FMO DATABASE

FMODB ID: YRM32

Calculation Name: 3HCS-A-Xray547

Preferred Name: TNF receptor-associated factor 6

Target Type: SINGLE PROTEIN

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3HCS

Chain ID: A

ChEMBL ID: CHEMBL3588728

UniProt ID: Q9Y4K3

Base Structure: X-ray

Registration Date: 2025-10-05

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	157
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1333781.987915
FMO2-HF: Nuclear repulsion	1265919.939491
FMO2-HF: Total energy	-67862.048424
FMO2-MP2: Total energy	-68044.811204

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(A:54:GLN)

Summations of interaction energy for fragment #1(A:54:GLN)

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.
-77.679	-71.202	5.383	-4.68	-7.18	-0.047

Interaction energy analysis for fragmet #1(A:54:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.860 / q_NPA : 0.924

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	A	56	TYR	0	-0.031	-0.016	3.799	-9.246	-6.990	0.006	-1.231	-1.030	-0.003
20	A	73	CYS	0	-0.087	-0.050	2.805	-11.237	-9.964	1.030	-0.914	-1.390	-0.014
21	A	74	LEU	0	0.035	0.032	4.651	-2.574	-2.529	-0.001	-0.006	-0.038	0.000
22	A	75	MET	0	0.070	0.044	2.204	-6.956	-5.646	1.677	-1.236	-1.752	-0.023
25	A	78	ARG	1	0.928	0.931	3.429	54.477	55.261	0.007	-0.227	-0.564	0.000
37	A	90	CYS	0	-0.038	0.029	3.545	2.722	3.042	0.006	-0.101	-0.225	0.000
39	A	92	ALA	0	0.025	-0.002	2.744	0.784	1.285	0.283	-0.194	-0.589	-0.001
40	A	93	CYS	0	-0.040	-0.012	2.947	-4.971	-5.024	2.376	-0.763	-1.561	-0.006
41	A	94	ILE	0	0.055	0.027	4.878	3.319	3.360	-0.001	-0.008	-0.031	0.000
4	A	57	ASP	-1	-0.891	-0.942	5.509	-32.700	-32.700	0.000	0.000	0.000	0.000
5	A	58	VAL	0	0.009	-0.003	6.927	2.093	2.093	0.000	0.000	0.000	0.000
6	A	59	GLU	-1	-0.807	-0.891	10.656	-16.860	-16.860	0.000	0.000	0.000	0.000
7	A	60	PHE	0	-0.015	-0.020	9.900	0.511	0.511	0.000	0.000	0.000	0.000
8	A	61	ASP	-1	-0.836	-0.909	15.073	-13.841	-13.841	0.000	0.000	0.000	0.000
9	A	62	PRO	0	-0.012	-0.018	18.872	0.592	0.592	0.000	0.000	0.000	0.000
10	A	63	PRO	0	-0.007	-0.007	16.504	-0.762	-0.762	0.000	0.000	0.000	0.000
11	A	64	LEU	0	-0.026	0.003	10.546	0.187	0.187	0.000	0.000	0.000	0.000
12	A	65	GLU	-1	-0.853	-0.931	14.741	-15.794	-15.794	0.000	0.000	0.000	0.000
13	A	66	SER	0	0.065	0.022	13.752	-0.947	-0.947	0.000	0.000	0.000	0.000
14	A	67	LYS	1	0.821	0.928	13.755	15.208	15.208	0.000	0.000	0.000	0.000
15	A	68	TYR	0	-0.067	-0.070	12.813	-0.033	-0.033	0.000	0.000	0.000	0.000
16	A	69	GLU	-1	-0.870	-0.930	9.377	-28.157	-28.157	0.000	0.000	0.000	0.000
17	A	70	CYS	0	-0.061	-0.020	5.072	2.812	2.812	0.000	0.000	0.000	0.000
18	A	71	PRO	0	0.020	-0.002	7.315	-2.676	-2.676	0.000	0.000	0.000	0.000
19	A	72	ILE	0	-0.029	-0.006	5.774	0.863	0.863	0.000	0.000	0.000	0.000
23	A	76	ALA	0	0.032	0.029	6.422	-0.079	-0.079	0.000	0.000	0.000	0.000
24	A	77	LEU	0	-0.043	-0.029	6.881	-6.697	-6.697	0.000	0.000	0.000	0.000
26	A	79	GLU	-1	-0.869	-0.931	5.958	-28.626	-28.626	0.000	0.000	0.000	0.000
27	A	80	ALA	0	0.022	0.023	8.337	-0.837	-0.837	0.000	0.000	0.000	0.000
28	A	81	VAL	0	-0.038	-0.015	9.230	2.166	2.166	0.000	0.000	0.000	0.000
29	A	82	GLN	0	-0.020	-0.021	11.685	-0.387	-0.387	0.000	0.000	0.000	0.000
30	A	83	THR	0	0.010	-0.014	13.822	0.368	0.368	0.000	0.000	0.000	0.000
31	A	84	PRO	0	0.041	0.010	16.168	0.367	0.367	0.000	0.000	0.000	0.000
32	A	85	CYS	0	-0.051	0.025	18.382	0.067	0.067	0.000	0.000	0.000	0.000
33	A	86	GLY	0	0.031	0.024	18.892	-0.016	-0.016	0.000	0.000	0.000	0.000
34	A	87	HIS	1	0.849	0.912	14.487	16.927	16.927	0.000	0.000	0.000	0.000
35	A	88	ARG	1	0.835	0.923	11.968	19.328	19.328	0.000	0.000	0.000	0.000
36	A	89	PHE	0	0.069	0.000	7.980	-1.029	-1.029	0.000	0.000	0.000	0.000
38	A	91	LYS	1	0.992	1.005	5.750	23.164	23.164	0.000	0.000	0.000	0.000
42	A	95	ILE	0	-0.013	-0.001	7.790	2.200	2.200	0.000	0.000	0.000	0.000
43	A	96	LYS	1	0.858	0.918	6.075	32.147	32.147	0.000	0.000	0.000	0.000
44	A	97	SER	0	-0.008	-0.010	8.568	2.566	2.566	0.000	0.000	0.000	0.000
45	A	98	ILE	0	0.047	0.022	10.583	1.677	1.677	0.000	0.000	0.000	0.000
46	A	99	ARG	1	0.764	0.855	11.100	23.612	23.612	0.000	0.000	0.000	0.000
47	A	100	ASP	-1	-0.874	-0.919	11.226	-24.472	-24.472	0.000	0.000	0.000	0.000
48	A	101	ALA	0	-0.004	0.004	13.349	1.204	1.204	0.000	0.000	0.000	0.000
49	A	102	GLY	0	0.015	0.013	15.071	1.090	1.090	0.000	0.000	0.000	0.000
50	A	103	HIS	0	-0.057	-0.038	16.131	-0.351	-0.351	0.000	0.000	0.000	0.000
51	A	104	LYS	1	0.904	0.953	16.394	17.451	17.451	0.000	0.000	0.000	0.000
52	A	105	CYS	0	-0.044	-0.017	14.655	-1.974	-1.974	0.000	0.000	0.000	0.000
53	A	106	PRO	0	-0.022	-0.027	11.522	0.825	0.825	0.000	0.000	0.000	0.000
54	A	107	VAL	0	-0.006	-0.007	13.590	0.294	0.294	0.000	0.000	0.000	0.000
55	A	108	ASP	-1	-0.749	-0.878	16.061	-15.785	-15.785	0.000	0.000	0.000	0.000
56	A	109	ASN	0	-0.053	-0.015	18.510	0.431	0.431	0.000	0.000	0.000	0.000
57	A	110	GLU	-1	-0.909	-0.933	19.700	-12.667	-12.667	0.000	0.000	0.000	0.000
58	A	111	ILE	0	-0.003	-0.009	19.127	-0.875	-0.875	0.000	0.000	0.000	0.000
59	A	112	LEU	0	-0.032	-0.016	13.740	-0.073	-0.073	0.000	0.000	0.000	0.000
60	A	113	LEU	0	0.019	0.005	17.333	-0.403	-0.403	0.000	0.000	0.000	0.000
61	A	114	GLU	-1	-0.790	-0.883	12.877	-21.554	-21.554	0.000	0.000	0.000	0.000
62	A	115	ASN	0	-0.043	-0.032	15.320	-0.542	-0.542	0.000	0.000	0.000	0.000
63	A	116	GLN	0	0.018	0.009	17.462	0.395	0.395	0.000	0.000	0.000	0.000
64	A	117	LEU	0	-0.028	0.005	11.486	-0.159	-0.159	0.000	0.000	0.000	0.000
65	A	118	PHE	0	0.015	0.016	15.343	0.294	0.294	0.000	0.000	0.000	0.000
66	A	119	PRO	0	0.004	-0.005	13.593	-1.134	-1.134	0.000	0.000	0.000	0.000
67	A	120	ASP	-1	-0.743	-0.859	13.493	-17.454	-17.454	0.000	0.000	0.000	0.000
68	A	121	ASN	0	-0.006	-0.040	14.488	-1.416	-1.416	0.000	0.000	0.000	0.000
69	A	122	PHE	0	-0.069	-0.005	16.435	0.471	0.471	0.000	0.000	0.000	0.000
70	A	123	ALA	0	0.034	0.010	13.492	0.011	0.011	0.000	0.000	0.000	0.000
71	A	124	LYS	1	0.843	0.904	11.387	22.671	22.671	0.000	0.000	0.000	0.000
72	A	125	ARG	1	0.950	0.976	13.659	14.797	14.797	0.000	0.000	0.000	0.000
73	A	126	GLU	-1	-0.751	-0.879	16.651	-16.655	-16.655	0.000	0.000	0.000	0.000
74	A	127	ILE	0	0.022	0.017	10.851	0.279	0.279	0.000	0.000	0.000	0.000
75	A	128	LEU	0	-0.033	-0.018	11.962	-0.083	-0.083	0.000	0.000	0.000	0.000
76	A	129	SER	0	-0.048	-0.028	15.036	0.859	0.859	0.000	0.000	0.000	0.000
77	A	130	LEU	0	-0.021	0.005	14.086	0.725	0.725	0.000	0.000	0.000	0.000
78	A	131	MET	0	-0.020	0.002	17.008	-0.387	-0.387	0.000	0.000	0.000	0.000
79	A	132	VAL	0	-0.002	-0.007	13.530	-0.829	-0.829	0.000	0.000	0.000	0.000
80	A	133	LYS	1	0.829	0.910	16.566	16.672	16.672	0.000	0.000	0.000	0.000
81	A	134	CYS	0	-0.038	-0.014	16.237	-1.387	-1.387	0.000	0.000	0.000	0.000
82	A	135	PRO	0	0.005	0.001	14.017	0.303	0.303	0.000	0.000	0.000	0.000
83	A	136	ASN	0	-0.063	-0.089	16.358	-0.223	-0.223	0.000	0.000	0.000	0.000
84	A	137	GLU	-1	-0.842	-0.922	19.445	-13.053	-13.053	0.000	0.000	0.000	0.000
85	A	138	GLY	0	0.001	-0.011	22.000	0.369	0.369	0.000	0.000	0.000	0.000
86	A	139	CYS	0	-0.082	-0.032	21.435	0.494	0.494	0.000	0.000	0.000	0.000
87	A	140	LEU	0	-0.009	-0.009	22.354	-0.356	-0.356	0.000	0.000	0.000	0.000
88	A	141	HIS	0	-0.002	0.001	22.329	0.021	0.021	0.000	0.000	0.000	0.000
89	A	142	LYS	1	0.861	0.920	20.748	13.005	13.005	0.000	0.000	0.000	0.000
90	A	143	MET	0	-0.043	-0.008	18.059	0.446	0.446	0.000	0.000	0.000	0.000
91	A	144	GLU	-1	-0.761	-0.873	18.775	-15.282	-15.282	0.000	0.000	0.000	0.000
92	A	145	LEU	0	-0.018	-0.007	10.838	-0.325	-0.325	0.000	0.000	0.000	0.000
93	A	146	ARG	1	0.796	0.865	14.592	14.431	14.431	0.000	0.000	0.000	0.000
94	A	147	HIS	0	0.007	0.005	15.967	0.174	0.174	0.000	0.000	0.000	0.000
95	A	148	LEU	0	0.019	0.007	12.652	0.459	0.459	0.000	0.000	0.000	0.000
96	A	149	GLU	-1	-0.991	-0.986	11.721	-22.868	-22.868	0.000	0.000	0.000	0.000
97	A	150	ASP	-1	-0.901	-0.957	15.083	-14.858	-14.858	0.000	0.000	0.000	0.000
98	A	151	HIS	0	-0.043	-0.074	18.317	0.640	0.640	0.000	0.000	0.000	0.000
99	A	152	GLN	0	-0.004	0.005	14.771	0.680	0.680	0.000	0.000	0.000	0.000
100	A	153	ALA	0	-0.024	0.000	17.634	0.328	0.328	0.000	0.000	0.000	0.000
101	A	154	HIS	0	-0.019	-0.023	19.712	0.936	0.936	0.000	0.000	0.000	0.000
102	A	155	CYS	-1	-0.787	-0.764	20.663	-13.727	-13.727	0.000	0.000	0.000	0.000
103	A	156	GLU	-1	-0.884	-0.953	22.609	-11.900	-11.900	0.000	0.000	0.000	0.000
104	A	157	PHE	0	0.014	-0.012	22.829	0.346	0.346	0.000	0.000	0.000	0.000
105	A	158	ALA	0	0.023	0.030	19.894	-0.312	-0.312	0.000	0.000	0.000	0.000
106	A	159	LEU	0	-0.036	-0.023	19.712	0.715	0.715	0.000	0.000	0.000	0.000
107	A	160	MET	0	-0.015	-0.005	20.541	-0.292	-0.292	0.000	0.000	0.000	0.000
108	A	161	ASP	-1	-0.868	-0.929	20.871	-13.138	-13.138	0.000	0.000	0.000	0.000
109	A	162	CYS	0	-0.053	0.004	23.817	0.366	0.366	0.000	0.000	0.000	0.000
110	A	163	PRO	0	0.012	-0.005	27.088	0.032	0.032	0.000	0.000	0.000	0.000
111	A	164	GLN	0	0.017	-0.011	28.000	0.152	0.152	0.000	0.000	0.000	0.000
112	A	165	CYS	0	-0.090	-0.061	29.517	0.170	0.170	0.000	0.000	0.000	0.000
113	A	166	GLN	0	-0.028	-0.008	24.583	-0.057	-0.057	0.000	0.000	0.000	0.000
114	A	167	ARG	1	0.997	1.010	24.864	9.508	9.508	0.000	0.000	0.000	0.000
115	A	168	PRO	0	0.046	0.036	22.277	0.233	0.233	0.000	0.000	0.000	0.000
116	A	169	PHE	0	-0.036	-0.030	24.377	0.383	0.383	0.000	0.000	0.000	0.000
117	A	170	GLN	0	-0.012	-0.016	23.608	0.013	0.013	0.000	0.000	0.000	0.000
118	A	171	LYS	1	0.846	0.934	22.705	13.745	13.745	0.000	0.000	0.000	0.000
119	A	172	PHE	0	-0.004	-0.007	26.486	0.484	0.484	0.000	0.000	0.000	0.000
120	A	173	HIS	0	-0.014	0.000	29.267	0.368	0.368	0.000	0.000	0.000	0.000
121	A	174	ILE	0	-0.008	0.000	26.816	0.373	0.373	0.000	0.000	0.000	0.000
122	A	175	ASN	0	0.012	-0.012	29.906	0.193	0.193	0.000	0.000	0.000	0.000
123	A	176	ILE	0	-0.027	0.000	33.054	0.357	0.357	0.000	0.000	0.000	0.000
124	A	177	HIS	0	0.070	0.017	30.657	0.339	0.339	0.000	0.000	0.000	0.000
125	A	178	ILE	0	-0.025	-0.015	29.592	0.208	0.208	0.000	0.000	0.000	0.000
126	A	179	LEU	0	-0.001	-0.001	33.748	0.224	0.224	0.000	0.000	0.000	0.000
127	A	180	LYS	1	0.863	0.939	37.143	7.900	7.900	0.000	0.000	0.000	0.000
128	A	181	ASP	-1	-0.807	-0.907	35.284	-8.434	-8.434	0.000	0.000	0.000	0.000
129	A	182	CYS	0	-0.062	-0.022	33.060	0.055	0.055	0.000	0.000	0.000	0.000
130	A	183	PRO	0	0.018	0.014	34.506	0.141	0.141	0.000	0.000	0.000	0.000
131	A	184	ARG	1	0.804	0.872	33.406	8.336	8.336	0.000	0.000	0.000	0.000
132	A	185	ARG	1	0.839	0.931	35.800	7.898	7.898	0.000	0.000	0.000	0.000
133	A	186	GLN	0	0.013	0.010	36.796	0.298	0.298	0.000	0.000	0.000	0.000
134	A	187	VAL	0	-0.019	-0.007	39.179	0.004	0.004	0.000	0.000	0.000	0.000
135	A	188	SER	0	0.024	0.009	42.882	-0.018	-0.018	0.000	0.000	0.000	0.000
136	A	189	CYS	0	-0.062	-0.003	46.101	0.083	0.083	0.000	0.000	0.000	0.000
137	A	190	ASP	-1	-0.937	-0.977	49.336	-6.087	-6.087	0.000	0.000	0.000	0.000
138	A	191	ASN	0	-0.038	-0.013	52.218	0.147	0.147	0.000	0.000	0.000	0.000
139	A	192	CYS	0	0.029	0.012	51.369	-0.022	-0.022	0.000	0.000	0.000	0.000
140	A	193	ALA	0	-0.022	-0.005	49.656	-0.043	-0.043	0.000	0.000	0.000	0.000
141	A	194	ALA	0	-0.001	0.004	47.202	-0.140	-0.140	0.000	0.000	0.000	0.000
142	A	195	SER	0	-0.030	-0.032	41.168	0.004	0.004	0.000	0.000	0.000	0.000
143	A	196	MET	0	-0.031	0.000	41.942	0.027	0.027	0.000	0.000	0.000	0.000
144	A	197	ALA	0	-0.002	0.002	38.271	-0.114	-0.114	0.000	0.000	0.000	0.000
145	A	198	PHE	0	-0.005	-0.015	39.771	0.184	0.184	0.000	0.000	0.000	0.000
146	A	199	GLU	-1	-0.866	-0.931	37.554	-8.040	-8.040	0.000	0.000	0.000	0.000
147	A	200	ASP	-1	-0.832	-0.907	40.500	-7.435	-7.435	0.000	0.000	0.000	0.000
148	A	201	LYS	1	0.849	0.907	43.372	6.572	6.572	0.000	0.000	0.000	0.000
149	A	202	GLU	-1	-0.929	-0.955	45.973	-6.237	-6.237	0.000	0.000	0.000	0.000
150	A	203	ILE	0	0.027	0.008	45.731	0.140	0.140	0.000	0.000	0.000	0.000
151	A	204	HIS	0	0.012	-0.001	47.187	0.062	0.062	0.000	0.000	0.000	0.000
152	A	205	ASP	-1	-0.777	-0.897	49.106	-6.086	-6.086	0.000	0.000	0.000	0.000
153	A	206	GLN	0	-0.113	-0.052	51.823	0.119	0.119	0.000	0.000	0.000	0.000
154	A	207	ASN	0	-0.104	-0.056	51.772	0.188	0.188	0.000	0.000	0.000	0.000
155	A	208	CYS	0	-0.039	0.009	52.868	-0.009	-0.009	0.000	0.000	0.000	0.000
156	A	209	PRO	0	-0.069	-0.050	53.610	0.082	0.082	0.000	0.000	0.000	0.000
157	A	210	LEU	-1	-0.901	-0.941	56.009	-5.359	-5.359	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:54:GLN)