FMO DATABASE

FMODB ID: 172YZ

Calculation Name: 3TYY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3TYY

Chain ID: A

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	75
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-355886.534443
FMO2-HF: Nuclear repulsion	323291.100074
FMO2-HF: Total energy	-32595.434369
FMO2-MP2: Total energy	-32687.035072

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:311:GLN)

Summations of interaction energy for fragment #1(A:311:GLN)

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.
-18.814	-18.561	7.095	-3.535	-3.813	-0.027

Interaction energy analysis for fragmet #1(A:311:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.038 / q_NPA : 0.016

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	313	GLU	-1	-0.759	-0.879	1.954	-21.167	-20.974	7.096	-3.519	-3.771	-0.027
4	A	314	SER	0	-0.030	-0.008	4.627	1.997	2.057	-0.001	-0.016	-0.042	0.000
5	A	315	ARG	1	0.970	0.966	8.136	0.739	0.739	0.000	0.000	0.000	0.000
6	A	316	ALA	0	0.095	0.052	11.142	0.017	0.017	0.000	0.000	0.000	0.000
7	A	317	CYS	0	-0.061	-0.017	7.522	0.322	0.322	0.000	0.000	0.000	0.000
8	A	318	LEU	0	0.020	-0.006	6.978	0.125	0.125	0.000	0.000	0.000	0.000
9	A	319	GLU	-1	-0.932	-0.953	10.788	-0.796	-0.796	0.000	0.000	0.000	0.000
10	A	320	ARG	1	0.859	0.917	13.807	1.067	1.067	0.000	0.000	0.000	0.000
11	A	321	ILE	0	-0.026	-0.016	9.698	0.084	0.084	0.000	0.000	0.000	0.000
12	A	322	GLN	0	0.014	0.003	13.823	0.122	0.122	0.000	0.000	0.000	0.000
13	A	323	GLU	-1	-0.853	-0.905	15.677	-0.704	-0.704	0.000	0.000	0.000	0.000
14	A	324	LEU	0	-0.018	-0.015	16.327	0.119	0.119	0.000	0.000	0.000	0.000
15	A	325	GLU	-1	-0.924	-0.964	14.544	-1.241	-1.241	0.000	0.000	0.000	0.000
16	A	326	ASP	-1	-0.814	-0.897	18.524	-0.585	-0.585	0.000	0.000	0.000	0.000
17	A	327	LEU	0	-0.010	-0.008	21.197	0.087	0.087	0.000	0.000	0.000	0.000
18	A	328	LEU	0	-0.030	-0.008	19.871	0.069	0.069	0.000	0.000	0.000	0.000
19	A	329	ALA	0	-0.041	-0.024	22.484	0.047	0.047	0.000	0.000	0.000	0.000
20	A	330	LYS	1	0.857	0.900	23.501	0.590	0.590	0.000	0.000	0.000	0.000
21	A	331	GLU	-1	-0.839	-0.902	26.608	-0.342	-0.342	0.000	0.000	0.000	0.000
22	A	332	LYS	1	0.911	0.962	23.054	0.586	0.586	0.000	0.000	0.000	0.000
23	A	333	ASP	-1	-0.844	-0.905	28.167	-0.347	-0.347	0.000	0.000	0.000	0.000
24	A	334	ASN	0	-0.047	-0.026	30.664	0.046	0.046	0.000	0.000	0.000	0.000
25	A	335	SER	0	0.017	0.006	32.016	0.029	0.029	0.000	0.000	0.000	0.000
26	A	336	ARG	1	0.887	0.916	27.570	0.377	0.377	0.000	0.000	0.000	0.000
27	A	337	ARG	1	0.879	0.954	34.324	0.283	0.283	0.000	0.000	0.000	0.000
28	A	338	MET	0	0.014	0.013	36.638	0.011	0.011	0.000	0.000	0.000	0.000
29	A	339	LEU	0	0.006	0.001	36.594	0.014	0.014	0.000	0.000	0.000	0.000
30	A	340	THR	0	-0.034	-0.023	37.686	0.013	0.013	0.000	0.000	0.000	0.000
31	A	341	ASP	-1	-0.863	-0.929	40.268	-0.188	-0.188	0.000	0.000	0.000	0.000
32	A	342	LYS	1	0.812	0.883	42.243	0.179	0.179	0.000	0.000	0.000	0.000
33	A	343	GLU	-1	-0.796	-0.901	42.668	-0.144	-0.144	0.000	0.000	0.000	0.000
34	A	344	ARG	1	0.827	0.916	42.634	0.178	0.178	0.000	0.000	0.000	0.000
35	A	345	GLU	-1	-0.782	-0.865	46.308	-0.152	-0.152	0.000	0.000	0.000	0.000
36	A	346	MET	0	-0.027	-0.024	46.559	0.004	0.004	0.000	0.000	0.000	0.000
37	A	347	ALA	0	-0.045	-0.022	48.388	0.006	0.006	0.000	0.000	0.000	0.000
38	A	348	GLU	-1	-0.917	-0.953	50.186	-0.118	-0.118	0.000	0.000	0.000	0.000
39	A	349	ILE	0	0.017	0.009	51.458	0.006	0.006	0.000	0.000	0.000	0.000
40	A	350	ARG	1	0.831	0.897	47.783	0.138	0.138	0.000	0.000	0.000	0.000
41	A	351	ASP	-1	-0.943	-0.953	54.407	-0.095	-0.095	0.000	0.000	0.000	0.000
42	A	352	GLN	0	-0.040	-0.029	55.272	0.007	0.007	0.000	0.000	0.000	0.000
43	A	353	MET	0	-0.054	-0.028	56.617	0.002	0.002	0.000	0.000	0.000	0.000
44	A	354	GLN	0	-0.022	-0.006	58.651	0.002	0.002	0.000	0.000	0.000	0.000
45	A	355	GLN	0	-0.020	-0.020	60.373	0.003	0.003	0.000	0.000	0.000	0.000
46	A	356	GLN	0	-0.007	-0.019	61.996	0.002	0.002	0.000	0.000	0.000	0.000
47	A	357	LEU	0	-0.035	-0.002	62.877	0.002	0.002	0.000	0.000	0.000	0.000
48	A	358	ASN	0	0.021	0.010	63.100	0.003	0.003	0.000	0.000	0.000	0.000
49	A	359	ASP	-1	-0.859	-0.925	66.530	-0.072	-0.072	0.000	0.000	0.000	0.000
50	A	360	TYR	0	-0.062	-0.026	67.931	0.003	0.003	0.000	0.000	0.000	0.000
51	A	361	GLU	-1	-0.927	-0.970	67.603	-0.068	-0.068	0.000	0.000	0.000	0.000
52	A	362	GLN	0	-0.028	-0.011	70.617	0.004	0.004	0.000	0.000	0.000	0.000
53	A	363	LEU	0	-0.025	-0.013	72.592	0.002	0.002	0.000	0.000	0.000	0.000
54	A	364	LEU	0	-0.018	-0.008	72.876	0.002	0.002	0.000	0.000	0.000	0.000
55	A	365	ASP	-1	-0.858	-0.931	75.199	-0.054	-0.054	0.000	0.000	0.000	0.000
56	A	366	VAL	0	-0.048	-0.023	77.159	0.002	0.002	0.000	0.000	0.000	0.000
57	A	367	LYS	1	0.783	0.875	77.996	0.054	0.054	0.000	0.000	0.000	0.000
58	A	368	LEU	0	0.009	-0.002	77.272	0.002	0.002	0.000	0.000	0.000	0.000
59	A	369	ALA	0	0.003	0.004	81.002	0.002	0.002	0.000	0.000	0.000	0.000
60	A	370	LEU	0	0.020	0.011	81.993	0.002	0.002	0.000	0.000	0.000	0.000
61	A	371	ASP	-1	-0.811	-0.881	82.205	-0.049	-0.049	0.000	0.000	0.000	0.000
62	A	372	MET	0	-0.050	-0.018	84.926	0.001	0.001	0.000	0.000	0.000	0.000
63	A	373	GLU	-1	-0.845	-0.901	87.255	-0.042	-0.042	0.000	0.000	0.000	0.000
64	A	374	ILE	0	0.000	-0.005	87.965	0.001	0.001	0.000	0.000	0.000	0.000
65	A	375	SER	0	-0.067	-0.052	88.478	0.001	0.001	0.000	0.000	0.000	0.000
66	A	376	ALA	0	-0.053	-0.007	91.129	0.001	0.001	0.000	0.000	0.000	0.000
67	A	377	TYR	0	-0.044	-0.052	91.227	0.002	0.002	0.000	0.000	0.000	0.000
68	A	378	ARG	1	0.914	0.947	89.253	0.043	0.043	0.000	0.000	0.000	0.000
69	A	379	LYS	1	0.935	0.967	93.111	0.038	0.038	0.000	0.000	0.000	0.000
70	A	380	LEU	0	-0.055	-0.016	97.483	0.001	0.001	0.000	0.000	0.000	0.000
71	A	381	LEU	0	-0.047	-0.026	97.982	0.001	0.001	0.000	0.000	0.000	0.000
72	A	382	GLU	-1	-0.963	-0.965	99.657	-0.034	-0.034	0.000	0.000	0.000	0.000
73	A	383	GLY	0	-0.022	-0.015	102.038	0.000	0.000	0.000	0.000	0.000	0.000
74	A	384	GLU	-1	-0.986	-0.986	105.607	-0.027	-0.027	0.000	0.000	0.000	0.000
75	A	385	GLU	-1	-1.004	-0.997	107.362	-0.027	-0.027	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:311:GLN)