FMO DATABASE

FMODB ID: 17K9Z

Calculation Name: 5F67-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5F67

Chain ID: A

ChEMBL ID:

UniProt ID: Q24008

Base Structure: X-ray

Registration Date: 2023-09-19

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	98
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-695017.112919
FMO2-HF: Nuclear repulsion	657575.237743
FMO2-HF: Total energy	-37441.875176
FMO2-MP2: Total energy	-37551.090399

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:351:SER)

Summations of interaction energy for fragment #1(A:351:SER)

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.
-31.711	-36.191	18.563	-8.921	-5.162	-0.076

Interaction energy analysis for fragmet #1(A:351:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.045 / q_NPA : -0.049

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	353	GLU	-1	-0.845	-0.899	1.606	-34.574	-39.172	18.564	-8.911	-5.055	-0.076
4	A	354	THR	0	-0.048	-0.044	4.716	2.071	2.189	-0.001	-0.010	-0.107	0.000
5	A	355	LYS	1	0.850	0.920	5.622	2.827	2.827	0.000	0.000	0.000	0.000
6	A	356	PHE	0	0.043	0.021	7.401	0.618	0.618	0.000	0.000	0.000	0.000
7	A	357	ILE	0	0.015	0.008	9.395	0.376	0.376	0.000	0.000	0.000	0.000
8	A	358	PHE	0	-0.060	-0.034	11.047	0.229	0.229	0.000	0.000	0.000	0.000
9	A	359	ASP	-1	-0.908	-0.953	11.212	-0.715	-0.715	0.000	0.000	0.000	0.000
10	A	360	GLN	0	-0.046	-0.019	13.673	0.005	0.005	0.000	0.000	0.000	0.000
11	A	361	PHE	0	-0.016	-0.021	15.564	0.122	0.122	0.000	0.000	0.000	0.000
12	A	362	PRO	0	0.032	0.025	17.250	-0.021	-0.021	0.000	0.000	0.000	0.000
13	A	363	LYS	1	0.817	0.902	18.194	0.424	0.424	0.000	0.000	0.000	0.000
14	A	364	ALA	0	-0.022	-0.001	16.441	0.029	0.029	0.000	0.000	0.000	0.000
15	A	365	ARG	1	0.765	0.847	17.915	0.517	0.517	0.000	0.000	0.000	0.000
16	A	366	THR	0	0.036	0.008	13.883	-0.057	-0.057	0.000	0.000	0.000	0.000
17	A	367	VAL	0	-0.031	-0.003	16.807	0.104	0.104	0.000	0.000	0.000	0.000
18	A	368	GLN	0	0.028	0.007	14.692	-0.078	-0.078	0.000	0.000	0.000	0.000
19	A	369	VAL	0	-0.007	-0.002	19.559	0.069	0.069	0.000	0.000	0.000	0.000
20	A	370	ARG	1	0.931	0.980	21.703	0.252	0.252	0.000	0.000	0.000	0.000
21	A	371	LYS	1	0.824	0.907	22.891	0.483	0.483	0.000	0.000	0.000	0.000
22	A	372	GLU	-1	-0.868	-0.935	24.855	-0.238	-0.238	0.000	0.000	0.000	0.000
23	A	373	GLY	0	-0.003	0.014	28.361	0.014	0.014	0.000	0.000	0.000	0.000
24	A	374	PHE	0	-0.037	-0.043	27.928	-0.012	-0.012	0.000	0.000	0.000	0.000
25	A	375	LEU	0	0.050	0.022	21.938	0.007	0.007	0.000	0.000	0.000	0.000
26	A	376	GLY	0	0.005	-0.022	26.188	0.014	0.014	0.000	0.000	0.000	0.000
27	A	377	ILE	0	-0.004	0.016	23.383	0.009	0.009	0.000	0.000	0.000	0.000
28	A	378	MET	0	-0.057	-0.012	28.021	0.003	0.003	0.000	0.000	0.000	0.000
29	A	379	VAL	0	0.018	0.008	23.265	-0.016	-0.016	0.000	0.000	0.000	0.000
30	A	380	ILE	0	0.015	0.007	26.421	0.027	0.027	0.000	0.000	0.000	0.000
31	A	381	TYR	0	0.032	0.023	22.067	-0.011	-0.011	0.000	0.000	0.000	0.000
32	A	382	GLY	0	0.013	0.004	25.664	0.039	0.039	0.000	0.000	0.000	0.000
33	A	383	LYS	1	0.865	0.915	26.693	0.337	0.337	0.000	0.000	0.000	0.000
34	A	384	HIS	0	0.062	0.037	26.611	0.013	0.013	0.000	0.000	0.000	0.000
35	A	385	ALA	0	0.010	0.000	27.538	-0.014	-0.014	0.000	0.000	0.000	0.000
36	A	386	GLU	-1	-0.835	-0.917	25.756	-0.346	-0.346	0.000	0.000	0.000	0.000
37	A	387	VAL	0	-0.009	0.000	21.094	-0.010	-0.010	0.000	0.000	0.000	0.000
38	A	388	GLY	0	0.014	0.028	23.286	-0.021	-0.021	0.000	0.000	0.000	0.000
39	A	389	SER	0	-0.044	-0.052	24.144	0.037	0.037	0.000	0.000	0.000	0.000
40	A	390	GLY	0	0.096	0.056	21.351	-0.042	-0.042	0.000	0.000	0.000	0.000
41	A	391	ILE	0	-0.010	0.003	20.208	0.066	0.066	0.000	0.000	0.000	0.000
42	A	392	PHE	0	-0.015	-0.002	22.176	-0.028	-0.028	0.000	0.000	0.000	0.000
43	A	393	ILE	0	-0.009	-0.005	22.933	0.016	0.016	0.000	0.000	0.000	0.000
44	A	394	SER	0	-0.005	-0.018	26.189	0.014	0.014	0.000	0.000	0.000	0.000
45	A	395	ASP	-1	-0.869	-0.941	29.578	-0.244	-0.244	0.000	0.000	0.000	0.000
46	A	396	LEU	0	-0.045	-0.032	28.633	-0.035	-0.035	0.000	0.000	0.000	0.000
47	A	397	ARG	1	0.904	0.970	31.308	0.245	0.245	0.000	0.000	0.000	0.000
48	A	398	GLU	-1	-0.860	-0.926	32.889	-0.191	-0.191	0.000	0.000	0.000	0.000
49	A	399	GLY	0	-0.013	-0.008	34.706	0.004	0.004	0.000	0.000	0.000	0.000
50	A	400	SER	0	-0.079	-0.036	30.127	-0.009	-0.009	0.000	0.000	0.000	0.000
51	A	401	ASN	0	0.008	-0.030	26.193	0.010	0.010	0.000	0.000	0.000	0.000
52	A	402	ALA	0	-0.003	0.004	25.682	-0.016	-0.016	0.000	0.000	0.000	0.000
53	A	403	GLU	-1	-0.890	-0.939	26.715	-0.259	-0.259	0.000	0.000	0.000	0.000
54	A	404	LEU	0	0.000	-0.010	28.985	0.002	0.002	0.000	0.000	0.000	0.000
55	A	405	ALA	0	-0.038	-0.007	23.594	0.005	0.005	0.000	0.000	0.000	0.000
56	A	406	GLY	0	-0.006	-0.001	24.538	-0.026	-0.026	0.000	0.000	0.000	0.000
57	A	407	VAL	0	-0.022	0.004	23.354	-0.018	-0.018	0.000	0.000	0.000	0.000
58	A	408	LYS	1	0.838	0.911	25.762	0.358	0.358	0.000	0.000	0.000	0.000
59	A	409	VAL	0	0.031	0.024	27.281	-0.028	-0.028	0.000	0.000	0.000	0.000
60	A	410	GLY	0	0.000	0.002	28.339	0.018	0.018	0.000	0.000	0.000	0.000
61	A	411	ASP	-1	-0.750	-0.831	23.173	-0.486	-0.486	0.000	0.000	0.000	0.000
62	A	412	MET	0	-0.009	0.013	20.374	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	413	LEU	0	-0.027	-0.026	18.028	-0.021	-0.021	0.000	0.000	0.000	0.000
64	A	414	LEU	0	-0.004	0.001	15.308	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	415	ALA	0	0.056	0.024	11.981	-0.177	-0.177	0.000	0.000	0.000	0.000
66	A	416	VAL	0	-0.023	-0.008	13.645	0.200	0.200	0.000	0.000	0.000	0.000
67	A	417	ASN	0	0.002	-0.021	12.602	-0.063	-0.063	0.000	0.000	0.000	0.000
68	A	418	GLN	0	-0.026	-0.028	6.057	-1.619	-1.619	0.000	0.000	0.000	0.000
69	A	419	ASP	-1	-0.891	-0.935	8.575	-1.923	-1.923	0.000	0.000	0.000	0.000
70	A	420	VAL	0	0.013	-0.005	8.986	0.257	0.257	0.000	0.000	0.000	0.000
71	A	421	THR	0	-0.027	-0.038	11.747	0.118	0.118	0.000	0.000	0.000	0.000
72	A	422	LEU	0	-0.062	-0.017	13.669	0.138	0.138	0.000	0.000	0.000	0.000
73	A	423	GLU	-1	-0.892	-0.945	14.897	-0.761	-0.761	0.000	0.000	0.000	0.000
74	A	424	SER	0	-0.076	-0.025	16.817	0.032	0.032	0.000	0.000	0.000	0.000
75	A	425	ASN	0	0.008	-0.010	18.592	0.072	0.072	0.000	0.000	0.000	0.000
76	A	426	TYR	0	0.021	-0.010	21.651	-0.037	-0.037	0.000	0.000	0.000	0.000
77	A	427	ASP	-1	-0.867	-0.923	23.863	-0.397	-0.397	0.000	0.000	0.000	0.000
78	A	428	ASP	-1	-0.859	-0.924	18.462	-0.642	-0.642	0.000	0.000	0.000	0.000
79	A	429	ALA	0	-0.014	0.005	19.206	-0.049	-0.049	0.000	0.000	0.000	0.000
80	A	430	THR	0	-0.037	-0.036	20.256	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	431	GLY	0	0.003	-0.001	21.550	0.018	0.018	0.000	0.000	0.000	0.000
82	A	432	LEU	0	-0.019	-0.008	15.141	0.040	0.040	0.000	0.000	0.000	0.000
83	A	433	LEU	0	0.009	0.012	18.761	0.015	0.015	0.000	0.000	0.000	0.000
84	A	434	LYS	1	0.889	0.948	21.170	0.403	0.403	0.000	0.000	0.000	0.000
85	A	435	ARG	1	0.944	0.965	17.177	0.699	0.699	0.000	0.000	0.000	0.000
86	A	436	ALA	0	0.001	0.032	17.966	0.009	0.009	0.000	0.000	0.000	0.000
87	A	437	GLU	-1	-0.915	-0.959	18.870	-0.297	-0.297	0.000	0.000	0.000	0.000
88	A	438	GLY	0	0.011	0.007	19.111	-0.041	-0.041	0.000	0.000	0.000	0.000
89	A	439	VAL	0	-0.061	-0.039	18.514	0.024	0.024	0.000	0.000	0.000	0.000
90	A	440	VAL	0	0.030	0.028	17.397	-0.061	-0.061	0.000	0.000	0.000	0.000
91	A	441	THR	0	0.018	-0.001	13.366	0.020	0.020	0.000	0.000	0.000	0.000
92	A	442	MET	0	-0.032	-0.013	16.106	-0.043	-0.043	0.000	0.000	0.000	0.000
93	A	443	ILE	0	0.012	0.018	11.660	0.066	0.066	0.000	0.000	0.000	0.000
94	A	444	LEU	0	-0.004	0.004	16.069	0.020	0.020	0.000	0.000	0.000	0.000
95	A	445	LEU	0	0.029	0.009	19.398	0.024	0.024	0.000	0.000	0.000	0.000
96	A	446	THR	0	-0.041	-0.037	21.179	0.032	0.032	0.000	0.000	0.000	0.000
97	A	447	LEU	0	-0.031	-0.004	23.440	0.016	0.016	0.000	0.000	0.000	0.000
98	A	448	LYS	1	0.891	0.955	26.398	0.357	0.357	0.000	0.000	0.000	0.000

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Highlights

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Interactive mode: IFIE and PIEDA for fragment #1(A:351:SER)