FMO DATABASE

FMODB ID: MNR4Z

Calculation Name: 4HT1-T-Xray372

Preferred Name: Tumor necrosis factor ligand superfamily member 12

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4HT1

Chain ID: T

ChEMBL ID: CHEMBL3713023

UniProt ID: O43508

Base Structure: X-ray

Registration Date: 2023-09-22

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	136
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1227915.606715
FMO2-HF: Nuclear repulsion	1175021.860686
FMO2-HF: Total energy	-52893.746029
FMO2-MP2: Total energy	-53050.282135

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(T:10:ARG)

Summations of interaction energy for fragment #1(T:10:ARG)

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.
3.705	6.877	8.56	-5.163	-6.57	-0.046

Interaction energy analysis for fragmet #1(T:10:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.980 / q_NPA : 0.981

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	T	12	ILE	0	-0.024	-0.009	3.321	-5.206	-2.710	0.009	-1.021	-1.484	0.004
4	T	13	ALA	0	0.032	0.006	5.027	5.411	5.528	-0.001	-0.008	-0.108	0.000
5	T	14	ALA	0	-0.010	0.015	7.683	-3.098	-3.098	0.000	0.000	0.000	0.000
6	T	15	HIS	0	0.015	0.012	10.489	0.780	0.780	0.000	0.000	0.000	0.000
7	T	16	TYR	0	-0.021	-0.034	12.140	-0.082	-0.082	0.000	0.000	0.000	0.000
8	T	17	GLU	-1	-0.845	-0.926	16.671	-15.036	-15.036	0.000	0.000	0.000	0.000
9	T	18	VAL	0	0.030	0.020	20.046	-0.223	-0.223	0.000	0.000	0.000	0.000
10	T	19	HIS	0	-0.051	-0.028	20.352	-0.318	-0.318	0.000	0.000	0.000	0.000
11	T	20	PRO	0	0.004	0.009	24.555	0.087	0.087	0.000	0.000	0.000	0.000
12	T	21	ARG	1	0.843	0.910	28.394	9.189	9.189	0.000	0.000	0.000	0.000
13	T	22	PRO	0	0.007	-0.001	31.537	0.039	0.039	0.000	0.000	0.000	0.000
14	T	23	GLY	0	0.003	-0.006	33.860	0.154	0.154	0.000	0.000	0.000	0.000
15	T	24	GLN	0	0.011	0.023	33.714	0.165	0.165	0.000	0.000	0.000	0.000
16	T	25	ASP	-1	-0.824	-0.900	32.780	-9.787	-9.787	0.000	0.000	0.000	0.000
17	T	26	GLY	0	0.009	-0.028	30.413	-0.229	-0.229	0.000	0.000	0.000	0.000
18	T	27	ALA	0	-0.006	0.001	28.937	-0.048	-0.048	0.000	0.000	0.000	0.000
19	T	28	GLN	0	-0.018	-0.014	30.901	0.279	0.279	0.000	0.000	0.000	0.000
20	T	29	ALA	0	-0.015	0.014	30.245	-0.265	-0.265	0.000	0.000	0.000	0.000
21	T	30	GLY	0	0.031	0.014	30.334	0.300	0.300	0.000	0.000	0.000	0.000
22	T	31	VAL	0	0.023	-0.001	31.760	0.159	0.159	0.000	0.000	0.000	0.000
23	T	32	ASP	-1	-0.807	-0.875	29.831	-10.473	-10.473	0.000	0.000	0.000	0.000
24	T	33	GLY	0	0.028	0.017	31.895	-0.041	-0.041	0.000	0.000	0.000	0.000
25	T	34	THR	0	-0.080	-0.070	25.551	-0.381	-0.381	0.000	0.000	0.000	0.000
26	T	35	VAL	0	-0.001	0.003	24.962	0.285	0.285	0.000	0.000	0.000	0.000
27	T	36	SER	0	-0.013	-0.010	23.673	-0.515	-0.515	0.000	0.000	0.000	0.000
28	T	37	GLY	0	0.040	0.011	23.410	0.197	0.197	0.000	0.000	0.000	0.000
29	T	38	TRP	0	-0.052	-0.034	18.826	-0.214	-0.214	0.000	0.000	0.000	0.000
30	T	39	GLU	-1	-0.859	-0.914	16.758	-17.484	-17.484	0.000	0.000	0.000	0.000
31	T	40	GLU	-1	-0.816	-0.867	9.702	-28.509	-28.509	0.000	0.000	0.000	0.000
32	T	41	ALA	0	0.032	0.021	14.136	0.083	0.083	0.000	0.000	0.000	0.000
33	T	42	ARG	1	0.876	0.925	12.364	18.454	18.454	0.000	0.000	0.000	0.000
34	T	43	ILE	0	0.036	0.022	8.480	0.408	0.408	0.000	0.000	0.000	0.000
35	T	44	ASN	0	-0.026	-0.007	6.638	0.135	0.135	0.000	0.000	0.000	0.000
36	T	45	SER	0	-0.031	-0.017	4.568	-1.633	-1.489	-0.001	-0.011	-0.132	0.000
37	T	46	SER	0	-0.067	-0.049	1.893	-33.123	-32.983	8.554	-3.936	-4.758	-0.049
38	T	47	SER	0	0.048	0.008	4.124	1.250	1.525	-0.001	-0.187	-0.088	-0.001
39	T	48	PRO	0	-0.051	-0.019	6.989	-3.076	-3.076	0.000	0.000	0.000	0.000
40	T	49	LEU	0	0.008	0.008	9.181	2.865	2.865	0.000	0.000	0.000	0.000
41	T	50	ARG	1	0.975	0.977	9.593	23.148	23.148	0.000	0.000	0.000	0.000
42	T	51	TYR	0	0.006	0.014	12.932	1.471	1.471	0.000	0.000	0.000	0.000
43	T	52	ASN	0	-0.045	-0.022	16.184	-0.038	-0.038	0.000	0.000	0.000	0.000
44	T	53	ARG	1	0.880	0.921	18.926	15.303	15.303	0.000	0.000	0.000	0.000
45	T	54	GLN	0	-0.008	0.003	20.981	0.345	0.345	0.000	0.000	0.000	0.000
46	T	55	ILE	0	-0.012	0.008	23.422	0.440	0.440	0.000	0.000	0.000	0.000
47	T	56	GLY	0	-0.020	-0.006	22.671	0.500	0.500	0.000	0.000	0.000	0.000
48	T	57	GLU	-1	-0.825	-0.904	19.879	-13.740	-13.740	0.000	0.000	0.000	0.000
49	T	58	PHE	0	0.008	-0.008	15.557	-0.628	-0.628	0.000	0.000	0.000	0.000
50	T	59	ILE	0	0.009	0.009	15.058	0.183	0.183	0.000	0.000	0.000	0.000
51	T	60	VAL	0	0.015	0.008	13.627	-1.790	-1.790	0.000	0.000	0.000	0.000
52	T	61	THR	0	-0.047	-0.036	9.012	0.168	0.168	0.000	0.000	0.000	0.000
53	T	62	ARG	1	0.893	0.954	5.496	43.987	43.987	0.000	0.000	0.000	0.000
54	T	63	ALA	0	0.051	0.044	10.423	1.209	1.209	0.000	0.000	0.000	0.000
55	T	64	GLY	0	0.005	0.004	10.618	-2.314	-2.314	0.000	0.000	0.000	0.000
56	T	65	LEU	0	0.004	0.016	12.375	1.340	1.340	0.000	0.000	0.000	0.000
57	T	66	TYR	0	-0.005	-0.031	9.128	-3.107	-3.107	0.000	0.000	0.000	0.000
58	T	67	TYR	0	0.040	0.029	13.636	1.598	1.598	0.000	0.000	0.000	0.000
59	T	68	LEU	0	-0.019	-0.017	14.627	-1.320	-1.320	0.000	0.000	0.000	0.000
60	T	69	TYR	0	-0.029	-0.035	14.548	0.655	0.655	0.000	0.000	0.000	0.000
61	T	70	CYS	0	-0.060	-0.021	19.173	-0.475	-0.475	0.000	0.000	0.000	0.000
62	T	71	GLN	0	0.002	0.025	21.894	0.483	0.483	0.000	0.000	0.000	0.000
63	T	72	VAL	0	0.028	0.009	24.652	-0.339	-0.339	0.000	0.000	0.000	0.000
64	T	73	HIS	0	-0.013	-0.009	27.378	0.611	0.611	0.000	0.000	0.000	0.000
65	T	74	PHE	0	-0.025	-0.021	29.692	-0.143	-0.143	0.000	0.000	0.000	0.000
66	T	75	ASP	-1	-0.855	-0.927	33.466	-8.450	-8.450	0.000	0.000	0.000	0.000
67	T	76	GLU	-1	-0.795	-0.891	36.569	-8.183	-8.183	0.000	0.000	0.000	0.000
68	T	77	GLY	0	-0.005	0.000	39.113	0.139	0.139	0.000	0.000	0.000	0.000
69	T	78	LYS	1	0.933	0.943	42.761	6.859	6.859	0.000	0.000	0.000	0.000
70	T	79	ALA	0	0.011	0.022	39.461	0.103	0.103	0.000	0.000	0.000	0.000
71	T	80	VAL	0	-0.033	-0.006	41.441	0.001	0.001	0.000	0.000	0.000	0.000
72	T	81	TYR	0	0.035	0.044	36.722	-0.118	-0.118	0.000	0.000	0.000	0.000
73	T	82	LEU	0	-0.023	-0.008	33.736	-0.073	-0.073	0.000	0.000	0.000	0.000
74	T	83	LYS	1	0.815	0.877	32.065	9.803	9.803	0.000	0.000	0.000	0.000
75	T	84	LEU	0	-0.011	-0.004	25.506	-0.072	-0.072	0.000	0.000	0.000	0.000
76	T	85	ASP	-1	-0.718	-0.834	28.313	-10.263	-10.263	0.000	0.000	0.000	0.000
77	T	86	LEU	0	0.018	0.003	20.449	-0.332	-0.332	0.000	0.000	0.000	0.000
78	T	87	LEU	0	0.001	-0.007	24.730	0.215	0.215	0.000	0.000	0.000	0.000
79	T	88	VAL	0	0.012	-0.005	20.735	-0.766	-0.766	0.000	0.000	0.000	0.000
80	T	89	ASP	-1	-0.755	-0.867	22.350	-13.967	-13.967	0.000	0.000	0.000	0.000
81	T	90	GLY	0	-0.003	0.011	24.373	0.142	0.142	0.000	0.000	0.000	0.000
82	T	91	VAL	0	-0.036	-0.014	26.726	0.509	0.509	0.000	0.000	0.000	0.000
83	T	92	LEU	0	-0.040	-0.026	26.719	-0.440	-0.440	0.000	0.000	0.000	0.000
84	T	93	ALA	0	-0.041	0.000	23.308	0.036	0.036	0.000	0.000	0.000	0.000
85	T	94	LEU	0	0.004	0.000	21.655	0.092	0.092	0.000	0.000	0.000	0.000
86	T	95	ARG	1	0.860	0.903	25.868	9.747	9.747	0.000	0.000	0.000	0.000
87	T	96	CYS	0	-0.022	0.025	28.865	0.441	0.441	0.000	0.000	0.000	0.000
88	T	97	LEU	0	-0.030	-0.040	30.521	-0.071	-0.071	0.000	0.000	0.000	0.000
89	T	98	GLU	-1	-0.840	-0.888	34.285	-8.535	-8.535	0.000	0.000	0.000	0.000
90	T	99	GLU	-1	-0.910	-0.983	37.063	-7.598	-7.598	0.000	0.000	0.000	0.000
91	T	108	LEU	0	-0.011	-0.004	46.798	0.070	0.070	0.000	0.000	0.000	0.000
92	T	109	GLY	0	-0.006	0.007	44.394	-0.133	-0.133	0.000	0.000	0.000	0.000
93	T	110	PRO	0	-0.008	-0.025	41.526	0.182	0.182	0.000	0.000	0.000	0.000
94	T	111	GLN	0	-0.042	-0.017	39.683	0.106	0.106	0.000	0.000	0.000	0.000
95	T	112	LEU	0	-0.013	0.014	33.369	-0.166	-0.166	0.000	0.000	0.000	0.000
96	T	113	ARG	1	0.859	0.918	35.405	8.802	8.802	0.000	0.000	0.000	0.000
97	T	114	LEU	0	0.005	-0.007	28.292	-0.234	-0.234	0.000	0.000	0.000	0.000
98	T	116	GLN	0	0.001	-0.021	25.942	-0.115	-0.115	0.000	0.000	0.000	0.000
99	T	117	VAL	0	-0.002	-0.001	23.840	0.325	0.325	0.000	0.000	0.000	0.000
100	T	118	SER	0	-0.002	-0.004	20.781	-0.406	-0.406	0.000	0.000	0.000	0.000
101	T	119	GLY	0	0.030	0.019	20.237	0.693	0.693	0.000	0.000	0.000	0.000
102	T	120	LEU	0	-0.024	-0.006	16.961	-0.890	-0.890	0.000	0.000	0.000	0.000
103	T	121	LEU	0	0.022	0.009	17.559	0.762	0.762	0.000	0.000	0.000	0.000
104	T	122	ALA	0	-0.003	0.005	16.525	-1.120	-1.120	0.000	0.000	0.000	0.000
105	T	123	LEU	0	-0.028	-0.007	14.089	0.725	0.725	0.000	0.000	0.000	0.000
106	T	124	ARG	1	0.920	0.946	15.330	13.830	13.830	0.000	0.000	0.000	0.000
107	T	125	PRO	0	0.019	-0.014	13.273	0.077	0.077	0.000	0.000	0.000	0.000
108	T	126	GLY	0	-0.022	0.002	15.373	0.978	0.978	0.000	0.000	0.000	0.000
109	T	127	SER	0	-0.037	-0.025	17.849	0.873	0.873	0.000	0.000	0.000	0.000
110	T	128	SER	0	-0.075	-0.032	17.895	-0.791	-0.791	0.000	0.000	0.000	0.000
111	T	129	LEU	0	0.031	0.015	16.935	0.431	0.431	0.000	0.000	0.000	0.000
112	T	130	ARG	1	0.876	0.929	20.306	12.497	12.497	0.000	0.000	0.000	0.000
113	T	131	ILE	0	0.033	0.032	20.277	0.343	0.343	0.000	0.000	0.000	0.000
114	T	132	ARG	1	0.833	0.920	24.356	10.531	10.531	0.000	0.000	0.000	0.000
115	T	133	THR	0	0.041	0.031	28.153	0.022	0.022	0.000	0.000	0.000	0.000
116	T	134	LEU	0	-0.004	-0.011	31.343	0.061	0.061	0.000	0.000	0.000	0.000
117	T	135	PRO	0	0.002	-0.016	34.045	-0.207	-0.207	0.000	0.000	0.000	0.000
118	T	136	TRP	0	-0.027	-0.005	34.743	0.147	0.147	0.000	0.000	0.000	0.000
119	T	137	ALA	0	0.048	0.045	33.679	0.137	0.137	0.000	0.000	0.000	0.000
120	T	138	HIS	0	0.003	-0.007	33.455	-0.521	-0.521	0.000	0.000	0.000	0.000
121	T	139	LEU	0	-0.017	-0.013	27.821	0.006	0.006	0.000	0.000	0.000	0.000
122	T	140	LYS	1	0.806	0.886	30.462	9.135	9.135	0.000	0.000	0.000	0.000
123	T	141	ALA	0	-0.008	-0.002	26.944	-0.334	-0.334	0.000	0.000	0.000	0.000
124	T	142	ALA	0	0.049	0.044	26.056	-0.370	-0.370	0.000	0.000	0.000	0.000
125	T	143	PRO	0	0.035	0.027	21.815	0.059	0.059	0.000	0.000	0.000	0.000
126	T	144	PHE	0	0.019	-0.007	22.822	-0.290	-0.290	0.000	0.000	0.000	0.000
127	T	145	LEU	0	-0.038	-0.013	24.285	0.269	0.269	0.000	0.000	0.000	0.000
128	T	146	THR	0	-0.021	-0.011	24.557	0.212	0.212	0.000	0.000	0.000	0.000
129	T	147	TYR	0	-0.027	-0.017	19.592	-0.598	-0.598	0.000	0.000	0.000	0.000
130	T	148	PHE	0	0.001	-0.008	16.429	0.463	0.463	0.000	0.000	0.000	0.000
131	T	149	GLY	0	0.039	0.018	14.957	-0.769	-0.769	0.000	0.000	0.000	0.000
132	T	150	LEU	0	-0.032	-0.010	11.236	0.877	0.877	0.000	0.000	0.000	0.000
133	T	151	PHE	0	0.012	0.000	9.654	-1.967	-1.967	0.000	0.000	0.000	0.000
134	T	152	GLN	0	-0.026	-0.018	7.852	1.036	1.036	0.000	0.000	0.000	0.000
135	T	153	VAL	0	-0.049	-0.024	9.717	-0.136	-0.136	0.000	0.000	0.000	0.000
136	T	154	HIS	0	0.016	0.012	5.715	1.838	1.838	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(T:10:ARG)