FMO DATABASE

FMODB ID: 6NYJZ

Calculation Name: 2X7L-M-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2X7L

Chain ID: M

ChEMBL ID:

UniProt ID: P04616

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	57
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-307279.747253
FMO2-HF: Nuclear repulsion	283432.522077
FMO2-HF: Total energy	-23847.225176
FMO2-MP2: Total energy	-23918.954973

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(M:9:ASP)

Summations of interaction energy for fragment #1(M:9:ASP)

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.
-156.284	-146.999	2.241	-5.169	-6.358	0.056

Interaction energy analysis for fragmet #1(M:9:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.874 / q_NPA : -0.960

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	M	11	ASP	-1	-0.918	-0.952	2.395	36.922	40.930	1.950	-2.631	-3.327	0.032
4	M	12	LEU	0	0.025	0.019	2.798	-22.458	-18.363	0.265	-2.158	-2.203	0.023
5	M	13	LEU	0	-0.006	0.005	3.268	-11.866	-11.050	0.025	-0.288	-0.553	0.001
6	M	14	LYS	1	0.943	0.965	5.678	-43.512	-43.512	0.000	0.000	0.000	0.000
7	M	15	ALA	0	0.012	0.017	7.348	-4.899	-4.899	0.000	0.000	0.000	0.000
8	M	16	VAL	0	0.023	0.010	7.360	-4.164	-4.164	0.000	0.000	0.000	0.000
9	M	17	ARG	1	0.907	0.950	9.365	-27.608	-27.608	0.000	0.000	0.000	0.000
10	M	18	LEU	0	0.005	0.014	11.793	-2.290	-2.290	0.000	0.000	0.000	0.000
11	M	19	ILE	0	0.032	0.010	11.838	-1.969	-1.969	0.000	0.000	0.000	0.000
12	M	20	LYS	1	0.962	0.974	14.120	-18.372	-18.372	0.000	0.000	0.000	0.000
13	M	21	PHE	0	0.019	0.015	15.938	-1.274	-1.274	0.000	0.000	0.000	0.000
14	M	22	LEU	0	-0.011	-0.016	16.512	-1.222	-1.222	0.000	0.000	0.000	0.000
15	M	23	TYR	0	-0.054	-0.014	17.578	-0.729	-0.729	0.000	0.000	0.000	0.000
16	M	24	GLN	0	-0.075	-0.032	18.338	-0.049	-0.049	0.000	0.000	0.000	0.000
17	M	25	SER	0	-0.015	-0.005	21.806	-0.898	-0.898	0.000	0.000	0.000	0.000
18	M	26	ASN	0	-0.007	-0.016	23.898	0.536	0.536	0.000	0.000	0.000	0.000
19	M	27	PRO	0	0.123	0.080	26.045	0.086	0.086	0.000	0.000	0.000	0.000
20	M	28	PRO	0	-0.022	-0.030	27.202	-0.267	-0.267	0.000	0.000	0.000	0.000
21	M	29	PRO	0	-0.057	-0.041	30.448	-0.115	-0.115	0.000	0.000	0.000	0.000
22	M	30	ASN	0	0.029	0.036	33.696	0.019	0.019	0.000	0.000	0.000	0.000
23	M	31	PRO	0	0.019	0.020	36.412	0.053	0.053	0.000	0.000	0.000	0.000
24	M	32	GLU	-1	-0.831	-0.931	38.444	7.626	7.626	0.000	0.000	0.000	0.000
25	M	33	GLY	0	-0.065	-0.035	41.687	0.070	0.070	0.000	0.000	0.000	0.000
26	M	34	THR	0	0.111	0.033	44.589	-0.047	-0.047	0.000	0.000	0.000	0.000
27	M	35	ARG	1	0.987	1.001	45.693	-5.800	-5.800	0.000	0.000	0.000	0.000
28	M	36	GLN	0	0.011	0.004	45.348	0.140	0.140	0.000	0.000	0.000	0.000
29	M	37	ALA	0	0.105	0.047	43.373	0.177	0.177	0.000	0.000	0.000	0.000
30	M	38	ARG	1	0.912	0.976	39.686	-7.427	-7.427	0.000	0.000	0.000	0.000
31	M	39	ARG	1	0.930	0.940	39.835	-6.844	-6.844	0.000	0.000	0.000	0.000
32	M	40	ASN	0	0.037	0.028	39.286	0.164	0.164	0.000	0.000	0.000	0.000
33	M	41	ARG	1	0.943	0.956	36.001	-7.837	-7.837	0.000	0.000	0.000	0.000
34	M	42	ARG	1	0.927	0.991	34.772	-8.258	-8.258	0.000	0.000	0.000	0.000
35	M	43	ARG	1	0.960	0.976	33.980	-7.560	-7.560	0.000	0.000	0.000	0.000
36	M	44	ARG	1	1.075	1.048	32.796	-9.043	-9.043	0.000	0.000	0.000	0.000
37	M	45	TRP	0	-0.022	-0.023	26.620	0.109	0.109	0.000	0.000	0.000	0.000
38	M	46	ARG	1	0.912	0.960	29.277	-8.704	-8.704	0.000	0.000	0.000	0.000
39	M	47	GLU	-1	-0.935	-0.960	28.753	9.865	9.865	0.000	0.000	0.000	0.000
40	M	48	ARG	1	0.899	0.961	22.664	-12.736	-12.736	0.000	0.000	0.000	0.000
41	M	49	GLN	0	0.058	0.015	23.611	0.857	0.857	0.000	0.000	0.000	0.000
42	M	50	ARG	1	0.964	0.973	24.003	-9.823	-9.823	0.000	0.000	0.000	0.000
43	M	51	GLN	0	0.017	0.020	23.022	-0.068	-0.068	0.000	0.000	0.000	0.000
44	M	52	ILE	0	0.028	0.001	19.599	0.438	0.438	0.000	0.000	0.000	0.000
45	M	53	HIS	0	-0.028	0.014	19.268	0.734	0.734	0.000	0.000	0.000	0.000
46	M	54	SER	0	0.017	0.010	19.037	0.775	0.775	0.000	0.000	0.000	0.000
47	M	55	ILE	0	-0.035	-0.019	16.415	0.489	0.489	0.000	0.000	0.000	0.000
48	M	56	SER	0	0.041	-0.002	14.843	1.337	1.337	0.000	0.000	0.000	0.000
49	M	57	GLU	-1	-0.951	-0.963	14.105	16.545	16.545	0.000	0.000	0.000	0.000
50	M	58	ARG	1	0.956	0.974	14.758	-14.781	-14.781	0.000	0.000	0.000	0.000
51	M	59	ILE	0	-0.017	0.005	10.210	0.941	0.941	0.000	0.000	0.000	0.000
52	M	60	LEU	0	0.026	0.013	9.158	2.780	2.780	0.000	0.000	0.000	0.000
53	M	61	SER	0	-0.041	-0.023	9.923	1.701	1.701	0.000	0.000	0.000	0.000
54	M	62	THR	0	-0.058	-0.049	9.669	0.660	0.660	0.000	0.000	0.000	0.000
55	M	63	TYR	0	-0.020	-0.014	4.074	1.429	1.795	0.001	-0.092	-0.275	0.000
56	M	64	LEU	0	-0.049	-0.019	6.982	0.614	0.614	0.000	0.000	0.000	0.000
57	M	65	GLY	0	0.008	0.021	9.686	-0.731	-0.731	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(M:9:ASP)