FMO DATABASE

FMODB ID: 179KZ

Calculation Name: 5U1T-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5U1T

Chain ID: B

ChEMBL ID:

UniProt ID: Q03018

Base Structure: X-ray

Registration Date: 2023-06-22

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	66
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-220819.452929
FMO2-HF: Nuclear repulsion	194026.444743
FMO2-HF: Total energy	-26793.008186
FMO2-MP2: Total energy	-26871.503727

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(B:257:MET)

Summations of interaction energy for fragment #1(B:257: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.
-4.524	-2.225	0.108	-1.004	-1.403	-0.005

Interaction energy analysis for fragmet #1(B:257:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.034 / q_NPA : -0.044

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	B	259	ILE	0	-0.038	-0.006	3.042	-3.100	-0.801	0.108	-1.004	-1.403	-0.005
4	B	260	GLU	-1	-0.927	-0.963	5.392	-1.832	-1.832	0.000	0.000	0.000	0.000
5	B	261	ILE	0	-0.021	-0.023	7.849	0.264	0.264	0.000	0.000	0.000	0.000
6	B	262	ALA	0	-0.007	-0.009	11.516	0.087	0.087	0.000	0.000	0.000	0.000
7	B	263	PRO	0	-0.012	0.006	14.887	0.026	0.026	0.000	0.000	0.000	0.000
8	B	264	GLN	0	0.013	-0.006	18.222	0.039	0.039	0.000	0.000	0.000	0.000
9	B	265	ARG	1	0.929	0.962	20.406	0.395	0.395	0.000	0.000	0.000	0.000
10	B	266	GLN	0	0.002	-0.003	23.145	0.014	0.014	0.000	0.000	0.000	0.000
11	B	267	GLU	-1	-0.923	-0.952	26.402	-0.203	-0.203	0.000	0.000	0.000	0.000
12	B	268	PRO	0	-0.053	-0.014	29.533	-0.001	-0.001	0.000	0.000	0.000	0.000
13	B	269	LEU	0	0.033	-0.002	31.458	0.009	0.009	0.000	0.000	0.000	0.000
14	B	270	PRO	0	-0.009	0.013	34.785	0.001	0.001	0.000	0.000	0.000	0.000
15	B	271	TYR	0	0.015	-0.002	37.306	0.005	0.005	0.000	0.000	0.000	0.000
16	B	272	VAL	0	-0.002	-0.016	39.106	0.003	0.003	0.000	0.000	0.000	0.000
17	B	273	PRO	0	-0.017	0.016	42.893	0.001	0.001	0.000	0.000	0.000	0.000
18	B	274	GLU	-1	-0.939	-0.995	44.999	-0.085	-0.085	0.000	0.000	0.000	0.000
19	B	275	GLY	0	-0.017	0.000	47.735	0.004	0.004	0.000	0.000	0.000	0.000
20	B	276	TYR	0	-0.015	0.000	46.985	0.003	0.003	0.000	0.000	0.000	0.000
21	B	277	SER	0	-0.005	-0.006	48.539	-0.003	-0.003	0.000	0.000	0.000	0.000
22	B	278	PRO	0	-0.023	-0.018	47.067	0.003	0.003	0.000	0.000	0.000	0.000
23	B	279	PHE	0	-0.040	-0.007	49.800	0.003	0.003	0.000	0.000	0.000	0.000
24	B	280	GLN	0	0.023	0.010	51.120	-0.005	-0.005	0.000	0.000	0.000	0.000
25	B	281	GLN	0	0.003	-0.009	50.574	-0.001	-0.001	0.000	0.000	0.000	0.000
26	B	282	ASP	-1	-0.887	-0.951	52.672	-0.059	-0.059	0.000	0.000	0.000	0.000
27	B	283	ASP	-1	-0.871	-0.946	55.296	-0.063	-0.063	0.000	0.000	0.000	0.000
28	B	284	ILE	0	-0.013	-0.004	51.153	0.002	0.002	0.000	0.000	0.000	0.000
29	B	285	GLU	-1	-0.880	-0.942	55.145	-0.055	-0.055	0.000	0.000	0.000	0.000
30	B	286	LYS	1	0.915	0.958	57.828	0.053	0.053	0.000	0.000	0.000	0.000
31	B	287	LEU	0	-0.029	-0.010	56.483	0.002	0.002	0.000	0.000	0.000	0.000
32	B	288	LYS	1	0.865	0.943	54.834	0.057	0.057	0.000	0.000	0.000	0.000
33	B	289	THR	0	-0.057	-0.017	59.384	0.002	0.002	0.000	0.000	0.000	0.000
34	B	290	PHE	0	0.003	0.005	62.552	0.001	0.001	0.000	0.000	0.000	0.000
35	B	291	ASN	0	-0.001	-0.008	65.862	0.001	0.001	0.000	0.000	0.000	0.000
36	B	292	SER	0	-0.034	-0.015	69.061	0.000	0.000	0.000	0.000	0.000	0.000
37	B	293	PRO	0	0.057	0.018	72.136	0.000	0.000	0.000	0.000	0.000	0.000
38	B	294	TYR	0	-0.003	-0.018	73.986	0.000	0.000	0.000	0.000	0.000	0.000
39	B	295	LYS	1	0.887	0.975	70.886	0.036	0.036	0.000	0.000	0.000	0.000
40	B	296	LEU	0	0.018	0.009	76.463	0.000	0.000	0.000	0.000	0.000	0.000
41	B	297	ASP	-1	-0.945	-0.988	76.246	-0.034	-0.034	0.000	0.000	0.000	0.000
42	B	298	LEU	0	-0.012	0.016	78.724	0.000	0.000	0.000	0.000	0.000	0.000
43	B	306	ASP	-1	-0.971	-1.000	89.637	-0.026	-0.026	0.000	0.000	0.000	0.000
44	B	307	LYS	1	0.911	0.956	91.300	0.024	0.024	0.000	0.000	0.000	0.000
45	B	308	VAL	0	0.035	0.030	95.065	0.000	0.000	0.000	0.000	0.000	0.000
46	B	309	ASP	-1	-0.934	-0.969	97.644	-0.022	-0.022	0.000	0.000	0.000	0.000
47	B	310	LEU	0	-0.049	-0.030	100.242	0.000	0.000	0.000	0.000	0.000	0.000
48	B	311	LEU	0	0.017	0.010	101.886	0.000	0.000	0.000	0.000	0.000	0.000
49	B	312	PRO	0	-0.012	-0.009	104.006	0.000	0.000	0.000	0.000	0.000	0.000
50	B	313	LEU	0	-0.015	-0.010	107.331	0.000	0.000	0.000	0.000	0.000	0.000
51	B	314	GLU	-1	-0.929	-0.957	108.027	-0.018	-0.018	0.000	0.000	0.000	0.000
52	B	315	GLN	0	-0.039	-0.034	111.411	0.000	0.000	0.000	0.000	0.000	0.000
53	B	316	ILE	0	-0.015	0.013	114.256	0.000	0.000	0.000	0.000	0.000	0.000
54	B	361	GLU	-1	-0.989	-1.013	135.255	-0.008	-0.008	0.000	0.000	0.000	0.000
55	B	362	GLY	0	-0.068	-0.028	132.610	0.000	0.000	0.000	0.000	0.000	0.000
56	B	363	LEU	0	-0.006	-0.002	128.013	0.000	0.000	0.000	0.000	0.000	0.000
57	B	364	ASP	-1	-0.857	-0.925	131.647	-0.008	-0.008	0.000	0.000	0.000	0.000
58	B	365	PRO	0	-0.045	-0.052	129.044	0.000	0.000	0.000	0.000	0.000	0.000
59	B	366	GLU	-1	-0.858	-0.919	127.929	-0.008	-0.008	0.000	0.000	0.000	0.000
60	B	367	GLU	-1	-0.934	-0.962	127.968	-0.009	-0.009	0.000	0.000	0.000	0.000
61	B	368	LEU	0	-0.102	-0.058	125.592	0.000	0.000	0.000	0.000	0.000	0.000
62	B	369	GLU	-1	-0.951	-0.983	123.456	-0.009	-0.009	0.000	0.000	0.000	0.000
63	B	370	ASP	-1	-0.952	-0.970	123.035	-0.010	-0.010	0.000	0.000	0.000	0.000
64	B	371	LEU	0	-0.018	0.006	122.818	0.000	0.000	0.000	0.000	0.000	0.000
65	B	372	VAL	0	-0.108	-0.049	118.909	0.000	0.000	0.000	0.000	0.000	0.000
66	B	373	THR	0	-0.113	-0.044	118.526	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:257:MET)