FMO DATABASE

FMODB ID: 63QGZ

Calculation Name: 1DEV-B-Xray309

Preferred Name: Mothers against decapentaplegic homolog 2

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1DEV

Chain ID: B

ChEMBL ID: CHEMBL2396512

UniProt ID: Q15796

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:

Apendix: None

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	41
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-113471.961571
FMO2-HF: Nuclear repulsion	98628.746182
FMO2-HF: Total energy	-14843.215389
FMO2-MP2: Total energy	-14885.289325

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:669:SER )

Summations of interaction energy for fragment #1(B:669:SER )

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.
0.211	2.191	-0.015	-1.186	-0.779	0.004

Interaction energy analysis for fragmet #1(B:669:SER )

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

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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	671	SER	0	-0.031	-0.022	3.811	-0.422	1.558	-0.015	-1.186	-0.779	0.004
4	B	672	PRO	0	0.041	0.040	5.889	0.030	0.030	0.000	0.000	0.000	0.000
5	B	673	ASN	0	0.050	0.028	7.997	-0.324	-0.324	0.000	0.000	0.000	0.000
6	B	674	PRO	0	0.028	0.002	10.211	0.074	0.074	0.000	0.000	0.000	0.000
7	B	675	ASN	0	-0.031	-0.021	13.493	0.025	0.025	0.000	0.000	0.000	0.000
8	B	676	ASN	0	-0.057	-0.026	10.980	-0.043	-0.043	0.000	0.000	0.000	0.000
9	B	677	PRO	0	0.043	0.007	12.910	0.075	0.075	0.000	0.000	0.000	0.000
10	B	678	ALA	0	-0.028	0.000	13.721	0.020	0.020	0.000	0.000	0.000	0.000
11	B	679	GLU	-1	-0.854	-0.927	7.898	0.834	0.834	0.000	0.000	0.000	0.000
12	B	680	TYR	0	-0.062	-0.040	10.767	0.079	0.079	0.000	0.000	0.000	0.000
13	B	681	CYS	0	-0.074	-0.022	13.179	-0.065	-0.065	0.000	0.000	0.000	0.000
14	B	682	SER	0	0.055	0.029	16.034	0.057	0.057	0.000	0.000	0.000	0.000
15	B	683	THR	0	-0.007	-0.008	18.561	-0.029	-0.029	0.000	0.000	0.000	0.000
16	B	684	ILE	0	-0.025	-0.003	18.976	-0.022	-0.022	0.000	0.000	0.000	0.000
17	B	685	PRO	0	0.038	0.017	22.424	-0.010	-0.010	0.000	0.000	0.000	0.000
18	B	686	PRO	0	0.069	0.022	23.720	0.005	0.005	0.000	0.000	0.000	0.000
19	B	687	LEU	0	0.028	0.013	24.710	0.000	0.000	0.000	0.000	0.000	0.000
20	B	688	GLN	0	-0.012	-0.020	24.600	-0.005	-0.005	0.000	0.000	0.000	0.000
21	B	689	GLN	0	-0.053	-0.013	19.309	0.024	0.024	0.000	0.000	0.000	0.000
22	B	690	ALA	0	-0.012	-0.002	21.903	-0.004	-0.004	0.000	0.000	0.000	0.000
23	B	691	GLN	0	0.037	0.007	24.393	-0.001	-0.001	0.000	0.000	0.000	0.000
24	B	692	ALA	0	-0.036	-0.023	22.085	0.012	0.012	0.000	0.000	0.000	0.000
25	B	693	SER	0	-0.006	0.008	20.507	0.012	0.012	0.000	0.000	0.000	0.000
26	B	694	GLY	0	-0.008	-0.020	22.128	-0.015	-0.015	0.000	0.000	0.000	0.000
27	B	695	ALA	0	-0.045	0.004	25.074	0.000	0.000	0.000	0.000	0.000	0.000
28	B	696	LEU	0	-0.041	-0.029	26.708	-0.006	-0.006	0.000	0.000	0.000	0.000
29	B	697	SER	0	0.026	0.001	29.452	-0.005	-0.005	0.000	0.000	0.000	0.000
30	B	698	SER	0	-0.033	-0.006	25.940	-0.001	-0.001	0.000	0.000	0.000	0.000
31	B	699	PRO	0	0.011	0.010	28.354	-0.002	-0.002	0.000	0.000	0.000	0.000
32	B	700	PRO	0	0.007	0.003	29.089	-0.004	-0.004	0.000	0.000	0.000	0.000
33	B	701	PRO	0	0.019	0.008	26.614	-0.004	-0.004	0.000	0.000	0.000	0.000
34	B	702	THR	0	-0.004	0.004	28.637	0.003	0.003	0.000	0.000	0.000	0.000
35	B	703	VAL	0	-0.018	0.000	27.666	-0.008	-0.008	0.000	0.000	0.000	0.000
36	B	704	MET	0	-0.008	-0.014	30.197	0.010	0.010	0.000	0.000	0.000	0.000
37	B	705	VAL	0	-0.004	-0.006	32.194	-0.010	-0.010	0.000	0.000	0.000	0.000
38	B	706	PRO	0	-0.022	-0.007	33.702	0.006	0.006	0.000	0.000	0.000	0.000
39	B	707	VAL	0	0.018	-0.015	36.923	0.006	0.006	0.000	0.000	0.000	0.000
40	B	708	GLY	0	-0.045	-0.018	39.116	0.003	0.003	0.000	0.000	0.000	0.000
41	B	709	VAL	-1	-0.936	-0.939	37.896	-0.084	-0.084	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:669:SER )