FMO DATABASE

FMODB ID: 5J26Z

Calculation Name: 3DGP-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DGP

Chain ID: B

ChEMBL ID:

UniProt ID: Q02939

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:

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	63
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-342610.730171
FMO2-HF: Nuclear repulsion	317712.090633
FMO2-HF: Total energy	-24898.639537
FMO2-MP2: Total energy	-24971.371201

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:2:ALA)

Summations of interaction energy for fragment #1(B:2:ALA)

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.
1.02	2.412	-0.017	-0.758	-0.617	0.002

Interaction energy analysis for fragmet #1(B:2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.034 / q_NPA : 0.007

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	B	4	ALA	0	0.040	0.022	3.892	0.299	1.691	-0.017	-0.758	-0.617	0.002
4	B	5	ARG	1	0.922	0.963	6.576	-0.556	-0.556	0.000	0.000	0.000	0.000
5	B	6	LYS	1	0.963	0.977	10.278	0.159	0.159	0.000	0.000	0.000	0.000
6	B	7	GLY	0	0.036	0.005	13.367	0.031	0.031	0.000	0.000	0.000	0.000
7	B	8	ALA	0	-0.011	0.014	15.789	-0.030	-0.030	0.000	0.000	0.000	0.000
8	B	9	LEU	0	0.007	0.015	15.489	0.025	0.025	0.000	0.000	0.000	0.000
9	B	10	VAL	0	-0.023	-0.013	17.725	-0.031	-0.031	0.000	0.000	0.000	0.000
10	B	11	GLN	0	-0.008	-0.007	20.769	0.026	0.026	0.000	0.000	0.000	0.000
11	B	12	CYS	0	-0.084	-0.032	22.344	-0.016	-0.016	0.000	0.000	0.000	0.000
12	B	13	ASP	-1	-0.734	-0.836	25.403	0.105	0.105	0.000	0.000	0.000	0.000
13	B	14	PRO	0	0.074	0.016	27.188	0.002	0.002	0.000	0.000	0.000	0.000
14	B	15	SER	0	-0.077	-0.059	28.193	0.001	0.001	0.000	0.000	0.000	0.000
15	B	16	ILE	0	0.037	0.003	27.803	-0.001	-0.001	0.000	0.000	0.000	0.000
16	B	17	LYS	1	0.852	0.926	22.074	-0.227	-0.227	0.000	0.000	0.000	0.000
17	B	18	ALA	0	0.001	-0.002	26.510	0.004	0.004	0.000	0.000	0.000	0.000
18	B	19	LEU	0	0.002	0.006	29.071	-0.002	-0.002	0.000	0.000	0.000	0.000
19	B	20	ILE	0	-0.011	-0.011	24.811	-0.004	-0.004	0.000	0.000	0.000	0.000
20	B	21	LEU	0	0.022	0.014	23.500	-0.001	-0.001	0.000	0.000	0.000	0.000
21	B	22	GLN	0	-0.036	-0.014	27.202	-0.007	-0.007	0.000	0.000	0.000	0.000
22	B	23	ILE	0	-0.012	-0.008	29.167	-0.005	-0.005	0.000	0.000	0.000	0.000
23	B	24	ASP	-1	-0.835	-0.931	24.924	0.146	0.146	0.000	0.000	0.000	0.000
24	B	25	ALA	0	0.018	0.020	27.703	-0.004	-0.004	0.000	0.000	0.000	0.000
25	B	26	LYS	1	0.854	0.936	29.643	-0.078	-0.078	0.000	0.000	0.000	0.000
26	B	27	MET	0	-0.031	-0.013	29.878	-0.007	-0.007	0.000	0.000	0.000	0.000
27	B	28	SER	0	-0.035	-0.007	26.881	-0.004	-0.004	0.000	0.000	0.000	0.000
28	B	29	ASP	-1	-0.900	-0.961	23.460	0.091	0.091	0.000	0.000	0.000	0.000
29	B	30	ILE	0	-0.047	-0.017	24.216	-0.008	-0.008	0.000	0.000	0.000	0.000
30	B	31	VAL	0	-0.029	-0.029	20.494	0.005	0.005	0.000	0.000	0.000	0.000
31	B	32	LEU	0	-0.086	-0.044	16.308	0.004	0.004	0.000	0.000	0.000	0.000
32	B	33	GLU	-1	-0.908	-0.971	12.408	0.790	0.790	0.000	0.000	0.000	0.000
33	B	34	GLU	-1	-0.879	-0.940	17.037	0.205	0.205	0.000	0.000	0.000	0.000
34	B	35	LEU	0	-0.069	-0.034	13.423	0.035	0.035	0.000	0.000	0.000	0.000
35	B	36	ASP	-1	-0.774	-0.885	16.597	0.291	0.291	0.000	0.000	0.000	0.000
36	B	37	ASP	-1	-0.903	-0.947	19.326	0.187	0.187	0.000	0.000	0.000	0.000
37	B	38	THR	0	-0.060	-0.028	21.738	-0.020	-0.020	0.000	0.000	0.000	0.000
38	B	39	HIS	1	0.837	0.905	17.992	-0.230	-0.230	0.000	0.000	0.000	0.000
39	B	40	LEU	0	0.032	0.032	18.873	0.024	0.024	0.000	0.000	0.000	0.000
40	B	41	LEU	0	-0.010	0.005	13.232	-0.019	-0.019	0.000	0.000	0.000	0.000
41	B	42	VAL	0	0.019	0.001	17.109	-0.001	-0.001	0.000	0.000	0.000	0.000
42	B	43	ASN	0	0.053	0.025	19.020	-0.017	-0.017	0.000	0.000	0.000	0.000
43	B	44	PRO	0	0.017	0.002	18.398	-0.009	-0.009	0.000	0.000	0.000	0.000
44	B	45	SER	0	-0.066	-0.037	21.166	-0.009	-0.009	0.000	0.000	0.000	0.000
45	B	46	LYS	1	0.947	0.981	23.965	-0.069	-0.069	0.000	0.000	0.000	0.000
46	B	47	VAL	0	0.016	0.019	22.485	0.003	0.003	0.000	0.000	0.000	0.000
47	B	48	GLU	-1	-0.875	-0.953	25.409	0.041	0.041	0.000	0.000	0.000	0.000
48	B	49	PHE	0	-0.003	0.007	28.873	-0.002	-0.002	0.000	0.000	0.000	0.000
49	B	50	VAL	0	0.041	0.017	25.915	-0.001	-0.001	0.000	0.000	0.000	0.000
50	B	51	LYS	1	0.946	0.975	26.020	-0.057	-0.057	0.000	0.000	0.000	0.000
51	B	52	HIS	0	-0.006	-0.006	30.362	-0.002	-0.002	0.000	0.000	0.000	0.000
52	B	53	GLU	-1	-0.919	-0.958	32.014	0.057	0.057	0.000	0.000	0.000	0.000
53	B	54	LEU	0	-0.007	-0.005	28.639	-0.001	-0.001	0.000	0.000	0.000	0.000
54	B	55	ASN	0	0.025	0.014	33.168	-0.002	-0.002	0.000	0.000	0.000	0.000
55	B	56	ARG	1	0.922	0.975	35.902	-0.041	-0.041	0.000	0.000	0.000	0.000
56	B	57	LEU	0	0.017	0.003	33.696	-0.002	-0.002	0.000	0.000	0.000	0.000
57	B	58	LEU	0	-0.010	0.003	34.551	-0.001	-0.001	0.000	0.000	0.000	0.000
58	B	59	SER	0	-0.048	-0.046	38.240	-0.004	-0.004	0.000	0.000	0.000	0.000
59	B	60	LYS	1	0.852	0.913	40.929	-0.038	-0.038	0.000	0.000	0.000	0.000
60	B	61	ASN	0	0.039	0.044	40.966	-0.003	-0.003	0.000	0.000	0.000	0.000
61	B	62	ILE	0	0.009	-0.006	43.197	-0.002	-0.002	0.000	0.000	0.000	0.000
62	B	63	TYR	0	-0.066	-0.021	45.199	-0.003	-0.003	0.000	0.000	0.000	0.000
63	B	64	ASN	0	-0.018	0.002	42.529	0.003	0.003	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(B:2:ALA)