FMO DATABASE

FMODB ID: V51K1

Calculation Name: 3B5N-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B5N

Chain ID: A

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	61
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-237927.362711
FMO2-HF: Nuclear repulsion	213999.195148
FMO2-HF: Total energy	-23928.167563
FMO2-MP2: Total energy	-23997.231303

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:26:GLY)

Summations of interaction energy for fragment #1(A:26: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.
0.82	2.52	0.021	-0.637	-1.084	0

Interaction energy analysis for fragmet #1(A:26:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.039 / q_NPA : 0.004

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].
3	A	28	ARG	1	1.009	1.005	3.828	-0.139	0.931	-0.004	-0.451	-0.615
4	A	29	THR	0	-0.020	-0.018	3.348	0.107	0.579	0.026	-0.141	-0.356
5	A	30	ALA	0	0.014	0.013	4.482	0.749	0.907	-0.001	-0.045	-0.113
6	A	31	GLU	-1	-0.907	-0.948	6.368	-0.018	-0.018	0.000	0.000	0.000
7	A	32	LEU	0	-0.018	-0.008	8.163	0.168	0.168	0.000	0.000	0.000
8	A	33	GLN	0	-0.080	-0.051	8.666	0.118	0.118	0.000	0.000	0.000
9	A	34	ALA	0	0.040	0.020	10.417	0.135	0.135	0.000	0.000	0.000
10	A	35	GLU	-1	-0.915	-0.952	12.398	-0.299	-0.299	0.000	0.000	0.000
11	A	36	ILE	0	-0.026	-0.005	11.995	0.079	0.079	0.000	0.000	0.000
12	A	37	ASP	-1	-0.856	-0.923	14.030	-0.335	-0.335	0.000	0.000	0.000
13	A	38	ASP	-1	-0.888	-0.940	16.422	-0.175	-0.175	0.000	0.000	0.000
14	A	39	THR	0	-0.082	-0.048	17.762	0.046	0.046	0.000	0.000	0.000
15	A	40	VAL	0	-0.026	-0.020	18.694	0.033	0.033	0.000	0.000	0.000
16	A	41	GLY	0	-0.015	-0.004	20.541	0.024	0.024	0.000	0.000	0.000
17	A	42	ILE	0	0.018	0.001	21.601	0.022	0.022	0.000	0.000	0.000
18	A	43	MET	0	-0.013	-0.012	23.450	0.019	0.019	0.000	0.000	0.000
19	A	44	ARG	1	0.914	0.958	23.052	0.159	0.159	0.000	0.000	0.000
20	A	45	ASP	-1	-0.830	-0.903	26.632	-0.081	-0.081	0.000	0.000	0.000
21	A	46	ASN	0	-0.001	-0.015	27.302	0.016	0.016	0.000	0.000	0.000
22	A	47	ILE	0	-0.011	0.003	28.807	0.007	0.007	0.000	0.000	0.000
23	A	48	ASN	0	-0.002	0.001	30.482	0.007	0.007	0.000	0.000	0.000
24	A	49	LYS	1	0.863	0.924	29.782	0.095	0.095	0.000	0.000	0.000
25	A	50	VAL	0	-0.048	-0.022	33.332	0.005	0.005	0.000	0.000	0.000
26	A	51	ALA	0	0.014	0.011	35.262	0.004	0.004	0.000	0.000	0.000
27	A	52	GLU	-1	-0.906	-0.947	37.191	-0.050	-0.050	0.000	0.000	0.000
28	A	53	ARG	1	0.937	0.964	37.781	0.064	0.064	0.000	0.000	0.000
29	A	54	GLY	0	0.026	0.014	39.470	0.003	0.003	0.000	0.000	0.000
30	A	55	GLU	-1	-0.821	-0.867	41.215	-0.041	-0.041	0.000	0.000	0.000
31	A	56	ARG	1	0.808	0.868	42.892	0.048	0.048	0.000	0.000	0.000
32	A	57	LEU	0	-0.014	-0.017	41.961	0.002	0.002	0.000	0.000	0.000
33	A	58	THR	0	0.008	-0.001	44.886	0.002	0.002	0.000	0.000	0.000
34	A	59	SER	0	-0.027	-0.014	47.289	0.003	0.003	0.000	0.000	0.000
35	A	60	ILE	0	-0.034	-0.023	46.536	0.002	0.002	0.000	0.000	0.000
36	A	61	GLU	-1	-0.951	-0.969	48.909	-0.038	-0.038	0.000	0.000	0.000
37	A	62	ASP	-1	-0.800	-0.894	51.129	-0.029	-0.029	0.000	0.000	0.000
38	A	63	LYS	1	0.834	0.914	52.110	0.033	0.033	0.000	0.000	0.000
39	A	64	ALA	0	-0.006	0.002	53.136	0.001	0.001	0.000	0.000	0.000
40	A	65	ASP	-1	-0.909	-0.944	55.124	-0.027	-0.027	0.000	0.000	0.000
41	A	66	ASN	0	-0.002	-0.019	57.354	0.002	0.002	0.000	0.000	0.000
42	A	67	LEU	0	-0.008	0.021	57.188	0.001	0.001	0.000	0.000	0.000
43	A	68	ALA	0	0.023	0.013	59.035	0.001	0.001	0.000	0.000	0.000
44	A	69	VAL	0	-0.004	-0.005	60.835	0.001	0.001	0.000	0.000	0.000
45	A	70	SER	0	-0.019	-0.020	62.666	0.001	0.001	0.000	0.000	0.000
46	A	71	ALA	0	-0.007	-0.001	63.106	0.001	0.001	0.000	0.000	0.000
47	A	72	GLN	0	-0.006	0.002	64.964	0.002	0.002	0.000	0.000	0.000
48	A	73	GLY	0	0.005	-0.006	66.880	0.001	0.001	0.000	0.000	0.000
49	A	74	PHE	0	0.031	0.016	67.880	0.001	0.001	0.000	0.000	0.000
50	A	75	LYS	1	0.975	0.991	67.389	0.021	0.021	0.000	0.000	0.000
51	A	76	ARG	1	0.866	0.917	69.360	0.020	0.020	0.000	0.000	0.000
52	A	77	GLY	0	0.006	0.007	72.687	0.001	0.001	0.000	0.000	0.000
53	A	78	ALA	0	0.053	0.024	73.164	0.001	0.001	0.000	0.000	0.000
54	A	79	ASN	0	0.007	0.006	74.795	0.001	0.001	0.000	0.000	0.000
55	A	80	ARG	1	0.946	0.976	76.365	0.016	0.016	0.000	0.000	0.000
56	A	81	VAL	0	0.052	0.031	77.935	0.000	0.000	0.000	0.000	0.000
57	A	82	ARG	1	0.915	0.951	77.804	0.015	0.015	0.000	0.000	0.000
58	A	83	LYS	1	0.924	0.956	80.418	0.014	0.014	0.000	0.000	0.000
59	A	84	ALA	0	-0.003	0.000	82.676	0.000	0.000	0.000	0.000	0.000
60	A	85	MET	0	-0.024	-0.009	82.573	0.000	0.000	0.000	0.000	0.000
61	A	86	TRP	0	-0.067	-0.017	84.696	0.001	0.001	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:26:GLY)