FMO DATABASE

FMODB ID: 72G5K

Calculation Name: 3K2T-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K2T

Chain ID: A

ChEMBL ID:

UniProt ID: Q927Y2

Base Structure: X-ray

Registration Date: 2023-06-21

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

Total energy (hartree)

FMO2-HF: Electronic energy	-292455.879151
FMO2-HF: Nuclear repulsion	269860.399526
FMO2-HF: Total energy	-22595.479625
FMO2-MP2: Total energy	-22660.886308

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(A:1:GLU)

Summations of interaction energy for fragment #1(A:1:GLU)

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.
14.942	20.518	1.6	-2.683	-4.492	-0.005

Interaction energy analysis for fragmet #1(A:1:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.949 / q_NPA : -0.975

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	A	3	VAL	0	0.004	-0.002	3.882	-4.199	-2.718	-0.016	-0.722	-0.743	0.002
4	A	4	ARG	1	0.839	0.923	6.798	-22.613	-22.613	0.000	0.000	0.000	0.000
5	A	5	THR	0	0.045	0.011	10.301	-0.456	-0.456	0.000	0.000	0.000	0.000
6	A	6	LYS	1	0.925	0.973	12.132	-16.130	-16.130	0.000	0.000	0.000	0.000
7	A	7	GLN	0	-0.014	-0.008	13.882	-0.219	-0.219	0.000	0.000	0.000	0.000
8	A	8	PHE	0	0.065	0.018	15.303	-0.338	-0.338	0.000	0.000	0.000	0.000
9	A	9	SER	0	0.005	0.010	14.114	-0.392	-0.392	0.000	0.000	0.000	0.000
10	A	10	LEU	0	0.020	0.016	9.423	1.264	1.264	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.789	0.870	8.930	-25.164	-25.164	0.000	0.000	0.000	0.000
12	A	12	PRO	0	0.043	0.033	11.281	0.632	0.632	0.000	0.000	0.000	0.000
13	A	13	MET	0	-0.046	-0.012	7.836	1.491	1.491	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.681	-0.832	12.388	17.788	17.788	0.000	0.000	0.000	0.000
15	A	15	SER	0	-0.037	-0.019	12.418	0.841	0.841	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.943	-0.981	12.660	19.830	19.830	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.815	-0.907	9.125	26.847	26.847	0.000	0.000	0.000	0.000
18	A	18	ALA	0	-0.010	-0.005	7.885	2.470	2.470	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.015	-0.012	8.726	0.959	0.959	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.007	0.006	6.059	0.639	0.639	0.000	0.000	0.000	0.000
21	A	21	GLN	0	0.016	-0.008	2.566	2.924	4.366	0.574	-0.805	-1.212	-0.012
22	A	22	MET	0	-0.061	-0.010	5.005	0.888	0.969	-0.001	0.000	-0.079	0.000
23	A	23	ASN	0	-0.032	-0.023	7.629	-0.875	-0.875	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.043	-0.015	2.364	-1.776	-0.283	0.858	-0.673	-1.677	0.001
25	A	25	LEU	0	-0.056	-0.022	3.273	0.063	1.142	0.185	-0.483	-0.781	0.004
26	A	26	GLY	0	-0.017	0.004	5.457	-2.421	-2.421	0.000	0.000	0.000	0.000
27	A	27	HIS	0	-0.033	-0.001	8.028	-3.293	-3.293	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.009	-0.017	10.705	-0.057	-0.057	0.000	0.000	0.000	0.000
29	A	29	PHE	0	-0.023	-0.037	13.003	-0.853	-0.853	0.000	0.000	0.000	0.000
30	A	30	TYR	0	0.030	0.012	6.011	0.349	0.349	0.000	0.000	0.000	0.000
31	A	31	VAL	0	-0.014	-0.003	11.387	-0.871	-0.871	0.000	0.000	0.000	0.000
32	A	32	TYR	0	-0.037	-0.026	11.100	1.340	1.340	0.000	0.000	0.000	0.000
33	A	33	THR	0	-0.030	-0.005	12.707	-0.804	-0.804	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.778	-0.887	14.184	15.835	15.835	0.000	0.000	0.000	0.000
35	A	35	ALA	0	-0.015	-0.003	15.613	-0.220	-0.220	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.903	-0.953	17.126	13.872	13.872	0.000	0.000	0.000	0.000
37	A	37	THR	0	-0.044	-0.049	20.330	-0.607	-0.607	0.000	0.000	0.000	0.000
38	A	38	ASN	0	-0.089	-0.043	19.026	-0.251	-0.251	0.000	0.000	0.000	0.000
39	A	39	GLY	0	0.039	0.034	20.067	-0.135	-0.135	0.000	0.000	0.000	0.000
40	A	40	THR	0	-0.056	-0.035	16.981	0.865	0.865	0.000	0.000	0.000	0.000
41	A	41	ASN	0	0.041	0.037	16.605	-1.094	-1.094	0.000	0.000	0.000	0.000
42	A	42	ILE	0	-0.029	-0.025	15.027	0.864	0.864	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.012	0.026	12.014	-0.819	-0.819	0.000	0.000	0.000	0.000
44	A	44	TYR	0	0.005	-0.017	14.250	0.260	0.260	0.000	0.000	0.000	0.000
45	A	45	SER	0	0.046	0.022	14.223	-0.174	-0.174	0.000	0.000	0.000	0.000
46	A	46	ARG	1	0.829	0.913	16.704	-12.398	-12.398	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.974	0.969	20.516	-10.750	-10.750	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.816	-0.876	22.932	11.568	11.568	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.011	0.000	20.448	-0.187	-0.187	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.851	0.930	19.421	-11.023	-11.023	0.000	0.000	0.000	0.000
51	A	51	TYR	0	0.083	0.037	13.749	0.335	0.335	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.043	-0.027	17.813	-0.846	-0.846	0.000	0.000	0.000	0.000
53	A	53	LEU	0	0.004	0.003	17.017	0.830	0.830	0.000	0.000	0.000	0.000
54	A	54	ILE	0	-0.037	-0.020	18.782	-0.731	-0.731	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.880	-0.933	19.385	12.367	12.367	0.000	0.000	0.000	0.000
56	A	56	THR	0	-0.095	-0.049	21.148	-0.483	-0.483	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:1:GLU)