FMO DATABASE

FMODB ID: 82VMY

Calculation Name: 1OQD-K-Xray372

Preferred Name: Tumor necrosis factor ligand superfamily member 13B

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1OQD

Chain ID: K

ChEMBL ID: CHEMBL2364158

UniProt ID: Q9Y275

Base Structure: X-ray

Registration Date: 2023-06-20

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	36
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-162074.952642
FMO2-HF: Nuclear repulsion	145257.847875
FMO2-HF: Total energy	-16817.104767
FMO2-MP2: Total energy	-16861.080396

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:CYS)

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

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.
-46.575	-34.058	20.787	-13.595	-19.712	0.008

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : 0.011

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	GLN	0	0.067	0.039	2.809	-6.078	-1.253	0.293	-2.628	-2.490	-0.006
4	K	4	ASN	0	-0.035	-0.017	6.230	0.307	0.307	0.000	0.000	0.000	0.000
5	K	5	GLU	-1	-0.885	-0.943	2.748	-15.362	-11.090	0.818	-2.233	-2.858	-0.027
6	K	6	TYR	0	-0.010	-0.042	3.739	-0.115	0.436	0.003	-0.139	-0.416	0.000
7	K	7	PHE	0	-0.001	0.014	2.371	-1.727	-0.215	9.279	-2.693	-8.099	0.006
8	K	8	ASP	-1	-0.814	-0.907	1.821	-7.937	-12.774	10.447	-2.852	-2.758	0.036
9	K	9	SER	0	0.020	-0.018	3.720	-3.126	-2.843	0.009	0.016	-0.308	0.001
10	K	10	LEU	0	-0.038	-0.003	6.332	-1.566	-1.566	0.000	0.000	0.000	0.000
11	K	11	LEU	0	-0.029	-0.019	4.240	-1.280	-1.153	-0.002	-0.004	-0.121	0.000
12	K	12	HIS	0	-0.105	-0.035	3.827	-6.479	-3.128	-0.027	-1.870	-1.454	-0.009
15	K	16	PRO	0	0.055	0.012	3.792	-0.640	1.793	-0.033	-1.192	-1.208	0.007
16	K	17	CYS	0	-0.080	-0.017	6.558	0.865	0.865	0.000	0.000	0.000	0.000
17	K	18	GLN	0	0.008	0.013	8.675	0.351	0.351	0.000	0.000	0.000	0.000
18	K	19	LEU	0	0.035	0.015	8.404	0.148	0.148	0.000	0.000	0.000	0.000
19	K	20	ARG	1	0.891	0.956	8.324	-2.684	-2.684	0.000	0.000	0.000	0.000
20	K	21	CYS	0	-0.084	-0.038	11.662	-0.146	-0.146	0.000	0.000	0.000	0.000
21	K	22	SER	0	-0.034	-0.021	14.302	-0.031	-0.031	0.000	0.000	0.000	0.000
22	K	23	SER	0	-0.010	0.003	16.358	-0.027	-0.027	0.000	0.000	0.000	0.000
23	K	24	ASN	0	-0.022	0.011	13.127	0.264	0.264	0.000	0.000	0.000	0.000
24	K	25	THR	0	-0.014	-0.003	15.050	0.133	0.133	0.000	0.000	0.000	0.000
25	K	26	PRO	0	0.002	0.001	11.673	0.158	0.158	0.000	0.000	0.000	0.000
26	K	27	PRO	0	0.062	0.045	8.819	-0.100	-0.100	0.000	0.000	0.000	0.000
27	K	28	LEU	0	0.115	0.039	11.141	-0.298	-0.298	0.000	0.000	0.000	0.000
28	K	29	THR	0	-0.027	-0.019	8.530	-0.249	-0.249	0.000	0.000	0.000	0.000
29	K	31	GLN	0	0.014	-0.005	10.992	-0.288	-0.288	0.000	0.000	0.000	0.000
30	K	32	ARG	1	0.935	0.972	14.389	-0.515	-0.515	0.000	0.000	0.000	0.000
31	K	33	TYR	0	0.065	0.001	12.034	-0.116	-0.116	0.000	0.000	0.000	0.000
32	K	35	ASN	0	0.032	-0.003	15.952	0.032	0.032	0.000	0.000	0.000	0.000
33	K	36	ALA	0	-0.060	-0.013	16.097	-0.037	-0.037	0.000	0.000	0.000	0.000
34	K	37	SER	0	-0.024	-0.003	17.010	-0.018	-0.018	0.000	0.000	0.000	0.000
35	K	38	VAL	0	-0.002	-0.001	18.853	-0.011	-0.011	0.000	0.000	0.000	0.000
36	K	39	THR	0	-0.018	0.013	21.898	-0.003	-0.003	0.000	0.000	0.000	0.000

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