FMO DATABASE

FMODB ID: 4366N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-485276.676936
FMO2-HF: Nuclear repulsion	455614.979102
FMO2-HF: Total energy	-29661.697834
FMO2-MP2: Total energy	-29749.750546

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.
-8.215	-9.191	18.835	-5.388	-12.471	-0.016

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 : 0.036 / q_NPA : 0.009

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	0.055	0.014	3.057	-3.329	-0.337	0.176	-1.473	-1.695	0.004
4	A	4	TYR	0	0.001	-0.006	5.094	-0.205	-0.060	-0.001	-0.005	-0.139	0.000
5	A	5	MET	0	0.054	0.039	2.542	-0.049	-3.045	8.039	-1.273	-3.770	-0.009
6	A	6	LYS	1	1.007	1.014	4.339	1.022	1.256	-0.001	-0.020	-0.213	0.000
7	A	7	ALA	0	-0.028	-0.015	5.035	0.130	0.168	-0.001	-0.003	-0.035	0.000
8	A	8	LEU	0	0.005	0.017	7.645	0.043	0.043	0.000	0.000	0.000	0.000
9	A	9	ILE	0	0.043	0.027	4.109	-0.090	0.018	-0.001	-0.011	-0.096	0.000
10	A	10	TYR	0	0.000	-0.008	8.073	0.074	0.074	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.919	-0.963	10.237	-0.109	-0.109	0.000	0.000	0.000	0.000
12	A	12	THR	0	0.020	0.001	11.192	0.065	0.065	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.055	-0.032	10.585	0.027	0.027	0.000	0.000	0.000	0.000
14	A	14	VAL	0	0.012	0.015	13.730	0.029	0.029	0.000	0.000	0.000	0.000
15	A	15	ASN	0	-0.047	-0.027	15.946	0.038	0.038	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.051	-0.031	14.520	0.020	0.020	0.000	0.000	0.000	0.000
17	A	17	ALA	0	0.004	0.004	17.850	0.009	0.009	0.000	0.000	0.000	0.000
18	A	18	ASN	0	-0.084	-0.043	19.685	0.019	0.019	0.000	0.000	0.000	0.000
19	A	19	GLN	0	-0.061	-0.014	21.007	0.031	0.031	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.877	-0.945	22.955	-0.057	-0.057	0.000	0.000	0.000	0.000
21	A	21	PRO	0	0.018	-0.022	23.844	0.005	0.005	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.934	-0.937	24.468	-0.013	-0.013	0.000	0.000	0.000	0.000
23	A	23	GLN	0	-0.010	-0.006	22.749	0.013	0.013	0.000	0.000	0.000	0.000
24	A	24	HIS	0	0.006	0.006	20.094	0.006	0.006	0.000	0.000	0.000	0.000
25	A	25	ALA	0	-0.029	-0.020	19.075	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	26	THR	0	0.022	-0.001	19.433	0.014	0.014	0.000	0.000	0.000	0.000
27	A	27	ILE	0	-0.013	0.005	15.925	0.029	0.029	0.000	0.000	0.000	0.000
28	A	28	ARG	1	0.900	0.950	14.824	0.106	0.106	0.000	0.000	0.000	0.000
29	A	29	GLN	0	-0.053	-0.032	14.498	-0.025	-0.025	0.000	0.000	0.000	0.000
30	A	30	ASN	0	0.025	0.013	15.474	0.103	0.103	0.000	0.000	0.000	0.000
31	A	31	LEU	0	0.023	0.020	8.660	0.063	0.063	0.000	0.000	0.000	0.000
32	A	32	TYR	0	-0.066	-0.056	10.688	0.078	0.078	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.888	-0.935	11.909	0.482	0.482	0.000	0.000	0.000	0.000
34	A	34	GLN	0	-0.056	-0.026	10.607	0.061	0.061	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.096	-0.050	5.836	0.233	0.233	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.932	-0.945	7.839	1.379	1.379	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.041	-0.017	5.857	0.123	0.123	0.000	0.000	0.000	0.000
38	A	38	PRO	0	0.017	0.010	8.695	-0.111	-0.111	0.000	0.000	0.000	0.000
39	A	39	PHE	0	0.080	0.021	11.154	-0.119	-0.119	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.879	-0.940	11.463	-0.187	-0.187	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.930	0.958	5.931	0.741	0.741	0.000	0.000	0.000	0.000
42	A	42	GLN	0	0.000	0.009	8.733	-0.108	-0.108	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.006	0.006	10.669	-0.059	-0.059	0.000	0.000	0.000	0.000
44	A	44	ALA	0	0.013	0.010	8.794	-0.019	-0.019	0.000	0.000	0.000	0.000
45	A	45	LEU	0	0.034	0.015	7.081	-0.069	-0.069	0.000	0.000	0.000	0.000
46	A	46	TYR	0	-0.018	-0.017	9.253	0.024	0.024	0.000	0.000	0.000	0.000
47	A	47	ALA	0	-0.019	-0.020	13.010	0.005	0.005	0.000	0.000	0.000	0.000
48	A	48	GLY	0	-0.007	0.008	11.797	0.021	0.021	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.004	-0.007	10.204	-0.023	-0.023	0.000	0.000	0.000	0.000
50	A	50	LEU	0	0.009	0.003	10.907	0.066	0.066	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.011	0.015	13.805	0.046	0.046	0.000	0.000	0.000	0.000
52	A	52	PRO	0	-0.009	-0.012	14.869	0.037	0.037	0.000	0.000	0.000	0.000
53	A	53	ALA	0	0.008	0.011	14.949	0.023	0.023	0.000	0.000	0.000	0.000
54	A	54	SER	0	0.003	-0.006	16.951	0.039	0.039	0.000	0.000	0.000	0.000
55	A	55	SER	0	-0.130	-0.061	19.426	0.019	0.019	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.094	0.052	20.756	0.010	0.010	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.830	0.916	19.594	0.227	0.227	0.000	0.000	0.000	0.000
58	A	58	LEU	0	-0.018	-0.006	14.053	-0.025	-0.025	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.898	-0.950	18.172	-0.180	-0.180	0.000	0.000	0.000	0.000
60	A	60	ASN	0	-0.016	-0.009	18.966	0.001	0.001	0.000	0.000	0.000	0.000
61	A	61	HIS	0	0.043	0.020	16.255	-0.050	-0.050	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.879	-0.939	16.147	-0.499	-0.499	0.000	0.000	0.000	0.000
63	A	63	ALA	0	0.006	0.002	16.006	-0.053	-0.053	0.000	0.000	0.000	0.000
64	A	64	ILE	0	-0.017	-0.011	12.880	-0.050	-0.050	0.000	0.000	0.000	0.000
65	A	65	SER	0	0.017	0.001	11.892	-0.084	-0.084	0.000	0.000	0.000	0.000
66	A	66	ASN	0	-0.030	-0.009	11.129	-0.069	-0.069	0.000	0.000	0.000	0.000
67	A	67	ALA	0	0.020	0.019	11.441	-0.111	-0.111	0.000	0.000	0.000	0.000
68	A	68	VAL	0	-0.027	-0.019	6.604	-0.146	-0.146	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.914	-0.962	6.562	-1.620	-1.620	0.000	0.000	0.000	0.000
70	A	70	SER	0	-0.033	-0.018	7.215	-0.296	-0.296	0.000	0.000	0.000	0.000
71	A	71	VAL	0	-0.003	-0.008	5.675	-0.117	-0.117	0.000	0.000	0.000	0.000
72	A	72	VAL	0	-0.039	-0.025	2.086	1.294	-2.063	6.515	-0.784	-2.373	0.001
73	A	73	GLN	0	0.022	0.016	3.305	-2.365	-1.471	0.065	-0.398	-0.562	-0.003
74	A	74	LEU	0	-0.066	-0.031	5.786	0.081	0.081	0.000	0.000	0.000	0.000
75	A	75	LEU	0	-0.081	-0.037	2.439	-0.476	0.183	0.992	-0.358	-1.293	-0.003
76	A	76	GLU	-1	-0.990	-0.975	1.942	-5.244	-5.113	3.031	-1.060	-2.101	-0.006
77	A	77	ILE	0	-0.007	-0.007	3.618	0.908	1.084	0.021	-0.003	-0.194	0.000

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