FMO DATABASE

FMODB ID: V58N1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-355634.497813
FMO2-HF: Nuclear repulsion	323039.339188
FMO2-HF: Total energy	-32595.158626
FMO2-MP2: Total energy	-32686.793046

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.
-17.439	-15.693	4.61	-2.988	-3.368	-0.022

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 : -0.004 / q_NPA : -0.010

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	-0.778	-0.890	2.058	-19.829	-18.134	4.611	-2.977	-3.329	-0.022
4	A	314	SER	0	-0.023	-0.009	4.640	1.993	2.044	-0.001	-0.011	-0.039	0.000
5	A	315	ARG	1	0.995	0.970	8.042	0.757	0.757	0.000	0.000	0.000	0.000
6	A	316	ALA	0	0.062	0.043	11.222	0.067	0.067	0.000	0.000	0.000	0.000
7	A	317	CYS	0	-0.039	-0.014	7.768	0.314	0.314	0.000	0.000	0.000	0.000
8	A	318	LEU	0	0.028	0.006	7.571	0.143	0.143	0.000	0.000	0.000	0.000
9	A	319	GLU	-1	-0.957	-0.957	11.019	-0.751	-0.751	0.000	0.000	0.000	0.000
10	A	320	ARG	1	0.853	0.907	13.934	1.023	1.023	0.000	0.000	0.000	0.000
11	A	321	ILE	0	-0.014	-0.020	9.788	0.090	0.090	0.000	0.000	0.000	0.000
12	A	322	GLN	0	-0.003	0.008	13.983	0.110	0.110	0.000	0.000	0.000	0.000
13	A	323	GLU	-1	-0.821	-0.889	15.887	-0.680	-0.680	0.000	0.000	0.000	0.000
14	A	324	LEU	0	-0.021	-0.015	16.418	0.112	0.112	0.000	0.000	0.000	0.000
15	A	325	GLU	-1	-0.928	-0.969	14.502	-1.271	-1.271	0.000	0.000	0.000	0.000
16	A	326	ASP	-1	-0.832	-0.920	18.615	-0.603	-0.603	0.000	0.000	0.000	0.000
17	A	327	LEU	0	-0.017	-0.017	21.487	0.082	0.082	0.000	0.000	0.000	0.000
18	A	328	LEU	0	-0.024	0.002	20.496	0.068	0.068	0.000	0.000	0.000	0.000
19	A	329	ALA	0	-0.044	-0.029	22.734	0.055	0.055	0.000	0.000	0.000	0.000
20	A	330	LYS	1	0.883	0.932	23.799	0.596	0.596	0.000	0.000	0.000	0.000
21	A	331	GLU	-1	-0.875	-0.907	26.633	-0.335	-0.335	0.000	0.000	0.000	0.000
22	A	332	LYS	1	0.923	0.950	23.037	0.575	0.575	0.000	0.000	0.000	0.000
23	A	333	ASP	-1	-0.865	-0.918	28.449	-0.358	-0.358	0.000	0.000	0.000	0.000
24	A	334	ASN	0	-0.043	-0.032	30.536	0.046	0.046	0.000	0.000	0.000	0.000
25	A	335	SER	0	0.021	0.008	31.977	0.029	0.029	0.000	0.000	0.000	0.000
26	A	336	ARG	1	0.903	0.930	27.487	0.387	0.387	0.000	0.000	0.000	0.000
27	A	337	ARG	1	0.910	0.967	34.481	0.282	0.282	0.000	0.000	0.000	0.000
28	A	338	MET	0	-0.026	-0.003	36.620	0.010	0.010	0.000	0.000	0.000	0.000
29	A	339	LEU	0	0.015	-0.001	37.027	0.014	0.014	0.000	0.000	0.000	0.000
30	A	340	THR	0	-0.028	-0.017	37.872	0.013	0.013	0.000	0.000	0.000	0.000
31	A	341	ASP	-1	-0.861	-0.919	40.438	-0.188	-0.188	0.000	0.000	0.000	0.000
32	A	342	LYS	1	0.826	0.905	42.449	0.181	0.181	0.000	0.000	0.000	0.000
33	A	343	GLU	-1	-0.801	-0.914	42.586	-0.146	-0.146	0.000	0.000	0.000	0.000
34	A	344	ARG	1	0.817	0.900	42.903	0.179	0.179	0.000	0.000	0.000	0.000
35	A	345	GLU	-1	-0.812	-0.888	46.458	-0.148	-0.148	0.000	0.000	0.000	0.000
36	A	346	MET	0	-0.040	-0.023	47.056	0.004	0.004	0.000	0.000	0.000	0.000
37	A	347	ALA	0	-0.047	-0.023	48.564	0.006	0.006	0.000	0.000	0.000	0.000
38	A	348	GLU	-1	-0.921	-0.947	50.381	-0.120	-0.120	0.000	0.000	0.000	0.000
39	A	349	ILE	0	0.029	0.010	51.826	0.006	0.006	0.000	0.000	0.000	0.000
40	A	350	ARG	1	0.827	0.888	47.737	0.140	0.140	0.000	0.000	0.000	0.000
41	A	351	ASP	-1	-0.929	-0.944	54.711	-0.099	-0.099	0.000	0.000	0.000	0.000
42	A	352	GLN	0	-0.033	-0.023	55.627	0.006	0.006	0.000	0.000	0.000	0.000
43	A	353	MET	0	-0.046	-0.023	56.968	0.002	0.002	0.000	0.000	0.000	0.000
44	A	354	GLN	0	-0.020	-0.004	58.635	0.001	0.001	0.000	0.000	0.000	0.000
45	A	355	GLN	0	-0.057	-0.036	60.402	0.002	0.002	0.000	0.000	0.000	0.000
46	A	356	GLN	0	-0.007	-0.023	62.123	0.002	0.002	0.000	0.000	0.000	0.000
47	A	357	LEU	0	-0.020	0.007	62.881	0.003	0.003	0.000	0.000	0.000	0.000
48	A	358	ASN	0	0.062	0.032	63.352	0.003	0.003	0.000	0.000	0.000	0.000
49	A	359	ASP	-1	-0.860	-0.922	66.830	-0.073	-0.073	0.000	0.000	0.000	0.000
50	A	360	TYR	0	-0.053	-0.016	68.159	0.003	0.003	0.000	0.000	0.000	0.000
51	A	361	GLU	-1	-0.938	-0.973	67.822	-0.068	-0.068	0.000	0.000	0.000	0.000
52	A	362	GLN	0	-0.017	0.004	70.710	0.004	0.004	0.000	0.000	0.000	0.000
53	A	363	LEU	0	-0.025	-0.018	72.739	0.002	0.002	0.000	0.000	0.000	0.000
54	A	364	LEU	0	-0.050	-0.031	73.226	0.002	0.002	0.000	0.000	0.000	0.000
55	A	365	ASP	-1	-0.847	-0.929	75.303	-0.054	-0.054	0.000	0.000	0.000	0.000
56	A	366	VAL	0	-0.059	-0.021	77.315	0.002	0.002	0.000	0.000	0.000	0.000
57	A	367	LYS	1	0.793	0.876	78.303	0.054	0.054	0.000	0.000	0.000	0.000
58	A	368	LEU	0	0.009	-0.003	77.311	0.002	0.002	0.000	0.000	0.000	0.000
59	A	369	ALA	0	0.011	0.009	81.040	0.002	0.002	0.000	0.000	0.000	0.000
60	A	370	LEU	0	-0.011	-0.008	82.072	0.002	0.002	0.000	0.000	0.000	0.000
61	A	371	ASP	-1	-0.790	-0.870	82.518	-0.049	-0.049	0.000	0.000	0.000	0.000
62	A	372	MET	0	-0.049	-0.022	85.178	0.001	0.001	0.000	0.000	0.000	0.000
63	A	373	GLU	-1	-0.851	-0.915	87.559	-0.042	-0.042	0.000	0.000	0.000	0.000
64	A	374	ILE	0	-0.002	-0.006	88.092	0.001	0.001	0.000	0.000	0.000	0.000
65	A	375	SER	0	-0.083	-0.055	88.890	0.001	0.001	0.000	0.000	0.000	0.000
66	A	376	ALA	0	-0.028	-0.012	91.548	0.001	0.001	0.000	0.000	0.000	0.000
67	A	377	TYR	0	-0.017	-0.008	91.728	0.002	0.002	0.000	0.000	0.000	0.000
68	A	378	ARG	1	0.906	0.946	89.885	0.042	0.042	0.000	0.000	0.000	0.000
69	A	379	LYS	1	0.931	0.960	92.926	0.038	0.038	0.000	0.000	0.000	0.000
70	A	380	LEU	0	-0.037	-0.001	97.672	0.001	0.001	0.000	0.000	0.000	0.000
71	A	381	LEU	0	-0.058	-0.043	98.020	0.001	0.001	0.000	0.000	0.000	0.000
72	A	382	GLU	-1	-1.010	-0.977	100.358	-0.033	-0.033	0.000	0.000	0.000	0.000
73	A	383	GLY	0	-0.008	0.001	102.310	0.000	0.000	0.000	0.000	0.000	0.000
74	A	384	GLU	-1	-0.969	-0.990	105.577	-0.027	-0.027	0.000	0.000	0.000	0.000
75	A	385	GLU	-1	-1.011	-0.998	107.826	-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)