FMO DATABASE

FMODB ID: Z658N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-585834.220781
FMO2-HF: Nuclear repulsion	550684.859112
FMO2-HF: Total energy	-35149.36167
FMO2-MP2: Total energy	-35248.351065

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.
-25.276	-15.491	16.226	-9.259	-16.752	-0.053

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 : -0.011 / q_NPA : 0.002

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	-0.018	-0.004	2.698	0.389	3.273	0.252	-1.194	-1.943	0.005
4	A	256	THR	0	-0.010	-0.005	4.921	-0.661	-0.625	-0.001	-0.006	-0.028	0.000
5	A	257	LEU	0	0.005	0.002	8.573	0.366	0.366	0.000	0.000	0.000	0.000
6	A	258	ASN	0	-0.017	-0.030	10.851	0.008	0.008	0.000	0.000	0.000	0.000
7	A	259	MET	0	0.025	0.035	14.368	-0.031	-0.031	0.000	0.000	0.000	0.000
8	A	260	GLU	-1	-0.872	-0.940	16.520	-0.182	-0.182	0.000	0.000	0.000	0.000
9	A	261	LYS	1	0.887	0.952	16.854	-0.183	-0.183	0.000	0.000	0.000	0.000
10	A	262	TYR	0	-0.023	-0.026	13.684	0.042	0.042	0.000	0.000	0.000	0.000
11	A	263	ASN	0	0.003	0.000	18.066	-0.008	-0.008	0.000	0.000	0.000	0.000
12	A	264	PHE	0	0.025	0.024	17.411	-0.048	-0.048	0.000	0.000	0.000	0.000
13	A	265	LEU	0	0.042	0.017	10.550	0.062	0.062	0.000	0.000	0.000	0.000
14	A	266	GLY	0	0.024	0.005	12.494	0.030	0.030	0.000	0.000	0.000	0.000
15	A	267	ILE	0	0.029	0.018	9.115	0.039	0.039	0.000	0.000	0.000	0.000
16	A	268	SER	0	-0.013	0.018	12.549	0.006	0.006	0.000	0.000	0.000	0.000
17	A	269	ILE	0	-0.009	0.009	11.327	-0.069	-0.069	0.000	0.000	0.000	0.000
18	A	270	VAL	0	-0.004	-0.010	13.854	0.132	0.132	0.000	0.000	0.000	0.000
19	A	271	GLY	0	0.033	0.019	14.753	-0.115	-0.115	0.000	0.000	0.000	0.000
20	A	272	GLN	0	-0.069	-0.034	14.711	0.129	0.129	0.000	0.000	0.000	0.000
21	A	273	SER	0	0.037	0.022	17.150	-0.061	-0.061	0.000	0.000	0.000	0.000
22	A	274	ASN	0	-0.008	0.000	19.739	0.032	0.032	0.000	0.000	0.000	0.000
23	A	275	GLU	-1	-0.906	-0.973	21.998	-0.214	-0.214	0.000	0.000	0.000	0.000
24	A	276	ARG	1	0.781	0.887	22.518	0.298	0.298	0.000	0.000	0.000	0.000
25	A	277	GLY	0	-0.002	0.003	22.548	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	278	ASP	-1	-0.829	-0.888	18.121	-0.427	-0.427	0.000	0.000	0.000	0.000
27	A	279	GLY	0	0.012	-0.019	15.879	0.055	0.055	0.000	0.000	0.000	0.000
28	A	280	GLY	0	0.024	0.024	13.622	-0.094	-0.094	0.000	0.000	0.000	0.000
29	A	281	ILE	0	-0.029	-0.012	12.302	0.147	0.147	0.000	0.000	0.000	0.000
30	A	282	TYR	0	0.013	0.010	9.896	-0.291	-0.291	0.000	0.000	0.000	0.000
31	A	283	ILE	0	-0.007	-0.009	6.371	0.167	0.167	0.000	0.000	0.000	0.000
32	A	284	GLY	0	0.007	0.000	9.770	0.161	0.161	0.000	0.000	0.000	0.000
33	A	285	SER	0	-0.065	-0.032	12.378	0.122	0.122	0.000	0.000	0.000	0.000
34	A	286	ILE	0	0.070	0.035	7.164	-0.086	-0.086	0.000	0.000	0.000	0.000
35	A	287	MET	0	-0.064	-0.033	11.584	0.120	0.120	0.000	0.000	0.000	0.000
36	A	288	LYS	1	0.963	0.960	14.377	-0.095	-0.095	0.000	0.000	0.000	0.000
37	A	289	GLY	0	0.009	-0.003	15.370	0.002	0.002	0.000	0.000	0.000	0.000
38	A	290	GLY	0	-0.003	0.019	14.574	0.021	0.021	0.000	0.000	0.000	0.000
39	A	291	ALA	0	0.007	-0.009	12.205	0.081	0.081	0.000	0.000	0.000	0.000
40	A	292	VAL	0	0.021	0.009	6.864	0.128	0.128	0.000	0.000	0.000	0.000
41	A	293	ALA	0	-0.006	0.003	8.313	0.143	0.143	0.000	0.000	0.000	0.000
42	A	294	ALA	0	-0.060	-0.027	10.578	0.175	0.175	0.000	0.000	0.000	0.000
43	A	295	ASP	-1	-0.895	-0.958	6.298	1.631	1.631	0.000	0.000	0.000	0.000
44	A	296	GLY	0	0.006	0.007	7.753	0.460	0.460	0.000	0.000	0.000	0.000
45	A	297	ARG	1	0.837	0.930	2.568	-7.400	-5.550	1.440	-0.804	-2.485	0.001
46	A	298	ILE	0	-0.049	-0.022	2.340	-3.403	-1.097	1.767	-1.605	-2.468	-0.017
47	A	299	GLU	-1	-0.876	-0.944	3.251	1.809	1.685	0.027	0.357	-0.260	-0.001
48	A	300	PRO	0	-0.031	-0.035	5.922	-0.452	-0.452	0.000	0.000	0.000	0.000
49	A	301	GLY	0	0.002	0.006	9.010	0.160	0.160	0.000	0.000	0.000	0.000
50	A	302	ASP	-1	-0.739	-0.862	3.375	-3.292	-2.421	0.083	-0.423	-0.532	-0.003
51	A	303	MET	0	-0.002	0.006	6.284	0.067	0.067	0.000	0.000	0.000	0.000
52	A	304	LEU	0	-0.053	-0.032	6.647	-1.147	-1.147	0.000	0.000	0.000	0.000
53	A	305	LEU	0	0.015	0.013	4.938	0.459	0.459	0.000	0.000	0.000	0.000
54	A	306	GLN	0	-0.016	-0.009	7.813	0.636	0.636	0.000	0.000	0.000	0.000
55	A	307	VAL	0	0.012	0.013	8.740	-0.456	-0.456	0.000	0.000	0.000	0.000
56	A	308	ASN	0	-0.034	-0.031	11.110	0.129	0.129	0.000	0.000	0.000	0.000
57	A	309	ASP	-1	-0.879	-0.950	11.881	-1.350	-1.350	0.000	0.000	0.000	0.000
58	A	310	ILE	0	-0.027	0.011	13.347	0.148	0.148	0.000	0.000	0.000	0.000
59	A	311	ASN	0	-0.044	-0.050	11.636	-0.068	-0.068	0.000	0.000	0.000	0.000
60	A	312	PHE	0	-0.025	-0.061	11.430	0.211	0.211	0.000	0.000	0.000	0.000
61	A	313	GLU	-1	-0.872	-0.911	10.859	-1.584	-1.584	0.000	0.000	0.000	0.000
62	A	314	ASN	0	-0.034	-0.015	13.118	0.193	0.193	0.000	0.000	0.000	0.000
63	A	315	MET	0	-0.062	0.002	15.957	0.133	0.133	0.000	0.000	0.000	0.000
64	A	316	SER	0	0.009	-0.013	17.734	0.008	0.008	0.000	0.000	0.000	0.000
65	A	317	ASN	0	0.088	0.003	18.307	-0.036	-0.036	0.000	0.000	0.000	0.000
66	A	318	ASP	-1	-0.867	-0.912	19.237	-0.441	-0.441	0.000	0.000	0.000	0.000
67	A	319	ASP	-1	-0.782	-0.870	21.022	-0.519	-0.519	0.000	0.000	0.000	0.000
68	A	320	ALA	0	-0.007	0.004	15.588	-0.021	-0.021	0.000	0.000	0.000	0.000
69	A	321	VAL	0	0.011	0.009	16.813	-0.041	-0.041	0.000	0.000	0.000	0.000
70	A	322	ARG	1	0.756	0.852	18.198	0.469	0.469	0.000	0.000	0.000	0.000
71	A	323	VAL	0	0.036	0.017	17.092	0.027	0.027	0.000	0.000	0.000	0.000
72	A	324	LEU	0	0.002	0.009	12.535	-0.018	-0.018	0.000	0.000	0.000	0.000
73	A	325	ARG	1	0.828	0.880	16.189	0.482	0.482	0.000	0.000	0.000	0.000
74	A	326	ASP	-1	-0.818	-0.893	19.100	-0.437	-0.437	0.000	0.000	0.000	0.000
75	A	327	ILE	0	-0.085	-0.045	14.948	0.051	0.051	0.000	0.000	0.000	0.000
76	A	328	VAL	0	-0.015	-0.012	15.161	0.019	0.019	0.000	0.000	0.000	0.000
77	A	329	HIS	0	-0.023	-0.004	17.618	0.063	0.063	0.000	0.000	0.000	0.000
78	A	330	LYS	1	0.841	0.944	19.596	0.612	0.612	0.000	0.000	0.000	0.000
79	A	331	PRO	0	0.017	0.009	19.857	-0.014	-0.014	0.000	0.000	0.000	0.000
80	A	332	GLY	0	0.043	0.022	18.551	-0.019	-0.019	0.000	0.000	0.000	0.000
81	A	333	PRO	0	-0.028	-0.009	13.618	-0.020	-0.020	0.000	0.000	0.000	0.000
82	A	334	ILE	0	0.005	0.008	11.422	-0.093	-0.093	0.000	0.000	0.000	0.000
83	A	335	VAL	0	-0.023	-0.019	8.451	0.051	0.051	0.000	0.000	0.000	0.000
84	A	336	LEU	0	0.039	0.036	5.966	0.017	0.017	0.000	0.000	0.000	0.000
85	A	337	THR	0	-0.025	-0.020	4.140	-0.959	-0.723	-0.001	-0.086	-0.149	0.000
86	A	338	VAL	0	-0.017	-0.018	2.306	0.072	2.161	1.381	-0.883	-2.587	-0.003
87	A	339	ALA	0	0.065	0.037	2.004	-9.359	-9.041	5.261	-3.004	-2.575	-0.038
88	A	340	LYS	1	0.770	0.869	2.583	-2.930	-3.792	6.014	-1.567	-3.585	0.003
89	A	341	CYS	0	-0.032	-0.031	3.999	0.299	0.480	0.003	-0.044	-0.140	0.000
90	A	342	TRP	0	-0.026	0.012	7.211	0.289	0.289	0.000	0.000	0.000	0.000

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