FMO DATABASE

FMODB ID: 6NV2Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-584628.53328
FMO2-HF: Nuclear repulsion	549479.893327
FMO2-HF: Total energy	-35148.639953
FMO2-MP2: Total energy	-35247.657217

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.
-39.033	-30.479	20.142	-10.444	-18.253	-0.051

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 : -0.019 / q_NPA : 0.000

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	255	VAL	0	-0.029	-0.007	2.653	0.445	3.285	0.359	-1.200	-1.999	0.003
4	A	256	THR	0	0.010	0.001	4.931	-0.623	-0.584	-0.001	-0.006	-0.031	0.000
5	A	257	LEU	0	0.028	0.010	8.477	0.412	0.412	0.000	0.000	0.000	0.000
6	A	258	ASN	0	-0.017	-0.025	10.849	0.048	0.048	0.000	0.000	0.000	0.000
7	A	259	MET	0	0.010	0.028	14.375	-0.034	-0.034	0.000	0.000	0.000	0.000
8	A	260	GLU	-1	-0.878	-0.937	16.582	-0.232	-0.232	0.000	0.000	0.000	0.000
9	A	261	LYS	1	0.885	0.951	16.872	-0.136	-0.136	0.000	0.000	0.000	0.000
10	A	262	TYR	0	-0.024	-0.030	13.442	0.055	0.055	0.000	0.000	0.000	0.000
11	A	263	ASN	0	0.032	0.009	18.089	-0.007	-0.007	0.000	0.000	0.000	0.000
12	A	264	PHE	0	-0.010	0.016	17.511	-0.053	-0.053	0.000	0.000	0.000	0.000
13	A	265	LEU	0	0.040	0.013	11.148	0.062	0.062	0.000	0.000	0.000	0.000
14	A	266	GLY	0	0.021	0.004	12.591	0.018	0.018	0.000	0.000	0.000	0.000
15	A	267	ILE	0	0.024	0.021	9.398	0.039	0.039	0.000	0.000	0.000	0.000
16	A	268	SER	0	-0.024	0.003	12.784	0.014	0.014	0.000	0.000	0.000	0.000
17	A	269	ILE	0	0.009	0.016	11.691	-0.085	-0.085	0.000	0.000	0.000	0.000
18	A	270	VAL	0	-0.001	-0.007	14.065	0.152	0.152	0.000	0.000	0.000	0.000
19	A	271	GLY	0	0.028	0.017	14.958	-0.126	-0.126	0.000	0.000	0.000	0.000
20	A	272	GLN	0	-0.060	-0.031	15.035	0.164	0.164	0.000	0.000	0.000	0.000
21	A	273	SER	0	0.037	0.022	17.338	-0.072	-0.072	0.000	0.000	0.000	0.000
22	A	274	ASN	0	0.029	0.023	19.920	0.037	0.037	0.000	0.000	0.000	0.000
23	A	275	GLU	-1	-0.915	-0.978	22.159	-0.240	-0.240	0.000	0.000	0.000	0.000
24	A	276	ARG	1	0.860	0.933	23.486	0.282	0.282	0.000	0.000	0.000	0.000
25	A	277	GLY	0	-0.019	-0.004	22.587	0.000	0.000	0.000	0.000	0.000	0.000
26	A	278	ASP	-1	-0.926	-0.937	18.021	-0.506	-0.506	0.000	0.000	0.000	0.000
27	A	279	GLY	0	0.010	-0.029	15.983	0.061	0.061	0.000	0.000	0.000	0.000
28	A	280	GLY	0	0.024	0.027	13.671	-0.105	-0.105	0.000	0.000	0.000	0.000
29	A	281	ILE	0	-0.033	-0.014	12.672	0.167	0.167	0.000	0.000	0.000	0.000
30	A	282	TYR	0	0.006	0.008	9.915	-0.308	-0.308	0.000	0.000	0.000	0.000
31	A	283	ILE	0	-0.008	-0.010	6.814	0.176	0.176	0.000	0.000	0.000	0.000
32	A	284	GLY	0	0.006	-0.003	10.032	0.189	0.189	0.000	0.000	0.000	0.000
33	A	285	SER	0	-0.067	-0.028	12.553	0.140	0.140	0.000	0.000	0.000	0.000
34	A	286	ILE	0	0.087	0.041	7.410	-0.107	-0.107	0.000	0.000	0.000	0.000
35	A	287	MET	0	-0.073	-0.038	11.740	0.146	0.146	0.000	0.000	0.000	0.000
36	A	288	LYS	1	0.972	0.967	14.436	-0.071	-0.071	0.000	0.000	0.000	0.000
37	A	289	GLY	0	0.006	-0.014	15.449	0.010	0.010	0.000	0.000	0.000	0.000
38	A	290	GLY	0	0.001	0.020	14.716	0.027	0.027	0.000	0.000	0.000	0.000
39	A	291	ALA	0	0.009	-0.009	12.195	0.088	0.088	0.000	0.000	0.000	0.000
40	A	292	VAL	0	0.013	0.007	7.017	0.126	0.126	0.000	0.000	0.000	0.000
41	A	293	ALA	0	-0.006	0.000	8.379	0.129	0.129	0.000	0.000	0.000	0.000
42	A	294	ALA	0	-0.066	-0.027	10.562	0.200	0.200	0.000	0.000	0.000	0.000
43	A	295	ASP	-1	-0.910	-0.968	6.398	1.444	1.444	0.000	0.000	0.000	0.000
44	A	296	GLY	0	-0.001	0.004	7.670	0.541	0.541	0.000	0.000	0.000	0.000
45	A	297	ARG	1	0.852	0.933	2.552	-10.441	-9.145	3.745	-1.274	-3.768	0.003
46	A	298	ILE	0	-0.082	-0.037	2.486	-4.673	-1.822	1.915	-2.057	-2.710	-0.027
47	A	299	GLU	-1	-0.871	-0.937	3.370	1.743	1.774	0.020	0.173	-0.223	-0.001
48	A	300	PRO	0	-0.042	-0.041	6.001	-0.482	-0.482	0.000	0.000	0.000	0.000
49	A	301	GLY	0	0.001	0.006	9.118	0.191	0.191	0.000	0.000	0.000	0.000
50	A	302	ASP	-1	-0.790	-0.878	3.884	-2.648	-2.257	0.007	-0.128	-0.270	-0.001
51	A	303	MET	0	-0.014	-0.004	6.437	0.069	0.069	0.000	0.000	0.000	0.000
52	A	304	LEU	0	-0.045	-0.031	6.770	-1.308	-1.308	0.000	0.000	0.000	0.000
53	A	305	LEU	0	0.017	0.011	4.731	0.388	0.476	-0.001	-0.003	-0.083	0.000
54	A	306	GLN	0	-0.007	-0.003	7.866	1.059	1.059	0.000	0.000	0.000	0.000
55	A	307	VAL	0	0.016	0.016	8.843	-0.540	-0.540	0.000	0.000	0.000	0.000
56	A	308	ASN	0	-0.006	-0.001	11.256	0.133	0.133	0.000	0.000	0.000	0.000
57	A	309	ASP	-1	-0.918	-0.972	11.917	-1.298	-1.298	0.000	0.000	0.000	0.000
58	A	310	ILE	0	-0.013	0.019	13.356	0.172	0.172	0.000	0.000	0.000	0.000
59	A	311	ASN	0	-0.012	-0.025	11.708	-0.129	-0.129	0.000	0.000	0.000	0.000
60	A	312	PHE	0	-0.030	-0.053	11.505	0.232	0.232	0.000	0.000	0.000	0.000
61	A	313	GLU	-1	-0.903	-0.944	10.874	-1.707	-1.707	0.000	0.000	0.000	0.000
62	A	314	ASN	0	-0.036	-0.015	13.168	0.191	0.191	0.000	0.000	0.000	0.000
63	A	315	MET	0	-0.060	0.004	16.001	0.147	0.147	0.000	0.000	0.000	0.000
64	A	316	SER	0	0.056	0.045	17.776	0.015	0.015	0.000	0.000	0.000	0.000
65	A	317	ASN	0	0.093	0.001	18.548	-0.043	-0.043	0.000	0.000	0.000	0.000
66	A	318	ASP	-1	-0.890	-0.944	19.489	-0.516	-0.516	0.000	0.000	0.000	0.000
67	A	319	ASP	-1	-0.865	-0.947	21.058	-0.604	-0.604	0.000	0.000	0.000	0.000
68	A	320	ALA	0	-0.005	0.001	15.826	-0.028	-0.028	0.000	0.000	0.000	0.000
69	A	321	VAL	0	0.004	0.008	17.070	-0.053	-0.053	0.000	0.000	0.000	0.000
70	A	322	ARG	1	0.800	0.892	18.444	0.544	0.544	0.000	0.000	0.000	0.000
71	A	323	VAL	0	0.058	0.031	17.087	0.029	0.029	0.000	0.000	0.000	0.000
72	A	324	LEU	0	-0.001	0.005	12.619	-0.027	-0.027	0.000	0.000	0.000	0.000
73	A	325	ARG	1	0.837	0.902	16.428	0.574	0.574	0.000	0.000	0.000	0.000
74	A	326	ASP	-1	-0.858	-0.923	19.318	-0.532	-0.532	0.000	0.000	0.000	0.000
75	A	327	ILE	0	-0.082	-0.040	15.041	0.053	0.053	0.000	0.000	0.000	0.000
76	A	328	VAL	0	-0.023	-0.016	15.383	0.016	0.016	0.000	0.000	0.000	0.000
77	A	329	HIS	0	-0.022	-0.009	17.801	0.065	0.065	0.000	0.000	0.000	0.000
78	A	330	LYS	1	0.869	0.961	19.747	0.722	0.722	0.000	0.000	0.000	0.000
79	A	331	PRO	0	0.023	0.013	19.955	-0.019	-0.019	0.000	0.000	0.000	0.000
80	A	332	GLY	0	0.035	0.012	18.556	-0.018	-0.018	0.000	0.000	0.000	0.000
81	A	333	PRO	0	-0.031	-0.012	13.735	-0.023	-0.023	0.000	0.000	0.000	0.000
82	A	334	ILE	0	0.003	0.003	11.321	-0.096	-0.096	0.000	0.000	0.000	0.000
83	A	335	VAL	0	-0.025	-0.021	8.147	0.008	0.008	0.000	0.000	0.000	0.000
84	A	336	LEU	0	0.026	0.031	5.973	0.046	0.046	0.000	0.000	0.000	0.000
85	A	337	THR	0	-0.040	-0.030	4.293	-0.838	-0.657	-0.001	-0.073	-0.108	0.000
86	A	338	VAL	0	0.003	-0.010	2.353	0.247	2.095	1.451	-0.788	-2.512	-0.004
87	A	339	ALA	0	0.042	0.023	2.054	-9.836	-8.793	4.220	-2.772	-2.492	-0.037
88	A	340	LYS	1	0.880	0.942	2.553	-12.985	-15.210	8.426	-2.273	-3.927	0.013
89	A	341	CYS	0	0.011	-0.025	4.027	0.294	0.465	0.002	-0.043	-0.130	0.000
90	A	342	TRP	0	-0.040	0.004	7.205	0.406	0.406	0.000	0.000	0.000	0.000

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