FMO DATABASE

FMODB ID: ZYK6N

Calculation Name: 2VSZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VSZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q92556

Base Structure: X-ray

Registration Date: 2023-06-19

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	147
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1318213.278015
FMO2-HF: Nuclear repulsion	1258834.748903
FMO2-HF: Total energy	-59378.529112
FMO2-MP2: Total energy	-59550.99067

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:527:GLY)

Summations of interaction energy for fragment #1(A:527: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.
9.509	0.73	0.013	9.541	-0.775	-0.009

Interaction energy analysis for fragmet #1(A:527:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : 0.036

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	529	LEU	0	0.014	-0.010	2.594	11.675	2.867	0.015	9.608	-0.815	-0.009
4	A	530	GLY	0	0.019	0.025	4.104	-1.698	-1.734	-0.001	-0.063	0.099	0.000
5	A	531	SER	0	0.020	-0.005	4.857	0.250	0.315	-0.001	-0.004	-0.059	0.000
6	A	532	PRO	0	0.096	0.043	5.295	-0.123	-0.123	0.000	0.000	0.000	0.000
7	A	533	ILE	0	-0.050	-0.017	8.428	0.018	0.018	0.000	0.000	0.000	0.000
8	A	534	LEU	0	-0.003	-0.008	9.754	0.025	0.025	0.000	0.000	0.000	0.000
9	A	535	GLU	-1	-0.890	-0.938	8.568	-0.537	-0.537	0.000	0.000	0.000	0.000
10	A	536	LEU	0	0.024	0.019	12.741	0.025	0.025	0.000	0.000	0.000	0.000
11	A	537	LYS	1	0.890	0.944	15.895	0.226	0.226	0.000	0.000	0.000	0.000
12	A	538	GLU	-1	-0.911	-0.981	12.245	-0.697	-0.697	0.000	0.000	0.000	0.000
13	A	539	LYS	1	0.901	0.966	12.949	0.378	0.378	0.000	0.000	0.000	0.000
14	A	540	ILE	0	0.036	0.020	15.869	0.029	0.029	0.000	0.000	0.000	0.000
15	A	541	GLN	0	-0.053	-0.034	18.206	0.002	0.002	0.000	0.000	0.000	0.000
16	A	542	PRO	0	0.031	0.008	18.489	0.019	0.019	0.000	0.000	0.000	0.000
17	A	543	GLU	-1	-0.867	-0.939	17.644	-0.264	-0.264	0.000	0.000	0.000	0.000
18	A	544	ILE	0	-0.002	0.010	21.557	0.020	0.020	0.000	0.000	0.000	0.000
19	A	545	LEU	0	-0.029	-0.018	23.992	0.011	0.011	0.000	0.000	0.000	0.000
20	A	546	GLU	-1	-0.841	-0.912	24.299	-0.159	-0.159	0.000	0.000	0.000	0.000
21	A	547	LEU	0	-0.024	-0.025	24.639	0.012	0.012	0.000	0.000	0.000	0.000
22	A	548	ILE	0	-0.008	0.003	27.431	0.012	0.012	0.000	0.000	0.000	0.000
23	A	549	LYS	1	0.937	0.966	29.433	0.155	0.155	0.000	0.000	0.000	0.000
24	A	550	GLN	0	-0.023	-0.026	28.939	0.016	0.016	0.000	0.000	0.000	0.000
25	A	551	GLN	0	-0.001	0.020	31.490	0.003	0.003	0.000	0.000	0.000	0.000
26	A	552	ARG	1	0.820	0.900	33.460	0.088	0.088	0.000	0.000	0.000	0.000
27	A	553	LEU	0	-0.004	-0.004	33.153	0.003	0.003	0.000	0.000	0.000	0.000
28	A	554	ASN	0	0.024	-0.014	33.169	0.002	0.002	0.000	0.000	0.000	0.000
29	A	555	ARG	1	0.901	0.957	36.963	0.061	0.061	0.000	0.000	0.000	0.000
30	A	556	LEU	0	0.029	0.026	39.732	0.003	0.003	0.000	0.000	0.000	0.000
31	A	557	VAL	0	-0.117	-0.027	37.790	0.001	0.001	0.000	0.000	0.000	0.000
32	A	558	GLU	-1	-0.916	-0.948	40.982	-0.044	-0.044	0.000	0.000	0.000	0.000
33	A	559	GLY	0	-0.035	-0.011	42.834	0.002	0.002	0.000	0.000	0.000	0.000
34	A	560	THR	0	0.005	0.005	45.551	0.001	0.001	0.000	0.000	0.000	0.000
35	A	561	CYS	0	-0.026	0.002	48.705	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	562	PHE	0	0.022	0.000	49.605	0.002	0.002	0.000	0.000	0.000	0.000
37	A	563	ARG	1	0.978	0.981	54.735	0.025	0.025	0.000	0.000	0.000	0.000
38	A	564	LYS	1	0.847	0.919	58.496	0.033	0.033	0.000	0.000	0.000	0.000
39	A	565	LEU	0	-0.026	-0.016	59.494	0.002	0.002	0.000	0.000	0.000	0.000
40	A	566	ASN	0	-0.025	-0.014	62.762	0.002	0.002	0.000	0.000	0.000	0.000
41	A	567	ALA	0	0.007	0.008	64.396	0.000	0.000	0.000	0.000	0.000	0.000
42	A	568	ARG	1	0.943	0.970	66.142	0.025	0.025	0.000	0.000	0.000	0.000
43	A	569	ARG	1	0.933	0.983	66.641	0.026	0.026	0.000	0.000	0.000	0.000
44	A	570	ARG	1	0.978	0.979	69.593	0.019	0.019	0.000	0.000	0.000	0.000
45	A	571	GLN	0	-0.003	-0.007	65.653	0.000	0.000	0.000	0.000	0.000	0.000
46	A	572	ASP	-1	-0.858	-0.913	62.596	-0.022	-0.022	0.000	0.000	0.000	0.000
47	A	573	LYS	1	0.883	0.936	61.986	0.026	0.026	0.000	0.000	0.000	0.000
48	A	574	PHE	0	0.041	0.007	56.809	0.001	0.001	0.000	0.000	0.000	0.000
49	A	575	TRP	0	-0.003	0.008	52.092	0.000	0.000	0.000	0.000	0.000	0.000
50	A	576	TYR	0	0.025	-0.002	46.957	0.002	0.002	0.000	0.000	0.000	0.000
51	A	577	CYS	0	-0.047	-0.004	48.728	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	578	ARG	1	0.882	0.923	42.294	0.062	0.062	0.000	0.000	0.000	0.000
53	A	579	LEU	0	-0.052	-0.013	38.421	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	580	SER	0	0.047	0.011	40.849	0.001	0.001	0.000	0.000	0.000	0.000
55	A	581	PRO	0	0.054	0.016	38.601	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	582	ASN	0	-0.020	-0.007	36.016	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	583	HIS	1	0.842	0.908	33.597	0.096	0.096	0.000	0.000	0.000	0.000
58	A	584	LYS	1	0.987	1.001	35.427	0.127	0.127	0.000	0.000	0.000	0.000
59	A	585	VAL	0	-0.009	0.008	39.892	0.001	0.001	0.000	0.000	0.000	0.000
60	A	586	LEU	0	0.018	0.015	43.567	0.001	0.001	0.000	0.000	0.000	0.000
61	A	587	HIS	0	0.028	0.006	45.312	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	588	TYR	0	0.045	-0.009	48.309	0.000	0.000	0.000	0.000	0.000	0.000
63	A	589	GLY	0	-0.002	0.001	51.502	0.000	0.000	0.000	0.000	0.000	0.000
64	A	590	ASP	-1	-0.831	-0.919	54.999	-0.035	-0.035	0.000	0.000	0.000	0.000
65	A	591	LEU	0	-0.036	-0.011	53.387	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	592	GLU	-1	-0.996	-1.011	57.815	-0.028	-0.028	0.000	0.000	0.000	0.000
67	A	593	GLU	-1	-0.940	-0.976	58.785	-0.023	-0.023	0.000	0.000	0.000	0.000
68	A	594	SER	0	-0.008	-0.009	55.447	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	595	PRO	0	-0.010	0.009	51.848	0.001	0.001	0.000	0.000	0.000	0.000
70	A	596	GLN	0	-0.018	-0.021	52.645	0.000	0.000	0.000	0.000	0.000	0.000
71	A	597	GLY	0	-0.002	-0.011	48.986	0.001	0.001	0.000	0.000	0.000	0.000
72	A	598	GLU	-1	-0.852	-0.902	44.637	-0.054	-0.054	0.000	0.000	0.000	0.000
73	A	599	VAL	0	0.011	0.012	47.475	0.002	0.002	0.000	0.000	0.000	0.000
74	A	600	PRO	0	0.004	0.007	47.157	-0.004	-0.004	0.000	0.000	0.000	0.000
75	A	601	HIS	0	0.023	-0.004	43.587	0.002	0.002	0.000	0.000	0.000	0.000
76	A	602	ASP	-1	-0.929	-0.972	46.730	-0.065	-0.065	0.000	0.000	0.000	0.000
77	A	603	SER	0	-0.081	-0.038	49.113	0.001	0.001	0.000	0.000	0.000	0.000
78	A	604	LEU	0	-0.067	-0.013	49.328	0.002	0.002	0.000	0.000	0.000	0.000
79	A	605	GLN	0	0.052	0.047	52.836	0.000	0.000	0.000	0.000	0.000	0.000
80	A	606	ASP	-1	-0.906	-0.946	53.405	-0.048	-0.048	0.000	0.000	0.000	0.000
81	A	607	LYS	1	0.912	0.933	48.290	0.065	0.065	0.000	0.000	0.000	0.000
82	A	608	LEU	0	0.005	0.013	47.545	0.001	0.001	0.000	0.000	0.000	0.000
83	A	609	PRO	0	-0.006	0.004	44.760	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	610	VAL	0	0.050	0.014	39.928	0.002	0.002	0.000	0.000	0.000	0.000
85	A	611	ALA	0	-0.066	-0.030	41.644	0.000	0.000	0.000	0.000	0.000	0.000
86	A	612	ASP	-1	-0.856	-0.924	42.762	-0.079	-0.079	0.000	0.000	0.000	0.000
87	A	613	ILE	0	-0.083	-0.046	43.697	0.005	0.005	0.000	0.000	0.000	0.000
88	A	614	LYS	1	0.860	0.952	44.856	0.057	0.057	0.000	0.000	0.000	0.000
89	A	615	ALA	0	0.000	-0.011	45.611	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	616	VAL	0	0.017	0.017	44.982	0.002	0.002	0.000	0.000	0.000	0.000
91	A	617	VAL	0	-0.018	0.000	47.249	0.000	0.000	0.000	0.000	0.000	0.000
92	A	618	THR	0	0.070	0.012	48.059	0.000	0.000	0.000	0.000	0.000	0.000
93	A	619	GLY	0	0.060	0.036	51.013	0.001	0.001	0.000	0.000	0.000	0.000
94	A	620	LYS	1	0.959	0.956	54.291	0.035	0.035	0.000	0.000	0.000	0.000
95	A	621	ASP	-1	-0.954	-0.971	52.741	-0.041	-0.041	0.000	0.000	0.000	0.000
96	A	622	CYS	0	-0.070	0.003	53.339	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	623	PRO	0	0.027	0.005	55.505	0.002	0.002	0.000	0.000	0.000	0.000
98	A	624	HIS	0	-0.063	-0.033	55.159	0.001	0.001	0.000	0.000	0.000	0.000
99	A	625	MET	0	-0.034	-0.007	57.212	0.002	0.002	0.000	0.000	0.000	0.000
100	A	626	LYS	1	0.890	0.957	58.061	0.038	0.038	0.000	0.000	0.000	0.000
101	A	627	GLU	-1	-0.774	-0.895	62.558	-0.024	-0.024	0.000	0.000	0.000	0.000
102	A	628	LYS	1	0.756	0.871	61.258	0.025	0.025	0.000	0.000	0.000	0.000
103	A	629	GLY	0	0.098	0.068	64.963	0.001	0.001	0.000	0.000	0.000	0.000
104	A	630	ALA	0	0.023	0.011	65.993	0.001	0.001	0.000	0.000	0.000	0.000
105	A	631	LEU	0	-0.021	0.002	65.864	0.000	0.000	0.000	0.000	0.000	0.000
106	A	632	LYS	1	0.952	0.963	65.287	0.014	0.014	0.000	0.000	0.000	0.000
107	A	633	GLN	0	-0.017	-0.007	64.342	0.001	0.001	0.000	0.000	0.000	0.000
108	A	634	ASN	0	0.049	0.032	61.747	0.001	0.001	0.000	0.000	0.000	0.000
109	A	635	LYS	1	0.933	0.929	59.125	0.019	0.019	0.000	0.000	0.000	0.000
110	A	636	GLU	-1	-0.899	-0.931	57.665	-0.021	-0.021	0.000	0.000	0.000	0.000
111	A	637	VAL	0	0.013	0.002	56.906	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	638	LEU	0	-0.035	-0.027	56.539	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	639	GLU	-1	-0.991	-0.997	53.066	-0.028	-0.028	0.000	0.000	0.000	0.000
114	A	640	LEU	0	-0.001	0.016	52.044	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	641	ALA	0	-0.044	-0.003	53.008	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	642	PHE	0	0.025	-0.012	48.619	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	643	SER	0	-0.014	-0.041	51.001	0.002	0.002	0.000	0.000	0.000	0.000
118	A	644	ILE	0	0.007	0.013	46.999	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	645	LEU	0	-0.023	-0.021	49.556	0.002	0.002	0.000	0.000	0.000	0.000
120	A	646	TYR	0	0.056	0.016	49.204	-0.003	-0.003	0.000	0.000	0.000	0.000
121	A	647	ASP	-1	-0.844	-0.917	50.239	-0.060	-0.060	0.000	0.000	0.000	0.000
122	A	648	SER	0	-0.021	-0.021	52.156	0.000	0.000	0.000	0.000	0.000	0.000
123	A	649	ASN	0	-0.087	-0.070	54.882	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	650	CYS	0	0.009	0.044	54.447	0.003	0.003	0.000	0.000	0.000	0.000
125	A	651	GLN	0	-0.021	-0.023	53.778	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	652	LEU	0	0.001	0.029	50.448	0.002	0.002	0.000	0.000	0.000	0.000
127	A	653	ASN	0	0.030	0.020	52.766	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	654	PHE	0	0.054	0.028	49.827	0.000	0.000	0.000	0.000	0.000	0.000
129	A	655	ILE	0	-0.033	-0.029	54.163	0.001	0.001	0.000	0.000	0.000	0.000
130	A	656	ALA	0	-0.013	-0.005	50.969	0.000	0.000	0.000	0.000	0.000	0.000
131	A	657	PRO	0	0.009	0.006	51.758	0.002	0.002	0.000	0.000	0.000	0.000
132	A	658	ASP	-1	-0.811	-0.904	50.166	-0.027	-0.027	0.000	0.000	0.000	0.000
133	A	659	LYS	1	1.004	0.986	48.807	0.019	0.019	0.000	0.000	0.000	0.000
134	A	660	HIS	0	-0.007	-0.005	46.283	-0.003	-0.003	0.000	0.000	0.000	0.000
135	A	661	GLU	-1	-0.805	-0.886	45.796	-0.041	-0.041	0.000	0.000	0.000	0.000
136	A	662	TYR	0	-0.030	-0.023	46.999	-0.003	-0.003	0.000	0.000	0.000	0.000
137	A	663	CYS	0	-0.061	-0.026	43.529	-0.003	-0.003	0.000	0.000	0.000	0.000
138	A	664	ILE	0	-0.007	0.006	42.267	-0.004	-0.004	0.000	0.000	0.000	0.000
139	A	665	TRP	0	0.024	-0.005	42.334	-0.007	-0.007	0.000	0.000	0.000	0.000
140	A	666	THR	0	-0.038	-0.020	43.536	-0.004	-0.004	0.000	0.000	0.000	0.000
141	A	667	ASP	-1	-0.800	-0.885	38.072	-0.070	-0.070	0.000	0.000	0.000	0.000
142	A	668	GLY	0	0.021	0.003	38.791	-0.006	-0.006	0.000	0.000	0.000	0.000
143	A	669	LEU	0	-0.015	-0.021	39.159	-0.006	-0.006	0.000	0.000	0.000	0.000
144	A	670	ASN	0	-0.006	-0.008	38.653	-0.005	-0.005	0.000	0.000	0.000	0.000
145	A	671	ALA	0	-0.104	-0.041	34.923	-0.006	-0.006	0.000	0.000	0.000	0.000
146	A	672	LEU	0	-0.045	-0.016	35.315	-0.008	-0.008	0.000	0.000	0.000	0.000
147	A	673	LEU	0	-0.052	-0.006	36.650	-0.006	-0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:527:GLY)