FMO DATABASE

FMODB ID: N6JLQ

Calculation Name: 1D0G-R-Xray547

Preferred Name: Tumor necrosis factor ligand superfamily member 10

Target Type: SINGLE PROTEIN

Ligand Name: zinc ion | chloride ion

Ligand 3-letter code: ZN | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1D0G

Chain ID: R

ChEMBL ID: CHEMBL5813

UniProt ID: P50591

Base Structure: X-ray

Registration Date: 2025-10-06

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	101
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-708749.75917
FMO2-HF: Nuclear repulsion	662194.107162
FMO2-HF: Total energy	-46555.652008
FMO2-MP2: Total energy	-46677.280211

3D Structure Molmil

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.
-145.512	-137.035	2.076	-5.002	-5.552	-0.05

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 : 1 / q_Mulliken : 0.819 / q_NPA : 0.899

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

Sort

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	0.016	0.013	3.790	-2.784	-1.113	-0.004	-0.672	-0.995	-0.002
8	R	28	CYS	0	-0.130	-0.031	2.262	4.749	6.025	0.890	-0.730	-1.436	-0.002
9	R	29	PRO	0	0.025	0.011	4.516	4.116	4.194	-0.001	-0.006	-0.071	0.000
12	R	32	HIS	0	-0.082	-0.041	3.688	-10.055	-9.293	0.011	-0.318	-0.455	-0.002
20	R	40	ASP	-1	-0.852	-0.932	3.476	-70.768	-70.037	0.005	-0.445	-0.292	-0.003
21	R	42	ILE	0	-0.032	-0.024	2.298	-29.052	-25.165	1.176	-2.830	-2.233	-0.041
22	R	43	SER	0	-0.004	-0.018	5.138	3.445	3.517	-0.001	-0.001	-0.070	0.000
4	R	24	SER	0	-0.042	-0.028	6.041	2.289	2.289	0.000	0.000	0.000	0.000
5	R	25	GLU	-1	-0.927	-0.968	8.293	-20.239	-20.239	0.000	0.000	0.000	0.000
6	R	26	GLY	0	-0.005	0.006	10.827	1.369	1.369	0.000	0.000	0.000	0.000
7	R	27	LEU	0	0.001	0.011	9.806	-0.033	-0.033	0.000	0.000	0.000	0.000
10	R	30	PRO	0	0.025	0.011	7.402	-0.474	-0.474	0.000	0.000	0.000	0.000
11	R	31	GLY	0	-0.022	-0.005	7.966	-2.775	-2.775	0.000	0.000	0.000	0.000
13	R	33	HIS	1	0.907	0.979	7.156	34.284	34.284	0.000	0.000	0.000	0.000
14	R	34	ILE	0	0.036	0.019	6.943	-6.599	-6.599	0.000	0.000	0.000	0.000
15	R	35	SER	0	-0.078	-0.066	7.663	1.453	1.453	0.000	0.000	0.000	0.000
16	R	36	GLU	-1	-0.897	-0.966	9.169	-19.455	-19.455	0.000	0.000	0.000	0.000
17	R	37	ASP	-1	-0.804	-0.865	10.394	-29.187	-29.187	0.000	0.000	0.000	0.000
18	R	38	GLY	0	0.015	0.008	10.396	0.922	0.922	0.000	0.000	0.000	0.000
19	R	39	ARG	1	0.773	0.870	6.795	36.539	36.539	0.000	0.000	0.000	0.000
23	R	44	CYS	0	-0.091	-0.007	7.256	1.200	1.200	0.000	0.000	0.000	0.000
24	R	45	LYS	1	0.888	0.949	10.871	18.108	18.108	0.000	0.000	0.000	0.000
25	R	46	TYR	0	0.106	0.022	13.150	1.153	1.153	0.000	0.000	0.000	0.000
26	R	47	GLY	0	0.003	0.014	14.873	0.591	0.591	0.000	0.000	0.000	0.000
27	R	48	GLN	0	-0.053	-0.024	17.302	0.406	0.406	0.000	0.000	0.000	0.000
28	R	49	ASP	-1	-0.858	-0.945	13.880	-21.082	-21.082	0.000	0.000	0.000	0.000
29	R	50	TYR	0	0.002	-0.005	13.516	-1.026	-1.026	0.000	0.000	0.000	0.000
30	R	51	SER	0	0.002	-0.031	10.008	0.510	0.510	0.000	0.000	0.000	0.000
31	R	52	THR	0	0.030	0.003	12.358	-0.882	-0.882	0.000	0.000	0.000	0.000
32	R	53	HIS	0	-0.030	0.000	13.381	-0.110	-0.110	0.000	0.000	0.000	0.000
33	R	54	TRP	0	0.018	0.004	6.848	-2.081	-2.081	0.000	0.000	0.000	0.000
34	R	55	ASN	0	-0.062	-0.044	9.560	2.172	2.172	0.000	0.000	0.000	0.000
35	R	56	ASP	-1	-0.821	-0.913	10.189	-23.292	-23.292	0.000	0.000	0.000	0.000
36	R	57	LEU	0	-0.010	0.009	12.149	0.626	0.626	0.000	0.000	0.000	0.000
37	R	58	LEU	0	0.050	0.019	11.540	-2.376	-2.376	0.000	0.000	0.000	0.000
38	R	59	PHE	0	-0.064	-0.036	12.918	-0.572	-0.572	0.000	0.000	0.000	0.000
39	R	61	LEU	0	0.019	0.018	13.971	1.266	1.266	0.000	0.000	0.000	0.000
40	R	62	ARG	1	0.966	0.968	17.171	14.674	14.674	0.000	0.000	0.000	0.000
41	R	63	CYS	0	-0.102	-0.030	18.574	-0.503	-0.503	0.000	0.000	0.000	0.000
42	R	64	THR	0	0.031	0.020	20.726	0.188	0.188	0.000	0.000	0.000	0.000
43	R	65	ARG	1	0.906	0.966	24.370	11.300	11.300	0.000	0.000	0.000	0.000
44	R	66	CYS	0	0.000	0.012	25.621	0.078	0.078	0.000	0.000	0.000	0.000
45	R	67	ASP	-1	-0.858	-0.930	29.563	-9.185	-9.185	0.000	0.000	0.000	0.000
46	R	68	SER	0	-0.037	-0.037	33.095	0.019	0.019	0.000	0.000	0.000	0.000
47	R	69	GLY	0	-0.017	0.009	36.102	0.196	0.196	0.000	0.000	0.000	0.000
48	R	70	GLU	-1	-0.816	-0.915	31.605	-9.971	-9.971	0.000	0.000	0.000	0.000
49	R	71	VAL	0	-0.008	0.002	32.407	-0.067	-0.067	0.000	0.000	0.000	0.000
50	R	72	GLU	-1	-0.910	-0.984	25.043	-12.529	-12.529	0.000	0.000	0.000	0.000
51	R	73	LEU	0	-0.038	-0.005	28.047	0.056	0.056	0.000	0.000	0.000	0.000
52	R	74	SER	0	-0.040	-0.030	23.200	-0.358	-0.358	0.000	0.000	0.000	0.000
53	R	75	PRO	0	0.063	0.043	21.103	-0.137	-0.137	0.000	0.000	0.000	0.000
54	R	77	THR	0	-0.017	-0.009	14.882	-0.214	-0.214	0.000	0.000	0.000	0.000
55	R	78	THR	0	0.010	0.002	10.057	0.754	0.754	0.000	0.000	0.000	0.000
56	R	79	THR	0	0.011	0.000	10.913	-0.481	-0.481	0.000	0.000	0.000	0.000
57	R	80	ARG	1	0.914	0.956	13.289	15.435	15.435	0.000	0.000	0.000	0.000
58	R	81	ASN	0	0.094	0.048	17.145	-0.240	-0.240	0.000	0.000	0.000	0.000
59	R	82	THR	0	-0.024	-0.030	19.841	-0.138	-0.138	0.000	0.000	0.000	0.000
60	R	83	VAL	0	-0.052	-0.009	22.677	0.115	0.115	0.000	0.000	0.000	0.000
61	R	85	GLN	0	0.025	0.006	28.947	-0.065	-0.065	0.000	0.000	0.000	0.000
62	R	86	CYS	0	-0.005	0.036	32.328	0.043	0.043	0.000	0.000	0.000	0.000
63	R	87	GLU	-1	-0.889	-0.943	35.910	-8.185	-8.185	0.000	0.000	0.000	0.000
64	R	88	GLU	-1	-0.932	-0.960	38.023	-7.247	-7.247	0.000	0.000	0.000	0.000
65	R	89	GLY	0	-0.030	-0.017	40.926	0.126	0.126	0.000	0.000	0.000	0.000
66	R	90	THR	0	-0.111	-0.080	40.091	0.115	0.115	0.000	0.000	0.000	0.000
67	R	91	PHE	0	0.001	0.002	39.412	-0.095	-0.095	0.000	0.000	0.000	0.000
68	R	92	ARG	1	0.860	0.916	31.800	9.489	9.489	0.000	0.000	0.000	0.000
69	R	93	GLU	-1	-0.773	-0.858	37.700	-7.699	-7.699	0.000	0.000	0.000	0.000
70	R	94	GLU	-1	-0.954	-0.975	36.365	-8.241	-8.241	0.000	0.000	0.000	0.000
71	R	95	ASP	-1	-0.899	-0.936	37.267	-7.809	-7.809	0.000	0.000	0.000	0.000
72	R	96	SER	0	-0.142	-0.097	38.898	0.119	0.119	0.000	0.000	0.000	0.000
73	R	97	PRO	0	0.028	-0.003	33.567	-0.057	-0.057	0.000	0.000	0.000	0.000
74	R	98	GLU	-1	-0.942	-0.974	33.906	-9.556	-9.556	0.000	0.000	0.000	0.000
75	R	99	MET	0	-0.040	-0.022	36.035	0.037	0.037	0.000	0.000	0.000	0.000
76	R	101	ARG	1	0.817	0.901	39.258	7.582	7.582	0.000	0.000	0.000	0.000
77	R	102	LYS	1	0.968	0.972	42.881	6.714	6.714	0.000	0.000	0.000	0.000
78	R	103	CYS	0	-0.059	0.009	44.108	-0.077	-0.077	0.000	0.000	0.000	0.000
79	R	104	ARG	1	0.788	0.876	46.580	6.469	6.469	0.000	0.000	0.000	0.000
80	R	105	THR	0	0.009	-0.008	49.775	-0.040	-0.040	0.000	0.000	0.000	0.000
81	R	106	GLY	0	0.000	0.000	51.821	0.029	0.029	0.000	0.000	0.000	0.000
82	R	107	CYS	0	-0.063	-0.033	49.141	0.016	0.016	0.000	0.000	0.000	0.000
83	R	108	PRO	0	0.028	0.008	55.062	0.090	0.090	0.000	0.000	0.000	0.000
84	R	109	ARG	1	0.972	0.974	58.264	4.827	4.827	0.000	0.000	0.000	0.000
85	R	110	GLY	0	-0.034	-0.019	61.919	0.027	0.027	0.000	0.000	0.000	0.000
86	R	111	MET	0	-0.035	0.008	55.691	0.023	0.023	0.000	0.000	0.000	0.000
87	R	112	VAL	0	-0.033	-0.012	55.876	0.026	0.026	0.000	0.000	0.000	0.000
88	R	113	LYS	1	0.888	0.922	49.000	6.341	6.341	0.000	0.000	0.000	0.000
89	R	114	VAL	0	-0.036	-0.024	49.974	0.070	0.070	0.000	0.000	0.000	0.000
90	R	115	GLY	0	0.056	0.041	46.921	-0.101	-0.101	0.000	0.000	0.000	0.000
91	R	116	ASP	-1	-0.871	-0.938	44.969	-6.495	-6.495	0.000	0.000	0.000	0.000
92	R	118	THR	0	0.004	-0.016	39.108	-0.131	-0.131	0.000	0.000	0.000	0.000
93	R	119	PRO	0	0.033	0.006	35.560	0.061	0.061	0.000	0.000	0.000	0.000
94	R	120	TRP	0	-0.033	-0.014	32.524	-0.092	-0.092	0.000	0.000	0.000	0.000
95	R	121	SER	0	0.010	0.025	37.794	0.016	0.016	0.000	0.000	0.000	0.000
96	R	122	ASP	-1	-0.725	-0.840	41.656	-6.626	-6.626	0.000	0.000	0.000	0.000
97	R	123	ILE	0	-0.089	-0.041	45.035	-0.001	-0.001	0.000	0.000	0.000	0.000
98	R	124	GLU	-1	-0.916	-0.948	46.976	-6.576	-6.576	0.000	0.000	0.000	0.000
99	R	126	VAL	0	0.026	0.021	52.953	-0.016	-0.016	0.000	0.000	0.000	0.000
100	R	127	HIS	0	-0.005	-0.021	55.286	0.109	0.109	0.000	0.000	0.000	0.000
101	R	128	LYS	0	0.045	0.035	58.810	-0.080	-0.080	0.000	0.000	0.000	0.000

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