FMO DATABASE

FMODB ID: R9JQ8

Calculation Name: 3B5N-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B5N

Chain ID: D

ChEMBL ID:

UniProt ID: P40357

Base Structure: X-ray

Registration Date: 2023-09-20

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	64
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-271147.64046
FMO2-HF: Nuclear repulsion	244827.568901
FMO2-HF: Total energy	-26320.071559
FMO2-MP2: Total energy	-26394.967975

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:587:GLY)

Summations of interaction energy for fragment #1(D:587: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.
-6.208	-0.923	3.093	-4.622	-3.756	-0.031

Interaction energy analysis for fragmet #1(D:587:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.047 / q_NPA : 0.030

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	D	589	GLU	-1	-0.845	-0.918	2.526	-6.573	-1.288	3.093	-4.622	-3.756	-0.031
4	D	590	MET	0	0.015	0.008	5.613	0.727	0.727	0.000	0.000	0.000	0.000
5	D	591	GLU	-1	-0.890	-0.941	7.107	-1.520	-1.520	0.000	0.000	0.000	0.000
6	D	592	LEU	0	-0.010	-0.010	6.190	0.480	0.480	0.000	0.000	0.000	0.000
7	D	593	GLU	-1	-0.911	-0.946	9.533	-0.235	-0.235	0.000	0.000	0.000	0.000
8	D	594	ILE	0	-0.007	-0.007	11.315	0.191	0.191	0.000	0.000	0.000	0.000
9	D	595	ASP	-1	-0.843	-0.906	12.665	-0.663	-0.663	0.000	0.000	0.000	0.000
10	D	596	ARG	1	0.748	0.818	13.029	0.787	0.787	0.000	0.000	0.000	0.000
11	D	597	ASN	0	-0.039	-0.026	15.047	0.147	0.147	0.000	0.000	0.000	0.000
12	D	598	LEU	0	-0.010	-0.005	16.759	0.083	0.083	0.000	0.000	0.000	0.000
13	D	599	ASP	-1	-0.812	-0.862	17.966	-0.412	-0.412	0.000	0.000	0.000	0.000
14	D	600	GLN	0	-0.046	-0.025	19.697	0.076	0.076	0.000	0.000	0.000	0.000
15	D	601	ILE	0	0.016	0.008	20.102	0.040	0.040	0.000	0.000	0.000	0.000
16	D	602	GLN	0	-0.008	-0.001	23.019	0.034	0.034	0.000	0.000	0.000	0.000
17	D	603	GLN	0	0.020	0.008	23.059	0.050	0.050	0.000	0.000	0.000	0.000
18	D	604	VAL	0	-0.012	-0.010	26.011	0.024	0.024	0.000	0.000	0.000	0.000
19	D	605	SER	0	0.012	0.016	27.319	0.023	0.023	0.000	0.000	0.000	0.000
20	D	606	ASN	0	-0.018	-0.013	29.008	0.023	0.023	0.000	0.000	0.000	0.000
21	D	607	ARG	1	0.928	0.953	26.585	0.182	0.182	0.000	0.000	0.000	0.000
22	D	608	LEU	0	0.041	0.019	30.162	0.011	0.011	0.000	0.000	0.000	0.000
23	D	609	LYS	1	0.975	0.994	33.235	0.175	0.175	0.000	0.000	0.000	0.000
24	D	610	LYS	1	0.929	0.965	34.922	0.140	0.140	0.000	0.000	0.000	0.000
25	D	611	MET	0	0.036	0.030	34.221	0.010	0.010	0.000	0.000	0.000	0.000
26	D	612	ALA	0	0.014	0.026	37.517	0.007	0.007	0.000	0.000	0.000	0.000
27	D	613	LEU	0	-0.024	-0.015	38.681	0.005	0.005	0.000	0.000	0.000	0.000
28	D	614	THR	0	-0.033	-0.026	40.713	0.006	0.006	0.000	0.000	0.000	0.000
29	D	615	THR	0	-0.008	-0.016	41.281	0.006	0.006	0.000	0.000	0.000	0.000
30	D	616	GLY	0	0.017	0.012	43.385	0.004	0.004	0.000	0.000	0.000	0.000
31	D	617	LYS	1	0.933	0.968	45.268	0.076	0.076	0.000	0.000	0.000	0.000
32	D	618	GLU	-1	-0.723	-0.836	46.863	-0.055	-0.055	0.000	0.000	0.000	0.000
33	D	619	LEU	0	0.005	0.010	46.032	0.003	0.003	0.000	0.000	0.000	0.000
34	D	620	ASP	-1	-0.865	-0.923	49.391	-0.063	-0.063	0.000	0.000	0.000	0.000
35	D	621	SER	0	-0.085	-0.044	51.281	0.004	0.004	0.000	0.000	0.000	0.000
36	D	622	GLN	0	-0.052	-0.051	50.261	0.003	0.003	0.000	0.000	0.000	0.000
37	D	623	GLN	0	-0.024	-0.010	53.508	0.001	0.001	0.000	0.000	0.000	0.000
38	D	624	LYS	1	0.854	0.914	54.164	0.061	0.061	0.000	0.000	0.000	0.000
39	D	625	ARG	1	0.848	0.901	52.768	0.054	0.054	0.000	0.000	0.000	0.000
40	D	626	LEU	0	0.003	-0.002	54.936	0.002	0.002	0.000	0.000	0.000	0.000
41	D	627	ASN	0	0.012	0.018	59.083	0.000	0.000	0.000	0.000	0.000	0.000
42	D	628	ASN	0	-0.003	-0.002	61.459	0.000	0.000	0.000	0.000	0.000	0.000
43	D	629	ILE	0	-0.039	-0.002	59.926	0.002	0.002	0.000	0.000	0.000	0.000
44	D	630	GLU	-1	-0.912	-0.946	62.665	-0.040	-0.040	0.000	0.000	0.000	0.000
45	D	631	GLU	-1	-0.887	-0.944	64.535	-0.036	-0.036	0.000	0.000	0.000	0.000
46	D	632	SER	0	-0.031	-0.037	66.843	0.001	0.001	0.000	0.000	0.000	0.000
47	D	633	THR	0	-0.089	-0.056	66.136	0.001	0.001	0.000	0.000	0.000	0.000
48	D	634	ASP	-1	-0.922	-0.956	68.730	-0.030	-0.030	0.000	0.000	0.000	0.000
49	D	635	ASP	-1	-0.909	-0.949	70.796	-0.028	-0.028	0.000	0.000	0.000	0.000
50	D	636	LEU	0	-0.044	-0.029	70.402	0.001	0.001	0.000	0.000	0.000	0.000
51	D	637	ASP	-1	-0.856	-0.915	72.383	-0.025	-0.025	0.000	0.000	0.000	0.000
52	D	638	ILE	0	0.019	0.011	74.357	0.001	0.001	0.000	0.000	0.000	0.000
53	D	639	ASN	0	-0.002	-0.010	76.727	0.002	0.002	0.000	0.000	0.000	0.000
54	D	640	LEU	0	-0.009	0.001	74.812	0.001	0.001	0.000	0.000	0.000	0.000
55	D	641	HIS	0	0.000	0.005	75.486	0.002	0.002	0.000	0.000	0.000	0.000
56	D	642	MET	0	-0.049	0.002	80.276	0.001	0.001	0.000	0.000	0.000	0.000
57	D	643	ASN	0	-0.039	-0.047	81.418	0.001	0.001	0.000	0.000	0.000	0.000
58	D	644	THR	0	-0.024	-0.017	81.263	0.001	0.001	0.000	0.000	0.000	0.000
59	D	645	ASN	0	-0.050	-0.043	83.224	0.001	0.001	0.000	0.000	0.000	0.000
60	D	646	ARG	1	0.904	0.957	86.246	0.020	0.020	0.000	0.000	0.000	0.000
61	D	647	LEU	0	-0.016	-0.011	85.059	0.001	0.001	0.000	0.000	0.000	0.000
62	D	648	ALA	0	-0.009	0.002	87.743	0.001	0.001	0.000	0.000	0.000	0.000
63	D	649	GLY	0	-0.024	0.003	89.603	0.000	0.000	0.000	0.000	0.000	0.000
64	D	650	ILE	0	-0.095	-0.038	91.043	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:587:GLY)