FMO DATABASE

FMODB ID: 5JR3Z

Calculation Name: 4E5R-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4E5R

Chain ID: A

ChEMBL ID:

UniProt ID: Q6IRB5

Base Structure: X-ray

Registration Date: 2023-09-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	56
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-275986.877557
FMO2-HF: Nuclear repulsion	253750.516745
FMO2-HF: Total energy	-22236.360813
FMO2-MP2: Total energy	-22301.334105

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:300:PRO)

Summations of interaction energy for fragment #1(A:300:PRO)

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.
-0.882	0.977	0.027	-0.731	-1.156	0.003

Interaction energy analysis for fragmet #1(A:300:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : -0.021

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

Sort

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	A	302	THR	0	-0.031	-0.028	3.817	-1.271	0.052	-0.009	-0.620	-0.694	0.003
4	A	303	GLU	-1	-0.868	-0.920	5.968	-0.429	-0.429	0.000	0.000	0.000	0.000
5	A	304	PRO	0	0.008	0.006	7.662	0.065	0.065	0.000	0.000	0.000	0.000
6	A	305	LEU	0	-0.037	-0.014	11.359	-0.027	-0.027	0.000	0.000	0.000	0.000
7	A	306	PRO	0	0.000	0.005	14.035	0.040	0.040	0.000	0.000	0.000	0.000
8	A	307	ASP	-1	-0.840	-0.921	16.284	-0.204	-0.204	0.000	0.000	0.000	0.000
9	A	308	GLY	0	-0.040	-0.027	19.606	0.000	0.000	0.000	0.000	0.000	0.000
10	A	309	TRP	0	-0.051	-0.031	17.942	0.001	0.001	0.000	0.000	0.000	0.000
11	A	310	ILE	0	-0.023	-0.010	19.088	-0.001	-0.001	0.000	0.000	0.000	0.000
12	A	311	MET	0	-0.015	0.003	14.690	-0.027	-0.027	0.000	0.000	0.000	0.000
13	A	312	THR	0	-0.012	-0.007	18.469	0.025	0.025	0.000	0.000	0.000	0.000
14	A	313	PHE	0	0.032	0.005	17.113	-0.036	-0.036	0.000	0.000	0.000	0.000
15	A	314	HIS	0	0.039	0.052	22.413	0.022	0.022	0.000	0.000	0.000	0.000
16	A	315	ASN	0	0.033	-0.001	25.023	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	316	SER	0	-0.038	-0.032	25.335	0.001	0.001	0.000	0.000	0.000	0.000
18	A	317	GLY	0	0.011	0.007	23.626	0.003	0.003	0.000	0.000	0.000	0.000
19	A	318	LEU	0	-0.027	-0.004	19.925	-0.025	-0.025	0.000	0.000	0.000	0.000
20	A	319	PRO	0	-0.007	0.005	16.262	0.022	0.022	0.000	0.000	0.000	0.000
21	A	320	VAL	0	-0.032	-0.016	19.150	0.002	0.002	0.000	0.000	0.000	0.000
22	A	321	TYR	0	0.008	-0.007	14.260	-0.033	-0.033	0.000	0.000	0.000	0.000
23	A	322	LEU	0	-0.008	-0.004	19.434	0.020	0.020	0.000	0.000	0.000	0.000
24	A	323	HIS	0	0.079	0.061	21.720	0.000	0.000	0.000	0.000	0.000	0.000
25	A	324	ARG	1	0.849	0.883	23.233	0.176	0.176	0.000	0.000	0.000	0.000
26	A	325	GLU	-1	-0.835	-0.906	26.121	-0.144	-0.144	0.000	0.000	0.000	0.000
27	A	326	THR	0	-0.015	-0.024	25.863	0.007	0.007	0.000	0.000	0.000	0.000
28	A	327	ARG	1	0.900	0.957	27.795	0.151	0.151	0.000	0.000	0.000	0.000
29	A	328	VAL	0	0.033	0.038	23.640	0.002	0.002	0.000	0.000	0.000	0.000
30	A	329	VAL	0	-0.004	-0.014	22.868	-0.012	-0.012	0.000	0.000	0.000	0.000
31	A	330	THR	0	-0.003	0.004	18.311	0.009	0.009	0.000	0.000	0.000	0.000
32	A	331	TRP	0	0.040	0.000	19.676	-0.011	-0.011	0.000	0.000	0.000	0.000
33	A	332	SER	0	-0.031	-0.003	15.042	-0.015	-0.015	0.000	0.000	0.000	0.000
34	A	333	ARG	1	0.874	0.936	9.910	0.944	0.944	0.000	0.000	0.000	0.000
35	A	334	PRO	0	0.009	0.027	12.954	-0.055	-0.055	0.000	0.000	0.000	0.000
36	A	335	TYR	0	-0.004	-0.046	10.893	-0.074	-0.074	0.000	0.000	0.000	0.000
37	A	336	PHE	0	0.018	0.015	12.736	0.072	0.072	0.000	0.000	0.000	0.000
38	A	337	LEU	0	0.000	0.016	12.785	-0.028	-0.028	0.000	0.000	0.000	0.000
39	A	338	GLY	0	0.038	0.011	14.631	0.015	0.015	0.000	0.000	0.000	0.000
40	A	339	THR	0	-0.037	-0.027	16.670	0.000	0.000	0.000	0.000	0.000	0.000
41	A	340	GLY	0	0.035	0.034	15.096	0.016	0.016	0.000	0.000	0.000	0.000
42	A	341	SER	0	-0.020	-0.017	16.043	0.008	0.008	0.000	0.000	0.000	0.000
43	A	342	ILE	0	0.078	0.023	16.707	-0.023	-0.023	0.000	0.000	0.000	0.000
44	A	343	ARG	1	0.932	0.949	17.708	0.143	0.143	0.000	0.000	0.000	0.000
45	A	344	LYS	1	0.925	0.954	16.848	0.138	0.138	0.000	0.000	0.000	0.000
46	A	345	HIS	0	-0.022	0.038	11.698	-0.041	-0.041	0.000	0.000	0.000	0.000
47	A	346	ASP	-1	-0.846	-0.914	8.555	-0.419	-0.419	0.000	0.000	0.000	0.000
48	A	347	PRO	0	-0.044	-0.020	9.307	-0.039	-0.039	0.000	0.000	0.000	0.000
49	A	348	PRO	0	0.063	0.034	5.720	-0.183	-0.183	0.000	0.000	0.000	0.000
50	A	349	ILE	0	0.079	0.021	3.266	-0.325	0.211	0.036	-0.111	-0.462	0.000
51	A	350	SER	0	-0.045	-0.026	5.798	0.277	0.277	0.000	0.000	0.000	0.000
52	A	351	SER	0	-0.068	-0.062	7.718	0.223	0.223	0.000	0.000	0.000	0.000
53	A	352	ILE	0	-0.056	0.005	8.495	0.175	0.175	0.000	0.000	0.000	0.000
54	A	353	PRO	0	-0.010	0.012	11.407	-0.007	-0.007	0.000	0.000	0.000	0.000
55	A	354	CYS	0	-0.020	-0.031	14.313	-0.026	-0.026	0.000	0.000	0.000	0.000
56	A	355	LEU	0	0.019	0.022	13.406	0.023	0.023	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:300:PRO)