FMO DATABASE

FMODB ID: JLMK9

Calculation Name: 1AVY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1AVY

Chain ID: A

ChEMBL ID:

UniProt ID: P10104

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	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	68
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-270252.172077
FMO2-HF: Nuclear repulsion	244882.748115
FMO2-HF: Total energy	-25369.423962
FMO2-MP2: Total energy	-25445.122393

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:419:THR)

Summations of interaction energy for fragment #1(A:419: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.
-7.63	-3.514	0.117	-1.671	-2.561	0.006

Interaction energy analysis for fragmet #1(A:419:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : -0.010

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	421	LYS	1	0.962	0.983	2.880	-6.211	-2.676	0.091	-1.589	-2.037	0.006
4	A	422	ILE	0	0.095	0.027	3.206	-0.899	-0.391	0.027	-0.080	-0.455	0.000
5	A	423	LYS	1	0.937	0.997	5.383	-0.652	-0.579	-0.001	-0.002	-0.069	0.000
6	A	424	ALA	0	-0.024	-0.019	7.381	-0.005	-0.005	0.000	0.000	0.000	0.000
7	A	425	ILE	0	0.036	0.021	6.646	-0.111	-0.111	0.000	0.000	0.000	0.000
8	A	426	GLU	-1	-0.904	-0.957	9.375	-0.293	-0.293	0.000	0.000	0.000	0.000
9	A	427	THR	0	-0.028	-0.019	11.322	-0.015	-0.015	0.000	0.000	0.000	0.000
10	A	428	ASP	-1	-0.894	-0.935	12.566	0.605	0.605	0.000	0.000	0.000	0.000
11	A	429	ILE	0	-0.036	-0.015	12.493	-0.064	-0.064	0.000	0.000	0.000	0.000
12	A	430	ALA	0	-0.045	-0.029	15.306	-0.036	-0.036	0.000	0.000	0.000	0.000
13	A	431	SER	0	0.022	0.009	17.072	-0.017	-0.017	0.000	0.000	0.000	0.000
14	A	432	VAL	0	0.036	0.024	18.258	-0.026	-0.026	0.000	0.000	0.000	0.000
15	A	433	ARG	1	0.950	0.961	19.295	-0.018	-0.018	0.000	0.000	0.000	0.000
16	A	434	GLN	0	-0.016	0.004	21.349	-0.008	-0.008	0.000	0.000	0.000	0.000
17	A	435	GLU	-1	-0.883	-0.940	23.109	0.186	0.186	0.000	0.000	0.000	0.000
18	A	436	VAL	0	-0.014	-0.010	23.558	-0.016	-0.016	0.000	0.000	0.000	0.000
19	A	437	ASN	0	-0.049	-0.044	24.895	-0.027	-0.027	0.000	0.000	0.000	0.000
20	A	438	THR	0	-0.006	0.004	27.448	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	439	ALA	0	-0.001	0.000	28.732	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	440	LYS	1	0.916	0.961	27.495	-0.032	-0.032	0.000	0.000	0.000	0.000
23	A	441	GLY	0	0.011	0.016	31.558	-0.007	-0.007	0.000	0.000	0.000	0.000
24	A	442	ASN	0	0.029	-0.001	33.107	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	443	ILE	0	-0.031	-0.007	32.512	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	444	SER	0	-0.001	-0.006	35.762	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	445	SER	0	-0.016	-0.004	37.689	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	446	LEU	0	-0.006	-0.003	37.382	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	447	GLN	0	-0.032	-0.020	38.310	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	448	GLY	0	0.035	0.027	41.847	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	449	ASP	-1	-0.897	-0.948	43.649	0.040	0.040	0.000	0.000	0.000	0.000
32	A	450	VAL	0	-0.075	-0.049	43.795	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	451	GLN	0	-0.043	-0.004	45.837	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	452	ALA	0	0.049	0.025	47.768	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	453	LEU	0	-0.066	-0.035	47.876	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	454	GLN	0	-0.066	-0.041	47.646	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	455	GLU	-1	-0.917	-0.966	50.662	0.013	0.013	0.000	0.000	0.000	0.000
38	A	456	ALA	0	-0.061	-0.011	53.900	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	457	GLY	0	-0.016	0.003	55.845	0.000	0.000	0.000	0.000	0.000	0.000
40	A	458	TYR	0	-0.035	-0.015	53.790	0.000	0.000	0.000	0.000	0.000	0.000
41	A	459	ILE	0	-0.017	-0.012	58.760	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	460	PRO	0	-0.004	-0.003	60.351	0.001	0.001	0.000	0.000	0.000	0.000
43	A	461	GLU	-1	-0.899	-0.941	61.476	0.022	0.022	0.000	0.000	0.000	0.000
44	A	462	ALA	0	-0.039	-0.014	63.692	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	463	PRO	0	-0.008	-0.014	66.975	0.001	0.001	0.000	0.000	0.000	0.000
46	A	464	ARG	1	0.952	0.974	61.977	-0.021	-0.021	0.000	0.000	0.000	0.000
47	A	465	ASP	-1	-0.786	-0.891	69.326	0.014	0.014	0.000	0.000	0.000	0.000
48	A	466	GLY	0	-0.033	-0.013	72.856	0.000	0.000	0.000	0.000	0.000	0.000
49	A	467	GLN	0	-0.029	0.004	74.436	0.000	0.000	0.000	0.000	0.000	0.000
50	A	468	ALA	0	-0.008	0.004	73.919	0.001	0.001	0.000	0.000	0.000	0.000
51	A	469	TYR	0	-0.050	-0.064	71.535	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	470	VAL	0	-0.006	0.004	72.804	0.001	0.001	0.000	0.000	0.000	0.000
53	A	471	ARG	1	0.918	0.954	64.731	-0.015	-0.015	0.000	0.000	0.000	0.000
54	A	472	LYS	1	0.935	0.956	71.021	-0.008	-0.008	0.000	0.000	0.000	0.000
55	A	473	ASP	-1	-0.866	-0.923	70.448	0.008	0.008	0.000	0.000	0.000	0.000
56	A	474	GLY	0	-0.032	-0.005	66.717	0.000	0.000	0.000	0.000	0.000	0.000
57	A	475	GLU	-1	-0.936	-0.972	66.792	0.009	0.009	0.000	0.000	0.000	0.000
58	A	476	TRP	0	-0.064	-0.031	65.482	0.000	0.000	0.000	0.000	0.000	0.000
59	A	477	VAL	0	0.006	0.004	70.529	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	478	LEU	0	0.033	0.010	74.325	0.001	0.001	0.000	0.000	0.000	0.000
61	A	479	LEU	0	0.058	0.014	76.786	0.000	0.000	0.000	0.000	0.000	0.000
62	A	480	SER	0	0.008	-0.018	78.374	0.000	0.000	0.000	0.000	0.000	0.000
63	A	481	THR	0	-0.037	0.000	79.654	0.000	0.000	0.000	0.000	0.000	0.000
64	A	482	PHE	0	-0.016	-0.013	77.454	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	483	LEU	0	-0.077	-0.011	82.207	0.000	0.000	0.000	0.000	0.000	0.000
66	A	484	SER	0	-0.006	-0.031	84.923	0.000	0.000	0.000	0.000	0.000	0.000
67	A	485	PRO	0	-0.053	0.003	86.388	0.000	0.000	0.000	0.000	0.000	0.000
68	A	486	ALA	0	0.038	0.018	84.575	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:419:THR)