FMO DATABASE

FMODB ID: 7675K

Calculation Name: 3TYS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3TYS

Chain ID: A

ChEMBL ID:

UniProt ID: Q6WRY9

Base Structure: X-ray

Registration Date: 2023-09-23

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

Total energy (hartree)

FMO2-HF: Electronic energy	-462206.258962
FMO2-HF: Nuclear repulsion	431717.632353
FMO2-HF: Total energy	-30488.626609
FMO2-MP2: Total energy	-30576.068119

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:-7:ARG)

Summations of interaction energy for fragment #1(A:-7:ARG)

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.
21.907	23.262	0.016	-0.513	-0.859	0.001

Interaction energy analysis for fragmet #1(A:-7:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.920 / q_NPA : 0.939

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	-5	ASN	0	-0.001	-0.003	3.585	5.710	7.065	0.016	-0.513	-0.859	0.001
4	A	-4	LEU	0	0.004	0.004	6.191	1.584	1.584	0.000	0.000	0.000	0.000
5	A	-3	TYR	0	0.012	0.000	8.731	1.385	1.385	0.000	0.000	0.000	0.000
6	A	-2	PHE	0	0.000	0.000	11.618	1.651	1.651	0.000	0.000	0.000	0.000
7	A	-1	GLN	0	-0.059	-0.046	9.483	-0.370	-0.370	0.000	0.000	0.000	0.000
8	A	0	GLY	0	0.071	0.056	12.456	0.414	0.414	0.000	0.000	0.000	0.000
9	A	1	MET	0	-0.056	-0.019	15.118	0.814	0.814	0.000	0.000	0.000	0.000
10	A	2	ARG	1	0.850	0.932	14.911	12.989	12.989	0.000	0.000	0.000	0.000
11	A	3	VAL	0	0.008	0.012	16.303	0.441	0.441	0.000	0.000	0.000	0.000
12	A	4	SER	0	0.008	0.001	18.052	0.556	0.556	0.000	0.000	0.000	0.000
13	A	5	TYR	0	0.036	-0.011	17.321	-0.304	-0.304	0.000	0.000	0.000	0.000
14	A	6	ASN	0	-0.012	-0.013	23.388	0.363	0.363	0.000	0.000	0.000	0.000
15	A	7	LYS	1	0.924	0.970	25.703	11.699	11.699	0.000	0.000	0.000	0.000
16	A	8	LEU	0	0.076	0.053	24.088	0.256	0.256	0.000	0.000	0.000	0.000
17	A	9	TRP	0	-0.051	-0.028	24.992	0.341	0.341	0.000	0.000	0.000	0.000
18	A	10	LYS	1	0.938	0.964	29.735	9.875	9.875	0.000	0.000	0.000	0.000
19	A	11	LEU	0	0.067	0.049	28.438	0.240	0.240	0.000	0.000	0.000	0.000
20	A	12	LEU	0	-0.037	-0.034	28.946	0.150	0.150	0.000	0.000	0.000	0.000
21	A	13	ILE	0	-0.005	0.007	32.474	0.225	0.225	0.000	0.000	0.000	0.000
22	A	14	ASP	-1	-0.911	-0.947	34.746	-8.388	-8.388	0.000	0.000	0.000	0.000
23	A	15	ARG	1	0.780	0.888	31.823	9.472	9.472	0.000	0.000	0.000	0.000
24	A	16	ASP	-1	-0.932	-0.957	36.268	-7.542	-7.542	0.000	0.000	0.000	0.000
25	A	17	MET	0	-0.029	-0.005	32.465	-0.037	-0.037	0.000	0.000	0.000	0.000
26	A	18	LYS	1	0.910	0.946	34.171	7.787	7.787	0.000	0.000	0.000	0.000
27	A	19	LYS	1	1.007	0.981	28.096	9.863	9.863	0.000	0.000	0.000	0.000
28	A	20	GLY	0	-0.093	-0.056	29.420	-0.305	-0.305	0.000	0.000	0.000	0.000
29	A	21	GLU	-1	-0.766	-0.882	30.845	-8.646	-8.646	0.000	0.000	0.000	0.000
30	A	22	LEU	0	0.037	0.035	25.817	-0.128	-0.128	0.000	0.000	0.000	0.000
31	A	23	ARG	1	0.834	0.918	25.594	10.006	10.006	0.000	0.000	0.000	0.000
32	A	24	GLU	-1	-0.965	-1.000	26.728	-9.667	-9.667	0.000	0.000	0.000	0.000
33	A	25	ALA	0	0.000	0.023	29.328	-0.024	-0.024	0.000	0.000	0.000	0.000
34	A	26	VAL	0	-0.006	0.000	23.324	-0.155	-0.155	0.000	0.000	0.000	0.000
35	A	27	GLY	0	0.035	0.036	24.615	-0.346	-0.346	0.000	0.000	0.000	0.000
36	A	28	VAL	0	-0.080	-0.033	20.567	-0.519	-0.519	0.000	0.000	0.000	0.000
37	A	29	SER	0	0.054	0.024	19.732	0.489	0.489	0.000	0.000	0.000	0.000
38	A	30	LYS	1	1.014	0.981	22.667	10.417	10.417	0.000	0.000	0.000	0.000
39	A	31	SER	0	0.009	0.002	19.139	-0.010	-0.010	0.000	0.000	0.000	0.000
40	A	32	THR	0	0.011	-0.001	17.498	-0.569	-0.569	0.000	0.000	0.000	0.000
41	A	33	PHE	0	0.076	0.035	19.322	-0.076	-0.076	0.000	0.000	0.000	0.000
42	A	34	ALA	0	-0.021	-0.020	21.667	0.187	0.187	0.000	0.000	0.000	0.000
43	A	35	LYS	1	0.916	0.974	13.694	17.779	17.779	0.000	0.000	0.000	0.000
44	A	36	LEU	0	0.055	0.041	19.445	-0.066	-0.066	0.000	0.000	0.000	0.000
45	A	37	GLY	0	-0.053	-0.016	21.704	0.263	0.263	0.000	0.000	0.000	0.000
46	A	38	LYS	1	0.882	0.949	19.960	12.971	12.971	0.000	0.000	0.000	0.000
47	A	39	ASN	0	0.029	0.017	20.031	-0.284	-0.284	0.000	0.000	0.000	0.000
48	A	40	GLU	-1	-0.891	-0.947	15.617	-15.067	-15.067	0.000	0.000	0.000	0.000
49	A	41	ASN	0	0.056	0.030	10.902	1.255	1.255	0.000	0.000	0.000	0.000
50	A	42	VAL	0	-0.014	-0.009	14.353	0.000	0.000	0.000	0.000	0.000	0.000
51	A	43	SER	0	-0.006	-0.004	12.275	-0.505	-0.505	0.000	0.000	0.000	0.000
52	A	44	LEU	0	0.126	0.044	11.904	1.051	1.051	0.000	0.000	0.000	0.000
53	A	45	THR	0	0.003	0.002	13.980	0.546	0.546	0.000	0.000	0.000	0.000
54	A	46	VAL	0	-0.012	-0.002	15.956	0.975	0.975	0.000	0.000	0.000	0.000
55	A	47	LEU	0	-0.004	-0.006	16.169	0.778	0.778	0.000	0.000	0.000	0.000
56	A	48	LEU	0	0.037	0.019	16.478	0.548	0.548	0.000	0.000	0.000	0.000
57	A	49	ALA	0	0.035	0.032	19.848	0.635	0.635	0.000	0.000	0.000	0.000
58	A	50	ILE	0	-0.037	-0.021	21.702	0.647	0.647	0.000	0.000	0.000	0.000
59	A	51	CYS	0	-0.045	-0.024	21.888	0.469	0.469	0.000	0.000	0.000	0.000
60	A	52	GLU	-1	-0.933	-0.963	23.989	-11.541	-11.541	0.000	0.000	0.000	0.000
61	A	53	TYR	0	-0.026	-0.011	25.826	0.468	0.468	0.000	0.000	0.000	0.000
62	A	54	LEU	0	-0.047	-0.035	27.081	0.436	0.436	0.000	0.000	0.000	0.000
63	A	55	ASN	0	0.003	0.020	28.583	0.202	0.202	0.000	0.000	0.000	0.000
64	A	56	CYS	0	-0.085	-0.029	25.547	0.243	0.243	0.000	0.000	0.000	0.000
65	A	57	ASP	-1	-0.802	-0.893	23.162	-13.210	-13.210	0.000	0.000	0.000	0.000
66	A	58	PHE	0	0.007	-0.025	17.453	-0.086	-0.086	0.000	0.000	0.000	0.000
67	A	59	GLY	0	-0.024	-0.016	21.951	-0.028	-0.028	0.000	0.000	0.000	0.000
68	A	60	ASP	-1	-0.841	-0.919	24.210	-10.490	-10.490	0.000	0.000	0.000	0.000
69	A	61	ILE	0	-0.062	-0.052	21.430	0.257	0.257	0.000	0.000	0.000	0.000
70	A	62	ILE	0	-0.069	-0.034	17.929	-0.201	-0.201	0.000	0.000	0.000	0.000
71	A	63	GLU	-1	-0.960	-0.982	21.511	-11.259	-11.259	0.000	0.000	0.000	0.000
72	A	64	ALA	0	-0.022	-0.007	18.476	-0.406	-0.406	0.000	0.000	0.000	0.000
73	A	65	LEU	0	-0.005	-0.013	19.823	0.582	0.582	0.000	0.000	0.000	0.000
74	A	66	PRO	0	0.031	0.017	19.581	-0.678	-0.678	0.000	0.000	0.000	0.000
75	A	67	GLU	-1	-0.992	-0.992	17.253	-14.205	-14.205	0.000	0.000	0.000	0.000

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Overview

Highlights

Manual

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Interactive mode: IFIE and PIEDA for fragment #1(A:-7:ARG)