FMO DATABASE

FMODB ID: M3LQZ

Calculation Name: 3U28-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3U28

Chain ID: B

ChEMBL ID:

UniProt ID: P33322

Base Structure: X-ray

Registration Date: 2023-03-14

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	48
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-203078.750564
FMO2-HF: Nuclear repulsion	183610.501361
FMO2-HF: Total energy	-19468.249203
FMO2-MP2: Total energy	-19524.496371

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(B:1:MET)

Summations of interaction energy for fragment #1(B:1: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.
-8.849	-5.292	6.776	-3.62	-6.713	0.002

Interaction energy analysis for fragmet #1(B:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.047 / q_NPA : 0.025

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	B	3	LEU	0	-0.034	-0.011	3.244	-3.897	-0.362	0.009	-1.832	-1.712	0.005
4	B	4	MET	0	0.013	0.028	4.021	-1.025	-0.791	0.001	-0.085	-0.150	0.000
5	B	5	TYR	0	-0.030	-0.029	6.769	0.286	0.286	0.000	0.000	0.000	0.000
6	B	6	THR	0	-0.006	0.009	10.194	-0.124	-0.124	0.000	0.000	0.000	0.000
7	B	7	LEU	0	0.000	-0.001	13.604	0.051	0.051	0.000	0.000	0.000	0.000
8	B	8	GLY	0	0.057	0.037	16.698	-0.011	-0.011	0.000	0.000	0.000	0.000
9	B	9	PRO	0	0.000	-0.009	19.654	-0.008	-0.008	0.000	0.000	0.000	0.000
10	B	10	ASP	-1	-0.814	-0.897	21.133	0.041	0.041	0.000	0.000	0.000	0.000
11	B	11	GLY	0	0.005	0.006	20.762	0.004	0.004	0.000	0.000	0.000	0.000
12	B	12	LYS	1	0.813	0.898	17.856	-0.043	-0.043	0.000	0.000	0.000	0.000
13	B	13	ARG	1	0.837	0.907	9.099	-0.156	-0.156	0.000	0.000	0.000	0.000
14	B	14	ILE	0	0.049	0.038	14.654	0.047	0.047	0.000	0.000	0.000	0.000
15	B	15	TYR	0	0.014	-0.004	8.795	-0.027	-0.027	0.000	0.000	0.000	0.000
16	B	16	THR	0	0.006	0.000	9.638	-0.050	-0.050	0.000	0.000	0.000	0.000
17	B	17	LEU	0	0.056	0.027	7.492	0.170	0.170	0.000	0.000	0.000	0.000
18	B	18	LYS	1	0.853	0.936	8.958	-0.288	-0.288	0.000	0.000	0.000	0.000
19	B	19	LYS	1	0.887	0.933	5.963	1.639	1.639	0.000	0.000	0.000	0.000
20	B	20	VAL	0	0.013	0.020	11.092	-0.012	-0.012	0.000	0.000	0.000	0.000
21	B	21	THR	0	0.004	0.001	14.523	0.037	0.037	0.000	0.000	0.000	0.000
22	B	22	GLU	-1	-0.781	-0.902	16.505	-0.048	-0.048	0.000	0.000	0.000	0.000
23	B	23	SER	0	-0.039	-0.014	19.827	0.002	0.002	0.000	0.000	0.000	0.000
24	B	24	GLY	0	0.020	0.021	19.607	-0.001	-0.001	0.000	0.000	0.000	0.000
25	B	25	GLU	-1	-0.842	-0.911	16.113	-0.184	-0.184	0.000	0.000	0.000	0.000
26	B	26	ILE	0	0.023	0.006	12.605	-0.008	-0.008	0.000	0.000	0.000	0.000
27	B	27	THR	0	-0.056	-0.041	9.995	-0.029	-0.029	0.000	0.000	0.000	0.000
28	B	28	LYS	1	0.843	0.903	9.231	0.123	0.123	0.000	0.000	0.000	0.000
29	B	29	SER	0	0.007	-0.008	4.728	-0.031	0.062	-0.001	-0.003	-0.089	0.000
30	B	30	ALA	0	0.009	0.003	4.917	0.077	0.077	0.000	0.000	0.000	0.000
31	B	31	HIS	0	0.013	0.013	2.505	-5.395	-5.700	6.767	-1.700	-4.762	-0.003
32	B	32	PRO	0	0.038	0.025	5.456	-0.129	-0.129	0.000	0.000	0.000	0.000
33	B	33	ALA	0	0.022	0.007	6.637	-0.179	-0.179	0.000	0.000	0.000	0.000
34	B	34	ARG	1	0.905	0.941	8.935	0.184	0.184	0.000	0.000	0.000	0.000
35	B	35	PHE	0	0.033	0.022	9.829	0.053	0.053	0.000	0.000	0.000	0.000
36	B	36	SER	0	-0.015	-0.053	13.120	0.001	0.001	0.000	0.000	0.000	0.000
37	B	37	PRO	0	-0.016	0.006	16.143	-0.001	-0.001	0.000	0.000	0.000	0.000
38	B	38	ASP	-1	-0.828	-0.874	19.100	-0.103	-0.103	0.000	0.000	0.000	0.000
39	B	39	ASP	-1	-0.817	-0.883	17.119	-0.177	-0.177	0.000	0.000	0.000	0.000
40	B	40	LYS	1	0.963	0.972	19.740	0.095	0.095	0.000	0.000	0.000	0.000
41	B	41	TYR	0	-0.023	-0.007	19.060	0.011	0.011	0.000	0.000	0.000	0.000
42	B	42	SER	0	0.036	0.015	21.935	-0.010	-0.010	0.000	0.000	0.000	0.000
43	B	43	ARG	1	0.974	1.002	22.761	0.083	0.083	0.000	0.000	0.000	0.000
44	B	44	GLN	0	0.072	0.036	22.897	0.003	0.003	0.000	0.000	0.000	0.000
45	B	45	ARG	1	0.802	0.862	17.101	0.172	0.172	0.000	0.000	0.000	0.000
46	B	46	VAL	0	-0.028	-0.006	21.806	-0.002	-0.002	0.000	0.000	0.000	0.000
47	B	47	THR	0	-0.053	-0.041	24.695	0.007	0.007	0.000	0.000	0.000	0.000
48	B	48	LEU	0	-0.020	0.010	21.131	0.003	0.003	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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