FMO DATABASE

FMODB ID: ZYK3N

Calculation Name: 3L4F-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3L4F

Chain ID: A

ChEMBL ID:

UniProt ID: O55043

Base Structure: X-ray

Registration Date: 2023-06-19

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	61
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-271204.888659
FMO2-HF: Nuclear repulsion	245185.837847
FMO2-HF: Total energy	-26019.050812
FMO2-MP2: Total energy	-26093.630581

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:586:MET)

Summations of interaction energy for fragment #1(A:586:MET)

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.
-17.345	-15.35	16.254	-7.741	-10.505	-0.058

Interaction energy analysis for fragmet #1(A:586:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.065 / q_NPA : -0.037

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	588	LYS	1	0.924	0.969	3.230	-7.363	-3.684	0.060	-1.855	-1.883	0.000
4	A	589	SER	0	0.078	0.040	4.929	-0.477	-0.379	-0.001	-0.001	-0.095	0.000
5	A	590	LEU	0	0.025	0.067	7.506	0.096	0.096	0.000	0.000	0.000	0.000
6	A	591	VAL	0	-0.006	-0.025	2.444	-0.781	0.185	0.709	-0.347	-1.329	0.000
7	A	592	ASP	-1	-0.789	-0.908	2.038	-5.307	-9.481	14.942	-5.116	-5.652	-0.058
8	A	593	THR	0	-0.030	-0.058	4.445	0.312	0.513	0.000	-0.027	-0.173	0.000
9	A	594	VAL	0	-0.044	-0.029	6.666	0.068	0.068	0.000	0.000	0.000	0.000
10	A	595	TYR	0	-0.007	-0.030	3.429	-1.352	-0.157	0.545	-0.380	-1.359	0.000
11	A	596	ALA	0	0.072	0.074	5.492	-0.324	-0.294	-0.001	-0.015	-0.014	0.000
12	A	597	LEU	0	0.083	0.043	7.564	-0.102	-0.102	0.000	0.000	0.000	0.000
13	A	598	LYS	1	0.832	0.943	7.739	-1.543	-1.543	0.000	0.000	0.000	0.000
14	A	599	ASP	-1	-0.890	-0.954	6.713	0.038	0.038	0.000	0.000	0.000	0.000
15	A	600	GLU	-1	-0.953	-0.991	10.032	-0.025	-0.025	0.000	0.000	0.000	0.000
16	A	601	VAL	0	-0.060	-0.035	12.870	-0.043	-0.043	0.000	0.000	0.000	0.000
17	A	602	GLN	0	-0.094	-0.058	12.640	0.017	0.017	0.000	0.000	0.000	0.000
18	A	603	GLU	-1	-0.862	-0.934	13.906	-0.113	-0.113	0.000	0.000	0.000	0.000
19	A	604	LEU	0	0.059	0.034	16.119	-0.009	-0.009	0.000	0.000	0.000	0.000
20	A	605	ARG	1	0.888	0.951	15.991	-0.226	-0.226	0.000	0.000	0.000	0.000
21	A	606	GLN	0	-0.078	-0.050	17.017	0.004	0.004	0.000	0.000	0.000	0.000
22	A	607	ASP	-1	-0.851	-0.919	20.184	-0.044	-0.044	0.000	0.000	0.000	0.000
23	A	608	ASN	0	0.031	0.010	22.342	-0.012	-0.012	0.000	0.000	0.000	0.000
24	A	609	LYS	1	0.887	0.951	20.775	-0.100	-0.100	0.000	0.000	0.000	0.000
25	A	610	LYS	1	0.948	0.981	22.190	0.057	0.057	0.000	0.000	0.000	0.000
26	A	611	MET	0	0.050	0.027	26.223	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	612	LYS	1	0.909	0.944	28.060	-0.055	-0.055	0.000	0.000	0.000	0.000
28	A	613	LYS	1	0.964	0.980	27.816	-0.016	-0.016	0.000	0.000	0.000	0.000
29	A	614	SER	0	0.073	0.037	30.653	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	615	LEU	0	0.003	0.018	32.082	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	616	GLU	-1	-0.947	-0.963	32.974	0.026	0.026	0.000	0.000	0.000	0.000
32	A	617	GLU	-1	-0.954	-0.988	33.062	-0.016	-0.016	0.000	0.000	0.000	0.000
33	A	618	GLU	-1	-0.884	-0.950	36.502	-0.013	-0.013	0.000	0.000	0.000	0.000
34	A	619	GLN	0	-0.087	-0.055	37.227	0.002	0.002	0.000	0.000	0.000	0.000
35	A	620	ARG	1	0.869	0.938	39.364	0.004	0.004	0.000	0.000	0.000	0.000
36	A	621	ALA	0	0.022	0.027	41.197	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	622	ARG	1	0.911	0.938	42.545	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	623	LYS	1	0.928	0.936	43.455	-0.016	-0.016	0.000	0.000	0.000	0.000
39	A	624	ASP	-1	-0.886	-0.943	45.894	0.000	0.000	0.000	0.000	0.000	0.000
40	A	625	LEU	0	0.043	0.021	47.228	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	626	GLU	-1	-0.869	-0.910	47.937	0.006	0.006	0.000	0.000	0.000	0.000
42	A	627	LYS	1	0.888	0.952	48.018	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	628	LEU	0	0.020	0.018	51.098	0.000	0.000	0.000	0.000	0.000	0.000
44	A	629	VAL	0	0.054	0.027	52.388	0.000	0.000	0.000	0.000	0.000	0.000
45	A	630	ARG	1	0.952	0.961	51.551	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	631	LYS	1	0.892	0.940	56.324	0.002	0.002	0.000	0.000	0.000	0.000
47	A	632	VAL	0	-0.008	0.007	56.966	0.000	0.000	0.000	0.000	0.000	0.000
48	A	633	LEU	0	0.002	-0.006	57.953	0.000	0.000	0.000	0.000	0.000	0.000
49	A	634	LYS	1	0.902	0.951	60.708	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	635	ASN	0	0.054	0.012	61.877	0.001	0.001	0.000	0.000	0.000	0.000
51	A	636	MET	0	-0.042	-0.001	62.387	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	637	ASN	0	-0.046	-0.025	65.345	0.000	0.000	0.000	0.000	0.000	0.000
53	A	638	ASP	-1	-0.944	-0.951	66.875	0.001	0.001	0.000	0.000	0.000	0.000
54	A	639	PRO	0	-0.001	-0.003	67.391	0.000	0.000	0.000	0.000	0.000	0.000
55	A	640	ALA	0	-0.046	-0.015	67.036	0.000	0.000	0.000	0.000	0.000	0.000
56	A	641	TRP	0	-0.074	-0.039	67.263	0.000	0.000	0.000	0.000	0.000	0.000
57	A	642	ASP	-1	-0.874	-0.930	70.281	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	643	GLU	-1	-0.985	-0.993	73.828	-0.007	-0.007	0.000	0.000	0.000	0.000
59	A	644	THR	0	-0.020	-0.025	76.739	0.001	0.001	0.000	0.000	0.000	0.000
60	A	645	ASN	0	-0.037	-0.006	80.493	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	646	LEU	0	-0.016	-0.004	82.353	0.001	0.001	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:586:MET)