FMO DATABASE

FMODB ID: 494QN

Calculation Name: 3B5N-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B5N

Chain ID: C

ChEMBL ID:

UniProt ID: P40357

Base Structure: X-ray

Registration Date: 2023-09-20

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	70
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-280849.106176
FMO2-HF: Nuclear repulsion	253246.299444
FMO2-HF: Total energy	-27602.806732
FMO2-MP2: Total energy	-27680.79876

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(C:431:GLY)

Summations of interaction energy for fragment #1(C:431:GLY)

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.
-3.843	-1.416	0.06	-1.015	-1.47	0.004

Interaction energy analysis for fragmet #1(C:431:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.067 / q_NPA : 0.027

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	C	433	ILE	0	0.052	0.045	3.306	-0.302	1.234	0.013	-0.706	-0.842	0.003
4	C	434	LYS	1	0.926	0.958	3.191	-2.283	-1.633	0.048	-0.212	-0.486	0.001
5	C	435	PHE	0	0.044	0.023	4.246	-0.298	-0.057	-0.001	-0.097	-0.142	0.000
6	C	436	THR	0	0.053	0.018	6.181	0.272	0.272	0.000	0.000	0.000	0.000
7	C	437	LYS	1	0.968	0.988	8.078	-1.159	-1.159	0.000	0.000	0.000	0.000
8	C	438	GLN	0	0.027	0.014	7.426	0.082	0.082	0.000	0.000	0.000	0.000
9	C	439	SER	0	0.012	0.003	10.107	-0.015	-0.015	0.000	0.000	0.000	0.000
10	C	440	SER	0	-0.002	-0.007	12.144	0.005	0.005	0.000	0.000	0.000	0.000
11	C	441	VAL	0	-0.016	0.004	13.309	-0.006	-0.006	0.000	0.000	0.000	0.000
12	C	442	ALA	0	-0.018	-0.006	14.412	-0.011	-0.011	0.000	0.000	0.000	0.000
13	C	443	SER	0	0.046	0.021	16.201	-0.010	-0.010	0.000	0.000	0.000	0.000
14	C	444	THR	0	-0.029	-0.016	17.451	0.001	0.001	0.000	0.000	0.000	0.000
15	C	445	ARG	1	0.960	0.980	16.379	-0.123	-0.123	0.000	0.000	0.000	0.000
16	C	446	ASN	0	0.021	0.009	20.474	-0.003	-0.003	0.000	0.000	0.000	0.000
17	C	447	THR	0	0.001	-0.015	21.881	-0.005	-0.005	0.000	0.000	0.000	0.000
18	C	448	LEU	0	0.004	0.008	23.709	-0.002	-0.002	0.000	0.000	0.000	0.000
19	C	449	LYS	1	0.936	0.972	24.382	-0.010	-0.010	0.000	0.000	0.000	0.000
20	C	450	MET	0	-0.006	-0.006	24.633	-0.005	-0.005	0.000	0.000	0.000	0.000
21	C	451	ALA	0	0.010	0.014	28.121	-0.002	-0.002	0.000	0.000	0.000	0.000
22	C	452	GLN	0	0.048	0.022	28.921	-0.002	-0.002	0.000	0.000	0.000	0.000
23	C	453	ASP	-1	-0.852	-0.919	30.532	0.012	0.012	0.000	0.000	0.000	0.000
24	C	454	ALA	0	-0.036	-0.017	32.529	-0.002	-0.002	0.000	0.000	0.000	0.000
25	C	455	GLU	-1	-0.929	-0.961	34.021	0.034	0.034	0.000	0.000	0.000	0.000
26	C	456	ARG	1	0.840	0.911	34.126	-0.015	-0.015	0.000	0.000	0.000	0.000
27	C	457	ALA	0	-0.028	-0.019	37.000	-0.001	-0.001	0.000	0.000	0.000	0.000
28	C	458	GLY	0	0.036	0.027	38.419	-0.001	-0.001	0.000	0.000	0.000	0.000
29	C	459	MET	0	0.026	0.002	39.776	-0.001	-0.001	0.000	0.000	0.000	0.000
30	C	460	ASN	0	-0.006	-0.001	41.616	0.000	0.000	0.000	0.000	0.000	0.000
31	C	461	THR	0	-0.044	-0.030	42.317	-0.001	-0.001	0.000	0.000	0.000	0.000
32	C	462	LEU	0	0.006	-0.003	43.326	-0.001	-0.001	0.000	0.000	0.000	0.000
33	C	463	GLY	0	0.016	0.019	46.054	0.000	0.000	0.000	0.000	0.000	0.000
34	C	464	MET	0	-0.057	-0.030	45.373	-0.001	-0.001	0.000	0.000	0.000	0.000
35	C	465	LEU	0	0.002	0.001	47.378	-0.001	-0.001	0.000	0.000	0.000	0.000
36	C	466	GLY	0	0.020	0.014	50.380	0.000	0.000	0.000	0.000	0.000	0.000
37	C	467	HIS	0	-0.010	-0.012	52.119	0.000	0.000	0.000	0.000	0.000	0.000
38	C	468	GLN	0	-0.004	-0.020	50.759	-0.001	-0.001	0.000	0.000	0.000	0.000
39	C	469	SER	0	0.017	0.020	54.779	-0.001	-0.001	0.000	0.000	0.000	0.000
40	C	470	GLU	-1	-0.922	-0.950	56.630	0.010	0.010	0.000	0.000	0.000	0.000
41	C	471	GLN	0	-0.068	-0.037	57.098	-0.001	-0.001	0.000	0.000	0.000	0.000
42	C	472	LEU	0	-0.012	-0.009	57.038	-0.001	-0.001	0.000	0.000	0.000	0.000
43	C	473	ASN	0	0.001	-0.002	60.713	0.000	0.000	0.000	0.000	0.000	0.000
44	C	474	ASN	0	0.011	0.004	62.766	0.000	0.000	0.000	0.000	0.000	0.000
45	C	475	VAL	0	-0.031	-0.007	63.371	0.000	0.000	0.000	0.000	0.000	0.000
46	C	476	GLU	-1	-0.882	-0.934	63.229	0.006	0.006	0.000	0.000	0.000	0.000
47	C	477	GLY	0	0.052	0.027	66.503	0.000	0.000	0.000	0.000	0.000	0.000
48	C	478	ASN	0	-0.075	-0.051	68.149	0.000	0.000	0.000	0.000	0.000	0.000
49	C	479	LEU	0	0.013	0.007	67.092	0.000	0.000	0.000	0.000	0.000	0.000
50	C	480	ASP	-1	-0.857	-0.921	70.202	0.004	0.004	0.000	0.000	0.000	0.000
51	C	481	LEU	0	-0.014	0.005	72.632	0.000	0.000	0.000	0.000	0.000	0.000
52	C	482	MET	0	0.022	0.002	71.312	0.000	0.000	0.000	0.000	0.000	0.000
53	C	483	LYS	1	0.790	0.885	70.374	-0.004	-0.004	0.000	0.000	0.000	0.000
54	C	484	VAL	0	-0.036	-0.012	76.303	0.000	0.000	0.000	0.000	0.000	0.000
55	C	485	GLN	0	-0.002	-0.018	77.305	0.000	0.000	0.000	0.000	0.000	0.000
56	C	486	ASN	0	0.020	0.003	77.555	0.000	0.000	0.000	0.000	0.000	0.000
57	C	487	LYS	1	0.957	1.003	79.365	-0.003	-0.003	0.000	0.000	0.000	0.000
58	C	488	VAL	0	0.030	0.023	83.299	0.000	0.000	0.000	0.000	0.000	0.000
59	C	489	ALA	0	0.026	0.011	83.747	0.000	0.000	0.000	0.000	0.000	0.000
60	C	490	ASP	-1	-0.888	-0.952	83.398	0.002	0.002	0.000	0.000	0.000	0.000
61	C	491	GLU	-1	-0.908	-0.947	86.433	0.003	0.003	0.000	0.000	0.000	0.000
62	C	492	LYS	1	0.812	0.899	88.855	-0.003	-0.003	0.000	0.000	0.000	0.000
63	C	493	VAL	0	0.011	0.011	87.221	0.000	0.000	0.000	0.000	0.000	0.000
64	C	494	ALA	0	-0.004	-0.001	90.352	0.000	0.000	0.000	0.000	0.000	0.000
65	C	495	GLU	-1	-0.948	-0.976	92.401	0.002	0.002	0.000	0.000	0.000	0.000
66	C	496	LEU	0	0.022	0.001	91.723	0.000	0.000	0.000	0.000	0.000	0.000
67	C	497	LYS	1	0.878	0.933	93.852	-0.001	-0.001	0.000	0.000	0.000	0.000
68	C	498	LYS	1	0.913	0.962	95.739	-0.001	-0.001	0.000	0.000	0.000	0.000
69	C	499	LEU	0	-0.022	0.006	97.601	0.000	0.000	0.000	0.000	0.000	0.000
70	C	500	GLN	0	-0.062	-0.027	97.108	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(C:431:GLY)