FMO DATABASE

FMODB ID: 665LZ

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	OptHSide
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	-343595.08067
FMO2-HF: Nuclear repulsion	317935.025823
FMO2-HF: Total energy	-25660.054847
FMO2-MP2: Total energy	-25735.170673

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.
-109.904	-103.83	0.352	-2.838	-3.587	0.025

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 : -0.873 / q_NPA : -0.945

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	0.834	0.930	3.370	-45.622	-42.114	0.096	-1.728	-1.875	0.016
4	A	15	ARG	1	0.936	0.960	3.207	-46.661	-44.719	0.256	-0.923	-1.275	0.009
5	A	16	GLU	-1	-0.855	-0.931	4.190	35.692	36.316	0.000	-0.187	-0.437	0.000
6	A	17	ILE	0	-0.027	-0.009	5.873	-5.630	-5.630	0.000	0.000	0.000	0.000
7	A	18	TYR	0	-0.031	-0.023	8.066	-2.911	-2.911	0.000	0.000	0.000	0.000
8	A	19	LYS	1	0.946	0.974	8.227	-29.170	-29.170	0.000	0.000	0.000	0.000
9	A	20	HIS	0	0.000	-0.014	10.011	-1.638	-1.638	0.000	0.000	0.000	0.000
10	A	21	ILE	0	0.000	0.004	11.955	-1.804	-1.804	0.000	0.000	0.000	0.000
11	A	22	VAL	0	-0.045	-0.014	13.411	-1.461	-1.461	0.000	0.000	0.000	0.000
12	A	23	LYS	1	0.932	0.958	14.155	-20.165	-20.165	0.000	0.000	0.000	0.000
13	A	24	SER	0	-0.013	0.011	15.825	-1.341	-1.341	0.000	0.000	0.000	0.000
14	A	25	PRO	0	-0.001	-0.004	17.651	0.316	0.316	0.000	0.000	0.000	0.000
15	A	26	GLY	0	-0.008	-0.004	19.508	-0.499	-0.499	0.000	0.000	0.000	0.000
16	A	27	LEU	0	-0.033	0.006	16.316	-0.474	-0.474	0.000	0.000	0.000	0.000
17	A	28	HIS	0	-0.012	-0.016	19.657	0.128	0.128	0.000	0.000	0.000	0.000
18	A	29	GLU	-1	-0.862	-0.942	17.075	17.612	17.612	0.000	0.000	0.000	0.000
19	A	30	ARG	1	0.926	0.935	16.398	-12.770	-12.770	0.000	0.000	0.000	0.000
20	A	31	GLN	0	-0.033	-0.018	17.488	0.480	0.480	0.000	0.000	0.000	0.000
21	A	32	LEU	0	0.047	0.027	12.528	0.555	0.555	0.000	0.000	0.000	0.000
22	A	33	ALA	0	-0.005	0.000	12.381	1.546	1.546	0.000	0.000	0.000	0.000
23	A	34	LYS	1	0.828	0.919	13.184	-16.284	-16.284	0.000	0.000	0.000	0.000
24	A	35	GLU	-1	-0.848	-0.921	14.276	18.278	18.278	0.000	0.000	0.000	0.000
25	A	36	LEU	0	-0.032	-0.016	8.762	0.951	0.951	0.000	0.000	0.000	0.000
26	A	37	ASP	-1	-0.933	-0.943	8.951	28.661	28.661	0.000	0.000	0.000	0.000
27	A	38	VAL	0	-0.037	-0.004	6.968	2.915	2.915	0.000	0.000	0.000	0.000
28	A	39	PRO	0	0.032	0.003	9.563	-2.815	-2.815	0.000	0.000	0.000	0.000
29	A	40	LEU	0	0.049	0.015	11.962	1.190	1.190	0.000	0.000	0.000	0.000
30	A	41	SER	0	0.030	0.007	14.403	0.027	0.027	0.000	0.000	0.000	0.000
31	A	42	THR	0	-0.012	-0.005	7.815	-0.471	-0.471	0.000	0.000	0.000	0.000
32	A	43	LEU	0	0.017	0.006	10.450	1.488	1.488	0.000	0.000	0.000	0.000
33	A	44	VAL	0	0.047	0.029	11.364	-0.024	-0.024	0.000	0.000	0.000	0.000
34	A	45	TYR	0	0.004	0.011	8.842	-0.011	-0.011	0.000	0.000	0.000	0.000
35	A	46	HIS	0	0.016	0.000	6.495	-2.132	-2.132	0.000	0.000	0.000	0.000
36	A	47	LEU	0	0.035	0.018	10.157	-0.371	-0.371	0.000	0.000	0.000	0.000
37	A	48	HIS	0	0.029	0.011	13.099	-1.125	-1.125	0.000	0.000	0.000	0.000
38	A	49	TYR	0	-0.100	-0.052	9.968	-0.974	-0.974	0.000	0.000	0.000	0.000
39	A	50	LEU	0	-0.002	-0.017	9.171	-0.612	-0.612	0.000	0.000	0.000	0.000
40	A	51	GLU	-1	-0.836	-0.902	12.779	15.753	15.753	0.000	0.000	0.000	0.000
41	A	52	ARG	1	0.924	0.973	14.232	-18.493	-18.493	0.000	0.000	0.000	0.000
42	A	53	ARG	1	0.850	0.919	12.890	-17.110	-17.110	0.000	0.000	0.000	0.000
43	A	54	GLU	-1	-0.931	-0.953	15.961	13.188	13.188	0.000	0.000	0.000	0.000
44	A	55	LEU	0	-0.060	-0.024	11.877	0.126	0.126	0.000	0.000	0.000	0.000
45	A	56	ILE	0	-0.040	-0.021	13.432	0.338	0.338	0.000	0.000	0.000	0.000
46	A	57	MET	0	-0.001	-0.003	16.396	-0.629	-0.629	0.000	0.000	0.000	0.000
47	A	58	MET	0	0.029	0.022	19.825	0.212	0.212	0.000	0.000	0.000	0.000
48	A	59	LYS	1	0.936	0.952	21.829	-12.646	-12.646	0.000	0.000	0.000	0.000
49	A	60	SER	0	0.018	0.010	24.972	0.438	0.438	0.000	0.000	0.000	0.000
50	A	61	ASP	-1	-0.790	-0.900	26.619	11.484	11.484	0.000	0.000	0.000	0.000
51	A	62	GLU	-1	-0.869	-0.944	28.525	10.045	10.045	0.000	0.000	0.000	0.000
52	A	63	ARG	1	0.872	0.945	29.060	-11.120	-11.120	0.000	0.000	0.000	0.000
53	A	64	TYR	0	-0.044	-0.026	27.868	0.088	0.088	0.000	0.000	0.000	0.000
54	A	65	ALA	0	-0.014	0.016	31.412	0.005	0.005	0.000	0.000	0.000	0.000
55	A	66	ARG	1	0.921	0.958	33.556	-9.375	-9.375	0.000	0.000	0.000	0.000
56	A	67	TYR	0	0.022	0.011	36.591	-0.110	-0.110	0.000	0.000	0.000	0.000
57	A	68	TYR	0	-0.012	-0.016	37.688	0.026	0.026	0.000	0.000	0.000	0.000
58	A	69	ALA	0	0.023	0.023	42.921	-0.028	-0.028	0.000	0.000	0.000	0.000
59	A	70	THR	0	0.013	0.008	45.271	0.075	0.075	0.000	0.000	0.000	0.000
60	A	71	LYS	1	0.982	0.993	46.237	-7.045	-7.045	0.000	0.000	0.000	0.000

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