FMO DATABASE

FMODB ID: 89M4Y

Calculation Name: 3UE7-B-Xray372

Preferred Name:

Target Type:

Ligand Name: d-arginine

ligand 3-letter code: DAR

PDB ID: 3UE7

Chain ID: B

ChEMBL ID:

UniProt ID: P01542

Base Structure: X-ray

Registration Date: 2023-09-23

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	43
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-186101.997304
FMO2-HF: Nuclear repulsion	168284.305642
FMO2-HF: Total energy	-17817.691662
FMO2-MP2: Total energy	-17864.612803

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(B:1:THR)

Summations of interaction energy for fragment #1(B:1:THR)

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.
-27.212	-25.995	26.993	-12.685	-15.526	-0.086

Interaction energy analysis for fragmet #1(B:1:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.045 / q_NPA : -0.045

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	B	3	CYS	0	-0.056	0.017	3.044	-4.337	-1.917	1.737	-1.309	-2.848	0.003
4	B	4	CYS	0	-0.141	-0.032	4.654	0.232	0.307	-0.002	-0.010	-0.063	0.000
5	B	5	PRO	0	0.064	0.037	8.281	-0.064	-0.064	0.000	0.000	0.000	0.000
6	B	6	SER	0	0.038	0.014	11.462	0.081	0.081	0.000	0.000	0.000	0.000
7	B	7	ILE	0	0.075	0.017	11.699	0.025	0.025	0.000	0.000	0.000	0.000
8	B	8	VAL	0	0.018	0.021	13.088	0.089	0.089	0.000	0.000	0.000	0.000
9	B	9	ALA	0	0.027	0.019	12.125	0.075	0.075	0.000	0.000	0.000	0.000
10	B	10	LYS	1	0.880	0.924	6.500	-0.847	-0.847	0.000	0.000	0.000	0.000
11	B	11	SER	0	0.010	0.001	10.744	0.200	0.200	0.000	0.000	0.000	0.000
12	B	12	ASN	0	0.011	0.000	14.059	0.099	0.099	0.000	0.000	0.000	0.000
13	B	13	PHE	0	0.020	0.007	7.194	0.042	0.042	0.000	0.000	0.000	0.000
14	B	14	ASN	0	0.012	-0.017	9.540	0.345	0.345	0.000	0.000	0.000	0.000
15	B	15	ALA	0	0.004	0.006	11.813	0.054	0.054	0.000	0.000	0.000	0.000
16	B	16	CYS	0	-0.007	0.007	10.905	-0.112	-0.112	0.000	0.000	0.000	0.000
17	B	17	ARG	1	0.838	0.887	8.738	-2.163	-2.163	0.000	0.000	0.000	0.000
18	B	18	LEU	0	-0.031	0.016	12.636	0.052	0.052	0.000	0.000	0.000	0.000
19	B	19	PRO	0	-0.039	-0.020	15.273	-0.002	-0.002	0.000	0.000	0.000	0.000
20	B	20	GLY	0	0.021	0.012	14.579	-0.048	-0.048	0.000	0.000	0.000	0.000
21	B	21	THR	0	-0.052	-0.031	14.563	0.021	0.021	0.000	0.000	0.000	0.000
22	B	22	PRO	0	0.038	0.015	12.480	0.208	0.208	0.000	0.000	0.000	0.000
23	B	23	GLU	-1	-0.788	-0.885	6.969	1.988	1.988	0.000	0.000	0.000	0.000
24	B	24	ALA	0	0.040	0.010	9.513	-0.239	-0.239	0.000	0.000	0.000	0.000
25	B	25	LEU	0	0.000	0.017	11.094	-0.216	-0.216	0.000	0.000	0.000	0.000
26	B	27	ALA	0	0.006	0.017	9.244	-0.118	-0.118	0.000	0.000	0.000	0.000
27	B	28	THR	0	-0.021	-0.024	11.063	-0.190	-0.190	0.000	0.000	0.000	0.000
28	B	29	TYR	0	-0.068	-0.026	14.675	-0.058	-0.058	0.000	0.000	0.000	0.000
29	B	30	THR	0	-0.044	-0.047	12.229	-0.061	-0.061	0.000	0.000	0.000	0.000
30	B	31	GLY	0	0.015	0.016	13.262	-0.061	-0.061	0.000	0.000	0.000	0.000
31	B	33	ILE	0	0.050	0.035	6.526	0.226	0.226	0.000	0.000	0.000	0.000
32	B	34	ILE	0	-0.009	-0.022	3.227	-0.872	-0.203	0.058	-0.272	-0.456	0.001
33	B	35	ILE	0	-0.013	-0.002	2.338	0.169	1.651	0.878	-0.702	-1.658	-0.001
34	B	36	PRO	0	0.035	0.004	1.962	-7.648	-8.920	7.453	-3.252	-2.929	-0.037
35	B	37	GLY	0	0.010	0.027	3.781	0.808	1.631	0.002	-0.388	-0.437	-0.001
36	B	38	ALA	0	0.017	0.012	1.732	-17.199	-21.492	15.379	-6.543	-4.543	-0.043
37	B	39	THR	0	0.000	-0.003	3.008	2.731	3.057	0.147	0.452	-0.925	-0.001
38	B	41	PRO	0	0.012	-0.005	4.576	0.527	0.592	-0.001	-0.013	-0.051	0.000
39	B	42	GLY	0	-0.007	-0.010	8.309	0.157	0.157	0.000	0.000	0.000	0.000
40	B	43	ASP	-1	-0.888	-0.937	10.216	-0.814	-0.814	0.000	0.000	0.000	0.000
41	B	44	TYR	0	-0.043	-0.011	6.816	0.090	0.090	0.000	0.000	0.000	0.000
42	B	45	ALA	0	0.000	0.001	7.117	-0.082	-0.082	0.000	0.000	0.000	0.000
43	B	46	ASN	0	0.000	-0.026	2.548	-0.300	0.622	1.342	-0.648	-1.616	-0.007

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Interactive mode: IFIE and PIEDA for fragment #1(B:1:THR)