FMO DATABASE

FMODB ID: R8N28

Calculation Name: 2PJW-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2PJW

Chain ID: H

ChEMBL ID:

UniProt ID: P38753

Base Structure: X-ray

Registration Date: 2023-09-20

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	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	88
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-469816.170338
FMO2-HF: Nuclear repulsion	434726.46046
FMO2-HF: Total energy	-35089.709878
FMO2-MP2: Total energy	-35190.547993

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(H:288:LYS)

Summations of interaction energy for fragment #1(H:288:LYS)

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.
104.017	101.078	19.492	-6.59	-9.962	-0.017

Interaction energy analysis for fragmet #1(H:288:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.028 / q_NPA : 0.987

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	H	290	ALA	0	0.020	0.011	2.762	1.048	3.161	0.098	-0.839	-1.372	0.002
4	H	291	ILE	0	-0.010	0.011	1.885	4.530	0.332	11.890	-3.578	-4.115	-0.004
5	H	292	VAL	0	0.008	0.005	4.560	3.402	3.585	-0.001	-0.031	-0.151	0.000
6	H	293	PHE	0	-0.035	-0.026	6.776	3.534	3.534	0.000	0.000	0.000	0.000
7	H	294	SER	0	0.011	0.020	7.320	2.924	2.924	0.000	0.000	0.000	0.000
8	H	295	GLN	0	-0.024	-0.022	9.407	2.683	2.683	0.000	0.000	0.000	0.000
9	H	296	LYS	1	0.943	0.975	11.765	20.214	20.214	0.000	0.000	0.000	0.000
10	H	297	THR	0	0.058	0.020	13.821	0.499	0.499	0.000	0.000	0.000	0.000
11	H	298	THR	0	0.039	0.034	14.711	0.928	0.928	0.000	0.000	0.000	0.000
12	H	299	ILE	0	-0.010	0.005	12.522	0.590	0.590	0.000	0.000	0.000	0.000
13	H	300	ASP	-1	-0.923	-0.947	16.719	-14.114	-14.114	0.000	0.000	0.000	0.000
14	H	301	GLN	0	0.011	-0.010	19.611	0.250	0.250	0.000	0.000	0.000	0.000
15	H	302	LEU	0	0.043	0.016	18.446	0.556	0.556	0.000	0.000	0.000	0.000
16	H	303	HIS	0	-0.038	-0.008	20.593	0.363	0.363	0.000	0.000	0.000	0.000
17	H	304	ASN	0	-0.027	-0.021	22.168	0.325	0.325	0.000	0.000	0.000	0.000
18	H	305	SER	0	0.002	0.008	23.915	0.457	0.457	0.000	0.000	0.000	0.000
19	H	306	LEU	0	0.066	0.022	22.699	0.445	0.445	0.000	0.000	0.000	0.000
20	H	307	ASN	0	-0.089	-0.050	26.070	0.687	0.687	0.000	0.000	0.000	0.000
21	H	308	ALA	0	-0.010	-0.005	27.827	0.380	0.380	0.000	0.000	0.000	0.000
22	H	309	ALA	0	0.056	0.035	29.614	0.367	0.367	0.000	0.000	0.000	0.000
23	H	310	SER	0	-0.069	-0.045	29.648	0.305	0.305	0.000	0.000	0.000	0.000
24	H	311	LYS	1	0.895	0.945	31.549	9.181	9.181	0.000	0.000	0.000	0.000
25	H	312	THR	0	-0.022	-0.007	34.455	0.294	0.294	0.000	0.000	0.000	0.000
26	H	313	GLY	0	-0.023	-0.002	34.946	0.206	0.206	0.000	0.000	0.000	0.000
27	H	314	ASN	0	-0.018	-0.039	32.586	0.009	0.009	0.000	0.000	0.000	0.000
28	H	315	SER	0	-0.032	-0.032	32.488	-0.051	-0.051	0.000	0.000	0.000	0.000
29	H	316	ASN	0	0.031	0.024	31.913	-0.387	-0.387	0.000	0.000	0.000	0.000
30	H	317	GLU	-1	-0.846	-0.893	31.856	-8.852	-8.852	0.000	0.000	0.000	0.000
31	H	318	VAL	0	0.021	-0.001	27.337	-0.194	-0.194	0.000	0.000	0.000	0.000
32	H	319	LEU	0	-0.071	-0.031	27.753	-0.308	-0.308	0.000	0.000	0.000	0.000
33	H	320	GLN	0	-0.106	-0.035	27.619	-0.390	-0.390	0.000	0.000	0.000	0.000
34	H	321	ASP	-1	-0.828	-0.914	27.173	-11.095	-11.095	0.000	0.000	0.000	0.000
35	H	322	PRO	0	0.016	-0.010	25.510	-0.328	-0.328	0.000	0.000	0.000	0.000
36	H	323	HIS	0	0.078	0.062	21.306	-0.669	-0.669	0.000	0.000	0.000	0.000
37	H	324	ILE	0	0.017	0.010	21.973	-0.763	-0.763	0.000	0.000	0.000	0.000
38	H	325	GLY	0	0.000	0.005	21.548	-0.620	-0.620	0.000	0.000	0.000	0.000
39	H	326	ASP	-1	-0.862	-0.942	19.719	-14.329	-14.329	0.000	0.000	0.000	0.000
40	H	327	MET	0	-0.085	-0.041	17.595	-1.001	-1.001	0.000	0.000	0.000	0.000
41	H	328	TYR	0	0.025	0.008	16.616	-1.232	-1.232	0.000	0.000	0.000	0.000
42	H	329	GLY	0	-0.018	0.002	16.487	-1.033	-1.033	0.000	0.000	0.000	0.000
43	H	330	SER	0	-0.047	-0.011	13.025	-1.094	-1.094	0.000	0.000	0.000	0.000
44	H	331	VAL	0	0.011	-0.004	11.905	-1.974	-1.974	0.000	0.000	0.000	0.000
45	H	332	THR	0	-0.059	-0.045	12.677	-1.333	-1.333	0.000	0.000	0.000	0.000
46	H	333	PRO	0	0.002	-0.005	10.918	-0.690	-0.690	0.000	0.000	0.000	0.000
47	H	334	LEU	0	-0.022	-0.019	8.114	-3.435	-3.435	0.000	0.000	0.000	0.000
48	H	335	ARG	1	0.977	1.013	9.511	17.451	17.451	0.000	0.000	0.000	0.000
49	H	336	PRO	0	0.065	0.062	8.579	-0.738	-0.738	0.000	0.000	0.000	0.000
50	H	337	GLN	0	0.038	0.012	3.137	-10.954	-9.617	0.084	-0.577	-0.843	-0.005
51	H	338	VAL	0	0.048	0.017	6.433	-2.241	-2.241	0.000	0.000	0.000	0.000
52	H	339	THR	0	-0.040	-0.064	8.816	2.002	2.002	0.000	0.000	0.000	0.000
53	H	340	ARG	1	0.848	0.933	2.132	64.124	61.280	7.409	-1.428	-3.136	-0.009
54	H	341	MET	0	-0.076	-0.039	3.420	1.536	2.006	0.012	-0.137	-0.345	-0.001
55	H	342	LEU	0	0.026	0.026	7.366	2.248	2.248	0.000	0.000	0.000	0.000
56	H	343	GLY	0	0.065	0.032	10.770	1.733	1.733	0.000	0.000	0.000	0.000
57	H	344	LYS	1	0.835	0.904	6.020	35.154	35.154	0.000	0.000	0.000	0.000
58	H	345	TYR	0	-0.047	-0.063	7.193	2.930	2.930	0.000	0.000	0.000	0.000
59	H	346	ALA	0	-0.039	0.001	11.920	1.933	1.933	0.000	0.000	0.000	0.000
60	H	347	LYS	1	0.853	0.926	12.737	18.801	18.801	0.000	0.000	0.000	0.000
61	H	348	GLU	-1	-0.770	-0.864	10.339	-25.758	-25.758	0.000	0.000	0.000	0.000
62	H	349	LYS	1	0.912	0.962	14.535	16.670	16.670	0.000	0.000	0.000	0.000
63	H	350	GLU	-1	-0.893	-0.961	17.198	-13.258	-13.258	0.000	0.000	0.000	0.000
64	H	351	ASP	-1	-0.820	-0.905	15.780	-17.342	-17.342	0.000	0.000	0.000	0.000
65	H	352	MET	0	-0.034	-0.018	17.011	1.051	1.051	0.000	0.000	0.000	0.000
66	H	353	LEU	0	-0.060	-0.026	20.239	0.884	0.884	0.000	0.000	0.000	0.000
67	H	354	SER	0	0.011	0.003	22.231	0.844	0.844	0.000	0.000	0.000	0.000
68	H	355	LEU	0	-0.003	-0.012	21.560	0.577	0.577	0.000	0.000	0.000	0.000
69	H	356	ARG	1	0.968	0.985	24.072	12.392	12.392	0.000	0.000	0.000	0.000
70	H	357	GLN	0	-0.019	-0.001	26.016	0.643	0.643	0.000	0.000	0.000	0.000
71	H	358	VAL	0	0.048	0.023	26.841	0.420	0.420	0.000	0.000	0.000	0.000
72	H	359	LEU	0	-0.027	-0.016	26.938	0.373	0.373	0.000	0.000	0.000	0.000
73	H	360	ALA	0	0.045	0.023	29.782	0.390	0.390	0.000	0.000	0.000	0.000
74	H	361	ASN	0	-0.081	-0.043	31.792	0.150	0.150	0.000	0.000	0.000	0.000
75	H	362	ALA	0	0.038	0.023	32.793	0.328	0.328	0.000	0.000	0.000	0.000
76	H	363	GLU	-1	-0.919	-0.949	32.916	-9.193	-9.193	0.000	0.000	0.000	0.000
77	H	364	ARG	1	0.936	0.969	34.117	9.090	9.090	0.000	0.000	0.000	0.000
78	H	365	SER	0	-0.019	-0.007	37.355	0.292	0.292	0.000	0.000	0.000	0.000
79	H	366	TYR	0	-0.025	-0.010	37.713	0.234	0.234	0.000	0.000	0.000	0.000
80	H	367	ASN	0	0.039	-0.011	38.016	0.224	0.224	0.000	0.000	0.000	0.000
81	H	368	GLN	0	-0.017	0.014	41.405	0.297	0.297	0.000	0.000	0.000	0.000
82	H	369	LEU	0	-0.069	-0.043	42.324	0.204	0.204	0.000	0.000	0.000	0.000
83	H	370	MET	0	-0.041	-0.042	42.138	0.164	0.164	0.000	0.000	0.000	0.000
84	H	371	ASP	-1	-0.801	-0.886	45.029	-6.898	-6.898	0.000	0.000	0.000	0.000
85	H	372	ARG	1	0.827	0.933	47.407	6.653	6.653	0.000	0.000	0.000	0.000
86	H	373	ALA	0	-0.034	-0.025	47.828	0.105	0.105	0.000	0.000	0.000	0.000
87	H	374	ALA	0	-0.068	-0.018	49.750	0.066	0.066	0.000	0.000	0.000	0.000
88	H	375	ASN	0	-0.024	-0.013	51.075	0.151	0.151	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(H:288:LYS)