FMO DATABASE

FMODB ID: 6Y83Z

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	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	56
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-297414.453647
FMO2-HF: Nuclear repulsion	275075.083257
FMO2-HF: Total energy	-22339.37039
FMO2-MP2: Total energy	-22404.768002

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.
-5.828	-3.749	8.161	-3.565	-6.677	-0.001

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 : 0.010 / q_NPA : -0.003

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	-0.039	-0.058	3.020	-2.615	0.345	0.380	-1.527	-1.812	-0.005
4	D	388	ARG	1	0.909	0.964	4.953	0.120	0.160	-0.001	-0.005	-0.034	0.000
5	D	389	ALA	0	0.057	0.038	8.701	-0.025	-0.025	0.000	0.000	0.000	0.000
6	D	390	LEU	0	-0.045	-0.019	11.434	0.072	0.072	0.000	0.000	0.000	0.000
7	D	391	TYR	0	-0.051	-0.033	13.930	0.058	0.058	0.000	0.000	0.000	0.000
8	D	392	ASP	-1	-0.844	-0.919	15.720	-0.169	-0.169	0.000	0.000	0.000	0.000
9	D	393	TYR	0	-0.010	-0.025	15.638	-0.005	-0.005	0.000	0.000	0.000	0.000
10	D	394	ASP	-1	-0.920	-0.959	17.944	-0.171	-0.171	0.000	0.000	0.000	0.000
11	D	395	GLY	0	0.010	0.007	19.579	-0.016	-0.016	0.000	0.000	0.000	0.000
12	D	396	GLN	0	-0.114	-0.042	20.043	0.052	0.052	0.000	0.000	0.000	0.000
13	D	397	GLU	-1	-0.905	-0.970	20.104	-0.263	-0.263	0.000	0.000	0.000	0.000
14	D	398	GLN	0	-0.080	-0.036	21.196	0.009	0.009	0.000	0.000	0.000	0.000
15	D	399	ASP	-1	-0.936	-0.966	17.181	-0.329	-0.329	0.000	0.000	0.000	0.000
16	D	400	GLU	-1	-0.857	-0.912	16.442	-0.373	-0.373	0.000	0.000	0.000	0.000
17	D	401	LEU	0	-0.068	-0.027	12.204	0.041	0.041	0.000	0.000	0.000	0.000
18	D	402	SER	0	0.007	-0.002	15.968	0.021	0.021	0.000	0.000	0.000	0.000
19	D	403	PHE	0	-0.045	-0.029	12.394	-0.018	-0.018	0.000	0.000	0.000	0.000
20	D	404	LYS	1	0.933	0.977	16.206	0.112	0.112	0.000	0.000	0.000	0.000
21	D	405	ALA	0	0.008	0.002	15.201	-0.029	-0.029	0.000	0.000	0.000	0.000
22	D	406	GLY	0	-0.073	-0.037	14.220	0.034	0.034	0.000	0.000	0.000	0.000
23	D	407	ASP	-1	-0.901	-0.946	13.465	-0.099	-0.099	0.000	0.000	0.000	0.000
24	D	408	GLU	-1	-0.917	-0.974	9.035	0.114	0.114	0.000	0.000	0.000	0.000
25	D	409	LEU	0	0.013	0.014	7.393	0.050	0.050	0.000	0.000	0.000	0.000
26	D	410	THR	0	-0.083	-0.046	3.558	0.045	0.251	0.001	-0.046	-0.162	0.000
27	D	411	LYS	1	0.965	0.985	2.031	2.807	0.719	7.734	-1.628	-4.019	0.007
28	D	412	LEU	0	-0.077	-0.056	3.317	-1.904	-1.057	0.048	-0.356	-0.540	-0.003
29	D	413	GLY	0	-0.039	-0.018	5.415	0.345	0.345	0.000	0.000	0.000	0.000
30	D	414	GLU	-1	-0.988	-0.991	4.982	-2.264	-2.150	-0.001	-0.003	-0.110	0.000
31	D	415	GLU	-1	-0.919	-0.982	6.759	-0.587	-0.587	0.000	0.000	0.000	0.000
32	D	416	ASP	-1	-0.832	-0.911	9.574	-0.494	-0.494	0.000	0.000	0.000	0.000
33	D	417	GLU	-1	-0.953	-0.988	13.107	-0.352	-0.352	0.000	0.000	0.000	0.000
34	D	418	GLN	0	-0.120	-0.060	15.745	0.024	0.024	0.000	0.000	0.000	0.000
35	D	419	GLY	0	0.042	0.036	13.107	0.035	0.035	0.000	0.000	0.000	0.000
36	D	420	TRP	0	-0.069	-0.018	12.433	-0.062	-0.062	0.000	0.000	0.000	0.000
37	D	421	CYS	0	-0.019	0.003	7.462	-0.135	-0.135	0.000	0.000	0.000	0.000
38	D	422	ARG	1	0.995	1.004	8.569	0.801	0.801	0.000	0.000	0.000	0.000
39	D	423	GLY	0	0.030	0.017	7.078	-0.444	-0.444	0.000	0.000	0.000	0.000
40	D	424	ARG	1	0.890	0.945	8.281	0.357	0.357	0.000	0.000	0.000	0.000
41	D	425	LEU	0	0.055	0.037	9.493	-0.039	-0.039	0.000	0.000	0.000	0.000
42	D	426	ASP	-1	-0.876	-0.956	11.905	0.049	0.049	0.000	0.000	0.000	0.000
43	D	427	SER	0	-0.139	-0.051	13.692	-0.011	-0.011	0.000	0.000	0.000	0.000
44	D	428	GLY	0	0.054	-0.007	14.507	0.018	0.018	0.000	0.000	0.000	0.000
45	D	429	GLN	0	-0.026	0.004	15.352	-0.019	-0.019	0.000	0.000	0.000	0.000
46	D	430	LEU	0	-0.041	-0.033	12.419	-0.056	-0.056	0.000	0.000	0.000	0.000
47	D	431	GLY	0	0.057	0.038	12.489	0.063	0.063	0.000	0.000	0.000	0.000
48	D	432	LEU	0	-0.017	-0.024	11.926	-0.144	-0.144	0.000	0.000	0.000	0.000
49	D	433	TYR	0	-0.004	-0.002	6.087	-0.123	-0.123	0.000	0.000	0.000	0.000
50	D	434	PRO	0	0.055	0.042	12.113	-0.068	-0.068	0.000	0.000	0.000	0.000
51	D	435	ALA	0	0.032	0.003	8.915	-0.024	-0.024	0.000	0.000	0.000	0.000
52	D	436	ASN	0	-0.042	-0.025	9.749	-0.015	-0.015	0.000	0.000	0.000	0.000
53	D	437	TYR	0	-0.005	-0.010	11.866	0.075	0.075	0.000	0.000	0.000	0.000
54	D	438	VAL	0	0.038	0.083	6.391	-0.097	-0.097	0.000	0.000	0.000	0.000
55	D	439	GLU	-1	-0.939	-0.968	8.741	-0.085	-0.085	0.000	0.000	0.000	0.000
56	D	440	ALA	0	-0.049	-0.034	5.711	-0.095	-0.095	0.000	0.000	0.000	0.000

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