FMO DATABASE

FMODB ID: R5JN8

Calculation Name: 4N6J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4N6J

Chain ID: A

ChEMBL ID:

UniProt ID: Q13033

Base Structure: X-ray

Registration Date: 2023-06-20

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	OptH
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	49
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-202472.588827
FMO2-HF: Nuclear repulsion	181380.081419
FMO2-HF: Total energy	-21092.507409
FMO2-MP2: Total energy	-21151.440447

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:82:SER)

Summations of interaction energy for fragment #1(A:82:SER)

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.
-11.988	-6.218	2.979	-3.977	-4.772	0.031

Interaction energy analysis for fragmet #1(A:82:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.038 / q_NPA : 0.017

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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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	84	MET	0	-0.008	0.005	2.226	-8.609	-3.337	2.960	-3.892	-4.340	0.030
4	A	85	ASP	-1	-0.843	-0.923	3.898	-3.274	-2.776	0.019	-0.085	-0.432	0.001
5	A	86	TRP	0	0.003	-0.002	6.146	0.189	0.189	0.000	0.000	0.000	0.000
6	A	87	GLU	-1	-0.957	-0.983	6.995	0.237	0.237	0.000	0.000	0.000	0.000
7	A	88	VAL	0	-0.013	-0.005	7.940	-0.080	-0.080	0.000	0.000	0.000	0.000
8	A	89	GLU	-1	-0.898	-0.946	9.926	-0.642	-0.642	0.000	0.000	0.000	0.000
9	A	90	ARG	1	0.942	0.965	11.445	0.109	0.109	0.000	0.000	0.000	0.000
10	A	91	ALA	0	-0.018	-0.018	12.616	-0.006	-0.006	0.000	0.000	0.000	0.000
11	A	92	GLU	-1	-0.910	-0.943	14.238	-0.023	-0.023	0.000	0.000	0.000	0.000
12	A	93	LEU	0	-0.030	-0.026	15.614	-0.005	-0.005	0.000	0.000	0.000	0.000
13	A	94	GLN	0	-0.015	-0.019	17.081	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	95	ALA	0	0.010	0.020	18.528	0.003	0.003	0.000	0.000	0.000	0.000
15	A	96	ARG	1	0.973	0.983	19.924	0.083	0.083	0.000	0.000	0.000	0.000
16	A	97	ILE	0	-0.020	0.000	21.169	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	98	ALA	0	-0.001	-0.001	22.884	0.001	0.001	0.000	0.000	0.000	0.000
18	A	99	MET	0	-0.014	0.000	24.581	0.004	0.004	0.000	0.000	0.000	0.000
19	A	100	LEU	0	0.030	0.016	25.710	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	101	GLN	0	-0.051	-0.037	26.388	0.006	0.006	0.000	0.000	0.000	0.000
21	A	102	GLY	0	0.004	0.002	28.724	0.001	0.001	0.000	0.000	0.000	0.000
22	A	103	GLU	-1	-0.918	-0.950	30.532	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	104	ARG	1	0.971	0.981	30.913	0.034	0.034	0.000	0.000	0.000	0.000
24	A	105	LYS	1	0.929	0.968	32.815	-0.013	-0.013	0.000	0.000	0.000	0.000
25	A	106	GLY	0	0.008	0.004	34.714	0.001	0.001	0.000	0.000	0.000	0.000
26	A	107	GLN	0	0.028	0.005	36.539	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	108	GLU	-1	-0.862	-0.926	37.773	-0.019	-0.019	0.000	0.000	0.000	0.000
28	A	109	ASN	0	-0.031	-0.039	38.270	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	110	LEU	0	0.057	0.047	40.692	0.000	0.000	0.000	0.000	0.000	0.000
30	A	111	LYS	1	0.902	0.947	41.515	0.017	0.017	0.000	0.000	0.000	0.000
31	A	112	LYS	1	0.888	0.937	40.797	0.010	0.010	0.000	0.000	0.000	0.000
32	A	113	ASP	-1	-0.851	-0.915	44.875	0.005	0.005	0.000	0.000	0.000	0.000
33	A	114	LEU	0	-0.031	-0.020	45.967	0.000	0.000	0.000	0.000	0.000	0.000
34	A	115	VAL	0	0.006	0.010	48.244	0.000	0.000	0.000	0.000	0.000	0.000
35	A	116	ARG	1	0.882	0.928	47.239	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	117	ARG	1	0.968	0.989	51.285	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	118	ILE	0	0.025	0.015	51.619	0.000	0.000	0.000	0.000	0.000	0.000
38	A	119	LYS	1	0.956	0.984	54.246	0.010	0.010	0.000	0.000	0.000	0.000
39	A	120	MET	0	-0.002	-0.004	55.737	0.000	0.000	0.000	0.000	0.000	0.000
40	A	121	LEU	0	-0.005	0.001	55.836	0.001	0.001	0.000	0.000	0.000	0.000
41	A	122	GLU	-1	-0.922	-0.960	58.255	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	123	MET	0	-0.064	-0.030	60.140	0.000	0.000	0.000	0.000	0.000	0.000
43	A	124	ALA	0	0.041	0.013	61.802	0.000	0.000	0.000	0.000	0.000	0.000
44	A	125	LEU	0	0.001	0.008	63.088	0.000	0.000	0.000	0.000	0.000	0.000
45	A	126	LYS	1	0.926	0.954	64.874	0.005	0.005	0.000	0.000	0.000	0.000
46	A	127	GLN	0	-0.054	-0.043	65.802	0.000	0.000	0.000	0.000	0.000	0.000
47	A	128	GLU	-1	-0.915	-0.943	67.447	0.001	0.001	0.000	0.000	0.000	0.000
48	A	129	ARG	1	0.876	0.938	66.568	0.005	0.005	0.000	0.000	0.000	0.000
49	A	130	ALA	0	-0.033	0.009	71.007	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:82:SER)