0.000
13	A	344	GLU	-1	-0.839	-0.913	15.477	0.314	0.314	0.000	0.000	0.000	0.000
14	A	345	LEU	0	-0.030	-0.015	17.021	-0.058	-0.058	0.000	0.000	0.000	0.000
15	A	346	GLN	0	-0.002	-0.009	17.463	-0.083	-0.083	0.000	0.000	0.000	0.000
16	A	347	SER	0	0.012	0.021	19.891	-0.038	-0.038	0.000	0.000	0.000	0.000
17	A	348	GLN	0	-0.027	-0.022	21.719	-0.055	-0.055	0.000	0.000	0.000	0.000
18	A	349	LEU	0	-0.027	-0.011	21.372	-0.030	-0.030	0.000	0.000	0.000	0.000
19	A	350	SER	0	-0.040	-0.024	23.684	-0.026	-0.026	0.000	0.000	0.000	0.000
20	A	351	MET	0	-0.029	-0.027	25.895	-0.014	-0.014	0.000	0.000	0.000	0.000
21	A	352	LYS	1	0.825	0.911	27.294	-0.196	-0.196	0.000	0.000	0.000	0.000
22	A	353	ALA	0	0.059	0.037	28.658	-0.016	-0.016	0.000	0.000	0.000	0.000
23	A	354	SER	0	-0.007	-0.003	30.463	-0.011	-0.011	0.000	0.000	0.000	0.000
24	A	355	LEU	0	0.002	-0.004	31.195	-0.012	-0.012	0.000	0.000	0.000	0.000
25	A	356	GLU	-1	-0.838	-0.908	31.797	0.152	0.152	0.000	0.000	0.000	0.000
26	A	357	ASN	0	-0.048	-0.037	33.917	-0.014	-0.014	0.000	0.000	0.000	0.000
27	A	358	SER	0	-0.001	0.016	36.268	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	359	LEU	0	-0.003	0.002	37.765	-0.008	-0.008	0.000	0.000	0.000	0.000
29	A	360	GLU	-1	-0.863	-0.943	39.351	0.094	0.094	0.000	0.000	0.000	0.000
30	A	361	GLU	-1	-0.846	-0.917	40.754	0.089	0.089	0.000	0.000	0.000	0.000
31	A	362	THR	0	-0.017	-0.019	41.841	-0.007	-0.007	0.000	0.000	0.000	0.000
32	A	363	LYS	1	0.828	0.922	41.658	-0.102	-0.102	0.000	0.000	0.000	0.000
33	A	364	GLY	0	0.031	0.018	45.451	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	365	ARG	1	0.864	0.937	43.964	-0.087	-0.087	0.000	0.000	0.000	0.000
35	A	366	TYR	0	0.002	-0.008	46.880	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	367	CYS	0	-0.042	-0.010	49.790	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	368	MET	0	0.023	0.003	50.928	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	369	GLN	0	0.000	-0.008	51.188	0.000	0.000	0.000	0.000	0.000	0.000
39	A	370	LEU	0	-0.024	-0.004	54.271	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	371	ALA	0	0.011	-0.003	55.734	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	372	GLN	0	0.024	0.010	55.342	0.000	0.000	0.000	0.000	0.000	0.000
42	A	373	ILE	0	-0.020	-0.009	58.599	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	374	GLN	0	-0.018	-0.018	58.880	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	375	GLU	-1	-0.911	-0.941	61.746	0.043	0.043	0.000	0.000	0.000	0.000
45	A	376	MET	0	-0.058	-0.029	62.690	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	377	ILE	0	-0.026	-0.015	63.601	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	378	GLY	0	0.072	0.053	66.163	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	379	SER	0	0.010	-0.002	67.562	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	380	VAL	0	-0.027	-0.015	69.489	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	381	GLU	-1	-0.945	-0.968	69.065	0.036	0.036	0.000	0.000	0.000	0.000
51	A	382	GLU	-1	-0.936	-0.963	71.764	0.033	0.033	0.000	0.000	0.000	0.000
52	A	383	GLN	0	-0.013	-0.003	73.743	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	384	LEU	0	-0.079	-0.052	75.177	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	385	ALA	0	-0.025	-0.021	76.388	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	386	GLN	0	-0.025	-0.026	77.941	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	387	LEU	0	0.020	0.013	79.732	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	388	ARG	1	0.931	0.952	78.011	-0.030	-0.030	0.000	0.000	0.000	0.000
58	A	389	CYS	0	-0.019	-0.009	82.351	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	390	GLU	-1	-0.875	-0.925	83.589	0.025	0.025	0.000	0.000	0.000	0.000
60	A	391	MET	0	-0.083	-0.041	84.731	0.000	0.000	0.000	0.000	0.000	0.000
61	A	392	GLU	-1	-0.851	-0.898	86.935	0.022	0.022	0.000	0.000	0.000	0.000
62	A	393	GLN	0	-0.032	-0.036	88.539	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	394	GLN	0	-0.020	-0.001	90.106	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	395	ASN	0	-0.027	-0.021	89.858	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	396	GLN	0	-0.077	-0.049	91.110	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	397	GLU	-1	-0.855	-0.916	92.862	0.020	0.020	0.000	0.000	0.000	0.000
67	A	398	TYR	0	-0.023	-0.013	96.051	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	399	LYS	1	0.796	0.878	97.545	-0.018	-0.018	0.000	0.000	0.000	0.000
69	A	400	ILE	0	0.018	0.009	98.267	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	401	LEU	0	-0.007	0.000	100.768	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	402	LEU	0	-0.002	-0.011	101.463	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	403	ASP	-1	-0.784	-0.878	103.501	0.017	0.017	0.000	0.000	0.000	0.000
73	A	404	VAL	0	-0.056	-0.023	105.511	0.000	0.000	0.000	0.000	0.000	0.000
74	A	405	LYS	1	0.817	0.903	106.374	-0.016	-0.016	0.000	0.000	0.000	0.000
75	A	406	THR	0	-0.011	-0.015	107.165	0.000	0.000	0.000	0.000	0.000	0.000
76	A	407	ARG	1	0.930	0.975	109.391	-0.015	-0.015	0.000	0.000	0.000	0.000
77	A	408	LEU	0	0.003	-0.002	110.225	0.000	0.000	0.000	0.000	0.000	0.000
78	A	409	GLU	-1	-0.822	-0.904	110.660	0.015	0.015	0.000	0.000	0.000	0.000
79	A	410	GLN	0	-0.021	-0.023	113.603	0.000	0.000	0.000	0.000	0.000	0.000
80	A	411	GLU	-1	-0.884	-0.916	114.835	0.014	0.014	0.000	0.000	0.000	0.000
81	A	412	ILE	0	0.016	0.001	115.314	0.000	0.000	0.000	0.000	0.000	0.000
82	A	413	ALA	0	-0.018	-0.001	118.381	0.000	0.000	0.000	0.000	0.000	0.000
83	A	414	THR	0	-0.063	-0.037	120.145	0.000	0.000	0.000	0.000	0.000	0.000
84	A	415	TYR	0	0.048	0.013	119.413	0.000	0.000	0.000	0.000	0.000	0.000
85	A	416	ARG	1	0.894	0.945	118.459	-0.013	-0.013	0.000	0.000	0.000	0.000
86	A	417	ARG	1	0.953	0.990	124.431	-0.012	-0.012	0.000	0.000	0.000	0.000
87	A	418	LEU	0	-0.054	-0.044	125.901	0.000	0.000	0.000	0.000	0.000	0.000
88	A	419	LEU	0	-0.051	-0.011	126.514	0.000	0.000	0.000	0.000	0.000	0.000
89	A	420	GLU	-1	-0.927	-0.958	129.609	0.011	0.011	0.000	0.000	0.000	0.000
90	A	421	GLY	0	-0.053	-0.009	130.790	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:332:SER)