FMO DATABASE

FMODB ID: R9G28

Calculation Name: 3FY5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FY5

Chain ID: A

ChEMBL ID:

UniProt ID: P51142

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	90
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-587193.27767
FMO2-HF: Nuclear repulsion	552043.635654
FMO2-HF: Total energy	-35149.642016
FMO2-MP2: Total energy	-35248.685418

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:253:MET)

Summations of interaction energy for fragment #1(A:253:MET)

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.
-23.148	-15.686	21.57	-11.219	-17.81	-0.059

Interaction energy analysis for fragmet #1(A:253:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : 0.010

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

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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	255	VAL	0	-0.061	-0.037	2.940	-0.146	2.709	0.177	-1.286	-1.745	0.005
4	A	256	THR	0	0.028	0.016	5.221	-0.185	-0.130	-0.001	-0.002	-0.051	0.000
5	A	257	LEU	0	-0.027	-0.002	8.860	0.356	0.356	0.000	0.000	0.000	0.000
6	A	258	ASN	0	-0.030	-0.042	10.791	0.034	0.034	0.000	0.000	0.000	0.000
7	A	259	MET	0	0.049	0.049	14.341	-0.004	-0.004	0.000	0.000	0.000	0.000
8	A	260	GLU	-1	-0.853	-0.935	16.443	-0.234	-0.234	0.000	0.000	0.000	0.000
9	A	261	LYS	1	0.863	0.945	16.914	-0.087	-0.087	0.000	0.000	0.000	0.000
10	A	262	TYR	0	0.000	-0.018	13.929	0.050	0.050	0.000	0.000	0.000	0.000
11	A	263	ASN	0	-0.012	0.001	18.242	-0.009	-0.009	0.000	0.000	0.000	0.000
12	A	264	PHE	0	0.010	0.013	17.544	-0.044	-0.044	0.000	0.000	0.000	0.000
13	A	265	LEU	0	0.065	0.031	10.621	0.054	0.054	0.000	0.000	0.000	0.000
14	A	266	GLY	0	0.015	0.009	12.384	0.006	0.006	0.000	0.000	0.000	0.000
15	A	267	ILE	0	0.021	0.013	9.163	0.026	0.026	0.000	0.000	0.000	0.000
16	A	268	SER	0	-0.020	0.012	12.559	0.037	0.037	0.000	0.000	0.000	0.000
17	A	269	ILE	0	0.000	0.004	11.168	-0.094	-0.094	0.000	0.000	0.000	0.000
18	A	270	VAL	0	0.009	0.000	13.587	0.143	0.143	0.000	0.000	0.000	0.000
19	A	271	GLY	0	0.034	0.020	14.267	-0.137	-0.137	0.000	0.000	0.000	0.000
20	A	272	GLN	0	-0.068	-0.032	14.743	0.137	0.137	0.000	0.000	0.000	0.000
21	A	273	SER	0	0.046	0.013	16.598	-0.088	-0.088	0.000	0.000	0.000	0.000
22	A	274	ASN	0	-0.043	-0.030	19.181	0.034	0.034	0.000	0.000	0.000	0.000
23	A	275	GLU	-1	-0.919	-0.978	21.577	-0.201	-0.201	0.000	0.000	0.000	0.000
24	A	276	ARG	1	0.787	0.885	22.356	0.281	0.281	0.000	0.000	0.000	0.000
25	A	277	GLY	0	0.028	0.021	22.367	0.000	0.000	0.000	0.000	0.000	0.000
26	A	278	ASP	-1	-0.834	-0.883	18.232	-0.399	-0.399	0.000	0.000	0.000	0.000
27	A	279	GLY	0	0.024	-0.004	15.931	0.055	0.055	0.000	0.000	0.000	0.000
28	A	280	GLY	0	0.023	0.032	13.370	-0.078	-0.078	0.000	0.000	0.000	0.000
29	A	281	ILE	0	-0.026	-0.007	11.962	0.137	0.137	0.000	0.000	0.000	0.000
30	A	282	TYR	0	0.000	0.000	9.557	-0.297	-0.297	0.000	0.000	0.000	0.000
31	A	283	ILE	0	-0.021	-0.007	6.176	0.212	0.212	0.000	0.000	0.000	0.000
32	A	284	GLY	0	0.006	0.006	9.504	0.153	0.153	0.000	0.000	0.000	0.000
33	A	285	SER	0	-0.075	-0.050	12.078	0.152	0.152	0.000	0.000	0.000	0.000
34	A	286	ILE	0	0.058	0.028	6.990	-0.106	-0.106	0.000	0.000	0.000	0.000
35	A	287	MET	0	-0.071	-0.022	11.545	0.120	0.120	0.000	0.000	0.000	0.000
36	A	288	LYS	1	0.988	0.967	14.528	-0.073	-0.073	0.000	0.000	0.000	0.000
37	A	289	GLY	0	0.010	0.004	15.444	0.014	0.014	0.000	0.000	0.000	0.000
38	A	290	GLY	0	0.011	0.018	15.213	0.007	0.007	0.000	0.000	0.000	0.000
39	A	291	ALA	0	0.000	-0.016	12.712	0.052	0.052	0.000	0.000	0.000	0.000
40	A	292	VAL	0	0.018	0.001	7.053	0.108	0.108	0.000	0.000	0.000	0.000
41	A	293	ALA	0	-0.014	-0.005	8.822	0.186	0.186	0.000	0.000	0.000	0.000
42	A	294	ALA	0	-0.055	-0.020	11.089	0.147	0.147	0.000	0.000	0.000	0.000
43	A	295	ASP	-1	-0.852	-0.914	6.183	1.239	1.239	0.000	0.000	0.000	0.000
44	A	296	GLY	0	-0.011	-0.006	7.979	0.412	0.412	0.000	0.000	0.000	0.000
45	A	297	ARG	1	0.825	0.902	3.395	-3.394	-2.135	0.487	-0.424	-1.322	0.001
46	A	298	ILE	0	-0.020	-0.010	2.218	-3.399	-1.096	2.493	-1.925	-2.871	-0.020
47	A	299	GLU	-1	-0.890	-0.956	3.201	2.133	1.814	0.010	0.611	-0.302	0.000
48	A	300	PRO	0	-0.061	-0.045	5.469	-0.492	-0.492	0.000	0.000	0.000	0.000
49	A	301	GLY	0	0.021	0.014	8.725	0.195	0.195	0.000	0.000	0.000	0.000
50	A	302	ASP	-1	-0.734	-0.854	2.899	-4.231	-2.994	0.309	-0.646	-0.900	-0.007
51	A	303	MET	0	0.005	0.006	6.028	0.107	0.107	0.000	0.000	0.000	0.000
52	A	304	LEU	0	-0.064	-0.036	6.368	-1.236	-1.236	0.000	0.000	0.000	0.000
53	A	305	LEU	0	0.020	0.010	5.189	0.494	0.494	0.000	0.000	0.000	0.000
54	A	306	GLN	0	-0.012	-0.014	8.040	0.591	0.591	0.000	0.000	0.000	0.000
55	A	307	VAL	0	-0.001	-0.008	8.901	-0.448	-0.448	0.000	0.000	0.000	0.000
56	A	308	ASN	0	-0.018	-0.022	11.380	0.154	0.154	0.000	0.000	0.000	0.000
57	A	309	ASP	-1	-0.863	-0.925	11.674	-1.333	-1.333	0.000	0.000	0.000	0.000
58	A	310	ILE	0	-0.027	0.008	13.421	0.135	0.135	0.000	0.000	0.000	0.000
59	A	311	ASN	0	-0.043	-0.043	11.662	-0.076	-0.076	0.000	0.000	0.000	0.000
60	A	312	PHE	0	-0.021	-0.048	11.477	0.199	0.199	0.000	0.000	0.000	0.000
61	A	313	GLU	-1	-0.890	-0.919	10.626	-1.508	-1.508	0.000	0.000	0.000	0.000
62	A	314	ASN	0	-0.027	-0.015	12.971	0.191	0.191	0.000	0.000	0.000	0.000
63	A	315	MET	0	-0.045	0.006	16.028	0.138	0.138	0.000	0.000	0.000	0.000
64	A	316	SER	0	0.020	-0.018	17.841	0.004	0.004	0.000	0.000	0.000	0.000
65	A	317	ASN	0	0.058	-0.001	17.855	-0.046	-0.046	0.000	0.000	0.000	0.000
66	A	318	ASP	-1	-0.843	-0.893	18.832	-0.454	-0.454	0.000	0.000	0.000	0.000
67	A	319	ASP	-1	-0.802	-0.874	21.045	-0.517	-0.517	0.000	0.000	0.000	0.000
68	A	320	ALA	0	0.025	0.011	15.370	-0.020	-0.020	0.000	0.000	0.000	0.000
69	A	321	VAL	0	-0.013	-0.001	16.665	-0.045	-0.045	0.000	0.000	0.000	0.000
70	A	322	ARG	1	0.751	0.846	18.299	0.473	0.473	0.000	0.000	0.000	0.000
71	A	323	VAL	0	0.029	0.016	16.842	0.021	0.021	0.000	0.000	0.000	0.000
72	A	324	LEU	0	0.013	0.008	12.376	-0.011	-0.011	0.000	0.000	0.000	0.000
73	A	325	ARG	1	0.819	0.879	16.088	0.474	0.474	0.000	0.000	0.000	0.000
74	A	326	ASP	-1	-0.788	-0.878	19.013	-0.428	-0.428	0.000	0.000	0.000	0.000
75	A	327	ILE	0	-0.081	-0.028	14.925	0.046	0.046	0.000	0.000	0.000	0.000
76	A	328	VAL	0	0.000	-0.011	15.481	0.030	0.030	0.000	0.000	0.000	0.000
77	A	329	HIS	0	-0.058	-0.017	17.862	0.056	0.056	0.000	0.000	0.000	0.000
78	A	330	LYS	1	0.849	0.925	19.764	0.599	0.599	0.000	0.000	0.000	0.000
79	A	331	PRO	0	0.003	0.000	19.731	-0.027	-0.027	0.000	0.000	0.000	0.000
80	A	332	GLY	0	0.047	0.038	18.848	-0.011	-0.011	0.000	0.000	0.000	0.000
81	A	333	PRO	0	-0.052	-0.019	13.784	-0.025	-0.025	0.000	0.000	0.000	0.000
82	A	334	ILE	0	0.030	0.016	11.389	-0.083	-0.083	0.000	0.000	0.000	0.000
83	A	335	VAL	0	-0.017	-0.033	8.879	0.047	0.047	0.000	0.000	0.000	0.000
84	A	336	LEU	0	0.036	0.037	6.382	-0.027	-0.027	0.000	0.000	0.000	0.000
85	A	337	THR	0	-0.026	-0.023	3.863	-0.689	-0.389	0.000	-0.106	-0.194	0.000
86	A	338	VAL	0	-0.007	-0.005	2.477	0.259	2.341	0.944	-0.745	-2.281	-0.001
87	A	339	ALA	0	0.046	0.035	1.881	-10.877	-12.011	8.613	-4.211	-3.268	-0.048
88	A	340	LYS	1	0.770	0.866	2.457	-2.995	-4.371	8.523	-2.460	-4.686	0.011
89	A	341	CYS	0	-0.055	-0.035	3.686	0.497	0.697	0.015	-0.025	-0.190	0.000
90	A	342	TRP	0	-0.016	0.008	6.698	0.411	0.411	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:253:MET)