FMO DATABASE

FMODB ID: 3N29L

Calculation Name: 3IBW-A-Xray312

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3IBW

Chain ID: A

ChEMBL ID:

UniProt ID: Q8KC80

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	81
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-513881.002281
FMO2-HF: Nuclear repulsion	482386.432361
FMO2-HF: Total energy	-31494.56992
FMO2-MP2: Total energy	-31585.030621

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:652:ACE )

Summations of interaction energy for fragment #1(A:652: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.
0.575	1.444	-0.006	-0.396	-0.468	0

Interaction energy analysis for fragmet #1(A:652:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : -0.010

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].
3	A	654	ASP	-1	-0.892	-0.934	3.847	-0.274	0.595	-0.006	-0.396	-0.468
4	A	655	PHE	0	-0.030	-0.006	7.095	0.167	0.167	0.000	0.000	0.000
5	A	656	LEU	0	-0.028	-0.015	8.621	0.003	0.003	0.000	0.000	0.000
6	A	657	ALA	0	-0.025	-0.012	12.344	0.068	0.068	0.000	0.000	0.000
7	A	658	GLY	0	0.066	0.010	14.339	-0.021	-0.021	0.000	0.000	0.000
8	A	659	ILE	0	-0.021	-0.005	17.694	0.016	0.016	0.000	0.000	0.000
9	A	660	ARG	1	0.958	0.979	20.501	0.014	0.014	0.000	0.000	0.000
10	A	661	ILE	0	-0.018	-0.008	23.526	0.004	0.004	0.000	0.000	0.000
11	A	662	VAL	0	0.009	0.000	26.798	-0.001	-0.001	0.000	0.000	0.000
12	A	663	GLY	0	0.031	0.012	30.514	0.001	0.001	0.000	0.000	0.000
13	A	664	GLU	-1	-0.901	-0.948	33.093	-0.023	-0.023	0.000	0.000	0.000
14	A	665	ASP	-1	-0.962	-0.989	36.127	-0.034	-0.034	0.000	0.000	0.000
15	A	666	LYS	1	0.974	0.981	37.886	0.021	0.021	0.000	0.000	0.000
16	A	667	ASN	0	-0.017	-0.018	38.336	-0.002	-0.002	0.000	0.000	0.000
17	A	668	GLY	0	0.057	0.041	37.894	-0.001	-0.001	0.000	0.000	0.000
18	A	669	MET	0	-0.015	0.005	32.480	-0.005	-0.005	0.000	0.000	0.000
19	A	670	THR	0	0.035	0.027	32.597	-0.004	-0.004	0.000	0.000	0.000
20	A	671	ASN	0	0.028	0.010	31.726	-0.004	-0.004	0.000	0.000	0.000
21	A	672	GLN	0	-0.003	0.002	31.355	-0.007	-0.007	0.000	0.000	0.000
22	A	673	ILE	0	0.013	-0.003	27.086	-0.006	-0.006	0.000	0.000	0.000
23	A	674	THR	0	-0.003	-0.009	27.081	-0.009	-0.009	0.000	0.000	0.000
24	A	675	GLY	0	0.018	0.008	27.015	-0.009	-0.009	0.000	0.000	0.000
25	A	676	VAL	0	-0.070	-0.023	24.271	-0.009	-0.009	0.000	0.000	0.000
26	A	677	ILE	0	0.008	-0.002	21.905	-0.011	-0.011	0.000	0.000	0.000
27	A	678	SER	0	-0.087	-0.045	22.158	-0.016	-0.016	0.000	0.000	0.000
28	A	679	LYS	1	0.950	0.965	23.144	0.077	0.077	0.000	0.000	0.000
29	A	680	PHE	0	-0.022	0.001	18.592	-0.002	-0.002	0.000	0.000	0.000
30	A	681	ASP	-1	-0.911	-0.945	15.562	-0.325	-0.325	0.000	0.000	0.000
31	A	682	THR	0	-0.068	-0.049	13.916	-0.031	-0.031	0.000	0.000	0.000
32	A	683	ASN	0	0.053	0.044	13.887	0.082	0.082	0.000	0.000	0.000
33	A	684	ILE	0	0.034	0.014	15.971	0.003	0.003	0.000	0.000	0.000
34	A	685	ARG	1	0.842	0.923	15.810	0.235	0.235	0.000	0.000	0.000
35	A	686	THR	0	0.007	-0.005	18.960	0.015	0.015	0.000	0.000	0.000
36	A	687	ILE	0	0.053	0.022	22.009	-0.002	-0.002	0.000	0.000	0.000
37	A	688	VAL	0	-0.014	0.005	24.756	0.003	0.003	0.000	0.000	0.000
38	A	689	LEU	0	0.005	0.000	27.683	0.003	0.003	0.000	0.000	0.000
39	A	690	ASN	0	-0.051	-0.037	30.074	0.002	0.002	0.000	0.000	0.000
40	A	691	ALA	0	0.024	0.021	33.615	0.001	0.001	0.000	0.000	0.000
41	A	692	LYS	1	0.949	0.961	36.326	0.022	0.022	0.000	0.000	0.000
42	A	693	ASP	-1	-0.880	-0.937	38.631	-0.015	-0.015	0.000	0.000	0.000
43	A	694	GLY	0	0.000	0.015	40.886	0.001	0.001	0.000	0.000	0.000
44	A	695	ILE	0	-0.016	0.004	34.846	-0.001	-0.001	0.000	0.000	0.000
45	A	696	PHE	0	0.018	0.009	29.566	-0.002	-0.002	0.000	0.000	0.000
46	A	697	THR	0	-0.071	-0.025	30.224	0.002	0.002	0.000	0.000	0.000
47	A	698	CYS	0	0.004	-0.014	26.415	-0.006	-0.006	0.000	0.000	0.000
48	A	699	ASN	0	0.042	0.038	24.127	0.004	0.004	0.000	0.000	0.000
49	A	700	LEU	0	0.018	0.007	19.655	-0.006	-0.006	0.000	0.000	0.000
50	A	701	MET	0	-0.019	0.009	17.156	0.012	0.012	0.000	0.000	0.000
51	A	702	ILE	0	0.027	0.006	14.654	-0.012	-0.012	0.000	0.000	0.000
52	A	703	PHE	0	0.009	-0.001	10.614	0.033	0.033	0.000	0.000	0.000
53	A	704	VAL	0	-0.013	-0.021	10.420	-0.006	-0.006	0.000	0.000	0.000
54	A	705	LYS	1	1.046	1.023	7.265	0.382	0.382	0.000	0.000	0.000
55	A	706	ASN	0	0.035	0.011	6.211	-0.095	-0.095	0.000	0.000	0.000
56	A	707	THR	0	0.073	0.009	8.193	-0.027	-0.027	0.000	0.000	0.000
57	A	708	ASP	-1	-0.842	-0.901	11.270	0.048	0.048	0.000	0.000	0.000
58	A	709	LYS	1	0.903	0.956	11.495	0.246	0.246	0.000	0.000	0.000
59	A	710	LEU	0	0.028	0.022	12.642	0.003	0.003	0.000	0.000	0.000
60	A	711	THR	0	0.018	0.001	14.436	0.010	0.010	0.000	0.000	0.000
61	A	712	THR	0	-0.039	-0.027	16.076	-0.007	-0.007	0.000	0.000	0.000
62	A	713	LEU	0	-0.044	-0.015	15.471	-0.004	-0.004	0.000	0.000	0.000
63	A	714	MET	0	-0.015	-0.009	17.464	0.009	0.009	0.000	0.000	0.000
64	A	715	ASP	-1	-0.858	-0.932	20.678	-0.014	-0.014	0.000	0.000	0.000
65	A	716	LYS	1	0.867	0.929	21.844	0.087	0.087	0.000	0.000	0.000
66	A	717	LEU	0	0.003	0.001	21.867	0.003	0.003	0.000	0.000	0.000
67	A	718	ARG	1	0.898	0.948	22.277	0.018	0.018	0.000	0.000	0.000
68	A	719	LYS	1	0.923	0.965	24.891	0.038	0.038	0.000	0.000	0.000
69	A	720	VAL	0	-0.035	0.007	28.054	0.000	0.000	0.000	0.000	0.000
70	A	721	GLN	0	0.012	-0.003	30.500	0.005	0.005	0.000	0.000	0.000
71	A	722	GLY	0	0.110	0.051	34.064	-0.002	-0.002	0.000	0.000	0.000
72	A	723	VAL	0	-0.071	-0.030	28.252	0.000	0.000	0.000	0.000	0.000
73	A	724	PHE	0	-0.031	-0.019	31.708	0.003	0.003	0.000	0.000	0.000
74	A	725	THR	0	-0.022	-0.012	28.327	0.003	0.003	0.000	0.000	0.000
75	A	726	VAL	0	0.015	-0.001	22.598	-0.006	-0.006	0.000	0.000	0.000
76	A	727	GLU	-1	-0.958	-0.963	22.818	0.007	0.007	0.000	0.000	0.000
77	A	728	ARG	1	0.985	0.982	12.388	-0.078	-0.078	0.000	0.000	0.000
78	A	729	LEU	0	-0.040	-0.015	19.476	0.009	0.009	0.000	0.000	0.000
79	A	730	SER	0	-0.025	-0.022	18.373	-0.001	-0.001	0.000	0.000	0.000
80	A	731	ASN	0	-0.006	-0.007	18.504	-0.001	-0.001	0.000	0.000	0.000
81	A	732	NME	0	0.011	0.019	16.865	-0.006	-0.006	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:652:ACE )