FMO DATABASE

FMODB ID: G5GJ1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-333325.050678
FMO2-HF: Nuclear repulsion	308347.032195
FMO2-HF: Total energy	-24978.018483
FMO2-MP2: Total energy	-25051.075541

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.
-4.349	-1.009	1.604	-1.24	-3.702	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 : 0.068 / 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	D	138	THR	0	0.051	0.019	3.611	-3.357	-1.651	0.024	-0.580	-1.150	0.004
4	D	139	GLN	0	0.020	0.026	3.315	-0.341	0.325	0.034	-0.168	-0.531	0.000
5	D	140	LEU	0	-0.027	-0.020	2.360	-1.002	-0.034	1.546	-0.492	-2.021	0.001
6	D	141	TYR	0	0.055	0.014	5.679	0.172	0.172	0.000	0.000	0.000	0.000
7	D	142	TYR	0	-0.024	0.022	8.168	-0.027	-0.027	0.000	0.000	0.000	0.000
8	D	143	LYS	1	0.927	0.958	7.518	0.234	0.234	0.000	0.000	0.000	0.000
9	D	144	ILE	0	-0.038	-0.016	8.561	0.034	0.034	0.000	0.000	0.000	0.000
10	D	145	SER	0	-0.003	-0.023	11.565	-0.022	-0.022	0.000	0.000	0.000	0.000
11	D	146	ARG	1	0.851	0.933	12.989	0.043	0.043	0.000	0.000	0.000	0.000
12	D	147	ILE	0	0.041	0.016	13.840	-0.004	-0.004	0.000	0.000	0.000	0.000
13	D	148	ASP	-1	-0.894	-0.929	13.219	-0.154	-0.154	0.000	0.000	0.000	0.000
14	D	149	TRP	0	-0.030	-0.029	12.162	0.017	0.017	0.000	0.000	0.000	0.000
15	D	150	ASP	-1	-0.829	-0.906	15.607	-0.035	-0.035	0.000	0.000	0.000	0.000
16	D	151	TYR	0	-0.026	-0.032	11.681	0.024	0.024	0.000	0.000	0.000	0.000
17	D	152	GLU	-1	-0.934	-0.954	16.794	-0.040	-0.040	0.000	0.000	0.000	0.000
18	D	153	VAL	0	-0.098	-0.037	20.032	0.003	0.003	0.000	0.000	0.000	0.000
19	D	154	GLU	-1	-0.853	-0.936	20.670	0.032	0.032	0.000	0.000	0.000	0.000
20	D	155	PRO	0	-0.018	-0.026	19.644	0.005	0.005	0.000	0.000	0.000	0.000
21	D	156	ALA	0	0.012	0.027	20.779	0.012	0.012	0.000	0.000	0.000	0.000
22	D	157	ARG	1	0.880	0.959	23.136	-0.020	-0.020	0.000	0.000	0.000	0.000
23	D	158	ILE	0	0.042	0.025	19.442	-0.002	-0.002	0.000	0.000	0.000	0.000
24	D	159	LYS	1	0.865	0.910	20.048	-0.005	-0.005	0.000	0.000	0.000	0.000
25	D	160	GLY	0	0.028	0.009	18.450	0.005	0.005	0.000	0.000	0.000	0.000
26	D	161	ILE	0	-0.073	-0.022	18.361	0.002	0.002	0.000	0.000	0.000	0.000
27	D	162	HIS	0	0.013	0.023	17.822	-0.012	-0.012	0.000	0.000	0.000	0.000
28	D	163	TYR	0	0.009	-0.011	16.880	-0.006	-0.006	0.000	0.000	0.000	0.000
29	D	164	GLY	0	0.027	-0.006	18.580	0.013	0.013	0.000	0.000	0.000	0.000
30	D	165	PRO	0	-0.083	-0.025	19.524	-0.011	-0.011	0.000	0.000	0.000	0.000
31	D	166	ASP	-1	-0.900	-0.945	22.285	0.021	0.021	0.000	0.000	0.000	0.000
32	D	167	ILE	0	-0.038	-0.027	23.338	-0.007	-0.007	0.000	0.000	0.000	0.000
33	D	168	ALA	0	0.009	0.012	21.632	0.006	0.006	0.000	0.000	0.000	0.000
34	D	169	GLN	0	-0.031	-0.016	22.575	0.004	0.004	0.000	0.000	0.000	0.000
35	D	170	PRO	0	-0.018	-0.001	22.580	0.000	0.000	0.000	0.000	0.000	0.000
36	D	171	ILE	0	0.020	0.015	19.542	0.007	0.007	0.000	0.000	0.000	0.000
37	D	172	ASN	0	0.013	-0.019	23.043	-0.009	-0.009	0.000	0.000	0.000	0.000
38	D	173	MET	0	-0.070	-0.005	24.413	0.000	0.000	0.000	0.000	0.000	0.000
39	D	174	ASP	-1	-0.769	-0.863	25.156	0.060	0.060	0.000	0.000	0.000	0.000
40	D	175	SER	0	-0.042	-0.060	23.862	0.004	0.004	0.000	0.000	0.000	0.000
41	D	176	SER	0	-0.061	-0.072	25.878	0.006	0.006	0.000	0.000	0.000	0.000
42	D	177	HIS	0	-0.054	-0.013	28.220	0.001	0.001	0.000	0.000	0.000	0.000
43	D	178	HIS	0	0.004	0.017	27.150	0.002	0.002	0.000	0.000	0.000	0.000
44	D	179	SER	0	-0.001	0.006	27.229	0.009	0.009	0.000	0.000	0.000	0.000
45	D	180	ARG	1	1.021	0.984	20.362	-0.166	-0.166	0.000	0.000	0.000	0.000
46	D	181	CYS	0	-0.039	0.002	21.924	0.018	0.018	0.000	0.000	0.000	0.000
47	D	182	PHE	0	0.103	0.047	22.910	0.005	0.005	0.000	0.000	0.000	0.000
48	D	183	ILE	0	0.007	0.015	21.107	-0.003	-0.003	0.000	0.000	0.000	0.000
49	D	184	SER	0	-0.033	-0.028	18.766	0.014	0.014	0.000	0.000	0.000	0.000
50	D	185	ASP	-1	-0.903	-0.959	19.979	0.156	0.156	0.000	0.000	0.000	0.000
51	D	186	TYR	0	-0.014	-0.002	22.434	-0.006	-0.006	0.000	0.000	0.000	0.000
52	D	187	LEU	0	0.011	0.015	17.912	-0.007	-0.007	0.000	0.000	0.000	0.000
53	D	188	TRP	0	-0.017	-0.022	12.598	0.006	0.006	0.000	0.000	0.000	0.000
54	D	189	SER	0	-0.089	-0.051	19.264	-0.013	-0.013	0.000	0.000	0.000	0.000
55	D	190	LEU	0	0.001	0.010	19.898	-0.012	-0.012	0.000	0.000	0.000	0.000
56	D	191	VAL	0	-0.051	-0.024	15.737	-0.011	-0.011	0.000	0.000	0.000	0.000
57	D	192	PRO	0	-0.003	0.009	18.827	0.008	0.008	0.000	0.000	0.000	0.000
58	D	193	THR	0	0.009	-0.013	19.424	0.002	0.002	0.000	0.000	0.000	0.000
59	D	194	ALA	0	-0.033	-0.004	21.262	0.001	0.001	0.000	0.000	0.000	0.000
60	D	195	TRP	0	-0.016	-0.003	17.685	-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)