FMO DATABASE

FMODB ID: 2JR7R

Calculation Name: 1T3G-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1T3G

Chain ID: A

ChEMBL ID:

UniProt ID: Q9NZN1

Base Structure: X-ray

Registration Date: 2023-06-22

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	152
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1639269.233124
FMO2-HF: Nuclear repulsion	1575478.041664
FMO2-HF: Total energy	-63791.19146
FMO2-MP2: Total energy	-63975.556196

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(A:403:LYS)

Summations of interaction energy for fragment #1(A:403:LYS)

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.
-15.821	-7.837	1.506	-4.482	-5.008	-0.029

Interaction energy analysis for fragmet #1(A:403:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.918 / q_NPA : 0.945

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	405	TYR	0	-0.028	-0.020	2.799	7.267	9.644	0.025	-1.101	-1.302	-0.002
4	A	406	ASP	-1	-0.846	-0.934	3.648	-24.054	-23.655	0.005	-0.144	-0.260	-0.001
5	A	407	ALA	0	-0.044	-0.046	6.309	1.362	1.362	0.000	0.000	0.000	0.000
6	A	408	TYR	0	0.044	0.047	8.025	-0.106	-0.106	0.000	0.000	0.000	0.000
7	A	409	LEU	0	-0.016	-0.008	9.452	1.141	1.141	0.000	0.000	0.000	0.000
8	A	410	SER	0	0.033	0.024	13.137	0.351	0.351	0.000	0.000	0.000	0.000
9	A	411	TYR	0	-0.033	-0.061	15.602	0.334	0.334	0.000	0.000	0.000	0.000
10	A	412	THR	0	-0.008	-0.014	19.171	-0.017	-0.017	0.000	0.000	0.000	0.000
11	A	413	LYS	1	0.944	0.981	22.540	11.819	11.819	0.000	0.000	0.000	0.000
12	A	414	VAL	0	-0.021	-0.002	24.997	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	415	ASP	-1	-0.952	-0.967	28.518	-8.883	-8.883	0.000	0.000	0.000	0.000
14	A	423	THR	0	0.029	-0.010	30.920	0.102	0.102	0.000	0.000	0.000	0.000
15	A	424	GLY	0	-0.004	-0.003	30.212	-0.245	-0.245	0.000	0.000	0.000	0.000
16	A	425	GLU	-1	-0.930	-0.957	30.352	-8.393	-8.393	0.000	0.000	0.000	0.000
17	A	426	GLU	-1	-0.903	-0.975	26.896	-9.259	-9.259	0.000	0.000	0.000	0.000
18	A	427	GLU	-1	-0.823	-0.928	25.296	-10.481	-10.481	0.000	0.000	0.000	0.000
19	A	428	ARG	1	0.951	0.999	25.193	8.954	8.954	0.000	0.000	0.000	0.000
20	A	429	PHE	0	-0.020	-0.019	21.048	-0.364	-0.364	0.000	0.000	0.000	0.000
21	A	430	ALA	0	0.026	0.001	21.031	-0.418	-0.418	0.000	0.000	0.000	0.000
22	A	431	LEU	0	-0.017	-0.009	20.046	-0.530	-0.530	0.000	0.000	0.000	0.000
23	A	432	GLU	-1	-0.937	-0.951	21.190	-10.968	-10.968	0.000	0.000	0.000	0.000
24	A	433	ILE	0	-0.031	-0.022	21.584	-0.240	-0.240	0.000	0.000	0.000	0.000
25	A	434	LEU	0	-0.052	-0.013	17.151	-0.213	-0.213	0.000	0.000	0.000	0.000
26	A	435	PRO	0	0.017	-0.007	16.495	-0.476	-0.476	0.000	0.000	0.000	0.000
27	A	436	ASP	-1	-0.865	-0.918	17.080	-12.908	-12.908	0.000	0.000	0.000	0.000
28	A	437	MET	0	-0.062	-0.038	19.334	-0.152	-0.152	0.000	0.000	0.000	0.000
29	A	438	LEU	0	-0.018	-0.024	13.562	-0.118	-0.118	0.000	0.000	0.000	0.000
30	A	439	GLU	-1	-0.791	-0.879	13.256	-18.333	-18.333	0.000	0.000	0.000	0.000
31	A	440	LYS	1	0.897	0.957	15.581	13.938	13.938	0.000	0.000	0.000	0.000
32	A	441	HIS	0	-0.061	-0.019	19.083	0.469	0.469	0.000	0.000	0.000	0.000
33	A	442	TYR	0	-0.084	-0.060	15.811	0.367	0.367	0.000	0.000	0.000	0.000
34	A	443	GLY	0	0.038	0.041	15.191	-0.338	-0.338	0.000	0.000	0.000	0.000
35	A	444	TYR	0	-0.043	-0.029	10.312	-0.426	-0.426	0.000	0.000	0.000	0.000
36	A	445	LYS	1	0.950	0.973	7.732	28.736	28.736	0.000	0.000	0.000	0.000
37	A	446	LEU	0	-0.024	-0.019	8.040	-1.521	-1.521	0.000	0.000	0.000	0.000
38	A	447	PHE	0	0.049	0.034	8.230	-0.260	-0.260	0.000	0.000	0.000	0.000
39	A	448	ILE	0	-0.003	-0.022	10.087	0.960	0.960	0.000	0.000	0.000	0.000
40	A	449	PRO	0	0.038	0.018	13.367	0.145	0.145	0.000	0.000	0.000	0.000
41	A	450	ASP	-1	-0.853	-0.913	15.493	-13.311	-13.311	0.000	0.000	0.000	0.000
42	A	451	ARG	1	0.682	0.832	12.799	18.815	18.815	0.000	0.000	0.000	0.000
43	A	452	ASP	-1	-0.821	-0.909	12.772	-19.989	-19.989	0.000	0.000	0.000	0.000
44	A	453	LEU	0	-0.036	-0.008	13.977	-1.128	-1.128	0.000	0.000	0.000	0.000
45	A	454	ILE	0	0.008	0.015	15.951	1.057	1.057	0.000	0.000	0.000	0.000
46	A	455	PRO	0	-0.036	-0.031	19.123	-0.328	-0.328	0.000	0.000	0.000	0.000
47	A	456	THR	0	0.034	0.016	19.120	0.621	0.621	0.000	0.000	0.000	0.000
48	A	457	GLY	0	-0.018	-0.013	21.931	0.232	0.232	0.000	0.000	0.000	0.000
49	A	458	THR	0	0.013	0.007	17.350	0.485	0.485	0.000	0.000	0.000	0.000
50	A	459	TYR	0	-0.016	0.006	17.488	-0.789	-0.789	0.000	0.000	0.000	0.000
51	A	460	ILE	0	0.015	0.005	16.876	-0.675	-0.675	0.000	0.000	0.000	0.000
52	A	461	GLU	-1	-0.830	-0.934	15.433	-17.119	-17.119	0.000	0.000	0.000	0.000
53	A	462	ASP	-1	-0.925	-0.961	13.241	-21.928	-21.928	0.000	0.000	0.000	0.000
54	A	463	VAL	0	-0.008	0.000	12.045	-1.754	-1.754	0.000	0.000	0.000	0.000
55	A	464	ALA	0	0.011	-0.002	11.244	-1.266	-1.266	0.000	0.000	0.000	0.000
56	A	465	ARG	1	0.945	0.973	8.488	24.981	24.981	0.000	0.000	0.000	0.000
57	A	466	CYS	0	-0.053	-0.025	7.476	-3.802	-3.802	0.000	0.000	0.000	0.000
58	A	467	VAL	0	-0.018	0.002	6.668	-1.638	-1.638	0.000	0.000	0.000	0.000
59	A	468	ASP	-1	-0.901	-0.952	6.343	-35.454	-35.454	0.000	0.000	0.000	0.000
60	A	469	GLN	0	-0.049	-0.009	3.272	-0.243	0.709	0.039	-0.262	-0.728	-0.001
61	A	470	SER	0	-0.021	-0.031	2.435	-9.563	-6.985	1.277	-2.288	-1.567	-0.030
62	A	471	LYS	1	0.897	0.959	3.131	26.056	27.702	0.161	-0.681	-1.126	0.005
63	A	472	ARG	1	0.786	0.876	4.923	20.248	20.280	-0.001	-0.006	-0.025	0.000
64	A	473	LEU	0	0.043	0.057	8.198	-1.058	-1.058	0.000	0.000	0.000	0.000
65	A	474	ILE	0	-0.003	-0.016	10.696	1.030	1.030	0.000	0.000	0.000	0.000
66	A	475	ILE	0	0.022	0.027	13.570	-0.084	-0.084	0.000	0.000	0.000	0.000
67	A	476	VAL	0	-0.004	-0.010	16.856	0.465	0.465	0.000	0.000	0.000	0.000
68	A	477	MET	0	-0.004	0.002	19.565	0.265	0.265	0.000	0.000	0.000	0.000
69	A	478	THR	0	0.023	0.004	22.679	0.336	0.336	0.000	0.000	0.000	0.000
70	A	479	PRO	0	0.068	0.016	25.573	-0.100	-0.100	0.000	0.000	0.000	0.000
71	A	480	ASN	0	0.011	0.004	26.878	0.219	0.219	0.000	0.000	0.000	0.000
72	A	481	TYR	0	-0.006	-0.003	17.968	0.138	0.138	0.000	0.000	0.000	0.000
73	A	482	VAL	0	-0.021	-0.007	24.587	-0.146	-0.146	0.000	0.000	0.000	0.000
74	A	483	VAL	0	-0.047	-0.021	26.848	0.090	0.090	0.000	0.000	0.000	0.000
75	A	484	ARG	1	0.907	0.949	25.765	9.843	9.843	0.000	0.000	0.000	0.000
76	A	485	ARG	1	0.825	0.899	25.134	9.226	9.226	0.000	0.000	0.000	0.000
77	A	486	GLY	0	0.022	0.011	21.751	-0.277	-0.277	0.000	0.000	0.000	0.000
78	A	487	TRP	0	0.006	0.007	19.153	-0.643	-0.643	0.000	0.000	0.000	0.000
79	A	488	SER	0	-0.011	-0.029	19.641	-0.310	-0.310	0.000	0.000	0.000	0.000
80	A	489	ILE	0	0.017	0.010	16.722	0.048	0.048	0.000	0.000	0.000	0.000
81	A	490	PHE	0	-0.014	-0.018	13.229	-0.415	-0.415	0.000	0.000	0.000	0.000
82	A	491	GLU	-1	-0.858	-0.937	17.320	-12.876	-12.876	0.000	0.000	0.000	0.000
83	A	492	LEU	0	-0.047	-0.020	20.512	0.247	0.247	0.000	0.000	0.000	0.000
84	A	493	GLU	-1	-0.825	-0.904	15.907	-17.538	-17.538	0.000	0.000	0.000	0.000
85	A	494	THR	0	0.019	0.000	17.861	-0.117	-0.117	0.000	0.000	0.000	0.000
86	A	495	ARG	1	0.966	0.975	9.721	25.019	25.019	0.000	0.000	0.000	0.000
87	A	496	LEU	0	-0.004	-0.003	11.934	-0.470	-0.470	0.000	0.000	0.000	0.000
88	A	497	ARG	1	0.924	0.977	14.286	12.507	12.507	0.000	0.000	0.000	0.000
89	A	498	ASN	0	-0.055	-0.033	15.345	0.430	0.430	0.000	0.000	0.000	0.000
90	A	499	MET	0	0.006	0.041	9.849	0.301	0.301	0.000	0.000	0.000	0.000
91	A	500	LEU	0	-0.025	-0.007	12.707	0.127	0.127	0.000	0.000	0.000	0.000
92	A	501	VAL	0	0.030	0.023	14.883	0.471	0.471	0.000	0.000	0.000	0.000
93	A	502	THR	0	-0.093	-0.084	14.656	0.264	0.264	0.000	0.000	0.000	0.000
94	A	503	GLY	0	-0.050	-0.028	13.791	-0.034	-0.034	0.000	0.000	0.000	0.000
95	A	504	GLU	-1	-0.965	-0.963	9.339	-22.437	-22.437	0.000	0.000	0.000	0.000
96	A	505	ILE	0	-0.013	-0.004	7.118	-1.477	-1.477	0.000	0.000	0.000	0.000
97	A	506	LYS	1	0.806	0.906	9.416	16.473	16.473	0.000	0.000	0.000	0.000
98	A	507	VAL	0	0.037	0.011	10.941	-0.649	-0.649	0.000	0.000	0.000	0.000
99	A	508	ILE	0	-0.039	-0.027	12.735	0.854	0.854	0.000	0.000	0.000	0.000
100	A	509	LEU	0	0.018	0.011	15.335	-0.156	-0.156	0.000	0.000	0.000	0.000
101	A	510	ILE	0	-0.002	-0.018	17.389	0.466	0.466	0.000	0.000	0.000	0.000
102	A	511	GLU	-1	-0.824	-0.907	20.507	-9.941	-9.941	0.000	0.000	0.000	0.000
103	A	512	CYS	0	-0.071	-0.030	23.218	0.115	0.115	0.000	0.000	0.000	0.000
104	A	513	SER	0	0.059	0.039	25.936	0.327	0.327	0.000	0.000	0.000	0.000
105	A	514	GLU	-1	-0.983	-0.988	28.688	-8.418	-8.418	0.000	0.000	0.000	0.000
106	A	515	LEU	0	0.002	0.017	27.962	0.235	0.235	0.000	0.000	0.000	0.000
107	A	516	ARG	1	0.997	1.003	30.874	7.805	7.805	0.000	0.000	0.000	0.000
108	A	517	GLY	0	0.000	-0.012	34.199	-0.037	-0.037	0.000	0.000	0.000	0.000
109	A	518	ILE	0	-0.013	-0.020	34.302	-0.192	-0.192	0.000	0.000	0.000	0.000
110	A	519	MET	0	0.038	0.017	34.152	-0.110	-0.110	0.000	0.000	0.000	0.000
111	A	520	ASN	0	0.069	0.035	30.358	-0.281	-0.281	0.000	0.000	0.000	0.000
112	A	521	TYR	0	0.002	-0.013	29.489	-0.234	-0.234	0.000	0.000	0.000	0.000
113	A	522	GLN	0	0.043	0.006	29.715	-0.371	-0.371	0.000	0.000	0.000	0.000
114	A	523	GLU	-1	-0.821	-0.862	27.775	-9.554	-9.554	0.000	0.000	0.000	0.000
115	A	524	VAL	0	0.005	-0.004	24.436	-0.366	-0.366	0.000	0.000	0.000	0.000
116	A	525	GLU	-1	-0.952	-0.979	25.004	-9.808	-9.808	0.000	0.000	0.000	0.000
117	A	526	ALA	0	-0.006	-0.009	25.944	-0.211	-0.211	0.000	0.000	0.000	0.000
118	A	527	LEU	0	-0.022	-0.004	19.810	-0.304	-0.304	0.000	0.000	0.000	0.000
119	A	528	LYS	1	0.851	0.897	21.337	9.861	9.861	0.000	0.000	0.000	0.000
120	A	529	HIS	0	-0.021	0.003	21.543	-0.464	-0.464	0.000	0.000	0.000	0.000
121	A	530	THR	0	-0.075	-0.020	19.301	0.040	0.040	0.000	0.000	0.000	0.000
122	A	531	ILE	0	-0.037	-0.021	15.789	-0.649	-0.649	0.000	0.000	0.000	0.000
123	A	532	LYS	1	0.930	0.986	16.250	13.700	13.700	0.000	0.000	0.000	0.000
124	A	533	LEU	0	-0.043	-0.017	12.015	0.470	0.470	0.000	0.000	0.000	0.000
125	A	534	LEU	0	0.041	0.018	15.016	-0.459	-0.459	0.000	0.000	0.000	0.000
126	A	535	THR	0	-0.053	-0.001	16.103	0.682	0.682	0.000	0.000	0.000	0.000
127	A	536	VAL	0	0.044	0.023	18.418	-0.192	-0.192	0.000	0.000	0.000	0.000
128	A	537	ILE	0	-0.044	-0.022	18.302	0.371	0.371	0.000	0.000	0.000	0.000
129	A	538	LYS	1	0.893	0.954	22.152	9.603	9.603	0.000	0.000	0.000	0.000
130	A	539	TRP	0	-0.001	-0.009	23.964	0.150	0.150	0.000	0.000	0.000	0.000
131	A	540	HIS	0	0.017	-0.006	25.858	0.247	0.247	0.000	0.000	0.000	0.000
132	A	541	GLY	0	0.067	0.031	28.973	0.226	0.226	0.000	0.000	0.000	0.000
133	A	542	PRO	0	0.050	-0.008	28.881	-0.222	-0.222	0.000	0.000	0.000	0.000
134	A	543	LYS	1	0.952	0.970	29.702	7.703	7.703	0.000	0.000	0.000	0.000
135	A	544	CYS	0	-0.065	-0.026	26.036	0.069	0.069	0.000	0.000	0.000	0.000
136	A	545	ASN	0	0.109	0.082	25.518	-0.478	-0.478	0.000	0.000	0.000	0.000
137	A	546	LYS	1	0.934	0.995	26.233	8.075	8.075	0.000	0.000	0.000	0.000
138	A	547	LEU	0	0.106	0.039	24.606	-0.112	-0.112	0.000	0.000	0.000	0.000
139	A	548	ASN	0	-0.035	-0.018	24.822	0.297	0.297	0.000	0.000	0.000	0.000
140	A	549	SER	0	0.010	0.029	25.596	0.248	0.248	0.000	0.000	0.000	0.000
141	A	550	LYS	1	0.961	0.943	25.382	8.535	8.535	0.000	0.000	0.000	0.000
142	A	551	PHE	0	0.004	0.015	20.889	-0.110	-0.110	0.000	0.000	0.000	0.000
143	A	552	TRP	0	0.040	0.008	19.227	-0.438	-0.438	0.000	0.000	0.000	0.000
144	A	553	LYS	1	0.933	0.983	20.252	10.622	10.622	0.000	0.000	0.000	0.000
145	A	554	ARG	1	0.805	0.873	20.072	11.176	11.176	0.000	0.000	0.000	0.000
146	A	555	LEU	0	0.040	0.015	15.542	-0.290	-0.290	0.000	0.000	0.000	0.000
147	A	556	GLN	0	0.008	0.001	15.994	-0.228	-0.228	0.000	0.000	0.000	0.000
148	A	557	TYR	0	-0.052	-0.015	15.493	-0.520	-0.520	0.000	0.000	0.000	0.000
149	A	558	GLU	-1	-0.769	-0.859	15.204	-13.404	-13.404	0.000	0.000	0.000	0.000
150	A	559	MET	0	-0.008	0.035	10.239	-0.844	-0.844	0.000	0.000	0.000	0.000
151	A	560	PRO	0	-0.034	-0.017	7.451	0.206	0.206	0.000	0.000	0.000	0.000
152	A	561	PHE	0	0.046	0.030	9.372	0.875	0.875	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:403:LYS)