FMO DATABASE

FMODB ID: 1NKMZ

Calculation Name: 3VZ9-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VZ9

Chain ID: D

ChEMBL ID:

UniProt ID: E1C4Y2

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	60
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-333812.927565
FMO2-HF: Nuclear repulsion	308834.984024
FMO2-HF: Total energy	-24977.943541
FMO2-MP2: Total energy	-25051.011604

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(D:136:TYR)

Summations of interaction energy for fragment #1(D:136:TYR)

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.
-4.791	-1.257	1.506	-1.228	-3.811	0.005

Interaction energy analysis for fragmet #1(D:136:TYR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.064 / q_NPA : 0.010

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	D	138	THR	0	0.055	0.017	3.501	-3.671	-1.837	0.023	-0.569	-1.287	0.004
4	D	139	GLN	0	0.029	0.024	3.167	-0.561	0.079	0.063	-0.145	-0.558	0.000
5	D	140	LEU	0	-0.016	-0.014	2.468	-1.127	-0.067	1.420	-0.514	-1.966	0.001
6	D	141	TYR	0	0.050	0.018	5.646	0.181	0.181	0.000	0.000	0.000	0.000
7	D	142	TYR	0	0.035	0.062	8.098	-0.037	-0.037	0.000	0.000	0.000	0.000
8	D	143	LYS	1	0.909	0.949	7.780	0.275	0.275	0.000	0.000	0.000	0.000
9	D	144	ILE	0	-0.036	-0.020	8.027	0.029	0.029	0.000	0.000	0.000	0.000
10	D	145	SER	0	0.018	-0.008	11.386	-0.010	-0.010	0.000	0.000	0.000	0.000
11	D	146	ARG	1	0.847	0.922	12.861	0.053	0.053	0.000	0.000	0.000	0.000
12	D	147	ILE	0	0.015	0.012	13.880	-0.010	-0.010	0.000	0.000	0.000	0.000
13	D	148	ASP	-1	-0.919	-0.946	12.999	-0.066	-0.066	0.000	0.000	0.000	0.000
14	D	149	TRP	0	-0.055	-0.045	12.355	-0.006	-0.006	0.000	0.000	0.000	0.000
15	D	150	ASP	-1	-0.828	-0.905	15.597	0.022	0.022	0.000	0.000	0.000	0.000
16	D	151	TYR	0	-0.024	-0.033	11.418	0.037	0.037	0.000	0.000	0.000	0.000
17	D	152	GLU	-1	-0.935	-0.955	16.868	0.030	0.030	0.000	0.000	0.000	0.000
18	D	153	VAL	0	-0.104	-0.037	20.416	-0.002	-0.002	0.000	0.000	0.000	0.000
19	D	154	GLU	-1	-0.873	-0.943	20.736	0.069	0.069	0.000	0.000	0.000	0.000
20	D	155	PRO	0	-0.005	-0.022	20.080	0.003	0.003	0.000	0.000	0.000	0.000
21	D	156	ALA	0	-0.003	0.016	21.198	0.010	0.010	0.000	0.000	0.000	0.000
22	D	157	ARG	1	0.896	0.961	23.269	-0.056	-0.056	0.000	0.000	0.000	0.000
23	D	158	ILE	0	0.035	0.026	19.651	0.006	0.006	0.000	0.000	0.000	0.000
24	D	159	LYS	1	0.869	0.900	20.152	-0.050	-0.050	0.000	0.000	0.000	0.000
25	D	160	GLY	0	0.029	0.013	18.406	0.009	0.009	0.000	0.000	0.000	0.000
26	D	161	ILE	0	-0.067	-0.015	18.239	-0.004	-0.004	0.000	0.000	0.000	0.000
27	D	162	HIS	0	0.012	0.017	17.931	-0.002	-0.002	0.000	0.000	0.000	0.000
28	D	163	TYR	0	0.016	-0.013	16.707	-0.008	-0.008	0.000	0.000	0.000	0.000
29	D	164	GLY	0	-0.007	-0.004	17.824	0.009	0.009	0.000	0.000	0.000	0.000
30	D	165	PRO	0	-0.069	-0.032	18.847	-0.007	-0.007	0.000	0.000	0.000	0.000
31	D	166	ASP	-1	-0.905	-0.942	21.778	0.020	0.020	0.000	0.000	0.000	0.000
32	D	167	ILE	0	-0.029	-0.026	23.066	-0.004	-0.004	0.000	0.000	0.000	0.000
33	D	168	ALA	0	-0.002	0.007	21.662	0.005	0.005	0.000	0.000	0.000	0.000
34	D	169	GLN	0	-0.010	-0.005	22.683	0.001	0.001	0.000	0.000	0.000	0.000
35	D	170	PRO	0	-0.024	-0.004	22.688	0.003	0.003	0.000	0.000	0.000	0.000
36	D	171	ILE	0	0.021	0.017	19.291	0.004	0.004	0.000	0.000	0.000	0.000
37	D	172	ASN	0	0.013	-0.020	23.027	-0.002	-0.002	0.000	0.000	0.000	0.000
38	D	173	MET	0	-0.061	-0.006	24.530	-0.002	-0.002	0.000	0.000	0.000	0.000
39	D	174	ASP	-1	-0.769	-0.851	25.207	0.078	0.078	0.000	0.000	0.000	0.000
40	D	175	SER	0	-0.042	-0.051	24.149	0.002	0.002	0.000	0.000	0.000	0.000
41	D	176	SER	0	-0.056	-0.064	26.159	0.004	0.004	0.000	0.000	0.000	0.000
42	D	177	HIS	0	-0.060	-0.022	28.608	0.001	0.001	0.000	0.000	0.000	0.000
43	D	178	HIS	0	0.013	0.019	27.163	-0.001	-0.001	0.000	0.000	0.000	0.000
44	D	179	SER	0	-0.007	0.004	26.857	0.009	0.009	0.000	0.000	0.000	0.000
45	D	180	ARG	1	1.034	0.989	19.754	-0.159	-0.159	0.000	0.000	0.000	0.000
46	D	181	CYS	0	-0.018	-0.005	21.878	0.015	0.015	0.000	0.000	0.000	0.000
47	D	182	PHE	0	0.091	0.051	22.982	0.003	0.003	0.000	0.000	0.000	0.000
48	D	183	ILE	0	0.015	0.017	20.926	-0.002	-0.002	0.000	0.000	0.000	0.000
49	D	184	SER	0	-0.043	-0.035	18.463	0.014	0.014	0.000	0.000	0.000	0.000
50	D	185	ASP	-1	-0.906	-0.949	19.813	0.145	0.145	0.000	0.000	0.000	0.000
51	D	186	TYR	0	-0.007	-0.004	22.141	-0.006	-0.006	0.000	0.000	0.000	0.000
52	D	187	LEU	0	-0.002	0.012	18.283	-0.006	-0.006	0.000	0.000	0.000	0.000
53	D	188	TRP	0	-0.011	-0.021	12.271	0.003	0.003	0.000	0.000	0.000	0.000
54	D	189	SER	0	-0.093	-0.050	18.997	-0.014	-0.014	0.000	0.000	0.000	0.000
55	D	190	LEU	0	-0.007	-0.001	20.004	-0.011	-0.011	0.000	0.000	0.000	0.000
56	D	191	VAL	0	-0.069	-0.025	15.802	-0.011	-0.011	0.000	0.000	0.000	0.000
57	D	192	PRO	0	0.009	0.012	18.878	0.005	0.005	0.000	0.000	0.000	0.000
58	D	193	THR	0	0.015	-0.013	19.221	0.002	0.002	0.000	0.000	0.000	0.000
59	D	194	ALA	0	-0.051	-0.009	21.026	0.000	0.000	0.000	0.000	0.000	0.000
60	D	195	TRP	0	0.004	0.005	17.232	-0.003	-0.003	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(D:136:TYR)