FMO DATABASE

FMODB ID: 6YN2Z

Calculation Name: 3DQG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DQG

Chain ID: A

ChEMBL ID:

UniProt ID: P11141

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:

Apendix: None

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	148
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1242495.118919
FMO2-HF: Nuclear repulsion	1186836.868092
FMO2-HF: Total energy	-55658.250828
FMO2-MP2: Total energy	-55821.462125

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:418:ASP)

Summations of interaction energy for fragment #1(A:418:ASP)

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.
11.027	16.224	0.195	-2.276	-3.115	0.001

Interaction energy analysis for fragmet #1(A:418:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.891 / q_NPA : -0.960

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	420	THR	0	0.013	0.012	3.854	5.575	7.622	-0.018	-1.035	-0.994	0.001
4	A	421	PRO	0	0.035	0.027	6.020	-2.795	-2.795	0.000	0.000	0.000	0.000
5	A	422	LEU	0	-0.031	-0.041	8.042	-3.916	-3.916	0.000	0.000	0.000	0.000
6	A	423	SER	0	-0.080	-0.096	11.314	1.388	1.388	0.000	0.000	0.000	0.000
7	A	424	LEU	0	-0.022	-0.003	10.552	-0.530	-0.530	0.000	0.000	0.000	0.000
8	A	425	GLY	0	0.029	0.004	14.739	-0.257	-0.257	0.000	0.000	0.000	0.000
9	A	426	ILE	0	-0.001	0.006	18.096	0.115	0.115	0.000	0.000	0.000	0.000
10	A	427	GLU	-1	-0.824	-0.887	21.574	11.594	11.594	0.000	0.000	0.000	0.000
11	A	428	THR	0	-0.058	-0.040	24.812	-0.397	-0.397	0.000	0.000	0.000	0.000
12	A	429	LEU	0	0.044	-0.002	27.458	-0.075	-0.075	0.000	0.000	0.000	0.000
13	A	430	GLY	0	0.037	0.027	30.903	0.056	0.056	0.000	0.000	0.000	0.000
14	A	431	GLY	0	0.008	0.019	28.690	-0.060	-0.060	0.000	0.000	0.000	0.000
15	A	432	ILE	0	0.004	0.015	25.829	0.352	0.352	0.000	0.000	0.000	0.000
16	A	433	MET	0	-0.047	-0.006	18.045	0.002	0.002	0.000	0.000	0.000	0.000
17	A	434	THR	0	-0.016	0.001	21.965	-0.181	-0.181	0.000	0.000	0.000	0.000
18	A	435	LYS	1	0.871	0.939	17.129	-16.027	-16.027	0.000	0.000	0.000	0.000
19	A	436	LEU	0	0.023	0.011	16.528	-0.458	-0.458	0.000	0.000	0.000	0.000
20	A	437	ILE	0	-0.023	-0.010	10.269	0.205	0.205	0.000	0.000	0.000	0.000
21	A	438	THR	0	0.023	0.014	12.937	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	439	ARG	1	0.931	0.973	10.632	-22.963	-22.963	0.000	0.000	0.000	0.000
23	A	440	ASN	0	-0.039	-0.033	7.584	0.925	0.925	0.000	0.000	0.000	0.000
24	A	441	THR	0	-0.072	-0.020	8.173	-1.379	-1.379	0.000	0.000	0.000	0.000
25	A	442	THR	0	0.025	-0.002	3.151	3.900	4.138	0.012	-0.099	-0.151	0.000
26	A	443	ILE	0	-0.063	-0.009	2.939	-7.817	-5.908	0.183	-0.748	-1.343	0.003
27	A	444	PRO	0	0.012	0.005	3.460	1.818	2.239	0.012	-0.260	-0.173	-0.002
28	A	445	THR	0	-0.059	-0.033	7.014	-1.852	-1.852	0.000	0.000	0.000	0.000
29	A	446	LYS	1	0.973	0.994	9.654	-16.599	-16.599	0.000	0.000	0.000	0.000
30	A	447	LYS	1	0.903	0.962	12.002	-20.553	-20.553	0.000	0.000	0.000	0.000
31	A	448	SER	0	0.011	0.010	15.677	0.050	0.050	0.000	0.000	0.000	0.000
32	A	449	GLN	0	0.027	0.018	19.459	0.473	0.473	0.000	0.000	0.000	0.000
33	A	450	VAL	0	-0.028	-0.007	22.399	-0.071	-0.071	0.000	0.000	0.000	0.000
34	A	451	PHE	0	0.006	0.002	22.586	-0.058	-0.058	0.000	0.000	0.000	0.000
35	A	452	SER	0	0.030	0.002	27.956	-0.272	-0.272	0.000	0.000	0.000	0.000
36	A	453	THR	0	-0.039	-0.015	31.283	0.237	0.237	0.000	0.000	0.000	0.000
37	A	454	ALA	0	0.014	-0.002	33.951	-0.031	-0.031	0.000	0.000	0.000	0.000
38	A	455	ALA	0	-0.011	-0.007	35.637	-0.202	-0.202	0.000	0.000	0.000	0.000
39	A	456	ASP	-1	-0.836	-0.920	39.032	7.521	7.521	0.000	0.000	0.000	0.000
40	A	457	GLY	0	-0.059	-0.034	41.270	-0.079	-0.079	0.000	0.000	0.000	0.000
41	A	458	GLN	0	-0.019	-0.006	33.477	-0.110	-0.110	0.000	0.000	0.000	0.000
42	A	459	THR	0	0.034	0.018	37.483	0.167	0.167	0.000	0.000	0.000	0.000
43	A	460	GLN	0	-0.003	0.008	33.075	0.403	0.403	0.000	0.000	0.000	0.000
44	A	461	VAL	0	0.015	0.013	29.183	-0.086	-0.086	0.000	0.000	0.000	0.000
45	A	462	GLN	0	0.030	0.018	27.964	0.089	0.089	0.000	0.000	0.000	0.000
46	A	463	ILE	0	-0.001	0.005	22.324	0.081	0.081	0.000	0.000	0.000	0.000
47	A	464	LYS	1	0.825	0.898	23.473	-11.657	-11.657	0.000	0.000	0.000	0.000
48	A	465	VAL	0	0.037	0.021	16.944	0.075	0.075	0.000	0.000	0.000	0.000
49	A	466	PHE	0	0.040	0.014	18.664	-0.103	-0.103	0.000	0.000	0.000	0.000
50	A	467	GLN	0	0.027	-0.005	10.902	-0.745	-0.745	0.000	0.000	0.000	0.000
51	A	468	GLY	0	0.020	0.008	15.518	-0.691	-0.691	0.000	0.000	0.000	0.000
52	A	469	GLU	-1	-0.727	-0.837	14.562	21.497	21.497	0.000	0.000	0.000	0.000
53	A	470	ARG	1	0.803	0.889	18.348	-13.403	-13.403	0.000	0.000	0.000	0.000
54	A	471	GLU	-1	-0.904	-0.952	22.105	12.231	12.231	0.000	0.000	0.000	0.000
55	A	472	MET	0	-0.007	0.029	24.479	-0.323	-0.323	0.000	0.000	0.000	0.000
56	A	473	ALA	0	0.021	-0.001	23.184	0.445	0.445	0.000	0.000	0.000	0.000
57	A	474	THR	0	-0.019	-0.022	22.967	0.540	0.540	0.000	0.000	0.000	0.000
58	A	475	SER	0	-0.036	-0.020	24.305	-0.209	-0.209	0.000	0.000	0.000	0.000
59	A	476	ASN	0	-0.066	-0.031	19.041	0.809	0.809	0.000	0.000	0.000	0.000
60	A	477	LYS	1	0.964	0.983	14.663	-20.743	-20.743	0.000	0.000	0.000	0.000
61	A	478	LEU	0	-0.037	-0.011	18.273	0.563	0.563	0.000	0.000	0.000	0.000
62	A	479	LEU	0	-0.063	-0.042	13.660	0.301	0.301	0.000	0.000	0.000	0.000
63	A	480	GLY	0	0.039	0.020	17.965	0.016	0.016	0.000	0.000	0.000	0.000
64	A	481	GLN	0	-0.043	-0.031	20.596	0.211	0.211	0.000	0.000	0.000	0.000
65	A	482	PHE	0	-0.002	0.004	21.619	-0.227	-0.227	0.000	0.000	0.000	0.000
66	A	483	SER	0	0.011	-0.012	26.131	0.152	0.152	0.000	0.000	0.000	0.000
67	A	484	LEU	0	-0.030	0.017	27.545	0.020	0.020	0.000	0.000	0.000	0.000
68	A	485	VAL	0	0.022	-0.006	30.482	-0.185	-0.185	0.000	0.000	0.000	0.000
69	A	486	GLY	0	-0.017	-0.013	34.253	0.013	0.013	0.000	0.000	0.000	0.000
70	A	487	ILE	0	-0.023	-0.010	32.019	-0.059	-0.059	0.000	0.000	0.000	0.000
71	A	488	PRO	0	0.001	-0.005	36.266	-0.190	-0.190	0.000	0.000	0.000	0.000
72	A	489	PRO	0	0.019	0.012	39.091	0.121	0.121	0.000	0.000	0.000	0.000
73	A	490	ALA	0	0.010	0.008	39.157	-0.143	-0.143	0.000	0.000	0.000	0.000
74	A	491	PRO	0	0.007	0.007	40.685	0.073	0.073	0.000	0.000	0.000	0.000
75	A	492	ARG	1	0.845	0.895	37.922	-7.737	-7.737	0.000	0.000	0.000	0.000
76	A	493	GLY	0	-0.016	-0.012	35.044	-0.115	-0.115	0.000	0.000	0.000	0.000
77	A	494	VAL	0	-0.024	0.000	35.690	0.057	0.057	0.000	0.000	0.000	0.000
78	A	495	PRO	0	-0.023	-0.007	33.887	0.137	0.137	0.000	0.000	0.000	0.000
79	A	496	GLN	0	0.018	0.025	30.420	0.098	0.098	0.000	0.000	0.000	0.000
80	A	497	VAL	0	0.012	-0.002	26.598	-0.014	-0.014	0.000	0.000	0.000	0.000
81	A	498	GLU	-1	-0.807	-0.884	24.557	11.387	11.387	0.000	0.000	0.000	0.000
82	A	499	VAL	0	-0.015	-0.003	20.170	0.048	0.048	0.000	0.000	0.000	0.000
83	A	500	THR	0	0.005	-0.011	17.227	0.219	0.219	0.000	0.000	0.000	0.000
84	A	501	PHE	0	-0.030	-0.011	13.788	-0.051	-0.051	0.000	0.000	0.000	0.000
85	A	502	ASP	-1	-0.944	-0.982	13.024	20.104	20.104	0.000	0.000	0.000	0.000
86	A	503	ILE	0	0.004	0.013	7.352	0.032	0.032	0.000	0.000	0.000	0.000
87	A	504	ASP	-1	-0.751	-0.891	8.213	31.430	31.430	0.000	0.000	0.000	0.000
88	A	505	ALA	0	-0.003	-0.028	4.419	2.480	2.454	-0.001	-0.008	0.035	0.000
89	A	506	ASN	0	-0.018	-0.006	3.723	14.495	15.060	0.008	-0.126	-0.447	-0.001
90	A	507	GLY	0	0.032	0.023	5.913	-0.233	-0.233	0.000	0.000	0.000	0.000
91	A	508	ILE	0	-0.034	0.026	6.970	-4.048	-4.048	0.000	0.000	0.000	0.000
92	A	509	VAL	0	-0.009	-0.016	10.512	0.049	0.049	0.000	0.000	0.000	0.000
93	A	510	ASN	0	-0.017	0.002	12.658	-1.635	-1.635	0.000	0.000	0.000	0.000
94	A	511	VAL	0	0.016	-0.004	15.823	0.250	0.250	0.000	0.000	0.000	0.000
95	A	512	SER	0	0.048	0.020	18.039	-0.573	-0.573	0.000	0.000	0.000	0.000
96	A	513	ALA	0	-0.013	-0.008	21.290	0.173	0.173	0.000	0.000	0.000	0.000
97	A	514	ARG	1	0.938	0.960	24.402	-10.959	-10.959	0.000	0.000	0.000	0.000
98	A	515	ASP	-1	-0.860	-0.923	26.988	9.297	9.297	0.000	0.000	0.000	0.000
99	A	516	ARG	1	0.872	0.908	26.880	-10.638	-10.638	0.000	0.000	0.000	0.000
100	A	517	GLY	0	-0.036	-0.008	31.076	-0.172	-0.172	0.000	0.000	0.000	0.000
101	A	518	THR	0	-0.067	-0.051	33.828	-0.163	-0.163	0.000	0.000	0.000	0.000
102	A	519	GLY	0	-0.019	-0.004	30.813	-0.115	-0.115	0.000	0.000	0.000	0.000
103	A	520	LYS	1	0.918	0.966	30.282	-8.488	-8.488	0.000	0.000	0.000	0.000
104	A	521	GLU	-1	-0.902	-0.957	25.531	11.704	11.704	0.000	0.000	0.000	0.000
105	A	522	GLN	0	-0.044	-0.015	25.983	-0.065	-0.065	0.000	0.000	0.000	0.000
106	A	523	GLN	0	0.013	-0.004	20.484	0.216	0.216	0.000	0.000	0.000	0.000
107	A	524	ILE	0	-0.022	0.007	19.166	-0.419	-0.419	0.000	0.000	0.000	0.000
108	A	525	VAL	0	0.010	0.005	15.591	0.557	0.557	0.000	0.000	0.000	0.000
109	A	526	ILE	0	-0.020	-0.010	14.291	-0.497	-0.497	0.000	0.000	0.000	0.000
110	A	527	GLN	0	0.019	0.012	10.954	3.049	3.049	0.000	0.000	0.000	0.000
111	A	528	SER	0	-0.076	-0.074	9.304	-0.217	-0.217	0.000	0.000	0.000	0.000
112	A	529	SER	0	0.043	0.011	5.108	-1.090	-1.047	-0.001	0.000	-0.042	0.000
113	A	530	GLY	0	0.009	0.004	8.188	-2.750	-2.750	0.000	0.000	0.000	0.000
114	A	531	GLY	0	-0.019	0.000	9.833	-2.255	-2.255	0.000	0.000	0.000	0.000
115	A	532	LEU	0	-0.067	-0.040	11.614	-2.195	-2.195	0.000	0.000	0.000	0.000
116	A	533	SER	0	0.057	0.032	11.247	2.498	2.498	0.000	0.000	0.000	0.000
117	A	534	LYS	1	0.996	0.986	10.165	-24.713	-24.713	0.000	0.000	0.000	0.000
118	A	535	ASP	-1	-0.883	-0.949	11.664	19.133	19.133	0.000	0.000	0.000	0.000
119	A	536	GLN	0	-0.006	0.007	14.866	-0.027	-0.027	0.000	0.000	0.000	0.000
120	A	537	ILE	0	0.011	0.006	9.017	-0.571	-0.571	0.000	0.000	0.000	0.000
121	A	538	GLU	-1	-0.928	-0.972	13.156	21.782	21.782	0.000	0.000	0.000	0.000
122	A	539	ASN	0	-0.016	-0.011	14.811	-0.871	-0.871	0.000	0.000	0.000	0.000
123	A	540	MET	0	0.031	0.019	15.744	-0.549	-0.549	0.000	0.000	0.000	0.000
124	A	541	ILE	0	-0.021	0.001	12.361	-0.616	-0.616	0.000	0.000	0.000	0.000
125	A	542	LYS	1	0.985	0.996	16.975	-15.844	-15.844	0.000	0.000	0.000	0.000
126	A	543	GLU	-1	-0.969	-1.001	19.912	13.761	13.761	0.000	0.000	0.000	0.000
127	A	544	ALA	0	-0.013	-0.007	19.648	-0.841	-0.841	0.000	0.000	0.000	0.000
128	A	545	GLU	-1	-0.936	-0.971	19.066	15.783	15.783	0.000	0.000	0.000	0.000
129	A	546	LYS	1	0.874	0.938	22.564	-12.771	-12.771	0.000	0.000	0.000	0.000
130	A	547	ASN	0	-0.072	-0.043	24.874	-1.001	-1.001	0.000	0.000	0.000	0.000
131	A	548	ALA	0	0.047	0.038	24.380	-0.293	-0.293	0.000	0.000	0.000	0.000
132	A	549	ALA	0	-0.009	-0.011	26.262	-0.330	-0.330	0.000	0.000	0.000	0.000
133	A	550	GLU	-1	-0.897	-0.954	29.623	9.314	9.314	0.000	0.000	0.000	0.000
134	A	551	ASP	-1	-0.749	-0.853	26.184	11.909	11.909	0.000	0.000	0.000	0.000
135	A	552	ALA	0	-0.002	0.005	29.624	-0.221	-0.221	0.000	0.000	0.000	0.000
136	A	553	LYS	1	0.827	0.923	31.301	-9.679	-9.679	0.000	0.000	0.000	0.000
137	A	554	ARG	1	0.825	0.892	30.594	-10.522	-10.522	0.000	0.000	0.000	0.000
138	A	555	LYS	1	0.906	0.942	34.867	-8.426	-8.426	0.000	0.000	0.000	0.000
139	A	556	GLU	-1	-0.880	-0.919	35.359	8.889	8.889	0.000	0.000	0.000	0.000
140	A	557	LEU	0	0.006	0.011	36.949	0.088	0.088	0.000	0.000	0.000	0.000
141	A	558	VAL	0	-0.005	0.002	33.010	0.049	0.049	0.000	0.000	0.000	0.000
142	A	559	GLU	-1	-0.830	-0.896	36.381	7.945	7.945	0.000	0.000	0.000	0.000
143	A	560	VAL	0	-0.020	-0.012	34.851	0.301	0.301	0.000	0.000	0.000	0.000
144	A	561	ILE	0	0.016	0.008	34.129	-0.279	-0.279	0.000	0.000	0.000	0.000
145	A	562	ASN	0	-0.028	-0.036	36.245	0.264	0.264	0.000	0.000	0.000	0.000
146	A	563	GLN	0	-0.040	-0.010	35.936	-0.478	-0.478	0.000	0.000	0.000	0.000
147	A	564	ALA	0	0.015	0.026	34.944	0.229	0.229	0.000	0.000	0.000	0.000
148	A	565	GLU	-1	-0.962	-0.983	31.621	9.190	9.190	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:418:ASP)