FMO DATABASE

FMODB ID: VR3Y1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-954716.108756
FMO2-HF: Nuclear repulsion	901155.294503
FMO2-HF: Total energy	-53560.814253
FMO2-MP2: Total energy	-53712.67415

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.
-14.857	-8.525	7.001	-6.053	-7.282	-0.031

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 : 0.024 / q_NPA : 0.017

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	0.020	0.008	2.096	-4.141	-0.118	4.507	-3.733	-4.798	0.001
4	A	261	THR	0	0.066	0.027	5.351	-0.352	-0.292	-0.001	-0.006	-0.053	0.000
5	A	262	GLU	-1	-0.892	-0.947	2.256	-12.262	-10.013	2.495	-2.314	-2.431	-0.032
6	A	263	MET	0	0.021	0.019	5.958	0.586	0.586	0.000	0.000	0.000	0.000
7	A	264	GLU	-1	-0.875	-0.926	7.773	-0.396	-0.396	0.000	0.000	0.000	0.000
8	A	265	ASN	0	0.035	0.008	9.021	0.344	0.344	0.000	0.000	0.000	0.000
9	A	266	LEU	0	0.047	0.032	7.336	0.185	0.185	0.000	0.000	0.000	0.000
10	A	267	ARG	1	0.877	0.932	10.157	0.958	0.958	0.000	0.000	0.000	0.000
11	A	268	VAL	0	0.026	0.026	13.519	0.105	0.105	0.000	0.000	0.000	0.000
12	A	269	GLN	0	-0.073	-0.053	11.600	-0.030	-0.030	0.000	0.000	0.000	0.000
13	A	270	LEU	0	-0.018	-0.025	12.647	0.067	0.067	0.000	0.000	0.000	0.000
14	A	271	GLU	-1	-0.804	-0.864	15.893	-0.278	-0.278	0.000	0.000	0.000	0.000
15	A	272	GLU	-1	-0.785	-0.878	18.471	-0.228	-0.228	0.000	0.000	0.000	0.000
16	A	273	ALA	0	-0.062	-0.032	17.963	0.036	0.036	0.000	0.000	0.000	0.000
17	A	274	GLU	-1	-0.947	-0.972	19.781	-0.280	-0.280	0.000	0.000	0.000	0.000
18	A	275	ARG	1	0.783	0.859	21.910	0.299	0.299	0.000	0.000	0.000	0.000
19	A	276	ARG	1	0.681	0.802	21.918	0.294	0.294	0.000	0.000	0.000	0.000
20	A	277	LEU	0	-0.071	-0.020	21.543	0.015	0.015	0.000	0.000	0.000	0.000
21	A	278	GLU	-1	-0.966	-0.961	25.202	-0.159	-0.159	0.000	0.000	0.000	0.000
22	A	279	ALA	0	-0.023	-0.020	28.310	0.005	0.005	0.000	0.000	0.000	0.000
23	A	280	ASN	0	0.000	0.005	26.690	0.019	0.019	0.000	0.000	0.000	0.000
24	A	281	SER	0	0.016	0.008	30.059	0.012	0.012	0.000	0.000	0.000	0.000
25	A	282	ASN	0	-0.041	-0.012	30.703	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	283	GLY	0	0.001	-0.003	30.426	0.008	0.008	0.000	0.000	0.000	0.000
27	A	284	SER	0	-0.057	-0.030	28.634	0.000	0.000	0.000	0.000	0.000	0.000
28	A	285	GLN	0	0.037	0.031	24.970	-0.015	-0.015	0.000	0.000	0.000	0.000
29	A	286	ALA	0	-0.012	0.008	22.451	0.013	0.013	0.000	0.000	0.000	0.000
30	A	287	PRO	0	0.023	-0.005	20.282	-0.022	-0.022	0.000	0.000	0.000	0.000
31	A	288	LEU	0	0.096	0.049	16.599	-0.015	-0.015	0.000	0.000	0.000	0.000
32	A	289	ALA	0	-0.022	0.001	14.522	-0.064	-0.064	0.000	0.000	0.000	0.000
33	A	290	LEU	0	0.007	-0.008	14.847	-0.035	-0.035	0.000	0.000	0.000	0.000
34	A	291	GLN	0	0.045	0.036	13.074	-0.105	-0.105	0.000	0.000	0.000	0.000
35	A	292	PRO	0	0.032	0.014	10.597	0.006	0.006	0.000	0.000	0.000	0.000
36	A	293	LEU	0	-0.072	-0.030	12.753	0.035	0.035	0.000	0.000	0.000	0.000
37	A	294	LEU	0	0.027	0.004	14.825	0.050	0.050	0.000	0.000	0.000	0.000
38	A	295	ARG	1	0.836	0.926	13.136	0.588	0.588	0.000	0.000	0.000	0.000
39	A	296	ARG	1	0.973	0.991	10.342	0.562	0.562	0.000	0.000	0.000	0.000
40	A	297	THR	0	-0.084	-0.049	14.472	0.065	0.065	0.000	0.000	0.000	0.000
41	A	298	CYS	0	0.006	0.013	18.122	0.038	0.038	0.000	0.000	0.000	0.000
42	A	299	GLU	-1	-0.850	-0.923	13.855	-0.431	-0.431	0.000	0.000	0.000	0.000
43	A	300	ASN	0	-0.034	-0.027	16.389	0.034	0.034	0.000	0.000	0.000	0.000
44	A	301	GLU	-1	-0.792	-0.841	19.075	-0.117	-0.117	0.000	0.000	0.000	0.000
45	A	302	MET	0	0.044	0.015	21.335	0.025	0.025	0.000	0.000	0.000	0.000
46	A	303	ALA	0	0.007	0.019	19.614	0.019	0.019	0.000	0.000	0.000	0.000
47	A	304	PHE	0	-0.038	-0.032	21.533	0.021	0.021	0.000	0.000	0.000	0.000
48	A	305	LEU	0	0.000	0.001	24.319	0.016	0.016	0.000	0.000	0.000	0.000
49	A	306	GLU	-1	-0.864	-0.930	24.016	-0.069	-0.069	0.000	0.000	0.000	0.000
50	A	307	LYS	1	0.936	0.970	24.608	0.043	0.043	0.000	0.000	0.000	0.000
51	A	308	GLN	0	-0.025	-0.024	26.437	0.016	0.016	0.000	0.000	0.000	0.000
52	A	309	ARG	1	0.881	0.947	29.051	0.081	0.081	0.000	0.000	0.000	0.000
53	A	310	GLN	0	-0.026	-0.017	24.351	0.015	0.015	0.000	0.000	0.000	0.000
54	A	311	ASP	-1	-0.855	-0.921	29.853	-0.025	-0.025	0.000	0.000	0.000	0.000
55	A	312	CYS	0	-0.012	0.004	32.085	0.004	0.004	0.000	0.000	0.000	0.000
56	A	313	PHE	0	0.016	0.010	32.745	0.004	0.004	0.000	0.000	0.000	0.000
57	A	314	LYS	1	0.871	0.911	28.861	0.030	0.030	0.000	0.000	0.000	0.000
58	A	315	GLU	-1	-0.752	-0.856	34.820	-0.019	-0.019	0.000	0.000	0.000	0.000
59	A	316	MET	0	-0.068	-0.039	37.662	0.001	0.001	0.000	0.000	0.000	0.000
60	A	317	LYS	1	0.926	0.969	36.430	0.022	0.022	0.000	0.000	0.000	0.000
61	A	318	GLU	-1	-0.832	-0.900	39.075	-0.009	-0.009	0.000	0.000	0.000	0.000
62	A	319	ALA	0	0.020	0.000	40.830	0.002	0.002	0.000	0.000	0.000	0.000
63	A	320	ILE	0	-0.021	-0.008	42.382	0.001	0.001	0.000	0.000	0.000	0.000
64	A	321	GLU	-1	-0.906	-0.946	41.878	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	322	MET	0	-0.091	-0.037	44.188	0.001	0.001	0.000	0.000	0.000	0.000
66	A	323	VAL	0	0.013	0.002	47.220	0.001	0.001	0.000	0.000	0.000	0.000
67	A	324	ASP	-1	-0.796	-0.877	47.668	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	325	ARG	1	0.904	0.942	48.871	0.003	0.003	0.000	0.000	0.000	0.000
69	A	326	LEU	0	-0.067	-0.038	50.545	0.001	0.001	0.000	0.000	0.000	0.000
70	A	327	GLN	0	-0.029	-0.014	52.370	0.000	0.000	0.000	0.000	0.000	0.000
71	A	328	LYS	1	0.821	0.915	49.453	0.004	0.004	0.000	0.000	0.000	0.000
72	A	329	LYS	1	0.862	0.937	54.711	0.002	0.002	0.000	0.000	0.000	0.000
73	A	330	GLN	0	0.094	0.067	55.736	0.000	0.000	0.000	0.000	0.000	0.000
74	A	331	GLY	0	-0.027	-0.040	57.493	0.001	0.001	0.000	0.000	0.000	0.000
75	A	332	SER	0	0.027	0.011	61.297	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	333	VAL	0	0.077	0.048	64.707	0.001	0.001	0.000	0.000	0.000	0.000
77	A	334	LEU	0	0.045	0.037	67.156	0.000	0.000	0.000	0.000	0.000	0.000
78	A	335	SER	0	0.007	0.000	68.238	0.000	0.000	0.000	0.000	0.000	0.000
79	A	336	SER	0	-0.008	-0.018	63.725	0.000	0.000	0.000	0.000	0.000	0.000
80	A	337	LEU	0	-0.043	-0.011	60.920	0.000	0.000	0.000	0.000	0.000	0.000
81	A	338	LYS	1	0.868	0.912	63.950	0.002	0.002	0.000	0.000	0.000	0.000
82	A	339	LEU	0	0.032	0.024	65.721	0.000	0.000	0.000	0.000	0.000	0.000
83	A	340	ALA	0	-0.003	-0.007	60.990	0.000	0.000	0.000	0.000	0.000	0.000
84	A	341	THR	0	-0.017	-0.005	61.679	0.000	0.000	0.000	0.000	0.000	0.000
85	A	342	GLY	0	0.031	0.023	63.129	0.000	0.000	0.000	0.000	0.000	0.000
86	A	343	ALA	0	-0.016	-0.016	57.915	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	344	ALA	0	0.019	0.020	55.413	0.000	0.000	0.000	0.000	0.000	0.000
88	A	345	SER	0	-0.016	-0.033	56.759	0.001	0.001	0.000	0.000	0.000	0.000
89	A	346	THR	0	0.024	-0.008	52.608	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	347	SER	0	0.064	0.015	52.692	0.000	0.000	0.000	0.000	0.000	0.000
91	A	348	ASP	-1	-0.818	-0.863	53.199	-0.013	-0.013	0.000	0.000	0.000	0.000
92	A	349	GLN	0	-0.068	-0.031	51.033	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	350	VAL	0	0.009	0.004	47.898	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	351	ASP	-1	-0.908	-0.945	48.224	-0.020	-0.020	0.000	0.000	0.000	0.000
95	A	352	SER	0	-0.045	-0.031	49.171	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	353	LYS	1	0.838	0.900	40.910	0.014	0.014	0.000	0.000	0.000	0.000
97	A	354	ILE	0	0.018	-0.001	44.297	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	355	PHE	0	0.006	0.019	44.549	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	356	ALA	0	0.020	0.011	43.606	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	357	LEU	0	-0.024	-0.009	38.967	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	358	LYS	1	0.985	0.982	40.055	0.027	0.027	0.000	0.000	0.000	0.000
102	A	359	SER	0	0.012	0.011	41.214	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	360	ARG	1	0.740	0.853	35.760	0.028	0.028	0.000	0.000	0.000	0.000
104	A	361	MET	0	0.042	0.011	33.292	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	362	GLU	-1	-0.873	-0.928	36.642	-0.059	-0.059	0.000	0.000	0.000	0.000
106	A	363	LYS	1	0.910	0.949	36.639	0.041	0.041	0.000	0.000	0.000	0.000
107	A	364	ILE	0	-0.023	-0.017	31.800	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	365	HIS	0	0.092	0.042	32.940	-0.008	-0.008	0.000	0.000	0.000	0.000
109	A	366	THR	0	-0.020	0.012	34.013	-0.005	-0.005	0.000	0.000	0.000	0.000
110	A	367	LEU	0	0.037	0.031	30.387	-0.005	-0.005	0.000	0.000	0.000	0.000
111	A	368	THR	0	0.033	0.003	28.943	-0.005	-0.005	0.000	0.000	0.000	0.000
112	A	369	ARG	1	0.850	0.920	29.617	0.064	0.064	0.000	0.000	0.000	0.000
113	A	370	GLU	-1	-0.871	-0.939	31.439	-0.090	-0.090	0.000	0.000	0.000	0.000
114	A	371	THR	0	-0.084	-0.049	26.032	-0.006	-0.006	0.000	0.000	0.000	0.000
115	A	372	GLN	0	-0.029	-0.019	26.614	-0.007	-0.007	0.000	0.000	0.000	0.000
116	A	373	GLU	-1	-0.918	-0.947	27.615	-0.112	-0.112	0.000	0.000	0.000	0.000
117	A	374	ARG	1	0.852	0.897	26.158	0.125	0.125	0.000	0.000	0.000	0.000
118	A	375	TRP	0	0.015	-0.026	21.176	-0.018	-0.018	0.000	0.000	0.000	0.000
119	A	376	LEU	0	0.025	0.035	24.820	-0.015	-0.015	0.000	0.000	0.000	0.000
120	A	377	GLN	0	0.007	0.003	26.864	-0.005	-0.005	0.000	0.000	0.000	0.000
121	A	378	ILE	0	-0.027	-0.006	23.145	-0.003	-0.003	0.000	0.000	0.000	0.000
122	A	379	GLU	-1	-0.747	-0.882	22.060	-0.263	-0.263	0.000	0.000	0.000	0.000
123	A	380	SER	0	-0.085	-0.047	24.190	-0.003	-0.003	0.000	0.000	0.000	0.000
124	A	381	LEU	0	-0.029	-0.026	27.329	0.005	0.005	0.000	0.000	0.000	0.000
125	A	382	CYS	0	-0.079	-0.045	22.082	0.000	0.000	0.000	0.000	0.000	0.000
126	A	383	GLY	0	0.077	0.042	23.528	-0.008	-0.008	0.000	0.000	0.000	0.000
127	A	384	PHE	0	-0.018	-0.020	18.941	-0.025	-0.025	0.000	0.000	0.000	0.000
128	A	385	PRO	0	0.011	0.012	18.318	0.014	0.014	0.000	0.000	0.000	0.000
129	A	386	LEU	0	-0.104	-0.067	17.505	-0.048	-0.048	0.000	0.000	0.000	0.000
130	A	387	LEU	0	-0.030	-0.005	18.621	-0.003	-0.003	0.000	0.000	0.000	0.000

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