FMO DATABASE

FMODB ID: VRV91

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:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
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
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-113044.866559
FMO2-HF: Nuclear repulsion	98200.457047
FMO2-HF: Total energy	-14844.409512
FMO2-MP2: Total energy	-14886.342219

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.
-0.26	1.89	-0.014	-1.177	-0.959	0.001

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 : 0.003 / q_NPA : 0.005

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	-0.019	-0.026	3.896	-0.641	1.509	-0.014	-1.177	-0.959	0.001
4	B	672	PRO	0	0.004	0.035	5.543	-0.175	-0.175	0.000	0.000	0.000	0.000
5	B	673	ASN	0	0.056	0.018	7.526	-0.380	-0.380	0.000	0.000	0.000	0.000
6	B	674	PRO	0	0.041	0.008	9.686	0.024	0.024	0.000	0.000	0.000	0.000
7	B	675	ASN	0	-0.076	-0.036	13.245	-0.014	-0.014	0.000	0.000	0.000	0.000
8	B	676	ASN	0	-0.046	-0.031	11.107	-0.063	-0.063	0.000	0.000	0.000	0.000
9	B	677	PRO	0	0.054	0.013	12.817	0.082	0.082	0.000	0.000	0.000	0.000
10	B	678	ALA	0	-0.015	-0.005	13.577	0.022	0.022	0.000	0.000	0.000	0.000
11	B	679	GLU	-1	-0.841	-0.904	7.936	0.839	0.839	0.000	0.000	0.000	0.000
12	B	680	TYR	0	-0.069	-0.050	10.018	0.139	0.139	0.000	0.000	0.000	0.000
13	B	681	CYS	0	-0.065	-0.001	12.572	-0.090	-0.090	0.000	0.000	0.000	0.000
14	B	682	SER	0	0.014	0.000	15.425	0.041	0.041	0.000	0.000	0.000	0.000
15	B	683	THR	0	-0.002	-0.007	17.992	-0.022	-0.022	0.000	0.000	0.000	0.000
16	B	684	ILE	0	-0.002	0.016	18.831	-0.025	-0.025	0.000	0.000	0.000	0.000
17	B	685	PRO	0	0.040	0.018	22.225	-0.001	-0.001	0.000	0.000	0.000	0.000
18	B	686	PRO	0	0.055	0.013	23.475	0.002	0.002	0.000	0.000	0.000	0.000
19	B	687	LEU	0	0.009	0.011	24.466	-0.001	-0.001	0.000	0.000	0.000	0.000
20	B	688	GLN	0	-0.008	-0.031	24.508	-0.005	-0.005	0.000	0.000	0.000	0.000
21	B	689	GLN	0	-0.042	-0.011	18.694	0.034	0.034	0.000	0.000	0.000	0.000
22	B	690	ALA	0	-0.009	0.008	21.416	-0.001	-0.001	0.000	0.000	0.000	0.000
23	B	691	GLN	0	0.028	0.002	24.116	-0.006	-0.006	0.000	0.000	0.000	0.000
24	B	692	ALA	0	-0.037	-0.030	21.958	0.011	0.011	0.000	0.000	0.000	0.000
25	B	693	SER	0	-0.021	0.017	19.867	0.005	0.005	0.000	0.000	0.000	0.000
26	B	694	GLY	0	0.017	-0.007	21.476	-0.014	-0.014	0.000	0.000	0.000	0.000
27	B	695	ALA	0	0.006	0.003	24.499	-0.003	-0.003	0.000	0.000	0.000	0.000
28	B	696	LEU	0	0.008	0.012	26.254	-0.008	-0.008	0.000	0.000	0.000	0.000
29	B	697	SER	0	-0.027	-0.013	28.410	-0.004	-0.004	0.000	0.000	0.000	0.000
30	B	698	SER	0	-0.032	-0.012	25.270	-0.001	-0.001	0.000	0.000	0.000	0.000
31	B	699	PRO	0	0.001	-0.003	27.872	-0.001	-0.001	0.000	0.000	0.000	0.000
32	B	700	PRO	0	0.017	0.005	28.727	0.000	0.000	0.000	0.000	0.000	0.000
33	B	701	PRO	0	0.004	0.006	26.059	-0.006	-0.006	0.000	0.000	0.000	0.000
34	B	702	THR	0	-0.016	-0.001	28.338	0.000	0.000	0.000	0.000	0.000	0.000
35	B	703	VAL	0	-0.020	-0.012	28.142	-0.005	-0.005	0.000	0.000	0.000	0.000
36	B	704	MET	0	0.002	0.004	30.822	0.005	0.005	0.000	0.000	0.000	0.000
37	B	705	VAL	0	-0.005	-0.007	32.553	-0.005	-0.005	0.000	0.000	0.000	0.000
38	B	706	PRO	0	-0.009	-0.005	34.252	0.003	0.003	0.000	0.000	0.000	0.000
39	B	707	VAL	0	0.017	0.006	37.489	0.003	0.003	0.000	0.000	0.000	0.000
40	B	708	GLY	0	0.010	0.005	40.400	0.000	0.000	0.000	0.000	0.000	0.000
41	B	709	VAL	0	-0.014	0.008	38.487	0.001	0.001	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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