FMO DATABASE

FMODB ID: VQL91

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

Total energy (hartree)

FMO2-HF: Electronic energy	-334119.802054
FMO2-HF: Nuclear repulsion	309141.966409
FMO2-HF: Total energy	-24977.835645
FMO2-MP2: Total energy	-25050.895915

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.
-5.266	-1.949	1.704	-0.977	-4.044	0.006

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 : 0.060 / q_NPA : 0.013

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

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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	0.050	0.016	3.606	-3.861	-2.153	0.048	-0.330	-1.426	0.005
4	D	139	GLN	0	0.038	0.026	3.279	-0.668	-0.065	0.043	-0.128	-0.518	0.000
5	D	140	LEU	0	-0.016	-0.015	2.406	-1.259	-0.253	1.613	-0.519	-2.100	0.001
6	D	141	TYR	0	0.043	0.017	5.520	0.126	0.126	0.000	0.000	0.000	0.000
7	D	142	TYR	0	0.047	0.061	8.108	-0.071	-0.071	0.000	0.000	0.000	0.000
8	D	143	LYS	1	0.903	0.944	7.830	0.265	0.265	0.000	0.000	0.000	0.000
9	D	144	ILE	0	-0.033	-0.021	7.710	0.018	0.018	0.000	0.000	0.000	0.000
10	D	145	SER	0	0.016	-0.002	11.272	-0.020	-0.020	0.000	0.000	0.000	0.000
11	D	146	ARG	1	0.862	0.933	12.647	0.036	0.036	0.000	0.000	0.000	0.000
12	D	147	ILE	0	0.014	0.011	13.901	-0.016	-0.016	0.000	0.000	0.000	0.000
13	D	148	ASP	-1	-0.929	-0.945	13.092	-0.006	-0.006	0.000	0.000	0.000	0.000
14	D	149	TRP	0	-0.057	-0.048	12.530	-0.020	-0.020	0.000	0.000	0.000	0.000
15	D	150	ASP	-1	-0.830	-0.910	15.651	0.044	0.044	0.000	0.000	0.000	0.000
16	D	151	TYR	0	-0.030	-0.036	11.298	0.042	0.042	0.000	0.000	0.000	0.000
17	D	152	GLU	-1	-0.930	-0.958	16.919	0.049	0.049	0.000	0.000	0.000	0.000
18	D	153	VAL	0	-0.111	-0.043	20.465	-0.004	-0.004	0.000	0.000	0.000	0.000
19	D	154	GLU	-1	-0.868	-0.940	20.805	0.078	0.078	0.000	0.000	0.000	0.000
20	D	155	PRO	0	-0.005	-0.022	20.220	0.004	0.004	0.000	0.000	0.000	0.000
21	D	156	ALA	0	-0.003	0.015	21.285	0.010	0.010	0.000	0.000	0.000	0.000
22	D	157	ARG	1	0.901	0.961	23.329	-0.067	-0.067	0.000	0.000	0.000	0.000
23	D	158	ILE	0	0.031	0.022	19.750	0.008	0.008	0.000	0.000	0.000	0.000
24	D	159	LYS	1	0.867	0.910	20.232	-0.068	-0.068	0.000	0.000	0.000	0.000
25	D	160	GLY	0	0.024	0.010	18.460	0.013	0.013	0.000	0.000	0.000	0.000
26	D	161	ILE	0	-0.070	-0.015	18.280	-0.007	-0.007	0.000	0.000	0.000	0.000
27	D	162	HIS	0	0.014	0.018	17.861	0.002	0.002	0.000	0.000	0.000	0.000
28	D	163	TYR	0	0.013	-0.014	16.576	-0.012	-0.012	0.000	0.000	0.000	0.000
29	D	164	GLY	0	-0.009	-0.007	17.850	0.008	0.008	0.000	0.000	0.000	0.000
30	D	165	PRO	0	-0.063	-0.028	18.845	-0.008	-0.008	0.000	0.000	0.000	0.000
31	D	166	ASP	-1	-0.903	-0.943	21.772	0.025	0.025	0.000	0.000	0.000	0.000
32	D	167	ILE	0	-0.026	-0.023	23.068	-0.004	-0.004	0.000	0.000	0.000	0.000
33	D	168	ALA	0	0.003	0.008	21.688	0.005	0.005	0.000	0.000	0.000	0.000
34	D	169	GLN	0	-0.020	-0.009	22.695	-0.004	-0.004	0.000	0.000	0.000	0.000
35	D	170	PRO	0	-0.023	-0.003	22.704	0.005	0.005	0.000	0.000	0.000	0.000
36	D	171	ILE	0	0.017	0.016	19.371	0.003	0.003	0.000	0.000	0.000	0.000
37	D	172	ASN	0	0.017	-0.019	23.085	0.002	0.002	0.000	0.000	0.000	0.000
38	D	173	MET	0	-0.059	-0.005	24.570	-0.004	-0.004	0.000	0.000	0.000	0.000
39	D	174	ASP	-1	-0.785	-0.852	25.288	0.082	0.082	0.000	0.000	0.000	0.000
40	D	175	SER	0	-0.045	-0.048	24.239	0.001	0.001	0.000	0.000	0.000	0.000
41	D	176	SER	0	-0.038	-0.058	26.253	0.003	0.003	0.000	0.000	0.000	0.000
42	D	177	HIS	0	-0.058	-0.022	28.705	0.001	0.001	0.000	0.000	0.000	0.000
43	D	178	HIS	0	0.011	0.019	26.857	-0.002	-0.002	0.000	0.000	0.000	0.000
44	D	179	SER	0	-0.012	0.001	26.373	0.009	0.009	0.000	0.000	0.000	0.000
45	D	180	ARG	1	1.030	0.987	19.338	-0.143	-0.143	0.000	0.000	0.000	0.000
46	D	181	CYS	0	-0.012	-0.011	21.512	0.016	0.016	0.000	0.000	0.000	0.000
47	D	182	PHE	0	0.084	0.049	22.728	0.004	0.004	0.000	0.000	0.000	0.000
48	D	183	ILE	0	0.018	0.020	20.709	-0.001	-0.001	0.000	0.000	0.000	0.000
49	D	184	SER	0	-0.036	-0.026	18.236	0.017	0.017	0.000	0.000	0.000	0.000
50	D	185	ASP	-1	-0.894	-0.942	19.517	0.147	0.147	0.000	0.000	0.000	0.000
51	D	186	TYR	0	-0.007	-0.007	21.853	-0.005	-0.005	0.000	0.000	0.000	0.000
52	D	187	LEU	0	-0.001	0.011	18.034	-0.005	-0.005	0.000	0.000	0.000	0.000
53	D	188	TRP	0	-0.015	-0.022	12.031	0.004	0.004	0.000	0.000	0.000	0.000
54	D	189	SER	0	-0.096	-0.049	18.671	-0.014	-0.014	0.000	0.000	0.000	0.000
55	D	190	LEU	0	-0.008	-0.003	19.876	-0.012	-0.012	0.000	0.000	0.000	0.000
56	D	191	VAL	0	-0.067	-0.022	15.553	-0.011	-0.011	0.000	0.000	0.000	0.000
57	D	192	PRO	0	0.009	0.009	18.798	0.003	0.003	0.000	0.000	0.000	0.000
58	D	193	THR	0	0.011	-0.010	19.014	0.002	0.002	0.000	0.000	0.000	0.000
59	D	194	ALA	0	-0.047	-0.008	20.706	-0.002	-0.002	0.000	0.000	0.000	0.000
60	D	195	TRP	0	0.000	0.004	16.946	-0.004	-0.004	0.000	0.000	0.000	0.000

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