FMO DATABASE

FMODB ID: ZY9RN

Calculation Name: 5DUK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DUK

Chain ID: A

ChEMBL ID:

UniProt ID: M7T6A0

Base Structure: X-ray

Registration Date: 2023-03-14

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	60
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-345453.599285
FMO2-HF: Nuclear repulsion	319793.271338
FMO2-HF: Total energy	-25660.327946
FMO2-MP2: Total energy	-25735.444718

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:12:ASP)

Summations of interaction energy for fragment #1(A:12:ASP)

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.
-111.964	-106.713	0.477	-2.698	-3.031	0.021

Interaction energy analysis for fragmet #1(A:12:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.795 / q_NPA : -0.882

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	14	ARG	1	0.840	0.922	3.567	-46.628	-43.486	0.102	-1.795	-1.449	0.015
4	A	15	ARG	1	0.948	0.976	3.097	-47.824	-46.243	0.376	-0.768	-1.189	0.006
5	A	16	GLU	-1	-0.846	-0.939	4.326	34.722	35.250	-0.001	-0.135	-0.393	0.000
6	A	17	ILE	0	-0.013	-0.003	6.103	-5.145	-5.145	0.000	0.000	0.000	0.000
7	A	18	TYR	0	-0.023	-0.012	8.190	-3.021	-3.021	0.000	0.000	0.000	0.000
8	A	19	LYS	1	0.936	0.970	8.123	-30.024	-30.024	0.000	0.000	0.000	0.000
9	A	20	HIS	0	-0.016	-0.024	10.114	-1.913	-1.913	0.000	0.000	0.000	0.000
10	A	21	ILE	0	0.004	0.003	12.084	-1.832	-1.832	0.000	0.000	0.000	0.000
11	A	22	VAL	0	-0.041	-0.021	13.360	-1.478	-1.478	0.000	0.000	0.000	0.000
12	A	23	LYS	1	0.906	0.953	14.087	-20.149	-20.149	0.000	0.000	0.000	0.000
13	A	24	SER	0	-0.009	0.001	15.824	-1.234	-1.234	0.000	0.000	0.000	0.000
14	A	25	PRO	0	0.010	0.003	17.723	0.193	0.193	0.000	0.000	0.000	0.000
15	A	26	GLY	0	-0.015	-0.007	19.430	-0.583	-0.583	0.000	0.000	0.000	0.000
16	A	27	LEU	0	-0.041	0.000	16.428	-0.498	-0.498	0.000	0.000	0.000	0.000
17	A	28	HIS	0	-0.009	-0.010	19.151	0.400	0.400	0.000	0.000	0.000	0.000
18	A	29	GLU	-1	-0.868	-0.940	16.493	18.021	18.021	0.000	0.000	0.000	0.000
19	A	30	ARG	1	0.906	0.922	16.246	-12.747	-12.747	0.000	0.000	0.000	0.000
20	A	31	GLN	0	-0.051	-0.010	18.253	-0.025	-0.025	0.000	0.000	0.000	0.000
21	A	32	LEU	0	0.061	0.022	12.124	0.614	0.614	0.000	0.000	0.000	0.000
22	A	33	ALA	0	0.004	0.003	12.439	1.563	1.563	0.000	0.000	0.000	0.000
23	A	34	LYS	1	0.829	0.903	12.886	-16.082	-16.082	0.000	0.000	0.000	0.000
24	A	35	GLU	-1	-0.816	-0.899	14.507	17.872	17.872	0.000	0.000	0.000	0.000
25	A	36	LEU	0	-0.064	-0.025	8.906	0.665	0.665	0.000	0.000	0.000	0.000
26	A	37	ASP	-1	-0.914	-0.937	9.004	29.345	29.345	0.000	0.000	0.000	0.000
27	A	38	VAL	0	-0.028	-0.002	7.075	2.847	2.847	0.000	0.000	0.000	0.000
28	A	39	PRO	0	0.019	-0.002	9.484	-2.873	-2.873	0.000	0.000	0.000	0.000
29	A	40	LEU	0	0.041	0.016	11.894	1.227	1.227	0.000	0.000	0.000	0.000
30	A	41	SER	0	0.035	0.008	14.124	0.156	0.156	0.000	0.000	0.000	0.000
31	A	42	THR	0	-0.008	0.002	7.721	-0.512	-0.512	0.000	0.000	0.000	0.000
32	A	43	LEU	0	0.000	0.007	10.085	1.999	1.999	0.000	0.000	0.000	0.000
33	A	44	VAL	0	0.045	0.026	11.320	0.299	0.299	0.000	0.000	0.000	0.000
34	A	45	TYR	0	-0.004	0.002	8.885	0.090	0.090	0.000	0.000	0.000	0.000
35	A	46	HIS	0	0.021	0.009	6.142	-2.750	-2.750	0.000	0.000	0.000	0.000
36	A	47	LEU	0	0.019	0.012	10.427	-0.397	-0.397	0.000	0.000	0.000	0.000
37	A	48	HIS	0	0.039	0.001	13.283	-1.018	-1.018	0.000	0.000	0.000	0.000
38	A	49	TYR	0	-0.089	-0.048	9.946	-0.887	-0.887	0.000	0.000	0.000	0.000
39	A	50	LEU	0	0.001	-0.011	8.822	-0.692	-0.692	0.000	0.000	0.000	0.000
40	A	51	GLU	-1	-0.859	-0.922	12.563	16.066	16.066	0.000	0.000	0.000	0.000
41	A	52	ARG	1	0.898	0.960	14.637	-18.994	-18.994	0.000	0.000	0.000	0.000
42	A	53	ARG	1	0.789	0.877	13.152	-16.502	-16.502	0.000	0.000	0.000	0.000
43	A	54	GLU	-1	-0.842	-0.904	15.529	14.001	14.001	0.000	0.000	0.000	0.000
44	A	55	LEU	0	-0.038	-0.006	11.322	-0.074	-0.074	0.000	0.000	0.000	0.000
45	A	56	ILE	0	-0.045	-0.021	13.453	0.303	0.303	0.000	0.000	0.000	0.000
46	A	57	MET	0	-0.006	-0.005	16.466	-0.650	-0.650	0.000	0.000	0.000	0.000
47	A	58	MET	0	0.040	0.033	19.763	0.184	0.184	0.000	0.000	0.000	0.000
48	A	59	LYS	1	0.931	0.949	21.536	-12.833	-12.833	0.000	0.000	0.000	0.000
49	A	60	SER	0	0.022	0.010	24.917	0.374	0.374	0.000	0.000	0.000	0.000
50	A	61	ASP	-1	-0.742	-0.852	26.315	11.731	11.731	0.000	0.000	0.000	0.000
51	A	62	GLU	-1	-0.851	-0.938	28.343	10.211	10.211	0.000	0.000	0.000	0.000
52	A	63	ARG	1	0.790	0.883	28.824	-11.107	-11.107	0.000	0.000	0.000	0.000
53	A	64	TYR	0	-0.029	-0.012	27.572	0.137	0.137	0.000	0.000	0.000	0.000
54	A	65	ALA	0	-0.008	0.019	31.121	0.031	0.031	0.000	0.000	0.000	0.000
55	A	66	ARG	1	0.887	0.937	33.472	-9.390	-9.390	0.000	0.000	0.000	0.000
56	A	67	TYR	0	0.031	0.016	36.355	-0.078	-0.078	0.000	0.000	0.000	0.000
57	A	68	TYR	0	0.016	-0.001	37.062	0.008	0.008	0.000	0.000	0.000	0.000
58	A	69	ALA	0	0.028	0.021	42.865	-0.031	-0.031	0.000	0.000	0.000	0.000
59	A	70	THR	0	-0.001	0.006	45.740	0.077	0.077	0.000	0.000	0.000	0.000
60	A	71	LYS	1	0.993	0.999	46.133	-7.129	-7.129	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:12:ASP)