FMO DATABASE

FMODB ID: 4355N

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	OptAll
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	-509795.914356
FMO2-HF: Nuclear repulsion	478471.616382
FMO2-HF: Total energy	-31324.297974
FMO2-MP2: Total energy	-31414.210832

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.
-3.013	-0.11	0.3	-1.626	-1.576	-0.005

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 : 0.014 / q_NPA : 0.006

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	-0.026	-0.004	2.833	-4.010	-1.203	0.303	-1.599	-1.511	-0.005
4	A	656	LEU	0	-0.014	-0.012	5.176	0.758	0.814	-0.001	-0.003	-0.052	0.000
5	A	657	ALA	0	-0.006	-0.001	8.470	0.004	0.004	0.000	0.000	0.000	0.000
6	A	658	GLY	0	0.061	0.006	11.441	0.091	0.091	0.000	0.000	0.000	0.000
7	A	659	ILE	0	-0.041	-0.019	15.091	-0.006	-0.006	0.000	0.000	0.000	0.000
8	A	660	ARG	1	0.920	0.954	18.058	0.228	0.228	0.000	0.000	0.000	0.000
9	A	661	ILE	0	-0.012	-0.004	21.116	0.005	0.005	0.000	0.000	0.000	0.000
10	A	662	VAL	0	0.032	0.014	24.680	0.000	0.000	0.000	0.000	0.000	0.000
11	A	663	GLY	0	0.067	0.031	28.489	0.003	0.003	0.000	0.000	0.000	0.000
12	A	664	GLU	-1	-0.802	-0.879	31.339	-0.059	-0.059	0.000	0.000	0.000	0.000
13	A	665	ASP	-1	-0.916	-0.966	33.911	-0.071	-0.071	0.000	0.000	0.000	0.000
14	A	666	LYS	1	0.884	0.928	35.070	0.063	0.063	0.000	0.000	0.000	0.000
15	A	667	ASN	0	-0.029	-0.026	35.735	0.002	0.002	0.000	0.000	0.000	0.000
16	A	668	GLY	0	0.065	0.049	34.915	0.004	0.004	0.000	0.000	0.000	0.000
17	A	669	MET	0	-0.027	0.005	30.383	0.004	0.004	0.000	0.000	0.000	0.000
18	A	670	THR	0	0.038	0.024	29.467	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	671	ASN	0	-0.012	0.003	28.521	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	672	GLN	0	-0.008	-0.005	28.293	0.012	0.012	0.000	0.000	0.000	0.000
21	A	673	ILE	0	0.004	-0.004	24.509	0.006	0.006	0.000	0.000	0.000	0.000
22	A	674	THR	0	0.000	-0.011	24.164	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	675	GLY	0	0.021	0.010	23.570	0.009	0.009	0.000	0.000	0.000	0.000
24	A	676	VAL	0	-0.068	-0.034	21.768	0.021	0.021	0.000	0.000	0.000	0.000
25	A	677	ILE	0	0.017	0.006	18.782	0.013	0.013	0.000	0.000	0.000	0.000
26	A	678	SER	0	-0.082	-0.046	18.874	0.019	0.019	0.000	0.000	0.000	0.000
27	A	679	LYS	1	0.925	0.967	19.786	-0.017	-0.017	0.000	0.000	0.000	0.000
28	A	680	PHE	0	-0.020	-0.010	15.233	0.010	0.010	0.000	0.000	0.000	0.000
29	A	681	ASP	-1	-0.825	-0.885	11.998	0.559	0.559	0.000	0.000	0.000	0.000
30	A	682	THR	0	0.003	-0.001	10.118	0.033	0.033	0.000	0.000	0.000	0.000
31	A	683	ASN	0	0.035	0.028	8.293	-0.139	-0.139	0.000	0.000	0.000	0.000
32	A	684	ILE	0	0.027	0.011	10.958	-0.182	-0.182	0.000	0.000	0.000	0.000
33	A	685	ARG	1	0.860	0.929	10.171	0.369	0.369	0.000	0.000	0.000	0.000
34	A	686	THR	0	-0.010	-0.014	13.840	-0.009	-0.009	0.000	0.000	0.000	0.000
35	A	687	ILE	0	0.018	0.009	17.217	-0.010	-0.010	0.000	0.000	0.000	0.000
36	A	688	VAL	0	-0.003	0.005	20.267	0.011	0.011	0.000	0.000	0.000	0.000
37	A	689	LEU	0	0.023	0.012	23.288	-0.008	-0.008	0.000	0.000	0.000	0.000
38	A	690	ASN	0	-0.066	-0.038	26.015	0.009	0.009	0.000	0.000	0.000	0.000
39	A	691	ALA	0	0.044	0.020	29.645	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	692	LYS	1	0.874	0.914	32.823	0.112	0.112	0.000	0.000	0.000	0.000
41	A	693	ASP	-1	-0.833	-0.898	35.972	-0.103	-0.103	0.000	0.000	0.000	0.000
42	A	694	GLY	0	0.031	0.031	38.125	0.002	0.002	0.000	0.000	0.000	0.000
43	A	695	ILE	0	-0.057	-0.022	33.077	0.002	0.002	0.000	0.000	0.000	0.000
44	A	696	PHE	0	0.027	0.007	27.228	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	697	THR	0	-0.048	-0.018	27.682	-0.013	-0.013	0.000	0.000	0.000	0.000
46	A	698	CYS	0	-0.013	-0.008	23.041	0.002	0.002	0.000	0.000	0.000	0.000
47	A	699	ASN	0	0.047	0.041	20.644	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	700	LEU	0	0.022	0.007	16.560	0.021	0.021	0.000	0.000	0.000	0.000
49	A	701	MET	0	-0.005	0.014	13.516	-0.031	-0.031	0.000	0.000	0.000	0.000
50	A	702	ILE	0	0.010	-0.003	11.211	0.088	0.088	0.000	0.000	0.000	0.000
51	A	703	PHE	0	0.003	0.003	6.235	-0.252	-0.252	0.000	0.000	0.000	0.000
52	A	704	VAL	0	0.005	-0.014	7.184	0.514	0.514	0.000	0.000	0.000	0.000
53	A	705	LYS	1	0.894	0.965	4.736	-0.794	-0.752	-0.001	-0.012	-0.028	0.000
54	A	706	ASN	0	0.021	-0.017	4.717	-1.145	-1.147	-0.001	-0.012	0.015	0.000
55	A	707	THR	0	0.079	0.029	7.324	0.253	0.253	0.000	0.000	0.000	0.000
56	A	708	ASP	-1	-0.763	-0.843	10.907	-0.276	-0.276	0.000	0.000	0.000	0.000
57	A	709	LYS	1	0.828	0.894	9.473	-0.211	-0.211	0.000	0.000	0.000	0.000
58	A	710	LEU	0	0.045	0.022	11.246	0.099	0.099	0.000	0.000	0.000	0.000
59	A	711	THR	0	-0.014	-0.026	13.012	0.073	0.073	0.000	0.000	0.000	0.000
60	A	712	THR	0	-0.059	-0.041	14.614	0.072	0.072	0.000	0.000	0.000	0.000
61	A	713	LEU	0	-0.026	-0.002	12.814	0.041	0.041	0.000	0.000	0.000	0.000
62	A	714	MET	0	-0.011	-0.006	16.369	0.015	0.015	0.000	0.000	0.000	0.000
63	A	715	ASP	-1	-0.827	-0.900	19.365	-0.108	-0.108	0.000	0.000	0.000	0.000
64	A	716	LYS	1	0.911	0.957	19.003	0.011	0.011	0.000	0.000	0.000	0.000
65	A	717	LEU	0	0.015	0.011	20.074	0.012	0.012	0.000	0.000	0.000	0.000
66	A	718	ARG	1	0.848	0.904	21.367	0.196	0.196	0.000	0.000	0.000	0.000
67	A	719	LYS	1	0.880	0.949	23.763	0.077	0.077	0.000	0.000	0.000	0.000
68	A	720	VAL	0	-0.023	0.004	25.833	0.015	0.015	0.000	0.000	0.000	0.000
69	A	721	GLN	0	-0.014	-0.023	28.566	-0.009	-0.009	0.000	0.000	0.000	0.000
70	A	722	GLY	0	0.085	0.037	32.251	0.005	0.005	0.000	0.000	0.000	0.000
71	A	723	VAL	0	-0.072	-0.031	26.883	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	724	PHE	0	-0.036	-0.021	30.133	0.005	0.005	0.000	0.000	0.000	0.000
73	A	725	THR	0	-0.032	-0.025	26.788	0.002	0.002	0.000	0.000	0.000	0.000
74	A	726	VAL	0	0.001	-0.009	21.442	0.003	0.003	0.000	0.000	0.000	0.000
75	A	727	GLU	-1	-0.889	-0.925	22.075	-0.237	-0.237	0.000	0.000	0.000	0.000
76	A	728	ARG	1	0.951	0.962	11.788	0.883	0.883	0.000	0.000	0.000	0.000
77	A	729	LEU	0	-0.034	-0.006	17.414	0.014	0.014	0.000	0.000	0.000	0.000
78	A	730	SER	0	-0.030	-0.020	16.394	-0.067	-0.067	0.000	0.000	0.000	0.000
79	A	731	ASN	0	0.029	0.022	15.421	0.022	0.022	0.000	0.000	0.000	0.000

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