FMO DATABASE

FMODB ID: R8928

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	OptAll
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	-1244214.84795
FMO2-HF: Nuclear repulsion	1188555.330659
FMO2-HF: Total energy	-55659.517292
FMO2-MP2: Total energy	-55822.611492

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.
-5.692	1.992	0.86	-3.743	-4.802	0.004

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 : -0.841 / q_NPA : -0.909

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	0.017	0.005	3.921	5.533	8.941	0.003	-1.907	-1.504	0.007
4	A	421	PRO	0	0.010	0.012	5.190	-3.893	-3.754	-0.001	-0.002	-0.137	0.000
5	A	422	LEU	0	-0.040	-0.047	7.232	-4.585	-4.585	0.000	0.000	0.000	0.000
6	A	423	SER	0	-0.061	-0.070	10.653	1.643	1.643	0.000	0.000	0.000	0.000
7	A	424	LEU	0	-0.031	-0.013	10.163	-0.598	-0.598	0.000	0.000	0.000	0.000
8	A	425	GLY	0	0.012	0.000	14.167	-0.433	-0.433	0.000	0.000	0.000	0.000
9	A	426	ILE	0	-0.010	0.009	17.685	0.135	0.135	0.000	0.000	0.000	0.000
10	A	427	GLU	-1	-0.803	-0.880	21.163	11.971	11.971	0.000	0.000	0.000	0.000
11	A	428	THR	0	-0.039	-0.022	24.348	-0.410	-0.410	0.000	0.000	0.000	0.000
12	A	429	LEU	0	0.033	-0.001	27.266	-0.056	-0.056	0.000	0.000	0.000	0.000
13	A	430	GLY	0	0.053	0.032	30.727	0.030	0.030	0.000	0.000	0.000	0.000
14	A	431	GLY	0	-0.013	0.005	28.020	-0.020	-0.020	0.000	0.000	0.000	0.000
15	A	432	ILE	0	0.010	0.016	25.288	0.398	0.398	0.000	0.000	0.000	0.000
16	A	433	MET	0	-0.052	-0.024	17.365	-0.032	-0.032	0.000	0.000	0.000	0.000
17	A	434	THR	0	-0.019	-0.003	21.766	0.034	0.034	0.000	0.000	0.000	0.000
18	A	435	LYS	1	0.805	0.904	16.756	-16.501	-16.501	0.000	0.000	0.000	0.000
19	A	436	LEU	0	0.044	0.020	16.622	-0.351	-0.351	0.000	0.000	0.000	0.000
20	A	437	ILE	0	-0.040	-0.024	10.112	0.293	0.293	0.000	0.000	0.000	0.000
21	A	438	THR	0	0.048	0.038	12.711	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	439	ARG	1	0.923	0.986	9.758	-24.246	-24.246	0.000	0.000	0.000	0.000
23	A	440	ASN	0	-0.040	-0.029	7.242	-0.308	-0.308	0.000	0.000	0.000	0.000
24	A	441	THR	0	-0.043	-0.019	7.907	-1.247	-1.247	0.000	0.000	0.000	0.000
25	A	442	THR	0	0.010	-0.003	3.265	2.653	2.909	0.010	-0.103	-0.163	0.000
26	A	443	ILE	0	-0.055	-0.003	2.619	-7.662	-5.479	0.609	-0.909	-1.884	0.004
27	A	444	PRO	0	0.011	0.008	2.838	0.445	1.389	0.218	-0.614	-0.548	-0.006
28	A	445	THR	0	-0.048	-0.037	6.335	-2.164	-2.164	0.000	0.000	0.000	0.000
29	A	446	LYS	1	0.864	0.927	9.379	-18.228	-18.228	0.000	0.000	0.000	0.000
30	A	447	LYS	1	0.874	0.941	11.714	-20.845	-20.845	0.000	0.000	0.000	0.000
31	A	448	SER	0	0.014	0.009	15.528	0.021	0.021	0.000	0.000	0.000	0.000
32	A	449	GLN	0	0.034	0.028	19.259	0.473	0.473	0.000	0.000	0.000	0.000
33	A	450	VAL	0	-0.022	-0.009	22.490	-0.100	-0.100	0.000	0.000	0.000	0.000
34	A	451	PHE	0	0.011	0.006	22.639	-0.042	-0.042	0.000	0.000	0.000	0.000
35	A	452	SER	0	0.019	-0.019	28.103	-0.285	-0.285	0.000	0.000	0.000	0.000
36	A	453	THR	0	-0.032	-0.004	31.590	0.257	0.257	0.000	0.000	0.000	0.000
37	A	454	ALA	0	0.023	0.006	33.686	-0.051	-0.051	0.000	0.000	0.000	0.000
38	A	455	ALA	0	-0.011	-0.011	35.410	-0.200	-0.200	0.000	0.000	0.000	0.000
39	A	456	ASP	-1	-0.815	-0.915	38.763	7.726	7.726	0.000	0.000	0.000	0.000
40	A	457	GLY	0	-0.032	-0.016	41.134	-0.108	-0.108	0.000	0.000	0.000	0.000
41	A	458	GLN	0	-0.036	-0.026	33.618	-0.088	-0.088	0.000	0.000	0.000	0.000
42	A	459	THR	0	0.034	0.021	36.978	0.226	0.226	0.000	0.000	0.000	0.000
43	A	460	GLN	0	-0.001	0.002	32.714	0.331	0.331	0.000	0.000	0.000	0.000
44	A	461	VAL	0	0.012	0.019	29.029	-0.090	-0.090	0.000	0.000	0.000	0.000
45	A	462	GLN	0	0.016	0.008	27.739	0.053	0.053	0.000	0.000	0.000	0.000
46	A	463	ILE	0	-0.018	-0.001	22.200	0.026	0.026	0.000	0.000	0.000	0.000
47	A	464	LYS	1	0.813	0.900	23.316	-11.876	-11.876	0.000	0.000	0.000	0.000
48	A	465	VAL	0	0.032	0.012	16.742	0.126	0.126	0.000	0.000	0.000	0.000
49	A	466	PHE	0	0.025	-0.003	18.019	-0.160	-0.160	0.000	0.000	0.000	0.000
50	A	467	GLN	0	0.043	0.003	10.236	-0.667	-0.667	0.000	0.000	0.000	0.000
51	A	468	GLY	0	0.016	0.004	15.030	-0.624	-0.624	0.000	0.000	0.000	0.000
52	A	469	GLU	-1	-0.697	-0.845	13.676	22.546	22.546	0.000	0.000	0.000	0.000
53	A	470	ARG	1	0.823	0.917	17.584	-13.616	-13.616	0.000	0.000	0.000	0.000
54	A	471	GLU	-1	-0.863	-0.937	21.315	12.109	12.109	0.000	0.000	0.000	0.000
55	A	472	MET	0	0.008	0.017	24.000	-0.134	-0.134	0.000	0.000	0.000	0.000
56	A	473	ALA	0	0.003	0.000	22.595	0.526	0.526	0.000	0.000	0.000	0.000
57	A	474	THR	0	0.016	-0.013	22.490	0.602	0.602	0.000	0.000	0.000	0.000
58	A	475	SER	0	-0.045	-0.018	23.625	-0.281	-0.281	0.000	0.000	0.000	0.000
59	A	476	ASN	0	-0.059	-0.016	18.391	1.178	1.178	0.000	0.000	0.000	0.000
60	A	477	LYS	1	0.898	0.952	13.089	-23.440	-23.440	0.000	0.000	0.000	0.000
61	A	478	LEU	0	-0.027	-0.009	17.424	0.679	0.679	0.000	0.000	0.000	0.000
62	A	479	LEU	0	-0.046	-0.030	13.052	0.461	0.461	0.000	0.000	0.000	0.000
63	A	480	GLY	0	0.032	0.013	17.465	0.010	0.010	0.000	0.000	0.000	0.000
64	A	481	GLN	0	-0.043	-0.031	20.436	0.231	0.231	0.000	0.000	0.000	0.000
65	A	482	PHE	0	0.023	0.020	21.378	-0.247	-0.247	0.000	0.000	0.000	0.000
66	A	483	SER	0	0.018	-0.006	25.939	0.105	0.105	0.000	0.000	0.000	0.000
67	A	484	LEU	0	-0.025	0.018	27.563	0.029	0.029	0.000	0.000	0.000	0.000
68	A	485	VAL	0	0.049	0.007	30.436	-0.175	-0.175	0.000	0.000	0.000	0.000
69	A	486	GLY	0	0.013	0.014	34.177	-0.032	-0.032	0.000	0.000	0.000	0.000
70	A	487	ILE	0	-0.014	-0.014	32.005	-0.022	-0.022	0.000	0.000	0.000	0.000
71	A	488	PRO	0	0.020	-0.002	36.260	-0.176	-0.176	0.000	0.000	0.000	0.000
72	A	489	PRO	0	-0.011	-0.006	39.083	0.119	0.119	0.000	0.000	0.000	0.000
73	A	490	ALA	0	0.020	0.019	38.974	-0.154	-0.154	0.000	0.000	0.000	0.000
74	A	491	PRO	0	0.021	0.006	40.316	0.084	0.084	0.000	0.000	0.000	0.000
75	A	492	ARG	1	0.756	0.841	37.624	-7.807	-7.807	0.000	0.000	0.000	0.000
76	A	493	GLY	0	0.006	0.004	34.919	-0.112	-0.112	0.000	0.000	0.000	0.000
77	A	494	VAL	0	-0.044	-0.005	35.568	0.062	0.062	0.000	0.000	0.000	0.000
78	A	495	PRO	0	-0.014	-0.009	33.801	0.101	0.101	0.000	0.000	0.000	0.000
79	A	496	GLN	0	0.048	0.044	30.602	0.352	0.352	0.000	0.000	0.000	0.000
80	A	497	VAL	0	0.003	0.008	26.600	0.074	0.074	0.000	0.000	0.000	0.000
81	A	498	GLU	-1	-0.769	-0.870	24.782	11.486	11.486	0.000	0.000	0.000	0.000
82	A	499	VAL	0	-0.035	-0.019	20.466	0.005	0.005	0.000	0.000	0.000	0.000
83	A	500	THR	0	-0.011	-0.015	17.347	0.230	0.230	0.000	0.000	0.000	0.000
84	A	501	PHE	0	0.003	-0.001	13.760	0.012	0.012	0.000	0.000	0.000	0.000
85	A	502	ASP	-1	-0.860	-0.922	13.310	18.863	18.863	0.000	0.000	0.000	0.000
86	A	503	ILE	0	0.006	0.019	7.128	-0.120	-0.120	0.000	0.000	0.000	0.000
87	A	504	ASP	-1	-0.752	-0.889	8.063	32.870	32.870	0.000	0.000	0.000	0.000
88	A	505	ALA	0	0.009	-0.011	4.512	2.548	2.561	-0.001	-0.009	-0.003	0.000
89	A	506	ASN	0	-0.038	-0.020	3.493	9.627	10.284	0.023	-0.188	-0.491	-0.001
90	A	507	GLY	0	0.031	0.021	5.739	1.274	1.274	0.000	0.000	0.000	0.000
91	A	508	ILE	0	-0.005	0.002	6.738	-3.860	-3.860	0.000	0.000	0.000	0.000
92	A	509	VAL	0	-0.024	-0.023	9.862	0.659	0.659	0.000	0.000	0.000	0.000
93	A	510	ASN	0	-0.007	-0.003	12.227	-1.601	-1.601	0.000	0.000	0.000	0.000
94	A	511	VAL	0	-0.007	-0.011	15.370	0.468	0.468	0.000	0.000	0.000	0.000
95	A	512	SER	0	0.016	0.004	17.688	-0.561	-0.561	0.000	0.000	0.000	0.000
96	A	513	ALA	0	0.003	-0.001	21.053	0.191	0.191	0.000	0.000	0.000	0.000
97	A	514	ARG	1	0.864	0.898	24.265	-11.154	-11.154	0.000	0.000	0.000	0.000
98	A	515	ASP	-1	-0.814	-0.878	27.014	9.343	9.343	0.000	0.000	0.000	0.000
99	A	516	ARG	1	0.831	0.891	26.686	-10.813	-10.813	0.000	0.000	0.000	0.000
100	A	517	GLY	0	-0.040	-0.008	31.062	-0.195	-0.195	0.000	0.000	0.000	0.000
101	A	518	THR	0	-0.067	-0.076	33.687	-0.231	-0.231	0.000	0.000	0.000	0.000
102	A	519	GLY	0	-0.018	0.004	30.906	-0.114	-0.114	0.000	0.000	0.000	0.000
103	A	520	LYS	1	0.827	0.918	30.681	-8.739	-8.739	0.000	0.000	0.000	0.000
104	A	521	GLU	-1	-0.833	-0.903	25.684	11.561	11.561	0.000	0.000	0.000	0.000
105	A	522	GLN	0	-0.068	-0.034	25.968	-0.238	-0.238	0.000	0.000	0.000	0.000
106	A	523	GLN	0	0.030	0.010	20.512	0.359	0.359	0.000	0.000	0.000	0.000
107	A	524	ILE	0	-0.027	0.007	19.036	-0.465	-0.465	0.000	0.000	0.000	0.000
108	A	525	VAL	0	0.011	0.004	15.339	0.616	0.616	0.000	0.000	0.000	0.000
109	A	526	ILE	0	-0.010	0.006	14.068	-0.546	-0.546	0.000	0.000	0.000	0.000
110	A	527	GLN	0	-0.006	-0.010	11.155	2.493	2.493	0.000	0.000	0.000	0.000
111	A	528	SER	0	-0.061	-0.028	8.846	-0.356	-0.356	0.000	0.000	0.000	0.000
112	A	529	SER	0	0.076	0.037	4.357	-1.773	-1.689	-0.001	-0.011	-0.072	0.000
113	A	530	GLY	0	0.019	0.018	7.357	-3.793	-3.793	0.000	0.000	0.000	0.000
114	A	531	GLY	0	-0.029	-0.015	9.294	-2.158	-2.158	0.000	0.000	0.000	0.000
115	A	532	LEU	0	-0.035	-0.029	10.887	-1.906	-1.906	0.000	0.000	0.000	0.000
116	A	533	SER	0	0.001	-0.010	10.651	2.309	2.309	0.000	0.000	0.000	0.000
117	A	534	LYS	1	0.916	0.932	10.037	-24.382	-24.382	0.000	0.000	0.000	0.000
118	A	535	ASP	-1	-0.840	-0.913	11.258	21.462	21.462	0.000	0.000	0.000	0.000
119	A	536	GLN	0	0.013	0.012	14.205	-0.119	-0.119	0.000	0.000	0.000	0.000
120	A	537	ILE	0	0.022	0.021	8.560	-0.820	-0.820	0.000	0.000	0.000	0.000
121	A	538	GLU	-1	-0.860	-0.915	12.714	22.148	22.148	0.000	0.000	0.000	0.000
122	A	539	ASN	0	-0.009	-0.004	14.418	-1.459	-1.459	0.000	0.000	0.000	0.000
123	A	540	MET	0	-0.014	-0.012	15.158	-0.595	-0.595	0.000	0.000	0.000	0.000
124	A	541	ILE	0	-0.013	0.006	11.814	-0.652	-0.652	0.000	0.000	0.000	0.000
125	A	542	LYS	1	0.881	0.906	16.423	-18.038	-18.038	0.000	0.000	0.000	0.000
126	A	543	GLU	-1	-0.867	-0.918	19.630	12.947	12.947	0.000	0.000	0.000	0.000
127	A	544	ALA	0	-0.002	0.000	18.880	-0.825	-0.825	0.000	0.000	0.000	0.000
128	A	545	GLU	-1	-0.854	-0.915	18.488	16.007	16.007	0.000	0.000	0.000	0.000
129	A	546	LYS	1	0.807	0.894	21.901	-13.881	-13.881	0.000	0.000	0.000	0.000
130	A	547	ASN	0	-0.035	-0.028	24.263	-1.008	-1.008	0.000	0.000	0.000	0.000
131	A	548	ALA	0	0.023	0.029	23.424	-0.320	-0.320	0.000	0.000	0.000	0.000
132	A	549	ALA	0	0.000	-0.008	25.407	-0.348	-0.348	0.000	0.000	0.000	0.000
133	A	550	GLU	-1	-0.828	-0.896	28.347	9.465	9.465	0.000	0.000	0.000	0.000
134	A	551	ASP	-1	-0.747	-0.858	25.104	12.427	12.427	0.000	0.000	0.000	0.000
135	A	552	ALA	0	-0.006	-0.001	28.666	-0.301	-0.301	0.000	0.000	0.000	0.000
136	A	553	LYS	1	0.752	0.873	30.467	-10.067	-10.067	0.000	0.000	0.000	0.000
137	A	554	ARG	1	0.800	0.882	29.353	-10.894	-10.894	0.000	0.000	0.000	0.000
138	A	555	LYS	1	0.848	0.907	33.878	-8.731	-8.731	0.000	0.000	0.000	0.000
139	A	556	GLU	-1	-0.845	-0.895	34.381	9.229	9.229	0.000	0.000	0.000	0.000
140	A	557	LEU	0	-0.001	0.009	36.109	0.146	0.146	0.000	0.000	0.000	0.000
141	A	558	VAL	0	-0.002	-0.009	33.077	0.082	0.082	0.000	0.000	0.000	0.000
142	A	559	GLU	-1	-0.812	-0.858	36.462	7.984	7.984	0.000	0.000	0.000	0.000
143	A	560	VAL	0	-0.023	-0.015	34.860	0.300	0.300	0.000	0.000	0.000	0.000
144	A	561	ILE	0	0.007	0.006	34.180	-0.260	-0.260	0.000	0.000	0.000	0.000
145	A	562	ASN	0	-0.027	-0.021	36.562	0.285	0.285	0.000	0.000	0.000	0.000
146	A	563	GLN	0	-0.074	-0.041	36.071	-0.401	-0.401	0.000	0.000	0.000	0.000
147	A	564	ALA	0	0.026	0.008	35.014	0.170	0.170	0.000	0.000	0.000	0.000
148	A	565	GLU	-1	-0.923	-0.940	32.265	8.895	8.895	0.000	0.000	0.000	0.000

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