FMO DATABASE

FMODB ID: ZV12N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-297567.296299
FMO2-HF: Nuclear repulsion	275226.975459
FMO2-HF: Total energy	-22340.32084
FMO2-MP2: Total energy	-22405.665857

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.
-6.631	-2.195	4.212	-2.975	-5.67	-0.003

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 : -0.009 / q_NPA : -0.014

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	D	387	VAL	0	0.011	0.021	3.228	-2.873	0.054	0.168	-1.450	-1.645	-0.003
4	D	388	ARG	1	0.880	0.933	5.201	0.290	0.324	-0.001	-0.003	-0.029	0.000
5	D	389	ALA	0	0.037	0.028	8.939	-0.035	-0.035	0.000	0.000	0.000	0.000
6	D	390	LEU	0	-0.050	-0.019	11.633	0.075	0.075	0.000	0.000	0.000	0.000
7	D	391	TYR	0	-0.037	-0.034	14.088	0.060	0.060	0.000	0.000	0.000	0.000
8	D	392	ASP	-1	-0.815	-0.883	15.882	-0.160	-0.160	0.000	0.000	0.000	0.000
9	D	393	TYR	0	-0.064	-0.066	16.100	-0.012	-0.012	0.000	0.000	0.000	0.000
10	D	394	ASP	-1	-0.930	-0.964	18.077	-0.152	-0.152	0.000	0.000	0.000	0.000
11	D	395	GLY	0	0.017	0.014	19.674	-0.015	-0.015	0.000	0.000	0.000	0.000
12	D	396	GLN	0	-0.130	-0.068	20.469	0.041	0.041	0.000	0.000	0.000	0.000
13	D	397	GLU	-1	-0.898	-0.975	20.538	-0.217	-0.217	0.000	0.000	0.000	0.000
14	D	398	GLN	0	-0.117	-0.055	21.387	0.012	0.012	0.000	0.000	0.000	0.000
15	D	399	ASP	-1	-0.902	-0.941	17.853	-0.226	-0.226	0.000	0.000	0.000	0.000
16	D	400	GLU	-1	-0.780	-0.847	16.593	-0.339	-0.339	0.000	0.000	0.000	0.000
17	D	401	LEU	0	-0.078	-0.023	12.229	0.034	0.034	0.000	0.000	0.000	0.000
18	D	402	SER	0	0.009	-0.004	16.210	0.012	0.012	0.000	0.000	0.000	0.000
19	D	403	PHE	0	-0.083	-0.039	12.977	-0.014	-0.014	0.000	0.000	0.000	0.000
20	D	404	LYS	1	0.840	0.902	16.476	0.122	0.122	0.000	0.000	0.000	0.000
21	D	405	ALA	0	-0.003	-0.006	15.427	-0.029	-0.029	0.000	0.000	0.000	0.000
22	D	406	GLY	0	-0.050	-0.027	14.445	0.035	0.035	0.000	0.000	0.000	0.000
23	D	407	ASP	-1	-0.850	-0.914	13.734	-0.103	-0.103	0.000	0.000	0.000	0.000
24	D	408	GLU	-1	-0.830	-0.903	9.287	0.110	0.110	0.000	0.000	0.000	0.000
25	D	409	LEU	0	-0.016	0.001	7.718	0.095	0.095	0.000	0.000	0.000	0.000
26	D	410	THR	0	-0.065	-0.040	3.842	-0.028	0.155	0.000	-0.045	-0.137	0.000
27	D	411	LYS	1	0.910	0.956	2.135	2.001	2.309	4.024	-1.076	-3.255	0.002
28	D	412	LEU	0	-0.085	-0.055	3.530	-1.359	-0.677	0.020	-0.308	-0.394	-0.002
29	D	413	GLY	0	-0.038	-0.021	5.388	0.309	0.309	0.000	0.000	0.000	0.000
30	D	414	GLU	-1	-0.916	-0.953	4.011	-2.780	-2.478	0.001	-0.093	-0.210	0.000
31	D	415	GLU	-1	-0.915	-0.980	6.845	-0.655	-0.655	0.000	0.000	0.000	0.000
32	D	416	ASP	-1	-0.807	-0.902	9.768	-0.411	-0.411	0.000	0.000	0.000	0.000
33	D	417	GLU	-1	-0.959	-0.983	13.276	-0.323	-0.323	0.000	0.000	0.000	0.000
34	D	418	GLN	0	-0.128	-0.070	16.018	0.044	0.044	0.000	0.000	0.000	0.000
35	D	419	GLY	0	0.042	0.035	13.321	0.027	0.027	0.000	0.000	0.000	0.000
36	D	420	TRP	0	-0.081	-0.021	12.557	-0.067	-0.067	0.000	0.000	0.000	0.000
37	D	421	CYS	0	-0.023	0.000	7.725	-0.139	-0.139	0.000	0.000	0.000	0.000
38	D	422	ARG	1	0.974	0.992	8.546	0.636	0.636	0.000	0.000	0.000	0.000
39	D	423	GLY	0	0.048	0.023	7.196	-0.370	-0.370	0.000	0.000	0.000	0.000
40	D	424	ARG	1	0.897	0.948	8.594	0.162	0.162	0.000	0.000	0.000	0.000
41	D	425	LEU	0	0.066	0.039	9.579	-0.010	-0.010	0.000	0.000	0.000	0.000
42	D	426	ASP	-1	-0.890	-0.957	11.738	0.233	0.233	0.000	0.000	0.000	0.000
43	D	427	SER	0	-0.133	-0.050	13.800	-0.017	-0.017	0.000	0.000	0.000	0.000
44	D	428	GLY	0	0.063	-0.010	14.600	0.007	0.007	0.000	0.000	0.000	0.000
45	D	429	GLN	0	-0.045	0.001	15.443	-0.010	-0.010	0.000	0.000	0.000	0.000
46	D	430	LEU	0	-0.014	-0.020	12.276	-0.040	-0.040	0.000	0.000	0.000	0.000
47	D	431	GLY	0	0.042	0.026	12.747	0.049	0.049	0.000	0.000	0.000	0.000
48	D	432	LEU	0	-0.036	-0.033	12.118	-0.115	-0.115	0.000	0.000	0.000	0.000
49	D	433	TYR	0	0.023	0.008	6.332	-0.100	-0.100	0.000	0.000	0.000	0.000
50	D	434	PRO	0	0.059	0.048	12.098	-0.067	-0.067	0.000	0.000	0.000	0.000
51	D	435	ALA	0	0.049	0.010	8.964	-0.027	-0.027	0.000	0.000	0.000	0.000
52	D	436	ASN	0	-0.024	-0.020	9.731	-0.036	-0.036	0.000	0.000	0.000	0.000
53	D	437	TYR	0	-0.026	-0.013	11.890	0.067	0.067	0.000	0.000	0.000	0.000
54	D	438	VAL	0	-0.030	0.000	6.731	0.002	0.002	0.000	0.000	0.000	0.000
55	D	439	GLU	-1	-0.860	-0.894	8.839	-0.185	-0.185	0.000	0.000	0.000	0.000
56	D	440	ALA	0	-0.109	-0.093	5.704	-0.140	-0.140	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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