FMO DATABASE

FMODB ID: KG9Y3

Calculation Name: 3GRC-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3GRC

Chain ID: A

ChEMBL ID:
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UniProt ID: Q121U0

Base Structure: X-ray

Registration Date: 2023-09-21

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	125
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1087575.938812
FMO2-HF: Nuclear repulsion	1038295.8518
FMO2-HF: Total energy	-49280.087013
FMO2-MP2: Total energy	-49422.664444

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:PRO)

Summations of interaction energy for fragment #1(A:546:PRO)

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.
-15.301	-13.906	20.262	-8.03	-13.627	-0.059

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : 0.007

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

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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	PRO	0	-0.001	0.008	3.841	-5.625	-0.302	-0.039	-2.919	-2.364	0.009
4	A	549	ARG	1	0.898	0.949	5.690	1.008	1.008	0.000	0.000	0.000	0.000
5	A	550	ILE	0	0.005	0.002	7.339	-0.088	-0.088	0.000	0.000	0.000	0.000
6	A	551	LEU	0	-0.035	-0.022	9.533	-0.118	-0.118	0.000	0.000	0.000	0.000
7	A	552	ILE	0	-0.003	-0.006	10.055	0.026	0.026	0.000	0.000	0.000	0.000
8	A	553	CYS	0	-0.068	-0.023	13.762	-0.017	-0.017	0.000	0.000	0.000	0.000
9	A	554	GLU	-1	-0.804	-0.912	17.189	-0.090	-0.090	0.000	0.000	0.000	0.000
10	A	555	ASP	-1	-0.884	-0.935	18.940	-0.103	-0.103	0.000	0.000	0.000	0.000
11	A	556	ASP	-1	-0.866	-0.939	20.991	-0.132	-0.132	0.000	0.000	0.000	0.000
12	A	557	PRO	0	-0.019	-0.027	19.220	-0.020	-0.020	0.000	0.000	0.000	0.000
13	A	558	ASP	-1	-0.899	-0.936	17.694	-0.195	-0.195	0.000	0.000	0.000	0.000
14	A	559	ILE	0	-0.051	-0.024	16.932	-0.025	-0.025	0.000	0.000	0.000	0.000
15	A	560	ALA	0	0.033	0.018	15.329	-0.020	-0.020	0.000	0.000	0.000	0.000
16	A	561	ARG	1	0.933	0.959	10.090	0.527	0.527	0.000	0.000	0.000	0.000
17	A	562	LEU	0	-0.017	-0.003	12.105	-0.074	-0.074	0.000	0.000	0.000	0.000
18	A	563	LEU	0	0.029	0.010	11.672	-0.041	-0.041	0.000	0.000	0.000	0.000
19	A	564	ASN	0	-0.022	-0.024	7.805	-0.063	-0.063	0.000	0.000	0.000	0.000
20	A	565	LEU	0	-0.030	-0.025	7.394	-0.210	-0.210	0.000	0.000	0.000	0.000
21	A	566	MET	0	-0.030	-0.014	7.661	-0.096	-0.096	0.000	0.000	0.000	0.000
22	A	567	LEU	0	-0.008	-0.014	6.071	0.039	0.039	0.000	0.000	0.000	0.000
23	A	568	GLU	-1	-0.950	-0.951	2.827	-2.725	-1.973	0.151	-0.241	-0.663	-0.001
24	A	569	LYS	1	0.889	0.940	3.500	-0.596	0.252	0.032	-0.321	-0.559	-0.002
25	A	570	GLY	0	-0.019	-0.001	5.770	0.207	0.207	0.000	0.000	0.000	0.000
26	A	571	GLY	0	-0.036	-0.018	1.969	1.805	-0.548	5.233	-1.167	-1.713	0.000
27	A	572	PHE	0	-0.043	-0.037	2.254	3.386	-0.496	7.878	-0.414	-3.582	-0.029
28	A	573	ASP	-1	-0.857	-0.910	1.987	-11.982	-11.485	6.995	-2.890	-4.603	-0.036
29	A	574	SER	0	-0.011	-0.031	3.750	0.015	0.225	0.012	-0.078	-0.143	0.000
30	A	575	ASP	-1	-0.820	-0.861	7.418	-0.567	-0.567	0.000	0.000	0.000	0.000
31	A	576	MET	0	-0.015	0.002	10.652	0.052	0.052	0.000	0.000	0.000	0.000
32	A	577	VAL	0	-0.064	-0.031	13.659	0.003	0.003	0.000	0.000	0.000	0.000
33	A	578	HIS	0	0.050	0.012	17.166	0.008	0.008	0.000	0.000	0.000	0.000
34	A	579	SER	0	0.054	0.038	20.382	0.007	0.007	0.000	0.000	0.000	0.000
35	A	580	ALA	0	0.068	0.031	21.619	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	581	ALA	0	0.000	0.009	23.184	0.003	0.003	0.000	0.000	0.000	0.000
37	A	582	GLN	0	0.021	0.004	19.876	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	583	ALA	0	0.008	0.007	18.615	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	584	LEU	0	-0.031	-0.021	19.442	0.009	0.009	0.000	0.000	0.000	0.000
40	A	585	GLU	-1	-0.984	-0.979	21.439	-0.083	-0.083	0.000	0.000	0.000	0.000
41	A	586	GLN	0	0.013	-0.019	14.250	0.003	0.003	0.000	0.000	0.000	0.000
42	A	587	VAL	0	-0.021	-0.015	16.439	0.002	0.002	0.000	0.000	0.000	0.000
43	A	588	ALA	0	-0.009	0.004	17.460	0.016	0.016	0.000	0.000	0.000	0.000
44	A	589	ARG	1	0.840	0.930	16.966	0.132	0.132	0.000	0.000	0.000	0.000
45	A	590	ARG	1	0.884	0.948	9.384	0.218	0.218	0.000	0.000	0.000	0.000
46	A	591	PRO	0	-0.008	-0.005	12.783	0.008	0.008	0.000	0.000	0.000	0.000
47	A	592	TYR	0	-0.063	-0.059	10.586	-0.005	-0.005	0.000	0.000	0.000	0.000
48	A	593	ALA	0	-0.014	-0.002	9.956	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	594	ALA	0	0.025	-0.007	11.801	-0.017	-0.017	0.000	0.000	0.000	0.000
50	A	595	MET	0	-0.025	0.008	12.529	-0.012	-0.012	0.000	0.000	0.000	0.000
51	A	596	THR	0	0.021	0.010	12.462	0.003	0.003	0.000	0.000	0.000	0.000
52	A	597	VAL	0	-0.039	-0.034	15.243	-0.017	-0.017	0.000	0.000	0.000	0.000
53	A	598	ASP	-1	-0.719	-0.859	18.842	-0.061	-0.061	0.000	0.000	0.000	0.000
54	A	599	LEU	0	-0.049	-0.055	21.005	0.005	0.005	0.000	0.000	0.000	0.000
55	A	600	ASN	0	-0.088	-0.041	24.520	0.007	0.007	0.000	0.000	0.000	0.000
56	A	601	LEU	0	-0.001	0.016	21.781	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	602	PRO	0	-0.024	-0.003	25.165	0.006	0.006	0.000	0.000	0.000	0.000
58	A	603	ASP	-1	-0.831	-0.919	26.594	-0.054	-0.054	0.000	0.000	0.000	0.000
59	A	604	GLN	0	-0.097	-0.060	27.529	0.002	0.002	0.000	0.000	0.000	0.000
60	A	605	ASP	-1	-0.806	-0.902	27.068	-0.026	-0.026	0.000	0.000	0.000	0.000
61	A	606	GLY	0	0.061	0.008	24.272	0.002	0.002	0.000	0.000	0.000	0.000
62	A	607	VAL	0	-0.002	-0.002	24.837	0.006	0.006	0.000	0.000	0.000	0.000
63	A	608	SER	0	-0.034	-0.003	27.102	0.004	0.004	0.000	0.000	0.000	0.000
64	A	609	LEU	0	0.020	0.010	21.246	0.003	0.003	0.000	0.000	0.000	0.000
65	A	610	ILE	0	0.039	0.010	22.023	0.005	0.005	0.000	0.000	0.000	0.000
66	A	611	ARG	1	0.917	0.957	24.328	0.002	0.002	0.000	0.000	0.000	0.000
67	A	612	ALA	0	-0.060	-0.030	26.490	0.004	0.004	0.000	0.000	0.000	0.000
68	A	613	LEU	0	0.037	0.019	20.586	0.002	0.002	0.000	0.000	0.000	0.000
69	A	614	ARG	1	0.803	0.913	20.337	-0.048	-0.048	0.000	0.000	0.000	0.000
70	A	615	ARG	1	0.865	0.934	26.086	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	616	ASP	-1	-0.858	-0.917	25.363	0.010	0.010	0.000	0.000	0.000	0.000
72	A	617	SER	0	0.013	-0.018	25.619	0.004	0.004	0.000	0.000	0.000	0.000
73	A	618	ARG	1	0.870	0.941	22.344	0.005	0.005	0.000	0.000	0.000	0.000
74	A	619	THR	0	0.000	-0.010	20.114	0.004	0.004	0.000	0.000	0.000	0.000
75	A	620	ARG	1	0.909	0.963	21.897	-0.055	-0.055	0.000	0.000	0.000	0.000
76	A	621	ASP	-1	-0.907	-0.953	20.824	0.077	0.077	0.000	0.000	0.000	0.000
77	A	622	LEU	0	-0.043	0.008	15.164	0.017	0.017	0.000	0.000	0.000	0.000
78	A	623	ALA	0	0.067	0.035	14.998	-0.017	-0.017	0.000	0.000	0.000	0.000
79	A	624	ILE	0	0.011	-0.004	15.973	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	625	VAL	0	-0.030	-0.008	14.787	0.006	0.006	0.000	0.000	0.000	0.000
81	A	626	VAL	0	0.009	0.019	17.228	-0.015	-0.015	0.000	0.000	0.000	0.000
82	A	627	VAL	0	-0.004	0.000	15.449	0.005	0.005	0.000	0.000	0.000	0.000
83	A	628	SER	0	-0.041	-0.030	18.907	-0.010	-0.010	0.000	0.000	0.000	0.000
84	A	629	ALA	0	0.018	0.012	22.204	0.005	0.005	0.000	0.000	0.000	0.000
85	A	630	ASN	0	0.016	0.024	25.071	0.000	0.000	0.000	0.000	0.000	0.000
86	A	631	ALA	0	0.037	0.018	23.268	0.004	0.004	0.000	0.000	0.000	0.000
87	A	632	ARG	1	1.008	1.012	25.310	0.007	0.007	0.000	0.000	0.000	0.000
88	A	633	GLU	-1	-0.903	-0.968	27.852	-0.013	-0.013	0.000	0.000	0.000	0.000
89	A	634	GLY	0	0.049	0.023	28.029	0.001	0.001	0.000	0.000	0.000	0.000
90	A	635	GLU	-1	-0.957	-0.985	26.392	0.023	0.023	0.000	0.000	0.000	0.000
91	A	636	LEU	0	-0.077	-0.052	28.232	0.003	0.003	0.000	0.000	0.000	0.000
92	A	637	GLU	-1	-0.977	-0.973	31.654	-0.007	-0.007	0.000	0.000	0.000	0.000
93	A	638	PHE	0	-0.026	-0.025	29.388	0.001	0.001	0.000	0.000	0.000	0.000
94	A	639	ASN	0	0.011	0.012	26.767	0.004	0.004	0.000	0.000	0.000	0.000
95	A	640	SER	0	-0.044	-0.027	28.434	0.000	0.000	0.000	0.000	0.000	0.000
96	A	641	GLN	0	0.067	0.012	28.145	0.004	0.004	0.000	0.000	0.000	0.000
97	A	642	PRO	0	-0.060	-0.031	27.756	0.003	0.003	0.000	0.000	0.000	0.000
98	A	643	LEU	0	-0.019	0.001	25.793	0.001	0.001	0.000	0.000	0.000	0.000
99	A	644	ALA	0	-0.007	0.012	23.570	0.001	0.001	0.000	0.000	0.000	0.000
100	A	645	VAL	0	0.017	0.037	20.911	0.008	0.008	0.000	0.000	0.000	0.000
101	A	646	SER	0	-0.013	-0.010	18.350	0.003	0.003	0.000	0.000	0.000	0.000
102	A	647	THR	0	-0.037	-0.032	18.605	0.005	0.005	0.000	0.000	0.000	0.000
103	A	648	TRP	0	0.035	0.025	19.948	-0.007	-0.007	0.000	0.000	0.000	0.000
104	A	649	LEU	0	-0.039	-0.025	16.226	0.001	0.001	0.000	0.000	0.000	0.000
105	A	650	GLU	-1	-0.888	-0.955	20.437	-0.020	-0.020	0.000	0.000	0.000	0.000
106	A	651	LYS	1	0.828	0.912	19.472	0.081	0.081	0.000	0.000	0.000	0.000
107	A	652	PRO	0	-0.013	-0.023	21.376	0.003	0.003	0.000	0.000	0.000	0.000
108	A	653	ILE	0	0.031	0.014	15.225	0.009	0.009	0.000	0.000	0.000	0.000
109	A	654	ASP	-1	-0.870	-0.913	17.870	-0.010	-0.010	0.000	0.000	0.000	0.000
110	A	655	GLU	-1	-0.870	-0.957	11.604	-0.162	-0.162	0.000	0.000	0.000	0.000
111	A	656	ASN	0	-0.009	-0.012	12.950	0.022	0.022	0.000	0.000	0.000	0.000
112	A	657	LEU	0	-0.010	-0.001	14.349	0.031	0.031	0.000	0.000	0.000	0.000
113	A	658	LEU	0	0.017	0.014	11.399	0.021	0.021	0.000	0.000	0.000	0.000
114	A	659	ILE	0	0.011	0.005	7.963	0.035	0.035	0.000	0.000	0.000	0.000
115	A	660	LEU	0	-0.040	-0.009	10.924	0.058	0.058	0.000	0.000	0.000	0.000
116	A	661	SER	0	-0.014	-0.034	13.798	0.024	0.024	0.000	0.000	0.000	0.000
117	A	662	LEU	0	0.002	0.011	9.459	0.005	0.005	0.000	0.000	0.000	0.000
118	A	663	HIS	0	0.035	0.020	7.500	0.023	0.023	0.000	0.000	0.000	0.000
119	A	664	ARG	1	0.931	0.963	12.239	-0.141	-0.141	0.000	0.000	0.000	0.000
120	A	665	ALA	0	-0.006	-0.006	15.015	-0.004	-0.004	0.000	0.000	0.000	0.000
121	A	666	ILE	0	-0.038	-0.020	10.292	-0.002	-0.002	0.000	0.000	0.000	0.000
122	A	667	ASP	-1	-0.928	-0.966	13.448	0.317	0.317	0.000	0.000	0.000	0.000
123	A	668	ASN	0	-0.139	-0.064	15.726	-0.026	-0.026	0.000	0.000	0.000	0.000
124	A	669	MET	0	-0.007	-0.003	17.958	-0.018	-0.018	0.000	0.000	0.000	0.000
125	A	670	ALA	0	-0.067	-0.011	15.985	-0.015	-0.015	0.000	0.000	0.000	0.000

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