FMO DATABASE

FMODB ID: MM7ZZ

Calculation Name: 1OQE-K-Xray310

Preferred Name: Tumor necrosis factor ligand superfamily member 13B

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1OQE

Chain ID: K

ChEMBL ID: CHEMBL2364158

UniProt ID: Q9Y275

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:

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	29
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-100669.401469
FMO2-HF: Nuclear repulsion	88149.053463
FMO2-HF: Total energy	-12520.348006
FMO2-MP2: Total energy	-12553.966095

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(K:1:PRO )

Summations of interaction energy for fragment #1(K:1:PRO )

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.
5.215	12.042	0.383	-3.498	-3.713	-0.025

Interaction energy analysis for fragmet #1(K:1:PRO )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.858 / q_NPA : 0.902

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	K	3	PRO	0	0.051	0.021	2.873	0.206	5.805	0.229	-2.848	-2.981	-0.018
4	K	17	CYS	0	-0.056	0.024	5.834	0.044	0.044	0.000	0.000	0.000	0.000
5	K	5	VAL	0	0.054	0.035	8.175	1.464	1.464	0.000	0.000	0.000	0.000
6	K	6	PRO	0	0.046	0.016	11.679	-0.201	-0.201	0.000	0.000	0.000	0.000
7	K	7	ALA	0	-0.009	-0.011	14.244	0.643	0.643	0.000	0.000	0.000	0.000
8	K	8	GLU	-1	-0.955	-0.980	11.070	-22.199	-22.199	0.000	0.000	0.000	0.000
9	K	20	CYS	0	-0.088	-0.052	10.693	-0.963	-0.963	0.000	0.000	0.000	0.000
10	K	10	PHE	0	0.046	0.013	2.972	-4.575	-3.347	0.154	-0.650	-0.732	-0.007
11	K	11	ASP	-1	-0.809	-0.901	7.777	-23.327	-23.327	0.000	0.000	0.000	0.000
12	K	12	LEU	0	-0.024	-0.034	6.590	-2.856	-2.856	0.000	0.000	0.000	0.000
13	K	13	LEU	0	-0.068	-0.013	8.418	-0.006	-0.006	0.000	0.000	0.000	0.000
14	K	14	VAL	0	-0.012	-0.006	10.091	-0.189	-0.189	0.000	0.000	0.000	0.000
15	K	15	ARG	1	0.872	0.944	5.200	31.564	31.564	0.000	0.000	0.000	0.000
16	K	16	HIS	0	0.001	-0.024	5.201	-3.647	-3.647	0.000	0.000	0.000	0.000
17	K	18	VAL	0	0.069	0.040	8.352	2.173	2.173	0.000	0.000	0.000	0.000
18	K	19	ALA	0	0.093	0.040	12.107	-0.191	-0.191	0.000	0.000	0.000	0.000
19	K	21	GLY	0	-0.002	0.011	15.619	0.499	0.499	0.000	0.000	0.000	0.000
20	K	22	LEU	0	-0.031	-0.015	15.886	0.618	0.618	0.000	0.000	0.000	0.000
21	K	23	LEU	0	-0.031	0.005	12.184	0.379	0.379	0.000	0.000	0.000	0.000
22	K	24	ARG	1	0.953	0.965	16.856	15.725	15.725	0.000	0.000	0.000	0.000
23	K	25	THR	0	0.029	0.008	17.920	-0.733	-0.733	0.000	0.000	0.000	0.000
24	K	26	PRO	0	0.009	0.001	15.331	0.582	0.582	0.000	0.000	0.000	0.000
25	K	27	ARG	1	0.941	0.976	17.432	14.140	14.140	0.000	0.000	0.000	0.000
26	K	28	PRO	0	0.029	-0.001	18.666	-0.660	-0.660	0.000	0.000	0.000	0.000
27	K	29	LYS	1	0.885	0.936	18.517	14.806	14.806	0.000	0.000	0.000	0.000
28	K	30	PRO	0	-0.042	-0.027	14.358	0.504	0.504	0.000	0.000	0.000	0.000
29	K	31	ALA	-1	-0.861	-0.889	16.355	-18.585	-18.585	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(K:1:PRO )