FMO DATABASE

FMODB ID: 52Z5Z

Calculation Name: 3TYY-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3TYY

Chain ID: B

ChEMBL ID:

UniProt ID: P20700

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	71
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-334426.687399
FMO2-HF: Nuclear repulsion	303645.789673
FMO2-HF: Total energy	-30780.897725
FMO2-MP2: Total energy	-30867.243984

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(B:313:GLU)

Summations of interaction energy for fragment #1(B:313:GLU)

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.
-18.955	-22.469	21.541	-8.733	-9.292	0.072

Interaction energy analysis for fragmet #1(B:313:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.786 / q_NPA : -0.883

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	B	315	ARG	1	0.849	0.883	3.339	-29.232	-27.196	0.035	-0.794	-1.277	0.006
4	B	316	ALA	0	0.020	0.009	5.975	-1.768	-1.768	0.000	0.000	0.000	0.000
5	B	317	CYS	0	-0.054	-0.019	1.821	-21.531	-27.115	18.978	-7.237	-6.157	0.067
6	B	318	LEU	0	0.049	0.013	2.399	-7.699	-7.876	2.530	-0.690	-1.662	-0.001
7	B	319	GLU	-1	-0.833	-0.883	4.928	22.356	22.427	-0.001	-0.005	-0.064	0.000
8	B	320	ARG	1	0.841	0.913	7.887	-27.982	-27.982	0.000	0.000	0.000	0.000
9	B	321	ILE	0	0.007	-0.002	4.543	-2.223	-2.083	-0.001	-0.007	-0.132	0.000
10	B	322	GLN	0	-0.027	-0.018	8.557	-1.989	-1.989	0.000	0.000	0.000	0.000
11	B	323	GLU	-1	-0.835	-0.900	10.692	20.588	20.588	0.000	0.000	0.000	0.000
12	B	324	LEU	0	-0.020	-0.022	11.077	-1.963	-1.963	0.000	0.000	0.000	0.000
13	B	325	GLU	-1	-0.952	-0.972	10.321	23.448	23.448	0.000	0.000	0.000	0.000
14	B	326	ASP	-1	-0.861	-0.921	14.033	17.277	17.277	0.000	0.000	0.000	0.000
15	B	327	LEU	0	-0.024	-0.017	16.337	-1.435	-1.435	0.000	0.000	0.000	0.000
16	B	328	LEU	0	-0.034	-0.008	15.862	-1.306	-1.306	0.000	0.000	0.000	0.000
17	B	329	ALA	0	-0.012	-0.011	18.220	-0.983	-0.983	0.000	0.000	0.000	0.000
18	B	330	LYS	1	0.823	0.895	20.117	-13.055	-13.055	0.000	0.000	0.000	0.000
19	B	331	GLU	-1	-0.809	-0.897	21.736	11.934	11.934	0.000	0.000	0.000	0.000
20	B	332	LYS	1	0.942	0.987	19.162	-15.696	-15.696	0.000	0.000	0.000	0.000
21	B	333	ASP	-1	-0.746	-0.849	24.276	10.631	10.631	0.000	0.000	0.000	0.000
22	B	334	ASN	0	-0.049	-0.034	25.806	-0.723	-0.723	0.000	0.000	0.000	0.000
23	B	335	SER	0	0.000	-0.018	26.439	-0.475	-0.475	0.000	0.000	0.000	0.000
24	B	336	ARG	1	0.868	0.935	27.764	-10.907	-10.907	0.000	0.000	0.000	0.000
25	B	337	ARG	1	0.835	0.919	28.268	-10.814	-10.814	0.000	0.000	0.000	0.000
26	B	338	MET	0	0.004	0.001	29.273	-0.346	-0.346	0.000	0.000	0.000	0.000
27	B	339	LEU	0	-0.022	0.007	32.947	-0.202	-0.202	0.000	0.000	0.000	0.000
28	B	340	THR	0	0.011	-0.008	34.356	-0.275	-0.275	0.000	0.000	0.000	0.000
29	B	341	ASP	-1	-0.858	-0.930	36.658	7.995	7.995	0.000	0.000	0.000	0.000
30	B	342	LYS	1	0.765	0.870	37.629	-8.191	-8.191	0.000	0.000	0.000	0.000
31	B	343	GLU	-1	-0.916	-0.971	37.510	8.153	8.153	0.000	0.000	0.000	0.000
32	B	344	ARG	1	0.760	0.839	40.681	-7.644	-7.644	0.000	0.000	0.000	0.000
33	B	345	GLU	-1	-0.780	-0.872	41.683	7.504	7.504	0.000	0.000	0.000	0.000
34	B	346	MET	0	-0.061	-0.021	43.170	-0.189	-0.189	0.000	0.000	0.000	0.000
35	B	347	ALA	0	-0.013	-0.010	44.911	-0.167	-0.167	0.000	0.000	0.000	0.000
36	B	348	GLU	-1	-0.790	-0.867	46.286	6.798	6.798	0.000	0.000	0.000	0.000
37	B	349	ILE	0	-0.028	-0.004	47.475	-0.163	-0.163	0.000	0.000	0.000	0.000
38	B	350	ARG	1	0.927	0.950	45.314	-6.916	-6.916	0.000	0.000	0.000	0.000
39	B	351	ASP	-1	-0.860	-0.903	50.989	5.796	5.796	0.000	0.000	0.000	0.000
40	B	352	GLN	0	-0.007	-0.018	51.092	-0.185	-0.185	0.000	0.000	0.000	0.000
41	B	353	MET	0	-0.053	-0.024	53.094	-0.082	-0.082	0.000	0.000	0.000	0.000
42	B	354	GLN	0	-0.034	-0.018	55.100	-0.040	-0.040	0.000	0.000	0.000	0.000
43	B	355	GLN	0	-0.031	-0.033	55.988	-0.200	-0.200	0.000	0.000	0.000	0.000
44	B	356	GLN	0	0.003	0.007	58.204	-0.102	-0.102	0.000	0.000	0.000	0.000
45	B	357	LEU	0	-0.046	-0.013	59.251	-0.089	-0.089	0.000	0.000	0.000	0.000
46	B	358	ASN	0	0.018	-0.006	60.688	-0.022	-0.022	0.000	0.000	0.000	0.000
47	B	359	ASP	-1	-0.924	-0.945	62.731	5.006	5.006	0.000	0.000	0.000	0.000
48	B	360	TYR	0	-0.067	-0.033	64.287	-0.119	-0.119	0.000	0.000	0.000	0.000
49	B	361	GLU	-1	-0.885	-0.941	63.597	4.990	4.990	0.000	0.000	0.000	0.000
50	B	362	GLN	0	0.007	-0.013	65.721	-0.123	-0.123	0.000	0.000	0.000	0.000
51	B	363	LEU	0	-0.034	-0.009	68.851	-0.093	-0.093	0.000	0.000	0.000	0.000
52	B	364	LEU	0	-0.015	-0.010	69.810	-0.090	-0.090	0.000	0.000	0.000	0.000
53	B	365	ASP	-1	-0.871	-0.935	71.149	4.438	4.438	0.000	0.000	0.000	0.000
54	B	366	VAL	0	-0.038	-0.019	73.400	-0.090	-0.090	0.000	0.000	0.000	0.000
55	B	367	LYS	1	0.784	0.871	74.369	-4.265	-4.265	0.000	0.000	0.000	0.000
56	B	368	LEU	0	-0.012	-0.011	73.909	-0.067	-0.067	0.000	0.000	0.000	0.000
57	B	369	ALA	0	-0.010	-0.004	77.497	-0.069	-0.069	0.000	0.000	0.000	0.000
58	B	370	LEU	0	0.014	0.005	78.345	-0.072	-0.072	0.000	0.000	0.000	0.000
59	B	371	ASP	-1	-0.803	-0.872	79.177	4.041	4.041	0.000	0.000	0.000	0.000
60	B	372	MET	0	-0.017	0.002	81.111	-0.084	-0.084	0.000	0.000	0.000	0.000
61	B	373	GLU	-1	-0.860	-0.909	83.635	3.772	3.772	0.000	0.000	0.000	0.000
62	B	374	ILE	0	0.000	-0.001	84.395	-0.066	-0.066	0.000	0.000	0.000	0.000
63	B	375	SER	0	-0.038	-0.040	85.603	-0.061	-0.061	0.000	0.000	0.000	0.000
64	B	376	ALA	0	-0.037	-0.006	88.008	-0.054	-0.054	0.000	0.000	0.000	0.000
65	B	377	TYR	0	-0.064	-0.067	87.257	-0.080	-0.080	0.000	0.000	0.000	0.000
66	B	378	ARG	1	0.873	0.939	87.570	-3.687	-3.687	0.000	0.000	0.000	0.000
67	B	379	LYS	1	0.919	0.973	92.106	-3.464	-3.464	0.000	0.000	0.000	0.000
68	B	380	LEU	0	-0.062	-0.029	93.603	-0.044	-0.044	0.000	0.000	0.000	0.000
69	B	381	LEU	0	-0.031	-0.004	94.694	-0.034	-0.034	0.000	0.000	0.000	0.000
70	B	382	GLU	-1	-0.900	-0.960	93.066	3.485	3.485	0.000	0.000	0.000	0.000
71	B	383	GLY	0	-0.048	-0.015	97.333	-0.011	-0.011	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(B:313:GLU)