FMO DATABASE

FMODB ID: K3JJ3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-509456.148935
FMO2-HF: Nuclear repulsion	478132.033471
FMO2-HF: Total energy	-31324.115464
FMO2-MP2: Total energy	-31414.003081

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.
-4.341	-1.381	0.24	-1.69	-1.509	-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 : 0.006 / q_NPA : 0.000

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	-0.005	2.889	-4.529	-1.553	0.242	-1.666	-1.552	-0.003
4	A	656	LEU	0	-0.020	-0.013	5.554	0.792	0.792	0.000	0.000	0.000	0.000
5	A	657	ALA	0	-0.023	-0.009	8.830	-0.033	-0.033	0.000	0.000	0.000	0.000
6	A	658	GLY	0	0.069	0.015	11.915	0.093	0.093	0.000	0.000	0.000	0.000
7	A	659	ILE	0	-0.030	-0.013	15.540	-0.001	-0.001	0.000	0.000	0.000	0.000
8	A	660	ARG	1	0.939	0.972	18.368	0.206	0.206	0.000	0.000	0.000	0.000
9	A	661	ILE	0	-0.017	-0.009	20.991	0.008	0.008	0.000	0.000	0.000	0.000
10	A	662	VAL	0	0.021	0.008	24.681	-0.001	-0.001	0.000	0.000	0.000	0.000
11	A	663	GLY	0	0.037	0.013	28.413	0.004	0.004	0.000	0.000	0.000	0.000
12	A	664	GLU	-1	-0.817	-0.891	31.039	-0.045	-0.045	0.000	0.000	0.000	0.000
13	A	665	ASP	-1	-0.940	-0.984	33.658	-0.056	-0.056	0.000	0.000	0.000	0.000
14	A	666	LYS	1	0.869	0.913	35.096	0.047	0.047	0.000	0.000	0.000	0.000
15	A	667	ASN	0	-0.018	-0.016	35.710	0.002	0.002	0.000	0.000	0.000	0.000
16	A	668	GLY	0	0.067	0.046	34.916	0.004	0.004	0.000	0.000	0.000	0.000
17	A	669	MET	0	0.000	0.020	30.208	0.006	0.006	0.000	0.000	0.000	0.000
18	A	670	THR	0	0.045	0.032	29.412	0.001	0.001	0.000	0.000	0.000	0.000
19	A	671	ASN	0	0.001	0.005	28.360	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	672	GLN	0	-0.016	-0.010	28.289	0.013	0.013	0.000	0.000	0.000	0.000
21	A	673	ILE	0	0.003	-0.011	24.564	0.008	0.008	0.000	0.000	0.000	0.000
22	A	674	THR	0	-0.005	-0.012	24.040	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	675	GLY	0	0.018	0.010	23.380	0.010	0.010	0.000	0.000	0.000	0.000
24	A	676	VAL	0	-0.064	-0.028	21.677	0.022	0.022	0.000	0.000	0.000	0.000
25	A	677	ILE	0	0.012	0.004	18.574	0.015	0.015	0.000	0.000	0.000	0.000
26	A	678	SER	0	-0.079	-0.037	18.610	0.022	0.022	0.000	0.000	0.000	0.000
27	A	679	LYS	1	0.941	0.963	19.026	-0.038	-0.038	0.000	0.000	0.000	0.000
28	A	680	PHE	0	-0.022	-0.003	15.400	0.024	0.024	0.000	0.000	0.000	0.000
29	A	681	ASP	-1	-0.828	-0.897	12.158	0.653	0.653	0.000	0.000	0.000	0.000
30	A	682	THR	0	-0.017	-0.011	10.360	0.053	0.053	0.000	0.000	0.000	0.000
31	A	683	ASN	0	0.036	0.035	8.493	-0.142	-0.142	0.000	0.000	0.000	0.000
32	A	684	ILE	0	0.037	0.016	11.284	-0.141	-0.141	0.000	0.000	0.000	0.000
33	A	685	ARG	1	0.857	0.927	10.222	0.323	0.323	0.000	0.000	0.000	0.000
34	A	686	THR	0	-0.005	-0.013	13.959	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	687	ILE	0	0.053	0.021	17.320	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	688	VAL	0	-0.017	0.007	20.372	0.009	0.009	0.000	0.000	0.000	0.000
37	A	689	LEU	0	0.010	-0.002	23.459	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	690	ASN	0	-0.071	-0.038	26.187	0.009	0.009	0.000	0.000	0.000	0.000
39	A	691	ALA	0	0.043	0.025	29.813	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	692	LYS	1	0.909	0.951	32.816	0.102	0.102	0.000	0.000	0.000	0.000
41	A	693	ASP	-1	-0.852	-0.935	35.596	-0.088	-0.088	0.000	0.000	0.000	0.000
42	A	694	GLY	0	0.009	0.021	37.984	0.001	0.001	0.000	0.000	0.000	0.000
43	A	695	ILE	0	-0.021	0.000	32.819	0.003	0.003	0.000	0.000	0.000	0.000
44	A	696	PHE	0	0.020	0.013	27.076	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	697	THR	0	-0.069	-0.028	27.440	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	698	CYS	0	0.008	-0.007	23.101	0.003	0.003	0.000	0.000	0.000	0.000
47	A	699	ASN	0	0.025	0.032	20.807	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	700	LEU	0	0.024	0.010	16.377	0.014	0.014	0.000	0.000	0.000	0.000
49	A	701	MET	0	-0.011	0.013	13.608	-0.030	-0.030	0.000	0.000	0.000	0.000
50	A	702	ILE	0	0.024	0.004	12.023	0.075	0.075	0.000	0.000	0.000	0.000
51	A	703	PHE	0	-0.007	-0.006	6.730	-0.219	-0.219	0.000	0.000	0.000	0.000
52	A	704	VAL	0	-0.010	-0.019	7.685	0.484	0.484	0.000	0.000	0.000	0.000
53	A	705	LYS	1	1.041	1.031	4.771	-1.433	-1.430	-0.001	-0.013	0.011	0.000
54	A	706	ASN	0	-0.002	-0.027	4.779	-1.162	-1.181	-0.001	-0.011	0.032	0.000
55	A	707	THR	0	0.062	0.013	7.212	0.165	0.165	0.000	0.000	0.000	0.000
56	A	708	ASP	-1	-0.806	-0.884	10.648	-0.105	-0.105	0.000	0.000	0.000	0.000
57	A	709	LYS	1	0.804	0.894	9.798	-0.327	-0.327	0.000	0.000	0.000	0.000
58	A	710	LEU	0	0.038	0.027	11.425	0.072	0.072	0.000	0.000	0.000	0.000
59	A	711	THR	0	-0.002	-0.016	13.101	0.050	0.050	0.000	0.000	0.000	0.000
60	A	712	THR	0	-0.048	-0.031	14.678	0.061	0.061	0.000	0.000	0.000	0.000
61	A	713	LEU	0	-0.028	-0.004	12.925	0.035	0.035	0.000	0.000	0.000	0.000
62	A	714	MET	0	-0.014	-0.009	16.273	0.002	0.002	0.000	0.000	0.000	0.000
63	A	715	ASP	-1	-0.815	-0.899	19.286	-0.067	-0.067	0.000	0.000	0.000	0.000
64	A	716	LYS	1	0.890	0.943	19.268	-0.040	-0.040	0.000	0.000	0.000	0.000
65	A	717	LEU	0	0.000	0.005	19.869	0.008	0.008	0.000	0.000	0.000	0.000
66	A	718	ARG	1	0.893	0.938	21.071	0.146	0.146	0.000	0.000	0.000	0.000
67	A	719	LYS	1	0.864	0.934	23.276	0.031	0.031	0.000	0.000	0.000	0.000
68	A	720	VAL	0	-0.031	0.006	25.795	0.012	0.012	0.000	0.000	0.000	0.000
69	A	721	GLN	0	0.000	-0.005	28.453	-0.010	-0.010	0.000	0.000	0.000	0.000
70	A	722	GLY	0	0.091	0.039	32.143	0.003	0.003	0.000	0.000	0.000	0.000
71	A	723	VAL	0	-0.059	-0.028	26.523	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	724	PHE	0	-0.031	-0.017	29.956	0.004	0.004	0.000	0.000	0.000	0.000
73	A	725	THR	0	-0.001	-0.005	27.119	0.003	0.003	0.000	0.000	0.000	0.000
74	A	726	VAL	0	0.001	-0.005	21.271	0.000	0.000	0.000	0.000	0.000	0.000
75	A	727	GLU	-1	-0.940	-0.961	21.755	-0.215	-0.215	0.000	0.000	0.000	0.000
76	A	728	ARG	1	0.974	0.977	11.467	0.815	0.815	0.000	0.000	0.000	0.000
77	A	729	LEU	0	-0.045	-0.017	17.837	0.017	0.017	0.000	0.000	0.000	0.000
78	A	730	SER	0	-0.041	-0.026	16.809	-0.067	-0.067	0.000	0.000	0.000	0.000
79	A	731	ASN	0	0.031	0.021	15.298	0.023	0.023	0.000	0.000	0.000	0.000

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