FMO DATABASE

FMODB ID: MN1QZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1566525.032563
FMO2-HF: Nuclear repulsion	1504587.85492
FMO2-HF: Total energy	-61937.177643
FMO2-MP2: Total energy	-62118.290477

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.
-1.179	3.149	3.279	-3.671	-3.937	-0.018

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 : 0.031 / 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	0.079	0.020	3.797	0.160	1.642	-0.007	-0.843	-0.633	0.005
4	A	540	ASN	0	-0.032	-0.026	6.620	0.400	0.400	0.000	0.000	0.000	0.000
5	A	541	GLY	0	0.044	0.026	9.685	0.179	0.179	0.000	0.000	0.000	0.000
6	A	542	PRO	0	0.030	0.007	10.139	-0.062	-0.062	0.000	0.000	0.000	0.000
7	A	543	GLU	-1	-0.760	-0.847	9.041	-0.969	-0.969	0.000	0.000	0.000	0.000
8	A	544	SER	0	-0.041	-0.031	5.831	0.096	0.096	0.000	0.000	0.000	0.000
9	A	545	VAL	0	0.010	0.015	6.186	0.275	0.275	0.000	0.000	0.000	0.000
10	A	546	LEU	0	-0.011	0.010	8.461	0.294	0.294	0.000	0.000	0.000	0.000
11	A	547	VAL	0	0.005	-0.006	4.370	0.192	0.242	-0.001	-0.005	-0.043	0.000
12	A	548	ASN	0	0.016	-0.004	2.535	-0.323	0.719	2.186	-1.592	-1.636	-0.014
13	A	549	THR	0	0.018	0.009	4.873	0.552	0.582	-0.001	-0.005	-0.024	0.000
14	A	550	TYR	0	-0.043	-0.051	8.452	0.083	0.083	0.000	0.000	0.000	0.000
15	A	551	GLN	0	-0.005	0.007	2.597	3.608	4.969	1.098	-1.069	-1.390	-0.010
16	A	552	TRP	0	0.009	0.024	6.617	0.054	0.054	0.000	0.000	0.000	0.000
17	A	553	ILE	0	-0.006	-0.013	8.369	-0.198	-0.198	0.000	0.000	0.000	0.000
18	A	554	ILE	0	-0.031	-0.009	9.644	-0.107	-0.107	0.000	0.000	0.000	0.000
19	A	555	ARG	1	0.883	0.932	3.518	-8.402	-8.039	0.004	-0.157	-0.211	0.001
20	A	556	ASN	0	-0.039	-0.011	10.798	-0.249	-0.249	0.000	0.000	0.000	0.000
21	A	557	TRP	0	0.062	0.033	13.554	-0.151	-0.151	0.000	0.000	0.000	0.000
22	A	558	GLU	-1	-0.776	-0.888	15.679	0.406	0.406	0.000	0.000	0.000	0.000
23	A	559	THR	0	-0.021	0.003	17.314	-0.073	-0.073	0.000	0.000	0.000	0.000
24	A	560	VAL	0	-0.032	-0.026	14.929	-0.072	-0.072	0.000	0.000	0.000	0.000
25	A	561	LYS	1	0.879	0.938	18.233	-0.487	-0.487	0.000	0.000	0.000	0.000
26	A	562	ILE	0	0.063	0.041	20.855	-0.050	-0.050	0.000	0.000	0.000	0.000
27	A	563	GLN	0	0.029	0.006	19.811	-0.013	-0.013	0.000	0.000	0.000	0.000
28	A	564	TRP	0	0.024	0.002	21.169	-0.029	-0.029	0.000	0.000	0.000	0.000
29	A	565	SER	0	0.015	-0.002	23.092	-0.037	-0.037	0.000	0.000	0.000	0.000
30	A	566	GLN	0	-0.025	-0.001	25.999	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	567	ASN	0	-0.049	-0.038	25.910	-0.023	-0.023	0.000	0.000	0.000	0.000
32	A	568	PRO	0	0.073	0.043	23.771	0.019	0.019	0.000	0.000	0.000	0.000
33	A	569	THR	0	0.012	-0.001	23.511	0.012	0.012	0.000	0.000	0.000	0.000
34	A	570	MET	0	-0.014	0.013	22.428	0.014	0.014	0.000	0.000	0.000	0.000
35	A	571	LEU	0	0.007	0.004	17.633	0.017	0.017	0.000	0.000	0.000	0.000
36	A	572	TYR	0	-0.019	-0.027	19.375	0.024	0.024	0.000	0.000	0.000	0.000
37	A	573	ASN	0	-0.067	-0.051	20.271	-0.022	-0.022	0.000	0.000	0.000	0.000
38	A	574	LYS	1	0.881	0.966	16.544	-0.510	-0.510	0.000	0.000	0.000	0.000
39	A	575	MET	0	0.067	0.019	16.628	0.010	0.010	0.000	0.000	0.000	0.000
40	A	576	GLU	-1	-0.940	-0.961	9.985	1.033	1.033	0.000	0.000	0.000	0.000
41	A	577	PHE	0	0.020	-0.001	12.300	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	578	GLU	-1	-0.902	-0.949	14.692	0.102	0.102	0.000	0.000	0.000	0.000
43	A	579	PRO	0	-0.002	-0.010	11.140	-0.078	-0.078	0.000	0.000	0.000	0.000
44	A	580	PHE	0	0.059	0.017	11.959	-0.086	-0.086	0.000	0.000	0.000	0.000
45	A	581	GLN	0	0.013	-0.010	13.920	-0.083	-0.083	0.000	0.000	0.000	0.000
46	A	582	SER	0	-0.074	-0.041	16.133	-0.030	-0.030	0.000	0.000	0.000	0.000
47	A	583	LEU	0	-0.012	0.003	12.138	-0.041	-0.041	0.000	0.000	0.000	0.000
48	A	584	VAL	0	0.000	0.024	16.828	-0.017	-0.017	0.000	0.000	0.000	0.000
49	A	585	PRO	0	0.031	0.024	19.694	0.002	0.002	0.000	0.000	0.000	0.000
50	A	586	LYS	1	1.029	1.001	22.978	0.032	0.032	0.000	0.000	0.000	0.000
51	A	587	ALA	0	-0.033	-0.016	24.846	0.012	0.012	0.000	0.000	0.000	0.000
52	A	588	ILE	0	0.000	-0.003	24.351	0.005	0.005	0.000	0.000	0.000	0.000
53	A	589	ARG	1	0.913	0.980	20.899	0.015	0.015	0.000	0.000	0.000	0.000
54	A	590	GLY	0	0.040	0.023	24.060	0.015	0.015	0.000	0.000	0.000	0.000
55	A	591	GLN	0	0.036	0.007	26.747	0.014	0.014	0.000	0.000	0.000	0.000
56	A	592	TYR	0	-0.005	0.005	22.025	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	593	SER	0	0.021	0.008	23.584	0.014	0.014	0.000	0.000	0.000	0.000
58	A	594	GLY	0	0.021	0.007	24.739	0.012	0.012	0.000	0.000	0.000	0.000
59	A	595	PHE	0	-0.008	-0.002	25.605	0.004	0.004	0.000	0.000	0.000	0.000
60	A	596	VAL	0	0.012	0.006	21.637	0.002	0.002	0.000	0.000	0.000	0.000
61	A	597	ARG	1	0.856	0.919	23.400	-0.151	-0.151	0.000	0.000	0.000	0.000
62	A	598	THR	0	-0.003	-0.008	26.415	0.005	0.005	0.000	0.000	0.000	0.000
63	A	599	LEU	0	-0.009	0.008	25.619	0.000	0.000	0.000	0.000	0.000	0.000
64	A	600	PHE	0	0.002	-0.015	20.405	0.007	0.007	0.000	0.000	0.000	0.000
65	A	601	GLN	0	-0.102	-0.056	26.702	0.002	0.002	0.000	0.000	0.000	0.000
66	A	602	GLN	0	0.007	0.009	29.969	-0.007	-0.007	0.000	0.000	0.000	0.000
67	A	603	MET	0	-0.017	-0.021	25.744	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	604	ARG	1	0.835	0.926	25.230	-0.204	-0.204	0.000	0.000	0.000	0.000
69	A	605	ASP	-1	-0.865	-0.914	29.562	0.129	0.129	0.000	0.000	0.000	0.000
70	A	606	VAL	0	-0.055	-0.033	32.787	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	607	LEU	0	-0.051	-0.020	29.331	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	608	GLY	0	0.022	0.028	29.290	0.007	0.007	0.000	0.000	0.000	0.000
73	A	609	THR	0	-0.055	-0.056	24.115	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	610	PHE	0	-0.007	0.016	24.503	0.018	0.018	0.000	0.000	0.000	0.000
75	A	611	ASP	-1	-0.850	-0.923	24.081	0.177	0.177	0.000	0.000	0.000	0.000
76	A	612	THR	0	0.007	-0.003	18.135	0.001	0.001	0.000	0.000	0.000	0.000
77	A	613	THR	0	-0.011	-0.022	17.692	0.038	0.038	0.000	0.000	0.000	0.000
78	A	614	GLN	0	-0.015	-0.020	18.225	-0.005	-0.005	0.000	0.000	0.000	0.000
79	A	615	ILE	0	0.019	0.017	19.162	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	616	ILE	0	0.016	0.003	13.593	0.013	0.013	0.000	0.000	0.000	0.000
81	A	617	LYS	1	0.764	0.887	15.559	-0.110	-0.110	0.000	0.000	0.000	0.000
82	A	618	LEU	0	-0.029	-0.022	16.789	-0.028	-0.028	0.000	0.000	0.000	0.000
83	A	619	LEU	0	0.031	0.029	15.938	-0.023	-0.023	0.000	0.000	0.000	0.000
84	A	620	PRO	0	0.042	0.029	13.757	-0.016	-0.016	0.000	0.000	0.000	0.000
85	A	621	PHE	0	-0.015	-0.021	16.321	-0.040	-0.040	0.000	0.000	0.000	0.000
86	A	622	ALA	0	-0.007	0.011	19.452	-0.026	-0.026	0.000	0.000	0.000	0.000
87	A	623	ALA	0	0.046	0.030	18.279	-0.009	-0.009	0.000	0.000	0.000	0.000
88	A	624	ALA	0	-0.039	0.001	20.277	-0.010	-0.010	0.000	0.000	0.000	0.000
89	A	625	PRO	0	0.023	0.014	22.754	0.006	0.006	0.000	0.000	0.000	0.000
90	A	626	PRO	0	-0.028	0.006	26.312	-0.012	-0.012	0.000	0.000	0.000	0.000
91	A	627	LYS	1	0.905	0.942	27.976	-0.035	-0.035	0.000	0.000	0.000	0.000
92	A	628	GLN	0	0.025	0.007	30.647	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	629	SER	0	-0.029	-0.022	31.881	-0.009	-0.009	0.000	0.000	0.000	0.000
94	A	630	ARG	1	1.020	0.999	33.894	-0.033	-0.033	0.000	0.000	0.000	0.000
95	A	631	MET	0	-0.021	0.008	31.575	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	632	GLN	0	0.009	0.003	31.190	0.011	0.011	0.000	0.000	0.000	0.000
97	A	633	PHE	0	-0.017	-0.002	26.843	-0.009	-0.009	0.000	0.000	0.000	0.000
98	A	634	SER	0	0.062	0.027	27.847	0.008	0.008	0.000	0.000	0.000	0.000
99	A	635	SER	0	-0.052	-0.035	23.598	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	636	LEU	0	-0.016	0.009	20.800	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	637	THR	0	-0.011	0.003	20.446	-0.011	-0.011	0.000	0.000	0.000	0.000
102	A	638	VAL	0	0.038	0.013	15.214	0.019	0.019	0.000	0.000	0.000	0.000
103	A	639	ASN	0	-0.044	-0.032	18.030	-0.019	-0.019	0.000	0.000	0.000	0.000
104	A	640	VAL	0	0.040	0.015	13.187	-0.035	-0.035	0.000	0.000	0.000	0.000
105	A	641	ARG	1	0.830	0.870	12.540	0.644	0.644	0.000	0.000	0.000	0.000
106	A	642	GLY	0	0.062	0.050	17.571	0.003	0.003	0.000	0.000	0.000	0.000
107	A	643	SER	0	-0.019	-0.006	20.972	0.001	0.001	0.000	0.000	0.000	0.000
108	A	644	GLY	0	0.012	0.007	21.077	0.023	0.023	0.000	0.000	0.000	0.000
109	A	645	MET	0	-0.047	-0.018	17.744	-0.016	-0.016	0.000	0.000	0.000	0.000
110	A	646	ARG	1	0.959	0.977	19.290	0.075	0.075	0.000	0.000	0.000	0.000
111	A	647	ILE	0	0.043	0.047	15.150	-0.016	-0.016	0.000	0.000	0.000	0.000
112	A	648	LEU	0	-0.004	-0.010	19.504	0.006	0.006	0.000	0.000	0.000	0.000
113	A	649	VAL	0	0.049	0.023	21.663	0.017	0.017	0.000	0.000	0.000	0.000
114	A	650	ARG	1	0.977	0.996	23.254	-0.025	-0.025	0.000	0.000	0.000	0.000
115	A	651	GLY	0	0.027	0.013	23.187	-0.015	-0.015	0.000	0.000	0.000	0.000
116	A	652	ASN	0	0.004	0.000	19.540	0.023	0.023	0.000	0.000	0.000	0.000
117	A	653	SER	0	-0.044	-0.053	18.972	-0.008	-0.008	0.000	0.000	0.000	0.000
118	A	654	PRO	0	0.024	0.002	18.076	0.002	0.002	0.000	0.000	0.000	0.000
119	A	655	VAL	0	-0.028	0.004	14.370	-0.039	-0.039	0.000	0.000	0.000	0.000
120	A	656	PHE	0	0.057	0.033	13.723	-0.019	-0.019	0.000	0.000	0.000	0.000
121	A	657	ASN	0	-0.020	-0.020	14.702	0.022	0.022	0.000	0.000	0.000	0.000
122	A	658	TYR	0	0.011	-0.013	15.319	0.008	0.008	0.000	0.000	0.000	0.000
123	A	659	ASN	0	0.040	0.032	17.026	-0.022	-0.022	0.000	0.000	0.000	0.000
124	A	660	LYS	1	0.921	0.951	18.956	-0.070	-0.070	0.000	0.000	0.000	0.000
125	A	661	THR	0	-0.002	0.007	21.525	0.007	0.007	0.000	0.000	0.000	0.000
126	A	662	THR	0	-0.007	-0.020	16.715	0.019	0.019	0.000	0.000	0.000	0.000
127	A	663	LYS	1	0.923	0.982	17.578	-0.156	-0.156	0.000	0.000	0.000	0.000
128	A	664	ARG	1	0.846	0.893	9.266	-0.475	-0.475	0.000	0.000	0.000	0.000
129	A	665	LEU	0	-0.022	-0.003	11.287	-0.086	-0.086	0.000	0.000	0.000	0.000
130	A	666	THR	0	-0.031	-0.007	10.984	0.011	0.011	0.000	0.000	0.000	0.000
131	A	667	ILE	0	-0.022	-0.017	8.982	0.039	0.039	0.000	0.000	0.000	0.000
132	A	668	LEU	0	-0.026	-0.022	10.072	-0.158	-0.158	0.000	0.000	0.000	0.000
133	A	669	GLY	0	-0.012	-0.010	11.913	-0.117	-0.117	0.000	0.000	0.000	0.000
134	A	670	LYS	1	0.828	0.925	7.143	1.843	1.843	0.000	0.000	0.000	0.000
135	A	671	ASP	-1	-0.771	-0.852	7.694	0.767	0.767	0.000	0.000	0.000	0.000
136	A	672	ALA	0	-0.008	-0.022	6.359	-0.047	-0.047	0.000	0.000	0.000	0.000
137	A	673	GLY	0	0.031	0.016	7.652	0.509	0.509	0.000	0.000	0.000	0.000
138	A	674	THR	0	-0.032	-0.027	9.883	-0.189	-0.189	0.000	0.000	0.000	0.000
139	A	675	LEU	0	-0.031	-0.009	13.418	0.096	0.096	0.000	0.000	0.000	0.000
140	A	676	ILE	0	0.043	0.021	15.792	-0.026	-0.026	0.000	0.000	0.000	0.000
141	A	677	GLU	-1	-0.860	-0.912	19.005	0.216	0.216	0.000	0.000	0.000	0.000
142	A	678	ASP	-1	-0.851	-0.921	21.740	0.200	0.200	0.000	0.000	0.000	0.000
143	A	679	PRO	0	-0.093	-0.043	23.514	0.023	0.023	0.000	0.000	0.000	0.000
144	A	680	ASP	-1	-0.879	-0.933	24.537	0.223	0.223	0.000	0.000	0.000	0.000
145	A	681	GLU	-1	-0.963	-0.982	21.015	0.319	0.319	0.000	0.000	0.000	0.000
146	A	682	SER	0	-0.004	-0.012	24.055	0.022	0.022	0.000	0.000	0.000	0.000
147	A	683	THR	0	-0.075	-0.035	22.133	0.024	0.024	0.000	0.000	0.000	0.000
148	A	684	SER	0	0.041	0.033	17.520	-0.010	-0.010	0.000	0.000	0.000	0.000
149	A	685	GLY	0	-0.042	-0.027	17.565	-0.010	-0.010	0.000	0.000	0.000	0.000
150	A	686	VAL	0	-0.058	-0.040	18.304	-0.030	-0.030	0.000	0.000	0.000	0.000
151	A	687	GLU	-1	-0.743	-0.866	20.349	0.118	0.118	0.000	0.000	0.000	0.000
152	A	688	SER	0	0.039	0.006	24.003	-0.010	-0.010	0.000	0.000	0.000	0.000
153	A	689	ALA	0	0.004	0.002	27.010	-0.005	-0.005	0.000	0.000	0.000	0.000
154	A	690	VAL	0	0.015	0.029	22.509	-0.013	-0.013	0.000	0.000	0.000	0.000
155	A	691	LEU	0	-0.007	-0.011	23.662	-0.017	-0.017	0.000	0.000	0.000	0.000
156	A	692	ARG	1	0.862	0.919	25.806	-0.019	-0.019	0.000	0.000	0.000	0.000
157	A	693	GLY	0	0.049	0.038	27.688	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:537:GLY)