FMO DATABASE

FMODB ID: 53RVZ

Calculation Name: 1DEV-B-Xray372

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: 2023-03-13

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	41
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-113528.606583
FMO2-HF: Nuclear repulsion	98684.813971
FMO2-HF: Total energy	-14843.792612
FMO2-MP2: Total energy	-14885.858775

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.
-1.634	0.435	-0.02	-1.242	-0.807	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 : 0.023 / q_NPA : 0.007

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	B	671	SER	0	-0.037	-0.025	3.807	-0.578	1.491	-0.020	-1.242	-0.807	0.004
4	B	672	PRO	0	0.040	0.040	5.891	-0.145	-0.145	0.000	0.000	0.000	0.000
5	B	673	ASN	0	0.050	0.028	8.000	0.233	0.233	0.000	0.000	0.000	0.000
6	B	674	PRO	0	0.028	0.002	10.213	0.064	0.064	0.000	0.000	0.000	0.000
7	B	675	ASN	0	-0.033	-0.022	13.493	0.112	0.112	0.000	0.000	0.000	0.000
8	B	676	ASN	0	-0.056	-0.025	10.984	0.164	0.164	0.000	0.000	0.000	0.000
9	B	677	PRO	0	0.045	0.008	12.914	-0.082	-0.082	0.000	0.000	0.000	0.000
10	B	678	ALA	0	-0.029	-0.002	13.632	-0.003	-0.003	0.000	0.000	0.000	0.000
11	B	679	GLU	-1	-0.855	-0.928	7.902	-1.450	-1.450	0.000	0.000	0.000	0.000
12	B	680	TYR	0	-0.063	-0.040	10.256	-0.043	-0.043	0.000	0.000	0.000	0.000
13	B	681	CYS	0	-0.074	-0.022	12.805	0.071	0.071	0.000	0.000	0.000	0.000
14	B	682	SER	0	0.054	0.028	15.337	-0.020	-0.020	0.000	0.000	0.000	0.000
15	B	683	THR	0	-0.005	-0.007	17.846	0.015	0.015	0.000	0.000	0.000	0.000
16	B	684	ILE	0	-0.024	-0.002	18.199	0.029	0.029	0.000	0.000	0.000	0.000
17	B	685	PRO	0	0.038	0.017	21.682	-0.009	-0.009	0.000	0.000	0.000	0.000
18	B	686	PRO	0	0.069	0.021	23.158	0.001	0.001	0.000	0.000	0.000	0.000
19	B	687	LEU	0	0.027	0.012	24.177	0.000	0.000	0.000	0.000	0.000	0.000
20	B	688	GLN	0	-0.011	-0.019	23.934	0.005	0.005	0.000	0.000	0.000	0.000
21	B	689	GLN	0	-0.053	-0.012	18.752	-0.023	-0.023	0.000	0.000	0.000	0.000
22	B	690	ALA	0	-0.013	-0.001	21.428	-0.001	-0.001	0.000	0.000	0.000	0.000
23	B	691	GLN	0	0.036	0.007	23.948	0.003	0.003	0.000	0.000	0.000	0.000
24	B	692	ALA	0	-0.034	-0.022	21.534	-0.009	-0.009	0.000	0.000	0.000	0.000
25	B	693	SER	0	-0.007	0.006	20.162	-0.006	-0.006	0.000	0.000	0.000	0.000
26	B	694	GLY	0	-0.008	-0.020	21.751	0.015	0.015	0.000	0.000	0.000	0.000
27	B	695	ALA	0	-0.042	0.003	24.805	0.004	0.004	0.000	0.000	0.000	0.000
28	B	696	LEU	0	-0.044	-0.029	26.427	0.008	0.008	0.000	0.000	0.000	0.000
29	B	697	SER	0	0.028	0.002	29.148	0.004	0.004	0.000	0.000	0.000	0.000
30	B	698	SER	0	-0.033	-0.006	25.772	0.003	0.003	0.000	0.000	0.000	0.000
31	B	699	PRO	0	0.011	0.011	28.197	-0.003	-0.003	0.000	0.000	0.000	0.000
32	B	700	PRO	0	0.007	0.003	29.106	-0.007	-0.007	0.000	0.000	0.000	0.000
33	B	701	PRO	0	0.022	0.008	26.745	0.007	0.007	0.000	0.000	0.000	0.000
34	B	702	THR	0	-0.006	0.003	28.927	0.003	0.003	0.000	0.000	0.000	0.000
35	B	703	VAL	0	-0.017	0.001	27.915	-0.001	-0.001	0.000	0.000	0.000	0.000
36	B	704	MET	0	-0.001	-0.011	30.453	0.004	0.004	0.000	0.000	0.000	0.000
37	B	705	VAL	0	-0.006	-0.007	32.308	-0.003	-0.003	0.000	0.000	0.000	0.000
38	B	706	PRO	0	-0.015	-0.003	33.752	0.004	0.004	0.000	0.000	0.000	0.000
39	B	707	VAL	0	0.038	-0.002	36.961	0.000	0.000	0.000	0.000	0.000	0.000
40	B	708	GLY	0	-0.018	-0.001	39.081	0.004	0.004	0.000	0.000	0.000	0.000
41	B	709	VAL	0	0.003	0.023	37.820	-0.004	-0.004	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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