FMO DATABASE

FMODB ID: 53YYZ

Calculation Name: 2B8I-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2B8I

Chain ID: A

ChEMBL ID:

UniProt ID: Q56GA4

Base Structure: X-ray

Registration Date: 2023-03-13

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	77
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-485193.172882
FMO2-HF: Nuclear repulsion	455530.984289
FMO2-HF: Total energy	-29662.188593
FMO2-MP2: Total energy	-29750.166414

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:1:ILE)

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

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.
-10.435	-6.145	13.192	-4.804	-12.68	-0.012

Interaction energy analysis for fragmet #1(A:1:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / q_NPA : 0.008

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	3	PRO	0	0.069	0.016	3.282	-3.256	-0.266	0.092	-1.460	-1.622	0.005
4	A	4	TYR	0	0.001	-0.001	5.285	-0.222	-0.073	-0.001	-0.005	-0.143	0.000
5	A	5	MET	0	0.030	0.026	2.387	-0.476	-2.396	7.265	-1.108	-4.237	-0.005
6	A	6	LYS	1	0.910	0.947	4.468	0.843	1.090	-0.001	-0.023	-0.223	0.000
7	A	7	ALA	0	-0.020	-0.009	5.084	0.111	0.149	-0.001	-0.003	-0.034	0.000
8	A	8	LEU	0	0.006	0.015	7.457	0.042	0.042	0.000	0.000	0.000	0.000
9	A	9	ILE	0	0.040	0.026	3.788	-0.141	0.020	0.002	-0.029	-0.135	0.000
10	A	10	TYR	0	-0.005	-0.014	7.803	0.067	0.067	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.877	-0.933	10.144	-0.111	-0.111	0.000	0.000	0.000	0.000
12	A	12	THR	0	0.002	-0.011	10.853	0.058	0.058	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.049	-0.028	10.453	0.023	0.023	0.000	0.000	0.000	0.000
14	A	14	VAL	0	0.013	0.014	13.504	0.028	0.028	0.000	0.000	0.000	0.000
15	A	15	ASN	0	-0.070	-0.043	15.701	0.044	0.044	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.043	-0.027	14.282	0.018	0.018	0.000	0.000	0.000	0.000
17	A	17	ALA	0	-0.014	-0.002	17.624	0.009	0.009	0.000	0.000	0.000	0.000
18	A	18	ASN	0	-0.076	-0.042	19.465	0.017	0.017	0.000	0.000	0.000	0.000
19	A	19	GLN	0	-0.042	0.002	20.525	0.028	0.028	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.856	-0.931	22.659	-0.064	-0.064	0.000	0.000	0.000	0.000
21	A	21	PRO	0	0.021	-0.022	23.478	0.003	0.003	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.945	-0.946	24.067	-0.028	-0.028	0.000	0.000	0.000	0.000
23	A	23	GLN	0	-0.034	-0.024	22.487	0.012	0.012	0.000	0.000	0.000	0.000
24	A	24	HIS	0	-0.002	0.000	19.691	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	25	ALA	0	-0.038	-0.020	18.633	-0.006	-0.006	0.000	0.000	0.000	0.000
26	A	26	THR	0	0.026	0.001	18.898	0.007	0.007	0.000	0.000	0.000	0.000
27	A	27	ILE	0	0.001	0.009	15.630	0.022	0.022	0.000	0.000	0.000	0.000
28	A	28	ARG	1	0.888	0.936	14.359	0.126	0.126	0.000	0.000	0.000	0.000
29	A	29	GLN	0	-0.040	-0.032	13.914	-0.029	-0.029	0.000	0.000	0.000	0.000
30	A	30	ASN	0	0.010	0.011	14.648	0.071	0.071	0.000	0.000	0.000	0.000
31	A	31	LEU	0	0.016	0.013	8.236	0.052	0.052	0.000	0.000	0.000	0.000
32	A	32	TYR	0	-0.064	-0.063	9.834	0.057	0.057	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.891	-0.930	11.601	0.332	0.332	0.000	0.000	0.000	0.000
34	A	34	GLN	0	-0.064	-0.032	10.494	0.049	0.049	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.090	-0.053	5.449	0.191	0.191	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.939	-0.942	7.853	1.011	1.011	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.021	-0.010	4.762	-0.009	0.082	-0.001	-0.002	-0.088	0.000
38	A	38	PRO	0	0.000	0.012	8.204	-0.052	-0.052	0.000	0.000	0.000	0.000
39	A	39	PHE	0	0.077	0.014	10.619	-0.110	-0.110	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.883	-0.952	11.197	-0.313	-0.313	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.873	0.933	5.770	1.240	1.240	0.000	0.000	0.000	0.000
42	A	42	GLN	0	-0.002	0.009	8.364	-0.106	-0.106	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.010	0.009	10.165	-0.040	-0.040	0.000	0.000	0.000	0.000
44	A	44	ALA	0	0.014	0.011	8.684	-0.009	-0.009	0.000	0.000	0.000	0.000
45	A	45	LEU	0	0.033	0.011	6.553	-0.051	-0.051	0.000	0.000	0.000	0.000
46	A	46	TYR	0	-0.001	-0.001	8.991	0.031	0.031	0.000	0.000	0.000	0.000
47	A	47	ALA	0	-0.030	-0.027	12.707	0.012	0.012	0.000	0.000	0.000	0.000
48	A	48	GLY	0	-0.003	0.009	11.841	0.024	0.024	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.000	-0.011	9.899	-0.016	-0.016	0.000	0.000	0.000	0.000
50	A	50	LEU	0	0.018	0.010	10.419	0.063	0.063	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.013	0.024	13.468	0.046	0.046	0.000	0.000	0.000	0.000
52	A	52	PRO	0	-0.011	-0.014	14.685	0.036	0.036	0.000	0.000	0.000	0.000
53	A	53	ALA	0	0.005	0.010	14.708	0.025	0.025	0.000	0.000	0.000	0.000
54	A	54	SER	0	-0.001	-0.007	16.725	0.037	0.037	0.000	0.000	0.000	0.000
55	A	55	SER	0	-0.135	-0.065	19.121	0.018	0.018	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.092	0.051	20.505	0.010	0.010	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.835	0.917	19.522	0.213	0.213	0.000	0.000	0.000	0.000
58	A	58	LEU	0	-0.020	-0.009	14.028	-0.022	-0.022	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.891	-0.948	18.049	-0.166	-0.166	0.000	0.000	0.000	0.000
60	A	60	ASN	0	-0.022	-0.009	18.924	0.001	0.001	0.000	0.000	0.000	0.000
61	A	61	HIS	0	0.061	0.027	16.198	-0.039	-0.039	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.851	-0.916	16.270	-0.459	-0.459	0.000	0.000	0.000	0.000
63	A	63	ALA	0	0.020	0.010	16.163	-0.047	-0.047	0.000	0.000	0.000	0.000
64	A	64	ILE	0	-0.012	-0.007	12.927	-0.049	-0.049	0.000	0.000	0.000	0.000
65	A	65	SER	0	0.008	-0.001	12.040	-0.076	-0.076	0.000	0.000	0.000	0.000
66	A	66	ASN	0	-0.069	-0.037	11.332	-0.086	-0.086	0.000	0.000	0.000	0.000
67	A	67	ALA	0	0.017	0.031	11.599	-0.104	-0.104	0.000	0.000	0.000	0.000
68	A	68	VAL	0	-0.018	-0.013	6.697	-0.139	-0.139	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.845	-0.914	6.694	-1.492	-1.492	0.000	0.000	0.000	0.000
70	A	70	SER	0	-0.026	-0.022	7.331	-0.262	-0.262	0.000	0.000	0.000	0.000
71	A	71	VAL	0	0.005	-0.004	5.648	-0.124	-0.124	0.000	0.000	0.000	0.000
72	A	72	VAL	0	-0.025	-0.016	2.246	-1.033	-0.620	1.609	-0.363	-1.659	0.001
73	A	73	GLN	0	0.011	0.007	3.237	-2.728	-1.525	0.063	-0.583	-0.684	-0.005
74	A	74	LEU	0	-0.036	-0.013	5.883	0.063	0.063	0.000	0.000	0.000	0.000
75	A	75	LEU	0	-0.045	-0.028	2.545	-0.496	0.121	1.412	-0.397	-1.632	-0.002
76	A	76	GLU	-1	-0.971	-0.957	2.055	-4.184	-3.900	2.708	-0.967	-2.025	-0.006
77	A	77	ILE	0	-0.023	-0.013	3.486	1.071	1.088	0.045	0.136	-0.198	0.000

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