FMO DATABASE

FMODB ID: J3V79

Calculation Name: 3LE4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LE4

Chain ID: A

ChEMBL ID:

UniProt ID: Q8WYQ5

Base Structure: X-ray

Registration Date: 2023-03-14

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	55
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-267182.696987
FMO2-HF: Nuclear repulsion	245387.256793
FMO2-HF: Total energy	-21795.440194
FMO2-MP2: Total energy	-21859.024739

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:298:PRO)

Summations of interaction energy for fragment #1(A:298: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.
-5.539	-1.297	3.394	-2.648	-4.989	-0.013

Interaction energy analysis for fragmet #1(A:298:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.004

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	300	THR	0	-0.045	-0.032	3.265	-2.414	-0.658	0.054	-0.877	-0.934	-0.001
4	A	301	GLU	-1	-0.826	-0.910	5.278	-0.286	-0.160	-0.001	-0.005	-0.120	0.000
5	A	302	PRO	0	0.003	-0.009	7.963	-0.008	-0.008	0.000	0.000	0.000	0.000
6	A	303	LEU	0	-0.006	0.009	11.192	-0.069	-0.069	0.000	0.000	0.000	0.000
7	A	304	PRO	0	-0.002	0.001	13.252	0.046	0.046	0.000	0.000	0.000	0.000
8	A	305	ASP	-1	-0.840	-0.921	16.220	-0.161	-0.161	0.000	0.000	0.000	0.000
9	A	306	GLY	0	-0.024	-0.018	19.746	-0.004	-0.004	0.000	0.000	0.000	0.000
10	A	307	TRP	0	-0.044	-0.027	16.202	0.000	0.000	0.000	0.000	0.000	0.000
11	A	308	ILE	0	-0.032	-0.006	16.400	0.014	0.014	0.000	0.000	0.000	0.000
12	A	309	MET	0	0.003	0.008	10.108	-0.064	-0.064	0.000	0.000	0.000	0.000
13	A	310	THR	0	-0.026	-0.021	14.051	0.054	0.054	0.000	0.000	0.000	0.000
14	A	311	PHE	0	0.045	0.027	14.819	-0.023	-0.023	0.000	0.000	0.000	0.000
15	A	312	HIS	0	0.067	0.054	16.442	-0.007	-0.007	0.000	0.000	0.000	0.000
16	A	313	ASN	0	0.017	-0.015	17.901	0.008	0.008	0.000	0.000	0.000	0.000
17	A	314	SER	0	-0.023	-0.021	17.656	0.007	0.007	0.000	0.000	0.000	0.000
18	A	315	GLY	0	-0.016	0.000	16.484	0.005	0.005	0.000	0.000	0.000	0.000
19	A	316	VAL	0	-0.035	-0.010	11.879	0.021	0.021	0.000	0.000	0.000	0.000
20	A	317	PRO	0	-0.018	-0.014	9.423	0.004	0.004	0.000	0.000	0.000	0.000
21	A	318	VAL	0	-0.014	0.005	12.138	-0.069	-0.069	0.000	0.000	0.000	0.000
22	A	319	TYR	0	0.028	0.002	8.153	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	320	LEU	0	-0.002	0.001	14.905	0.004	0.004	0.000	0.000	0.000	0.000
24	A	321	HIS	0	0.054	0.050	18.592	0.008	0.008	0.000	0.000	0.000	0.000
25	A	322	ARG	1	0.816	0.881	20.685	0.112	0.112	0.000	0.000	0.000	0.000
26	A	323	GLU	-1	-0.827	-0.897	23.233	-0.095	-0.095	0.000	0.000	0.000	0.000
27	A	324	SER	0	-0.010	-0.028	23.461	0.003	0.003	0.000	0.000	0.000	0.000
28	A	325	ARG	1	0.909	0.955	24.205	0.093	0.093	0.000	0.000	0.000	0.000
29	A	326	VAL	0	0.036	0.036	19.912	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	327	VAL	0	-0.010	-0.015	18.121	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	328	THR	0	-0.020	-0.004	13.676	0.002	0.002	0.000	0.000	0.000	0.000
32	A	329	TRP	0	0.036	0.011	13.618	0.007	0.007	0.000	0.000	0.000	0.000
33	A	330	SER	0	-0.037	-0.024	9.705	-0.068	-0.068	0.000	0.000	0.000	0.000
34	A	331	ARG	1	0.860	0.940	7.002	0.901	0.901	0.000	0.000	0.000	0.000
35	A	332	PRO	0	0.002	0.019	9.619	-0.064	-0.064	0.000	0.000	0.000	0.000
36	A	333	TYR	0	-0.013	-0.033	9.948	-0.057	-0.057	0.000	0.000	0.000	0.000
37	A	334	PHE	0	0.012	-0.001	12.011	0.069	0.069	0.000	0.000	0.000	0.000
38	A	335	LEU	0	-0.014	0.008	14.775	0.005	0.005	0.000	0.000	0.000	0.000
39	A	336	GLY	0	0.039	0.023	15.890	0.021	0.021	0.000	0.000	0.000	0.000
40	A	337	THR	0	-0.038	-0.025	18.976	0.002	0.002	0.000	0.000	0.000	0.000
41	A	338	GLY	0	0.027	0.026	17.652	0.012	0.012	0.000	0.000	0.000	0.000
42	A	339	SER	0	-0.008	-0.019	18.734	0.003	0.003	0.000	0.000	0.000	0.000
43	A	340	ILE	0	0.057	0.029	17.914	-0.018	-0.018	0.000	0.000	0.000	0.000
44	A	341	ARG	1	0.931	0.950	18.243	0.153	0.153	0.000	0.000	0.000	0.000
45	A	342	LYS	1	0.910	0.948	18.449	0.169	0.169	0.000	0.000	0.000	0.000
46	A	343	HIS	0	-0.003	0.035	12.931	-0.024	-0.024	0.000	0.000	0.000	0.000
47	A	344	ASP	-1	-0.851	-0.921	10.518	-0.366	-0.366	0.000	0.000	0.000	0.000
48	A	345	PRO	0	-0.038	-0.011	9.053	0.002	0.002	0.000	0.000	0.000	0.000
49	A	346	PRO	0	0.059	0.024	6.865	-0.087	-0.087	0.000	0.000	0.000	0.000
50	A	347	LEU	0	0.059	0.014	2.424	-0.833	-0.540	2.334	-0.812	-1.816	-0.001
51	A	348	SER	0	-0.042	-0.012	2.669	-3.271	-1.245	0.991	-1.076	-1.940	-0.011
52	A	349	SER	0	-0.058	-0.053	3.512	0.532	0.573	0.016	0.122	-0.179	0.000
53	A	350	ILE	0	-0.033	0.009	5.118	0.373	0.373	0.000	0.000	0.000	0.000
54	A	351	PRO	0	-0.011	0.000	6.147	-0.171	-0.171	0.000	0.000	0.000	0.000
55	A	352	CYS	0	-0.013	-0.001	8.510	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:298:PRO)