FMO DATABASE

FMODB ID: 5221Z

Calculation Name: 5F5S-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5F5S

Chain ID: B

ChEMBL ID:

UniProt ID: P55081

Base Structure: X-ray

Registration Date: 2023-06-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	53
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-247197.436139
FMO2-HF: Nuclear repulsion	223696.280264
FMO2-HF: Total energy	-23501.155875
FMO2-MP2: Total energy	-23569.91709

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:270:GLU)

Summations of interaction energy for fragment #1(B:270:GLU)

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.
52.738	57.983	3.351	-3.916	-4.681	-0.018

Interaction energy analysis for fragmet #1(B:270:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.914 / q_NPA : -0.958

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	B	272	ASP	-1	-0.929	-0.958	2.184	25.170	29.305	3.341	-3.596	-3.881	-0.018
4	B	273	GLU	-1	-0.880	-0.943	3.256	23.415	24.342	0.011	-0.307	-0.632	0.000
5	B	274	GLU	-1	-0.939	-0.988	4.683	27.405	27.588	-0.001	-0.013	-0.168	0.000
6	B	275	GLU	-1	-0.866	-0.906	7.045	18.043	18.043	0.000	0.000	0.000	0.000
7	B	276	TYR	0	-0.001	-0.006	7.561	-2.779	-2.779	0.000	0.000	0.000	0.000
8	B	277	GLU	-1	-0.790	-0.884	8.958	16.885	16.885	0.000	0.000	0.000	0.000
9	B	278	ALA	0	0.012	0.005	10.988	-1.663	-1.663	0.000	0.000	0.000	0.000
10	B	279	TRP	0	-0.074	-0.023	12.226	-1.272	-1.272	0.000	0.000	0.000	0.000
11	B	280	LYS	1	0.860	0.917	12.108	-18.752	-18.752	0.000	0.000	0.000	0.000
12	B	281	VAL	0	0.002	0.009	15.120	-1.086	-1.086	0.000	0.000	0.000	0.000
13	B	282	ARG	1	0.739	0.831	13.261	-17.983	-17.983	0.000	0.000	0.000	0.000
14	B	283	GLU	-1	-0.797	-0.881	17.869	11.768	11.768	0.000	0.000	0.000	0.000
15	B	284	LEU	0	0.003	0.002	18.392	-0.653	-0.653	0.000	0.000	0.000	0.000
16	B	285	LYS	1	0.886	0.947	20.756	-13.247	-13.247	0.000	0.000	0.000	0.000
17	B	286	ARG	1	0.829	0.900	18.709	-13.092	-13.092	0.000	0.000	0.000	0.000
18	B	287	ILE	0	0.047	0.029	21.709	-0.420	-0.420	0.000	0.000	0.000	0.000
19	B	288	LYS	1	0.777	0.869	25.198	-9.777	-9.777	0.000	0.000	0.000	0.000
20	B	289	ARG	1	0.875	0.930	27.041	-10.081	-10.081	0.000	0.000	0.000	0.000
21	B	290	ASP	-1	-0.821	-0.904	27.294	9.505	9.505	0.000	0.000	0.000	0.000
22	B	291	ARG	1	0.830	0.907	29.235	-9.131	-9.131	0.000	0.000	0.000	0.000
23	B	292	GLU	-1	-0.789	-0.882	30.907	8.747	8.747	0.000	0.000	0.000	0.000
24	B	293	ASP	-1	-0.883	-0.938	32.927	8.182	8.182	0.000	0.000	0.000	0.000
25	B	294	ARG	1	0.806	0.888	33.012	-8.281	-8.281	0.000	0.000	0.000	0.000
26	B	295	GLU	-1	-0.864	-0.926	33.743	8.072	8.072	0.000	0.000	0.000	0.000
27	B	296	ALA	0	-0.028	-0.005	36.969	-0.250	-0.250	0.000	0.000	0.000	0.000
28	B	297	LEU	0	0.019	0.002	38.517	-0.220	-0.220	0.000	0.000	0.000	0.000
29	B	298	GLU	-1	-0.854	-0.917	37.019	7.467	7.467	0.000	0.000	0.000	0.000
30	B	299	LYS	1	0.953	0.974	40.726	-6.828	-6.828	0.000	0.000	0.000	0.000
31	B	300	GLU	-1	-0.941	-0.966	42.979	6.528	6.528	0.000	0.000	0.000	0.000
32	B	301	LYS	1	0.906	0.946	42.664	-6.788	-6.788	0.000	0.000	0.000	0.000
33	B	302	ALA	0	0.017	0.018	44.789	-0.135	-0.135	0.000	0.000	0.000	0.000
34	B	303	GLU	-1	-0.849	-0.909	46.577	5.657	5.657	0.000	0.000	0.000	0.000
35	B	304	ILE	0	-0.013	-0.016	47.723	-0.135	-0.135	0.000	0.000	0.000	0.000
36	B	305	GLU	-1	-0.862	-0.921	48.125	5.741	5.741	0.000	0.000	0.000	0.000
37	B	306	ARG	1	0.867	0.932	50.694	-5.755	-5.755	0.000	0.000	0.000	0.000
38	B	307	MET	0	-0.020	-0.011	52.504	-0.128	-0.128	0.000	0.000	0.000	0.000
39	B	308	ARG	1	0.871	0.932	50.108	-5.835	-5.835	0.000	0.000	0.000	0.000
40	B	309	ASN	0	0.025	0.002	52.492	-0.106	-0.106	0.000	0.000	0.000	0.000
41	B	310	LEU	0	-0.001	0.015	56.328	-0.075	-0.075	0.000	0.000	0.000	0.000
42	B	311	THR	0	0.016	-0.003	58.575	-0.110	-0.110	0.000	0.000	0.000	0.000
43	B	312	GLU	-1	-0.983	-0.989	57.572	5.070	5.070	0.000	0.000	0.000	0.000
44	B	313	GLU	-1	-1.025	-1.022	58.306	5.017	5.017	0.000	0.000	0.000	0.000
45	B	314	GLU	-1	-0.914	-0.967	62.081	4.705	4.705	0.000	0.000	0.000	0.000
46	B	315	ARG	1	1.001	1.017	64.139	-4.603	-4.603	0.000	0.000	0.000	0.000
47	B	316	ARG	1	0.917	0.951	60.292	-4.947	-4.947	0.000	0.000	0.000	0.000
48	B	317	ALA	0	-0.039	-0.019	66.298	-0.076	-0.076	0.000	0.000	0.000	0.000
49	B	318	GLU	-1	-0.897	-0.946	68.102	4.324	4.324	0.000	0.000	0.000	0.000
50	B	319	LEU	0	-0.050	-0.027	68.864	-0.073	-0.073	0.000	0.000	0.000	0.000
51	B	320	ARG	1	0.878	0.938	66.820	-4.496	-4.496	0.000	0.000	0.000	0.000
52	B	321	ALA	0	-0.032	0.005	72.244	-0.054	-0.054	0.000	0.000	0.000	0.000
53	B	322	ASN	0	-0.074	-0.031	73.563	-0.132	-0.132	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:270:GLU)