FMO DATABASE

FMODB ID: K9L43

Calculation Name: 3L4F-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3L4F

Chain ID: D

ChEMBL ID:

UniProt ID: O55043

Base Structure: X-ray

Registration Date: 2023-09-19

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	107
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-776045.939843
FMO2-HF: Nuclear repulsion	734883.120415
FMO2-HF: Total energy	-41162.819428
FMO2-MP2: Total energy	-41282.34954

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(D:652:GLY)

Summations of interaction energy for fragment #1(D:652:GLY)

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.
0.536	1.535	-0.006	-0.444	-0.549	0

Interaction energy analysis for fragmet #1(D:652:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / q_NPA : -0.003

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

Sort

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	D	654	GLY	0	0.029	0.024	3.863	0.757	1.756	-0.006	-0.444	-0.549
4	D	655	SER	0	-0.058	-0.056	5.601	0.608	0.608	0.000	0.000	0.000
5	D	656	ASP	-1	-0.893	-0.913	6.620	-1.644	-1.644	0.000	0.000	0.000
6	D	657	TYR	0	0.003	-0.015	9.445	0.068	0.068	0.000	0.000	0.000
7	D	658	ILE	0	-0.056	-0.023	11.083	0.026	0.026	0.000	0.000	0.000
8	D	659	ILE	0	0.007	0.003	14.682	0.045	0.045	0.000	0.000	0.000
9	D	660	LYS	1	0.915	0.968	18.067	0.239	0.239	0.000	0.000	0.000
10	D	661	GLU	-1	-0.855	-0.935	20.456	-0.133	-0.133	0.000	0.000	0.000
11	D	662	LYS	1	0.742	0.851	23.511	0.181	0.181	0.000	0.000	0.000
12	D	663	THR	0	0.033	0.009	26.401	0.007	0.007	0.000	0.000	0.000
13	D	664	VAL	0	-0.020	-0.004	29.614	-0.002	-0.002	0.000	0.000	0.000
14	D	665	LEU	0	0.010	0.000	32.341	0.004	0.004	0.000	0.000	0.000
15	D	666	LEU	0	-0.017	0.000	33.212	0.000	0.000	0.000	0.000	0.000
16	D	667	GLN	0	0.008	-0.013	37.133	0.006	0.006	0.000	0.000	0.000
17	D	668	LYS	1	0.799	0.931	40.236	0.050	0.050	0.000	0.000	0.000
18	D	669	LYS	1	0.928	0.953	42.391	0.055	0.055	0.000	0.000	0.000
19	D	670	ASP	-1	-0.832	-0.929	45.326	-0.045	-0.045	0.000	0.000	0.000
20	D	671	SER	0	-0.040	-0.015	46.225	0.000	0.000	0.000	0.000	0.000
21	D	672	GLU	-1	-0.822	-0.885	40.642	-0.062	-0.062	0.000	0.000	0.000
22	D	673	GLY	0	0.041	0.011	41.108	0.002	0.002	0.000	0.000	0.000
23	D	674	PHE	0	0.001	-0.019	36.568	-0.002	-0.002	0.000	0.000	0.000
24	D	675	GLY	0	0.016	0.031	35.620	-0.005	-0.005	0.000	0.000	0.000
25	D	676	PHE	0	0.003	-0.010	32.228	-0.007	-0.007	0.000	0.000	0.000
26	D	677	VAL	0	-0.005	0.012	32.628	0.006	0.006	0.000	0.000	0.000
27	D	678	LEU	0	-0.014	-0.006	31.960	-0.006	-0.006	0.000	0.000	0.000
28	D	679	ARG	1	0.857	0.912	31.020	0.072	0.072	0.000	0.000	0.000
29	D	680	GLY	0	0.078	0.023	31.577	-0.008	-0.008	0.000	0.000	0.000
30	D	681	ALA	0	0.010	0.043	32.850	0.006	0.006	0.000	0.000	0.000
31	D	682	LYS	1	0.932	0.955	34.845	0.039	0.039	0.000	0.000	0.000
32	D	683	ALA	0	0.118	0.063	38.211	0.001	0.001	0.000	0.000	0.000
33	D	684	GLN	0	-0.053	-0.014	40.205	0.002	0.002	0.000	0.000	0.000
34	D	685	THR	0	0.010	-0.009	43.440	0.001	0.001	0.000	0.000	0.000
35	D	686	PRO	0	-0.041	-0.007	38.807	0.001	0.001	0.000	0.000	0.000
36	D	687	ILE	0	0.014	-0.006	39.276	0.002	0.002	0.000	0.000	0.000
37	D	688	GLU	-1	-0.885	-0.946	34.528	-0.054	-0.054	0.000	0.000	0.000
38	D	689	GLU	-1	-0.898	-0.953	30.530	-0.050	-0.050	0.000	0.000	0.000
39	D	690	PHE	0	-0.057	-0.024	31.548	-0.007	-0.007	0.000	0.000	0.000
40	D	691	THR	0	0.001	-0.008	28.214	0.002	0.002	0.000	0.000	0.000
41	D	692	PRO	0	-0.008	0.013	27.548	-0.005	-0.005	0.000	0.000	0.000
42	D	693	THR	0	0.016	-0.005	23.158	-0.011	-0.011	0.000	0.000	0.000
43	D	694	PRO	0	-0.009	-0.030	19.366	-0.001	-0.001	0.000	0.000	0.000
44	D	695	ALA	0	-0.004	0.018	19.593	-0.026	-0.026	0.000	0.000	0.000
45	D	696	PHE	0	-0.031	-0.021	20.832	0.001	0.001	0.000	0.000	0.000
46	D	697	PRO	0	-0.009	0.002	22.446	0.012	0.012	0.000	0.000	0.000
47	D	698	ALA	0	0.003	0.011	25.217	0.008	0.008	0.000	0.000	0.000
48	D	699	LEU	0	-0.023	-0.003	28.527	-0.002	-0.002	0.000	0.000	0.000
49	D	700	GLN	0	-0.025	-0.025	30.597	0.006	0.006	0.000	0.000	0.000
50	D	701	TYR	0	0.006	-0.016	26.651	-0.008	-0.008	0.000	0.000	0.000
51	D	702	LEU	0	-0.019	-0.006	27.796	0.012	0.012	0.000	0.000	0.000
52	D	703	GLU	-1	-0.800	-0.859	27.393	-0.088	-0.088	0.000	0.000	0.000
53	D	704	SER	0	0.017	0.005	28.310	-0.003	-0.003	0.000	0.000	0.000
54	D	705	VAL	0	-0.041	-0.026	28.516	0.001	0.001	0.000	0.000	0.000
55	D	706	ASP	-1	-0.874	-0.929	30.016	-0.077	-0.077	0.000	0.000	0.000
56	D	707	GLU	-1	-0.889	-0.952	29.065	-0.104	-0.104	0.000	0.000	0.000
57	D	708	GLY	0	0.003	0.009	31.702	0.006	0.006	0.000	0.000	0.000
58	D	709	GLY	0	0.012	-0.003	34.145	0.005	0.005	0.000	0.000	0.000
59	D	710	VAL	0	-0.032	-0.028	34.216	-0.005	-0.005	0.000	0.000	0.000
60	D	711	ALA	0	0.024	0.008	31.572	-0.004	-0.004	0.000	0.000	0.000
61	D	712	TRP	0	0.039	0.023	26.092	-0.011	-0.011	0.000	0.000	0.000
62	D	713	ARG	1	0.799	0.886	29.917	0.066	0.066	0.000	0.000	0.000
63	D	714	ALA	0	0.003	0.019	31.279	0.001	0.001	0.000	0.000	0.000
64	D	715	GLY	0	-0.025	-0.012	27.080	-0.006	-0.006	0.000	0.000	0.000
65	D	716	LEU	0	-0.020	0.000	25.783	-0.015	-0.015	0.000	0.000	0.000
66	D	717	ARG	1	0.817	0.899	23.571	0.148	0.148	0.000	0.000	0.000
67	D	718	MET	0	0.012	0.008	23.917	0.000	0.000	0.000	0.000	0.000
68	D	719	GLY	0	0.016	0.006	22.669	-0.017	-0.017	0.000	0.000	0.000
69	D	720	ASP	-1	-0.763	-0.866	23.418	-0.185	-0.185	0.000	0.000	0.000
70	D	721	PHE	0	0.024	0.014	22.149	0.015	0.015	0.000	0.000	0.000
71	D	722	LEU	0	-0.015	-0.024	26.408	-0.003	-0.003	0.000	0.000	0.000
72	D	723	ILE	0	0.007	0.007	26.013	0.004	0.004	0.000	0.000	0.000
73	D	724	GLU	-1	-0.794	-0.905	30.446	-0.093	-0.093	0.000	0.000	0.000
74	D	725	VAL	0	-0.010	-0.004	33.676	-0.003	-0.003	0.000	0.000	0.000
75	D	726	ASN	0	0.005	-0.015	36.549	0.003	0.003	0.000	0.000	0.000
76	D	727	GLY	0	-0.002	0.002	38.054	0.001	0.001	0.000	0.000	0.000
77	D	728	GLN	0	-0.013	0.004	38.320	0.000	0.000	0.000	0.000	0.000
78	D	729	ASN	0	0.000	-0.017	32.103	0.000	0.000	0.000	0.000	0.000
79	D	730	VAL	0	-0.041	-0.046	32.965	0.006	0.006	0.000	0.000	0.000
80	D	731	VAL	0	0.011	0.029	29.547	0.002	0.002	0.000	0.000	0.000
81	D	732	LYS	1	0.973	0.991	31.766	0.064	0.064	0.000	0.000	0.000
82	D	733	VAL	0	-0.006	0.008	34.373	0.007	0.007	0.000	0.000	0.000
83	D	734	GLY	0	0.045	0.016	35.802	-0.003	-0.003	0.000	0.000	0.000
84	D	735	HIS	0	-0.026	-0.023	35.334	0.005	0.005	0.000	0.000	0.000
85	D	736	ARG	1	0.892	0.925	37.748	0.041	0.041	0.000	0.000	0.000
86	D	737	GLN	0	0.029	0.031	40.740	0.003	0.003	0.000	0.000	0.000
87	D	738	VAL	0	0.056	0.025	35.147	0.000	0.000	0.000	0.000	0.000
88	D	739	VAL	0	0.016	0.005	38.506	-0.001	-0.001	0.000	0.000	0.000
89	D	740	ASN	0	-0.057	-0.032	40.240	0.001	0.001	0.000	0.000	0.000
90	D	741	MET	0	-0.019	-0.004	39.857	0.000	0.000	0.000	0.000	0.000
91	D	742	ILE	0	-0.009	-0.005	35.983	0.000	0.000	0.000	0.000	0.000
92	D	743	ARG	1	0.916	0.952	40.302	0.049	0.049	0.000	0.000	0.000
93	D	744	GLN	0	-0.011	0.011	43.783	0.001	0.001	0.000	0.000	0.000
94	D	745	GLY	0	0.031	0.034	42.984	0.001	0.001	0.000	0.000	0.000
95	D	746	GLY	0	0.015	0.004	44.042	0.000	0.000	0.000	0.000	0.000
96	D	747	ASN	0	-0.035	-0.037	44.280	-0.002	-0.002	0.000	0.000	0.000
97	D	748	THR	0	-0.073	-0.039	41.726	-0.002	-0.002	0.000	0.000	0.000
98	D	749	LEU	0	0.022	-0.001	36.374	0.001	0.001	0.000	0.000	0.000
99	D	750	MET	0	-0.009	0.026	34.558	-0.004	-0.004	0.000	0.000	0.000
100	D	751	VAL	0	-0.005	-0.015	32.014	0.003	0.003	0.000	0.000	0.000
101	D	752	LYS	1	0.845	0.931	29.041	0.114	0.114	0.000	0.000	0.000
102	D	753	VAL	0	-0.011	0.001	25.933	0.006	0.006	0.000	0.000	0.000
103	D	754	VAL	0	0.023	0.019	22.213	-0.006	-0.006	0.000	0.000	0.000
104	D	755	MET	0	-0.001	0.017	19.207	0.007	0.007	0.000	0.000	0.000
105	D	756	VAL	0	0.039	0.002	16.785	-0.013	-0.013	0.000	0.000	0.000
106	D	757	THR	0	-0.019	-0.002	12.892	0.026	0.026	0.000	0.000	0.000
107	D	758	ARG	1	1.026	1.019	9.822	0.453	0.453	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:652:GLY)