FMO DATABASE

FMODB ID: 22VGR

Calculation Name: 3TUF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3TUF

Chain ID: A

ChEMBL ID:

UniProt ID: P71044

Base Structure: X-ray

Registration Date: 2023-06-20

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	115
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-844089.041183
FMO2-HF: Nuclear repulsion	799299.250278
FMO2-HF: Total energy	-44789.790904
FMO2-MP2: Total energy	-44921.217105

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:103:ASP)

Summations of interaction energy for fragment #1(A:103:ASP)

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.
56.517	61.797	0.555	-2.426	-3.41	0.021

Interaction energy analysis for fragmet #1(A:103:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.923 / q_NPA : -0.973

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	105	LEU	0	0.033	0.024	2.788	-8.590	-3.711	0.556	-2.355	-3.079	0.021
4	A	106	PHE	0	-0.018	-0.009	4.461	-8.176	-8.025	0.000	-0.035	-0.117	0.000
5	A	107	THR	0	-0.063	-0.061	6.592	-2.516	-2.516	0.000	0.000	0.000	0.000
6	A	108	THR	0	-0.020	-0.002	4.003	-3.249	-2.999	-0.001	-0.036	-0.214	0.000
7	A	109	TYR	0	0.056	0.035	6.651	-5.541	-5.541	0.000	0.000	0.000	0.000
8	A	110	ARG	1	0.772	0.857	9.080	-25.864	-25.864	0.000	0.000	0.000	0.000
9	A	111	LEU	0	-0.037	-0.015	8.777	-2.661	-2.661	0.000	0.000	0.000	0.000
10	A	112	ASP	-1	-0.873	-0.937	9.296	29.670	29.670	0.000	0.000	0.000	0.000
11	A	113	LEU	0	-0.065	-0.034	12.126	-2.052	-2.052	0.000	0.000	0.000	0.000
12	A	114	GLU	-1	-0.835	-0.909	14.579	14.807	14.807	0.000	0.000	0.000	0.000
13	A	115	ASP	-1	-0.831	-0.898	15.034	17.618	17.618	0.000	0.000	0.000	0.000
14	A	116	ALA	0	-0.038	-0.030	16.244	-1.363	-1.363	0.000	0.000	0.000	0.000
15	A	117	ARG	1	0.757	0.814	18.068	-16.997	-16.997	0.000	0.000	0.000	0.000
16	A	118	SER	0	-0.067	-0.037	19.744	-1.207	-1.207	0.000	0.000	0.000	0.000
17	A	119	LYS	1	0.873	0.936	17.244	-18.302	-18.302	0.000	0.000	0.000	0.000
18	A	120	GLH	0	0.001	-0.024	22.208	-0.941	-0.941	0.000	0.000	0.000	0.000
19	A	121	ARG	1	0.744	0.855	20.981	-15.029	-15.029	0.000	0.000	0.000	0.000
20	A	122	GLU	-1	-0.948	-0.967	25.595	11.652	11.652	0.000	0.000	0.000	0.000
21	A	123	GLU	-1	-0.934	-0.964	25.499	12.073	12.073	0.000	0.000	0.000	0.000
22	A	124	LEU	0	-0.034	-0.019	27.403	-0.557	-0.557	0.000	0.000	0.000	0.000
23	A	125	ASN	0	-0.012	-0.027	30.094	-0.649	-0.649	0.000	0.000	0.000	0.000
24	A	126	ALA	0	0.002	0.020	31.352	-0.426	-0.426	0.000	0.000	0.000	0.000
25	A	127	ILE	0	-0.016	-0.013	31.905	-0.393	-0.393	0.000	0.000	0.000	0.000
26	A	128	VAL	0	-0.030	-0.024	34.521	-0.373	-0.373	0.000	0.000	0.000	0.000
27	A	129	SER	0	-0.076	-0.044	35.439	-0.356	-0.356	0.000	0.000	0.000	0.000
28	A	130	SER	0	0.001	0.019	37.311	-0.258	-0.258	0.000	0.000	0.000	0.000
29	A	131	ASP	-1	-0.920	-0.972	39.134	7.309	7.309	0.000	0.000	0.000	0.000
30	A	132	ASP	-1	-0.982	-0.987	40.434	7.536	7.536	0.000	0.000	0.000	0.000
31	A	133	ALA	0	-0.034	0.011	38.536	0.028	0.028	0.000	0.000	0.000	0.000
32	A	134	THR	0	-0.054	-0.080	40.542	-0.265	-0.265	0.000	0.000	0.000	0.000
33	A	135	ALA	0	0.018	-0.006	41.405	0.153	0.153	0.000	0.000	0.000	0.000
34	A	136	LYS	1	0.928	0.964	40.731	-7.428	-7.428	0.000	0.000	0.000	0.000
35	A	137	GLU	-1	-0.757	-0.840	37.741	8.354	8.354	0.000	0.000	0.000	0.000
36	A	138	LYS	1	0.834	0.924	36.998	-7.593	-7.593	0.000	0.000	0.000	0.000
37	A	139	SER	0	0.007	0.002	37.272	0.124	0.124	0.000	0.000	0.000	0.000
38	A	140	GLU	-1	-0.880	-0.937	35.322	9.010	9.010	0.000	0.000	0.000	0.000
39	A	141	ALA	0	-0.021	-0.008	32.874	0.315	0.315	0.000	0.000	0.000	0.000
40	A	142	TYR	0	0.000	-0.011	32.670	0.310	0.310	0.000	0.000	0.000	0.000
41	A	143	ASP	-1	-0.908	-0.958	33.757	8.909	8.909	0.000	0.000	0.000	0.000
42	A	144	LYS	1	0.849	0.923	29.514	-9.575	-9.575	0.000	0.000	0.000	0.000
43	A	145	MET	0	0.019	0.023	29.102	0.372	0.372	0.000	0.000	0.000	0.000
44	A	146	THR	0	-0.014	-0.018	29.355	0.299	0.299	0.000	0.000	0.000	0.000
45	A	147	ALA	0	-0.012	-0.005	29.719	0.155	0.155	0.000	0.000	0.000	0.000
46	A	148	LEU	0	0.035	0.026	22.921	0.266	0.266	0.000	0.000	0.000	0.000
47	A	149	SER	0	-0.013	0.001	25.402	0.486	0.486	0.000	0.000	0.000	0.000
48	A	150	GLU	-1	-0.906	-0.940	26.964	10.519	10.519	0.000	0.000	0.000	0.000
49	A	151	VAL	0	-0.034	0.005	22.629	0.174	0.174	0.000	0.000	0.000	0.000
50	A	152	GLU	-1	-0.806	-0.890	21.409	15.162	15.162	0.000	0.000	0.000	0.000
51	A	153	GLY	0	-0.042	-0.028	23.026	0.369	0.369	0.000	0.000	0.000	0.000
52	A	154	THR	0	-0.068	-0.054	24.607	-0.043	-0.043	0.000	0.000	0.000	0.000
53	A	155	GLU	-1	-0.738	-0.845	19.207	16.339	16.339	0.000	0.000	0.000	0.000
54	A	156	LYS	1	0.994	1.001	20.683	-13.497	-13.497	0.000	0.000	0.000	0.000
55	A	157	GLN	0	-0.001	0.007	21.930	0.021	0.021	0.000	0.000	0.000	0.000
56	A	158	LEU	0	0.006	0.008	22.065	-0.078	-0.078	0.000	0.000	0.000	0.000
57	A	159	GLU	-1	-0.765	-0.877	16.406	18.921	18.921	0.000	0.000	0.000	0.000
58	A	160	THR	0	-0.053	-0.043	20.438	0.075	0.075	0.000	0.000	0.000	0.000
59	A	161	LEU	0	-0.003	0.001	22.884	-0.222	-0.222	0.000	0.000	0.000	0.000
60	A	162	ILE	0	0.023	0.028	19.819	-0.285	-0.285	0.000	0.000	0.000	0.000
61	A	163	LYS	1	0.822	0.923	16.679	-17.905	-17.905	0.000	0.000	0.000	0.000
62	A	164	THR	0	-0.074	-0.059	21.623	-0.433	-0.433	0.000	0.000	0.000	0.000
63	A	165	GLN	0	-0.126	-0.066	24.393	-0.703	-0.703	0.000	0.000	0.000	0.000
64	A	166	GLY	0	-0.028	-0.003	23.904	-0.134	-0.134	0.000	0.000	0.000	0.000
65	A	167	TYR	0	-0.069	-0.033	18.831	0.265	0.265	0.000	0.000	0.000	0.000
66	A	168	GLU	-1	-0.809	-0.902	14.004	22.055	22.055	0.000	0.000	0.000	0.000
67	A	169	ASP	-1	-0.721	-0.841	13.153	21.836	21.836	0.000	0.000	0.000	0.000
68	A	170	ALA	0	-0.076	-0.052	15.499	-0.231	-0.231	0.000	0.000	0.000	0.000
69	A	171	LEU	0	0.004	0.019	10.805	-0.021	-0.021	0.000	0.000	0.000	0.000
70	A	172	VAL	0	-0.013	-0.004	14.859	-0.315	-0.315	0.000	0.000	0.000	0.000
71	A	173	ASN	0	0.011	0.024	16.267	-0.611	-0.611	0.000	0.000	0.000	0.000
72	A	174	ALA	0	-0.053	-0.060	18.175	-0.273	-0.273	0.000	0.000	0.000	0.000
73	A	175	GLU	-1	-0.777	-0.873	20.049	14.767	14.767	0.000	0.000	0.000	0.000
74	A	176	GLY	0	-0.002	0.017	22.144	-0.545	-0.545	0.000	0.000	0.000	0.000
75	A	177	ASP	-1	-0.901	-0.953	23.811	11.655	11.655	0.000	0.000	0.000	0.000
76	A	178	LYS	1	0.820	0.913	19.437	-16.291	-16.291	0.000	0.000	0.000	0.000
77	A	179	ILE	0	-0.020	0.007	21.428	0.212	0.212	0.000	0.000	0.000	0.000
78	A	180	ASN	0	-0.015	-0.007	16.624	-0.077	-0.077	0.000	0.000	0.000	0.000
79	A	181	ILE	0	0.048	0.031	17.387	0.218	0.218	0.000	0.000	0.000	0.000
80	A	182	THR	0	-0.033	-0.018	11.705	0.171	0.171	0.000	0.000	0.000	0.000
81	A	183	VAL	0	0.005	0.001	14.922	-0.210	-0.210	0.000	0.000	0.000	0.000
82	A	184	LYS	1	0.860	0.940	10.304	-25.197	-25.197	0.000	0.000	0.000	0.000
83	A	185	SER	0	-0.063	-0.084	14.425	-2.005	-2.005	0.000	0.000	0.000	0.000
84	A	186	ASP	-1	-0.814	-0.858	15.686	19.731	19.731	0.000	0.000	0.000	0.000
85	A	187	LYS	1	0.904	0.951	17.854	-13.342	-13.342	0.000	0.000	0.000	0.000
86	A	188	HIS	0	0.085	0.067	19.465	0.148	0.148	0.000	0.000	0.000	0.000
87	A	189	SER	0	-0.006	-0.023	21.509	-0.491	-0.491	0.000	0.000	0.000	0.000
88	A	190	LYS	1	1.030	0.998	24.947	-10.788	-10.788	0.000	0.000	0.000	0.000
89	A	191	SER	0	-0.006	-0.002	27.221	-0.034	-0.034	0.000	0.000	0.000	0.000
90	A	192	LYS	1	0.939	0.971	22.288	-14.075	-14.075	0.000	0.000	0.000	0.000
91	A	193	ALA	0	0.018	0.022	23.634	0.151	0.151	0.000	0.000	0.000	0.000
92	A	194	THR	0	0.050	0.025	24.569	0.027	0.027	0.000	0.000	0.000	0.000
93	A	195	ALA	0	-0.015	-0.002	27.023	-0.190	-0.190	0.000	0.000	0.000	0.000
94	A	196	ILE	0	-0.016	-0.004	20.890	-0.083	-0.083	0.000	0.000	0.000	0.000
95	A	197	ILE	0	0.020	0.008	24.791	-0.096	-0.096	0.000	0.000	0.000	0.000
96	A	198	ASP	-1	-0.920	-0.962	26.448	10.036	10.036	0.000	0.000	0.000	0.000
97	A	199	LEU	0	-0.068	-0.030	24.661	-0.309	-0.309	0.000	0.000	0.000	0.000
98	A	200	VAL	0	-0.035	0.000	24.945	-0.030	-0.030	0.000	0.000	0.000	0.000
99	A	201	ALA	0	0.062	0.027	27.689	-0.382	-0.382	0.000	0.000	0.000	0.000
100	A	202	LYS	1	0.989	0.972	30.730	-8.718	-8.718	0.000	0.000	0.000	0.000
101	A	203	GLU	-1	-0.866	-0.925	33.353	9.370	9.370	0.000	0.000	0.000	0.000
102	A	204	ILE	0	0.016	0.016	26.699	0.043	0.043	0.000	0.000	0.000	0.000
103	A	205	LYS	1	0.838	0.913	28.711	-10.641	-10.641	0.000	0.000	0.000	0.000
104	A	206	THR	0	-0.102	-0.063	30.404	-0.181	-0.181	0.000	0.000	0.000	0.000
105	A	207	MET	0	-0.070	-0.033	31.756	-0.275	-0.275	0.000	0.000	0.000	0.000
106	A	208	LYS	1	0.895	0.968	25.878	-12.131	-12.131	0.000	0.000	0.000	0.000
107	A	209	ASP	-1	-0.876	-0.928	24.725	12.864	12.864	0.000	0.000	0.000	0.000
108	A	210	VAL	0	-0.025	-0.036	23.523	0.243	0.243	0.000	0.000	0.000	0.000
109	A	211	ALA	0	-0.030	-0.007	20.166	-0.168	-0.168	0.000	0.000	0.000	0.000
110	A	212	VAL	0	-0.001	-0.014	19.174	0.304	0.304	0.000	0.000	0.000	0.000
111	A	213	THR	0	-0.046	-0.019	13.914	-1.091	-1.091	0.000	0.000	0.000	0.000
112	A	214	PHE	0	-0.038	-0.041	16.065	-0.067	-0.067	0.000	0.000	0.000	0.000
113	A	215	GLU	-1	-0.864	-0.929	9.321	32.226	32.226	0.000	0.000	0.000	0.000
114	A	216	PRO	0	-0.024	-0.007	10.589	-1.575	-1.575	0.000	0.000	0.000	0.000
115	A	217	SER	0	-0.101	-0.068	11.370	3.273	3.273	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:103:ASP)