FMO DATABASE

FMODB ID: LNQY9

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	OptH
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	-1228461.124558
FMO2-HF: Nuclear repulsion	1175568.738486
FMO2-HF: Total energy	-52892.386072
FMO2-MP2: Total energy	-53048.820141

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.
24.676	30.957	6.307	-4.358	-8.226	-0.028

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 : 0.986 / q_NPA : 0.998

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	T	12	ILE	0	-0.042	-0.028	3.539	-7.810	-4.640	0.004	-1.397	-1.776	0.005
4	T	13	ALA	0	0.036	0.000	5.069	4.781	4.900	-0.001	-0.007	-0.110	0.000
5	T	14	ALA	0	0.016	0.025	8.179	-2.362	-2.362	0.000	0.000	0.000	0.000
6	T	15	HIS	0	0.067	0.080	10.897	0.625	0.625	0.000	0.000	0.000	0.000
7	T	16	TYR	0	-0.003	0.012	12.695	-0.885	-0.885	0.000	0.000	0.000	0.000
8	T	17	GLU	-1	-0.861	-0.948	16.932	-15.396	-15.396	0.000	0.000	0.000	0.000
9	T	18	VAL	0	0.006	0.020	20.286	-0.309	-0.309	0.000	0.000	0.000	0.000
10	T	19	HIS	0	-0.062	-0.031	21.253	-0.034	-0.034	0.000	0.000	0.000	0.000
11	T	20	PRO	0	0.004	0.001	24.934	0.065	0.065	0.000	0.000	0.000	0.000
12	T	21	ARG	1	0.858	0.921	28.705	9.307	9.307	0.000	0.000	0.000	0.000
13	T	22	PRO	0	0.021	0.008	31.931	0.000	0.000	0.000	0.000	0.000	0.000
14	T	23	GLY	0	-0.004	-0.011	34.251	0.115	0.115	0.000	0.000	0.000	0.000
15	T	24	GLN	0	0.015	0.027	34.566	0.160	0.160	0.000	0.000	0.000	0.000
16	T	25	ASP	-1	-0.829	-0.902	33.630	-9.680	-9.680	0.000	0.000	0.000	0.000
17	T	26	GLY	0	-0.059	-0.039	31.437	-0.261	-0.261	0.000	0.000	0.000	0.000
18	T	27	ALA	0	-0.024	-0.020	29.551	-0.043	-0.043	0.000	0.000	0.000	0.000
19	T	28	GLN	0	0.017	0.018	31.536	0.165	0.165	0.000	0.000	0.000	0.000
20	T	29	ALA	0	-0.024	0.007	30.535	-0.267	-0.267	0.000	0.000	0.000	0.000
21	T	30	GLY	0	0.023	0.005	30.651	0.322	0.322	0.000	0.000	0.000	0.000
22	T	31	VAL	0	0.022	-0.003	32.124	0.148	0.148	0.000	0.000	0.000	0.000
23	T	32	ASP	-1	-0.822	-0.832	30.129	-10.500	-10.500	0.000	0.000	0.000	0.000
24	T	33	GLY	0	-0.028	-0.021	31.713	-0.148	-0.148	0.000	0.000	0.000	0.000
25	T	34	THR	0	-0.094	-0.111	25.961	-0.314	-0.314	0.000	0.000	0.000	0.000
26	T	35	VAL	0	0.016	0.010	25.683	0.324	0.324	0.000	0.000	0.000	0.000
27	T	36	SER	0	-0.013	-0.013	23.947	-0.479	-0.479	0.000	0.000	0.000	0.000
28	T	37	GLY	0	0.024	-0.010	23.641	0.160	0.160	0.000	0.000	0.000	0.000
29	T	38	TRP	0	-0.025	-0.012	19.072	-0.179	-0.179	0.000	0.000	0.000	0.000
30	T	39	GLU	-1	-0.930	-0.973	17.200	-17.132	-17.132	0.000	0.000	0.000	0.000
31	T	40	GLU	-1	-0.935	-0.982	10.513	-29.343	-29.343	0.000	0.000	0.000	0.000
32	T	41	ALA	0	0.011	0.005	14.721	0.339	0.339	0.000	0.000	0.000	0.000
33	T	42	ARG	1	0.917	0.959	12.862	17.857	17.857	0.000	0.000	0.000	0.000
34	T	43	ILE	0	0.044	0.017	8.529	0.714	0.714	0.000	0.000	0.000	0.000
35	T	44	ASN	0	-0.025	-0.007	7.617	-0.249	-0.249	0.000	0.000	0.000	0.000
36	T	45	SER	0	-0.038	-0.024	4.410	-1.189	-1.004	-0.001	-0.021	-0.162	0.000
37	T	46	SER	0	-0.085	-0.049	2.401	-15.953	-15.306	5.209	-1.883	-3.972	-0.023
38	T	47	SER	0	0.100	0.062	4.477	0.248	0.376	-0.001	-0.040	-0.087	0.000
39	T	48	PRO	0	-0.068	-0.029	6.888	-4.250	-4.250	0.000	0.000	0.000	0.000
40	T	49	LEU	0	0.019	0.001	8.349	3.014	3.014	0.000	0.000	0.000	0.000
41	T	50	ARG	1	0.969	0.996	8.645	25.552	25.552	0.000	0.000	0.000	0.000
42	T	51	TYR	0	0.023	0.005	12.480	1.508	1.508	0.000	0.000	0.000	0.000
43	T	52	ASN	0	-0.026	-0.013	15.877	0.332	0.332	0.000	0.000	0.000	0.000
44	T	53	ARG	1	0.983	0.996	18.654	15.002	15.002	0.000	0.000	0.000	0.000
45	T	54	GLN	0	-0.002	0.001	20.528	0.565	0.565	0.000	0.000	0.000	0.000
46	T	55	ILE	0	-0.065	0.002	21.338	0.420	0.420	0.000	0.000	0.000	0.000
47	T	56	GLY	0	0.000	0.002	22.366	0.532	0.532	0.000	0.000	0.000	0.000
48	T	57	GLU	-1	-0.903	-0.964	19.430	-15.057	-15.057	0.000	0.000	0.000	0.000
49	T	58	PHE	0	0.002	0.000	15.442	-0.576	-0.576	0.000	0.000	0.000	0.000
50	T	59	ILE	0	0.010	0.012	13.903	0.315	0.315	0.000	0.000	0.000	0.000
51	T	60	VAL	0	0.019	0.009	11.840	-2.044	-2.044	0.000	0.000	0.000	0.000
52	T	61	THR	0	-0.038	-0.030	8.249	0.044	0.044	0.000	0.000	0.000	0.000
53	T	62	ARG	1	0.904	0.958	2.721	51.443	53.475	1.097	-1.010	-2.119	-0.010
54	T	63	ALA	0	0.044	0.044	7.923	1.351	1.351	0.000	0.000	0.000	0.000
55	T	64	GLY	0	0.016	0.012	9.907	-2.121	-2.121	0.000	0.000	0.000	0.000
56	T	65	LEU	0	-0.002	0.012	12.072	1.496	1.496	0.000	0.000	0.000	0.000
57	T	66	TYR	0	-0.012	-0.036	8.773	-3.255	-3.255	0.000	0.000	0.000	0.000
58	T	67	TYR	0	0.042	0.032	13.457	1.496	1.496	0.000	0.000	0.000	0.000
59	T	68	LEU	0	-0.013	-0.011	14.749	-1.156	-1.156	0.000	0.000	0.000	0.000
60	T	69	TYR	0	-0.046	-0.059	14.910	0.791	0.791	0.000	0.000	0.000	0.000
61	T	70	CYS	0	-0.033	-0.009	19.361	-0.498	-0.498	0.000	0.000	0.000	0.000
62	T	71	GLN	0	0.031	0.037	22.042	0.499	0.499	0.000	0.000	0.000	0.000
63	T	72	VAL	0	0.009	0.003	24.611	-0.316	-0.316	0.000	0.000	0.000	0.000
64	T	73	HIS	0	-0.038	-0.017	27.386	0.644	0.644	0.000	0.000	0.000	0.000
65	T	74	PHE	0	-0.009	-0.016	30.092	-0.106	-0.106	0.000	0.000	0.000	0.000
66	T	75	ASP	-1	-0.937	-0.993	33.500	-8.312	-8.312	0.000	0.000	0.000	0.000
67	T	76	GLU	-1	-0.869	-0.933	36.698	-8.442	-8.442	0.000	0.000	0.000	0.000
68	T	77	GLY	0	-0.021	-0.007	39.084	0.132	0.132	0.000	0.000	0.000	0.000
69	T	78	LYS	1	0.960	0.960	42.871	6.964	6.964	0.000	0.000	0.000	0.000
70	T	79	ALA	0	0.017	0.034	39.784	0.095	0.095	0.000	0.000	0.000	0.000
71	T	80	VAL	0	-0.062	-0.038	41.771	0.022	0.022	0.000	0.000	0.000	0.000
72	T	81	TYR	0	0.035	0.018	36.762	-0.114	-0.114	0.000	0.000	0.000	0.000
73	T	82	LEU	0	-0.028	-0.016	33.508	-0.083	-0.083	0.000	0.000	0.000	0.000
74	T	83	LYS	1	0.919	0.943	32.019	9.676	9.676	0.000	0.000	0.000	0.000
75	T	84	LEU	0	0.005	0.003	25.725	-0.122	-0.122	0.000	0.000	0.000	0.000
76	T	85	ASP	-1	-0.738	-0.830	27.838	-10.531	-10.531	0.000	0.000	0.000	0.000
77	T	86	LEU	0	0.035	0.003	20.519	-0.376	-0.376	0.000	0.000	0.000	0.000
78	T	87	LEU	0	-0.052	-0.029	24.143	0.302	0.302	0.000	0.000	0.000	0.000
79	T	88	VAL	0	0.004	-0.011	19.925	-0.690	-0.690	0.000	0.000	0.000	0.000
80	T	89	ASP	-1	-0.790	-0.906	21.038	-14.311	-14.311	0.000	0.000	0.000	0.000
81	T	90	GLY	0	-0.048	-0.022	22.680	0.120	0.120	0.000	0.000	0.000	0.000
82	T	91	VAL	0	-0.034	-0.024	25.328	0.528	0.528	0.000	0.000	0.000	0.000
83	T	92	LEU	0	-0.055	-0.026	25.662	-0.477	-0.477	0.000	0.000	0.000	0.000
84	T	93	ALA	0	-0.020	0.018	23.261	0.087	0.087	0.000	0.000	0.000	0.000
85	T	94	LEU	0	-0.007	-0.010	21.686	0.208	0.208	0.000	0.000	0.000	0.000
86	T	95	ARG	1	0.823	0.861	25.954	9.967	9.967	0.000	0.000	0.000	0.000
87	T	96	CYS	0	-0.048	0.013	29.002	0.421	0.421	0.000	0.000	0.000	0.000
88	T	97	LEU	0	-0.045	-0.052	30.606	-0.042	-0.042	0.000	0.000	0.000	0.000
89	T	98	GLU	-1	-0.879	-0.936	34.294	-8.601	-8.601	0.000	0.000	0.000	0.000
90	T	99	GLU	-1	-0.904	-0.933	36.930	-7.628	-7.628	0.000	0.000	0.000	0.000
91	T	108	LEU	0	-0.007	-0.001	46.721	0.071	0.071	0.000	0.000	0.000	0.000
92	T	109	GLY	0	-0.015	0.010	44.303	-0.137	-0.137	0.000	0.000	0.000	0.000
93	T	110	PRO	0	-0.008	-0.021	41.716	0.183	0.183	0.000	0.000	0.000	0.000
94	T	111	GLN	0	0.008	0.004	39.822	0.159	0.159	0.000	0.000	0.000	0.000
95	T	112	LEU	0	-0.026	0.008	33.242	-0.182	-0.182	0.000	0.000	0.000	0.000
96	T	113	ARG	1	0.917	0.960	35.375	8.915	8.915	0.000	0.000	0.000	0.000
97	T	114	LEU	0	0.016	0.000	28.310	-0.197	-0.197	0.000	0.000	0.000	0.000
98	T	116	GLN	0	0.003	-0.031	25.669	-0.154	-0.154	0.000	0.000	0.000	0.000
99	T	117	VAL	0	-0.016	0.008	23.538	0.320	0.320	0.000	0.000	0.000	0.000
100	T	118	SER	0	-0.011	-0.008	20.927	-0.620	-0.620	0.000	0.000	0.000	0.000
101	T	119	GLY	0	0.043	0.023	20.220	0.619	0.619	0.000	0.000	0.000	0.000
102	T	120	LEU	0	-0.034	-0.019	16.637	-0.781	-0.781	0.000	0.000	0.000	0.000
103	T	121	LEU	0	0.034	0.018	17.443	0.771	0.771	0.000	0.000	0.000	0.000
104	T	122	ALA	0	0.011	0.007	16.366	-1.195	-1.195	0.000	0.000	0.000	0.000
105	T	123	LEU	0	-0.030	-0.012	13.966	0.775	0.775	0.000	0.000	0.000	0.000
106	T	124	ARG	1	0.977	0.971	14.312	14.293	14.293	0.000	0.000	0.000	0.000
107	T	125	PRO	0	0.029	0.006	11.779	0.015	0.015	0.000	0.000	0.000	0.000
108	T	126	GLY	0	-0.024	-0.008	13.677	0.920	0.920	0.000	0.000	0.000	0.000
109	T	127	SER	0	-0.028	0.007	16.121	0.774	0.774	0.000	0.000	0.000	0.000
110	T	128	SER	0	-0.013	-0.003	16.698	-0.905	-0.905	0.000	0.000	0.000	0.000
111	T	129	LEU	0	0.002	0.004	16.273	0.411	0.411	0.000	0.000	0.000	0.000
112	T	130	ARG	1	0.972	0.970	19.756	12.795	12.795	0.000	0.000	0.000	0.000
113	T	131	ILE	0	0.033	0.035	20.769	0.240	0.240	0.000	0.000	0.000	0.000
114	T	132	ARG	1	0.866	0.951	24.582	10.814	10.814	0.000	0.000	0.000	0.000
115	T	133	THR	0	0.016	0.009	28.327	-0.044	-0.044	0.000	0.000	0.000	0.000
116	T	134	LEU	0	-0.036	-0.022	31.606	0.012	0.012	0.000	0.000	0.000	0.000
117	T	135	PRO	0	0.023	-0.011	34.655	-0.156	-0.156	0.000	0.000	0.000	0.000
118	T	136	TRP	0	-0.021	-0.007	34.848	0.131	0.131	0.000	0.000	0.000	0.000
119	T	137	ALA	0	0.036	0.037	33.608	0.092	0.092	0.000	0.000	0.000	0.000
120	T	138	HIS	0	0.033	0.027	33.958	-0.493	-0.493	0.000	0.000	0.000	0.000
121	T	139	LEU	0	0.005	0.005	28.301	0.044	0.044	0.000	0.000	0.000	0.000
122	T	140	LYS	1	0.908	0.925	29.991	9.373	9.373	0.000	0.000	0.000	0.000
123	T	141	ALA	0	-0.006	-0.019	27.031	-0.320	-0.320	0.000	0.000	0.000	0.000
124	T	142	ALA	0	0.035	0.043	25.932	-0.408	-0.408	0.000	0.000	0.000	0.000
125	T	143	PRO	0	0.061	0.026	22.031	0.068	0.068	0.000	0.000	0.000	0.000
126	T	144	PHE	0	0.016	0.006	22.427	-0.390	-0.390	0.000	0.000	0.000	0.000
127	T	145	LEU	0	-0.052	-0.034	24.454	0.203	0.203	0.000	0.000	0.000	0.000
128	T	146	THR	0	-0.005	-0.010	24.303	0.244	0.244	0.000	0.000	0.000	0.000
129	T	147	TYR	0	-0.023	-0.009	19.428	-0.519	-0.519	0.000	0.000	0.000	0.000
130	T	148	PHE	0	-0.005	-0.018	17.438	0.369	0.369	0.000	0.000	0.000	0.000
131	T	149	GLY	0	0.056	0.042	15.096	-0.865	-0.865	0.000	0.000	0.000	0.000
132	T	150	LEU	0	-0.038	-0.015	11.173	0.827	0.827	0.000	0.000	0.000	0.000
133	T	151	PHE	0	0.029	0.001	9.718	-1.725	-1.725	0.000	0.000	0.000	0.000
134	T	152	GLN	0	-0.040	-0.026	7.568	1.269	1.269	0.000	0.000	0.000	0.000
135	T	153	VAL	0	-0.038	-0.022	9.501	-0.174	-0.174	0.000	0.000	0.000	0.000
136	T	154	HIS	0	-0.010	0.003	5.849	2.019	2.019	0.000	0.000	0.000	0.000

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