FMO DATABASE

FMODB ID: MVN1Z

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	OptAll
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	-569521.863396
FMO2-HF: Nuclear repulsion	530005.769175
FMO2-HF: Total energy	-39516.094221
FMO2-MP2: Total energy	-39619.686033

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.
-11.852	-8.878	7.812	-5.159	-5.627	-0.038

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 : -0.042 / q_NPA : -0.036

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	0.014	-0.003	3.893	0.865	2.512	-0.017	-0.865	-0.765	0.001
4	R	24	SER	0	-0.009	0.011	6.528	0.093	0.093	0.000	0.000	0.000	0.000
5	R	25	GLU	-1	-0.959	-0.990	8.202	0.112	0.112	0.000	0.000	0.000	0.000
6	R	26	GLY	0	-0.019	0.003	10.562	-0.010	-0.010	0.000	0.000	0.000	0.000
7	R	27	LEU	0	-0.028	-0.007	10.011	-0.094	-0.094	0.000	0.000	0.000	0.000
8	R	28	CYS	0	-0.050	-0.004	2.202	0.774	1.737	1.893	-1.047	-1.810	0.003
9	R	29	PRO	0	0.019	0.004	5.005	-0.190	-0.190	0.000	0.000	0.000	0.000
10	R	30	PRO	0	0.013	0.007	7.976	-0.212	-0.212	0.000	0.000	0.000	0.000
11	R	31	GLY	0	-0.042	-0.023	8.681	0.065	0.065	0.000	0.000	0.000	0.000
12	R	32	HIS	0	-0.071	-0.046	3.502	-0.673	-0.371	0.007	-0.062	-0.246	0.000
13	R	33	HIS	0	-0.009	0.009	6.452	0.285	0.285	0.000	0.000	0.000	0.000
14	R	34	ILE	0	0.033	0.009	6.020	-0.640	-0.640	0.000	0.000	0.000	0.000
15	R	35	SER	0	-0.037	-0.033	7.769	0.002	0.002	0.000	0.000	0.000	0.000
16	R	36	GLU	-1	-0.921	-0.978	9.523	-0.445	-0.445	0.000	0.000	0.000	0.000
17	R	37	ASP	-1	-0.830	-0.874	11.083	-1.071	-1.071	0.000	0.000	0.000	0.000
18	R	38	GLY	0	-0.005	-0.002	10.466	0.070	0.070	0.000	0.000	0.000	0.000
19	R	39	ARG	1	0.733	0.843	8.236	1.479	1.479	0.000	0.000	0.000	0.000
20	R	40	ASP	-1	-0.816	-0.894	4.966	-2.944	-2.819	-0.001	-0.018	-0.106	0.000
21	R	42	ILE	0	-0.010	-0.001	2.002	-9.559	-9.680	5.931	-3.162	-2.648	-0.042
22	R	43	SER	0	-0.011	-0.003	4.665	0.688	0.746	-0.001	-0.005	-0.052	0.000
23	R	44	CYS	0	-0.084	-0.010	6.326	0.178	0.178	0.000	0.000	0.000	0.000
24	R	45	LYS	1	0.930	0.959	9.967	0.311	0.311	0.000	0.000	0.000	0.000
25	R	46	TYR	0	0.051	0.003	12.808	0.048	0.048	0.000	0.000	0.000	0.000
26	R	47	GLY	0	-0.008	0.001	14.868	0.015	0.015	0.000	0.000	0.000	0.000
27	R	48	GLN	0	-0.097	-0.040	16.611	-0.005	-0.005	0.000	0.000	0.000	0.000
28	R	49	ASP	-1	-0.824	-0.928	12.697	-0.479	-0.479	0.000	0.000	0.000	0.000
29	R	50	TYR	0	0.017	0.002	13.190	-0.005	-0.005	0.000	0.000	0.000	0.000
30	R	51	SER	0	-0.001	-0.012	10.718	0.001	0.001	0.000	0.000	0.000	0.000
31	R	52	THR	0	0.012	-0.014	12.422	0.019	0.019	0.000	0.000	0.000	0.000
32	R	53	HIS	0	0.000	0.018	13.413	0.043	0.043	0.000	0.000	0.000	0.000
33	R	54	TRP	0	0.019	0.013	8.275	-0.031	-0.031	0.000	0.000	0.000	0.000
34	R	55	ASN	0	-0.074	-0.048	9.376	-0.111	-0.111	0.000	0.000	0.000	0.000
35	R	56	ASP	-1	-0.840	-0.920	9.945	-0.343	-0.343	0.000	0.000	0.000	0.000
36	R	57	LEU	0	0.003	0.004	11.684	-0.013	-0.013	0.000	0.000	0.000	0.000
37	R	58	LEU	0	0.034	0.006	10.860	-0.122	-0.122	0.000	0.000	0.000	0.000
38	R	59	PHE	0	-0.043	-0.022	11.384	-0.065	-0.065	0.000	0.000	0.000	0.000
39	R	61	LEU	0	0.003	0.015	12.774	0.030	0.030	0.000	0.000	0.000	0.000
40	R	62	ARG	1	0.967	0.973	16.370	0.261	0.261	0.000	0.000	0.000	0.000
41	R	63	CYS	0	-0.068	-0.013	18.514	0.012	0.012	0.000	0.000	0.000	0.000
42	R	64	THR	0	0.007	0.013	20.241	0.000	0.000	0.000	0.000	0.000	0.000
43	R	65	ARG	1	0.919	0.949	23.932	0.100	0.100	0.000	0.000	0.000	0.000
44	R	66	CYS	0	-0.042	0.011	25.823	0.004	0.004	0.000	0.000	0.000	0.000
45	R	67	ASP	-1	-0.816	-0.888	29.187	-0.073	-0.073	0.000	0.000	0.000	0.000
46	R	68	SER	0	-0.084	-0.061	32.633	0.005	0.005	0.000	0.000	0.000	0.000
47	R	69	GLY	0	0.024	0.020	35.688	0.003	0.003	0.000	0.000	0.000	0.000
48	R	70	GLU	-1	-0.809	-0.910	31.390	-0.055	-0.055	0.000	0.000	0.000	0.000
49	R	71	VAL	0	-0.027	-0.006	32.522	0.000	0.000	0.000	0.000	0.000	0.000
50	R	72	GLU	-1	-0.843	-0.926	24.945	-0.071	-0.071	0.000	0.000	0.000	0.000
51	R	73	LEU	0	-0.024	0.010	28.601	0.006	0.006	0.000	0.000	0.000	0.000
52	R	74	SER	0	0.002	-0.025	24.164	0.011	0.011	0.000	0.000	0.000	0.000
53	R	75	PRO	0	0.030	0.048	21.916	-0.009	-0.009	0.000	0.000	0.000	0.000
54	R	77	THR	0	-0.052	-0.026	15.690	0.001	0.001	0.000	0.000	0.000	0.000
55	R	78	THR	0	0.042	0.020	10.738	0.025	0.025	0.000	0.000	0.000	0.000
56	R	79	THR	0	0.015	0.004	11.630	-0.044	-0.044	0.000	0.000	0.000	0.000
57	R	80	ARG	1	0.850	0.918	13.704	0.060	0.060	0.000	0.000	0.000	0.000
58	R	81	ASN	0	0.082	0.030	17.371	-0.021	-0.021	0.000	0.000	0.000	0.000
59	R	82	THR	0	-0.080	-0.074	19.598	0.017	0.017	0.000	0.000	0.000	0.000
60	R	83	VAL	0	-0.017	-0.006	22.622	-0.002	-0.002	0.000	0.000	0.000	0.000
61	R	85	GLN	0	0.015	-0.008	29.100	0.004	0.004	0.000	0.000	0.000	0.000
62	R	86	CYS	0	-0.011	0.049	32.758	-0.001	-0.001	0.000	0.000	0.000	0.000
63	R	87	GLU	-1	-0.917	-0.946	36.336	-0.018	-0.018	0.000	0.000	0.000	0.000
64	R	88	GLU	-1	-0.918	-0.961	38.448	-0.009	-0.009	0.000	0.000	0.000	0.000
65	R	89	GLY	0	-0.013	-0.007	41.346	-0.001	-0.001	0.000	0.000	0.000	0.000
66	R	90	THR	0	-0.101	-0.062	40.489	-0.002	-0.002	0.000	0.000	0.000	0.000
67	R	91	PHE	0	0.005	0.003	39.388	0.001	0.001	0.000	0.000	0.000	0.000
68	R	92	ARG	1	0.762	0.831	31.843	0.053	0.053	0.000	0.000	0.000	0.000
69	R	93	GLU	-1	-0.817	-0.888	37.460	-0.031	-0.031	0.000	0.000	0.000	0.000
70	R	94	GLU	-1	-0.939	-0.968	35.091	-0.056	-0.056	0.000	0.000	0.000	0.000
71	R	95	ASP	-1	-0.914	-0.950	36.963	-0.050	-0.050	0.000	0.000	0.000	0.000
72	R	96	SER	0	-0.129	-0.068	38.523	0.002	0.002	0.000	0.000	0.000	0.000
73	R	97	PRO	0	0.015	0.010	33.935	0.002	0.002	0.000	0.000	0.000	0.000
74	R	98	GLU	-1	-0.910	-0.951	35.417	-0.067	-0.067	0.000	0.000	0.000	0.000
75	R	99	MET	0	-0.048	-0.032	37.078	0.001	0.001	0.000	0.000	0.000	0.000
76	R	101	ARG	1	0.821	0.887	39.717	0.034	0.034	0.000	0.000	0.000	0.000
77	R	102	LYS	1	0.957	0.972	43.350	0.020	0.020	0.000	0.000	0.000	0.000
78	R	103	CYS	0	-0.177	-0.086	44.563	-0.001	-0.001	0.000	0.000	0.000	0.000
79	R	116	ASP	-1	-0.945	-0.985	45.912	-0.007	-0.007	0.000	0.000	0.000	0.000
80	R	118	THR	0	0.002	-0.006	39.935	0.001	0.001	0.000	0.000	0.000	0.000
81	R	119	PRO	0	0.011	-0.006	36.326	-0.002	-0.002	0.000	0.000	0.000	0.000
82	R	120	TRP	0	0.002	-0.010	33.281	-0.002	-0.002	0.000	0.000	0.000	0.000
83	R	121	SER	0	-0.011	0.009	38.426	-0.001	-0.001	0.000	0.000	0.000	0.000
84	R	122	ASP	-1	-0.756	-0.836	42.265	-0.019	-0.019	0.000	0.000	0.000	0.000
85	R	123	ILE	0	-0.076	-0.040	45.654	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)