FMO DATABASE

FMODB ID: R56R8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-270953.357381
FMO2-HF: Nuclear repulsion	244933.330464
FMO2-HF: Total energy	-26020.026917
FMO2-MP2: Total energy	-26094.551606

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.
-23.038	-13.696	7.09	-6.277	-10.154	-0.044

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 : -0.072 / q_NPA : -0.046

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	0.829	0.919	3.645	-1.999	0.962	-0.023	-1.516	-1.422	0.000
4	A	589	SER	0	0.093	0.044	5.071	-0.402	-0.314	-0.001	-0.001	-0.086	0.000
5	A	590	LEU	0	-0.022	0.011	7.551	0.095	0.095	0.000	0.000	0.000	0.000
6	A	591	VAL	0	0.012	-0.011	2.448	-0.909	-0.119	1.312	-0.563	-1.539	-0.001
7	A	592	ASP	-1	-0.782	-0.910	2.427	-13.792	-9.786	4.011	-3.445	-4.571	-0.044
8	A	593	THR	0	0.004	-0.007	4.230	0.030	0.181	0.001	0.017	-0.169	0.000
9	A	594	VAL	0	-0.047	-0.031	7.006	0.031	0.031	0.000	0.000	0.000	0.000
10	A	595	TYR	0	-0.002	-0.024	3.193	-1.960	-0.661	1.791	-0.732	-2.359	0.001
11	A	596	ALA	0	0.055	0.064	5.220	-0.636	-0.589	-0.001	-0.037	-0.008	0.000
12	A	597	LEU	0	0.104	0.056	6.997	-0.026	-0.026	0.000	0.000	0.000	0.000
13	A	598	LYS	1	0.817	0.937	6.735	-2.718	-2.718	0.000	0.000	0.000	0.000
14	A	599	ASP	-1	-0.892	-0.954	6.306	0.268	0.268	0.000	0.000	0.000	0.000
15	A	600	GLU	-1	-0.937	-0.985	9.408	-0.088	-0.088	0.000	0.000	0.000	0.000
16	A	601	VAL	0	-0.067	-0.043	12.155	-0.045	-0.045	0.000	0.000	0.000	0.000
17	A	602	GLN	0	-0.025	-0.015	12.580	-0.013	-0.013	0.000	0.000	0.000	0.000
18	A	603	GLU	-1	-0.806	-0.908	13.450	-0.050	-0.050	0.000	0.000	0.000	0.000
19	A	604	LEU	0	0.037	0.023	15.589	-0.016	-0.016	0.000	0.000	0.000	0.000
20	A	605	ARG	1	0.872	0.938	15.091	-0.405	-0.405	0.000	0.000	0.000	0.000
21	A	606	GLN	0	-0.103	-0.055	16.451	0.009	0.009	0.000	0.000	0.000	0.000
22	A	607	ASP	-1	-0.791	-0.890	19.827	-0.028	-0.028	0.000	0.000	0.000	0.000
23	A	608	ASN	0	-0.036	-0.019	21.823	-0.015	-0.015	0.000	0.000	0.000	0.000
24	A	609	LYS	1	0.899	0.958	21.392	-0.187	-0.187	0.000	0.000	0.000	0.000
25	A	610	LYS	1	0.873	0.936	20.085	0.005	0.005	0.000	0.000	0.000	0.000
26	A	611	MET	0	0.060	0.026	25.745	-0.008	-0.008	0.000	0.000	0.000	0.000
27	A	612	LYS	1	0.890	0.938	27.585	-0.095	-0.095	0.000	0.000	0.000	0.000
28	A	613	LYS	1	0.821	0.901	28.958	-0.062	-0.062	0.000	0.000	0.000	0.000
29	A	614	SER	0	0.082	0.040	30.249	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	615	LEU	0	0.011	0.020	31.430	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	616	GLU	-1	-0.836	-0.902	32.769	0.064	0.064	0.000	0.000	0.000	0.000
32	A	617	GLU	-1	-0.931	-0.973	33.062	0.010	0.010	0.000	0.000	0.000	0.000
33	A	618	GLU	-1	-0.889	-0.953	36.082	0.000	0.000	0.000	0.000	0.000	0.000
34	A	619	GLN	0	-0.072	-0.044	36.751	0.000	0.000	0.000	0.000	0.000	0.000
35	A	620	ARG	1	0.809	0.894	39.083	-0.017	-0.017	0.000	0.000	0.000	0.000
36	A	621	ALA	0	0.027	0.028	40.822	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	622	ARG	1	0.918	0.947	42.081	-0.022	-0.022	0.000	0.000	0.000	0.000
38	A	623	LYS	1	0.937	0.947	43.714	-0.034	-0.034	0.000	0.000	0.000	0.000
39	A	624	ASP	-1	-0.809	-0.885	45.442	0.017	0.017	0.000	0.000	0.000	0.000
40	A	625	LEU	0	0.046	0.026	46.516	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	626	GLU	-1	-0.845	-0.911	47.280	0.019	0.019	0.000	0.000	0.000	0.000
42	A	627	LYS	1	0.823	0.907	47.463	-0.020	-0.020	0.000	0.000	0.000	0.000
43	A	628	LEU	0	0.015	0.015	50.629	0.000	0.000	0.000	0.000	0.000	0.000
44	A	629	VAL	0	0.061	0.025	52.250	0.000	0.000	0.000	0.000	0.000	0.000
45	A	630	ARG	1	0.946	0.966	50.866	-0.018	-0.018	0.000	0.000	0.000	0.000
46	A	631	LYS	1	0.844	0.920	55.865	-0.006	-0.006	0.000	0.000	0.000	0.000
47	A	632	VAL	0	0.001	0.008	56.690	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	633	LEU	0	0.010	0.003	57.383	0.000	0.000	0.000	0.000	0.000	0.000
49	A	634	LYS	1	0.931	0.963	60.277	-0.012	-0.012	0.000	0.000	0.000	0.000
50	A	635	ASN	0	-0.004	-0.015	62.046	0.001	0.001	0.000	0.000	0.000	0.000
51	A	636	MET	0	-0.008	0.011	62.029	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	637	ASN	0	-0.066	-0.031	64.874	0.000	0.000	0.000	0.000	0.000	0.000
53	A	638	ASP	-1	-0.931	-0.952	66.454	0.007	0.007	0.000	0.000	0.000	0.000
54	A	639	PRO	0	0.011	0.006	67.012	0.001	0.001	0.000	0.000	0.000	0.000
55	A	640	ALA	0	-0.042	-0.017	66.696	0.000	0.000	0.000	0.000	0.000	0.000
56	A	641	TRP	0	-0.059	-0.030	67.161	0.000	0.000	0.000	0.000	0.000	0.000
57	A	642	ASP	-1	-0.874	-0.938	69.988	0.003	0.003	0.000	0.000	0.000	0.000
58	A	643	GLU	-1	-0.971	-0.979	73.269	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	644	THR	0	-0.034	-0.030	76.422	0.001	0.001	0.000	0.000	0.000	0.000
60	A	645	ASN	0	-0.039	-0.005	80.188	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	646	LEU	0	-0.002	0.001	82.461	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)