FMO DATABASE

FMODB ID: GNM61

Calculation Name: 1GXJ-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: 1GXJ

Chain ID: A

ChEMBL ID:
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UniProt ID: Q9X0R4

Base Structure: X-ray

Registration Date: 2023-06-21

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	161
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1439576.70896
FMO2-HF: Nuclear repulsion	1379261.298242
FMO2-HF: Total energy	-60315.410718
FMO2-MP2: Total energy	-60495.598767

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:498:GLY)

Summations of interaction energy for fragment #1(A:498: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.
-2.275	-1.183	-0.016	-0.555	-0.521	0.001

Interaction energy analysis for fragmet #1(A:498:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : 0.002

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	500	SER	0	0.025	0.005	3.811	2.287	3.247	-0.015	-0.533	-0.412	0.001
4	A	501	ARG	1	1.008	0.997	7.086	-0.256	-0.256	0.000	0.000	0.000	0.000
5	A	502	ALA	0	0.012	0.025	8.812	0.035	0.035	0.000	0.000	0.000	0.000
6	A	503	VAL	0	0.064	0.021	7.011	0.002	0.002	0.000	0.000	0.000	0.000
7	A	504	ARG	1	0.869	0.932	4.662	-4.287	-4.155	-0.001	-0.022	-0.109	0.000
8	A	505	ALA	0	0.048	0.031	7.429	-0.158	-0.158	0.000	0.000	0.000	0.000
9	A	506	VAL	0	-0.005	-0.017	11.134	-0.093	-0.093	0.000	0.000	0.000	0.000
10	A	507	PHE	0	-0.022	-0.009	8.376	-0.090	-0.090	0.000	0.000	0.000	0.000
11	A	508	GLU	-1	-1.010	-0.990	9.691	1.129	1.129	0.000	0.000	0.000	0.000
12	A	509	GLU	-1	-0.817	-0.901	11.311	0.272	0.272	0.000	0.000	0.000	0.000
13	A	510	LYS	1	0.987	0.992	12.032	-0.215	-0.215	0.000	0.000	0.000	0.000
14	A	511	GLU	-1	-0.925	-0.952	15.017	0.199	0.199	0.000	0.000	0.000	0.000
15	A	512	ARG	1	0.831	0.908	17.899	-0.232	-0.232	0.000	0.000	0.000	0.000
16	A	513	PHE	0	-0.060	-0.042	15.897	-0.026	-0.026	0.000	0.000	0.000	0.000
17	A	514	PRO	0	0.054	0.025	18.319	-0.012	-0.012	0.000	0.000	0.000	0.000
18	A	515	GLY	0	-0.007	0.009	20.683	-0.015	-0.015	0.000	0.000	0.000	0.000
19	A	516	LEU	0	-0.034	-0.029	12.736	-0.017	-0.017	0.000	0.000	0.000	0.000
20	A	517	VAL	0	-0.050	-0.017	15.926	0.003	0.003	0.000	0.000	0.000	0.000
21	A	518	ASP	-1	-0.783	-0.896	9.979	-0.377	-0.377	0.000	0.000	0.000	0.000
22	A	519	VAL	0	-0.064	-0.030	7.307	0.043	0.043	0.000	0.000	0.000	0.000
23	A	520	VAL	0	0.020	-0.003	10.673	-0.025	-0.025	0.000	0.000	0.000	0.000
24	A	521	SER	0	0.004	-0.008	8.233	-0.020	-0.020	0.000	0.000	0.000	0.000
25	A	522	ASN	0	-0.101	-0.056	7.022	-0.227	-0.227	0.000	0.000	0.000	0.000
26	A	523	LEU	0	-0.036	-0.012	10.717	0.082	0.082	0.000	0.000	0.000	0.000
27	A	524	ILE	0	-0.050	-0.009	13.662	0.051	0.051	0.000	0.000	0.000	0.000
28	A	525	GLU	-1	-0.829	-0.894	14.808	-0.220	-0.220	0.000	0.000	0.000	0.000
29	A	526	VAL	0	-0.018	-0.027	16.629	0.025	0.025	0.000	0.000	0.000	0.000
30	A	527	ASP	-1	-0.825	-0.885	18.372	-0.186	-0.186	0.000	0.000	0.000	0.000
31	A	528	GLU	-1	-0.876	-0.942	18.151	-0.230	-0.230	0.000	0.000	0.000	0.000
32	A	529	LYS	1	0.836	0.903	19.308	0.147	0.147	0.000	0.000	0.000	0.000
33	A	530	TYR	0	0.022	-0.007	21.134	0.009	0.009	0.000	0.000	0.000	0.000
34	A	531	SER	0	-0.027	-0.009	15.519	-0.014	-0.014	0.000	0.000	0.000	0.000
35	A	532	LEU	0	0.045	0.026	16.600	-0.034	-0.034	0.000	0.000	0.000	0.000
36	A	533	ALA	0	0.017	0.011	18.020	-0.008	-0.008	0.000	0.000	0.000	0.000
37	A	534	VAL	0	0.029	0.003	16.430	0.001	0.001	0.000	0.000	0.000	0.000
38	A	535	SER	0	0.023	0.012	13.797	-0.037	-0.037	0.000	0.000	0.000	0.000
39	A	536	VAL	0	-0.051	-0.019	15.665	-0.014	-0.014	0.000	0.000	0.000	0.000
40	A	537	LEU	0	-0.031	-0.010	18.312	0.016	0.016	0.000	0.000	0.000	0.000
41	A	538	LEU	0	0.017	0.029	14.153	0.017	0.017	0.000	0.000	0.000	0.000
42	A	539	GLY	0	0.038	0.041	16.333	0.017	0.017	0.000	0.000	0.000	0.000
43	A	540	GLY	0	-0.014	-0.025	13.534	-0.063	-0.063	0.000	0.000	0.000	0.000
44	A	541	THR	0	-0.049	-0.044	13.603	-0.030	-0.030	0.000	0.000	0.000	0.000
45	A	542	ALA	0	0.049	0.028	11.095	0.003	0.003	0.000	0.000	0.000	0.000
46	A	543	GLN	0	-0.046	-0.021	9.030	-0.051	-0.051	0.000	0.000	0.000	0.000
47	A	544	ASN	0	-0.015	-0.008	10.456	0.080	0.080	0.000	0.000	0.000	0.000
48	A	545	ILE	0	0.015	-0.002	11.176	-0.042	-0.042	0.000	0.000	0.000	0.000
49	A	546	VAL	0	0.016	0.020	13.489	0.033	0.033	0.000	0.000	0.000	0.000
50	A	547	VAL	0	-0.022	-0.013	16.003	0.019	0.019	0.000	0.000	0.000	0.000
51	A	548	ARG	1	0.866	0.896	18.541	0.057	0.057	0.000	0.000	0.000	0.000
52	A	549	ASN	0	0.044	0.042	22.019	0.000	0.000	0.000	0.000	0.000	0.000
53	A	550	VAL	0	0.027	0.001	22.722	0.005	0.005	0.000	0.000	0.000	0.000
54	A	551	ASP	-1	-0.917	-0.952	24.045	0.015	0.015	0.000	0.000	0.000	0.000
55	A	552	THR	0	0.009	-0.008	18.898	0.016	0.016	0.000	0.000	0.000	0.000
56	A	553	ALA	0	0.018	0.008	19.693	0.014	0.014	0.000	0.000	0.000	0.000
57	A	554	LYS	1	0.910	0.953	20.577	0.003	0.003	0.000	0.000	0.000	0.000
58	A	555	ALA	0	0.010	0.015	21.374	0.012	0.012	0.000	0.000	0.000	0.000
59	A	556	ILE	0	0.041	0.027	15.496	0.019	0.019	0.000	0.000	0.000	0.000
60	A	557	VAL	0	-0.013	-0.004	18.255	0.025	0.025	0.000	0.000	0.000	0.000
61	A	558	GLU	-1	-0.817	-0.888	19.991	0.106	0.106	0.000	0.000	0.000	0.000
62	A	559	PHE	0	-0.029	-0.024	14.271	0.004	0.004	0.000	0.000	0.000	0.000
63	A	560	LEU	0	-0.059	-0.037	13.699	0.026	0.026	0.000	0.000	0.000	0.000
64	A	561	LYS	1	0.767	0.883	17.818	-0.081	-0.081	0.000	0.000	0.000	0.000
65	A	562	GLN	0	-0.084	-0.046	21.081	0.006	0.006	0.000	0.000	0.000	0.000
66	A	563	ASN	0	-0.029	-0.007	15.807	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	564	GLU	-1	-0.928	-0.956	18.011	0.205	0.205	0.000	0.000	0.000	0.000
68	A	565	ALA	0	-0.033	-0.003	13.073	0.035	0.035	0.000	0.000	0.000	0.000
69	A	566	GLY	0	-0.013	-0.030	13.544	0.055	0.055	0.000	0.000	0.000	0.000
70	A	567	ARG	1	0.932	0.959	14.494	-0.040	-0.040	0.000	0.000	0.000	0.000
71	A	568	VAL	0	0.030	0.014	12.008	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	569	THR	0	-0.013	0.002	14.318	0.027	0.027	0.000	0.000	0.000	0.000
73	A	570	ILE	0	-0.024	-0.005	15.155	-0.028	-0.028	0.000	0.000	0.000	0.000
74	A	571	LEU	0	-0.014	-0.004	17.389	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	572	PRO	0	-0.027	-0.007	19.322	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	573	LEU	0	0.032	0.000	20.487	0.000	0.000	0.000	0.000	0.000	0.000
77	A	574	ASP	-1	-0.821	-0.915	23.226	-0.037	-0.037	0.000	0.000	0.000	0.000
78	A	575	LEU	0	-0.070	-0.036	25.403	0.005	0.005	0.000	0.000	0.000	0.000
79	A	576	ILE	0	-0.083	-0.025	21.728	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	577	ASP	-1	-0.815	-0.885	25.591	-0.073	-0.073	0.000	0.000	0.000	0.000
81	A	578	GLY	0	0.025	-0.002	26.871	-0.010	-0.010	0.000	0.000	0.000	0.000
82	A	579	SER	0	-0.085	-0.053	27.652	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	580	PHE	0	-0.014	-0.018	28.992	-0.005	-0.005	0.000	0.000	0.000	0.000
84	A	581	ASN	0	-0.018	-0.004	31.648	0.005	0.005	0.000	0.000	0.000	0.000
85	A	582	ARG	1	0.831	0.878	30.472	0.095	0.095	0.000	0.000	0.000	0.000
86	A	583	ILE	0	-0.016	-0.011	33.617	0.005	0.005	0.000	0.000	0.000	0.000
87	A	584	SER	0	0.022	-0.003	36.948	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	585	GLY	0	0.002	0.003	39.622	0.002	0.002	0.000	0.000	0.000	0.000
89	A	586	LEU	0	-0.006	0.007	33.212	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	587	GLU	-1	-0.806	-0.928	34.846	-0.078	-0.078	0.000	0.000	0.000	0.000
91	A	588	ASN	0	-0.072	-0.027	35.892	0.001	0.001	0.000	0.000	0.000	0.000
92	A	589	GLU	-1	-0.837	-0.867	36.436	-0.064	-0.064	0.000	0.000	0.000	0.000
93	A	590	ARG	1	0.986	0.983	36.585	0.072	0.072	0.000	0.000	0.000	0.000
94	A	591	GLY	0	0.035	0.017	33.500	0.000	0.000	0.000	0.000	0.000	0.000
95	A	592	PHE	0	-0.020	0.020	31.690	-0.010	-0.010	0.000	0.000	0.000	0.000
96	A	593	VAL	0	-0.010	0.005	26.793	0.002	0.002	0.000	0.000	0.000	0.000
97	A	594	GLY	0	0.041	-0.002	28.792	0.003	0.003	0.000	0.000	0.000	0.000
98	A	595	TYR	0	-0.012	-0.011	27.725	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	596	ALA	0	0.047	0.013	22.527	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	597	VAL	0	-0.042	-0.022	23.575	-0.010	-0.010	0.000	0.000	0.000	0.000
101	A	598	ASP	-1	-0.787	-0.853	25.098	-0.111	-0.111	0.000	0.000	0.000	0.000
102	A	599	LEU	0	-0.075	-0.031	23.466	0.000	0.000	0.000	0.000	0.000	0.000
103	A	600	VAL	0	-0.066	-0.023	18.630	-0.013	-0.013	0.000	0.000	0.000	0.000
104	A	601	LYS	1	0.851	0.927	20.495	0.187	0.187	0.000	0.000	0.000	0.000
105	A	602	PHE	0	0.050	0.023	17.230	-0.027	-0.027	0.000	0.000	0.000	0.000
106	A	603	PRO	0	0.033	0.014	18.446	0.017	0.017	0.000	0.000	0.000	0.000
107	A	604	SER	0	0.051	0.003	21.391	0.003	0.003	0.000	0.000	0.000	0.000
108	A	605	ASP	-1	-0.859	-0.900	22.332	-0.092	-0.092	0.000	0.000	0.000	0.000
109	A	606	LEU	0	-0.035	-0.029	18.250	0.003	0.003	0.000	0.000	0.000	0.000
110	A	607	GLU	-1	-0.919	-0.949	22.232	-0.110	-0.110	0.000	0.000	0.000	0.000
111	A	608	VAL	0	0.005	-0.009	24.769	-0.008	-0.008	0.000	0.000	0.000	0.000
112	A	609	LEU	0	0.001	0.005	17.183	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	610	GLY	0	0.044	0.021	21.690	-0.013	-0.013	0.000	0.000	0.000	0.000
114	A	611	GLY	0	0.001	-0.002	22.747	-0.003	-0.003	0.000	0.000	0.000	0.000
115	A	612	PHE	0	-0.010	-0.005	20.445	0.000	0.000	0.000	0.000	0.000	0.000
116	A	613	LEU	0	-0.058	-0.017	17.375	-0.006	-0.006	0.000	0.000	0.000	0.000
117	A	614	PHE	0	-0.016	-0.017	18.234	-0.009	-0.009	0.000	0.000	0.000	0.000
118	A	615	GLY	0	0.034	0.048	23.359	0.009	0.009	0.000	0.000	0.000	0.000
119	A	616	ASN	0	-0.055	-0.031	26.948	-0.006	-0.006	0.000	0.000	0.000	0.000
120	A	617	SER	0	-0.046	-0.033	24.904	0.004	0.004	0.000	0.000	0.000	0.000
121	A	618	VAL	0	-0.038	-0.022	27.013	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	619	VAL	0	0.019	0.023	23.687	-0.008	-0.008	0.000	0.000	0.000	0.000
123	A	620	VAL	0	-0.024	-0.028	26.630	0.011	0.011	0.000	0.000	0.000	0.000
124	A	621	GLU	-1	-0.901	-0.968	27.697	-0.111	-0.111	0.000	0.000	0.000	0.000
125	A	622	THR	0	-0.023	-0.037	28.620	-0.004	-0.004	0.000	0.000	0.000	0.000
126	A	623	LEU	0	0.063	0.018	28.671	0.003	0.003	0.000	0.000	0.000	0.000
127	A	624	ASP	-1	-0.923	-0.959	30.640	-0.074	-0.074	0.000	0.000	0.000	0.000
128	A	625	ASP	-1	-0.757	-0.858	32.410	-0.089	-0.089	0.000	0.000	0.000	0.000
129	A	626	ALA	0	0.006	0.012	29.978	0.003	0.003	0.000	0.000	0.000	0.000
130	A	627	ILE	0	-0.023	-0.025	32.036	0.005	0.005	0.000	0.000	0.000	0.000
131	A	628	ARG	1	0.787	0.893	34.679	0.084	0.084	0.000	0.000	0.000	0.000
132	A	629	MET	0	0.032	0.018	33.017	0.004	0.004	0.000	0.000	0.000	0.000
133	A	630	LYS	1	0.846	0.924	31.954	0.097	0.097	0.000	0.000	0.000	0.000
134	A	631	LYS	1	0.896	0.948	35.561	0.072	0.072	0.000	0.000	0.000	0.000
135	A	632	LYS	1	0.805	0.890	39.100	0.066	0.066	0.000	0.000	0.000	0.000
136	A	633	TYR	0	-0.018	-0.034	37.532	0.003	0.003	0.000	0.000	0.000	0.000
137	A	634	ARG	1	0.893	0.952	38.525	0.058	0.058	0.000	0.000	0.000	0.000
138	A	635	LEU	0	0.026	0.034	32.914	0.000	0.000	0.000	0.000	0.000	0.000
139	A	636	ASN	0	-0.023	-0.008	33.747	-0.004	-0.004	0.000	0.000	0.000	0.000
140	A	637	THR	0	0.000	-0.005	29.219	-0.005	-0.005	0.000	0.000	0.000	0.000
141	A	638	ARG	1	0.831	0.898	20.909	0.199	0.199	0.000	0.000	0.000	0.000
142	A	639	ILE	0	0.006	0.006	27.324	0.002	0.002	0.000	0.000	0.000	0.000
143	A	640	ALA	0	0.016	0.015	22.799	-0.003	-0.003	0.000	0.000	0.000	0.000
144	A	641	THR	0	-0.045	-0.045	24.695	0.004	0.004	0.000	0.000	0.000	0.000
145	A	642	LEU	0	0.015	0.005	23.578	-0.016	-0.016	0.000	0.000	0.000	0.000
146	A	643	ASP	-1	-0.865	-0.907	22.618	-0.168	-0.168	0.000	0.000	0.000	0.000
147	A	644	GLY	0	-0.001	0.003	20.869	-0.010	-0.010	0.000	0.000	0.000	0.000
148	A	645	GLU	-1	-0.888	-0.908	21.592	-0.138	-0.138	0.000	0.000	0.000	0.000
149	A	646	LEU	0	-0.010	-0.017	21.644	-0.003	-0.003	0.000	0.000	0.000	0.000
150	A	647	ILE	0	-0.023	-0.006	24.692	0.011	0.011	0.000	0.000	0.000	0.000
151	A	648	SER	0	0.020	-0.005	26.940	0.000	0.000	0.000	0.000	0.000	0.000
152	A	649	GLY	0	0.094	0.039	27.790	0.007	0.007	0.000	0.000	0.000	0.000
153	A	650	ARG	1	0.901	0.931	30.349	0.079	0.079	0.000	0.000	0.000	0.000
154	A	651	GLY	0	-0.028	-0.008	31.477	0.006	0.006	0.000	0.000	0.000	0.000
155	A	652	ALA	0	-0.020	0.010	28.245	0.003	0.003	0.000	0.000	0.000	0.000
156	A	653	ILE	0	0.033	0.012	28.286	-0.007	-0.007	0.000	0.000	0.000	0.000
157	A	654	THR	0	-0.036	-0.007	22.178	0.003	0.003	0.000	0.000	0.000	0.000
158	A	655	GLY	0	0.072	0.022	24.294	-0.006	-0.006	0.000	0.000	0.000	0.000
159	A	656	GLY	0	-0.011	0.007	24.410	0.006	0.006	0.000	0.000	0.000	0.000
160	A	657	ARG	1	0.812	0.874	21.073	0.140	0.140	0.000	0.000	0.000	0.000
161	A	658	GLU	-1	-0.926	-0.946	17.715	-0.161	-0.161	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:498:GLY)