FMO DATABASE

FMODB ID: 4J92N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1088645.320791
FMO2-HF: Nuclear repulsion	1039364.542753
FMO2-HF: Total energy	-49280.778038
FMO2-MP2: Total energy	-49423.319747

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.
-17.691	-7.438	7.622	-7.796	-10.078	-0.055

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 : -0.008 / 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	0.021	0.028	3.841	-4.515	-0.376	-0.041	-2.278	-1.820	0.004
4	A	549	ARG	1	0.801	0.874	5.461	1.415	1.415	0.000	0.000	0.000	0.000
5	A	550	ILE	0	0.006	0.000	7.332	-0.147	-0.147	0.000	0.000	0.000	0.000
6	A	551	LEU	0	-0.032	-0.016	9.641	-0.115	-0.115	0.000	0.000	0.000	0.000
7	A	552	ILE	0	-0.015	-0.009	10.101	0.020	0.020	0.000	0.000	0.000	0.000
8	A	553	CYS	0	-0.040	-0.011	13.839	-0.035	-0.035	0.000	0.000	0.000	0.000
9	A	554	GLU	-1	-0.843	-0.926	17.316	-0.006	-0.006	0.000	0.000	0.000	0.000
10	A	555	ASP	-1	-0.861	-0.930	19.094	-0.053	-0.053	0.000	0.000	0.000	0.000
11	A	556	ASP	-1	-0.848	-0.912	20.974	-0.074	-0.074	0.000	0.000	0.000	0.000
12	A	557	PRO	0	-0.008	-0.026	19.278	-0.008	-0.008	0.000	0.000	0.000	0.000
13	A	558	ASP	-1	-0.899	-0.938	17.786	-0.128	-0.128	0.000	0.000	0.000	0.000
14	A	559	ILE	0	-0.041	-0.022	16.967	-0.013	-0.013	0.000	0.000	0.000	0.000
15	A	560	ALA	0	0.024	0.016	15.317	0.000	0.000	0.000	0.000	0.000	0.000
16	A	561	ARG	1	0.926	0.943	9.746	0.425	0.425	0.000	0.000	0.000	0.000
17	A	562	LEU	0	-0.018	-0.001	12.197	-0.048	-0.048	0.000	0.000	0.000	0.000
18	A	563	LEU	0	0.036	0.013	11.580	-0.014	-0.014	0.000	0.000	0.000	0.000
19	A	564	ASN	0	-0.011	-0.012	8.069	-0.032	-0.032	0.000	0.000	0.000	0.000
20	A	565	LEU	0	-0.043	-0.028	7.405	-0.111	-0.111	0.000	0.000	0.000	0.000
21	A	566	MET	0	-0.011	-0.004	7.679	-0.073	-0.073	0.000	0.000	0.000	0.000
22	A	567	LEU	0	-0.013	-0.016	6.485	0.031	0.031	0.000	0.000	0.000	0.000
23	A	568	GLU	-1	-0.886	-0.908	3.013	-1.464	-0.929	0.077	-0.167	-0.444	0.000
24	A	569	LYS	1	0.817	0.894	3.335	-0.962	0.015	0.045	-0.430	-0.592	-0.003
25	A	570	GLY	0	-0.012	0.003	5.791	0.053	0.053	0.000	0.000	0.000	0.000
26	A	571	GLY	0	-0.048	-0.019	2.191	-0.412	-0.090	1.807	-1.018	-1.111	-0.001
27	A	572	PHE	0	-0.029	-0.035	2.585	0.180	2.350	1.444	-1.211	-2.403	-0.024
28	A	573	ASP	-1	-0.787	-0.864	2.081	-11.609	-9.680	4.277	-2.639	-3.567	-0.031
29	A	574	SER	0	0.009	-0.017	3.676	-0.092	0.089	0.013	-0.053	-0.141	0.000
30	A	575	ASP	-1	-0.829	-0.872	7.368	-0.499	-0.499	0.000	0.000	0.000	0.000
31	A	576	MET	0	-0.008	0.008	10.604	0.060	0.060	0.000	0.000	0.000	0.000
32	A	577	VAL	0	-0.056	-0.031	13.642	-0.014	-0.014	0.000	0.000	0.000	0.000
33	A	578	HIS	0	0.042	0.008	17.131	0.014	0.014	0.000	0.000	0.000	0.000
34	A	579	SER	0	-0.002	-0.013	20.361	0.004	0.004	0.000	0.000	0.000	0.000
35	A	580	ALA	0	0.076	0.034	21.561	0.002	0.002	0.000	0.000	0.000	0.000
36	A	581	ALA	0	-0.002	0.008	23.104	0.004	0.004	0.000	0.000	0.000	0.000
37	A	582	GLN	0	0.014	0.004	19.854	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	583	ALA	0	0.022	0.011	18.537	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	584	LEU	0	-0.028	-0.019	19.342	0.008	0.008	0.000	0.000	0.000	0.000
40	A	585	GLU	-1	-0.935	-0.948	20.992	-0.062	-0.062	0.000	0.000	0.000	0.000
41	A	586	GLN	0	-0.005	-0.034	13.802	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	587	VAL	0	-0.022	-0.015	16.310	0.002	0.002	0.000	0.000	0.000	0.000
43	A	588	ALA	0	-0.014	0.002	17.322	0.013	0.013	0.000	0.000	0.000	0.000
44	A	589	ARG	1	0.817	0.910	17.103	0.095	0.095	0.000	0.000	0.000	0.000
45	A	590	ARG	1	0.862	0.945	9.384	0.237	0.237	0.000	0.000	0.000	0.000
46	A	591	PRO	0	-0.005	-0.005	12.642	0.015	0.015	0.000	0.000	0.000	0.000
47	A	592	TYR	0	-0.042	-0.035	10.577	-0.014	-0.014	0.000	0.000	0.000	0.000
48	A	593	ALA	0	-0.022	-0.007	10.183	-0.015	-0.015	0.000	0.000	0.000	0.000
49	A	594	ALA	0	0.027	-0.003	12.073	-0.028	-0.028	0.000	0.000	0.000	0.000
50	A	595	MET	0	-0.024	0.002	12.793	0.001	0.001	0.000	0.000	0.000	0.000
51	A	596	THR	0	0.009	0.013	13.088	0.004	0.004	0.000	0.000	0.000	0.000
52	A	597	VAL	0	-0.035	-0.035	15.746	-0.021	-0.021	0.000	0.000	0.000	0.000
53	A	598	ASP	-1	-0.668	-0.797	19.289	0.004	0.004	0.000	0.000	0.000	0.000
54	A	599	LEU	0	-0.039	-0.046	21.329	0.001	0.001	0.000	0.000	0.000	0.000
55	A	600	ASN	0	-0.060	-0.023	24.819	0.001	0.001	0.000	0.000	0.000	0.000
56	A	601	LEU	0	-0.005	0.005	21.820	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	602	PRO	0	-0.004	-0.002	25.206	0.003	0.003	0.000	0.000	0.000	0.000
58	A	603	ASP	-1	-0.811	-0.893	26.463	-0.018	-0.018	0.000	0.000	0.000	0.000
59	A	604	GLN	0	-0.094	-0.046	27.427	0.001	0.001	0.000	0.000	0.000	0.000
60	A	605	ASP	-1	-0.784	-0.892	27.121	0.013	0.013	0.000	0.000	0.000	0.000
61	A	606	GLY	0	0.057	0.006	24.667	0.003	0.003	0.000	0.000	0.000	0.000
62	A	607	VAL	0	-0.001	-0.003	25.309	0.007	0.007	0.000	0.000	0.000	0.000
63	A	608	SER	0	-0.037	-0.009	27.639	0.004	0.004	0.000	0.000	0.000	0.000
64	A	609	LEU	0	0.000	0.010	21.188	0.001	0.001	0.000	0.000	0.000	0.000
65	A	610	ILE	0	0.034	0.006	22.492	0.004	0.004	0.000	0.000	0.000	0.000
66	A	611	ARG	1	0.913	0.960	24.715	-0.029	-0.029	0.000	0.000	0.000	0.000
67	A	612	ALA	0	-0.060	-0.029	26.438	0.002	0.002	0.000	0.000	0.000	0.000
68	A	613	LEU	0	0.030	0.015	20.593	0.000	0.000	0.000	0.000	0.000	0.000
69	A	614	ARG	1	0.802	0.900	20.985	-0.101	-0.101	0.000	0.000	0.000	0.000
70	A	615	ARG	1	0.881	0.941	26.309	-0.026	-0.026	0.000	0.000	0.000	0.000
71	A	616	ASP	-1	-0.808	-0.874	25.355	0.030	0.030	0.000	0.000	0.000	0.000
72	A	617	SER	0	-0.023	-0.023	25.479	0.006	0.006	0.000	0.000	0.000	0.000
73	A	618	ARG	1	0.849	0.902	21.838	-0.018	-0.018	0.000	0.000	0.000	0.000
74	A	619	THR	0	-0.006	-0.009	19.761	0.006	0.006	0.000	0.000	0.000	0.000
75	A	620	ARG	1	0.796	0.887	21.758	-0.079	-0.079	0.000	0.000	0.000	0.000
76	A	621	ASP	-1	-0.829	-0.895	21.115	0.103	0.103	0.000	0.000	0.000	0.000
77	A	622	LEU	0	-0.028	0.018	15.193	0.020	0.020	0.000	0.000	0.000	0.000
78	A	623	ALA	0	0.060	0.036	15.393	-0.020	-0.020	0.000	0.000	0.000	0.000
79	A	624	ILE	0	0.024	0.000	16.675	0.006	0.006	0.000	0.000	0.000	0.000
80	A	625	VAL	0	-0.031	-0.010	15.663	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	626	VAL	0	0.014	0.024	17.778	-0.008	-0.008	0.000	0.000	0.000	0.000
82	A	627	VAL	0	-0.011	-0.004	15.810	0.006	0.006	0.000	0.000	0.000	0.000
83	A	628	SER	0	-0.045	-0.062	19.279	-0.011	-0.011	0.000	0.000	0.000	0.000
84	A	629	ALA	0	0.003	0.008	22.502	0.004	0.004	0.000	0.000	0.000	0.000
85	A	630	ASN	0	-0.023	-0.010	25.293	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	631	ALA	0	0.023	0.013	23.631	0.002	0.002	0.000	0.000	0.000	0.000
87	A	632	ARG	1	0.985	1.000	25.720	-0.025	-0.025	0.000	0.000	0.000	0.000
88	A	633	GLU	-1	-0.857	-0.932	28.296	0.018	0.018	0.000	0.000	0.000	0.000
89	A	634	GLY	0	0.055	0.027	28.497	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	635	GLU	-1	-0.930	-0.972	26.978	0.063	0.063	0.000	0.000	0.000	0.000
91	A	636	LEU	0	-0.075	-0.052	28.796	0.001	0.001	0.000	0.000	0.000	0.000
92	A	637	GLU	-1	-0.972	-0.972	32.177	0.017	0.017	0.000	0.000	0.000	0.000
93	A	638	PHE	0	-0.018	-0.022	30.042	0.000	0.000	0.000	0.000	0.000	0.000
94	A	639	ASN	0	-0.033	-0.009	27.007	0.004	0.004	0.000	0.000	0.000	0.000
95	A	640	SER	0	-0.048	-0.025	29.145	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	641	GLN	0	0.032	0.002	28.645	0.007	0.007	0.000	0.000	0.000	0.000
97	A	642	PRO	0	-0.033	-0.024	28.334	0.004	0.004	0.000	0.000	0.000	0.000
98	A	643	LEU	0	-0.015	0.008	26.277	0.001	0.001	0.000	0.000	0.000	0.000
99	A	644	ALA	0	0.011	0.015	24.163	0.005	0.005	0.000	0.000	0.000	0.000
100	A	645	VAL	0	0.016	0.031	21.521	0.012	0.012	0.000	0.000	0.000	0.000
101	A	646	SER	0	-0.024	-0.012	19.104	0.001	0.001	0.000	0.000	0.000	0.000
102	A	647	THR	0	0.001	-0.016	19.042	0.000	0.000	0.000	0.000	0.000	0.000
103	A	648	TRP	0	0.033	0.028	20.560	0.000	0.000	0.000	0.000	0.000	0.000
104	A	649	LEU	0	-0.045	-0.030	16.716	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	650	GLU	-1	-0.880	-0.951	20.869	0.024	0.024	0.000	0.000	0.000	0.000
106	A	651	LYS	1	0.747	0.854	19.431	0.010	0.010	0.000	0.000	0.000	0.000
107	A	652	PRO	0	-0.004	-0.023	21.412	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	653	ILE	0	0.022	0.014	15.277	0.008	0.008	0.000	0.000	0.000	0.000
109	A	654	ASP	-1	-0.843	-0.907	17.944	0.049	0.049	0.000	0.000	0.000	0.000
110	A	655	GLU	-1	-0.866	-0.956	11.165	-0.054	-0.054	0.000	0.000	0.000	0.000
111	A	656	ASN	0	-0.029	-0.022	13.209	0.032	0.032	0.000	0.000	0.000	0.000
112	A	657	LEU	0	-0.009	0.002	14.752	0.035	0.035	0.000	0.000	0.000	0.000
113	A	658	LEU	0	0.027	0.023	11.875	0.023	0.023	0.000	0.000	0.000	0.000
114	A	659	ILE	0	0.007	0.006	8.201	0.056	0.056	0.000	0.000	0.000	0.000
115	A	660	LEU	0	-0.033	-0.008	11.430	0.058	0.058	0.000	0.000	0.000	0.000
116	A	661	SER	0	-0.032	-0.041	14.397	0.013	0.013	0.000	0.000	0.000	0.000
117	A	662	LEU	0	-0.001	0.009	10.338	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	663	HIS	0	0.031	0.019	7.425	0.014	0.014	0.000	0.000	0.000	0.000
119	A	664	ARG	1	0.938	0.966	12.370	-0.205	-0.205	0.000	0.000	0.000	0.000
120	A	665	ALA	0	-0.002	-0.003	15.591	-0.012	-0.012	0.000	0.000	0.000	0.000
121	A	666	ILE	0	-0.036	-0.022	10.295	-0.007	-0.007	0.000	0.000	0.000	0.000
122	A	667	ASP	-1	-0.904	-0.949	13.889	0.343	0.343	0.000	0.000	0.000	0.000
123	A	668	ASN	0	-0.141	-0.061	15.887	-0.035	-0.035	0.000	0.000	0.000	0.000
124	A	669	MET	0	-0.014	-0.008	18.212	-0.024	-0.024	0.000	0.000	0.000	0.000
125	A	670	ALA	0	-0.102	-0.035	16.172	-0.034	-0.034	0.000	0.000	0.000	0.000

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