FMO DATABASE

FMODB ID: YY5R2

Calculation Name: 3TER-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3TER

Chain ID: A

ChEMBL ID:

UniProt ID: G5EF60

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	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	130
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-955530.503007
FMO2-HF: Nuclear repulsion	901970.916151
FMO2-HF: Total energy	-53559.586856
FMO2-MP2: Total energy	-53711.555269

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:258:VAL)

Summations of interaction energy for fragment #1(A:258:VAL)

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.
-15.572	-14.165	15.898	-8.208	-9.097	-0.059

Interaction energy analysis for fragmet #1(A:258:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : 0.012

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	260	HIS	0	0.032	0.011	1.933	-1.786	-0.571	8.740	-4.245	-5.710	-0.008
4	A	261	THR	0	0.050	0.013	4.978	-0.410	-0.337	-0.001	-0.008	-0.064	0.000
5	A	262	GLU	-1	-0.866	-0.937	1.987	-15.013	-14.894	7.159	-3.955	-3.323	-0.051
6	A	263	MET	0	-0.015	-0.010	5.788	0.525	0.525	0.000	0.000	0.000	0.000
7	A	264	GLU	-1	-0.940	-0.963	7.737	-0.477	-0.477	0.000	0.000	0.000	0.000
8	A	265	ASN	0	0.037	0.006	9.192	0.323	0.323	0.000	0.000	0.000	0.000
9	A	266	LEU	0	0.024	0.022	8.228	0.211	0.211	0.000	0.000	0.000	0.000
10	A	267	ARG	1	0.925	0.960	10.228	1.010	1.010	0.000	0.000	0.000	0.000
11	A	268	VAL	0	0.029	0.029	13.556	0.116	0.116	0.000	0.000	0.000	0.000
12	A	269	GLN	0	-0.077	-0.064	11.578	-0.054	-0.054	0.000	0.000	0.000	0.000
13	A	270	LEU	0	-0.019	-0.023	13.086	0.071	0.071	0.000	0.000	0.000	0.000
14	A	271	GLU	-1	-0.888	-0.917	16.020	-0.323	-0.323	0.000	0.000	0.000	0.000
15	A	272	GLU	-1	-0.832	-0.921	18.623	-0.257	-0.257	0.000	0.000	0.000	0.000
16	A	273	ALA	0	-0.057	-0.028	18.104	0.039	0.039	0.000	0.000	0.000	0.000
17	A	274	GLU	-1	-0.935	-0.971	19.743	-0.328	-0.328	0.000	0.000	0.000	0.000
18	A	275	ARG	1	0.907	0.949	22.027	0.319	0.319	0.000	0.000	0.000	0.000
19	A	276	ARG	1	0.691	0.818	21.726	0.337	0.337	0.000	0.000	0.000	0.000
20	A	277	LEU	0	-0.063	-0.016	21.771	0.017	0.017	0.000	0.000	0.000	0.000
21	A	278	GLU	-1	-0.957	-0.955	25.297	-0.184	-0.184	0.000	0.000	0.000	0.000
22	A	279	ALA	0	-0.033	-0.021	28.416	0.005	0.005	0.000	0.000	0.000	0.000
23	A	280	ASN	0	-0.013	-0.001	26.703	0.020	0.020	0.000	0.000	0.000	0.000
24	A	281	SER	0	0.016	0.005	30.076	0.013	0.013	0.000	0.000	0.000	0.000
25	A	282	ASN	0	-0.048	-0.016	30.804	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	283	GLY	0	0.004	0.000	30.337	0.009	0.009	0.000	0.000	0.000	0.000
27	A	284	SER	0	-0.056	-0.029	28.577	0.000	0.000	0.000	0.000	0.000	0.000
28	A	285	GLN	0	0.065	0.037	25.161	-0.014	-0.014	0.000	0.000	0.000	0.000
29	A	286	ALA	0	-0.023	0.005	22.383	0.014	0.014	0.000	0.000	0.000	0.000
30	A	287	PRO	0	0.028	-0.004	20.319	-0.024	-0.024	0.000	0.000	0.000	0.000
31	A	288	LEU	0	0.103	0.049	16.706	-0.016	-0.016	0.000	0.000	0.000	0.000
32	A	289	ALA	0	-0.016	0.004	14.625	-0.070	-0.070	0.000	0.000	0.000	0.000
33	A	290	LEU	0	0.010	-0.010	14.916	-0.040	-0.040	0.000	0.000	0.000	0.000
34	A	291	GLN	0	0.046	0.040	12.854	-0.108	-0.108	0.000	0.000	0.000	0.000
35	A	292	PRO	0	0.037	0.030	10.465	0.006	0.006	0.000	0.000	0.000	0.000
36	A	293	LEU	0	-0.084	-0.046	12.609	0.043	0.043	0.000	0.000	0.000	0.000
37	A	294	LEU	0	0.030	0.002	14.721	0.057	0.057	0.000	0.000	0.000	0.000
38	A	295	ARG	1	0.999	1.023	13.459	0.559	0.559	0.000	0.000	0.000	0.000
39	A	296	ARG	1	0.972	0.990	10.912	0.598	0.598	0.000	0.000	0.000	0.000
40	A	297	THR	0	-0.079	-0.034	14.420	0.072	0.072	0.000	0.000	0.000	0.000
41	A	298	CYS	0	0.008	0.010	18.073	0.040	0.040	0.000	0.000	0.000	0.000
42	A	299	GLU	-1	-0.935	-0.978	13.762	-0.462	-0.462	0.000	0.000	0.000	0.000
43	A	300	ASN	0	-0.008	-0.014	16.616	0.026	0.026	0.000	0.000	0.000	0.000
44	A	301	GLU	-1	-0.804	-0.858	18.963	-0.128	-0.128	0.000	0.000	0.000	0.000
45	A	302	MET	0	0.034	0.007	21.169	0.027	0.027	0.000	0.000	0.000	0.000
46	A	303	ALA	0	0.011	0.022	19.172	0.021	0.021	0.000	0.000	0.000	0.000
47	A	304	PHE	0	-0.044	-0.036	21.320	0.024	0.024	0.000	0.000	0.000	0.000
48	A	305	LEU	0	0.007	0.005	23.869	0.018	0.018	0.000	0.000	0.000	0.000
49	A	306	GLU	-1	-0.853	-0.923	23.729	-0.075	-0.075	0.000	0.000	0.000	0.000
50	A	307	LYS	1	0.905	0.950	24.068	0.043	0.043	0.000	0.000	0.000	0.000
51	A	308	GLN	0	0.004	-0.007	26.001	0.016	0.016	0.000	0.000	0.000	0.000
52	A	309	ARG	1	0.949	0.977	28.829	0.083	0.083	0.000	0.000	0.000	0.000
53	A	310	GLN	0	-0.059	-0.033	24.070	0.016	0.016	0.000	0.000	0.000	0.000
54	A	311	ASP	-1	-0.890	-0.942	29.599	-0.027	-0.027	0.000	0.000	0.000	0.000
55	A	312	CYS	0	-0.050	-0.030	31.687	0.004	0.004	0.000	0.000	0.000	0.000
56	A	313	PHE	0	0.018	0.014	32.452	0.004	0.004	0.000	0.000	0.000	0.000
57	A	314	LYS	1	0.931	0.952	28.942	0.024	0.024	0.000	0.000	0.000	0.000
58	A	315	GLU	-1	-0.849	-0.932	34.523	-0.012	-0.012	0.000	0.000	0.000	0.000
59	A	316	MET	0	-0.088	-0.045	37.417	0.001	0.001	0.000	0.000	0.000	0.000
60	A	317	LYS	1	0.917	0.965	36.202	0.021	0.021	0.000	0.000	0.000	0.000
61	A	318	GLU	-1	-0.847	-0.923	38.786	-0.006	-0.006	0.000	0.000	0.000	0.000
62	A	319	ALA	0	-0.022	-0.022	40.547	0.002	0.002	0.000	0.000	0.000	0.000
63	A	320	ILE	0	-0.018	-0.006	41.919	0.001	0.001	0.000	0.000	0.000	0.000
64	A	321	GLU	-1	-0.879	-0.936	41.573	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	322	MET	0	-0.112	-0.046	43.436	0.001	0.001	0.000	0.000	0.000	0.000
66	A	323	VAL	0	-0.004	-0.003	46.939	0.001	0.001	0.000	0.000	0.000	0.000
67	A	324	ASP	-1	-0.826	-0.910	46.737	-0.008	-0.008	0.000	0.000	0.000	0.000
68	A	325	ARG	1	0.832	0.907	48.422	0.001	0.001	0.000	0.000	0.000	0.000
69	A	326	LEU	0	-0.059	-0.037	50.271	0.001	0.001	0.000	0.000	0.000	0.000
70	A	327	GLN	0	0.001	0.005	52.261	0.001	0.001	0.000	0.000	0.000	0.000
71	A	328	LYS	1	0.912	0.975	49.493	0.000	0.000	0.000	0.000	0.000	0.000
72	A	329	LYS	1	0.859	0.947	54.452	0.000	0.000	0.000	0.000	0.000	0.000
73	A	330	GLN	0	0.106	0.067	55.632	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	331	GLY	0	-0.044	-0.051	57.152	0.001	0.001	0.000	0.000	0.000	0.000
75	A	332	SER	0	0.034	0.014	60.926	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	333	VAL	0	0.076	0.048	64.339	0.001	0.001	0.000	0.000	0.000	0.000
77	A	334	LEU	0	0.040	0.035	66.821	0.000	0.000	0.000	0.000	0.000	0.000
78	A	335	SER	0	0.010	0.000	67.849	0.000	0.000	0.000	0.000	0.000	0.000
79	A	336	SER	0	-0.017	-0.026	63.427	0.000	0.000	0.000	0.000	0.000	0.000
80	A	337	LEU	0	-0.037	-0.009	60.504	0.000	0.000	0.000	0.000	0.000	0.000
81	A	338	LYS	1	0.876	0.927	63.602	0.001	0.001	0.000	0.000	0.000	0.000
82	A	339	LEU	0	0.032	0.018	65.359	0.000	0.000	0.000	0.000	0.000	0.000
83	A	340	ALA	0	0.001	-0.002	60.679	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	341	THR	0	-0.017	-0.009	61.312	0.000	0.000	0.000	0.000	0.000	0.000
85	A	342	GLY	0	0.026	0.022	62.744	0.000	0.000	0.000	0.000	0.000	0.000
86	A	343	ALA	0	-0.014	-0.014	57.460	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	344	ALA	0	0.031	0.023	55.022	0.000	0.000	0.000	0.000	0.000	0.000
88	A	345	SER	0	-0.024	0.002	56.374	0.001	0.001	0.000	0.000	0.000	0.000
89	A	346	THR	0	0.026	-0.001	52.114	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	347	SER	0	0.050	0.006	52.306	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	348	ASP	-1	-0.828	-0.901	52.871	-0.014	-0.014	0.000	0.000	0.000	0.000
92	A	349	GLN	0	-0.063	-0.039	50.122	0.000	0.000	0.000	0.000	0.000	0.000
93	A	350	VAL	0	-0.005	-0.009	47.470	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	351	ASP	-1	-0.894	-0.942	47.883	-0.021	-0.021	0.000	0.000	0.000	0.000
95	A	352	SER	0	-0.042	-0.022	48.831	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	353	LYS	1	0.914	0.960	41.246	0.012	0.012	0.000	0.000	0.000	0.000
97	A	354	ILE	0	0.014	0.003	43.890	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	355	PHE	0	-0.006	0.014	44.225	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	356	ALA	0	0.012	0.004	43.099	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	357	LEU	0	-0.032	-0.013	38.440	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	358	LYS	1	0.992	0.979	39.699	0.029	0.029	0.000	0.000	0.000	0.000
102	A	359	SER	0	0.045	0.037	40.874	-0.004	-0.004	0.000	0.000	0.000	0.000
103	A	360	ARG	1	0.823	0.925	34.940	0.031	0.031	0.000	0.000	0.000	0.000
104	A	361	MET	0	0.061	0.023	33.051	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	362	GLU	-1	-0.891	-0.942	36.296	-0.057	-0.057	0.000	0.000	0.000	0.000
106	A	363	LYS	1	0.946	0.956	36.049	0.042	0.042	0.000	0.000	0.000	0.000
107	A	364	ILE	0	-0.048	-0.025	31.452	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	365	HIS	0	0.007	-0.011	32.677	-0.010	-0.010	0.000	0.000	0.000	0.000
109	A	366	THR	0	-0.022	-0.003	33.786	-0.005	-0.005	0.000	0.000	0.000	0.000
110	A	367	LEU	0	0.030	0.031	30.433	-0.006	-0.006	0.000	0.000	0.000	0.000
111	A	368	THR	0	-0.016	-0.018	28.674	-0.007	-0.007	0.000	0.000	0.000	0.000
112	A	369	ARG	1	0.935	0.971	29.567	0.072	0.072	0.000	0.000	0.000	0.000
113	A	370	GLU	-1	-0.851	-0.929	31.367	-0.100	-0.100	0.000	0.000	0.000	0.000
114	A	371	THR	0	-0.093	-0.046	26.027	-0.007	-0.007	0.000	0.000	0.000	0.000
115	A	372	GLN	0	-0.032	-0.022	26.631	-0.012	-0.012	0.000	0.000	0.000	0.000
116	A	373	GLU	-1	-0.907	-0.941	27.518	-0.123	-0.123	0.000	0.000	0.000	0.000
117	A	374	ARG	1	0.846	0.902	25.877	0.139	0.139	0.000	0.000	0.000	0.000
118	A	375	TRP	0	-0.002	-0.021	20.730	-0.020	-0.020	0.000	0.000	0.000	0.000
119	A	376	LEU	0	0.035	0.036	24.695	-0.018	-0.018	0.000	0.000	0.000	0.000
120	A	377	GLN	0	0.011	0.006	26.737	-0.007	-0.007	0.000	0.000	0.000	0.000
121	A	378	ILE	0	-0.035	-0.023	22.988	-0.003	-0.003	0.000	0.000	0.000	0.000
122	A	379	GLU	-1	-0.773	-0.908	22.025	-0.289	-0.289	0.000	0.000	0.000	0.000
123	A	380	SER	0	-0.097	-0.039	24.037	-0.005	-0.005	0.000	0.000	0.000	0.000
124	A	381	LEU	0	-0.031	-0.023	27.152	0.005	0.005	0.000	0.000	0.000	0.000
125	A	382	CYS	0	-0.062	-0.033	21.985	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	383	GLY	0	0.060	0.035	23.573	-0.010	-0.010	0.000	0.000	0.000	0.000
127	A	384	PHE	0	-0.032	-0.023	18.865	-0.029	-0.029	0.000	0.000	0.000	0.000
128	A	385	PRO	0	0.029	0.023	18.099	0.017	0.017	0.000	0.000	0.000	0.000
129	A	386	LEU	0	-0.094	-0.063	17.132	-0.051	-0.051	0.000	0.000	0.000	0.000
130	A	387	LEU	0	-0.030	-0.005	18.513	-0.005	-0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:258:VAL)