FMO DATABASE

FMODB ID: 49RYN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-334162.512859
FMO2-HF: Nuclear repulsion	303381.808011
FMO2-HF: Total energy	-30780.704848
FMO2-MP2: Total energy	-30867.069163

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.
-9.56	-7.449	9.215	-4.699	-6.626	0.038

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 : -0.861 / q_NPA : -0.946

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	0.889	0.896	3.356	-27.040	-25.019	0.027	-1.038	-1.010	0.003
4	B	316	ALA	0	0.006	0.004	6.003	-1.910	-1.910	0.000	0.000	0.000	0.000
5	B	317	CYS	0	-0.047	-0.013	2.242	-17.389	-16.442	5.260	-2.708	-3.499	0.036
6	B	318	LEU	0	0.054	0.015	2.257	-4.691	-5.763	3.930	-0.937	-1.920	-0.001
7	B	319	GLU	-1	-0.834	-0.880	4.842	21.451	21.516	-0.001	-0.006	-0.058	0.000
8	B	320	ARG	1	0.857	0.935	7.936	-26.456	-26.456	0.000	0.000	0.000	0.000
9	B	321	ILE	0	0.009	-0.006	4.288	-2.312	-2.162	-0.001	-0.010	-0.139	0.000
10	B	322	GLN	0	-0.023	-0.012	8.433	-1.918	-1.918	0.000	0.000	0.000	0.000
11	B	323	GLU	-1	-0.826	-0.903	10.353	19.770	19.770	0.000	0.000	0.000	0.000
12	B	324	LEU	0	-0.028	-0.031	11.491	-1.908	-1.908	0.000	0.000	0.000	0.000
13	B	325	GLU	-1	-0.957	-0.966	9.977	23.582	23.582	0.000	0.000	0.000	0.000
14	B	326	ASP	-1	-0.878	-0.930	13.752	17.182	17.182	0.000	0.000	0.000	0.000
15	B	327	LEU	0	-0.042	-0.021	16.387	-1.355	-1.355	0.000	0.000	0.000	0.000
16	B	328	LEU	0	-0.007	0.003	15.972	-1.202	-1.202	0.000	0.000	0.000	0.000
17	B	329	ALA	0	-0.015	-0.009	17.942	-1.009	-1.009	0.000	0.000	0.000	0.000
18	B	330	LYS	1	0.887	0.924	19.874	-12.838	-12.838	0.000	0.000	0.000	0.000
19	B	331	GLU	-1	-0.843	-0.914	21.454	11.815	11.815	0.000	0.000	0.000	0.000
20	B	332	LYS	1	0.947	0.964	18.906	-15.605	-15.605	0.000	0.000	0.000	0.000
21	B	333	ASP	-1	-0.790	-0.860	23.943	10.693	10.693	0.000	0.000	0.000	0.000
22	B	334	ASN	0	-0.046	-0.028	25.714	-0.751	-0.751	0.000	0.000	0.000	0.000
23	B	335	SER	0	0.007	0.008	26.278	-0.414	-0.414	0.000	0.000	0.000	0.000
24	B	336	ARG	1	0.872	0.925	27.181	-10.945	-10.945	0.000	0.000	0.000	0.000
25	B	337	ARG	1	0.834	0.904	27.616	-10.868	-10.868	0.000	0.000	0.000	0.000
26	B	338	MET	0	0.009	0.009	29.413	-0.333	-0.333	0.000	0.000	0.000	0.000
27	B	339	LEU	0	-0.013	0.007	32.787	-0.221	-0.221	0.000	0.000	0.000	0.000
28	B	340	THR	0	-0.007	-0.019	33.985	-0.270	-0.270	0.000	0.000	0.000	0.000
29	B	341	ASP	-1	-0.868	-0.945	36.168	8.039	8.039	0.000	0.000	0.000	0.000
30	B	342	LYS	1	0.793	0.882	37.372	-8.138	-8.138	0.000	0.000	0.000	0.000
31	B	343	GLU	-1	-0.929	-0.974	37.450	8.123	8.123	0.000	0.000	0.000	0.000
32	B	344	ARG	1	0.801	0.888	40.402	-7.613	-7.613	0.000	0.000	0.000	0.000
33	B	345	GLU	-1	-0.812	-0.884	41.124	7.489	7.489	0.000	0.000	0.000	0.000
34	B	346	MET	0	-0.063	-0.026	42.952	-0.176	-0.176	0.000	0.000	0.000	0.000
35	B	347	ALA	0	-0.018	-0.018	44.664	-0.174	-0.174	0.000	0.000	0.000	0.000
36	B	348	GLU	-1	-0.825	-0.891	45.845	6.751	6.751	0.000	0.000	0.000	0.000
37	B	349	ILE	0	-0.013	-0.001	47.208	-0.159	-0.159	0.000	0.000	0.000	0.000
38	B	350	ARG	1	0.941	0.946	44.833	-6.914	-6.914	0.000	0.000	0.000	0.000
39	B	351	ASP	-1	-0.875	-0.906	50.602	5.792	5.792	0.000	0.000	0.000	0.000
40	B	352	GLN	0	0.011	-0.002	51.007	-0.174	-0.174	0.000	0.000	0.000	0.000
41	B	353	MET	0	-0.058	-0.027	52.868	-0.088	-0.088	0.000	0.000	0.000	0.000
42	B	354	GLN	0	-0.029	-0.016	54.823	-0.032	-0.032	0.000	0.000	0.000	0.000
43	B	355	GLN	0	-0.019	-0.026	55.682	-0.192	-0.192	0.000	0.000	0.000	0.000
44	B	356	GLN	0	-0.010	0.003	57.974	-0.099	-0.099	0.000	0.000	0.000	0.000
45	B	357	LEU	0	-0.043	-0.019	58.767	-0.094	-0.094	0.000	0.000	0.000	0.000
46	B	358	ASN	0	0.006	-0.008	60.424	-0.012	-0.012	0.000	0.000	0.000	0.000
47	B	359	ASP	-1	-0.908	-0.941	62.741	4.978	4.978	0.000	0.000	0.000	0.000
48	B	360	TYR	0	-0.075	-0.032	64.090	-0.119	-0.119	0.000	0.000	0.000	0.000
49	B	361	GLU	-1	-0.880	-0.946	63.143	4.986	4.986	0.000	0.000	0.000	0.000
50	B	362	GLN	0	0.003	0.003	65.454	-0.104	-0.104	0.000	0.000	0.000	0.000
51	B	363	LEU	0	-0.027	-0.008	68.601	-0.094	-0.094	0.000	0.000	0.000	0.000
52	B	364	LEU	0	-0.028	-0.016	69.417	-0.088	-0.088	0.000	0.000	0.000	0.000
53	B	365	ASP	-1	-0.853	-0.928	71.220	4.422	4.422	0.000	0.000	0.000	0.000
54	B	366	VAL	0	-0.047	-0.016	73.099	-0.086	-0.086	0.000	0.000	0.000	0.000
55	B	367	LYS	1	0.778	0.869	74.250	-4.281	-4.281	0.000	0.000	0.000	0.000
56	B	368	LEU	0	-0.001	-0.010	73.602	-0.068	-0.068	0.000	0.000	0.000	0.000
57	B	369	ALA	0	-0.015	0.005	77.150	-0.068	-0.068	0.000	0.000	0.000	0.000
58	B	370	LEU	0	0.009	-0.010	78.266	-0.071	-0.071	0.000	0.000	0.000	0.000
59	B	371	ASP	-1	-0.816	-0.878	78.817	4.050	4.050	0.000	0.000	0.000	0.000
60	B	372	MET	0	-0.031	-0.021	80.488	-0.079	-0.079	0.000	0.000	0.000	0.000
61	B	373	GLU	-1	-0.850	-0.923	83.462	3.760	3.760	0.000	0.000	0.000	0.000
62	B	374	ILE	0	-0.016	-0.003	84.208	-0.068	-0.068	0.000	0.000	0.000	0.000
63	B	375	SER	0	-0.048	-0.027	85.449	-0.057	-0.057	0.000	0.000	0.000	0.000
64	B	376	ALA	0	-0.018	0.002	87.899	-0.055	-0.055	0.000	0.000	0.000	0.000
65	B	377	TYR	0	-0.043	-0.042	87.217	-0.082	-0.082	0.000	0.000	0.000	0.000
66	B	378	ARG	1	0.949	0.980	86.531	-3.709	-3.709	0.000	0.000	0.000	0.000
67	B	379	LYS	1	0.895	0.959	92.089	-3.469	-3.469	0.000	0.000	0.000	0.000
68	B	380	LEU	0	-0.044	-0.026	93.464	-0.044	-0.044	0.000	0.000	0.000	0.000
69	B	381	LEU	0	-0.040	-0.001	94.706	-0.040	-0.040	0.000	0.000	0.000	0.000
70	B	382	GLU	-1	-0.962	-0.997	93.306	3.454	3.454	0.000	0.000	0.000	0.000
71	B	383	GLY	0	-0.044	-0.011	97.462	-0.015	-0.015	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)