FMO DATABASE

FMODB ID: MN39Z

Calculation Name: 1B6Q-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1B6Q

Chain ID: A

ChEMBL ID:

UniProt ID: P03051

Base Structure: X-ray

Registration Date: 2023-09-21

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

DOI:

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	55
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-257542.290765
FMO2-HF: Nuclear repulsion	234281.048297
FMO2-HF: Total energy	-23261.242467
FMO2-MP2: Total energy	-23326.35467

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:1:MET)

Summations of interaction energy for fragment #1(A:1: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.
-16.126	-10.573	9.441	-4.463	-10.532	-0.011

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / 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

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	A	3	LYS	1	0.953	0.951	3.073	-0.788	1.260	0.170	-1.077	-1.142	-0.001
4	A	4	GLN	0	0.053	0.025	5.366	0.261	0.432	-0.001	-0.006	-0.164	0.000
5	A	5	GLU	-1	-0.739	-0.837	2.846	-10.767	-7.532	0.798	-1.733	-2.301	-0.015
6	A	6	LYS	1	0.903	0.953	2.107	-5.079	-4.878	7.429	-2.058	-5.572	0.007
7	A	7	THR	0	-0.046	-0.023	3.121	0.849	0.448	0.043	0.628	-0.269	0.000
8	A	8	ALA	0	0.047	0.032	5.879	0.201	0.201	0.000	0.000	0.000	0.000
9	A	9	LEU	0	0.016	0.011	2.408	-0.221	0.078	1.002	-0.217	-1.084	-0.002
10	A	10	ASN	0	0.006	-0.008	5.430	0.480	0.480	0.000	0.000	0.000	0.000
11	A	11	MET	0	0.029	0.030	7.808	0.062	0.062	0.000	0.000	0.000	0.000
12	A	12	ALA	0	0.036	0.019	8.331	0.065	0.065	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.855	0.906	5.208	-1.057	-1.057	0.000	0.000	0.000	0.000
14	A	14	PHE	0	0.012	0.014	10.400	0.044	0.044	0.000	0.000	0.000	0.000
15	A	15	ILE	0	0.051	0.024	13.101	0.014	0.014	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.937	0.981	8.603	0.308	0.308	0.000	0.000	0.000	0.000
17	A	17	SER	0	0.020	0.004	14.603	0.029	0.029	0.000	0.000	0.000	0.000
18	A	18	GLN	0	-0.018	-0.006	16.484	0.011	0.011	0.000	0.000	0.000	0.000
19	A	19	THR	0	0.014	-0.008	17.924	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.037	-0.020	17.824	0.004	0.004	0.000	0.000	0.000	0.000
21	A	21	THR	0	0.022	0.018	20.918	0.006	0.006	0.000	0.000	0.000	0.000
22	A	22	LEU	0	0.005	-0.006	22.382	0.000	0.000	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.011	0.016	23.955	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.969	-0.994	23.791	0.056	0.056	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.783	0.862	27.174	-0.024	-0.024	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.032	0.031	26.946	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	27	ASN	0	-0.062	-0.028	28.936	-0.006	-0.006	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.897	-0.938	32.069	0.023	0.023	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.045	-0.003	32.518	0.001	0.001	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.870	-0.928	35.634	-0.017	-0.017	0.000	0.000	0.000	0.000
31	A	31	PRO	0	-0.031	-0.036	36.254	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.888	-0.946	35.951	-0.046	-0.046	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.861	-0.919	35.669	-0.031	-0.031	0.000	0.000	0.000	0.000
34	A	34	GLN	0	-0.083	-0.053	32.095	-0.009	-0.009	0.000	0.000	0.000	0.000
35	A	35	ALA	0	-0.021	-0.005	31.604	-0.008	-0.008	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.860	-0.924	32.534	-0.068	-0.068	0.000	0.000	0.000	0.000
37	A	37	ILE	0	-0.071	-0.040	28.176	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	38	CYS	0	-0.086	-0.063	27.638	-0.010	-0.010	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.915	-0.950	27.796	-0.109	-0.109	0.000	0.000	0.000	0.000
40	A	40	SER	0	0.030	0.025	29.203	-0.016	-0.016	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.041	-0.016	23.284	-0.014	-0.014	0.000	0.000	0.000	0.000
42	A	42	HIS	0	-0.092	-0.045	24.351	-0.030	-0.030	0.000	0.000	0.000	0.000
43	A	43	ASP	-1	-0.814	-0.912	25.581	-0.159	-0.159	0.000	0.000	0.000	0.000
44	A	44	HIS	0	-0.042	-0.031	24.343	-0.013	-0.013	0.000	0.000	0.000	0.000
45	A	45	ALA	0	-0.065	-0.033	21.199	-0.025	-0.025	0.000	0.000	0.000	0.000
46	A	46	ASP	-1	-0.802	-0.891	22.026	-0.260	-0.260	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.918	-0.950	24.501	-0.180	-0.180	0.000	0.000	0.000	0.000
48	A	48	LEU	0	-0.019	0.001	19.112	-0.019	-0.019	0.000	0.000	0.000	0.000
49	A	49	TYR	0	-0.004	0.016	19.786	-0.049	-0.049	0.000	0.000	0.000	0.000
50	A	50	ARG	1	0.887	0.911	21.496	0.190	0.190	0.000	0.000	0.000	0.000
51	A	51	SER	0	-0.002	-0.009	22.982	0.004	0.004	0.000	0.000	0.000	0.000
52	A	52	CYS	0	-0.177	-0.088	18.984	-0.014	-0.014	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.015	0.005	20.974	-0.018	-0.018	0.000	0.000	0.000	0.000
54	A	54	ALA	0	-0.040	-0.003	23.085	0.003	0.003	0.000	0.000	0.000	0.000
55	A	55	ARG	1	0.840	0.910	20.230	0.321	0.321	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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