FMO DATABASE

FMODB ID: Q1ZQY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-271035.038543
FMO2-HF: Nuclear repulsion	245014.580745
FMO2-HF: Total energy	-26020.457798
FMO2-MP2: Total energy	-26094.897552

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.
-18.707	-10.252	7.073	-5.748	-9.779	-0.034

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 : -0.083 / q_NPA : -0.050

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	588	LYS	1	0.827	0.895	3.409	-0.921	1.223	-0.009	-1.076	-1.059	0.001
4	A	589	SER	0	0.066	0.033	4.998	0.109	0.230	-0.001	-0.002	-0.118	0.000
5	A	590	LEU	0	-0.003	0.023	7.500	0.186	0.186	0.000	0.000	0.000	0.000
6	A	591	VAL	0	0.014	0.006	2.512	-0.793	0.129	0.427	-0.268	-1.081	0.000
7	A	592	ASP	-1	-0.714	-0.882	2.446	-11.465	-6.994	2.660	-3.281	-3.850	-0.038
8	A	593	THR	0	0.001	-0.010	4.326	0.494	0.666	-0.001	0.062	-0.234	0.000
9	A	594	VAL	0	-0.033	-0.018	6.828	0.021	0.021	0.000	0.000	0.000	0.000
10	A	595	TYR	0	-0.038	-0.042	3.222	-2.034	-1.482	3.998	-1.130	-3.419	0.003
11	A	596	ALA	0	0.034	0.033	5.080	-0.751	-0.678	-0.001	-0.053	-0.018	0.000
12	A	597	LEU	0	0.084	0.029	7.201	-0.251	-0.251	0.000	0.000	0.000	0.000
13	A	598	LYS	1	0.848	0.947	6.206	-3.312	-3.312	0.000	0.000	0.000	0.000
14	A	599	ASP	-1	-0.900	-0.950	6.424	1.028	1.028	0.000	0.000	0.000	0.000
15	A	600	GLU	-1	-0.930	-0.968	9.747	0.296	0.296	0.000	0.000	0.000	0.000
16	A	601	VAL	0	-0.023	-0.020	12.381	-0.117	-0.117	0.000	0.000	0.000	0.000
17	A	602	GLN	0	0.000	0.011	11.907	-0.102	-0.102	0.000	0.000	0.000	0.000
18	A	603	GLU	-1	-0.767	-0.893	13.727	0.082	0.082	0.000	0.000	0.000	0.000
19	A	604	LEU	0	0.023	0.026	15.702	-0.044	-0.044	0.000	0.000	0.000	0.000
20	A	605	ARG	1	0.867	0.931	14.637	-0.559	-0.559	0.000	0.000	0.000	0.000
21	A	606	GLN	0	-0.114	-0.062	16.814	-0.021	-0.021	0.000	0.000	0.000	0.000
22	A	607	ASP	-1	-0.802	-0.898	19.738	0.091	0.091	0.000	0.000	0.000	0.000
23	A	608	ASN	0	-0.062	-0.036	21.756	-0.029	-0.029	0.000	0.000	0.000	0.000
24	A	609	LYS	1	0.914	0.960	21.685	-0.239	-0.239	0.000	0.000	0.000	0.000
25	A	610	LYS	1	0.820	0.909	19.037	-0.127	-0.127	0.000	0.000	0.000	0.000
26	A	611	MET	0	0.051	0.021	25.640	-0.014	-0.014	0.000	0.000	0.000	0.000
27	A	612	LYS	1	0.926	0.971	27.492	-0.138	-0.138	0.000	0.000	0.000	0.000
28	A	613	LYS	1	0.826	0.912	28.755	-0.100	-0.100	0.000	0.000	0.000	0.000
29	A	614	SER	0	0.099	0.042	30.107	-0.006	-0.006	0.000	0.000	0.000	0.000
30	A	615	LEU	0	0.002	0.007	31.247	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	616	GLU	-1	-0.900	-0.944	32.954	0.097	0.097	0.000	0.000	0.000	0.000
32	A	617	GLU	-1	-0.929	-0.972	32.530	0.048	0.048	0.000	0.000	0.000	0.000
33	A	618	GLU	-1	-0.886	-0.942	36.001	0.035	0.035	0.000	0.000	0.000	0.000
34	A	619	GLN	0	-0.065	-0.041	36.600	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	620	ARG	1	0.840	0.908	38.985	-0.042	-0.042	0.000	0.000	0.000	0.000
36	A	621	ALA	0	0.033	0.031	40.435	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	622	ARG	1	0.959	0.968	41.940	-0.051	-0.051	0.000	0.000	0.000	0.000
38	A	623	LYS	1	0.954	0.961	43.653	-0.057	-0.057	0.000	0.000	0.000	0.000
39	A	624	ASP	-1	-0.814	-0.883	44.552	0.036	0.036	0.000	0.000	0.000	0.000
40	A	625	LEU	0	0.027	0.013	46.047	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	626	GLU	-1	-0.884	-0.939	46.994	0.042	0.042	0.000	0.000	0.000	0.000
42	A	627	LYS	1	0.819	0.906	46.936	-0.040	-0.040	0.000	0.000	0.000	0.000
43	A	628	LEU	0	0.015	0.014	50.228	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	629	VAL	0	0.042	0.021	51.960	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	630	ARG	1	0.938	0.969	50.298	-0.037	-0.037	0.000	0.000	0.000	0.000
46	A	631	LYS	1	0.848	0.908	55.343	-0.020	-0.020	0.000	0.000	0.000	0.000
47	A	632	VAL	0	0.012	0.022	56.854	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	633	LEU	0	0.021	0.000	56.985	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	634	LYS	1	0.952	0.979	60.007	-0.023	-0.023	0.000	0.000	0.000	0.000
50	A	635	ASN	0	-0.016	-0.013	61.837	0.000	0.000	0.000	0.000	0.000	0.000
51	A	636	MET	0	-0.012	-0.004	61.802	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	637	ASN	0	-0.064	-0.014	64.625	0.000	0.000	0.000	0.000	0.000	0.000
53	A	638	ASP	-1	-0.929	-0.971	66.102	0.018	0.018	0.000	0.000	0.000	0.000
54	A	639	PRO	0	0.019	0.008	66.503	0.001	0.001	0.000	0.000	0.000	0.000
55	A	640	ALA	0	-0.041	-0.005	66.458	0.000	0.000	0.000	0.000	0.000	0.000
56	A	641	TRP	0	-0.051	-0.030	66.525	0.000	0.000	0.000	0.000	0.000	0.000
57	A	642	ASP	-1	-0.889	-0.945	69.733	0.012	0.012	0.000	0.000	0.000	0.000
58	A	643	GLU	-1	-0.974	-0.978	73.047	0.008	0.008	0.000	0.000	0.000	0.000
59	A	644	THR	0	-0.037	-0.035	76.329	0.000	0.000	0.000	0.000	0.000	0.000
60	A	645	ASN	0	-0.037	-0.004	80.169	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	646	LEU	0	-0.002	0.004	82.126	0.000	0.000	0.000	0.000	0.000	0.000

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