FMO DATABASE

FMODB ID: YV9Q2

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-275839.739612
FMO2-HF: Nuclear repulsion	253603.309357
FMO2-HF: Total energy	-22236.430255
FMO2-MP2: Total energy	-22301.40018

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.
-1.17	0.978	0.36	-0.912	-1.596	0.001

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 : 0.009 / q_NPA : -0.016

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	A	302	THR	0	-0.039	-0.032	3.814	-1.192	0.081	-0.002	-0.650	-0.621	0.002
4	A	303	GLU	-1	-0.861	-0.924	5.907	-0.364	-0.364	0.000	0.000	0.000	0.000
5	A	304	PRO	0	0.010	0.004	7.742	0.065	0.065	0.000	0.000	0.000	0.000
6	A	305	LEU	0	-0.030	-0.005	11.366	-0.035	-0.035	0.000	0.000	0.000	0.000
7	A	306	PRO	0	-0.006	-0.005	14.223	0.039	0.039	0.000	0.000	0.000	0.000
8	A	307	ASP	-1	-0.842	-0.920	16.473	-0.189	-0.189	0.000	0.000	0.000	0.000
9	A	308	GLY	0	-0.022	-0.019	19.815	0.001	0.001	0.000	0.000	0.000	0.000
10	A	309	TRP	0	-0.048	-0.030	18.138	0.000	0.000	0.000	0.000	0.000	0.000
11	A	310	ILE	0	-0.029	-0.003	19.342	0.005	0.005	0.000	0.000	0.000	0.000
12	A	311	MET	0	0.001	0.008	14.462	-0.036	-0.036	0.000	0.000	0.000	0.000
13	A	312	THR	0	-0.013	-0.010	18.413	0.027	0.027	0.000	0.000	0.000	0.000
14	A	313	PHE	0	0.027	0.009	17.191	-0.039	-0.039	0.000	0.000	0.000	0.000
15	A	314	HIS	0	0.043	0.052	22.079	0.019	0.019	0.000	0.000	0.000	0.000
16	A	315	ASN	0	0.007	-0.014	24.864	-0.009	-0.009	0.000	0.000	0.000	0.000
17	A	316	SER	0	-0.008	-0.020	25.061	0.001	0.001	0.000	0.000	0.000	0.000
18	A	317	GLY	0	0.005	0.007	23.718	0.001	0.001	0.000	0.000	0.000	0.000
19	A	318	LEU	0	-0.008	0.005	20.047	-0.026	-0.026	0.000	0.000	0.000	0.000
20	A	319	PRO	0	-0.016	0.002	15.991	0.023	0.023	0.000	0.000	0.000	0.000
21	A	320	VAL	0	-0.035	-0.022	18.710	0.000	0.000	0.000	0.000	0.000	0.000
22	A	321	TYR	0	0.031	0.002	13.678	-0.037	-0.037	0.000	0.000	0.000	0.000
23	A	322	LEU	0	-0.011	-0.004	19.261	0.019	0.019	0.000	0.000	0.000	0.000
24	A	323	HIS	0	0.053	0.047	21.618	0.002	0.002	0.000	0.000	0.000	0.000
25	A	324	ARG	1	0.823	0.884	23.171	0.172	0.172	0.000	0.000	0.000	0.000
26	A	325	GLU	-1	-0.830	-0.897	25.963	-0.139	-0.139	0.000	0.000	0.000	0.000
27	A	326	THR	0	-0.004	-0.027	25.628	0.005	0.005	0.000	0.000	0.000	0.000
28	A	327	ARG	1	0.905	0.957	27.535	0.149	0.149	0.000	0.000	0.000	0.000
29	A	328	VAL	0	0.036	0.035	23.270	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	329	VAL	0	-0.008	-0.015	22.843	-0.011	-0.011	0.000	0.000	0.000	0.000
31	A	330	THR	0	-0.021	-0.005	18.020	0.009	0.009	0.000	0.000	0.000	0.000
32	A	331	TRP	0	0.047	0.014	19.337	-0.009	-0.009	0.000	0.000	0.000	0.000
33	A	332	SER	0	-0.033	-0.022	14.804	-0.028	-0.028	0.000	0.000	0.000	0.000
34	A	333	ARG	1	0.842	0.929	9.681	0.903	0.903	0.000	0.000	0.000	0.000
35	A	334	PRO	0	0.007	0.025	12.745	-0.045	-0.045	0.000	0.000	0.000	0.000
36	A	335	TYR	0	0.016	-0.027	10.556	-0.065	-0.065	0.000	0.000	0.000	0.000
37	A	336	PHE	0	0.022	0.002	12.138	0.067	0.067	0.000	0.000	0.000	0.000
38	A	337	LEU	0	-0.011	0.010	12.591	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	338	GLY	0	0.040	0.021	14.289	0.025	0.025	0.000	0.000	0.000	0.000
40	A	339	THR	0	-0.033	-0.022	16.328	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	340	GLY	0	0.028	0.027	14.760	0.016	0.016	0.000	0.000	0.000	0.000
42	A	341	SER	0	-0.002	-0.018	15.683	0.000	0.000	0.000	0.000	0.000	0.000
43	A	342	ILE	0	0.059	0.029	16.482	-0.019	-0.019	0.000	0.000	0.000	0.000
44	A	343	ARG	1	0.933	0.953	17.427	0.120	0.120	0.000	0.000	0.000	0.000
45	A	344	LYS	1	0.898	0.942	16.306	0.114	0.114	0.000	0.000	0.000	0.000
46	A	345	HIS	0	-0.005	0.037	11.354	-0.019	-0.019	0.000	0.000	0.000	0.000
47	A	346	ASP	-1	-0.845	-0.919	7.829	-0.355	-0.355	0.000	0.000	0.000	0.000
48	A	347	PRO	0	-0.033	-0.008	8.919	-0.022	-0.022	0.000	0.000	0.000	0.000
49	A	348	PRO	0	0.045	0.026	5.545	-0.178	-0.178	0.000	0.000	0.000	0.000
50	A	349	ILE	0	0.079	0.017	2.755	-0.693	0.124	0.363	-0.259	-0.921	-0.001
51	A	350	SER	0	-0.036	-0.014	5.353	0.177	0.235	-0.001	-0.003	-0.054	0.000
52	A	351	SER	0	-0.067	-0.062	7.301	0.217	0.217	0.000	0.000	0.000	0.000
53	A	352	ILE	0	-0.046	0.007	7.822	0.166	0.166	0.000	0.000	0.000	0.000
54	A	353	PRO	0	-0.003	0.010	10.752	-0.011	-0.011	0.000	0.000	0.000	0.000
55	A	354	CYS	0	-0.033	-0.035	13.973	-0.027	-0.027	0.000	0.000	0.000	0.000
56	A	355	LEU	0	0.021	0.027	12.979	0.043	0.043	0.000	0.000	0.000	0.000

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