FMO DATABASE

FMODB ID: ZYMLN

Calculation Name: 1T3J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1T3J

Chain ID: A

ChEMBL ID:

UniProt ID: Q811U4

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	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	62
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-274758.396291
FMO2-HF: Nuclear repulsion	248687.822026
FMO2-HF: Total energy	-26070.574266
FMO2-MP2: Total energy	-26145.304054

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:674:ALA)

Summations of interaction energy for fragment #1(A:674:ALA)

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.
-1.649	1.584	0.286	-1.601	-1.919	0.003

Interaction energy analysis for fragmet #1(A:674:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.057 / q_NPA : 0.019

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	A	676	THR	0	0.063	0.023	3.820	-1.701	-0.006	-0.023	-0.957	-0.715	0.002
4	A	677	PHE	0	0.038	0.025	6.795	0.003	0.003	0.000	0.000	0.000	0.000
5	A	678	ALA	0	0.070	0.036	2.801	-0.735	-0.157	0.202	-0.296	-0.484	0.001
6	A	679	ARG	1	0.884	0.934	3.066	0.902	1.802	0.108	-0.346	-0.663	0.000
7	A	680	LEU	0	0.028	0.007	5.273	0.035	0.095	-0.001	-0.002	-0.057	0.000
8	A	681	CYS	0	-0.041	-0.015	7.481	0.025	0.025	0.000	0.000	0.000	0.000
9	A	682	GLN	0	0.017	0.014	6.987	-0.096	-0.096	0.000	0.000	0.000	0.000
10	A	683	GLN	0	-0.009	-0.009	8.809	-0.071	-0.071	0.000	0.000	0.000	0.000
11	A	684	VAL	0	0.013	0.011	11.046	0.013	0.013	0.000	0.000	0.000	0.000
12	A	685	ASP	-1	-0.819	-0.883	11.781	0.029	0.029	0.000	0.000	0.000	0.000
13	A	686	MET	0	-0.019	-0.015	12.028	-0.034	-0.034	0.000	0.000	0.000	0.000
14	A	687	THR	0	-0.032	-0.028	14.614	0.000	0.000	0.000	0.000	0.000	0.000
15	A	688	GLN	0	-0.068	-0.043	16.478	0.001	0.001	0.000	0.000	0.000	0.000
16	A	689	LYS	1	0.866	0.921	14.565	-0.013	-0.013	0.000	0.000	0.000	0.000
17	A	690	HIS	0	0.037	0.025	18.834	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	691	LEU	0	-0.016	-0.014	20.784	0.003	0.003	0.000	0.000	0.000	0.000
19	A	692	GLU	-1	-0.897	-0.938	21.192	0.029	0.029	0.000	0.000	0.000	0.000
20	A	693	GLU	-1	-0.942	-0.971	21.841	-0.035	-0.035	0.000	0.000	0.000	0.000
21	A	694	GLU	-1	-0.843	-0.884	24.823	-0.040	-0.040	0.000	0.000	0.000	0.000
22	A	695	ILE	0	-0.006	-0.014	25.862	0.002	0.002	0.000	0.000	0.000	0.000
23	A	696	ALA	0	-0.013	0.016	27.998	0.002	0.002	0.000	0.000	0.000	0.000
24	A	697	ARG	1	0.738	0.828	27.920	0.034	0.034	0.000	0.000	0.000	0.000
25	A	698	LEU	0	0.030	0.013	30.018	0.001	0.001	0.000	0.000	0.000	0.000
26	A	699	SER	0	-0.022	-0.019	32.269	0.002	0.002	0.000	0.000	0.000	0.000
27	A	700	LYS	1	0.948	0.980	34.067	0.015	0.015	0.000	0.000	0.000	0.000
28	A	701	GLU	-1	-0.909	-0.976	33.700	-0.024	-0.024	0.000	0.000	0.000	0.000
29	A	702	ILE	0	0.007	0.006	35.653	0.000	0.000	0.000	0.000	0.000	0.000
30	A	703	ASP	-1	-0.878	-0.927	38.570	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	704	GLN	0	-0.096	-0.052	38.491	0.000	0.000	0.000	0.000	0.000	0.000
32	A	705	LEU	0	0.022	0.002	39.767	0.000	0.000	0.000	0.000	0.000	0.000
33	A	706	GLU	-1	-0.826	-0.903	42.813	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	707	LYS	1	0.949	0.985	44.567	0.006	0.006	0.000	0.000	0.000	0.000
35	A	708	MET	0	-0.029	-0.018	44.838	0.000	0.000	0.000	0.000	0.000	0.000
36	A	709	GLN	0	0.043	0.037	46.343	0.000	0.000	0.000	0.000	0.000	0.000
37	A	710	ASN	0	-0.010	-0.026	48.150	0.000	0.000	0.000	0.000	0.000	0.000
38	A	711	ASN	0	-0.012	-0.012	50.384	0.001	0.001	0.000	0.000	0.000	0.000
39	A	712	SER	0	-0.020	-0.020	50.871	0.000	0.000	0.000	0.000	0.000	0.000
40	A	713	LYS	1	0.841	0.924	49.577	0.005	0.005	0.000	0.000	0.000	0.000
41	A	714	LEU	0	0.015	0.029	54.932	0.000	0.000	0.000	0.000	0.000	0.000
42	A	715	LEU	0	-0.020	-0.013	54.965	0.000	0.000	0.000	0.000	0.000	0.000
43	A	716	ARG	1	0.972	0.985	55.115	0.007	0.007	0.000	0.000	0.000	0.000
44	A	717	ASN	0	0.001	-0.017	58.463	0.000	0.000	0.000	0.000	0.000	0.000
45	A	718	LYS	1	0.969	1.001	60.740	0.005	0.005	0.000	0.000	0.000	0.000
46	A	719	ALA	0	-0.003	-0.010	62.104	0.000	0.000	0.000	0.000	0.000	0.000
47	A	720	VAL	0	0.048	0.030	62.923	0.000	0.000	0.000	0.000	0.000	0.000
48	A	721	GLN	0	-0.076	-0.034	65.098	0.000	0.000	0.000	0.000	0.000	0.000
49	A	722	LEU	0	-0.002	-0.019	65.706	0.000	0.000	0.000	0.000	0.000	0.000
50	A	723	GLU	-1	-0.962	-0.968	67.316	-0.006	-0.006	0.000	0.000	0.000	0.000
51	A	724	SER	0	-0.008	-0.005	69.381	0.000	0.000	0.000	0.000	0.000	0.000
52	A	725	GLU	-1	-0.874	-0.925	70.395	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	726	LEU	0	-0.020	-0.011	71.751	0.000	0.000	0.000	0.000	0.000	0.000
54	A	727	GLU	-1	-0.900	-0.954	73.239	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	728	ASN	0	-0.070	-0.048	74.723	0.000	0.000	0.000	0.000	0.000	0.000
56	A	729	PHE	0	0.003	0.003	77.027	0.000	0.000	0.000	0.000	0.000	0.000
57	A	730	SER	0	0.036	0.009	78.185	0.000	0.000	0.000	0.000	0.000	0.000
58	A	731	LYS	1	0.934	0.981	79.458	0.002	0.002	0.000	0.000	0.000	0.000
59	A	732	GLN	0	-0.071	-0.028	81.619	0.000	0.000	0.000	0.000	0.000	0.000
60	A	733	PHE	0	-0.045	-0.038	81.928	0.000	0.000	0.000	0.000	0.000	0.000
61	A	734	LEU	0	-0.056	-0.022	80.614	0.000	0.000	0.000	0.000	0.000	0.000
62	A	735	HIS	0	-0.062	-0.009	80.908	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:674:ALA)