FMO DATABASE

FMODB ID: 76GMK

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	OptAll
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
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-257507.557
FMO2-HF: Nuclear repulsion	234246.1239
FMO2-HF: Total energy	-23261.4331
FMO2-MP2: Total energy	-23326.510477

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.
-26.2	-19.295	14.971	-7.924	-13.95	-0.038

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 : 0.029 / q_NPA : 0.023

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	0.990	0.984	2.884	-0.927	1.410	0.278	-1.306	-1.308	-0.005
4	A	4	GLN	0	0.042	0.035	5.643	0.472	0.472	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.719	-0.830	2.336	-16.232	-11.039	4.545	-4.393	-5.344	-0.045
6	A	6	LYS	1	0.860	0.918	2.685	-9.244	-10.045	9.397	-2.476	-6.120	0.014
7	A	7	THR	0	-0.053	-0.030	3.214	0.347	0.098	0.047	0.430	-0.228	0.000
8	A	8	ALA	0	0.044	0.026	5.757	0.129	0.129	0.000	0.000	0.000	0.000
9	A	9	LEU	0	0.001	0.002	2.547	-0.329	0.096	0.704	-0.179	-0.950	-0.002
10	A	10	ASN	0	0.003	-0.007	5.519	0.346	0.346	0.000	0.000	0.000	0.000
11	A	11	MET	0	0.033	0.030	7.900	0.035	0.035	0.000	0.000	0.000	0.000
12	A	12	ALA	0	0.073	0.031	8.434	0.061	0.061	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.843	0.920	5.190	-0.758	-0.758	0.000	0.000	0.000	0.000
14	A	14	PHE	0	0.024	0.018	10.548	0.040	0.040	0.000	0.000	0.000	0.000
15	A	15	ILE	0	0.060	0.025	13.198	0.013	0.013	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.904	0.955	8.756	0.471	0.471	0.000	0.000	0.000	0.000
17	A	17	SER	0	0.043	0.017	14.763	0.033	0.033	0.000	0.000	0.000	0.000
18	A	18	GLN	0	-0.033	-0.006	16.665	0.020	0.020	0.000	0.000	0.000	0.000
19	A	19	THR	0	0.016	-0.010	18.018	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.053	-0.014	17.937	0.004	0.004	0.000	0.000	0.000	0.000
21	A	21	THR	0	0.040	0.014	20.647	0.010	0.010	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.018	-0.017	22.363	0.002	0.002	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.002	0.007	23.806	0.000	0.000	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.976	-1.003	23.333	0.039	0.039	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.788	0.861	27.090	-0.014	-0.014	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.018	0.023	26.896	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	27	ASN	0	-0.078	-0.037	28.969	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.885	-0.917	32.141	0.017	0.017	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.021	0.005	32.150	0.002	0.002	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.855	-0.928	35.626	-0.030	-0.030	0.000	0.000	0.000	0.000
31	A	31	PRO	0	-0.059	-0.040	36.378	-0.005	-0.005	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.902	-0.945	36.123	-0.062	-0.062	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.850	-0.919	35.558	-0.041	-0.041	0.000	0.000	0.000	0.000
34	A	34	GLN	0	-0.096	-0.067	32.265	-0.011	-0.011	0.000	0.000	0.000	0.000
35	A	35	ALA	0	0.006	0.013	31.611	-0.010	-0.010	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.869	-0.928	32.475	-0.084	-0.084	0.000	0.000	0.000	0.000
37	A	37	ILE	0	-0.061	-0.036	28.258	-0.010	-0.010	0.000	0.000	0.000	0.000
38	A	38	CYS	0	-0.079	-0.052	27.852	-0.012	-0.012	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.925	-0.958	27.958	-0.133	-0.133	0.000	0.000	0.000	0.000
40	A	40	SER	0	0.020	0.015	29.170	-0.017	-0.017	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.043	-0.024	23.500	-0.014	-0.014	0.000	0.000	0.000	0.000
42	A	42	HIS	0	-0.095	-0.051	24.287	-0.036	-0.036	0.000	0.000	0.000	0.000
43	A	43	ASP	-1	-0.818	-0.900	25.163	-0.195	-0.195	0.000	0.000	0.000	0.000
44	A	44	HIS	0	-0.030	-0.026	24.324	-0.012	-0.012	0.000	0.000	0.000	0.000
45	A	45	ALA	0	-0.046	-0.017	20.856	-0.025	-0.025	0.000	0.000	0.000	0.000
46	A	46	ASP	-1	-0.797	-0.881	21.684	-0.304	-0.304	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.925	-0.963	24.163	-0.198	-0.198	0.000	0.000	0.000	0.000
48	A	48	LEU	0	-0.017	0.000	18.836	-0.015	-0.015	0.000	0.000	0.000	0.000
49	A	49	TYR	0	-0.026	0.003	19.683	-0.054	-0.054	0.000	0.000	0.000	0.000
50	A	50	ARG	1	0.877	0.904	21.249	0.219	0.219	0.000	0.000	0.000	0.000
51	A	51	SER	0	0.001	-0.007	22.696	0.004	0.004	0.000	0.000	0.000	0.000
52	A	52	CYS	0	-0.173	-0.078	18.570	-0.018	-0.018	0.000	0.000	0.000	0.000
53	A	53	LEU	0	0.005	0.011	20.630	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	54	ALA	0	-0.031	-0.010	22.933	0.003	0.003	0.000	0.000	0.000	0.000
55	A	55	ARG	1	0.815	0.901	20.051	0.345	0.345	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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