FMO DATABASE

FMODB ID: YQ2V2

Calculation Name: 3LKU-B-Xray313

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: 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	53
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-185536.986626
FMO2-HF: Nuclear repulsion	165791.131846
FMO2-HF: Total energy	-19745.85478
FMO2-MP2: Total energy	-19805.145705

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.
-5.396	-0.46	0.025	-2.456	-2.505	0.007

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 : 0.041 / q_NPA : 0.006

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	5	ALA	0	0.031	0.021	3.243	-4.506	0.048	0.024	-2.383	-2.195	0.007
4	B	6	SER	0	0.002	0.006	3.519	-0.988	-0.606	0.001	-0.073	-0.310	0.000
5	B	7	GLY	0	0.028	0.017	5.718	-0.439	-0.439	0.000	0.000	0.000	0.000
6	B	8	PRO	0	0.015	-0.004	6.732	0.207	0.207	0.000	0.000	0.000	0.000
7	B	9	GLU	-1	-0.916	-0.951	9.035	-0.483	-0.483	0.000	0.000	0.000	0.000
8	B	10	HIS	0	-0.008	0.005	6.484	0.067	0.067	0.000	0.000	0.000	0.000
9	B	11	GLU	-1	-0.899	-0.968	8.605	-0.850	-0.850	0.000	0.000	0.000	0.000
10	B	12	PHE	0	-0.034	-0.014	11.364	0.170	0.170	0.000	0.000	0.000	0.000
11	B	13	VAL	0	0.024	0.005	11.615	0.108	0.108	0.000	0.000	0.000	0.000
12	B	14	SER	0	-0.013	-0.002	11.882	0.145	0.145	0.000	0.000	0.000	0.000
13	B	15	LYS	1	0.955	0.970	13.830	0.708	0.708	0.000	0.000	0.000	0.000
14	B	16	PHE	0	-0.005	0.007	16.553	0.079	0.079	0.000	0.000	0.000	0.000
15	B	17	LEU	0	0.008	0.002	16.403	0.055	0.055	0.000	0.000	0.000	0.000
16	B	18	THR	0	-0.009	0.008	17.701	0.047	0.047	0.000	0.000	0.000	0.000
17	B	19	LEU	0	-0.035	-0.027	20.074	0.043	0.043	0.000	0.000	0.000	0.000
18	B	20	ALA	0	-0.047	-0.016	21.726	0.032	0.032	0.000	0.000	0.000	0.000
19	B	21	THR	0	-0.105	-0.067	21.701	0.023	0.023	0.000	0.000	0.000	0.000
20	B	22	LEU	0	0.002	0.016	24.348	0.005	0.005	0.000	0.000	0.000	0.000
21	B	23	THR	0	-0.045	-0.007	26.183	0.018	0.018	0.000	0.000	0.000	0.000
22	B	24	GLU	-1	-0.898	-0.961	28.012	-0.198	-0.198	0.000	0.000	0.000	0.000
23	B	25	PRO	0	-0.001	0.006	26.408	0.011	0.011	0.000	0.000	0.000	0.000
24	B	26	LYS	1	0.942	0.975	29.174	0.125	0.125	0.000	0.000	0.000	0.000
25	B	27	LEU	0	-0.045	-0.023	31.175	0.011	0.011	0.000	0.000	0.000	0.000
26	B	28	PRO	0	0.068	0.043	30.016	-0.012	-0.012	0.000	0.000	0.000	0.000
27	B	29	LYS	1	1.007	0.978	23.578	0.248	0.248	0.000	0.000	0.000	0.000
28	B	30	SER	0	-0.018	0.001	28.772	0.003	0.003	0.000	0.000	0.000	0.000
29	B	31	TYR	0	-0.014	-0.005	31.989	0.012	0.012	0.000	0.000	0.000	0.000
30	B	32	THR	0	0.026	0.006	33.183	0.000	0.000	0.000	0.000	0.000	0.000
31	B	33	LYS	1	0.908	0.968	35.841	0.078	0.078	0.000	0.000	0.000	0.000
32	B	34	PRO	0	0.053	0.023	38.358	0.002	0.002	0.000	0.000	0.000	0.000
33	B	35	LEU	0	0.043	0.011	39.269	0.002	0.002	0.000	0.000	0.000	0.000
34	B	36	LYS	1	0.937	0.965	41.760	0.051	0.051	0.000	0.000	0.000	0.000
35	B	37	ASP	-1	-0.855	-0.923	42.734	-0.058	-0.058	0.000	0.000	0.000	0.000
36	B	38	VAL	0	-0.110	-0.051	39.329	-0.002	-0.002	0.000	0.000	0.000	0.000
37	B	39	THR	0	0.008	0.012	41.983	0.003	0.003	0.000	0.000	0.000	0.000
38	B	40	ASN	0	-0.030	-0.037	39.667	0.004	0.004	0.000	0.000	0.000	0.000
39	B	41	LEU	0	0.015	-0.005	38.050	-0.004	-0.004	0.000	0.000	0.000	0.000
40	B	42	GLY	0	-0.020	0.022	35.509	-0.001	-0.001	0.000	0.000	0.000	0.000
41	B	43	VAL	0	0.004	-0.001	33.787	0.005	0.005	0.000	0.000	0.000	0.000
42	B	44	PRO	0	0.009	0.003	34.682	-0.001	-0.001	0.000	0.000	0.000	0.000
43	B	45	LEU	0	0.022	0.015	29.636	-0.001	-0.001	0.000	0.000	0.000	0.000
44	B	46	PRO	0	-0.002	0.000	29.412	0.005	0.005	0.000	0.000	0.000	0.000
45	B	47	THR	0	0.010	0.009	32.120	-0.001	-0.001	0.000	0.000	0.000	0.000
46	B	48	LEU	0	-0.003	-0.006	27.991	0.005	0.005	0.000	0.000	0.000	0.000
47	B	49	LYS	1	0.945	0.958	28.488	-0.052	-0.052	0.000	0.000	0.000	0.000
48	B	50	TYR	0	0.021	0.021	24.873	0.007	0.007	0.000	0.000	0.000	0.000
49	B	51	LYS	1	1.004	1.003	31.418	-0.045	-0.045	0.000	0.000	0.000	0.000
50	B	52	TYR	0	0.042	0.024	33.252	0.003	0.003	0.000	0.000	0.000	0.000
51	B	53	LYS	1	0.874	0.923	34.871	-0.037	-0.037	0.000	0.000	0.000	0.000
52	B	54	GLN	0	0.058	0.016	35.753	-0.002	-0.002	0.000	0.000	0.000	0.000
53	B	1	NME	0	0.024	0.042	37.362	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 )