FMO DATABASE

FMODB ID: LJVK9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-202353.46526
FMO2-HF: Nuclear repulsion	182885.774735
FMO2-HF: Total energy	-19467.690525
FMO2-MP2: Total energy	-19523.894874

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.
-3.206	1.382	4.239	-2.921	-5.904	-0.013

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 : -0.018 / q_NPA : -0.016

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	B	3	LEU	0	-0.047	0.005	3.013	-2.540	0.524	-0.004	-1.426	-1.633	-0.001
4	B	4	MET	0	0.017	0.023	4.902	-0.958	-0.860	-0.001	-0.020	-0.078	0.000
5	B	5	TYR	0	-0.049	-0.034	7.399	0.265	0.265	0.000	0.000	0.000	0.000
6	B	6	THR	0	0.027	0.024	10.737	-0.030	-0.030	0.000	0.000	0.000	0.000
7	B	7	LEU	0	0.010	-0.006	14.044	-0.026	-0.026	0.000	0.000	0.000	0.000
8	B	8	GLY	0	0.058	0.039	17.071	0.027	0.027	0.000	0.000	0.000	0.000
9	B	9	PRO	0	0.011	-0.003	20.060	-0.007	-0.007	0.000	0.000	0.000	0.000
10	B	10	ASP	-1	-0.881	-0.948	21.625	-0.297	-0.297	0.000	0.000	0.000	0.000
11	B	11	GLY	0	-0.012	0.000	20.715	0.001	0.001	0.000	0.000	0.000	0.000
12	B	12	LYS	1	0.902	0.960	18.430	0.250	0.250	0.000	0.000	0.000	0.000
13	B	13	ARG	1	0.862	0.930	9.526	1.056	1.056	0.000	0.000	0.000	0.000
14	B	14	ILE	0	0.052	0.041	14.906	0.037	0.037	0.000	0.000	0.000	0.000
15	B	15	TYR	0	-0.002	-0.018	8.859	-0.134	-0.134	0.000	0.000	0.000	0.000
16	B	16	THR	0	0.009	0.004	10.096	0.139	0.139	0.000	0.000	0.000	0.000
17	B	17	LEU	0	0.047	0.018	8.033	-0.172	-0.172	0.000	0.000	0.000	0.000
18	B	18	LYS	1	0.911	0.969	9.412	0.138	0.138	0.000	0.000	0.000	0.000
19	B	19	LYS	1	0.982	0.976	5.135	1.265	1.265	0.000	0.000	0.000	0.000
20	B	20	VAL	0	0.038	0.029	10.922	-0.039	-0.039	0.000	0.000	0.000	0.000
21	B	21	THR	0	-0.023	-0.015	14.622	0.053	0.053	0.000	0.000	0.000	0.000
22	B	22	GLU	-1	-0.919	-0.968	16.517	-0.108	-0.108	0.000	0.000	0.000	0.000
23	B	23	SER	0	-0.023	-0.013	19.925	0.012	0.012	0.000	0.000	0.000	0.000
24	B	24	GLY	0	0.019	0.018	19.493	0.011	0.011	0.000	0.000	0.000	0.000
25	B	25	GLU	-1	-0.970	-0.976	15.745	-0.457	-0.457	0.000	0.000	0.000	0.000
26	B	26	ILE	0	0.009	0.000	12.482	-0.017	-0.017	0.000	0.000	0.000	0.000
27	B	27	THR	0	-0.058	-0.037	10.077	-0.085	-0.085	0.000	0.000	0.000	0.000
28	B	28	LYS	1	0.972	0.987	9.172	0.658	0.658	0.000	0.000	0.000	0.000
29	B	29	SER	0	0.024	0.004	3.946	-0.450	-0.235	0.002	-0.070	-0.146	0.000
30	B	30	ALA	0	-0.004	-0.006	5.284	0.331	0.331	0.000	0.000	0.000	0.000
31	B	31	HIS	0	-0.001	-0.001	2.381	-2.479	-1.322	4.243	-1.403	-3.997	-0.012
32	B	32	PRO	0	0.016	0.012	5.376	0.053	0.107	-0.001	-0.002	-0.050	0.000
33	B	33	ALA	0	0.007	-0.003	6.462	-0.257	-0.257	0.000	0.000	0.000	0.000
34	B	34	ARG	1	0.971	0.983	8.339	0.319	0.319	0.000	0.000	0.000	0.000
35	B	35	PHE	0	0.029	0.019	9.232	0.048	0.048	0.000	0.000	0.000	0.000
36	B	36	SER	0	-0.033	-0.029	12.698	0.056	0.056	0.000	0.000	0.000	0.000
37	B	37	PRO	0	0.023	-0.001	15.641	-0.017	-0.017	0.000	0.000	0.000	0.000
38	B	38	ASP	-1	-0.903	-0.929	18.911	-0.127	-0.127	0.000	0.000	0.000	0.000
39	B	39	ASP	-1	-0.870	-0.923	16.658	-0.323	-0.323	0.000	0.000	0.000	0.000
40	B	40	LYS	1	0.994	0.989	19.379	0.120	0.120	0.000	0.000	0.000	0.000
41	B	41	TYR	0	-0.066	-0.034	18.366	0.021	0.021	0.000	0.000	0.000	0.000
42	B	42	SER	0	0.030	0.008	21.319	-0.030	-0.030	0.000	0.000	0.000	0.000
43	B	43	ARG	1	0.993	0.999	22.739	0.138	0.138	0.000	0.000	0.000	0.000
44	B	44	GLN	0	0.040	0.018	22.658	-0.006	-0.006	0.000	0.000	0.000	0.000
45	B	45	ARG	1	0.902	0.940	17.167	0.352	0.352	0.000	0.000	0.000	0.000
46	B	46	VAL	0	-0.044	-0.017	21.631	-0.008	-0.008	0.000	0.000	0.000	0.000
47	B	47	THR	0	-0.055	-0.033	24.454	0.007	0.007	0.000	0.000	0.000	0.000
48	B	48	LEU	0	-0.015	0.017	20.704	0.004	0.004	0.000	0.000	0.000	0.000

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