FMO DATABASE

FMODB ID: 3J87L

Calculation Name: 3BID-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BID

Chain ID: A

ChEMBL ID:

UniProt ID: Q7DDI1

Base Structure: X-ray

Registration Date: 2023-09-23

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	58
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-288793.095286
FMO2-HF: Nuclear repulsion	265425.826836
FMO2-HF: Total energy	-23367.26845
FMO2-MP2: Total energy	-23435.151675

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.
-8.531	-1.86	7.6	-5.724	-8.547	-0.037

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 : 0.006 / q_NPA : 0.012

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	PHE	0	0.053	0.022	3.876	-0.911	1.785	-0.020	-1.440	-1.236	0.005
4	A	4	GLU	-1	-0.809	-0.893	6.381	-0.671	-0.671	0.000	0.000	0.000	0.000
5	A	5	ILE	0	-0.015	-0.019	9.587	0.232	0.232	0.000	0.000	0.000	0.000
6	A	6	TYR	0	-0.016	-0.006	12.866	0.039	0.039	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.903	0.954	15.968	0.255	0.255	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.836	-0.928	19.525	-0.122	-0.122	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.016	-0.011	21.009	-0.007	-0.007	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.872	0.948	23.486	0.075	0.075	0.000	0.000	0.000	0.000
11	A	11	GLY	0	-0.015	0.003	24.478	-0.001	-0.001	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.814	-0.887	21.452	-0.129	-0.129	0.000	0.000	0.000	0.000
13	A	13	TYR	0	-0.037	-0.048	18.058	-0.012	-0.012	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.852	0.931	15.392	0.164	0.164	0.000	0.000	0.000	0.000
15	A	15	TRP	0	0.054	0.017	8.463	-0.135	-0.135	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.875	0.939	8.657	0.418	0.418	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.002	0.000	2.476	-1.292	-1.209	2.509	-0.558	-2.034	-0.001
18	A	18	LYS	1	0.833	0.923	4.551	1.000	1.375	-0.001	-0.086	-0.288	0.000
19	A	19	ALA	0	0.058	0.015	2.410	-6.729	-4.005	4.034	-3.478	-3.280	-0.040
20	A	20	ALA	0	0.020	0.001	3.482	-0.484	-0.383	0.002	0.135	-0.238	0.000
21	A	21	ASN	0	-0.014	0.015	5.355	-0.788	-0.768	-0.001	-0.003	-0.016	0.000
22	A	22	HIS	0	-0.020	-0.039	7.050	-0.274	-0.274	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.877	-0.934	6.836	0.789	0.789	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.084	-0.044	6.227	0.003	0.003	0.000	0.000	0.000	0.000
25	A	25	ILE	0	0.011	0.018	2.639	-0.611	0.061	1.077	-0.294	-1.455	-0.001
26	A	26	ALA	0	0.017	0.004	6.887	-0.108	-0.108	0.000	0.000	0.000	0.000
27	A	27	GLN	0	0.026	-0.001	8.765	-0.278	-0.278	0.000	0.000	0.000	0.000
28	A	28	GLY	0	-0.013	0.000	11.563	0.009	0.009	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.846	-0.919	13.625	0.008	0.008	0.000	0.000	0.000	0.000
30	A	30	GLY	0	-0.051	-0.033	17.388	-0.051	-0.051	0.000	0.000	0.000	0.000
31	A	31	TYR	0	0.025	0.008	15.653	-0.014	-0.014	0.000	0.000	0.000	0.000
32	A	32	THR	0	0.023	0.003	20.603	0.000	0.000	0.000	0.000	0.000	0.000
33	A	33	SER	0	0.019	-0.003	21.831	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.962	0.994	18.132	0.502	0.502	0.000	0.000	0.000	0.000
35	A	35	GLN	0	0.036	0.020	18.466	-0.077	-0.077	0.000	0.000	0.000	0.000
36	A	36	ASN	0	-0.007	-0.020	19.206	-0.016	-0.016	0.000	0.000	0.000	0.000
37	A	37	CYS	0	0.005	0.022	14.291	0.003	0.003	0.000	0.000	0.000	0.000
38	A	38	GLN	0	-0.023	-0.017	14.381	-0.036	-0.036	0.000	0.000	0.000	0.000
39	A	39	HIS	0	0.038	0.027	14.609	-0.091	-0.091	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.017	0.014	14.933	-0.011	-0.011	0.000	0.000	0.000	0.000
41	A	41	VAL	0	-0.002	-0.004	9.156	-0.012	-0.012	0.000	0.000	0.000	0.000
42	A	42	ASP	-1	-0.865	-0.930	10.298	-1.137	-1.137	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.004	-0.001	12.130	-0.011	-0.011	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.001	0.016	8.940	0.028	0.028	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.866	0.938	7.212	1.438	1.438	0.000	0.000	0.000	0.000
46	A	46	SER	0	-0.102	-0.036	8.403	-0.023	-0.023	0.000	0.000	0.000	0.000
47	A	47	THR	0	-0.068	-0.037	9.677	0.146	0.146	0.000	0.000	0.000	0.000
48	A	48	THR	0	0.032	0.002	9.506	-0.120	-0.120	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.027	0.009	9.926	0.072	0.072	0.000	0.000	0.000	0.000
50	A	50	ALA	0	-0.021	-0.009	11.121	0.064	0.064	0.000	0.000	0.000	0.000
51	A	51	THR	0	-0.023	-0.014	12.800	0.003	0.003	0.000	0.000	0.000	0.000
52	A	52	PRO	0	-0.009	0.000	14.358	0.041	0.041	0.000	0.000	0.000	0.000
53	A	53	VAL	0	0.036	0.014	13.198	-0.014	-0.014	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.906	0.954	16.467	-0.027	-0.027	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.925	-0.959	18.360	0.247	0.247	0.000	0.000	0.000	0.000
56	A	56	VAL	0	-0.055	-0.025	20.703	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	57	LEU	0	0.007	-0.009	22.895	0.015	0.015	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.967	-0.964	25.835	0.123	0.123	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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