FMO DATABASE

FMODB ID: R8V18

Calculation Name: 2X3W-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2X3W

Chain ID: D

ChEMBL ID:

UniProt ID: Q61644

Base Structure: X-ray

Registration Date: 2023-09-23

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	-298802.618077
FMO2-HF: Nuclear repulsion	276462.078321
FMO2-HF: Total energy	-22340.539757
FMO2-MP2: Total energy	-22405.903469

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(D:385:VAL)

Summations of interaction energy for fragment #1(D:385:VAL)

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.
-6.736	-1.835	3.068	-2.67	-5.298	-0.002

Interaction energy analysis for fragmet #1(D:385:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / q_NPA : -0.018

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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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	D	387	VAL	0	-0.009	0.008	3.002	-3.514	-0.728	0.349	-1.420	-1.714	-0.003
4	D	388	ARG	1	0.835	0.912	5.073	0.390	0.416	-0.001	-0.003	-0.022	0.000
5	D	389	ALA	0	0.056	0.036	8.896	-0.035	-0.035	0.000	0.000	0.000	0.000
6	D	390	LEU	0	-0.048	-0.021	11.669	0.085	0.085	0.000	0.000	0.000	0.000
7	D	391	TYR	0	-0.059	-0.042	14.130	0.065	0.065	0.000	0.000	0.000	0.000
8	D	392	ASP	-1	-0.808	-0.881	15.757	-0.176	-0.176	0.000	0.000	0.000	0.000
9	D	393	TYR	0	-0.087	-0.075	15.951	-0.015	-0.015	0.000	0.000	0.000	0.000
10	D	394	ASP	-1	-0.920	-0.955	17.921	-0.165	-0.165	0.000	0.000	0.000	0.000
11	D	395	GLY	0	0.025	0.009	19.230	-0.015	-0.015	0.000	0.000	0.000	0.000
12	D	396	GLN	0	-0.121	-0.062	20.063	0.042	0.042	0.000	0.000	0.000	0.000
13	D	397	GLU	-1	-0.950	-0.980	20.462	-0.216	-0.216	0.000	0.000	0.000	0.000
14	D	398	GLN	0	-0.102	-0.062	20.818	0.008	0.008	0.000	0.000	0.000	0.000
15	D	399	ASP	-1	-0.867	-0.924	17.485	-0.234	-0.234	0.000	0.000	0.000	0.000
16	D	400	GLU	-1	-0.807	-0.864	16.211	-0.354	-0.354	0.000	0.000	0.000	0.000
17	D	401	LEU	0	-0.065	-0.024	11.409	0.037	0.037	0.000	0.000	0.000	0.000
18	D	402	SER	0	-0.001	-0.006	15.430	0.008	0.008	0.000	0.000	0.000	0.000
19	D	403	PHE	0	-0.074	-0.035	13.064	-0.013	-0.013	0.000	0.000	0.000	0.000
20	D	404	LYS	1	0.822	0.886	16.032	0.137	0.137	0.000	0.000	0.000	0.000
21	D	405	ALA	0	-0.005	-0.008	15.315	-0.031	-0.031	0.000	0.000	0.000	0.000
22	D	406	GLY	0	-0.046	-0.023	14.626	0.040	0.040	0.000	0.000	0.000	0.000
23	D	407	ASP	-1	-0.844	-0.910	13.191	-0.139	-0.139	0.000	0.000	0.000	0.000
24	D	408	GLU	-1	-0.835	-0.903	9.204	0.186	0.186	0.000	0.000	0.000	0.000
25	D	409	LEU	0	-0.007	0.003	7.252	0.099	0.099	0.000	0.000	0.000	0.000
26	D	410	THR	0	-0.060	-0.034	3.686	-0.131	0.176	0.002	-0.088	-0.221	0.000
27	D	411	LYS	1	0.901	0.950	2.150	1.832	2.803	2.687	-0.848	-2.810	0.003
28	D	412	LEU	0	-0.079	-0.048	3.399	-0.875	-0.252	0.032	-0.285	-0.370	-0.002
29	D	413	GLY	0	-0.041	-0.021	4.842	0.366	0.366	0.000	0.000	0.000	0.000
30	D	414	GLU	-1	-0.895	-0.946	4.380	-2.548	-2.360	-0.001	-0.026	-0.161	0.000
31	D	415	GLU	-1	-0.922	-0.969	6.800	-0.739	-0.739	0.000	0.000	0.000	0.000
32	D	416	ASP	-1	-0.804	-0.898	9.981	-0.384	-0.384	0.000	0.000	0.000	0.000
33	D	417	GLU	-1	-0.964	-0.995	13.541	-0.318	-0.318	0.000	0.000	0.000	0.000
34	D	418	GLN	0	-0.114	-0.056	15.960	0.048	0.048	0.000	0.000	0.000	0.000
35	D	419	GLY	0	0.039	0.038	12.879	0.021	0.021	0.000	0.000	0.000	0.000
36	D	420	TRP	0	-0.085	-0.040	12.285	-0.076	-0.076	0.000	0.000	0.000	0.000
37	D	421	CYS	0	-0.029	0.005	7.591	-0.121	-0.121	0.000	0.000	0.000	0.000
38	D	422	ARG	1	0.977	0.989	8.688	0.626	0.626	0.000	0.000	0.000	0.000
39	D	423	GLY	0	0.028	0.007	7.022	-0.371	-0.371	0.000	0.000	0.000	0.000
40	D	424	ARG	1	0.915	0.961	7.869	0.239	0.239	0.000	0.000	0.000	0.000
41	D	425	LEU	0	0.097	0.049	9.151	-0.075	-0.075	0.000	0.000	0.000	0.000
42	D	426	ASP	-1	-0.861	-0.927	10.704	0.292	0.292	0.000	0.000	0.000	0.000
43	D	427	SER	0	-0.100	-0.066	13.046	-0.021	-0.021	0.000	0.000	0.000	0.000
44	D	428	GLY	0	0.031	0.003	14.278	0.006	0.006	0.000	0.000	0.000	0.000
45	D	429	GLN	0	-0.015	0.023	15.074	-0.012	-0.012	0.000	0.000	0.000	0.000
46	D	430	LEU	0	-0.025	-0.022	11.630	-0.043	-0.043	0.000	0.000	0.000	0.000
47	D	431	GLY	0	0.049	0.029	12.085	0.059	0.059	0.000	0.000	0.000	0.000
48	D	432	LEU	0	-0.023	-0.020	11.596	-0.130	-0.130	0.000	0.000	0.000	0.000
49	D	433	TYR	0	0.049	0.018	6.320	-0.109	-0.109	0.000	0.000	0.000	0.000
50	D	434	PRO	0	0.040	0.042	11.632	-0.078	-0.078	0.000	0.000	0.000	0.000
51	D	435	ALA	0	0.044	0.009	9.270	-0.022	-0.022	0.000	0.000	0.000	0.000
52	D	436	ASN	0	-0.013	-0.021	10.180	-0.030	-0.030	0.000	0.000	0.000	0.000
53	D	437	TYR	0	-0.029	-0.014	12.367	0.064	0.064	0.000	0.000	0.000	0.000
54	D	438	VAL	0	-0.022	-0.001	6.990	-0.006	-0.006	0.000	0.000	0.000	0.000
55	D	439	GLU	-1	-0.851	-0.891	8.976	-0.212	-0.212	0.000	0.000	0.000	0.000
56	D	440	ALA	0	-0.082	-0.079	5.857	-0.178	-0.178	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:385:VAL)