FMO DATABASE

FMODB ID: QYG2Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-775636.381957
FMO2-HF: Nuclear repulsion	734474.410394
FMO2-HF: Total energy	-41161.971564
FMO2-MP2: Total energy	-41281.634751

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.
-0.106	1.075	-0.018	-0.546	-0.618	0.001

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 : 0.011 / q_NPA : -0.008

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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	D	654	GLY	0	0.017	0.017	3.792	0.497	1.678	-0.018	-0.546	-0.618	0.001
4	D	655	SER	0	-0.032	-0.035	6.074	0.625	0.625	0.000	0.000	0.000	0.000
5	D	656	ASP	-1	-0.922	-0.938	6.970	-1.893	-1.893	0.000	0.000	0.000	0.000
6	D	657	TYR	0	-0.012	-0.014	10.083	0.126	0.126	0.000	0.000	0.000	0.000
7	D	658	ILE	0	-0.028	-0.026	11.784	-0.023	-0.023	0.000	0.000	0.000	0.000
8	D	659	ILE	0	-0.011	-0.015	15.511	0.047	0.047	0.000	0.000	0.000	0.000
9	D	660	LYS	1	0.931	0.999	18.766	0.240	0.240	0.000	0.000	0.000	0.000
10	D	661	GLU	-1	-0.843	-0.943	21.176	-0.159	-0.159	0.000	0.000	0.000	0.000
11	D	662	LYS	1	0.765	0.893	23.437	0.178	0.178	0.000	0.000	0.000	0.000
12	D	663	THR	0	0.053	0.015	26.801	0.006	0.006	0.000	0.000	0.000	0.000
13	D	664	VAL	0	-0.051	-0.022	29.705	-0.001	-0.001	0.000	0.000	0.000	0.000
14	D	665	LEU	0	0.010	0.000	32.397	0.003	0.003	0.000	0.000	0.000	0.000
15	D	666	LEU	0	-0.030	-0.014	33.352	0.001	0.001	0.000	0.000	0.000	0.000
16	D	667	GLN	0	0.026	-0.008	37.456	0.004	0.004	0.000	0.000	0.000	0.000
17	D	668	LYS	1	0.765	0.916	40.134	0.043	0.043	0.000	0.000	0.000	0.000
18	D	669	LYS	1	0.938	0.962	42.335	0.042	0.042	0.000	0.000	0.000	0.000
19	D	670	ASP	-1	-0.830	-0.918	45.151	-0.037	-0.037	0.000	0.000	0.000	0.000
20	D	671	SER	0	-0.068	-0.037	46.072	0.001	0.001	0.000	0.000	0.000	0.000
21	D	672	GLU	-1	-0.843	-0.911	41.189	-0.046	-0.046	0.000	0.000	0.000	0.000
22	D	673	GLY	0	0.038	0.012	40.656	0.000	0.000	0.000	0.000	0.000	0.000
23	D	674	PHE	0	-0.012	-0.025	36.377	-0.001	-0.001	0.000	0.000	0.000	0.000
24	D	675	GLY	0	0.029	0.044	35.480	-0.004	-0.004	0.000	0.000	0.000	0.000
25	D	676	PHE	0	0.019	0.001	32.063	-0.005	-0.005	0.000	0.000	0.000	0.000
26	D	677	VAL	0	-0.030	-0.006	32.491	0.004	0.004	0.000	0.000	0.000	0.000
27	D	678	LEU	0	-0.017	-0.012	32.003	-0.005	-0.005	0.000	0.000	0.000	0.000
28	D	679	ARG	1	0.854	0.906	30.473	0.058	0.058	0.000	0.000	0.000	0.000
29	D	680	GLY	0	0.101	0.037	31.597	-0.008	-0.008	0.000	0.000	0.000	0.000
30	D	681	ALA	0	-0.004	0.035	33.109	0.007	0.007	0.000	0.000	0.000	0.000
31	D	682	LYS	1	0.939	0.961	35.307	0.035	0.035	0.000	0.000	0.000	0.000
32	D	683	ALA	0	0.124	0.047	38.138	-0.002	-0.002	0.000	0.000	0.000	0.000
33	D	684	GLN	0	-0.077	-0.003	40.433	0.004	0.004	0.000	0.000	0.000	0.000
34	D	685	THR	0	0.001	-0.020	43.348	0.000	0.000	0.000	0.000	0.000	0.000
35	D	686	PRO	0	-0.055	-0.013	38.632	0.002	0.002	0.000	0.000	0.000	0.000
36	D	687	ILE	0	0.034	0.013	39.332	0.001	0.001	0.000	0.000	0.000	0.000
37	D	688	GLU	-1	-0.930	-0.976	34.792	-0.062	-0.062	0.000	0.000	0.000	0.000
38	D	689	GLU	-1	-0.911	-0.944	30.873	-0.068	-0.068	0.000	0.000	0.000	0.000
39	D	690	PHE	0	-0.036	-0.035	32.636	-0.004	-0.004	0.000	0.000	0.000	0.000
40	D	691	THR	0	0.038	0.019	28.101	0.002	0.002	0.000	0.000	0.000	0.000
41	D	692	PRO	0	-0.002	0.029	27.627	-0.006	-0.006	0.000	0.000	0.000	0.000
42	D	693	THR	0	0.003	-0.024	23.386	-0.012	-0.012	0.000	0.000	0.000	0.000
43	D	694	PRO	0	-0.001	0.001	19.591	0.004	0.004	0.000	0.000	0.000	0.000
44	D	695	ALA	0	-0.056	-0.028	19.677	-0.027	-0.027	0.000	0.000	0.000	0.000
45	D	696	PHE	0	-0.018	-0.014	21.448	-0.002	-0.002	0.000	0.000	0.000	0.000
46	D	697	PRO	0	-0.032	-0.009	22.934	0.012	0.012	0.000	0.000	0.000	0.000
47	D	698	ALA	0	0.017	0.015	25.744	0.007	0.007	0.000	0.000	0.000	0.000
48	D	699	LEU	0	-0.006	0.008	29.025	-0.001	-0.001	0.000	0.000	0.000	0.000
49	D	700	GLN	0	-0.023	-0.023	31.370	0.007	0.007	0.000	0.000	0.000	0.000
50	D	701	TYR	0	0.002	-0.021	26.950	-0.009	-0.009	0.000	0.000	0.000	0.000
51	D	702	LEU	0	-0.013	0.010	27.701	0.012	0.012	0.000	0.000	0.000	0.000
52	D	703	GLU	-1	-0.814	-0.871	27.275	-0.066	-0.066	0.000	0.000	0.000	0.000
53	D	704	SER	0	0.018	-0.004	28.026	0.001	0.001	0.000	0.000	0.000	0.000
54	D	705	VAL	0	-0.032	-0.005	28.417	-0.002	-0.002	0.000	0.000	0.000	0.000
55	D	706	ASP	-1	-0.882	-0.939	29.929	-0.050	-0.050	0.000	0.000	0.000	0.000
56	D	707	GLU	-1	-0.921	-0.965	29.175	-0.058	-0.058	0.000	0.000	0.000	0.000
57	D	708	GLY	0	0.007	0.009	31.096	0.005	0.005	0.000	0.000	0.000	0.000
58	D	709	GLY	0	-0.004	-0.009	33.604	0.003	0.003	0.000	0.000	0.000	0.000
59	D	710	VAL	0	0.001	-0.029	33.837	-0.005	-0.005	0.000	0.000	0.000	0.000
60	D	711	ALA	0	0.010	-0.001	31.721	-0.004	-0.004	0.000	0.000	0.000	0.000
61	D	712	TRP	0	0.084	0.054	25.727	-0.011	-0.011	0.000	0.000	0.000	0.000
62	D	713	ARG	1	0.818	0.924	29.539	0.051	0.051	0.000	0.000	0.000	0.000
63	D	714	ALA	0	0.037	0.014	30.885	0.001	0.001	0.000	0.000	0.000	0.000
64	D	715	GLY	0	-0.045	-0.011	26.779	-0.007	-0.007	0.000	0.000	0.000	0.000
65	D	716	LEU	0	-0.006	-0.006	25.890	-0.010	-0.010	0.000	0.000	0.000	0.000
66	D	717	ARG	1	0.839	0.913	23.186	0.119	0.119	0.000	0.000	0.000	0.000
67	D	718	MET	0	0.013	0.006	23.041	0.001	0.001	0.000	0.000	0.000	0.000
68	D	719	GLY	0	-0.001	-0.005	22.706	-0.014	-0.014	0.000	0.000	0.000	0.000
69	D	720	ASP	-1	-0.768	-0.866	23.772	-0.175	-0.175	0.000	0.000	0.000	0.000
70	D	721	PHE	0	0.034	0.010	22.319	0.014	0.014	0.000	0.000	0.000	0.000
71	D	722	LEU	0	-0.020	-0.028	26.780	-0.004	-0.004	0.000	0.000	0.000	0.000
72	D	723	ILE	0	0.032	0.020	26.482	0.004	0.004	0.000	0.000	0.000	0.000
73	D	724	GLU	-1	-0.851	-0.931	30.838	-0.101	-0.101	0.000	0.000	0.000	0.000
74	D	725	VAL	0	-0.010	-0.003	34.223	-0.001	-0.001	0.000	0.000	0.000	0.000
75	D	726	ASN	0	-0.019	-0.009	36.983	0.004	0.004	0.000	0.000	0.000	0.000
76	D	727	GLY	0	0.038	0.007	38.576	-0.002	-0.002	0.000	0.000	0.000	0.000
77	D	728	GLN	0	-0.015	-0.014	38.026	-0.003	-0.003	0.000	0.000	0.000	0.000
78	D	729	ASN	0	-0.005	-0.019	32.466	0.000	0.000	0.000	0.000	0.000	0.000
79	D	730	VAL	0	-0.034	-0.031	33.795	0.005	0.005	0.000	0.000	0.000	0.000
80	D	731	VAL	0	0.027	0.037	30.190	0.002	0.002	0.000	0.000	0.000	0.000
81	D	732	LYS	1	0.963	0.981	32.409	0.078	0.078	0.000	0.000	0.000	0.000
82	D	733	VAL	0	-0.023	0.001	34.667	0.007	0.007	0.000	0.000	0.000	0.000
83	D	734	GLY	0	0.064	0.020	36.415	-0.002	-0.002	0.000	0.000	0.000	0.000
84	D	735	HIS	0	0.013	-0.005	35.640	0.005	0.005	0.000	0.000	0.000	0.000
85	D	736	ARG	1	0.918	0.937	37.985	0.040	0.040	0.000	0.000	0.000	0.000
86	D	737	GLN	0	-0.052	-0.005	40.567	0.004	0.004	0.000	0.000	0.000	0.000
87	D	738	VAL	0	0.067	0.016	35.496	0.001	0.001	0.000	0.000	0.000	0.000
88	D	739	VAL	0	-0.014	-0.012	38.704	0.000	0.000	0.000	0.000	0.000	0.000
89	D	740	ASN	0	-0.016	-0.016	40.327	0.001	0.001	0.000	0.000	0.000	0.000
90	D	741	MET	0	-0.026	0.005	40.535	0.000	0.000	0.000	0.000	0.000	0.000
91	D	742	ILE	0	0.014	-0.003	36.279	0.002	0.002	0.000	0.000	0.000	0.000
92	D	743	ARG	1	0.909	0.967	40.543	0.043	0.043	0.000	0.000	0.000	0.000
93	D	744	GLN	0	0.051	0.032	43.825	0.000	0.000	0.000	0.000	0.000	0.000
94	D	745	GLY	0	-0.029	0.018	43.547	0.002	0.002	0.000	0.000	0.000	0.000
95	D	746	GLY	0	0.073	0.023	44.097	-0.001	-0.001	0.000	0.000	0.000	0.000
96	D	747	ASN	0	-0.062	-0.045	43.975	-0.002	-0.002	0.000	0.000	0.000	0.000
97	D	748	THR	0	-0.098	-0.045	41.894	-0.001	-0.001	0.000	0.000	0.000	0.000
98	D	749	LEU	0	0.014	-0.003	36.586	0.000	0.000	0.000	0.000	0.000	0.000
99	D	750	MET	0	-0.019	0.017	35.076	-0.002	-0.002	0.000	0.000	0.000	0.000
100	D	751	VAL	0	0.021	-0.001	32.219	0.001	0.001	0.000	0.000	0.000	0.000
101	D	752	LYS	1	0.895	0.963	29.122	0.131	0.131	0.000	0.000	0.000	0.000
102	D	753	VAL	0	-0.014	-0.003	26.354	0.004	0.004	0.000	0.000	0.000	0.000
103	D	754	VAL	0	0.006	0.007	22.988	-0.007	-0.007	0.000	0.000	0.000	0.000
104	D	755	MET	0	-0.010	0.005	18.916	0.008	0.008	0.000	0.000	0.000	0.000
105	D	756	VAL	0	0.028	-0.007	16.844	-0.020	-0.020	0.000	0.000	0.000	0.000
106	D	757	THR	0	-0.032	-0.007	12.491	0.047	0.047	0.000	0.000	0.000	0.000
107	D	758	ARG	1	1.040	1.028	9.850	0.265	0.265	0.000	0.000	0.000	0.000

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