FMO DATABASE

FMODB ID: ZV68N

Calculation Name: 3DQG-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: 3DQG

Chain ID: A

ChEMBL ID:
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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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1243298.241226
FMO2-HF: Nuclear repulsion	1187639.225356
FMO2-HF: Total energy	-55659.01587
FMO2-MP2: Total energy	-55822.155684

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.
4.111	11.155	0.186	-3.414	-3.817	0.011

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 : -0.843 / q_NPA : -0.918

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	0.020	0.019	3.854	5.333	8.963	-0.005	-1.950	-1.675	0.008
4	A	421	PRO	0	0.032	0.023	5.665	-3.530	-3.530	0.000	0.000	0.000	0.000
5	A	422	LEU	0	-0.027	-0.037	7.599	-4.381	-4.381	0.000	0.000	0.000	0.000
6	A	423	SER	0	-0.057	-0.070	11.037	1.476	1.476	0.000	0.000	0.000	0.000
7	A	424	LEU	0	-0.033	-0.007	10.512	-0.517	-0.517	0.000	0.000	0.000	0.000
8	A	425	GLY	0	0.033	0.008	14.586	-0.270	-0.270	0.000	0.000	0.000	0.000
9	A	426	ILE	0	0.005	0.008	18.153	0.103	0.103	0.000	0.000	0.000	0.000
10	A	427	GLU	-1	-0.814	-0.884	21.559	11.813	11.813	0.000	0.000	0.000	0.000
11	A	428	THR	0	-0.050	-0.029	24.657	-0.329	-0.329	0.000	0.000	0.000	0.000
12	A	429	LEU	0	0.050	0.004	27.501	-0.070	-0.070	0.000	0.000	0.000	0.000
13	A	430	GLY	0	0.055	0.033	30.858	0.062	0.062	0.000	0.000	0.000	0.000
14	A	431	GLY	0	-0.005	0.007	28.523	-0.044	-0.044	0.000	0.000	0.000	0.000
15	A	432	ILE	0	0.022	0.021	25.786	0.351	0.351	0.000	0.000	0.000	0.000
16	A	433	MET	0	-0.054	-0.016	17.834	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	434	THR	0	-0.016	-0.005	22.255	-0.178	-0.178	0.000	0.000	0.000	0.000
18	A	435	LYS	1	0.818	0.907	16.910	-16.392	-16.392	0.000	0.000	0.000	0.000
19	A	436	LEU	0	0.026	0.011	16.893	-0.464	-0.464	0.000	0.000	0.000	0.000
20	A	437	ILE	0	-0.012	-0.004	10.465	0.213	0.213	0.000	0.000	0.000	0.000
21	A	438	THR	0	0.029	0.018	12.907	-0.050	-0.050	0.000	0.000	0.000	0.000
22	A	439	ARG	1	0.908	0.967	9.958	-23.210	-23.210	0.000	0.000	0.000	0.000
23	A	440	ASN	0	-0.051	-0.036	7.554	0.161	0.161	0.000	0.000	0.000	0.000
24	A	441	THR	0	-0.054	-0.023	7.987	-1.772	-1.772	0.000	0.000	0.000	0.000
25	A	442	THR	0	0.008	-0.005	3.143	2.825	3.191	0.024	-0.170	-0.221	0.001
26	A	443	ILE	0	-0.049	-0.003	2.972	-8.555	-6.446	0.149	-0.903	-1.355	0.005
27	A	444	PRO	0	0.009	0.003	3.397	1.659	2.060	0.014	-0.262	-0.153	-0.002
28	A	445	THR	0	-0.057	-0.036	7.000	-2.067	-2.067	0.000	0.000	0.000	0.000
29	A	446	LYS	1	0.879	0.939	9.802	-17.469	-17.469	0.000	0.000	0.000	0.000
30	A	447	LYS	1	0.905	0.960	12.252	-20.860	-20.860	0.000	0.000	0.000	0.000
31	A	448	SER	0	0.015	0.011	15.935	0.054	0.054	0.000	0.000	0.000	0.000
32	A	449	GLN	0	0.029	0.019	19.698	0.445	0.445	0.000	0.000	0.000	0.000
33	A	450	VAL	0	-0.027	-0.006	22.672	-0.060	-0.060	0.000	0.000	0.000	0.000
34	A	451	PHE	0	0.005	0.000	22.766	-0.074	-0.074	0.000	0.000	0.000	0.000
35	A	452	SER	0	0.029	-0.004	28.175	-0.273	-0.273	0.000	0.000	0.000	0.000
36	A	453	THR	0	-0.039	-0.013	31.499	0.240	0.240	0.000	0.000	0.000	0.000
37	A	454	ALA	0	0.011	-0.004	34.166	-0.036	-0.036	0.000	0.000	0.000	0.000
38	A	455	ALA	0	-0.009	-0.004	35.854	-0.203	-0.203	0.000	0.000	0.000	0.000
39	A	456	ASP	-1	-0.831	-0.920	39.246	7.634	7.634	0.000	0.000	0.000	0.000
40	A	457	GLY	0	-0.047	-0.025	41.482	-0.082	-0.082	0.000	0.000	0.000	0.000
41	A	458	GLN	0	-0.022	-0.014	33.787	-0.087	-0.087	0.000	0.000	0.000	0.000
42	A	459	THR	0	0.036	0.018	37.674	0.162	0.162	0.000	0.000	0.000	0.000
43	A	460	GLN	0	-0.008	0.003	33.067	0.338	0.338	0.000	0.000	0.000	0.000
44	A	461	VAL	0	0.014	0.015	29.462	-0.089	-0.089	0.000	0.000	0.000	0.000
45	A	462	GLN	0	0.014	0.005	27.828	0.090	0.090	0.000	0.000	0.000	0.000
46	A	463	ILE	0	-0.011	0.004	22.438	0.085	0.085	0.000	0.000	0.000	0.000
47	A	464	LYS	1	0.806	0.889	23.385	-11.806	-11.806	0.000	0.000	0.000	0.000
48	A	465	VAL	0	0.029	0.017	16.822	0.093	0.093	0.000	0.000	0.000	0.000
49	A	466	PHE	0	0.040	0.012	18.511	-0.103	-0.103	0.000	0.000	0.000	0.000
50	A	467	GLN	0	0.024	-0.008	10.705	-0.601	-0.601	0.000	0.000	0.000	0.000
51	A	468	GLY	0	0.019	0.006	15.337	-0.707	-0.707	0.000	0.000	0.000	0.000
52	A	469	GLU	-1	-0.715	-0.855	13.982	21.886	21.886	0.000	0.000	0.000	0.000
53	A	470	ARG	1	0.814	0.902	17.864	-13.474	-13.474	0.000	0.000	0.000	0.000
54	A	471	GLU	-1	-0.899	-0.948	21.630	12.319	12.319	0.000	0.000	0.000	0.000
55	A	472	MET	0	-0.012	0.021	23.980	-0.303	-0.303	0.000	0.000	0.000	0.000
56	A	473	ALA	0	0.013	-0.006	23.004	0.493	0.493	0.000	0.000	0.000	0.000
57	A	474	THR	0	0.007	-0.012	22.793	0.579	0.579	0.000	0.000	0.000	0.000
58	A	475	SER	0	-0.044	-0.021	24.075	-0.200	-0.200	0.000	0.000	0.000	0.000
59	A	476	ASN	0	-0.095	-0.034	18.863	1.050	1.050	0.000	0.000	0.000	0.000
60	A	477	LYS	1	0.956	0.983	14.104	-21.669	-21.669	0.000	0.000	0.000	0.000
61	A	478	LEU	0	-0.029	-0.007	18.123	0.602	0.602	0.000	0.000	0.000	0.000
62	A	479	LEU	0	-0.058	-0.039	13.460	0.318	0.318	0.000	0.000	0.000	0.000
63	A	480	GLY	0	0.038	0.018	17.855	0.006	0.006	0.000	0.000	0.000	0.000
64	A	481	GLN	0	-0.041	-0.031	20.505	0.189	0.189	0.000	0.000	0.000	0.000
65	A	482	PHE	0	0.012	0.012	21.747	-0.232	-0.232	0.000	0.000	0.000	0.000
66	A	483	SER	0	0.020	-0.004	26.055	0.155	0.155	0.000	0.000	0.000	0.000
67	A	484	LEU	0	-0.017	0.023	27.486	0.012	0.012	0.000	0.000	0.000	0.000
68	A	485	VAL	0	0.036	0.001	30.665	-0.194	-0.194	0.000	0.000	0.000	0.000
69	A	486	GLY	0	0.010	0.002	34.434	0.021	0.021	0.000	0.000	0.000	0.000
70	A	487	ILE	0	-0.009	-0.005	32.070	-0.055	-0.055	0.000	0.000	0.000	0.000
71	A	488	PRO	0	0.016	0.002	36.459	-0.180	-0.180	0.000	0.000	0.000	0.000
72	A	489	PRO	0	0.001	0.002	39.293	0.118	0.118	0.000	0.000	0.000	0.000
73	A	490	ALA	0	0.024	0.015	39.362	-0.144	-0.144	0.000	0.000	0.000	0.000
74	A	491	PRO	0	0.012	0.009	40.897	0.073	0.073	0.000	0.000	0.000	0.000
75	A	492	ARG	1	0.798	0.855	38.148	-7.796	-7.796	0.000	0.000	0.000	0.000
76	A	493	GLY	0	-0.011	-0.009	35.260	-0.115	-0.115	0.000	0.000	0.000	0.000
77	A	494	VAL	0	-0.024	-0.001	35.909	0.057	0.057	0.000	0.000	0.000	0.000
78	A	495	PRO	0	-0.026	-0.010	34.055	0.138	0.138	0.000	0.000	0.000	0.000
79	A	496	GLN	0	0.038	0.046	30.667	0.334	0.334	0.000	0.000	0.000	0.000
80	A	497	VAL	0	0.008	-0.004	26.847	-0.019	-0.019	0.000	0.000	0.000	0.000
81	A	498	GLU	-1	-0.795	-0.874	24.748	11.502	11.502	0.000	0.000	0.000	0.000
82	A	499	VAL	0	-0.012	-0.007	20.454	0.061	0.061	0.000	0.000	0.000	0.000
83	A	500	THR	0	0.012	-0.007	17.350	0.222	0.222	0.000	0.000	0.000	0.000
84	A	501	PHE	0	-0.026	-0.009	14.058	-0.023	-0.023	0.000	0.000	0.000	0.000
85	A	502	ASP	-1	-0.873	-0.933	13.386	19.661	19.661	0.000	0.000	0.000	0.000
86	A	503	ILE	0	0.008	0.014	7.516	-0.009	-0.009	0.000	0.000	0.000	0.000
87	A	504	ASP	-1	-0.755	-0.892	8.347	32.584	32.584	0.000	0.000	0.000	0.000
88	A	505	ALA	0	0.003	-0.012	4.486	2.749	2.724	-0.001	-0.008	0.034	0.000
89	A	506	ASN	0	-0.037	-0.019	3.734	11.966	12.490	0.006	-0.121	-0.409	-0.001
90	A	507	GLY	0	0.018	0.016	6.000	-0.264	-0.264	0.000	0.000	0.000	0.000
91	A	508	ILE	0	-0.024	-0.001	6.938	-4.068	-4.068	0.000	0.000	0.000	0.000
92	A	509	VAL	0	-0.009	-0.018	10.514	0.075	0.075	0.000	0.000	0.000	0.000
93	A	510	ASN	0	-0.008	-0.002	12.813	-1.559	-1.559	0.000	0.000	0.000	0.000
94	A	511	VAL	0	-0.001	-0.007	15.975	0.236	0.236	0.000	0.000	0.000	0.000
95	A	512	SER	0	0.031	0.015	18.217	-0.516	-0.516	0.000	0.000	0.000	0.000
96	A	513	ALA	0	-0.013	-0.006	21.468	0.179	0.179	0.000	0.000	0.000	0.000
97	A	514	ARG	1	0.916	0.943	24.593	-11.085	-11.085	0.000	0.000	0.000	0.000
98	A	515	ASP	-1	-0.824	-0.883	27.174	9.344	9.344	0.000	0.000	0.000	0.000
99	A	516	ARG	1	0.830	0.885	27.089	-10.749	-10.749	0.000	0.000	0.000	0.000
100	A	517	GLY	0	-0.045	-0.014	31.269	-0.175	-0.175	0.000	0.000	0.000	0.000
101	A	518	THR	0	-0.064	-0.076	34.050	-0.189	-0.189	0.000	0.000	0.000	0.000
102	A	519	GLY	0	-0.019	-0.001	30.988	-0.108	-0.108	0.000	0.000	0.000	0.000
103	A	520	LYS	1	0.834	0.925	30.450	-8.772	-8.772	0.000	0.000	0.000	0.000
104	A	521	GLU	-1	-0.861	-0.934	25.447	11.815	11.815	0.000	0.000	0.000	0.000
105	A	522	GLN	0	-0.092	-0.037	26.167	-0.230	-0.230	0.000	0.000	0.000	0.000
106	A	523	GLN	0	0.028	0.008	20.788	0.304	0.304	0.000	0.000	0.000	0.000
107	A	524	ILE	0	-0.018	0.012	19.140	-0.433	-0.433	0.000	0.000	0.000	0.000
108	A	525	VAL	0	0.020	0.007	15.726	0.600	0.600	0.000	0.000	0.000	0.000
109	A	526	ILE	0	-0.014	-0.004	14.186	-0.501	-0.501	0.000	0.000	0.000	0.000
110	A	527	GLN	0	0.017	0.012	11.492	2.903	2.903	0.000	0.000	0.000	0.000
111	A	528	SER	0	-0.063	-0.044	9.147	-0.275	-0.275	0.000	0.000	0.000	0.000
112	A	529	SER	0	0.051	0.020	5.054	-0.661	-0.622	-0.001	0.000	-0.038	0.000
113	A	530	GLY	0	0.007	0.001	8.108	-2.859	-2.859	0.000	0.000	0.000	0.000
114	A	531	GLY	0	-0.016	0.001	9.787	-2.292	-2.292	0.000	0.000	0.000	0.000
115	A	532	LEU	0	-0.060	-0.035	11.512	-2.170	-2.170	0.000	0.000	0.000	0.000
116	A	533	SER	0	0.047	0.024	11.138	2.440	2.440	0.000	0.000	0.000	0.000
117	A	534	LYS	1	0.920	0.935	10.242	-23.991	-23.991	0.000	0.000	0.000	0.000
118	A	535	ASP	-1	-0.887	-0.953	11.577	20.046	20.046	0.000	0.000	0.000	0.000
119	A	536	GLN	0	0.004	0.006	14.729	-0.010	-0.010	0.000	0.000	0.000	0.000
120	A	537	ILE	0	0.019	0.009	8.756	-0.631	-0.631	0.000	0.000	0.000	0.000
121	A	538	GLU	-1	-0.854	-0.912	12.877	22.394	22.394	0.000	0.000	0.000	0.000
122	A	539	ASN	0	-0.013	-0.011	14.529	-1.161	-1.161	0.000	0.000	0.000	0.000
123	A	540	MET	0	0.023	0.017	15.384	-0.569	-0.569	0.000	0.000	0.000	0.000
124	A	541	ILE	0	-0.027	-0.003	11.920	-0.698	-0.698	0.000	0.000	0.000	0.000
125	A	542	LYS	1	0.876	0.924	16.570	-16.507	-16.507	0.000	0.000	0.000	0.000
126	A	543	GLU	-1	-0.944	-0.988	19.545	13.748	13.748	0.000	0.000	0.000	0.000
127	A	544	ALA	0	-0.010	-0.004	19.174	-0.853	-0.853	0.000	0.000	0.000	0.000
128	A	545	GLU	-1	-0.860	-0.917	18.729	15.703	15.703	0.000	0.000	0.000	0.000
129	A	546	LYS	1	0.884	0.946	22.127	-12.980	-12.980	0.000	0.000	0.000	0.000
130	A	547	ASN	0	-0.072	-0.046	24.447	-1.007	-1.007	0.000	0.000	0.000	0.000
131	A	548	ALA	0	0.037	0.032	23.894	-0.292	-0.292	0.000	0.000	0.000	0.000
132	A	549	ALA	0	0.002	-0.005	25.789	-0.327	-0.327	0.000	0.000	0.000	0.000
133	A	550	GLU	-1	-0.804	-0.894	29.186	9.338	9.338	0.000	0.000	0.000	0.000
134	A	551	ASP	-1	-0.742	-0.845	25.629	12.087	12.087	0.000	0.000	0.000	0.000
135	A	552	ALA	0	-0.004	0.005	29.141	-0.222	-0.222	0.000	0.000	0.000	0.000
136	A	553	LYS	1	0.751	0.874	30.801	-9.844	-9.844	0.000	0.000	0.000	0.000
137	A	554	ARG	1	0.819	0.883	30.103	-10.616	-10.616	0.000	0.000	0.000	0.000
138	A	555	LYS	1	0.876	0.920	34.368	-8.548	-8.548	0.000	0.000	0.000	0.000
139	A	556	GLU	-1	-0.870	-0.899	35.099	9.144	9.144	0.000	0.000	0.000	0.000
140	A	557	LEU	0	0.015	0.014	36.569	0.086	0.086	0.000	0.000	0.000	0.000
141	A	558	VAL	0	-0.002	-0.001	32.949	0.047	0.047	0.000	0.000	0.000	0.000
142	A	559	GLU	-1	-0.808	-0.860	36.366	7.975	7.975	0.000	0.000	0.000	0.000
143	A	560	VAL	0	-0.023	-0.014	34.793	0.302	0.302	0.000	0.000	0.000	0.000
144	A	561	ILE	0	0.015	0.009	34.494	-0.275	-0.275	0.000	0.000	0.000	0.000
145	A	562	ASN	0	-0.024	-0.031	36.476	0.288	0.288	0.000	0.000	0.000	0.000
146	A	563	GLN	0	-0.038	-0.014	36.237	-0.417	-0.417	0.000	0.000	0.000	0.000
147	A	564	ALA	0	0.005	0.019	35.236	0.228	0.228	0.000	0.000	0.000	0.000
148	A	565	GLU	-1	-0.952	-0.976	31.859	9.144	9.144	0.000	0.000	0.000	0.000

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