FMO DATABASE

FMODB ID: K97V3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-333419.321537
FMO2-HF: Nuclear repulsion	302639.340438
FMO2-HF: Total energy	-30779.981099
FMO2-MP2: Total energy	-30866.31507

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.
6.964	5.791	12.086	-4.957	-5.955	0.019

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 : -0.900 / q_NPA : -0.960

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	B	315	ARG	1	0.965	0.967	3.472	-23.257	-21.727	0.016	-0.801	-0.745	0.002
4	B	316	ALA	0	0.013	0.011	6.170	-1.222	-1.222	0.000	0.000	0.000	0.000
5	B	317	CYS	0	-0.044	-0.015	2.520	-13.003	-10.095	1.344	-1.993	-2.259	0.024
6	B	318	LEU	0	0.043	0.007	2.002	0.791	-5.020	10.728	-2.155	-2.763	-0.007
7	B	319	GLU	-1	-0.875	-0.929	5.023	20.419	20.492	-0.001	-0.004	-0.067	0.000
8	B	320	ARG	1	0.887	0.964	7.979	-24.486	-24.486	0.000	0.000	0.000	0.000
9	B	321	ILE	0	0.010	-0.009	4.398	-1.752	-1.625	-0.001	-0.004	-0.121	0.000
10	B	322	GLN	0	-0.008	0.004	8.474	-1.395	-1.395	0.000	0.000	0.000	0.000
11	B	323	GLU	-1	-0.860	-0.933	10.511	18.194	18.194	0.000	0.000	0.000	0.000
12	B	324	LEU	0	-0.046	-0.044	11.387	-1.733	-1.733	0.000	0.000	0.000	0.000
13	B	325	GLU	-1	-0.946	-0.962	9.704	24.040	24.040	0.000	0.000	0.000	0.000
14	B	326	ASP	-1	-0.890	-0.935	13.605	16.569	16.569	0.000	0.000	0.000	0.000
15	B	327	LEU	0	-0.059	-0.032	16.400	-1.236	-1.236	0.000	0.000	0.000	0.000
16	B	328	LEU	0	-0.003	0.004	16.001	-1.069	-1.069	0.000	0.000	0.000	0.000
17	B	329	ALA	0	-0.005	-0.004	17.791	-0.910	-0.910	0.000	0.000	0.000	0.000
18	B	330	LYS	1	0.970	0.973	19.680	-12.760	-12.760	0.000	0.000	0.000	0.000
19	B	331	GLU	-1	-0.925	-0.961	21.377	11.753	11.753	0.000	0.000	0.000	0.000
20	B	332	LYS	1	0.949	0.959	18.944	-15.523	-15.523	0.000	0.000	0.000	0.000
21	B	333	ASP	-1	-0.876	-0.919	23.811	11.424	11.424	0.000	0.000	0.000	0.000
22	B	334	ASN	0	-0.060	-0.042	25.746	-0.734	-0.734	0.000	0.000	0.000	0.000
23	B	335	SER	0	0.013	0.014	26.453	-0.424	-0.424	0.000	0.000	0.000	0.000
24	B	336	ARG	1	0.857	0.919	26.913	-10.920	-10.920	0.000	0.000	0.000	0.000
25	B	337	ARG	1	0.915	0.951	27.099	-10.888	-10.888	0.000	0.000	0.000	0.000
26	B	338	MET	0	0.021	0.020	29.504	-0.275	-0.275	0.000	0.000	0.000	0.000
27	B	339	LEU	0	-0.005	0.009	32.407	-0.218	-0.218	0.000	0.000	0.000	0.000
28	B	340	THR	0	-0.001	0.000	34.193	-0.265	-0.265	0.000	0.000	0.000	0.000
29	B	341	ASP	-1	-0.902	-0.958	36.052	8.264	8.264	0.000	0.000	0.000	0.000
30	B	342	LYS	1	0.877	0.941	37.195	-8.086	-8.086	0.000	0.000	0.000	0.000
31	B	343	GLU	-1	-0.916	-0.964	37.439	8.168	8.168	0.000	0.000	0.000	0.000
32	B	344	ARG	1	0.891	0.953	40.266	-7.533	-7.533	0.000	0.000	0.000	0.000
33	B	345	GLU	-1	-0.878	-0.947	41.436	7.351	7.351	0.000	0.000	0.000	0.000
34	B	346	MET	0	-0.069	-0.026	42.813	-0.151	-0.151	0.000	0.000	0.000	0.000
35	B	347	ALA	0	-0.014	-0.020	44.542	-0.169	-0.169	0.000	0.000	0.000	0.000
36	B	348	GLU	-1	-0.893	-0.944	46.183	6.640	6.640	0.000	0.000	0.000	0.000
37	B	349	ILE	0	-0.024	-0.005	47.405	-0.155	-0.155	0.000	0.000	0.000	0.000
38	B	350	ARG	1	0.927	0.939	45.162	-6.851	-6.851	0.000	0.000	0.000	0.000
39	B	351	ASP	-1	-0.937	-0.941	50.512	5.803	5.803	0.000	0.000	0.000	0.000
40	B	352	GLN	0	0.045	0.011	51.578	-0.165	-0.165	0.000	0.000	0.000	0.000
41	B	353	MET	0	-0.055	-0.027	52.500	-0.097	-0.097	0.000	0.000	0.000	0.000
42	B	354	GLN	0	-0.028	-0.007	54.731	0.002	0.002	0.000	0.000	0.000	0.000
43	B	355	GLN	0	0.006	-0.006	56.508	-0.106	-0.106	0.000	0.000	0.000	0.000
44	B	356	GLN	0	-0.001	0.008	57.739	-0.093	-0.093	0.000	0.000	0.000	0.000
45	B	357	LEU	0	-0.059	-0.023	58.860	-0.089	-0.089	0.000	0.000	0.000	0.000
46	B	358	ASN	0	0.048	0.014	60.715	0.002	0.002	0.000	0.000	0.000	0.000
47	B	359	ASP	-1	-0.893	-0.935	62.647	4.983	4.983	0.000	0.000	0.000	0.000
48	B	360	TYR	0	-0.080	-0.038	64.017	-0.121	-0.121	0.000	0.000	0.000	0.000
49	B	361	GLU	-1	-0.919	-0.975	62.813	4.970	4.970	0.000	0.000	0.000	0.000
50	B	362	GLN	0	0.019	0.012	65.456	-0.024	-0.024	0.000	0.000	0.000	0.000
51	B	363	LEU	0	-0.032	-0.009	68.513	-0.094	-0.094	0.000	0.000	0.000	0.000
52	B	364	LEU	0	-0.026	-0.017	69.419	-0.090	-0.090	0.000	0.000	0.000	0.000
53	B	365	ASP	-1	-0.861	-0.931	70.771	4.446	4.446	0.000	0.000	0.000	0.000
54	B	366	VAL	0	-0.049	-0.019	72.999	-0.086	-0.086	0.000	0.000	0.000	0.000
55	B	367	LYS	1	0.814	0.893	74.256	-4.306	-4.306	0.000	0.000	0.000	0.000
56	B	368	LEU	0	-0.010	-0.020	73.539	-0.069	-0.069	0.000	0.000	0.000	0.000
57	B	369	ALA	0	-0.010	0.007	77.069	-0.066	-0.066	0.000	0.000	0.000	0.000
58	B	370	LEU	0	0.018	-0.003	78.196	-0.067	-0.067	0.000	0.000	0.000	0.000
59	B	371	ASP	-1	-0.838	-0.890	78.797	4.035	4.035	0.000	0.000	0.000	0.000
60	B	372	MET	0	-0.039	-0.028	80.218	-0.070	-0.070	0.000	0.000	0.000	0.000
61	B	373	GLU	-1	-0.892	-0.956	83.237	3.791	3.791	0.000	0.000	0.000	0.000
62	B	374	ILE	0	-0.028	-0.004	84.161	-0.070	-0.070	0.000	0.000	0.000	0.000
63	B	375	SER	0	-0.044	-0.022	85.598	-0.061	-0.061	0.000	0.000	0.000	0.000
64	B	376	ALA	0	-0.021	-0.003	87.809	-0.055	-0.055	0.000	0.000	0.000	0.000
65	B	377	TYR	0	0.007	-0.010	87.744	-0.077	-0.077	0.000	0.000	0.000	0.000
66	B	378	ARG	1	0.975	0.990	86.233	-3.723	-3.723	0.000	0.000	0.000	0.000
67	B	379	LYS	1	0.898	0.962	92.015	-3.478	-3.478	0.000	0.000	0.000	0.000
68	B	380	LEU	0	-0.050	-0.027	93.697	-0.043	-0.043	0.000	0.000	0.000	0.000
69	B	381	LEU	0	-0.035	-0.001	94.825	-0.039	-0.039	0.000	0.000	0.000	0.000
70	B	382	GLU	-1	-0.988	-1.002	93.560	3.440	3.440	0.000	0.000	0.000	0.000
71	B	383	GLY	0	-0.047	-0.013	97.415	-0.017	-0.017	0.000	0.000	0.000	0.000

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