FMO DATABASE

FMODB ID: Q1ZZY

Calculation Name: 3IBW-A-Xray372

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: 2023-06-19

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	79
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-509518.971087
FMO2-HF: Nuclear repulsion	478195.347358
FMO2-HF: Total energy	-31323.623729
FMO2-MP2: Total energy	-31413.546384

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:653:THR)

Summations of interaction energy for fragment #1(A:653: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.
-3.812	-0.9	0.259	-1.664	-1.506	-0.003

Interaction energy analysis for fragmet #1(A:653:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : -0.001

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	655	PHE	0	-0.029	-0.006	2.874	-4.383	-1.447	0.261	-1.640	-1.557	-0.003
4	A	656	LEU	0	-0.029	-0.016	5.539	0.774	0.774	0.000	0.000	0.000	0.000
5	A	657	ALA	0	-0.024	-0.011	8.816	-0.031	-0.031	0.000	0.000	0.000	0.000
6	A	658	GLY	0	0.065	0.011	11.900	0.092	0.092	0.000	0.000	0.000	0.000
7	A	659	ILE	0	-0.020	-0.005	15.526	-0.003	-0.003	0.000	0.000	0.000	0.000
8	A	660	ARG	1	0.955	0.978	18.354	0.209	0.209	0.000	0.000	0.000	0.000
9	A	661	ILE	0	-0.014	-0.006	21.121	0.007	0.007	0.000	0.000	0.000	0.000
10	A	662	VAL	0	0.008	0.000	24.667	0.000	0.000	0.000	0.000	0.000	0.000
11	A	663	GLY	0	0.030	0.011	28.400	0.003	0.003	0.000	0.000	0.000	0.000
12	A	664	GLU	-1	-0.902	-0.947	31.026	-0.050	-0.050	0.000	0.000	0.000	0.000
13	A	665	ASP	-1	-0.961	-0.989	33.646	-0.059	-0.059	0.000	0.000	0.000	0.000
14	A	666	LYS	1	0.973	0.981	35.084	0.047	0.047	0.000	0.000	0.000	0.000
15	A	667	ASN	0	-0.017	-0.018	35.699	0.002	0.002	0.000	0.000	0.000	0.000
16	A	668	GLY	0	0.058	0.042	34.907	0.003	0.003	0.000	0.000	0.000	0.000
17	A	669	MET	0	-0.009	0.007	29.902	0.005	0.005	0.000	0.000	0.000	0.000
18	A	670	THR	0	0.033	0.026	29.403	0.000	0.000	0.000	0.000	0.000	0.000
19	A	671	ASN	0	0.026	0.009	28.350	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	672	GLN	0	-0.007	0.000	28.301	0.012	0.012	0.000	0.000	0.000	0.000
21	A	673	ILE	0	0.017	-0.002	24.389	0.007	0.007	0.000	0.000	0.000	0.000
22	A	674	THR	0	-0.004	-0.010	24.031	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	675	GLY	0	0.019	0.009	23.393	0.009	0.009	0.000	0.000	0.000	0.000
24	A	676	VAL	0	-0.071	-0.023	21.538	0.021	0.021	0.000	0.000	0.000	0.000
25	A	677	ILE	0	0.005	-0.003	18.537	0.012	0.012	0.000	0.000	0.000	0.000
26	A	678	SER	0	-0.083	-0.043	18.623	0.020	0.020	0.000	0.000	0.000	0.000
27	A	679	LYS	1	0.950	0.965	19.041	-0.028	-0.028	0.000	0.000	0.000	0.000
28	A	680	PHE	0	-0.023	0.000	15.367	0.019	0.019	0.000	0.000	0.000	0.000
29	A	681	ASP	-1	-0.908	-0.946	12.106	0.617	0.617	0.000	0.000	0.000	0.000
30	A	682	THR	0	-0.068	-0.051	10.631	0.070	0.070	0.000	0.000	0.000	0.000
31	A	683	ASN	0	0.065	0.055	8.523	-0.073	-0.073	0.000	0.000	0.000	0.000
32	A	684	ILE	0	0.030	0.011	11.296	-0.149	-0.149	0.000	0.000	0.000	0.000
33	A	685	ARG	1	0.845	0.924	10.638	0.319	0.319	0.000	0.000	0.000	0.000
34	A	686	THR	0	0.005	-0.006	13.950	0.002	0.002	0.000	0.000	0.000	0.000
35	A	687	ILE	0	0.055	0.023	17.310	-0.008	-0.008	0.000	0.000	0.000	0.000
36	A	688	VAL	0	-0.018	0.003	20.361	0.009	0.009	0.000	0.000	0.000	0.000
37	A	689	LEU	0	0.010	0.002	23.448	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	690	ASN	0	-0.055	-0.038	26.176	0.013	0.013	0.000	0.000	0.000	0.000
39	A	691	ALA	0	0.029	0.022	29.801	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	692	LYS	1	0.944	0.959	32.804	0.107	0.107	0.000	0.000	0.000	0.000
41	A	693	ASP	-1	-0.878	-0.936	35.583	-0.087	-0.087	0.000	0.000	0.000	0.000
42	A	694	GLY	0	0.002	0.016	37.970	0.001	0.001	0.000	0.000	0.000	0.000
43	A	695	ILE	0	-0.016	0.004	32.385	0.002	0.002	0.000	0.000	0.000	0.000
44	A	696	PHE	0	0.019	0.010	26.890	0.000	0.000	0.000	0.000	0.000	0.000
45	A	697	THR	0	-0.076	-0.028	27.327	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	698	CYS	0	0.009	-0.012	23.022	0.003	0.003	0.000	0.000	0.000	0.000
47	A	699	ASN	0	0.038	0.036	20.697	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	700	LEU	0	0.021	0.008	16.322	0.014	0.014	0.000	0.000	0.000	0.000
49	A	701	MET	0	-0.014	0.011	13.623	-0.029	-0.029	0.000	0.000	0.000	0.000
50	A	702	ILE	0	0.006	-0.003	11.704	0.082	0.082	0.000	0.000	0.000	0.000
51	A	703	PHE	0	0.013	0.001	6.016	-0.147	-0.147	0.000	0.000	0.000	0.000
52	A	704	VAL	0	-0.014	-0.023	7.676	0.490	0.490	0.000	0.000	0.000	0.000
53	A	705	LYS	1	1.047	1.024	4.765	-1.393	-1.394	-0.001	-0.013	0.016	0.000
54	A	706	ASN	0	0.038	0.013	4.813	-1.144	-1.167	-0.001	-0.011	0.035	0.000
55	A	707	THR	0	0.070	0.009	7.251	0.154	0.154	0.000	0.000	0.000	0.000
56	A	708	ASP	-1	-0.841	-0.902	10.698	-0.121	-0.121	0.000	0.000	0.000	0.000
57	A	709	LYS	1	0.903	0.956	9.902	-0.070	-0.070	0.000	0.000	0.000	0.000
58	A	710	LEU	0	0.028	0.021	11.482	0.076	0.076	0.000	0.000	0.000	0.000
59	A	711	THR	0	0.016	0.000	13.151	0.053	0.053	0.000	0.000	0.000	0.000
60	A	712	THR	0	-0.039	-0.027	14.682	0.064	0.064	0.000	0.000	0.000	0.000
61	A	713	LEU	0	-0.045	-0.016	12.877	0.043	0.043	0.000	0.000	0.000	0.000
62	A	714	MET	0	-0.015	-0.008	16.445	0.006	0.006	0.000	0.000	0.000	0.000
63	A	715	ASP	-1	-0.859	-0.932	19.290	-0.103	-0.103	0.000	0.000	0.000	0.000
64	A	716	LYS	1	0.867	0.929	19.785	-0.021	-0.021	0.000	0.000	0.000	0.000
65	A	717	LEU	0	0.003	0.001	19.839	0.010	0.010	0.000	0.000	0.000	0.000
66	A	718	ARG	1	0.900	0.949	21.298	0.161	0.161	0.000	0.000	0.000	0.000
67	A	719	LYS	1	0.924	0.965	23.567	0.031	0.031	0.000	0.000	0.000	0.000
68	A	720	VAL	0	-0.036	0.007	25.847	0.012	0.012	0.000	0.000	0.000	0.000
69	A	721	GLN	0	0.010	-0.004	28.444	-0.010	-0.010	0.000	0.000	0.000	0.000
70	A	722	GLY	0	0.107	0.052	32.136	0.003	0.003	0.000	0.000	0.000	0.000
71	A	723	VAL	0	-0.070	-0.030	26.562	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	724	PHE	0	-0.031	-0.019	29.948	0.003	0.003	0.000	0.000	0.000	0.000
73	A	725	THR	0	-0.020	-0.012	27.225	-0.006	-0.006	0.000	0.000	0.000	0.000
74	A	726	VAL	0	0.017	0.000	21.332	0.001	0.001	0.000	0.000	0.000	0.000
75	A	727	GLU	-1	-0.962	-0.964	21.815	-0.227	-0.227	0.000	0.000	0.000	0.000
76	A	728	ARG	1	0.984	0.982	11.771	0.813	0.813	0.000	0.000	0.000	0.000
77	A	729	LEU	0	-0.046	-0.018	17.821	0.017	0.017	0.000	0.000	0.000	0.000
78	A	730	SER	0	-0.032	-0.021	16.794	-0.066	-0.066	0.000	0.000	0.000	0.000
79	A	731	ASN	0	0.023	0.017	15.241	0.021	0.021	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:653:THR)