FMO DATABASE

FMODB ID: 98LZ2

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	OptHSide
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	-1227924.908413
FMO2-HF: Nuclear repulsion	1175031.628172
FMO2-HF: Total energy	-52893.280242
FMO2-MP2: Total energy	-53049.713194

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.
13.446	15.886	10.21	-5.583	-7.067	-0.042

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 : 0.969 / q_NPA : 0.974

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	-0.039	-0.026	3.478	-7.581	-4.459	-0.002	-1.357	-1.764	0.005
4	T	13	ALA	0	0.043	0.006	5.361	4.710	4.807	-0.001	-0.005	-0.090	0.000
5	T	14	ALA	0	0.000	0.020	7.936	-2.399	-2.399	0.000	0.000	0.000	0.000
6	T	15	HIS	0	0.046	0.039	10.627	0.657	0.657	0.000	0.000	0.000	0.000
7	T	16	TYR	0	-0.051	-0.039	11.920	-0.187	-0.187	0.000	0.000	0.000	0.000
8	T	17	GLU	-1	-0.851	-0.948	16.623	-14.912	-14.912	0.000	0.000	0.000	0.000
9	T	18	VAL	0	0.017	0.026	19.953	-0.307	-0.307	0.000	0.000	0.000	0.000
10	T	19	HIS	0	-0.075	-0.039	20.731	-0.146	-0.146	0.000	0.000	0.000	0.000
11	T	20	PRO	0	0.017	0.011	24.484	0.056	0.056	0.000	0.000	0.000	0.000
12	T	21	ARG	1	0.845	0.915	28.242	9.157	9.157	0.000	0.000	0.000	0.000
13	T	22	PRO	0	0.016	0.004	31.555	-0.011	-0.011	0.000	0.000	0.000	0.000
14	T	23	GLY	0	-0.003	-0.010	33.873	0.124	0.124	0.000	0.000	0.000	0.000
15	T	24	GLN	0	0.015	0.029	33.901	0.170	0.170	0.000	0.000	0.000	0.000
16	T	25	ASP	-1	-0.831	-0.908	33.229	-9.613	-9.613	0.000	0.000	0.000	0.000
17	T	26	GLY	0	-0.054	-0.040	31.053	-0.250	-0.250	0.000	0.000	0.000	0.000
18	T	27	ALA	0	-0.029	-0.021	28.933	-0.042	-0.042	0.000	0.000	0.000	0.000
19	T	28	GLN	0	0.000	-0.004	30.933	0.216	0.216	0.000	0.000	0.000	0.000
20	T	29	ALA	0	-0.014	0.014	29.998	-0.259	-0.259	0.000	0.000	0.000	0.000
21	T	30	GLY	0	0.025	0.008	30.353	0.315	0.315	0.000	0.000	0.000	0.000
22	T	31	VAL	0	0.011	-0.006	31.923	0.143	0.143	0.000	0.000	0.000	0.000
23	T	32	ASP	-1	-0.833	-0.901	29.870	-10.450	-10.450	0.000	0.000	0.000	0.000
24	T	33	GLY	0	-0.008	-0.011	31.710	-0.146	-0.146	0.000	0.000	0.000	0.000
25	T	34	THR	0	-0.050	-0.032	25.667	-0.408	-0.408	0.000	0.000	0.000	0.000
26	T	35	VAL	0	0.009	0.006	24.897	0.319	0.319	0.000	0.000	0.000	0.000
27	T	36	SER	0	-0.018	-0.017	23.513	-0.488	-0.488	0.000	0.000	0.000	0.000
28	T	37	GLY	0	0.036	0.010	23.277	0.154	0.154	0.000	0.000	0.000	0.000
29	T	38	TRP	0	-0.026	-0.019	18.515	-0.162	-0.162	0.000	0.000	0.000	0.000
30	T	39	GLU	-1	-0.884	-0.944	17.091	-17.141	-17.141	0.000	0.000	0.000	0.000
31	T	40	GLU	-1	-0.839	-0.899	9.648	-28.377	-28.377	0.000	0.000	0.000	0.000
32	T	41	ALA	0	0.037	0.009	14.250	0.366	0.366	0.000	0.000	0.000	0.000
33	T	42	ARG	1	0.874	0.936	12.723	18.008	18.008	0.000	0.000	0.000	0.000
34	T	43	ILE	0	0.053	0.024	8.537	0.725	0.725	0.000	0.000	0.000	0.000
35	T	44	ASN	0	-0.030	-0.008	6.830	-0.227	-0.227	0.000	0.000	0.000	0.000
36	T	45	SER	0	-0.029	-0.017	4.433	-1.022	-0.884	-0.001	-0.018	-0.119	0.000
37	T	46	SER	0	-0.069	-0.034	1.855	-25.733	-27.440	10.214	-3.883	-4.624	-0.046
38	T	47	SER	0	0.069	0.041	4.124	0.615	1.051	0.000	-0.297	-0.140	-0.001
39	T	48	PRO	0	-0.064	-0.029	6.686	-3.918	-3.918	0.000	0.000	0.000	0.000
40	T	49	LEU	0	0.010	0.001	8.753	2.853	2.853	0.000	0.000	0.000	0.000
41	T	50	ARG	1	0.982	0.997	9.692	24.006	24.006	0.000	0.000	0.000	0.000
42	T	51	TYR	0	0.011	0.007	12.763	1.495	1.495	0.000	0.000	0.000	0.000
43	T	52	ASN	0	-0.068	-0.037	15.929	0.086	0.086	0.000	0.000	0.000	0.000
44	T	53	ARG	1	0.939	0.963	18.786	15.054	15.054	0.000	0.000	0.000	0.000
45	T	54	GLN	0	0.014	0.000	21.000	0.399	0.399	0.000	0.000	0.000	0.000
46	T	55	ILE	0	-0.060	0.000	22.574	0.454	0.454	0.000	0.000	0.000	0.000
47	T	56	GLY	0	0.000	0.006	22.545	0.522	0.522	0.000	0.000	0.000	0.000
48	T	57	GLU	-1	-0.892	-0.948	19.509	-14.435	-14.435	0.000	0.000	0.000	0.000
49	T	58	PHE	0	0.018	0.006	15.310	-0.553	-0.553	0.000	0.000	0.000	0.000
50	T	59	ILE	0	0.013	0.010	14.653	0.423	0.423	0.000	0.000	0.000	0.000
51	T	60	VAL	0	0.005	0.006	13.372	-1.916	-1.916	0.000	0.000	0.000	0.000
52	T	61	THR	0	-0.028	-0.025	8.772	-0.001	-0.001	0.000	0.000	0.000	0.000
53	T	62	ARG	1	0.897	0.954	4.653	47.953	48.307	0.000	-0.023	-0.330	0.000
54	T	63	ALA	0	0.040	0.046	9.756	1.185	1.185	0.000	0.000	0.000	0.000
55	T	64	GLY	0	0.017	0.008	10.751	-1.948	-1.948	0.000	0.000	0.000	0.000
56	T	65	LEU	0	0.000	0.016	12.154	1.425	1.425	0.000	0.000	0.000	0.000
57	T	66	TYR	0	-0.013	-0.031	8.956	-2.955	-2.955	0.000	0.000	0.000	0.000
58	T	67	TYR	0	0.042	0.028	13.630	1.507	1.507	0.000	0.000	0.000	0.000
59	T	68	LEU	0	-0.015	-0.009	14.999	-1.116	-1.116	0.000	0.000	0.000	0.000
60	T	69	TYR	0	-0.033	-0.029	14.765	0.655	0.655	0.000	0.000	0.000	0.000
61	T	70	CYS	0	-0.058	-0.021	19.252	-0.393	-0.393	0.000	0.000	0.000	0.000
62	T	71	GLN	0	0.038	0.041	21.877	0.532	0.532	0.000	0.000	0.000	0.000
63	T	72	VAL	0	0.009	-0.002	24.537	-0.314	-0.314	0.000	0.000	0.000	0.000
64	T	73	HIS	0	-0.030	-0.017	27.238	0.619	0.619	0.000	0.000	0.000	0.000
65	T	74	PHE	0	-0.008	-0.017	29.462	-0.116	-0.116	0.000	0.000	0.000	0.000
66	T	75	ASP	-1	-0.851	-0.930	33.281	-8.335	-8.335	0.000	0.000	0.000	0.000
67	T	76	GLU	-1	-0.819	-0.914	36.507	-8.266	-8.266	0.000	0.000	0.000	0.000
68	T	77	GLY	0	-0.020	0.001	38.796	0.129	0.129	0.000	0.000	0.000	0.000
69	T	78	LYS	1	0.953	0.955	42.584	6.868	6.868	0.000	0.000	0.000	0.000
70	T	79	ALA	0	0.015	0.035	39.401	0.091	0.091	0.000	0.000	0.000	0.000
71	T	80	VAL	0	-0.040	-0.023	41.381	0.022	0.022	0.000	0.000	0.000	0.000
72	T	81	TYR	0	0.022	0.036	36.568	-0.114	-0.114	0.000	0.000	0.000	0.000
73	T	82	LEU	0	-0.029	-0.017	33.374	-0.081	-0.081	0.000	0.000	0.000	0.000
74	T	83	LYS	1	0.846	0.906	31.764	9.779	9.779	0.000	0.000	0.000	0.000
75	T	84	LEU	0	0.014	0.012	25.495	-0.117	-0.117	0.000	0.000	0.000	0.000
76	T	85	ASP	-1	-0.752	-0.849	27.638	-10.288	-10.288	0.000	0.000	0.000	0.000
77	T	86	LEU	0	0.033	0.007	20.031	-0.356	-0.356	0.000	0.000	0.000	0.000
78	T	87	LEU	0	-0.034	-0.024	24.248	0.278	0.278	0.000	0.000	0.000	0.000
79	T	88	VAL	0	0.007	-0.012	20.672	-0.678	-0.678	0.000	0.000	0.000	0.000
80	T	89	ASP	-1	-0.765	-0.865	22.366	-14.084	-14.084	0.000	0.000	0.000	0.000
81	T	90	GLY	0	-0.041	-0.020	23.878	0.105	0.105	0.000	0.000	0.000	0.000
82	T	91	VAL	0	-0.027	-0.022	26.531	0.498	0.498	0.000	0.000	0.000	0.000
83	T	92	LEU	0	-0.058	-0.025	26.304	-0.462	-0.462	0.000	0.000	0.000	0.000
84	T	93	ALA	0	-0.020	0.018	23.463	0.082	0.082	0.000	0.000	0.000	0.000
85	T	94	LEU	0	0.002	-0.003	21.917	0.192	0.192	0.000	0.000	0.000	0.000
86	T	95	ARG	1	0.878	0.909	26.180	9.802	9.802	0.000	0.000	0.000	0.000
87	T	96	CYS	0	-0.042	0.013	29.040	0.379	0.379	0.000	0.000	0.000	0.000
88	T	97	LEU	0	-0.024	-0.037	30.677	-0.037	-0.037	0.000	0.000	0.000	0.000
89	T	98	GLU	-1	-0.842	-0.904	34.317	-8.494	-8.494	0.000	0.000	0.000	0.000
90	T	99	GLU	-1	-0.886	-0.959	36.927	-7.593	-7.593	0.000	0.000	0.000	0.000
91	T	108	LEU	0	-0.008	-0.002	46.771	0.069	0.069	0.000	0.000	0.000	0.000
92	T	109	GLY	0	-0.010	0.013	44.269	-0.135	-0.135	0.000	0.000	0.000	0.000
93	T	110	PRO	0	-0.014	-0.029	41.540	0.177	0.177	0.000	0.000	0.000	0.000
94	T	111	GLN	0	-0.009	-0.006	39.704	0.149	0.149	0.000	0.000	0.000	0.000
95	T	112	LEU	0	0.000	0.023	33.433	-0.177	-0.177	0.000	0.000	0.000	0.000
96	T	113	ARG	1	0.851	0.909	35.416	8.776	8.776	0.000	0.000	0.000	0.000
97	T	114	LEU	0	0.006	-0.001	28.353	-0.204	-0.204	0.000	0.000	0.000	0.000
98	T	116	GLN	0	-0.005	-0.030	25.828	-0.172	-0.172	0.000	0.000	0.000	0.000
99	T	117	VAL	0	-0.016	0.001	23.781	0.316	0.316	0.000	0.000	0.000	0.000
100	T	118	SER	0	-0.006	-0.004	21.139	-0.447	-0.447	0.000	0.000	0.000	0.000
101	T	119	GLY	0	0.045	0.028	20.454	0.598	0.598	0.000	0.000	0.000	0.000
102	T	120	LEU	0	-0.038	-0.016	16.981	-0.767	-0.767	0.000	0.000	0.000	0.000
103	T	121	LEU	0	0.034	0.013	17.610	0.731	0.731	0.000	0.000	0.000	0.000
104	T	122	ALA	0	0.005	0.008	16.516	-1.162	-1.162	0.000	0.000	0.000	0.000
105	T	123	LEU	0	-0.027	-0.011	14.379	0.734	0.734	0.000	0.000	0.000	0.000
106	T	124	ARG	1	0.971	0.976	15.426	14.079	14.079	0.000	0.000	0.000	0.000
107	T	125	PRO	0	0.017	-0.007	13.175	0.181	0.181	0.000	0.000	0.000	0.000
108	T	126	GLY	0	-0.018	-0.001	15.278	0.849	0.849	0.000	0.000	0.000	0.000
109	T	127	SER	0	-0.056	-0.038	17.631	0.851	0.851	0.000	0.000	0.000	0.000
110	T	128	SER	0	-0.039	-0.021	17.839	-0.844	-0.844	0.000	0.000	0.000	0.000
111	T	129	LEU	0	0.024	0.016	16.688	0.385	0.385	0.000	0.000	0.000	0.000
112	T	130	ARG	1	0.957	0.968	20.260	12.692	12.692	0.000	0.000	0.000	0.000
113	T	131	ILE	0	0.043	0.038	20.353	0.240	0.240	0.000	0.000	0.000	0.000
114	T	132	ARG	1	0.839	0.932	24.266	10.676	10.676	0.000	0.000	0.000	0.000
115	T	133	THR	0	0.036	0.017	28.050	-0.025	-0.025	0.000	0.000	0.000	0.000
116	T	134	LEU	0	-0.024	-0.016	31.150	0.019	0.019	0.000	0.000	0.000	0.000
117	T	135	PRO	0	0.020	-0.012	34.164	-0.150	-0.150	0.000	0.000	0.000	0.000
118	T	136	TRP	0	-0.037	-0.013	34.483	0.137	0.137	0.000	0.000	0.000	0.000
119	T	137	ALA	0	0.046	0.044	33.109	0.107	0.107	0.000	0.000	0.000	0.000
120	T	138	HIS	0	0.014	0.008	33.379	-0.462	-0.462	0.000	0.000	0.000	0.000
121	T	139	LEU	0	-0.005	-0.002	27.650	0.040	0.040	0.000	0.000	0.000	0.000
122	T	140	LYS	1	0.817	0.887	29.909	9.217	9.217	0.000	0.000	0.000	0.000
123	T	141	ALA	0	-0.001	-0.014	26.718	-0.319	-0.319	0.000	0.000	0.000	0.000
124	T	142	ALA	0	0.036	0.045	25.682	-0.412	-0.412	0.000	0.000	0.000	0.000
125	T	143	PRO	0	0.051	0.031	21.818	0.081	0.081	0.000	0.000	0.000	0.000
126	T	144	PHE	0	0.015	-0.004	22.473	-0.368	-0.368	0.000	0.000	0.000	0.000
127	T	145	LEU	0	-0.042	-0.022	24.503	0.202	0.202	0.000	0.000	0.000	0.000
128	T	146	THR	0	-0.018	-0.006	24.142	0.242	0.242	0.000	0.000	0.000	0.000
129	T	147	TYR	0	-0.046	-0.026	19.497	-0.581	-0.581	0.000	0.000	0.000	0.000
130	T	148	PHE	0	-0.013	-0.019	16.781	0.419	0.419	0.000	0.000	0.000	0.000
131	T	149	GLY	0	0.058	0.037	14.803	-0.833	-0.833	0.000	0.000	0.000	0.000
132	T	150	LEU	0	-0.039	-0.015	11.007	0.778	0.778	0.000	0.000	0.000	0.000
133	T	151	PHE	0	0.027	0.004	9.979	-1.675	-1.675	0.000	0.000	0.000	0.000
134	T	152	GLN	0	-0.037	-0.033	7.735	0.903	0.903	0.000	0.000	0.000	0.000
135	T	153	VAL	0	-0.043	-0.026	9.650	-0.220	-0.220	0.000	0.000	0.000	0.000
136	T	154	HIS	0	0.005	0.011	6.164	2.054	2.054	0.000	0.000	0.000	0.000

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