FMO DATABASE

FMODB ID: QVJYY

Calculation Name: 3AG7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3AG7

Chain ID: A

ChEMBL ID:

UniProt ID: Q9C9Q4

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	OptAll
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	105
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-806707.959814
FMO2-HF: Nuclear repulsion	765507.956762
FMO2-HF: Total energy	-41200.003052
FMO2-MP2: Total energy	-41321.040951

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:546:GLY)

Summations of interaction energy for fragment #1(A:546: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.
-6.806	-10.383	14.905	-6.941	-4.389	-0.054

Interaction energy analysis for fragmet #1(A:546:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.062 / q_NPA : 0.023

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	548	LEU	0	-0.026	-0.027	3.887	-0.269	0.967	-0.004	-0.607	-0.625	0.003
4	A	549	GLY	0	0.038	0.047	3.410	1.186	1.576	0.003	-0.166	-0.227	0.000
5	A	550	SER	0	0.035	0.000	4.396	0.611	0.684	-0.001	-0.010	-0.063	0.000
6	A	551	GLU	-1	-0.905	-0.954	6.012	-0.032	-0.032	0.000	0.000	0.000	0.000
7	A	552	GLU	-1	-0.802	-0.896	1.784	-13.726	-19.140	14.906	-6.045	-3.449	-0.057
8	A	553	ILE	0	-0.012	-0.002	5.402	0.757	0.757	0.000	0.000	0.000	0.000
9	A	554	LYS	1	0.896	0.938	7.778	1.558	1.558	0.000	0.000	0.000	0.000
10	A	555	ASN	0	-0.032	-0.015	8.006	0.440	0.440	0.000	0.000	0.000	0.000
11	A	556	ILE	0	-0.033	-0.013	6.684	0.239	0.239	0.000	0.000	0.000	0.000
12	A	557	ASP	-1	-0.780	-0.867	10.226	-0.778	-0.778	0.000	0.000	0.000	0.000
13	A	558	ALA	0	-0.049	-0.022	12.907	0.126	0.126	0.000	0.000	0.000	0.000
14	A	559	LYS	1	0.861	0.936	12.429	0.350	0.350	0.000	0.000	0.000	0.000
15	A	560	ILE	0	0.051	0.018	13.720	0.073	0.073	0.000	0.000	0.000	0.000
16	A	561	ARG	1	0.959	1.002	14.965	0.578	0.578	0.000	0.000	0.000	0.000
17	A	562	LYS	1	0.950	0.974	17.291	0.209	0.209	0.000	0.000	0.000	0.000
18	A	563	TRP	0	-0.067	-0.039	18.504	0.023	0.023	0.000	0.000	0.000	0.000
19	A	564	SER	0	0.020	-0.014	19.992	0.024	0.024	0.000	0.000	0.000	0.000
20	A	565	SER	0	0.017	0.011	22.144	0.015	0.015	0.000	0.000	0.000	0.000
21	A	566	GLY	0	0.022	0.010	24.493	0.013	0.013	0.000	0.000	0.000	0.000
22	A	567	LYS	1	0.751	0.868	22.739	0.174	0.174	0.000	0.000	0.000	0.000
23	A	568	SER	0	0.039	0.031	25.755	0.001	0.001	0.000	0.000	0.000	0.000
24	A	569	GLY	0	0.018	0.009	26.946	0.014	0.014	0.000	0.000	0.000	0.000
25	A	570	ASN	0	-0.011	-0.013	29.212	0.012	0.012	0.000	0.000	0.000	0.000
26	A	571	ILE	0	0.036	0.008	27.350	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	572	ARG	1	0.872	0.920	28.525	0.082	0.082	0.000	0.000	0.000	0.000
28	A	573	SER	0	0.032	0.034	28.124	0.008	0.008	0.000	0.000	0.000	0.000
29	A	574	LEU	0	0.013	0.033	23.179	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	575	LEU	0	0.010	-0.004	24.547	0.001	0.001	0.000	0.000	0.000	0.000
31	A	576	SER	0	-0.028	-0.030	25.787	0.006	0.006	0.000	0.000	0.000	0.000
32	A	577	THR	0	-0.025	-0.011	23.881	0.006	0.006	0.000	0.000	0.000	0.000
33	A	578	LEU	0	0.063	0.046	20.355	-0.011	-0.011	0.000	0.000	0.000	0.000
34	A	579	GLN	0	-0.006	-0.017	19.662	-0.026	-0.026	0.000	0.000	0.000	0.000
35	A	580	TYR	0	-0.038	-0.014	19.378	0.017	0.017	0.000	0.000	0.000	0.000
36	A	581	ILE	0	-0.043	-0.017	14.879	-0.014	-0.014	0.000	0.000	0.000	0.000
37	A	582	LEU	0	0.003	0.008	14.765	-0.050	-0.050	0.000	0.000	0.000	0.000
38	A	583	TRP	0	0.027	0.024	12.221	0.007	0.007	0.000	0.000	0.000	0.000
39	A	584	SER	0	0.029	0.006	14.211	-0.013	-0.013	0.000	0.000	0.000	0.000
40	A	585	GLY	0	0.042	0.011	15.905	0.007	0.007	0.000	0.000	0.000	0.000
41	A	586	SER	0	-0.052	-0.024	16.601	-0.009	-0.009	0.000	0.000	0.000	0.000
42	A	587	GLY	0	0.022	0.008	18.148	-0.017	-0.017	0.000	0.000	0.000	0.000
43	A	588	TRP	0	-0.029	-0.016	21.175	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	589	LYS	1	0.934	0.962	22.959	0.033	0.033	0.000	0.000	0.000	0.000
45	A	590	PRO	0	-0.001	0.011	25.423	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	591	VAL	0	0.015	0.010	27.052	0.007	0.007	0.000	0.000	0.000	0.000
47	A	592	PRO	0	0.032	0.022	29.971	-0.009	-0.009	0.000	0.000	0.000	0.000
48	A	593	LEU	0	0.051	-0.005	31.691	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	594	MET	0	0.001	-0.004	34.056	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	595	ASP	-1	-0.878	-0.930	33.885	-0.035	-0.035	0.000	0.000	0.000	0.000
51	A	596	MET	0	-0.089	-0.044	29.403	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	597	ILE	0	0.049	0.046	35.084	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	598	GLU	-1	-0.741	-0.855	38.389	-0.062	-0.062	0.000	0.000	0.000	0.000
54	A	599	GLY	0	0.007	-0.002	38.005	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	600	ASN	0	-0.001	-0.009	38.059	-0.006	-0.006	0.000	0.000	0.000	0.000
56	A	601	ALA	0	0.009	0.013	35.840	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	602	VAL	0	0.016	0.024	32.359	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	603	ARG	1	0.872	0.929	31.973	0.083	0.083	0.000	0.000	0.000	0.000
59	A	604	LYS	1	0.898	0.949	32.222	0.053	0.053	0.000	0.000	0.000	0.000
60	A	605	SER	0	-0.005	-0.018	29.392	0.001	0.001	0.000	0.000	0.000	0.000
61	A	606	TYR	0	0.022	0.003	26.972	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	607	GLN	0	-0.005	0.000	27.414	-0.007	-0.007	0.000	0.000	0.000	0.000
63	A	608	ARG	1	0.927	0.961	26.854	0.059	0.059	0.000	0.000	0.000	0.000
64	A	609	ALA	0	0.058	0.033	23.643	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	610	LEU	0	0.035	0.013	22.833	-0.021	-0.021	0.000	0.000	0.000	0.000
66	A	611	LEU	0	-0.056	-0.026	23.668	-0.014	-0.014	0.000	0.000	0.000	0.000
67	A	612	ILE	0	-0.097	-0.046	19.311	0.009	0.009	0.000	0.000	0.000	0.000
68	A	613	LEU	0	-0.001	-0.010	17.627	-0.027	-0.027	0.000	0.000	0.000	0.000
69	A	614	HIS	0	0.071	0.053	19.557	-0.045	-0.045	0.000	0.000	0.000	0.000
70	A	615	PRO	0	0.047	0.016	18.375	0.005	0.005	0.000	0.000	0.000	0.000
71	A	616	ASP	-1	-0.788	-0.885	18.955	-0.199	-0.199	0.000	0.000	0.000	0.000
72	A	617	LYS	1	0.780	0.879	21.183	0.179	0.179	0.000	0.000	0.000	0.000
73	A	618	LEU	0	0.009	0.005	15.549	0.016	0.016	0.000	0.000	0.000	0.000
74	A	619	GLN	0	0.003	0.009	16.165	-0.055	-0.055	0.000	0.000	0.000	0.000
75	A	620	GLN	0	-0.009	-0.010	17.828	0.041	0.041	0.000	0.000	0.000	0.000
76	A	621	LYS	1	0.869	0.949	17.520	0.159	0.159	0.000	0.000	0.000	0.000
77	A	622	GLY	0	0.023	0.025	15.905	0.033	0.033	0.000	0.000	0.000	0.000
78	A	623	ALA	0	-0.039	-0.005	13.025	0.012	0.012	0.000	0.000	0.000	0.000
79	A	624	SER	0	0.025	-0.027	7.462	-0.181	-0.181	0.000	0.000	0.000	0.000
80	A	625	ALA	0	0.027	0.002	7.617	0.028	0.028	0.000	0.000	0.000	0.000
81	A	626	ASN	0	0.052	0.027	3.441	0.868	1.006	0.001	-0.113	-0.025	0.000
82	A	627	GLN	0	0.031	0.046	7.632	0.221	0.221	0.000	0.000	0.000	0.000
83	A	628	LYS	1	0.895	0.950	10.563	0.649	0.649	0.000	0.000	0.000	0.000
84	A	629	TYR	0	0.004	-0.009	9.992	0.063	0.063	0.000	0.000	0.000	0.000
85	A	630	MET	0	-0.030	-0.019	10.621	0.117	0.117	0.000	0.000	0.000	0.000
86	A	631	ALA	0	-0.020	-0.022	12.415	0.110	0.110	0.000	0.000	0.000	0.000
87	A	632	GLU	-1	-0.860	-0.911	15.181	-0.611	-0.611	0.000	0.000	0.000	0.000
88	A	633	LYS	1	0.829	0.884	14.910	0.662	0.662	0.000	0.000	0.000	0.000
89	A	634	VAL	0	-0.030	-0.012	16.371	0.058	0.058	0.000	0.000	0.000	0.000
90	A	635	PHE	0	-0.027	-0.021	18.695	0.057	0.057	0.000	0.000	0.000	0.000
91	A	636	GLU	-1	-0.827	-0.906	19.884	-0.433	-0.433	0.000	0.000	0.000	0.000
92	A	637	LEU	0	0.017	0.011	20.072	0.034	0.034	0.000	0.000	0.000	0.000
93	A	638	LEU	0	-0.013	-0.014	22.021	0.033	0.033	0.000	0.000	0.000	0.000
94	A	639	GLN	0	-0.062	-0.031	24.700	0.020	0.020	0.000	0.000	0.000	0.000
95	A	640	GLU	-1	-0.800	-0.898	26.190	-0.204	-0.204	0.000	0.000	0.000	0.000
96	A	641	ALA	0	0.011	-0.003	27.408	0.018	0.018	0.000	0.000	0.000	0.000
97	A	642	TRP	0	-0.029	-0.011	28.846	0.021	0.021	0.000	0.000	0.000	0.000
98	A	643	ASP	-1	-0.893	-0.931	30.630	-0.131	-0.131	0.000	0.000	0.000	0.000
99	A	644	HIS	0	0.058	0.042	32.254	0.006	0.006	0.000	0.000	0.000	0.000
100	A	645	PHE	0	-0.065	-0.044	33.061	0.013	0.013	0.000	0.000	0.000	0.000
101	A	646	ASN	0	-0.081	-0.051	33.786	0.017	0.017	0.000	0.000	0.000	0.000
102	A	647	THR	0	-0.012	-0.007	36.445	0.005	0.005	0.000	0.000	0.000	0.000
103	A	648	LEU	0	-0.017	-0.001	37.172	0.006	0.006	0.000	0.000	0.000	0.000
104	A	649	GLY	0	-0.012	0.009	36.739	0.006	0.006	0.000	0.000	0.000	0.000
105	A	650	PRO	0	-0.030	-0.017	35.471	-0.001	-0.001	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:546:GLY)