FMO DATABASE

FMODB ID: VR491

Calculation Name: 2H4M-D-Xray372

Preferred Name: Heterogeneous nuclear ribonucleoprotein A1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2H4M

Chain ID: D

ChEMBL ID: CHEMBL1955709

UniProt ID: P09651

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	27
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-58273.471999
FMO2-HF: Nuclear repulsion	48107.18009
FMO2-HF: Total energy	-10166.291909
FMO2-MP2: Total energy	-10195.239338

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(D:263:PHE)

Summations of interaction energy for fragment #1(D:263:PHE)

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.
-0.719	2.597	-0.008	-1.577	-1.731	-0.001

Interaction energy analysis for fragmet #1(D:263:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / 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

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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	D	265	ASN	0	-0.028	-0.017	3.604	-1.135	1.784	-0.008	-1.532	-1.378	-0.001
4	D	266	TYR	0	-0.001	-0.005	4.214	1.061	1.458	0.000	-0.045	-0.353	0.000
5	D	267	ASN	0	-0.003	-0.027	6.611	-0.457	-0.457	0.000	0.000	0.000	0.000
6	D	268	ASN	0	-0.030	0.000	9.238	0.016	0.016	0.000	0.000	0.000	0.000
7	D	269	GLN	0	0.053	0.036	11.852	0.088	0.088	0.000	0.000	0.000	0.000
8	D	270	SER	0	0.012	0.018	14.503	-0.028	-0.028	0.000	0.000	0.000	0.000
9	D	271	SER	0	-0.039	-0.023	17.451	0.020	0.020	0.000	0.000	0.000	0.000
10	D	272	ASN	0	0.020	-0.003	18.347	-0.039	-0.039	0.000	0.000	0.000	0.000
11	D	273	PHE	0	-0.001	0.009	20.314	-0.012	-0.012	0.000	0.000	0.000	0.000
12	D	274	GLY	0	0.022	0.017	21.664	-0.010	-0.010	0.000	0.000	0.000	0.000
13	D	275	PRO	0	-0.034	-0.015	24.973	0.007	0.007	0.000	0.000	0.000	0.000
14	D	276	MET	0	0.042	0.010	23.740	0.002	0.002	0.000	0.000	0.000	0.000
15	D	277	LYS	1	0.928	0.967	28.127	-0.122	-0.122	0.000	0.000	0.000	0.000
16	D	278	GLY	0	0.051	0.030	31.443	0.006	0.006	0.000	0.000	0.000	0.000
17	D	279	GLY	0	-0.010	-0.004	33.910	0.000	0.000	0.000	0.000	0.000	0.000
18	D	280	ASN	0	-0.010	-0.012	35.255	-0.008	-0.008	0.000	0.000	0.000	0.000
19	D	281	PHE	0	0.022	-0.005	38.187	0.002	0.002	0.000	0.000	0.000	0.000
20	D	282	GLY	0	0.005	0.022	40.575	-0.004	-0.004	0.000	0.000	0.000	0.000
21	D	283	GLY	0	0.006	0.014	38.605	0.000	0.000	0.000	0.000	0.000	0.000
22	D	284	ARG	1	0.933	0.952	33.107	-0.110	-0.110	0.000	0.000	0.000	0.000
23	D	285	SER	0	0.015	0.004	39.399	-0.001	-0.001	0.000	0.000	0.000	0.000
24	D	286	SER	0	0.037	0.013	39.146	0.003	0.003	0.000	0.000	0.000	0.000
25	D	287	GLY	0	-0.001	0.014	39.200	0.004	0.004	0.000	0.000	0.000	0.000
26	D	288	PRO	0	-0.025	-0.023	40.023	-0.002	-0.002	0.000	0.000	0.000	0.000
27	D	289	TYR	0	0.011	0.021	36.502	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:263:PHE)