FMO DATABASE

FMODB ID: G5GZ1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-186006.50261
FMO2-HF: Nuclear repulsion	168188.847065
FMO2-HF: Total energy	-17817.655545
FMO2-MP2: Total energy	-17864.609764

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.
-30.087	-31.218	30.827	-14.431	-15.264	-0.093

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 : -0.060 / q_NPA : -0.046

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	-0.061	-0.004	3.040	-3.477	-1.076	1.982	-1.314	-3.069	0.004
4	B	4	CYS	0	-0.145	-0.050	4.665	0.106	0.172	-0.002	-0.010	-0.054	0.000
5	B	5	PRO	0	0.063	0.037	8.244	-0.046	-0.046	0.000	0.000	0.000	0.000
6	B	6	SER	0	0.053	0.024	11.401	0.037	0.037	0.000	0.000	0.000	0.000
7	B	7	ILE	0	0.078	0.023	11.619	0.048	0.048	0.000	0.000	0.000	0.000
8	B	8	VAL	0	0.022	0.017	13.035	0.084	0.084	0.000	0.000	0.000	0.000
9	B	9	ALA	0	0.023	0.021	12.190	0.066	0.066	0.000	0.000	0.000	0.000
10	B	10	LYS	1	0.888	0.927	6.316	-1.355	-1.355	0.000	0.000	0.000	0.000
11	B	11	SER	0	0.012	0.001	10.665	0.197	0.197	0.000	0.000	0.000	0.000
12	B	12	ASN	0	-0.005	-0.009	13.794	0.084	0.084	0.000	0.000	0.000	0.000
13	B	13	PHE	0	-0.001	-0.001	6.985	0.017	0.017	0.000	0.000	0.000	0.000
14	B	14	ASN	0	0.025	-0.017	9.313	0.333	0.333	0.000	0.000	0.000	0.000
15	B	15	ALA	0	0.012	0.020	11.570	0.039	0.039	0.000	0.000	0.000	0.000
16	B	16	CYS	0	-0.013	0.002	10.918	-0.112	-0.112	0.000	0.000	0.000	0.000
17	B	17	ARG	1	0.869	0.915	8.734	-2.074	-2.074	0.000	0.000	0.000	0.000
18	B	18	LEU	0	-0.037	0.016	12.431	0.039	0.039	0.000	0.000	0.000	0.000
19	B	19	PRO	0	-0.033	-0.018	14.877	-0.002	-0.002	0.000	0.000	0.000	0.000
20	B	20	GLY	0	0.021	0.009	14.519	-0.060	-0.060	0.000	0.000	0.000	0.000
21	B	21	THR	0	-0.064	-0.033	14.517	0.005	0.005	0.000	0.000	0.000	0.000
22	B	22	PRO	0	0.045	0.015	12.521	0.198	0.198	0.000	0.000	0.000	0.000
23	B	23	GLU	-1	-0.790	-0.897	6.920	1.883	1.883	0.000	0.000	0.000	0.000
24	B	24	ALA	0	0.018	0.005	9.596	-0.202	-0.202	0.000	0.000	0.000	0.000
25	B	25	LEU	0	0.009	0.007	10.814	-0.192	-0.192	0.000	0.000	0.000	0.000
26	B	27	ALA	0	-0.014	0.002	8.960	-0.094	-0.094	0.000	0.000	0.000	0.000
27	B	28	THR	0	-0.008	-0.008	10.973	-0.180	-0.180	0.000	0.000	0.000	0.000
28	B	29	TYR	0	-0.060	-0.019	14.255	-0.040	-0.040	0.000	0.000	0.000	0.000
29	B	30	THR	0	-0.032	-0.035	12.118	-0.051	-0.051	0.000	0.000	0.000	0.000
30	B	31	GLY	0	0.009	0.016	13.178	-0.042	-0.042	0.000	0.000	0.000	0.000
31	B	33	ILE	0	0.043	0.023	6.704	0.147	0.147	0.000	0.000	0.000	0.000
32	B	34	ILE	0	-0.007	-0.011	3.315	-1.086	-0.514	0.034	-0.232	-0.373	0.001
33	B	35	ILE	0	-0.018	-0.007	2.511	-0.118	1.633	0.481	-0.696	-1.536	-0.001
34	B	36	PRO	0	0.053	0.010	1.857	-8.318	-11.943	10.688	-4.271	-2.792	-0.040
35	B	37	GLY	0	-0.007	0.017	3.618	-0.656	0.492	0.006	-0.626	-0.528	-0.003
36	B	38	ALA	0	0.034	0.018	1.707	-17.311	-22.544	16.240	-6.738	-4.270	-0.045
37	B	39	THR	0	-0.002	0.001	3.041	2.528	3.306	0.305	0.046	-1.129	-0.004
38	B	41	PRO	0	0.019	0.002	4.601	0.500	0.567	-0.001	-0.014	-0.052	0.000
39	B	42	GLY	0	-0.008	-0.009	8.300	0.146	0.146	0.000	0.000	0.000	0.000
40	B	43	ASP	-1	-0.888	-0.944	10.015	-0.614	-0.614	0.000	0.000	0.000	0.000
41	B	44	TYR	0	-0.050	-0.012	6.850	0.060	0.060	0.000	0.000	0.000	0.000
42	B	45	ALA	0	0.003	0.008	7.698	0.066	0.066	0.000	0.000	0.000	0.000
43	B	46	ASN	0	0.009	-0.006	2.404	-0.640	0.304	1.094	-0.576	-1.461	-0.005

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