FMO DATABASE

FMODB ID: 98V12

Calculation Name: 2VY7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VY7

Chain ID: A

ChEMBL ID:

UniProt ID: P31345

Base Structure: X-ray

Registration Date: 2023-09-23

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	157
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1566426.747027
FMO2-HF: Nuclear repulsion	1504490.124352
FMO2-HF: Total energy	-61936.622675
FMO2-MP2: Total energy	-62117.769925

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:537:GLY)

Summations of interaction energy for fragment #1(A:537:GLY)

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.
0.775	5.176	1.882	-3.022	-3.261	-0.014

Interaction energy analysis for fragmet #1(A:537:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.021

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	539	ILE	0	0.074	0.018	3.797	0.240	1.725	-0.007	-0.846	-0.632	0.005
4	A	540	ASN	0	-0.024	-0.012	6.617	0.377	0.377	0.000	0.000	0.000	0.000
5	A	541	GLY	0	0.038	0.023	9.685	0.172	0.172	0.000	0.000	0.000	0.000
6	A	542	PRO	0	0.033	0.008	10.142	-0.057	-0.057	0.000	0.000	0.000	0.000
7	A	543	GLU	-1	-0.786	-0.871	8.995	-0.869	-0.869	0.000	0.000	0.000	0.000
8	A	544	SER	0	-0.045	-0.034	5.822	0.106	0.106	0.000	0.000	0.000	0.000
9	A	545	VAL	0	0.016	0.021	6.177	0.289	0.289	0.000	0.000	0.000	0.000
10	A	546	LEU	0	-0.018	0.004	8.451	0.293	0.293	0.000	0.000	0.000	0.000
11	A	547	VAL	0	0.005	-0.008	4.311	0.194	0.246	-0.001	-0.006	-0.045	0.000
12	A	548	ASN	0	0.023	-0.001	2.800	-1.000	0.403	0.762	-1.088	-1.077	-0.009
13	A	549	THR	0	0.019	0.013	4.863	0.552	0.577	-0.001	-0.004	-0.019	0.000
14	A	550	TYR	0	-0.057	-0.062	8.443	0.081	0.081	0.000	0.000	0.000	0.000
15	A	551	GLN	0	-0.002	0.012	2.615	3.806	5.148	1.130	-1.053	-1.420	-0.010
16	A	552	TRP	0	0.007	0.017	6.615	0.047	0.047	0.000	0.000	0.000	0.000
17	A	553	ILE	0	-0.006	-0.014	8.362	-0.197	-0.197	0.000	0.000	0.000	0.000
18	A	554	ILE	0	-0.026	-0.010	9.692	-0.102	-0.102	0.000	0.000	0.000	0.000
19	A	555	ARG	1	0.885	0.939	4.175	-5.935	-5.841	-0.001	-0.025	-0.068	0.000
20	A	556	ASN	0	-0.045	-0.011	10.796	-0.246	-0.246	0.000	0.000	0.000	0.000
21	A	557	TRP	0	0.073	0.037	13.550	-0.147	-0.147	0.000	0.000	0.000	0.000
22	A	558	GLU	-1	-0.832	-0.939	15.676	0.417	0.417	0.000	0.000	0.000	0.000
23	A	559	THR	0	-0.027	0.006	17.300	-0.070	-0.070	0.000	0.000	0.000	0.000
24	A	560	VAL	0	-0.028	-0.023	14.861	-0.069	-0.069	0.000	0.000	0.000	0.000
25	A	561	LYS	1	0.944	0.986	18.227	-0.460	-0.460	0.000	0.000	0.000	0.000
26	A	562	ILE	0	0.054	0.031	20.850	-0.049	-0.049	0.000	0.000	0.000	0.000
27	A	563	GLN	0	0.003	-0.015	19.425	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	564	TRP	0	0.013	-0.001	21.194	-0.027	-0.027	0.000	0.000	0.000	0.000
29	A	565	SER	0	-0.001	-0.010	23.085	-0.038	-0.038	0.000	0.000	0.000	0.000
30	A	566	GLN	0	-0.015	0.007	26.005	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	567	ASN	0	-0.044	-0.038	25.899	-0.026	-0.026	0.000	0.000	0.000	0.000
32	A	568	PRO	0	0.068	0.041	23.762	0.020	0.020	0.000	0.000	0.000	0.000
33	A	569	THR	0	0.014	-0.001	23.501	0.012	0.012	0.000	0.000	0.000	0.000
34	A	570	MET	0	-0.025	0.006	22.558	0.012	0.012	0.000	0.000	0.000	0.000
35	A	571	LEU	0	0.008	0.006	17.642	0.018	0.018	0.000	0.000	0.000	0.000
36	A	572	TYR	0	-0.029	-0.033	19.365	0.015	0.015	0.000	0.000	0.000	0.000
37	A	573	ASN	0	-0.058	-0.040	20.271	-0.020	-0.020	0.000	0.000	0.000	0.000
38	A	574	LYS	1	0.934	0.994	15.900	-0.553	-0.553	0.000	0.000	0.000	0.000
39	A	575	MET	0	0.047	0.009	16.803	0.011	0.011	0.000	0.000	0.000	0.000
40	A	576	GLU	-1	-0.922	-0.961	10.247	1.017	1.017	0.000	0.000	0.000	0.000
41	A	577	PHE	0	0.026	0.008	12.307	0.007	0.007	0.000	0.000	0.000	0.000
42	A	578	GLU	-1	-0.918	-0.953	14.699	0.108	0.108	0.000	0.000	0.000	0.000
43	A	579	PRO	0	0.000	-0.009	11.247	-0.079	-0.079	0.000	0.000	0.000	0.000
44	A	580	PHE	0	0.062	0.019	11.994	-0.085	-0.085	0.000	0.000	0.000	0.000
45	A	581	GLN	0	0.024	-0.007	13.909	-0.083	-0.083	0.000	0.000	0.000	0.000
46	A	582	SER	0	-0.059	-0.030	16.226	-0.031	-0.031	0.000	0.000	0.000	0.000
47	A	583	LEU	0	-0.021	0.005	12.173	-0.042	-0.042	0.000	0.000	0.000	0.000
48	A	584	VAL	0	0.000	0.022	16.819	-0.019	-0.019	0.000	0.000	0.000	0.000
49	A	585	PRO	0	0.027	0.024	19.685	0.002	0.002	0.000	0.000	0.000	0.000
50	A	586	LYS	1	1.021	0.993	22.969	0.024	0.024	0.000	0.000	0.000	0.000
51	A	587	ALA	0	-0.047	-0.027	24.835	0.011	0.011	0.000	0.000	0.000	0.000
52	A	588	ILE	0	-0.007	-0.003	24.164	0.004	0.004	0.000	0.000	0.000	0.000
53	A	589	ARG	1	0.914	0.974	20.972	0.005	0.005	0.000	0.000	0.000	0.000
54	A	590	GLY	0	0.034	0.015	24.051	0.015	0.015	0.000	0.000	0.000	0.000
55	A	591	GLN	0	0.043	0.013	26.737	0.013	0.013	0.000	0.000	0.000	0.000
56	A	592	TYR	0	-0.009	0.004	21.994	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	593	SER	0	0.024	0.015	23.600	0.013	0.013	0.000	0.000	0.000	0.000
58	A	594	GLY	0	-0.008	-0.009	24.730	0.011	0.011	0.000	0.000	0.000	0.000
59	A	595	PHE	0	-0.006	-0.003	25.474	0.004	0.004	0.000	0.000	0.000	0.000
60	A	596	VAL	0	0.013	0.006	21.688	0.002	0.002	0.000	0.000	0.000	0.000
61	A	597	ARG	1	0.856	0.919	23.525	-0.155	-0.155	0.000	0.000	0.000	0.000
62	A	598	THR	0	0.005	0.015	26.407	0.006	0.006	0.000	0.000	0.000	0.000
63	A	599	LEU	0	-0.009	0.007	25.514	0.000	0.000	0.000	0.000	0.000	0.000
64	A	600	PHE	0	-0.018	-0.028	20.477	0.008	0.008	0.000	0.000	0.000	0.000
65	A	601	GLN	0	-0.084	-0.044	26.696	0.003	0.003	0.000	0.000	0.000	0.000
66	A	602	GLN	0	-0.011	-0.005	29.962	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	603	MET	0	-0.013	-0.019	25.877	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	604	ARG	1	0.854	0.933	25.185	-0.202	-0.202	0.000	0.000	0.000	0.000
69	A	605	ASP	-1	-0.863	-0.909	29.557	0.124	0.124	0.000	0.000	0.000	0.000
70	A	606	VAL	0	-0.064	-0.035	32.790	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	607	LEU	0	-0.046	-0.024	29.648	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	608	GLY	0	0.024	0.033	29.287	0.007	0.007	0.000	0.000	0.000	0.000
73	A	609	THR	0	-0.060	-0.060	24.065	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	610	PHE	0	-0.012	0.015	24.501	0.017	0.017	0.000	0.000	0.000	0.000
75	A	611	ASP	-1	-0.846	-0.923	24.079	0.169	0.169	0.000	0.000	0.000	0.000
76	A	612	THR	0	0.018	0.006	18.074	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	613	THR	0	-0.003	-0.006	17.516	0.037	0.037	0.000	0.000	0.000	0.000
78	A	614	GLN	0	-0.011	-0.018	18.223	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	615	ILE	0	0.021	0.019	19.143	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	616	ILE	0	0.013	0.001	13.562	0.013	0.013	0.000	0.000	0.000	0.000
81	A	617	LYS	1	0.781	0.902	15.554	-0.107	-0.107	0.000	0.000	0.000	0.000
82	A	618	LEU	0	-0.019	-0.015	16.784	-0.025	-0.025	0.000	0.000	0.000	0.000
83	A	619	LEU	0	0.031	0.030	15.799	-0.022	-0.022	0.000	0.000	0.000	0.000
84	A	620	PRO	0	0.040	0.027	13.755	-0.015	-0.015	0.000	0.000	0.000	0.000
85	A	621	PHE	0	-0.019	-0.026	16.312	-0.038	-0.038	0.000	0.000	0.000	0.000
86	A	622	ALA	0	-0.011	0.012	19.444	-0.025	-0.025	0.000	0.000	0.000	0.000
87	A	623	ALA	0	0.039	0.024	18.218	-0.009	-0.009	0.000	0.000	0.000	0.000
88	A	624	ALA	0	-0.031	-0.001	20.267	-0.010	-0.010	0.000	0.000	0.000	0.000
89	A	625	PRO	0	0.012	0.010	22.743	0.005	0.005	0.000	0.000	0.000	0.000
90	A	626	PRO	0	-0.034	0.000	26.311	-0.013	-0.013	0.000	0.000	0.000	0.000
91	A	627	LYS	1	0.942	0.965	27.966	-0.040	-0.040	0.000	0.000	0.000	0.000
92	A	628	GLN	0	0.060	0.022	30.271	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	629	SER	0	-0.014	-0.009	31.977	-0.009	-0.009	0.000	0.000	0.000	0.000
94	A	630	ARG	1	1.017	0.996	33.886	-0.033	-0.033	0.000	0.000	0.000	0.000
95	A	631	MET	0	-0.038	-0.008	31.679	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	632	GLN	0	0.036	0.020	31.201	0.011	0.011	0.000	0.000	0.000	0.000
97	A	633	PHE	0	-0.013	0.000	26.824	-0.009	-0.009	0.000	0.000	0.000	0.000
98	A	634	SER	0	0.057	0.025	27.843	0.007	0.007	0.000	0.000	0.000	0.000
99	A	635	SER	0	-0.073	-0.043	23.580	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	636	LEU	0	-0.015	0.007	20.802	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	637	THR	0	-0.006	0.003	20.442	-0.013	-0.013	0.000	0.000	0.000	0.000
102	A	638	VAL	0	0.026	0.008	15.220	0.019	0.019	0.000	0.000	0.000	0.000
103	A	639	ASN	0	-0.030	-0.027	18.017	-0.023	-0.023	0.000	0.000	0.000	0.000
104	A	640	VAL	0	0.028	0.015	13.218	-0.033	-0.033	0.000	0.000	0.000	0.000
105	A	641	ARG	1	0.832	0.881	12.697	0.618	0.618	0.000	0.000	0.000	0.000
106	A	642	GLY	0	0.072	0.042	17.590	0.000	0.000	0.000	0.000	0.000	0.000
107	A	643	SER	0	-0.024	-0.006	20.905	0.001	0.001	0.000	0.000	0.000	0.000
108	A	644	GLY	0	0.006	0.004	21.069	0.023	0.023	0.000	0.000	0.000	0.000
109	A	645	MET	0	-0.055	-0.022	17.664	-0.018	-0.018	0.000	0.000	0.000	0.000
110	A	646	ARG	1	0.975	0.983	19.298	0.082	0.082	0.000	0.000	0.000	0.000
111	A	647	ILE	0	0.025	0.023	15.272	-0.016	-0.016	0.000	0.000	0.000	0.000
112	A	648	LEU	0	0.008	-0.003	19.501	0.007	0.007	0.000	0.000	0.000	0.000
113	A	649	VAL	0	0.050	0.020	21.661	0.016	0.016	0.000	0.000	0.000	0.000
114	A	650	ARG	1	0.968	0.995	23.252	-0.024	-0.024	0.000	0.000	0.000	0.000
115	A	651	GLY	0	0.012	0.004	23.189	-0.014	-0.014	0.000	0.000	0.000	0.000
116	A	652	ASN	0	0.009	0.003	19.433	0.022	0.022	0.000	0.000	0.000	0.000
117	A	653	SER	0	-0.020	-0.028	18.875	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	654	PRO	0	0.015	-0.003	18.078	0.001	0.001	0.000	0.000	0.000	0.000
119	A	655	VAL	0	-0.020	0.010	14.169	-0.039	-0.039	0.000	0.000	0.000	0.000
120	A	656	PHE	0	0.055	0.032	13.724	-0.020	-0.020	0.000	0.000	0.000	0.000
121	A	657	ASN	0	-0.022	-0.015	14.706	0.026	0.026	0.000	0.000	0.000	0.000
122	A	658	TYR	0	0.060	0.036	15.323	0.006	0.006	0.000	0.000	0.000	0.000
123	A	659	ASN	0	0.039	0.018	17.032	-0.026	-0.026	0.000	0.000	0.000	0.000
124	A	660	LYS	1	1.008	1.006	18.962	-0.047	-0.047	0.000	0.000	0.000	0.000
125	A	661	THR	0	0.041	0.033	21.598	0.007	0.007	0.000	0.000	0.000	0.000
126	A	662	THR	0	0.004	-0.019	16.765	0.020	0.020	0.000	0.000	0.000	0.000
127	A	663	LYS	1	0.924	0.984	17.531	-0.145	-0.145	0.000	0.000	0.000	0.000
128	A	664	ARG	1	0.846	0.903	9.332	-0.384	-0.384	0.000	0.000	0.000	0.000
129	A	665	LEU	0	-0.025	-0.002	11.180	-0.080	-0.080	0.000	0.000	0.000	0.000
130	A	666	THR	0	-0.033	-0.008	10.990	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	667	ILE	0	-0.023	-0.017	8.959	0.047	0.047	0.000	0.000	0.000	0.000
132	A	668	LEU	0	-0.026	-0.024	10.075	-0.152	-0.152	0.000	0.000	0.000	0.000
133	A	669	GLY	0	-0.014	-0.013	11.917	-0.112	-0.112	0.000	0.000	0.000	0.000
134	A	670	LYS	1	0.909	0.980	7.176	1.796	1.796	0.000	0.000	0.000	0.000
135	A	671	ASP	-1	-0.757	-0.854	7.609	0.646	0.646	0.000	0.000	0.000	0.000
136	A	672	ALA	0	-0.013	-0.023	6.367	-0.076	-0.076	0.000	0.000	0.000	0.000
137	A	673	GLY	0	0.021	0.008	7.657	0.495	0.495	0.000	0.000	0.000	0.000
138	A	674	THR	0	-0.042	-0.030	9.889	-0.220	-0.220	0.000	0.000	0.000	0.000
139	A	675	LEU	0	-0.037	-0.018	13.376	0.096	0.096	0.000	0.000	0.000	0.000
140	A	676	ILE	0	0.052	0.033	15.795	-0.026	-0.026	0.000	0.000	0.000	0.000
141	A	677	GLU	-1	-0.934	-0.990	19.008	0.196	0.196	0.000	0.000	0.000	0.000
142	A	678	ASP	-1	-0.852	-0.914	21.742	0.193	0.193	0.000	0.000	0.000	0.000
143	A	679	PRO	0	-0.096	-0.051	23.515	0.021	0.021	0.000	0.000	0.000	0.000
144	A	680	ASP	-1	-0.887	-0.934	24.538	0.215	0.215	0.000	0.000	0.000	0.000
145	A	681	GLU	-1	-0.959	-0.985	20.890	0.305	0.305	0.000	0.000	0.000	0.000
146	A	682	SER	0	0.008	-0.007	23.997	0.022	0.022	0.000	0.000	0.000	0.000
147	A	683	THR	0	-0.090	-0.042	21.958	0.023	0.023	0.000	0.000	0.000	0.000
148	A	684	SER	0	0.036	0.035	17.124	-0.017	-0.017	0.000	0.000	0.000	0.000
149	A	685	GLY	0	-0.034	-0.025	17.512	-0.012	-0.012	0.000	0.000	0.000	0.000
150	A	686	VAL	0	-0.073	-0.047	18.254	-0.028	-0.028	0.000	0.000	0.000	0.000
151	A	687	GLU	-1	-0.854	-0.928	20.305	0.116	0.116	0.000	0.000	0.000	0.000
152	A	688	SER	0	0.017	-0.003	23.957	-0.010	-0.010	0.000	0.000	0.000	0.000
153	A	689	ALA	0	0.007	0.007	26.967	-0.006	-0.006	0.000	0.000	0.000	0.000
154	A	690	VAL	0	0.023	0.025	22.530	-0.013	-0.013	0.000	0.000	0.000	0.000
155	A	691	LEU	0	-0.014	-0.012	23.743	-0.016	-0.016	0.000	0.000	0.000	0.000
156	A	692	ARG	1	0.854	0.917	25.777	-0.008	-0.008	0.000	0.000	0.000	0.000
157	A	693	GLY	0	0.054	0.039	27.670	0.005	0.005	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:537:GLY)