FMO DATABASE

FMODB ID: M3G8Z

Calculation Name: 3VBC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3VBC

Chain ID: A

ChEMBL ID:

UniProt ID: Q9JIP3

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:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	136
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1269458.615125
FMO2-HF: Nuclear repulsion	1214991.520917
FMO2-HF: Total energy	-54467.094208
FMO2-MP2: Total energy	-54624.316425

3D Structure Molmil

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:325:LEU)

Summations of interaction energy for fragment #1(A:325:LEU)

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.
-3.088	-0.096000000000001	0.011	-1.509	-1.494	0.006

Interaction energy analysis for fragmet #1(A:325:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : 0.010

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	327	PRO	0	0.010	0.021	3.439	-2.706	0.286	0.011	-1.509	-1.494	0.006
4	A	328	LEU	0	-0.057	-0.035	5.006	0.595	0.595	0.000	0.000	0.000	0.000
5	A	329	ILE	0	0.027	0.024	6.031	-0.047	-0.047	0.000	0.000	0.000	0.000
6	A	330	LYS	1	0.823	0.889	6.222	0.145	0.145	0.000	0.000	0.000	0.000
7	A	331	VAL	0	0.005	-0.003	10.060	0.017	0.017	0.000	0.000	0.000	0.000
8	A	332	LEU	0	-0.009	0.012	13.636	0.034	0.034	0.000	0.000	0.000	0.000
9	A	333	VAL	0	-0.024	-0.016	15.932	-0.014	-0.014	0.000	0.000	0.000	0.000
10	A	334	VAL	0	-0.005	0.009	19.424	0.019	0.019	0.000	0.000	0.000	0.000
11	A	335	TYR	0	0.007	-0.012	22.395	-0.009	-0.009	0.000	0.000	0.000	0.000
12	A	336	PRO	0	0.017	0.020	25.768	0.009	0.009	0.000	0.000	0.000	0.000
13	A	337	SER	0	-0.003	-0.015	29.417	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	338	GLU	-1	-0.807	-0.915	30.591	-0.033	-0.033	0.000	0.000	0.000	0.000
15	A	339	ILE	0	0.071	0.012	32.995	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	340	CYS	0	-0.041	-0.019	34.437	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	341	PHE	0	0.033	0.023	27.814	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	342	HIS	0	0.036	0.019	28.240	-0.007	-0.007	0.000	0.000	0.000	0.000
19	A	343	HIS	0	0.020	0.003	29.322	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	344	THR	0	-0.007	-0.003	28.350	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	345	VAL	0	0.008	0.013	24.548	-0.012	-0.012	0.000	0.000	0.000	0.000
22	A	346	CYS	0	-0.026	0.000	24.599	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	347	ARG	1	0.901	0.948	24.773	0.124	0.124	0.000	0.000	0.000	0.000
24	A	348	PHE	0	0.029	0.003	20.618	-0.016	-0.016	0.000	0.000	0.000	0.000
25	A	349	THR	0	0.022	0.009	20.404	-0.016	-0.016	0.000	0.000	0.000	0.000
26	A	350	ASP	-1	-0.853	-0.912	19.851	-0.172	-0.172	0.000	0.000	0.000	0.000
27	A	351	PHE	0	-0.029	-0.016	20.811	-0.026	-0.026	0.000	0.000	0.000	0.000
28	A	352	LEU	0	0.031	0.001	16.399	-0.028	-0.028	0.000	0.000	0.000	0.000
29	A	353	GLN	0	0.017	0.017	15.921	-0.032	-0.032	0.000	0.000	0.000	0.000
30	A	354	ASN	0	-0.075	-0.039	16.255	-0.056	-0.056	0.000	0.000	0.000	0.000
31	A	355	TYR	0	-0.056	-0.029	18.522	-0.029	-0.029	0.000	0.000	0.000	0.000
32	A	356	CYS	0	-0.032	-0.014	16.297	-0.013	-0.013	0.000	0.000	0.000	0.000
33	A	357	ARG	1	0.840	0.940	11.847	0.416	0.416	0.000	0.000	0.000	0.000
34	A	358	SER	0	0.025	0.009	11.762	-0.096	-0.096	0.000	0.000	0.000	0.000
35	A	359	GLU	-1	-0.820	-0.902	7.883	-0.083	-0.083	0.000	0.000	0.000	0.000
36	A	360	VAL	0	-0.041	-0.019	12.012	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	361	ILE	0	-0.026	-0.007	11.526	0.037	0.037	0.000	0.000	0.000	0.000
38	A	362	LEU	0	0.036	0.006	15.800	-0.009	-0.009	0.000	0.000	0.000	0.000
39	A	363	GLH	0	0.009	-0.036	19.553	0.013	0.013	0.000	0.000	0.000	0.000
40	A	364	ALA	0	-0.037	-0.019	22.285	0.011	0.011	0.000	0.000	0.000	0.000
41	A	365	TRP	0	-0.036	-0.023	17.770	0.003	0.003	0.000	0.000	0.000	0.000
42	A	366	GLN	0	0.024	0.014	15.034	0.026	0.026	0.000	0.000	0.000	0.000
43	A	367	ALA	0	0.041	0.021	20.593	0.007	0.007	0.000	0.000	0.000	0.000
44	A	368	ALA	0	0.026	0.012	22.387	0.002	0.002	0.000	0.000	0.000	0.000
45	A	369	ALA	0	0.059	0.028	19.202	0.006	0.006	0.000	0.000	0.000	0.000
46	A	370	ILE	0	0.001	-0.002	21.161	0.002	0.002	0.000	0.000	0.000	0.000
47	A	371	ALA	0	-0.061	-0.024	23.465	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	372	GLU	-1	-0.956	-0.972	23.253	0.129	0.129	0.000	0.000	0.000	0.000
49	A	373	MET	0	-0.090	-0.026	18.012	0.007	0.007	0.000	0.000	0.000	0.000
50	A	374	GLY	0	0.043	0.030	23.560	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	375	PRO	0	0.016	-0.020	24.000	0.004	0.004	0.000	0.000	0.000	0.000
52	A	376	VAL	0	0.036	0.017	23.462	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	377	GLN	0	0.059	0.031	20.404	-0.005	-0.005	0.000	0.000	0.000	0.000
54	A	378	TRP	0	0.014	-0.002	18.295	0.003	0.003	0.000	0.000	0.000	0.000
55	A	379	LEU	0	0.015	0.003	18.410	0.000	0.000	0.000	0.000	0.000	0.000
56	A	380	THR	0	-0.026	-0.014	18.230	-0.013	-0.013	0.000	0.000	0.000	0.000
57	A	381	THR	0	-0.023	-0.023	14.841	0.010	0.010	0.000	0.000	0.000	0.000
58	A	382	GLN	0	0.014	0.005	13.965	0.007	0.007	0.000	0.000	0.000	0.000
59	A	383	LYS	1	0.850	0.935	13.525	-0.039	-0.039	0.000	0.000	0.000	0.000
60	A	384	GLN	0	-0.084	-0.052	12.857	-0.034	-0.034	0.000	0.000	0.000	0.000
61	A	385	ALA	0	-0.016	0.006	9.559	0.010	0.010	0.000	0.000	0.000	0.000
62	A	386	ALA	0	-0.031	-0.002	8.737	-0.048	-0.048	0.000	0.000	0.000	0.000
63	A	387	ASP	-1	-0.804	-0.890	7.236	-0.591	-0.591	0.000	0.000	0.000	0.000
64	A	388	LYS	1	0.788	0.877	10.093	0.327	0.327	0.000	0.000	0.000	0.000
65	A	389	VAL	0	-0.026	-0.013	13.780	0.022	0.022	0.000	0.000	0.000	0.000
66	A	390	VAL	0	-0.007	-0.006	16.772	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	391	PHE	0	0.005	0.010	19.674	0.016	0.016	0.000	0.000	0.000	0.000
68	A	392	LEU	0	-0.029	-0.020	23.201	-0.008	-0.008	0.000	0.000	0.000	0.000
69	A	393	LEU	0	0.000	-0.013	25.129	0.013	0.013	0.000	0.000	0.000	0.000
70	A	394	PRO	0	-0.014	0.001	28.846	-0.007	-0.007	0.000	0.000	0.000	0.000
71	A	395	SER	0	-0.045	-0.031	31.967	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	417	GLN	0	-0.052	-0.010	30.770	0.004	0.004	0.000	0.000	0.000	0.000
73	A	418	ASP	-1	-0.828	-0.898	28.590	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	419	LEU	0	0.043	0.028	23.608	0.003	0.003	0.000	0.000	0.000	0.000
75	A	420	PHE	0	-0.016	0.010	25.971	0.000	0.000	0.000	0.000	0.000	0.000
76	A	421	PRO	0	0.012	0.008	27.038	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	422	LEU	0	-0.001	-0.001	26.328	0.002	0.002	0.000	0.000	0.000	0.000
78	A	423	ALA	0	0.043	0.013	22.687	0.003	0.003	0.000	0.000	0.000	0.000
79	A	424	PHE	0	0.011	0.003	24.083	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	425	ASN	0	-0.068	-0.036	26.282	0.004	0.004	0.000	0.000	0.000	0.000
81	A	426	LEU	0	-0.011	-0.009	23.248	0.002	0.002	0.000	0.000	0.000	0.000
82	A	427	PHE	0	0.013	-0.010	19.564	0.002	0.002	0.000	0.000	0.000	0.000
83	A	428	CYS	0	-0.029	0.001	22.766	-0.005	-0.005	0.000	0.000	0.000	0.000
84	A	429	SER	0	0.019	0.008	24.296	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	430	ASP	-1	-0.854	-0.912	19.900	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	431	PHE	0	-0.066	-0.024	21.157	-0.012	-0.012	0.000	0.000	0.000	0.000
87	A	432	SER	0	0.024	0.009	22.327	-0.010	-0.010	0.000	0.000	0.000	0.000
88	A	433	SER	0	-0.033	-0.009	19.793	0.001	0.001	0.000	0.000	0.000	0.000
89	A	434	GLN	0	0.031	0.001	20.338	-0.021	-0.021	0.000	0.000	0.000	0.000
90	A	435	THR	0	-0.067	-0.026	16.629	-0.008	-0.008	0.000	0.000	0.000	0.000
91	A	436	HIS	0	0.005	0.005	12.405	-0.039	-0.039	0.000	0.000	0.000	0.000
92	A	437	LEU	0	0.035	0.020	15.847	0.000	0.000	0.000	0.000	0.000	0.000
93	A	438	HIS	0	0.031	0.008	16.656	-0.025	-0.025	0.000	0.000	0.000	0.000
94	A	439	LYS	1	0.887	0.959	11.567	0.062	0.062	0.000	0.000	0.000	0.000
95	A	440	TYR	0	-0.029	-0.023	16.184	-0.009	-0.009	0.000	0.000	0.000	0.000
96	A	441	LEU	0	0.001	0.001	17.248	-0.004	-0.004	0.000	0.000	0.000	0.000
97	A	442	VAL	0	0.010	0.009	20.866	0.010	0.010	0.000	0.000	0.000	0.000
98	A	443	VAL	0	-0.025	-0.014	22.069	-0.010	-0.010	0.000	0.000	0.000	0.000
99	A	444	TYR	0	-0.046	-0.024	25.126	0.013	0.013	0.000	0.000	0.000	0.000
100	A	445	LEU	0	0.017	-0.014	26.522	-0.009	-0.009	0.000	0.000	0.000	0.000
101	A	446	GLY	0	0.043	0.026	29.701	0.006	0.006	0.000	0.000	0.000	0.000
102	A	447	GLY	0	0.020	0.014	32.566	0.000	0.000	0.000	0.000	0.000	0.000
103	A	448	ALA	0	-0.012	-0.025	33.885	0.001	0.001	0.000	0.000	0.000	0.000
104	A	449	ASP	-1	-0.934	-0.955	35.967	-0.037	-0.037	0.000	0.000	0.000	0.000
105	A	450	LEU	0	-0.023	-0.015	31.383	0.003	0.003	0.000	0.000	0.000	0.000
106	A	451	LYS	1	0.990	0.982	35.630	0.014	0.014	0.000	0.000	0.000	0.000
107	A	452	GLY	0	-0.060	-0.026	35.089	0.001	0.001	0.000	0.000	0.000	0.000
108	A	453	ASP	-1	-0.818	-0.891	35.369	-0.037	-0.037	0.000	0.000	0.000	0.000
109	A	454	TYR	0	-0.028	-0.042	29.936	0.004	0.004	0.000	0.000	0.000	0.000
110	A	455	ASN	0	0.023	-0.008	30.835	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	456	ALA	0	0.025	0.022	28.782	-0.005	-0.005	0.000	0.000	0.000	0.000
112	A	457	LEU	0	0.037	0.012	25.678	-0.005	-0.005	0.000	0.000	0.000	0.000
113	A	458	SER	0	-0.063	-0.030	27.408	-0.009	-0.009	0.000	0.000	0.000	0.000
114	A	459	VAL	0	-0.027	-0.013	25.806	-0.004	-0.004	0.000	0.000	0.000	0.000
115	A	460	CYS	0	-0.052	0.001	23.213	-0.005	-0.005	0.000	0.000	0.000	0.000
116	A	461	PRO	0	0.019	0.015	21.116	0.003	0.003	0.000	0.000	0.000	0.000
117	A	462	GLN	0	-0.029	-0.016	24.121	0.008	0.008	0.000	0.000	0.000	0.000
118	A	463	TYR	0	-0.009	-0.003	21.661	-0.011	-0.011	0.000	0.000	0.000	0.000
119	A	464	HIS	0	0.021	0.006	26.165	0.009	0.009	0.000	0.000	0.000	0.000
120	A	465	LEU	0	-0.032	0.027	23.510	-0.008	-0.008	0.000	0.000	0.000	0.000
121	A	466	MET	0	0.007	-0.032	25.347	0.012	0.012	0.000	0.000	0.000	0.000
122	A	467	LYS	1	0.940	0.965	28.231	0.092	0.092	0.000	0.000	0.000	0.000
123	A	468	ASP	-1	-0.795	-0.884	26.261	-0.150	-0.150	0.000	0.000	0.000	0.000
124	A	469	ALA	0	-0.016	-0.018	24.036	-0.016	-0.016	0.000	0.000	0.000	0.000
125	A	470	THR	0	0.038	0.012	22.448	-0.020	-0.020	0.000	0.000	0.000	0.000
126	A	471	ALA	0	0.015	0.021	21.851	-0.028	-0.028	0.000	0.000	0.000	0.000
127	A	472	PHE	0	0.044	0.010	18.967	-0.020	-0.020	0.000	0.000	0.000	0.000
128	A	473	HIS	0	0.031	0.013	15.987	-0.026	-0.026	0.000	0.000	0.000	0.000
129	A	474	THR	0	-0.034	-0.031	16.966	-0.050	-0.050	0.000	0.000	0.000	0.000
130	A	475	GLU	-1	-0.860	-0.910	16.984	-0.341	-0.341	0.000	0.000	0.000	0.000
131	A	476	LEU	0	0.004	-0.004	14.263	-0.023	-0.023	0.000	0.000	0.000	0.000
132	A	477	LEU	0	0.008	0.005	12.675	-0.084	-0.084	0.000	0.000	0.000	0.000
133	A	478	LYS	1	0.818	0.912	12.381	0.217	0.217	0.000	0.000	0.000	0.000
134	A	479	ALA	0	0.001	-0.006	10.606	-0.026	-0.026	0.000	0.000	0.000	0.000
135	A	480	THR	0	-0.042	-0.004	7.846	-0.052	-0.052	0.000	0.000	0.000	0.000
136	A	481	GLN	0	-0.063	-0.014	8.334	-0.250	-0.250	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:325:LEU)