FMO DATABASE

FMODB ID: 2K6ZR

Calculation Name: 3U28-B-Xray308

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	49
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-203166.344121
FMO2-HF: Nuclear repulsion	183679.665298
FMO2-HF: Total energy	-19486.678823
FMO2-MP2: Total energy	-19543.017535

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.
-3.241	1.333	4.248	-2.945	-5.878	-0.014

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 : -0.015

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	0.006	3.013	-2.547	0.492	0.009	-1.432	-1.616	-0.002
4	B	4	MET	0	0.017	0.023	4.902	-0.969	-0.873	0.000	-0.022	-0.074	0.000
5	B	5	TYR	0	-0.050	-0.034	7.399	0.273	0.273	0.000	0.000	0.000	0.000
6	B	6	THR	0	0.029	0.023	10.737	-0.026	-0.026	0.000	0.000	0.000	0.000
7	B	7	LEU	0	0.010	-0.006	14.044	-0.025	-0.025	0.000	0.000	0.000	0.000
8	B	8	GLY	0	0.057	0.038	17.071	0.030	0.030	0.000	0.000	0.000	0.000
9	B	9	PRO	0	0.012	-0.003	20.060	-0.007	-0.007	0.000	0.000	0.000	0.000
10	B	10	ASP	-1	-0.881	-0.947	21.625	-0.299	-0.299	0.000	0.000	0.000	0.000
11	B	11	GLY	0	-0.011	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	0.861	0.929	9.526	1.069	1.069	0.000	0.000	0.000	0.000
14	B	14	ILE	0	0.051	0.041	14.906	0.039	0.039	0.000	0.000	0.000	0.000
15	B	15	TYR	0	-0.002	-0.018	8.859	-0.137	-0.137	0.000	0.000	0.000	0.000
16	B	16	THR	0	0.010	0.005	10.096	0.144	0.144	0.000	0.000	0.000	0.000
17	B	17	LEU	0	0.048	0.018	8.032	-0.171	-0.171	0.000	0.000	0.000	0.000
18	B	18	LYS	1	0.911	0.969	9.412	0.133	0.133	0.000	0.000	0.000	0.000
19	B	19	LYS	1	0.981	0.976	5.133	1.210	1.210	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	-0.026	-0.017	14.622	0.057	0.057	0.000	0.000	0.000	0.000
22	B	22	GLU	-1	-0.918	-0.967	16.517	-0.102	-0.102	0.000	0.000	0.000	0.000
23	B	23	SER	0	-0.020	-0.011	19.928	0.012	0.012	0.000	0.000	0.000	0.000
24	B	24	GLY	0	0.018	0.017	19.493	0.010	0.010	0.000	0.000	0.000	0.000
25	B	25	GLU	-1	-0.972	-0.977	15.745	-0.458	-0.458	0.000	0.000	0.000	0.000
26	B	26	ILE	0	0.012	0.001	12.482	-0.017	-0.017	0.000	0.000	0.000	0.000
27	B	27	THR	0	-0.062	-0.038	10.077	-0.090	-0.090	0.000	0.000	0.000	0.000
28	B	28	LYS	1	0.975	0.987	9.172	0.654	0.654	0.000	0.000	0.000	0.000
29	B	29	SER	0	0.023	0.004	3.946	-0.470	-0.252	0.003	-0.072	-0.149	0.000
30	B	30	ALA	0	-0.003	-0.006	5.284	0.337	0.337	0.000	0.000	0.000	0.000
31	B	31	HIS	0	0.001	0.000	2.381	-2.502	-1.331	4.236	-1.416	-3.992	-0.012
32	B	32	PRO	0	0.015	0.012	5.376	0.078	0.128	0.000	-0.003	-0.047	0.000
33	B	33	ALA	0	0.006	-0.003	6.462	-0.262	-0.262	0.000	0.000	0.000	0.000
34	B	34	ARG	1	0.971	0.984	8.339	0.334	0.334	0.000	0.000	0.000	0.000
35	B	35	PHE	0	0.030	0.019	9.232	0.056	0.056	0.000	0.000	0.000	0.000
36	B	36	SER	0	-0.033	-0.030	12.698	0.059	0.059	0.000	0.000	0.000	0.000
37	B	37	PRO	0	0.022	-0.002	15.641	-0.016	-0.016	0.000	0.000	0.000	0.000
38	B	38	ASP	-1	-0.902	-0.928	18.912	-0.132	-0.132	0.000	0.000	0.000	0.000
39	B	39	ASP	-1	-0.873	-0.924	16.658	-0.330	-0.330	0.000	0.000	0.000	0.000
40	B	40	LYS	1	0.997	0.990	19.379	0.124	0.124	0.000	0.000	0.000	0.000
41	B	41	TYR	0	-0.068	-0.035	18.366	0.022	0.022	0.000	0.000	0.000	0.000
42	B	42	SER	0	0.031	0.007	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	0.141	0.141	0.000	0.000	0.000	0.000
44	B	44	GLN	0	0.041	0.018	22.658	-0.006	-0.006	0.000	0.000	0.000	0.000
45	B	45	ARG	1	0.897	0.936	17.166	0.358	0.358	0.000	0.000	0.000	0.000
46	B	46	VAL	0	-0.039	-0.014	21.631	-0.007	-0.007	0.000	0.000	0.000	0.000
47	B	47	THR	0	-0.056	-0.036	24.454	0.008	0.008	0.000	0.000	0.000	0.000
48	B	48	LEU	0	-0.035	0.019	20.552	0.003	0.003	0.000	0.000	0.000	0.000
49	B	49	NME	0	0.020	0.001	21.919	0.001	0.001	0.000	0.000	0.000	0.000

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