FMO DATABASE

FMODB ID: YZ612

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

Total energy (hartree)

FMO2-HF: Electronic energy	-355009.450864
FMO2-HF: Nuclear repulsion	322414.960373
FMO2-HF: Total energy	-32594.490491
FMO2-MP2: Total energy	-32686.104155

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.
-19.279	-15.928	2.4	-2.641	-3.108	-0.017

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 : 0.001 / q_NPA : -0.007

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	-0.810	-0.906	2.196	-21.518	-18.206	2.401	-2.635	-3.077	-0.017
4	A	314	SER	0	-0.022	-0.010	4.760	1.965	2.004	-0.001	-0.006	-0.031	0.000
5	A	315	ARG	1	1.012	0.978	8.167	0.821	0.821	0.000	0.000	0.000	0.000
6	A	316	ALA	0	0.053	0.038	11.349	0.079	0.079	0.000	0.000	0.000	0.000
7	A	317	CYS	0	-0.024	-0.006	7.766	0.281	0.281	0.000	0.000	0.000	0.000
8	A	318	LEU	0	0.025	0.007	7.650	0.138	0.138	0.000	0.000	0.000	0.000
9	A	319	GLU	-1	-0.979	-0.970	11.107	-0.747	-0.747	0.000	0.000	0.000	0.000
10	A	320	ARG	1	0.898	0.937	14.056	1.035	1.035	0.000	0.000	0.000	0.000
11	A	321	ILE	0	-0.022	-0.020	9.932	0.087	0.087	0.000	0.000	0.000	0.000
12	A	322	GLN	0	0.031	0.031	14.032	0.067	0.067	0.000	0.000	0.000	0.000
13	A	323	GLU	-1	-0.858	-0.912	15.874	-0.673	-0.673	0.000	0.000	0.000	0.000
14	A	324	LEU	0	-0.027	-0.022	16.659	0.115	0.115	0.000	0.000	0.000	0.000
15	A	325	GLU	-1	-0.927	-0.971	14.252	-1.296	-1.296	0.000	0.000	0.000	0.000
16	A	326	ASP	-1	-0.928	-0.970	18.619	-0.658	-0.658	0.000	0.000	0.000	0.000
17	A	327	LEU	0	-0.054	-0.040	21.482	0.082	0.082	0.000	0.000	0.000	0.000
18	A	328	LEU	0	-0.020	0.004	20.467	0.071	0.071	0.000	0.000	0.000	0.000
19	A	329	ALA	0	-0.034	-0.025	22.750	0.057	0.057	0.000	0.000	0.000	0.000
20	A	330	LYS	1	1.003	0.994	24.429	0.571	0.571	0.000	0.000	0.000	0.000
21	A	331	GLU	-1	-0.927	-0.935	26.643	-0.339	-0.339	0.000	0.000	0.000	0.000
22	A	332	LYS	1	0.912	0.940	23.466	0.549	0.549	0.000	0.000	0.000	0.000
23	A	333	ASP	-1	-0.906	-0.946	28.598	-0.350	-0.350	0.000	0.000	0.000	0.000
24	A	334	ASN	0	-0.027	-0.018	30.543	0.043	0.043	0.000	0.000	0.000	0.000
25	A	335	SER	0	0.002	0.001	31.974	0.029	0.029	0.000	0.000	0.000	0.000
26	A	336	ARG	1	0.975	0.975	27.759	0.370	0.370	0.000	0.000	0.000	0.000
27	A	337	ARG	1	0.938	0.968	34.494	0.280	0.280	0.000	0.000	0.000	0.000
28	A	338	MET	0	-0.031	-0.004	36.630	0.009	0.009	0.000	0.000	0.000	0.000
29	A	339	LEU	0	0.018	-0.002	37.207	0.014	0.014	0.000	0.000	0.000	0.000
30	A	340	THR	0	-0.026	-0.011	37.894	0.013	0.013	0.000	0.000	0.000	0.000
31	A	341	ASP	-1	-0.938	-0.965	40.451	-0.190	-0.190	0.000	0.000	0.000	0.000
32	A	342	LYS	1	0.926	0.966	42.409	0.189	0.189	0.000	0.000	0.000	0.000
33	A	343	GLU	-1	-0.902	-0.964	42.565	-0.147	-0.147	0.000	0.000	0.000	0.000
34	A	344	ARG	1	0.896	0.954	42.987	0.174	0.174	0.000	0.000	0.000	0.000
35	A	345	GLU	-1	-0.907	-0.955	46.471	-0.139	-0.139	0.000	0.000	0.000	0.000
36	A	346	MET	0	-0.005	-0.013	47.485	0.005	0.005	0.000	0.000	0.000	0.000
37	A	347	ALA	0	-0.068	-0.034	48.647	0.006	0.006	0.000	0.000	0.000	0.000
38	A	348	GLU	-1	-0.924	-0.952	50.398	-0.120	-0.120	0.000	0.000	0.000	0.000
39	A	349	ILE	0	0.040	0.023	51.901	0.006	0.006	0.000	0.000	0.000	0.000
40	A	350	ARG	1	0.877	0.921	48.421	0.131	0.131	0.000	0.000	0.000	0.000
41	A	351	ASP	-1	-0.929	-0.943	54.661	-0.098	-0.098	0.000	0.000	0.000	0.000
42	A	352	GLN	0	-0.002	-0.011	56.401	0.004	0.004	0.000	0.000	0.000	0.000
43	A	353	MET	0	-0.032	-0.018	57.337	0.002	0.002	0.000	0.000	0.000	0.000
44	A	354	GLN	0	-0.032	-0.003	58.609	0.001	0.001	0.000	0.000	0.000	0.000
45	A	355	GLN	0	-0.036	-0.012	60.422	0.002	0.002	0.000	0.000	0.000	0.000
46	A	356	GLN	0	-0.019	-0.029	62.023	0.002	0.002	0.000	0.000	0.000	0.000
47	A	357	LEU	0	-0.021	0.008	62.748	0.002	0.002	0.000	0.000	0.000	0.000
48	A	358	ASN	0	0.084	0.033	63.607	0.002	0.002	0.000	0.000	0.000	0.000
49	A	359	ASP	-1	-0.897	-0.949	66.850	-0.071	-0.071	0.000	0.000	0.000	0.000
50	A	360	TYR	0	-0.055	-0.018	68.202	0.003	0.003	0.000	0.000	0.000	0.000
51	A	361	GLU	-1	-0.940	-0.979	67.378	-0.066	-0.066	0.000	0.000	0.000	0.000
52	A	362	GLN	0	-0.002	0.014	70.694	0.004	0.004	0.000	0.000	0.000	0.000
53	A	363	LEU	0	-0.019	-0.014	72.757	0.002	0.002	0.000	0.000	0.000	0.000
54	A	364	LEU	0	-0.055	-0.035	72.998	0.002	0.002	0.000	0.000	0.000	0.000
55	A	365	ASP	-1	-0.849	-0.928	75.318	-0.053	-0.053	0.000	0.000	0.000	0.000
56	A	366	VAL	0	-0.061	-0.020	77.325	0.002	0.002	0.000	0.000	0.000	0.000
57	A	367	LYS	1	0.840	0.909	78.281	0.052	0.052	0.000	0.000	0.000	0.000
58	A	368	LEU	0	-0.016	-0.017	77.208	0.002	0.002	0.000	0.000	0.000	0.000
59	A	369	ALA	0	0.010	0.009	81.012	0.002	0.002	0.000	0.000	0.000	0.000
60	A	370	LEU	0	0.003	-0.001	82.113	0.001	0.001	0.000	0.000	0.000	0.000
61	A	371	ASP	-1	-0.825	-0.895	82.623	-0.046	-0.046	0.000	0.000	0.000	0.000
62	A	372	MET	0	-0.057	-0.038	85.286	0.001	0.001	0.000	0.000	0.000	0.000
63	A	373	GLU	-1	-0.887	-0.934	87.519	-0.041	-0.041	0.000	0.000	0.000	0.000
64	A	374	ILE	0	-0.009	-0.009	88.011	0.001	0.001	0.000	0.000	0.000	0.000
65	A	375	SER	0	-0.083	-0.052	88.984	0.001	0.001	0.000	0.000	0.000	0.000
66	A	376	ALA	0	-0.028	-0.012	91.493	0.001	0.001	0.000	0.000	0.000	0.000
67	A	377	TYR	0	0.016	0.008	92.172	0.001	0.001	0.000	0.000	0.000	0.000
68	A	378	ARG	1	0.897	0.945	89.897	0.040	0.040	0.000	0.000	0.000	0.000
69	A	379	LYS	1	0.957	0.978	92.732	0.036	0.036	0.000	0.000	0.000	0.000
70	A	380	LEU	0	-0.032	0.002	97.641	0.001	0.001	0.000	0.000	0.000	0.000
71	A	381	LEU	0	-0.062	-0.048	97.921	0.001	0.001	0.000	0.000	0.000	0.000
72	A	382	GLU	-1	-1.009	-0.977	100.448	-0.031	-0.031	0.000	0.000	0.000	0.000
73	A	383	GLY	0	-0.016	-0.002	102.261	0.000	0.000	0.000	0.000	0.000	0.000
74	A	384	GLU	-1	-0.964	-0.987	105.486	-0.026	-0.026	0.000	0.000	0.000	0.000
75	A	385	GLU	-1	-1.012	-1.000	107.775	-0.025	-0.025	0.000	0.000	0.000	0.000

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