FMO DATABASE

FMODB ID: 1NK8Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-186093.351125
FMO2-HF: Nuclear repulsion	168276.785681
FMO2-HF: Total energy	-17816.565443
FMO2-MP2: Total energy	-17863.579986

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.
-29.727	-35.451	37.294	-16.498	-15.076	-0.091

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 : -0.073 / q_NPA : -0.062

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	0.001	0.007	3.036	-3.023	-0.809	2.026	-1.201	-3.039	0.004
4	B	4	CYS	0	-0.132	-0.051	4.586	0.053	0.123	-0.002	-0.013	-0.055	0.000
5	B	5	PRO	0	0.052	0.029	8.201	-0.030	-0.030	0.000	0.000	0.000	0.000
6	B	6	SER	0	0.048	0.029	11.402	0.051	0.051	0.000	0.000	0.000	0.000
7	B	7	ILE	0	0.070	0.018	11.650	0.047	0.047	0.000	0.000	0.000	0.000
8	B	8	VAL	0	0.021	0.019	13.106	0.086	0.086	0.000	0.000	0.000	0.000
9	B	9	ALA	0	0.019	0.015	12.169	0.063	0.063	0.000	0.000	0.000	0.000
10	B	10	LYS	1	0.276	0.386	4.797	-1.237	-1.174	-0.001	-0.002	-0.060	0.000
11	B	11	SER	0	-0.024	-0.008	10.713	0.206	0.206	0.000	0.000	0.000	0.000
12	B	12	ASN	0	0.042	0.011	13.874	0.088	0.088	0.000	0.000	0.000	0.000
13	B	13	PHE	0	-0.025	-0.011	7.010	0.082	0.082	0.000	0.000	0.000	0.000
14	B	14	ASN	0	0.019	-0.019	9.289	0.316	0.316	0.000	0.000	0.000	0.000
15	B	15	ALA	0	0.004	0.018	11.596	0.041	0.041	0.000	0.000	0.000	0.000
16	B	16	CYS	0	-0.028	-0.010	10.996	-0.108	-0.108	0.000	0.000	0.000	0.000
17	B	17	ARG	1	0.906	0.941	8.247	-2.160	-2.160	0.000	0.000	0.000	0.000
18	B	18	LEU	0	-0.028	0.021	12.483	0.042	0.042	0.000	0.000	0.000	0.000
19	B	19	PRO	0	-0.036	-0.020	14.920	0.000	0.000	0.000	0.000	0.000	0.000
20	B	20	GLY	0	0.018	0.006	14.582	-0.059	-0.059	0.000	0.000	0.000	0.000
21	B	21	THR	0	-0.067	-0.031	14.573	0.006	0.006	0.000	0.000	0.000	0.000
22	B	22	PRO	0	0.047	0.015	12.524	0.188	0.188	0.000	0.000	0.000	0.000
23	B	23	GLU	-1	-0.827	-0.926	7.092	1.976	1.976	0.000	0.000	0.000	0.000
24	B	24	ALA	0	0.020	0.004	9.596	-0.224	-0.224	0.000	0.000	0.000	0.000
25	B	25	LEU	0	-0.001	0.001	10.741	-0.190	-0.190	0.000	0.000	0.000	0.000
26	B	27	ALA	0	-0.011	-0.003	8.859	-0.083	-0.083	0.000	0.000	0.000	0.000
27	B	28	THR	0	0.002	-0.002	10.907	-0.173	-0.173	0.000	0.000	0.000	0.000
28	B	29	TYR	0	-0.062	-0.020	14.181	-0.032	-0.032	0.000	0.000	0.000	0.000
29	B	30	THR	0	-0.031	-0.022	11.960	-0.059	-0.059	0.000	0.000	0.000	0.000
30	B	31	GLY	0	0.014	0.017	13.073	-0.033	-0.033	0.000	0.000	0.000	0.000
31	B	33	ILE	0	0.037	0.019	6.530	0.136	0.136	0.000	0.000	0.000	0.000
32	B	34	ILE	0	0.006	-0.003	3.333	-1.115	-0.614	0.022	-0.180	-0.344	0.001
33	B	35	ILE	0	-0.029	-0.017	2.536	0.015	1.852	0.567	-0.732	-1.672	0.000
34	B	36	PRO	0	0.050	0.011	1.888	-8.969	-12.040	10.346	-4.242	-3.034	-0.041
35	B	37	GLY	0	0.006	0.024	3.522	-0.739	0.757	0.012	-0.857	-0.651	-0.005
36	B	38	ALA	0	0.039	0.030	1.603	-16.746	-26.879	23.353	-9.062	-4.159	-0.047
37	B	39	THR	0	-0.052	-0.015	3.137	2.454	3.180	0.210	0.073	-1.010	-0.003
38	B	41	PRO	0	0.027	0.010	4.523	0.507	0.581	0.000	-0.017	-0.057	0.000
39	B	42	GLY	0	-0.009	-0.012	8.198	0.150	0.150	0.000	0.000	0.000	0.000
40	B	43	ASP	-1	-0.880	-0.938	10.017	-0.622	-0.622	0.000	0.000	0.000	0.000
41	B	44	TYR	0	-0.046	-0.012	6.761	0.057	0.057	0.000	0.000	0.000	0.000
42	B	45	ALA	0	0.020	0.015	7.743	0.101	0.101	0.000	0.000	0.000	0.000
43	B	46	ASN	0	0.597	0.522	2.472	-0.790	-0.291	0.761	-0.265	-0.995	0.000

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