FMO DATABASE

FMODB ID: K9VQ3

Calculation Name: 5EKQ-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5EKQ

Chain ID: E

ChEMBL ID:

UniProt ID: P0A940

Base Structure: X-ray

Registration Date: 2023-06-22

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	90
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-562809.198269
FMO2-HF: Nuclear repulsion	527785.483856
FMO2-HF: Total energy	-35023.714413
FMO2-MP2: Total energy	-35126.484932

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(E:22:THR)

Summations of interaction energy for fragment #1(E:22:THR)

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.
-0.614	1.517	-0.021	-0.842	-1.268	-0.001

Interaction energy analysis for fragmet #1(E:22:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / q_NPA : -0.048

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	E	24	GLU	-1	-0.874	-0.917	3.775	-1.184	0.947	-0.021	-0.842	-1.268	-0.001
4	E	25	ARG	1	0.910	0.937	5.738	0.795	0.795	0.000	0.000	0.000	0.000
5	E	26	VAL	0	-0.014	0.001	6.307	-0.365	-0.365	0.000	0.000	0.000	0.000
6	E	27	VAL	0	-0.011	0.005	8.533	0.232	0.232	0.000	0.000	0.000	0.000
7	E	28	TYR	0	0.037	0.010	11.367	-0.074	-0.074	0.000	0.000	0.000	0.000
8	E	29	ARG	1	0.937	0.953	14.565	0.235	0.235	0.000	0.000	0.000	0.000
9	E	30	PRO	0	-0.031	0.015	16.957	0.001	0.001	0.000	0.000	0.000	0.000
10	E	31	ASP	-1	-0.838	-0.936	20.241	-0.135	-0.135	0.000	0.000	0.000	0.000
11	E	32	ILE	0	-0.068	-0.020	20.157	0.011	0.011	0.000	0.000	0.000	0.000
12	E	33	ASN	0	-0.014	-0.015	23.601	-0.004	-0.004	0.000	0.000	0.000	0.000
13	E	34	GLN	0	-0.026	-0.025	25.140	0.008	0.008	0.000	0.000	0.000	0.000
14	E	35	GLY	0	0.041	0.013	27.854	0.000	0.000	0.000	0.000	0.000	0.000
15	E	36	ASN	0	-0.028	-0.009	30.992	0.000	0.000	0.000	0.000	0.000	0.000
16	E	37	TYR	0	0.040	0.010	32.831	-0.001	-0.001	0.000	0.000	0.000	0.000
17	E	38	LEU	0	-0.002	0.007	33.707	0.003	0.003	0.000	0.000	0.000	0.000
18	E	39	THR	0	-0.001	-0.011	35.120	-0.002	-0.002	0.000	0.000	0.000	0.000
19	E	40	ALA	0	0.042	0.030	36.552	0.000	0.000	0.000	0.000	0.000	0.000
20	E	41	ASN	0	0.022	-0.004	37.889	0.003	0.003	0.000	0.000	0.000	0.000
21	E	42	ASP	-1	-0.856	-0.933	40.359	-0.025	-0.025	0.000	0.000	0.000	0.000
22	E	43	VAL	0	0.004	-0.008	37.403	0.002	0.002	0.000	0.000	0.000	0.000
23	E	44	SER	0	-0.065	-0.035	40.826	0.002	0.002	0.000	0.000	0.000	0.000
24	E	45	LYS	1	0.891	0.971	43.468	0.022	0.022	0.000	0.000	0.000	0.000
25	E	46	ILE	0	-0.038	0.001	42.603	0.001	0.001	0.000	0.000	0.000	0.000
26	E	47	ARG	1	0.964	0.962	45.784	0.015	0.015	0.000	0.000	0.000	0.000
27	E	48	VAL	0	0.041	0.007	47.616	0.000	0.000	0.000	0.000	0.000	0.000
28	E	49	GLY	0	0.022	0.020	49.598	0.000	0.000	0.000	0.000	0.000	0.000
29	E	50	MET	0	-0.057	-0.015	47.948	0.000	0.000	0.000	0.000	0.000	0.000
30	E	51	THR	0	0.048	0.001	50.795	0.001	0.001	0.000	0.000	0.000	0.000
31	E	52	GLN	0	0.037	0.053	46.558	0.001	0.001	0.000	0.000	0.000	0.000
32	E	53	GLN	0	0.015	-0.007	47.907	0.000	0.000	0.000	0.000	0.000	0.000
33	E	54	GLN	0	-0.010	-0.033	49.494	0.000	0.000	0.000	0.000	0.000	0.000
34	E	55	VAL	0	0.004	0.010	43.957	-0.001	-0.001	0.000	0.000	0.000	0.000
35	E	56	ALA	0	0.000	-0.002	44.560	-0.001	-0.001	0.000	0.000	0.000	0.000
36	E	57	TYR	0	-0.067	-0.008	45.646	-0.001	-0.001	0.000	0.000	0.000	0.000
37	E	58	ALA	0	-0.018	-0.021	45.111	-0.001	-0.001	0.000	0.000	0.000	0.000
38	E	59	LEU	0	-0.001	-0.003	40.244	0.000	0.000	0.000	0.000	0.000	0.000
39	E	60	GLY	0	0.057	0.028	40.637	-0.002	-0.002	0.000	0.000	0.000	0.000
40	E	61	THR	0	0.017	0.055	40.641	0.001	0.001	0.000	0.000	0.000	0.000
41	E	62	PRO	0	-0.017	0.018	38.328	-0.002	-0.002	0.000	0.000	0.000	0.000
42	E	63	LEU	0	-0.016	-0.024	34.185	0.001	0.001	0.000	0.000	0.000	0.000
43	E	64	MET	0	-0.023	0.001	31.154	0.000	0.000	0.000	0.000	0.000	0.000
44	E	65	SER	0	-0.006	-0.007	35.675	0.000	0.000	0.000	0.000	0.000	0.000
45	E	66	ASP	-1	-0.756	-0.881	37.536	-0.005	-0.005	0.000	0.000	0.000	0.000
46	E	67	PRO	0	-0.108	-0.003	37.651	0.001	0.001	0.000	0.000	0.000	0.000
47	E	68	PHE	0	0.056	0.009	35.306	0.000	0.000	0.000	0.000	0.000	0.000
48	E	69	GLY	0	-0.011	-0.009	40.613	0.000	0.000	0.000	0.000	0.000	0.000
49	E	70	THR	0	-0.015	-0.006	41.835	0.000	0.000	0.000	0.000	0.000	0.000
50	E	71	ASN	0	-0.044	-0.016	43.505	-0.001	-0.001	0.000	0.000	0.000	0.000
51	E	72	THR	0	-0.020	-0.050	39.332	-0.001	-0.001	0.000	0.000	0.000	0.000
52	E	73	TRP	0	-0.043	-0.021	39.793	-0.001	-0.001	0.000	0.000	0.000	0.000
53	E	74	PHE	0	0.018	0.007	34.242	-0.001	-0.001	0.000	0.000	0.000	0.000
54	E	75	TYR	0	-0.047	-0.078	35.599	-0.001	-0.001	0.000	0.000	0.000	0.000
55	E	76	VAL	0	-0.008	-0.002	28.877	-0.001	-0.001	0.000	0.000	0.000	0.000
56	E	77	PHE	0	-0.012	0.014	29.557	-0.001	-0.001	0.000	0.000	0.000	0.000
57	E	78	ARG	1	0.946	0.974	20.617	0.052	0.052	0.000	0.000	0.000	0.000
58	E	79	GLN	0	0.010	0.011	24.954	0.001	0.001	0.000	0.000	0.000	0.000
59	E	80	GLN	0	-0.008	-0.004	17.554	-0.001	-0.001	0.000	0.000	0.000	0.000
60	E	81	PRO	0	0.085	0.036	20.975	-0.008	-0.008	0.000	0.000	0.000	0.000
61	E	82	GLY	0	0.072	0.043	18.363	-0.015	-0.015	0.000	0.000	0.000	0.000
62	E	83	HIS	0	-0.118	-0.074	11.767	-0.013	-0.013	0.000	0.000	0.000	0.000
63	E	84	GLU	-1	-0.946	-0.951	15.153	-0.172	-0.172	0.000	0.000	0.000	0.000
64	E	85	GLY	0	0.020	0.000	16.985	-0.010	-0.010	0.000	0.000	0.000	0.000
65	E	86	VAL	0	-0.088	-0.039	18.501	0.011	0.011	0.000	0.000	0.000	0.000
66	E	87	THR	0	0.024	0.013	20.824	0.005	0.005	0.000	0.000	0.000	0.000
67	E	88	GLN	0	0.054	-0.011	24.397	0.001	0.001	0.000	0.000	0.000	0.000
68	E	89	GLN	0	-0.025	0.008	26.816	0.004	0.004	0.000	0.000	0.000	0.000
69	E	90	THR	0	-0.063	-0.052	29.329	0.002	0.002	0.000	0.000	0.000	0.000
70	E	91	LEU	0	0.003	0.013	32.018	0.001	0.001	0.000	0.000	0.000	0.000
71	E	92	THR	0	0.004	0.017	35.051	0.000	0.000	0.000	0.000	0.000	0.000
72	E	93	LEU	0	-0.020	-0.015	37.403	0.000	0.000	0.000	0.000	0.000	0.000
73	E	94	THR	0	0.052	0.032	41.202	0.001	0.001	0.000	0.000	0.000	0.000
74	E	95	PHE	0	-0.003	0.016	43.359	-0.001	-0.001	0.000	0.000	0.000	0.000
75	E	96	ASN	0	0.026	0.020	46.763	0.001	0.001	0.000	0.000	0.000	0.000
76	E	97	SER	0	0.015	-0.008	49.773	0.000	0.000	0.000	0.000	0.000	0.000
77	E	98	SER	0	-0.039	-0.022	51.929	0.000	0.000	0.000	0.000	0.000	0.000
78	E	99	GLY	0	0.036	0.033	50.400	0.000	0.000	0.000	0.000	0.000	0.000
79	E	100	VAL	0	-0.036	-0.030	50.820	-0.001	-0.001	0.000	0.000	0.000	0.000
80	E	101	LEU	0	-0.019	0.006	45.423	0.001	0.001	0.000	0.000	0.000	0.000
81	E	102	THR	0	-0.028	-0.036	46.869	0.000	0.000	0.000	0.000	0.000	0.000
82	E	103	ASN	0	-0.017	-0.013	41.660	-0.001	-0.001	0.000	0.000	0.000	0.000
83	E	104	ILE	0	-0.017	-0.016	40.847	-0.001	-0.001	0.000	0.000	0.000	0.000
84	E	105	ASP	-1	-0.886	-0.921	36.516	-0.014	-0.014	0.000	0.000	0.000	0.000
85	E	106	ASN	0	-0.028	-0.029	35.389	-0.002	-0.002	0.000	0.000	0.000	0.000
86	E	107	LYS	1	0.978	1.004	29.506	0.020	0.020	0.000	0.000	0.000	0.000
87	E	108	PRO	0	0.017	-0.011	30.852	-0.002	-0.002	0.000	0.000	0.000	0.000
88	E	109	ALA	0	-0.008	0.008	26.012	0.000	0.000	0.000	0.000	0.000	0.000
89	E	110	LEU	0	-0.009	-0.025	22.991	0.004	0.004	0.000	0.000	0.000	0.000
90	E	111	SER	0	0.000	0.023	22.878	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:22:THR)