FMO DATABASE

FMODB ID: LZN39

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

Total energy (hartree)

FMO2-HF: Electronic energy	-568511.214145
FMO2-HF: Nuclear repulsion	528999.385822
FMO2-HF: Total energy	-39511.828323
FMO2-MP2: Total energy	-39615.499422

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.
-4.739	0.121	2.168	-3.132	-3.894	-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 : -0.025 / q_NPA : -0.028

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	-0.002	-0.001	3.805	0.813	3.119	-0.028	-1.272	-1.006	0.000
4	R	24	SER	0	-0.064	-0.012	6.536	-0.578	-0.578	0.000	0.000	0.000	0.000
5	R	25	GLU	-1	-0.935	-0.987	8.426	0.707	0.707	0.000	0.000	0.000	0.000
6	R	26	GLY	0	-0.024	-0.006	10.798	-0.066	-0.066	0.000	0.000	0.000	0.000
7	R	27	LEU	0	-0.017	0.005	9.959	-0.112	-0.112	0.000	0.000	0.000	0.000
8	R	28	CYS	0	-0.104	-0.011	2.172	1.022	1.463	2.033	-0.828	-1.645	0.004
9	R	29	PRO	0	0.011	0.004	4.585	-0.815	-0.703	-0.001	-0.007	-0.103	0.000
10	R	30	PRO	0	0.017	0.003	7.400	-0.195	-0.195	0.000	0.000	0.000	0.000
11	R	31	GLY	0	-0.049	-0.013	8.452	0.182	0.182	0.000	0.000	0.000	0.000
12	R	32	HIS	0	-0.065	-0.047	3.605	-0.152	0.114	0.003	-0.064	-0.205	0.000
13	R	33	HIS	0	0.001	0.023	7.081	0.034	0.034	0.000	0.000	0.000	0.000
14	R	34	ILE	0	0.043	0.029	6.458	0.032	0.032	0.000	0.000	0.000	0.000
15	R	35	SER	0	0.012	0.020	8.205	-0.031	-0.031	0.000	0.000	0.000	0.000
16	R	36	GLU	-1	-0.934	-0.983	10.351	-0.027	-0.027	0.000	0.000	0.000	0.000
17	R	37	ASP	-1	-0.872	-0.925	11.852	-0.510	-0.510	0.000	0.000	0.000	0.000
18	R	38	GLY	0	-0.012	-0.004	10.347	-0.003	-0.003	0.000	0.000	0.000	0.000
19	R	39	ARG	1	0.827	0.902	8.760	0.856	0.856	0.000	0.000	0.000	0.000
20	R	40	ASP	-1	-0.922	-0.962	4.877	-2.841	-2.841	0.000	0.000	0.000	0.000
21	R	42	ILE	0	-0.016	-0.023	3.134	-4.039	-2.339	0.162	-0.958	-0.904	-0.009
22	R	43	SER	0	-0.044	-0.031	5.373	0.324	0.359	-0.001	-0.003	-0.031	0.000
23	R	44	CYS	0	-0.080	0.010	6.523	-0.030	-0.030	0.000	0.000	0.000	0.000
24	R	45	LYS	1	0.969	0.995	10.176	-0.030	-0.030	0.000	0.000	0.000	0.000
25	R	46	TYR	0	-0.004	-0.029	12.839	0.017	0.017	0.000	0.000	0.000	0.000
26	R	47	GLY	0	0.005	0.010	15.015	-0.037	-0.037	0.000	0.000	0.000	0.000
27	R	48	GLN	0	-0.075	-0.029	16.629	-0.025	-0.025	0.000	0.000	0.000	0.000
28	R	49	ASP	-1	-0.861	-0.962	13.244	0.180	0.180	0.000	0.000	0.000	0.000
29	R	50	TYR	0	0.028	0.006	13.441	0.041	0.041	0.000	0.000	0.000	0.000
30	R	51	SER	0	-0.019	-0.017	10.836	-0.051	-0.051	0.000	0.000	0.000	0.000
31	R	52	THR	0	0.005	-0.008	12.355	0.071	0.071	0.000	0.000	0.000	0.000
32	R	53	HIS	0	0.017	0.016	13.742	0.075	0.075	0.000	0.000	0.000	0.000
33	R	54	TRP	0	0.023	0.015	7.932	0.106	0.106	0.000	0.000	0.000	0.000
34	R	55	ASN	0	-0.056	-0.048	9.159	-0.299	-0.299	0.000	0.000	0.000	0.000
35	R	56	ASP	-1	-0.845	-0.923	9.983	0.658	0.658	0.000	0.000	0.000	0.000
36	R	57	LEU	0	0.010	-0.007	11.596	-0.128	-0.128	0.000	0.000	0.000	0.000
37	R	58	LEU	0	0.024	0.002	11.368	0.018	0.018	0.000	0.000	0.000	0.000
38	R	59	PHE	0	-0.036	-0.031	12.011	-0.062	-0.062	0.000	0.000	0.000	0.000
39	R	61	LEU	0	0.004	0.009	13.297	-0.058	-0.058	0.000	0.000	0.000	0.000
40	R	62	ARG	1	0.969	0.970	16.909	-0.080	-0.080	0.000	0.000	0.000	0.000
41	R	63	CYS	0	-0.054	-0.011	18.574	0.036	0.036	0.000	0.000	0.000	0.000
42	R	64	THR	0	0.025	0.024	20.403	-0.015	-0.015	0.000	0.000	0.000	0.000
43	R	65	ARG	1	0.921	0.951	24.095	-0.081	-0.081	0.000	0.000	0.000	0.000
44	R	66	CYS	0	0.006	0.017	25.888	-0.006	-0.006	0.000	0.000	0.000	0.000
45	R	67	ASP	-1	-0.847	-0.914	29.352	0.084	0.084	0.000	0.000	0.000	0.000
46	R	68	SER	0	-0.050	-0.042	32.815	0.002	0.002	0.000	0.000	0.000	0.000
47	R	69	GLY	0	-0.007	0.009	35.951	-0.002	-0.002	0.000	0.000	0.000	0.000
48	R	70	GLU	-1	-0.227	-0.602	31.768	0.112	0.112	0.000	0.000	0.000	0.000
49	R	71	VAL	0	-0.001	0.006	32.503	-0.004	-0.004	0.000	0.000	0.000	0.000
50	R	72	GLU	-1	-0.960	-1.000	25.729	0.143	0.143	0.000	0.000	0.000	0.000
51	R	73	LEU	0	-0.039	0.013	28.189	-0.001	-0.001	0.000	0.000	0.000	0.000
52	R	74	SER	0	-0.089	-0.059	23.787	0.010	0.010	0.000	0.000	0.000	0.000
53	R	75	PRO	0	0.035	0.042	21.589	-0.001	-0.001	0.000	0.000	0.000	0.000
54	R	77	THR	0	-0.058	-0.041	15.813	-0.003	-0.003	0.000	0.000	0.000	0.000
55	R	78	THR	0	0.052	0.027	10.825	-0.027	-0.027	0.000	0.000	0.000	0.000
56	R	79	THR	0	0.024	0.004	11.384	-0.010	-0.010	0.000	0.000	0.000	0.000
57	R	80	ARG	1	0.962	0.984	13.730	-0.301	-0.301	0.000	0.000	0.000	0.000
58	R	81	ASN	0	0.106	0.043	17.393	-0.021	-0.021	0.000	0.000	0.000	0.000
59	R	82	THR	0	-0.064	-0.023	19.721	0.003	0.003	0.000	0.000	0.000	0.000
60	R	83	VAL	0	-0.002	0.008	22.788	0.001	0.001	0.000	0.000	0.000	0.000
61	R	85	GLN	0	0.030	-0.004	29.114	0.008	0.008	0.000	0.000	0.000	0.000
62	R	86	CYS	0	0.102	0.183	32.545	-0.002	-0.002	0.000	0.000	0.000	0.000
63	R	87	GLU	-1	-0.935	-0.959	36.090	0.074	0.074	0.000	0.000	0.000	0.000
64	R	88	GLU	-1	-0.929	-0.957	38.243	0.068	0.068	0.000	0.000	0.000	0.000
65	R	89	GLY	0	-0.004	0.005	41.096	-0.003	-0.003	0.000	0.000	0.000	0.000
66	R	90	THR	0	-0.099	-0.088	40.552	-0.004	-0.004	0.000	0.000	0.000	0.000
67	R	91	PHE	0	0.078	0.058	39.340	0.003	0.003	0.000	0.000	0.000	0.000
68	R	92	ARG	1	0.098	0.393	32.439	-0.103	-0.103	0.000	0.000	0.000	0.000
69	R	93	GLU	-1	-0.974	-0.985	37.220	0.080	0.080	0.000	0.000	0.000	0.000
70	R	94	GLU	-1	-0.963	-0.982	35.138	0.097	0.097	0.000	0.000	0.000	0.000
71	R	95	ASP	-1	-0.878	-0.922	36.782	0.075	0.075	0.000	0.000	0.000	0.000
72	R	96	SER	0	-0.137	-0.083	38.643	-0.005	-0.005	0.000	0.000	0.000	0.000
73	R	97	PRO	0	0.022	-0.007	33.979	0.001	0.001	0.000	0.000	0.000	0.000
74	R	98	GLU	-1	-0.929	-0.978	34.948	0.072	0.072	0.000	0.000	0.000	0.000
75	R	99	MET	0	-0.016	0.025	37.144	-0.002	-0.002	0.000	0.000	0.000	0.000
76	R	101	ARG	1	0.859	0.911	39.785	-0.069	-0.069	0.000	0.000	0.000	0.000
77	R	102	LYS	1	0.961	0.975	43.468	-0.046	-0.046	0.000	0.000	0.000	0.000
78	R	103	CYS	0	-0.062	0.004	44.187	0.001	0.001	0.000	0.000	0.000	0.000
79	R	116	ASP	-1	-0.952	-0.983	45.808	0.067	0.067	0.000	0.000	0.000	0.000
80	R	118	THR	0	-0.016	0.008	39.626	0.004	0.004	0.000	0.000	0.000	0.000
81	R	119	PRO	0	0.042	-0.001	36.312	-0.003	-0.003	0.000	0.000	0.000	0.000
82	R	120	TRP	0	0.000	-0.011	32.986	0.000	0.000	0.000	0.000	0.000	0.000
83	R	121	SER	0	-0.042	-0.023	38.216	0.000	0.000	0.000	0.000	0.000	0.000
84	R	122	ASP	-1	-0.863	-0.916	42.004	0.061	0.061	0.000	0.000	0.000	0.000
85	R	123	ILE	0	-0.077	-0.033	45.508	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)