FMO DATABASE

FMODB ID: 228GR

Calculation Name: 1OQE-K-Xray372

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: 2023-06-19

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	29
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-100659.746773
FMO2-HF: Nuclear repulsion	88139.236914
FMO2-HF: Total energy	-12520.50986
FMO2-MP2: Total energy	-12554.113454

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.
-4.79	0.939	0.448	-2.97	-3.208	-0.007

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 : 0 / q_Mulliken : 0.035 / q_NPA : 0.006

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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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	0.005	-0.007	2.861	-3.824	0.929	0.274	-2.551	-2.476	-0.003
4	K	4	CYS	0	-0.058	0.025	5.832	-0.211	-0.211	0.000	0.000	0.000	0.000
5	K	5	VAL	0	0.046	0.030	8.176	0.157	0.157	0.000	0.000	0.000	0.000
6	K	6	PRO	0	0.037	0.011	11.680	-0.070	-0.070	0.000	0.000	0.000	0.000
7	K	7	ALA	0	-0.014	-0.014	14.245	0.015	0.015	0.000	0.000	0.000	0.000
8	K	8	GLU	-1	-0.955	-0.981	11.073	-0.558	-0.558	0.000	0.000	0.000	0.000
9	K	9	CYS	0	-0.095	-0.056	10.696	-0.010	-0.010	0.000	0.000	0.000	0.000
10	K	10	PHE	0	0.071	0.026	2.953	-1.438	-0.462	0.174	-0.419	-0.732	-0.004
11	K	11	ASP	-1	-0.822	-0.908	7.776	-0.857	-0.857	0.000	0.000	0.000	0.000
12	K	12	LEU	0	-0.022	-0.032	6.584	-0.232	-0.232	0.000	0.000	0.000	0.000
13	K	13	LEU	0	-0.076	-0.017	8.418	0.061	0.061	0.000	0.000	0.000	0.000
14	K	14	VAL	0	-0.016	-0.009	10.101	0.021	0.021	0.000	0.000	0.000	0.000
15	K	15	ARG	1	0.876	0.945	5.211	1.177	1.177	0.000	0.000	0.000	0.000
16	K	16	HIS	0	0.011	-0.016	5.214	-0.153	-0.153	0.000	0.000	0.000	0.000
17	K	18	VAL	0	0.063	0.037	8.357	0.180	0.180	0.000	0.000	0.000	0.000
18	K	19	ALA	0	0.090	0.039	12.113	-0.007	-0.007	0.000	0.000	0.000	0.000
19	K	21	GLY	0	-0.009	0.007	15.623	0.017	0.017	0.000	0.000	0.000	0.000
20	K	22	LEU	0	-0.029	-0.014	15.891	0.026	0.026	0.000	0.000	0.000	0.000
21	K	23	LEU	0	-0.027	0.008	12.186	0.015	0.015	0.000	0.000	0.000	0.000
22	K	24	ARG	1	0.951	0.965	16.857	0.397	0.397	0.000	0.000	0.000	0.000
23	K	25	THR	0	0.031	0.008	17.917	-0.037	-0.037	0.000	0.000	0.000	0.000
24	K	26	PRO	0	0.013	0.004	15.328	0.031	0.031	0.000	0.000	0.000	0.000
25	K	27	ARG	1	0.946	0.978	17.428	0.271	0.271	0.000	0.000	0.000	0.000
26	K	28	PRO	0	0.033	0.003	18.664	-0.014	-0.014	0.000	0.000	0.000	0.000
27	K	29	LYS	1	0.910	0.952	18.516	0.209	0.209	0.000	0.000	0.000	0.000
28	K	30	PRO	0	0.009	0.004	14.357	0.034	0.034	0.000	0.000	0.000	0.000
29	K	31	ALA	0	0.046	0.054	16.306	0.010	0.010	0.000	0.000	0.000	0.000

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