FMO DATABASE

FMODB ID: 948V2

Calculation Name: 1ZA3-R-Xray372

Preferred Name: Tumor necrosis factor receptor superfamily member 10B

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1ZA3

Chain ID: R

ChEMBL ID: CHEMBL1075153

UniProt ID: O14763

Base Structure: X-ray

Registration Date: 2023-06-22

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	OptHSide
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	85
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-568926.106366
FMO2-HF: Nuclear repulsion	529411.951568
FMO2-HF: Total energy	-39514.154798
FMO2-MP2: Total energy	-39617.720631

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(R:21:SER)

Summations of interaction energy for fragment #1(R:21: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.
-8.221	-3.731	2.144	-2.779	-3.855	0.005

Interaction energy analysis for fragmet #1(R:21:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.026 / q_NPA : -0.025

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	R	23	PRO	0	0.007	-0.005	3.805	-1.352	1.016	-0.029	-1.279	-1.060	0.000
4	R	24	SER	0	-0.072	-0.019	5.802	-0.390	-0.390	0.000	0.000	0.000	0.000
5	R	25	GLU	-1	-0.929	-0.981	7.785	-0.329	-0.329	0.000	0.000	0.000	0.000
6	R	26	GLY	0	-0.031	-0.006	10.409	0.060	0.060	0.000	0.000	0.000	0.000
7	R	27	LEU	0	-0.006	0.010	9.709	0.058	0.058	0.000	0.000	0.000	0.000
8	R	28	CYS	0	-0.089	-0.012	2.555	-1.832	-1.257	2.028	-0.857	-1.745	0.009
9	R	29	PRO	0	0.010	0.008	4.432	-0.382	-0.273	-0.001	-0.007	-0.101	0.000
10	R	30	PRO	0	0.019	0.008	7.362	0.140	0.140	0.000	0.000	0.000	0.000
11	R	31	GLY	0	-0.045	-0.017	8.511	-0.068	-0.068	0.000	0.000	0.000	0.000
12	R	32	HIS	0	-0.075	-0.049	3.972	-0.792	-0.522	0.001	-0.056	-0.215	0.000
13	R	33	HIS	0	0.005	0.026	7.584	-0.105	-0.105	0.000	0.000	0.000	0.000
14	R	34	ILE	0	0.036	0.029	7.256	0.415	0.415	0.000	0.000	0.000	0.000
15	R	35	SER	0	-0.042	-0.037	8.681	-0.072	-0.072	0.000	0.000	0.000	0.000
16	R	36	GLU	-1	-0.927	-0.983	10.356	-0.073	-0.073	0.000	0.000	0.000	0.000
17	R	37	ASP	-1	-0.831	-0.887	11.319	-0.399	-0.399	0.000	0.000	0.000	0.000
18	R	38	GLY	0	-0.007	0.007	10.411	-0.032	-0.032	0.000	0.000	0.000	0.000
19	R	39	ARG	1	0.744	0.849	8.760	0.677	0.677	0.000	0.000	0.000	0.000
20	R	40	ASP	-1	-0.845	-0.914	4.839	-2.036	-2.036	0.000	0.000	0.000	0.000
21	R	42	ILE	0	-0.024	-0.025	3.132	-1.818	-0.650	0.145	-0.580	-0.734	-0.004
22	R	43	SER	0	-0.014	-0.003	5.695	0.050	0.050	0.000	0.000	0.000	0.000
23	R	44	CYS	0	-0.077	-0.001	6.798	-0.021	-0.021	0.000	0.000	0.000	0.000
24	R	45	LYS	1	0.936	0.969	10.317	-0.146	-0.146	0.000	0.000	0.000	0.000
25	R	46	TYR	0	0.004	-0.025	12.972	-0.019	-0.019	0.000	0.000	0.000	0.000
26	R	47	GLY	0	0.006	0.013	14.989	-0.002	-0.002	0.000	0.000	0.000	0.000
27	R	48	GLN	0	-0.090	-0.035	16.795	-0.008	-0.008	0.000	0.000	0.000	0.000
28	R	49	ASP	-1	-0.851	-0.953	13.551	0.145	0.145	0.000	0.000	0.000	0.000
29	R	50	TYR	0	0.038	0.008	13.737	0.008	0.008	0.000	0.000	0.000	0.000
30	R	51	SER	0	-0.036	-0.031	11.251	-0.016	-0.016	0.000	0.000	0.000	0.000
31	R	52	THR	0	0.007	-0.017	12.631	-0.001	-0.001	0.000	0.000	0.000	0.000
32	R	53	HIS	0	0.026	0.027	14.100	-0.019	-0.019	0.000	0.000	0.000	0.000
33	R	54	TRP	0	0.029	0.021	7.261	0.051	0.051	0.000	0.000	0.000	0.000
34	R	55	ASN	0	-0.080	-0.057	10.113	-0.035	-0.035	0.000	0.000	0.000	0.000
35	R	56	ASP	-1	-0.829	-0.916	10.366	0.115	0.115	0.000	0.000	0.000	0.000
36	R	57	LEU	0	0.001	-0.001	12.223	-0.049	-0.049	0.000	0.000	0.000	0.000
37	R	58	LEU	0	0.028	0.003	12.091	0.049	0.049	0.000	0.000	0.000	0.000
38	R	59	PHE	0	-0.038	-0.027	12.771	0.001	0.001	0.000	0.000	0.000	0.000
39	R	61	LEU	0	0.006	0.013	13.911	-0.022	-0.022	0.000	0.000	0.000	0.000
40	R	62	ARG	1	0.958	0.967	17.458	-0.055	-0.055	0.000	0.000	0.000	0.000
41	R	63	CYS	0	-0.057	0.003	18.849	-0.006	-0.006	0.000	0.000	0.000	0.000
42	R	64	THR	0	0.038	0.031	20.736	-0.002	-0.002	0.000	0.000	0.000	0.000
43	R	65	ARG	1	0.929	0.954	24.430	-0.045	-0.045	0.000	0.000	0.000	0.000
44	R	66	CYS	0	-0.062	-0.010	26.013	0.000	0.000	0.000	0.000	0.000	0.000
45	R	67	ASP	-1	-0.831	-0.900	29.574	0.028	0.028	0.000	0.000	0.000	0.000
46	R	68	SER	0	-0.067	-0.054	33.079	0.000	0.000	0.000	0.000	0.000	0.000
47	R	69	GLY	0	0.015	0.017	36.166	0.000	0.000	0.000	0.000	0.000	0.000
48	R	70	GLU	-1	-0.802	-0.929	31.571	0.026	0.026	0.000	0.000	0.000	0.000
49	R	71	VAL	0	-0.035	-0.019	32.507	0.002	0.002	0.000	0.000	0.000	0.000
50	R	72	GLU	-1	-0.896	-0.955	25.276	0.052	0.052	0.000	0.000	0.000	0.000
51	R	73	LEU	0	-0.018	0.016	28.266	0.000	0.000	0.000	0.000	0.000	0.000
52	R	74	SER	0	-0.052	-0.050	23.440	-0.001	-0.001	0.000	0.000	0.000	0.000
53	R	75	PRO	0	0.029	0.033	21.677	0.000	0.000	0.000	0.000	0.000	0.000
54	R	77	THR	0	-0.072	-0.047	15.772	0.006	0.006	0.000	0.000	0.000	0.000
55	R	78	THR	0	0.050	0.029	10.805	-0.002	-0.002	0.000	0.000	0.000	0.000
56	R	79	THR	0	0.022	0.006	11.461	0.017	0.017	0.000	0.000	0.000	0.000
57	R	80	ARG	1	0.923	0.969	13.796	-0.048	-0.048	0.000	0.000	0.000	0.000
58	R	81	ASN	0	0.101	0.042	17.496	0.013	0.013	0.000	0.000	0.000	0.000
59	R	82	THR	0	-0.091	-0.062	19.938	-0.006	-0.006	0.000	0.000	0.000	0.000
60	R	83	VAL	0	-0.018	0.000	22.933	-0.003	-0.003	0.000	0.000	0.000	0.000
61	R	85	GLN	0	0.041	0.002	29.272	-0.003	-0.003	0.000	0.000	0.000	0.000
62	R	86	CYS	0	0.025	0.106	32.665	0.001	0.001	0.000	0.000	0.000	0.000
63	R	87	GLU	-1	-0.943	-0.964	36.225	0.023	0.023	0.000	0.000	0.000	0.000
64	R	88	GLU	-1	-0.925	-0.966	38.304	0.015	0.015	0.000	0.000	0.000	0.000
65	R	89	GLY	0	-0.009	0.001	41.124	0.000	0.000	0.000	0.000	0.000	0.000
66	R	90	THR	0	-0.104	-0.075	40.577	0.000	0.000	0.000	0.000	0.000	0.000
67	R	91	PHE	0	0.084	0.063	39.508	0.000	0.000	0.000	0.000	0.000	0.000
68	R	92	ARG	1	0.763	0.822	31.871	-0.023	-0.023	0.000	0.000	0.000	0.000
69	R	93	GLU	-1	-0.894	-0.936	37.555	0.008	0.008	0.000	0.000	0.000	0.000
70	R	94	GLU	-1	-0.951	-0.974	35.738	0.008	0.008	0.000	0.000	0.000	0.000
71	R	95	ASP	-1	-0.875	-0.933	37.195	0.008	0.008	0.000	0.000	0.000	0.000
72	R	96	SER	0	-0.135	-0.066	39.025	0.000	0.000	0.000	0.000	0.000	0.000
73	R	97	PRO	0	0.032	0.000	34.359	0.001	0.001	0.000	0.000	0.000	0.000
74	R	98	GLU	-1	-0.936	-0.968	35.305	0.021	0.021	0.000	0.000	0.000	0.000
75	R	99	MET	0	-0.034	0.005	37.523	0.001	0.001	0.000	0.000	0.000	0.000
76	R	101	ARG	1	0.814	0.858	40.047	-0.011	-0.011	0.000	0.000	0.000	0.000
77	R	102	LYS	1	0.951	0.971	43.716	-0.013	-0.013	0.000	0.000	0.000	0.000
78	R	103	CYS	0	-0.135	-0.060	44.466	-0.001	-0.001	0.000	0.000	0.000	0.000
79	R	116	ASP	-1	-0.948	-0.983	45.938	0.008	0.008	0.000	0.000	0.000	0.000
80	R	118	THR	0	-0.014	0.005	39.748	0.001	0.001	0.000	0.000	0.000	0.000
81	R	119	PRO	0	0.043	0.002	36.412	0.000	0.000	0.000	0.000	0.000	0.000
82	R	120	TRP	0	-0.007	-0.016	33.180	0.000	0.000	0.000	0.000	0.000	0.000
83	R	121	SER	0	-0.016	-0.002	38.408	-0.001	-0.001	0.000	0.000	0.000	0.000
84	R	122	ASP	-1	-0.799	-0.863	42.209	0.010	0.010	0.000	0.000	0.000	0.000
85	R	123	ILE	0	-0.077	-0.038	45.704	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(R:21:SER)