FMO DATABASE

FMODB ID: V2741

Calculation Name: 5DUK-A-Xray308

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	62
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-347330.051607
FMO2-HF: Nuclear repulsion	321499.344731
FMO2-HF: Total energy	-25830.706876
FMO2-MP2: Total energy	-25906.34724

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:11:ACE )

Summations of interaction energy for fragment #1(A:11:ACE )

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.
-2.086	-0.527	0.479	-0.854	-1.185	-0.002

Interaction energy analysis for fragmet #1(A:11:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.069 / q_NPA : -0.051

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	13	THR	0	0.085	0.045	3.809	1.344	2.160	-0.006	-0.370	-0.440	-0.001
4	A	14	ARG	1	0.860	0.940	4.379	-0.781	-0.678	0.000	-0.019	-0.084	0.000
5	A	15	ARG	1	0.919	0.952	2.602	-1.879	-1.273	0.485	-0.443	-0.648	-0.001
6	A	16	GLU	-1	-0.857	-0.931	4.493	-0.919	-0.885	0.000	-0.022	-0.013	0.000
7	A	17	ILE	0	-0.023	-0.004	7.545	0.171	0.171	0.000	0.000	0.000	0.000
8	A	18	TYR	0	-0.029	-0.020	7.692	0.045	0.045	0.000	0.000	0.000	0.000
9	A	19	LYS	1	0.955	0.969	8.398	0.034	0.034	0.000	0.000	0.000	0.000
10	A	20	HIS	0	-0.016	-0.027	10.421	-0.008	-0.008	0.000	0.000	0.000	0.000
11	A	21	ILE	0	-0.004	0.002	12.578	0.014	0.014	0.000	0.000	0.000	0.000
12	A	22	VAL	0	-0.055	-0.017	12.361	0.003	0.003	0.000	0.000	0.000	0.000
13	A	23	LYS	1	0.942	0.958	14.713	0.095	0.095	0.000	0.000	0.000	0.000
14	A	24	SER	0	-0.016	0.015	16.551	-0.007	-0.007	0.000	0.000	0.000	0.000
15	A	25	PRO	0	-0.003	-0.007	18.349	0.005	0.005	0.000	0.000	0.000	0.000
16	A	26	GLY	0	-0.005	-0.003	19.719	-0.009	-0.009	0.000	0.000	0.000	0.000
17	A	27	LEU	0	-0.022	0.013	17.446	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	28	HIS	0	-0.055	-0.037	20.450	0.006	0.006	0.000	0.000	0.000	0.000
19	A	29	GLU	-1	-0.857	-0.938	18.513	0.019	0.019	0.000	0.000	0.000	0.000
20	A	30	ARG	1	0.977	0.967	18.804	0.011	0.011	0.000	0.000	0.000	0.000
21	A	31	GLN	0	-0.074	-0.052	20.832	-0.014	-0.014	0.000	0.000	0.000	0.000
22	A	32	LEU	0	0.065	0.043	14.048	-0.015	-0.015	0.000	0.000	0.000	0.000
23	A	33	ALA	0	0.001	-0.001	15.979	-0.029	-0.029	0.000	0.000	0.000	0.000
24	A	34	LYS	1	0.923	0.976	17.108	0.055	0.055	0.000	0.000	0.000	0.000
25	A	35	GLU	-1	-0.926	-0.954	17.437	-0.105	-0.105	0.000	0.000	0.000	0.000
26	A	36	LEU	0	-0.027	-0.013	11.438	-0.020	-0.020	0.000	0.000	0.000	0.000
27	A	37	ASP	-1	-0.933	-0.945	14.058	-0.302	-0.302	0.000	0.000	0.000	0.000
28	A	38	VAL	0	-0.029	-0.002	11.603	-0.034	-0.034	0.000	0.000	0.000	0.000
29	A	39	PRO	0	0.026	-0.002	14.248	0.050	0.050	0.000	0.000	0.000	0.000
30	A	40	LEU	0	0.063	0.019	15.630	0.007	0.007	0.000	0.000	0.000	0.000
31	A	41	SER	0	0.025	0.006	17.044	0.017	0.017	0.000	0.000	0.000	0.000
32	A	42	THR	0	-0.006	0.000	11.144	0.029	0.029	0.000	0.000	0.000	0.000
33	A	43	LEU	0	0.018	0.002	12.291	0.044	0.044	0.000	0.000	0.000	0.000
34	A	44	VAL	0	0.051	0.034	13.494	0.056	0.056	0.000	0.000	0.000	0.000
35	A	45	TYR	0	0.011	0.013	9.039	0.102	0.102	0.000	0.000	0.000	0.000
36	A	46	HIS	0	0.007	-0.008	6.753	0.275	0.275	0.000	0.000	0.000	0.000
37	A	47	LEU	0	0.035	0.016	10.785	0.093	0.093	0.000	0.000	0.000	0.000
38	A	48	HIS	0	0.050	0.030	13.498	0.016	0.016	0.000	0.000	0.000	0.000
39	A	49	TYR	0	-0.096	-0.044	8.803	0.033	0.033	0.000	0.000	0.000	0.000
40	A	50	LEU	0	-0.011	-0.023	8.274	0.065	0.065	0.000	0.000	0.000	0.000
41	A	51	GLU	-1	-0.854	-0.924	12.084	0.152	0.152	0.000	0.000	0.000	0.000
42	A	52	ARG	1	0.931	0.978	13.347	-0.350	-0.350	0.000	0.000	0.000	0.000
43	A	53	ARG	1	0.840	0.913	11.506	-0.486	-0.486	0.000	0.000	0.000	0.000
44	A	54	GLU	-1	-0.911	-0.943	14.611	0.236	0.236	0.000	0.000	0.000	0.000
45	A	55	LEU	0	-0.077	-0.033	10.059	0.024	0.024	0.000	0.000	0.000	0.000
46	A	56	ILE	0	-0.044	-0.021	12.711	-0.028	-0.028	0.000	0.000	0.000	0.000
47	A	57	MET	0	0.003	-0.003	15.461	0.000	0.000	0.000	0.000	0.000	0.000
48	A	58	MET	0	0.018	0.018	19.119	-0.018	-0.018	0.000	0.000	0.000	0.000
49	A	59	LYS	1	0.940	0.956	21.529	-0.071	-0.071	0.000	0.000	0.000	0.000
50	A	60	SER	0	0.007	0.005	24.885	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	61	ASP	-1	-0.786	-0.904	27.195	0.014	0.014	0.000	0.000	0.000	0.000
52	A	62	GLU	-1	-0.876	-0.946	28.870	0.029	0.029	0.000	0.000	0.000	0.000
53	A	63	ARG	1	0.865	0.941	29.960	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	64	TYR	0	-0.052	-0.022	29.203	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	65	ALA	0	-0.011	0.016	32.470	0.001	0.001	0.000	0.000	0.000	0.000
56	A	66	ARG	1	0.931	0.958	34.392	-0.013	-0.013	0.000	0.000	0.000	0.000
57	A	67	TYR	0	0.020	0.014	37.489	0.003	0.003	0.000	0.000	0.000	0.000
58	A	68	TYR	0	-0.007	-0.015	38.601	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	69	ALA	0	0.020	0.021	43.621	0.001	0.001	0.000	0.000	0.000	0.000
60	A	70	THR	0	0.002	-0.006	45.403	0.000	0.000	0.000	0.000	0.000	0.000
61	A	71	LYS	1	0.954	0.966	46.949	-0.020	-0.020	0.000	0.000	0.000	0.000
62	A	72	NME	0	0.029	0.035	50.106	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:11:ACE )