FMO DATABASE

FMODB ID: 1498Z

Calculation Name: 3LKU-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LKU

Chain ID: B

ChEMBL ID:

UniProt ID: Q12125

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:

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	52
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-184995.076653
FMO2-HF: Nuclear repulsion	165268.067606
FMO2-HF: Total energy	-19727.009047
FMO2-MP2: Total energy	-19786.193447

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:3:THR)

Summations of interaction energy for fragment #1(B:3:THR)

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.
-6.263	-0.894	0.045	-2.746	-2.668	0.012

Interaction energy analysis for fragmet #1(B:3:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.044 / 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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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	5	ALA	0	0.011	0.012	3.094	-5.246	-0.211	0.046	-2.672	-2.408	0.012
4	B	6	SER	0	0.024	0.016	4.177	-1.286	-0.952	-0.001	-0.074	-0.260	0.000
5	B	7	GLY	0	0.021	0.013	5.909	-0.312	-0.312	0.000	0.000	0.000	0.000
6	B	8	PRO	0	0.018	-0.002	6.977	0.195	0.195	0.000	0.000	0.000	0.000
7	B	9	GLU	-1	-0.914	-0.947	9.189	-0.639	-0.639	0.000	0.000	0.000	0.000
8	B	10	HIS	0	-0.018	-0.007	6.626	-0.020	-0.020	0.000	0.000	0.000	0.000
9	B	11	GLU	-1	-0.813	-0.911	8.743	-0.483	-0.483	0.000	0.000	0.000	0.000
10	B	12	PHE	0	-0.030	-0.010	11.319	0.149	0.149	0.000	0.000	0.000	0.000
11	B	13	VAL	0	0.025	0.005	11.740	0.101	0.101	0.000	0.000	0.000	0.000
12	B	14	SER	0	-0.018	-0.003	11.625	0.135	0.135	0.000	0.000	0.000	0.000
13	B	15	LYS	1	0.869	0.918	13.632	0.631	0.631	0.000	0.000	0.000	0.000
14	B	16	PHE	0	0.006	0.011	16.556	0.066	0.066	0.000	0.000	0.000	0.000
15	B	17	LEU	0	-0.002	-0.001	15.936	0.046	0.046	0.000	0.000	0.000	0.000
16	B	18	THR	0	-0.021	-0.003	17.260	0.044	0.044	0.000	0.000	0.000	0.000
17	B	19	LEU	0	-0.021	-0.020	19.770	0.034	0.034	0.000	0.000	0.000	0.000
18	B	20	ALA	0	-0.047	-0.016	21.613	0.026	0.026	0.000	0.000	0.000	0.000
19	B	21	THR	0	-0.104	-0.073	21.401	0.019	0.019	0.000	0.000	0.000	0.000
20	B	22	LEU	0	-0.019	0.011	23.879	0.007	0.007	0.000	0.000	0.000	0.000
21	B	23	THR	0	0.002	0.012	25.841	0.012	0.012	0.000	0.000	0.000	0.000
22	B	24	GLU	-1	-0.918	-0.965	27.751	-0.146	-0.146	0.000	0.000	0.000	0.000
23	B	25	PRO	0	-0.021	-0.006	26.170	0.008	0.008	0.000	0.000	0.000	0.000
24	B	26	LYS	1	0.951	0.978	29.048	0.107	0.107	0.000	0.000	0.000	0.000
25	B	27	LEU	0	-0.042	-0.017	31.181	0.009	0.009	0.000	0.000	0.000	0.000
26	B	28	PRO	0	0.062	0.038	29.967	-0.010	-0.010	0.000	0.000	0.000	0.000
27	B	29	LYS	1	0.999	0.974	23.160	0.184	0.184	0.000	0.000	0.000	0.000
28	B	30	SER	0	-0.009	0.003	28.691	0.000	0.000	0.000	0.000	0.000	0.000
29	B	31	TYR	0	-0.012	-0.003	31.956	0.009	0.009	0.000	0.000	0.000	0.000
30	B	32	THR	0	0.014	-0.002	33.249	-0.002	-0.002	0.000	0.000	0.000	0.000
31	B	33	LYS	1	0.878	0.963	35.930	0.070	0.070	0.000	0.000	0.000	0.000
32	B	34	PRO	0	0.050	0.023	38.516	0.001	0.001	0.000	0.000	0.000	0.000
33	B	35	LEU	0	0.041	0.011	39.664	0.001	0.001	0.000	0.000	0.000	0.000
34	B	36	LYS	1	0.937	0.964	41.945	0.047	0.047	0.000	0.000	0.000	0.000
35	B	37	ASP	-1	-0.848	-0.932	42.871	-0.056	-0.056	0.000	0.000	0.000	0.000
36	B	38	VAL	0	-0.092	-0.042	39.572	-0.002	-0.002	0.000	0.000	0.000	0.000
37	B	39	THR	0	0.008	0.010	42.178	0.002	0.002	0.000	0.000	0.000	0.000
38	B	40	ASN	0	-0.017	-0.023	39.664	0.001	0.001	0.000	0.000	0.000	0.000
39	B	41	LEU	0	0.018	0.001	38.179	-0.003	-0.003	0.000	0.000	0.000	0.000
40	B	42	GLY	0	-0.009	0.020	35.645	-0.003	-0.003	0.000	0.000	0.000	0.000
41	B	43	VAL	0	-0.009	-0.005	33.829	0.005	0.005	0.000	0.000	0.000	0.000
42	B	44	PRO	0	0.013	0.005	34.748	-0.002	-0.002	0.000	0.000	0.000	0.000
43	B	45	LEU	0	0.016	0.012	29.886	-0.003	-0.003	0.000	0.000	0.000	0.000
44	B	46	PRO	0	0.004	0.000	29.309	0.006	0.006	0.000	0.000	0.000	0.000
45	B	47	THR	0	0.001	0.003	32.037	-0.001	-0.001	0.000	0.000	0.000	0.000
46	B	48	LEU	0	0.011	0.004	27.896	0.000	0.000	0.000	0.000	0.000	0.000
47	B	49	LYS	1	0.944	0.957	28.582	0.026	0.026	0.000	0.000	0.000	0.000
48	B	50	TYR	0	0.020	0.022	24.805	0.002	0.002	0.000	0.000	0.000	0.000
49	B	51	LYS	1	0.962	0.986	31.382	0.007	0.007	0.000	0.000	0.000	0.000
50	B	52	TYR	0	0.031	0.011	33.307	0.000	0.000	0.000	0.000	0.000	0.000
51	B	53	LYS	1	0.916	0.938	34.866	0.003	0.003	0.000	0.000	0.000	0.000
52	B	54	GLN	0	0.095	0.074	35.753	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:3:THR)