FMO DATABASE

FMODB ID: 6Y28Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-463559.400744
FMO2-HF: Nuclear repulsion	433069.881723
FMO2-HF: Total energy	-30489.519022
FMO2-MP2: Total energy	-30576.92744

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.
28.332	29.651	0.017	-0.356	-0.98	0.002

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 : 0.892 / q_NPA : 0.908

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	A	-5	ASN	0	-0.048	-0.021	3.474	10.305	11.624	0.017	-0.356	-0.980	0.002
4	A	-4	LEU	0	0.005	0.002	6.321	2.110	2.110	0.000	0.000	0.000	0.000
5	A	-3	TYR	0	0.017	0.007	8.690	1.916	1.916	0.000	0.000	0.000	0.000
6	A	-2	PHE	0	-0.015	-0.006	11.618	1.772	1.772	0.000	0.000	0.000	0.000
7	A	-1	GLN	0	-0.025	-0.032	9.537	-0.405	-0.405	0.000	0.000	0.000	0.000
8	A	0	GLY	0	0.057	0.056	12.376	0.239	0.239	0.000	0.000	0.000	0.000
9	A	1	MET	0	-0.074	-0.040	14.841	0.876	0.876	0.000	0.000	0.000	0.000
10	A	2	ARG	1	0.852	0.928	14.605	13.410	13.410	0.000	0.000	0.000	0.000
11	A	3	VAL	0	0.013	0.018	16.125	0.482	0.482	0.000	0.000	0.000	0.000
12	A	4	SER	0	-0.008	-0.017	17.893	0.552	0.552	0.000	0.000	0.000	0.000
13	A	5	TYR	0	0.040	-0.007	17.487	-0.188	-0.188	0.000	0.000	0.000	0.000
14	A	6	ASN	0	-0.023	-0.024	23.593	0.385	0.385	0.000	0.000	0.000	0.000
15	A	7	LYS	1	0.795	0.921	24.904	12.371	12.371	0.000	0.000	0.000	0.000
16	A	8	LEU	0	0.066	0.046	23.806	0.335	0.335	0.000	0.000	0.000	0.000
17	A	9	TRP	0	-0.062	-0.051	24.659	0.337	0.337	0.000	0.000	0.000	0.000
18	A	10	LYS	1	0.900	0.964	29.636	9.970	9.970	0.000	0.000	0.000	0.000
19	A	11	LEU	0	0.080	0.040	28.478	0.233	0.233	0.000	0.000	0.000	0.000
20	A	12	LEU	0	-0.045	-0.024	29.028	0.108	0.108	0.000	0.000	0.000	0.000
21	A	13	ILE	0	0.010	0.007	32.530	0.243	0.243	0.000	0.000	0.000	0.000
22	A	14	ASP	-1	-0.913	-0.953	34.159	-8.598	-8.598	0.000	0.000	0.000	0.000
23	A	15	ARG	1	0.804	0.887	31.886	9.378	9.378	0.000	0.000	0.000	0.000
24	A	16	ASP	-1	-0.891	-0.929	36.885	-7.472	-7.472	0.000	0.000	0.000	0.000
25	A	17	MET	0	-0.064	-0.025	32.364	0.007	0.007	0.000	0.000	0.000	0.000
26	A	18	LYS	1	0.816	0.881	34.087	8.061	8.061	0.000	0.000	0.000	0.000
27	A	19	LYS	1	0.969	0.967	27.896	9.926	9.926	0.000	0.000	0.000	0.000
28	A	20	GLY	0	-0.029	-0.012	29.295	-0.300	-0.300	0.000	0.000	0.000	0.000
29	A	21	GLU	-1	-0.748	-0.854	30.993	-8.556	-8.556	0.000	0.000	0.000	0.000
30	A	22	LEU	0	0.026	0.022	25.813	-0.112	-0.112	0.000	0.000	0.000	0.000
31	A	23	ARG	1	0.748	0.840	25.854	9.769	9.769	0.000	0.000	0.000	0.000
32	A	24	GLU	-1	-0.796	-0.877	27.221	-9.980	-9.980	0.000	0.000	0.000	0.000
33	A	25	ALA	0	-0.032	-0.001	29.551	-0.082	-0.082	0.000	0.000	0.000	0.000
34	A	26	VAL	0	-0.006	0.003	23.651	-0.108	-0.108	0.000	0.000	0.000	0.000
35	A	27	GLY	0	0.015	0.023	24.717	-0.429	-0.429	0.000	0.000	0.000	0.000
36	A	28	VAL	0	-0.050	-0.016	21.125	-0.499	-0.499	0.000	0.000	0.000	0.000
37	A	29	SER	0	0.042	0.021	20.036	0.348	0.348	0.000	0.000	0.000	0.000
38	A	30	LYS	1	1.005	0.977	22.338	10.041	10.041	0.000	0.000	0.000	0.000
39	A	31	SER	0	0.015	0.012	19.171	0.171	0.171	0.000	0.000	0.000	0.000
40	A	32	THR	0	0.017	0.001	17.507	-0.592	-0.592	0.000	0.000	0.000	0.000
41	A	33	PHE	0	0.055	0.010	19.343	-0.135	-0.135	0.000	0.000	0.000	0.000
42	A	34	ALA	0	-0.019	-0.014	21.536	0.193	0.193	0.000	0.000	0.000	0.000
43	A	35	LYS	1	0.865	0.951	12.670	18.415	18.415	0.000	0.000	0.000	0.000
44	A	36	LEU	0	0.044	0.033	19.196	-0.013	-0.013	0.000	0.000	0.000	0.000
45	A	37	GLY	0	-0.059	-0.031	21.510	0.260	0.260	0.000	0.000	0.000	0.000
46	A	38	LYS	1	0.790	0.881	19.034	13.661	13.661	0.000	0.000	0.000	0.000
47	A	39	ASN	0	0.025	0.032	20.025	-0.359	-0.359	0.000	0.000	0.000	0.000
48	A	40	GLU	-1	-0.771	-0.863	15.577	-14.814	-14.814	0.000	0.000	0.000	0.000
49	A	41	ASN	0	0.056	0.029	10.907	1.459	1.459	0.000	0.000	0.000	0.000
50	A	42	VAL	0	0.006	0.014	13.755	-0.383	-0.383	0.000	0.000	0.000	0.000
51	A	43	SER	0	0.008	0.000	12.427	-0.555	-0.555	0.000	0.000	0.000	0.000
52	A	44	LEU	0	0.098	0.026	12.002	1.064	1.064	0.000	0.000	0.000	0.000
53	A	45	THR	0	0.030	0.014	14.384	0.503	0.503	0.000	0.000	0.000	0.000
54	A	46	VAL	0	-0.017	0.000	16.354	0.942	0.942	0.000	0.000	0.000	0.000
55	A	47	LEU	0	-0.012	-0.004	16.431	0.725	0.725	0.000	0.000	0.000	0.000
56	A	48	LEU	0	0.039	0.020	16.925	0.556	0.556	0.000	0.000	0.000	0.000
57	A	49	ALA	0	0.048	0.033	20.251	0.626	0.626	0.000	0.000	0.000	0.000
58	A	50	ILE	0	-0.034	-0.022	21.642	0.647	0.647	0.000	0.000	0.000	0.000
59	A	51	CYS	0	-0.038	-0.019	22.835	0.331	0.331	0.000	0.000	0.000	0.000
60	A	52	GLU	-1	-0.943	-0.963	24.294	-11.584	-11.584	0.000	0.000	0.000	0.000
61	A	53	TYR	0	0.005	-0.008	26.126	0.503	0.503	0.000	0.000	0.000	0.000
62	A	54	LEU	0	-0.028	-0.027	27.284	0.427	0.427	0.000	0.000	0.000	0.000
63	A	55	ASN	0	-0.058	-0.013	28.892	0.442	0.442	0.000	0.000	0.000	0.000
64	A	56	CYS	0	-0.083	-0.020	26.186	0.260	0.260	0.000	0.000	0.000	0.000
65	A	57	ASP	-1	-0.750	-0.879	23.570	-13.477	-13.477	0.000	0.000	0.000	0.000
66	A	58	PHE	0	0.002	-0.030	17.332	-0.145	-0.145	0.000	0.000	0.000	0.000
67	A	59	GLY	0	-0.024	-0.012	22.325	0.029	0.029	0.000	0.000	0.000	0.000
68	A	60	ASP	-1	-0.838	-0.912	24.832	-10.502	-10.502	0.000	0.000	0.000	0.000
69	A	61	ILE	0	-0.054	-0.044	21.613	0.243	0.243	0.000	0.000	0.000	0.000
70	A	62	ILE	0	-0.055	-0.037	18.481	-0.129	-0.129	0.000	0.000	0.000	0.000
71	A	63	GLU	-1	-0.856	-0.909	22.012	-11.491	-11.491	0.000	0.000	0.000	0.000
72	A	64	ALA	0	-0.006	-0.010	18.647	-0.608	-0.608	0.000	0.000	0.000	0.000
73	A	65	LEU	0	-0.006	-0.005	19.706	0.557	0.557	0.000	0.000	0.000	0.000
74	A	66	PRO	0	0.038	0.006	19.247	-0.705	-0.705	0.000	0.000	0.000	0.000
75	A	67	GLU	-1	-0.982	-0.977	16.909	-14.635	-14.635	0.000	0.000	0.000	0.000

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