FMO DATABASE

FMODB ID: J2299

Calculation Name: 5VSX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5VSX

Chain ID: A

ChEMBL ID:

UniProt ID: Q9NZJ4

Base Structure: X-ray

Registration Date: 2023-09-27

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	75
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-452012.186777
FMO2-HF: Nuclear repulsion	421849.563893
FMO2-HF: Total energy	-30162.622884
FMO2-MP2: Total energy	-30250.248008

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:6:ASN)

Summations of interaction energy for fragment #1(A:6:ASN)

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.
-1.089	0.184	-0.002	-0.595	-0.676	0.002

Interaction energy analysis for fragmet #1(A:6:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.050 / q_NPA : 0.007

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	A	8	TRP	0	0.033	0.010	3.752	-1.078	0.195	-0.002	-0.595	-0.676	0.002
4	A	9	VAL	0	-0.016	-0.024	5.601	0.542	0.542	0.000	0.000	0.000	0.000
5	A	10	PRO	0	0.007	0.009	8.240	-0.022	-0.022	0.000	0.000	0.000	0.000
6	A	11	VAL	0	0.012	0.008	10.842	0.086	0.086	0.000	0.000	0.000	0.000
7	A	12	THR	0	-0.021	-0.008	13.577	-0.050	-0.050	0.000	0.000	0.000	0.000
8	A	13	VAL	0	0.028	0.016	16.947	0.026	0.026	0.000	0.000	0.000	0.000
9	A	14	LEU	0	0.013	0.002	19.060	-0.034	-0.034	0.000	0.000	0.000	0.000
10	A	15	PRO	0	0.000	0.007	22.653	0.016	0.016	0.000	0.000	0.000	0.000
11	A	16	GLY	0	0.025	0.002	25.354	-0.014	-0.014	0.000	0.000	0.000	0.000
12	A	17	CYS	0	-0.162	-0.078	25.774	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	18	VAL	0	0.057	0.024	27.684	0.000	0.000	0.000	0.000	0.000	0.000
14	A	19	GLY	0	0.038	0.023	31.516	-0.009	-0.009	0.000	0.000	0.000	0.000
15	A	21	ARG	1	0.938	0.980	29.956	-0.098	-0.098	0.000	0.000	0.000	0.000
16	A	22	THR	0	-0.036	-0.027	27.086	0.013	0.013	0.000	0.000	0.000	0.000
17	A	23	VAL	0	0.000	0.009	29.546	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	24	ALA	0	-0.004	0.002	29.919	0.008	0.008	0.000	0.000	0.000	0.000
19	A	25	ALA	0	0.006	0.007	29.357	-0.010	-0.010	0.000	0.000	0.000	0.000
20	A	26	LEU	0	0.007	0.003	30.258	0.011	0.011	0.000	0.000	0.000	0.000
21	A	27	ALA	0	0.022	0.003	27.620	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	28	SER	0	0.030	0.014	29.116	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	29	TRP	0	0.026	0.016	31.776	-0.009	-0.009	0.000	0.000	0.000	0.000
24	A	30	THR	0	-0.034	-0.049	31.905	0.000	0.000	0.000	0.000	0.000	0.000
25	A	31	VAL	0	0.004	-0.013	29.423	0.007	0.007	0.000	0.000	0.000	0.000
26	A	32	ARG	1	0.811	0.886	32.052	-0.044	-0.044	0.000	0.000	0.000	0.000
27	A	33	ASP	-1	-0.781	-0.858	34.826	0.073	0.073	0.000	0.000	0.000	0.000
28	A	34	VAL	0	-0.027	-0.015	30.263	0.004	0.004	0.000	0.000	0.000	0.000
29	A	35	LYS	1	0.857	0.932	33.598	-0.045	-0.045	0.000	0.000	0.000	0.000
30	A	36	GLU	-1	-0.766	-0.874	35.854	0.053	0.053	0.000	0.000	0.000	0.000
31	A	37	ARG	1	0.858	0.929	35.331	-0.106	-0.106	0.000	0.000	0.000	0.000
32	A	38	ILE	0	0.014	-0.002	32.171	0.002	0.002	0.000	0.000	0.000	0.000
33	A	39	PHE	0	-0.024	0.015	36.572	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	40	ALA	0	0.014	0.004	40.241	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	41	GLU	-1	-0.848	-0.911	35.835	0.114	0.114	0.000	0.000	0.000	0.000
36	A	42	THR	0	-0.108	-0.085	37.097	0.002	0.002	0.000	0.000	0.000	0.000
37	A	43	GLY	0	0.037	0.036	40.412	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	44	PHE	0	-0.016	-0.015	37.990	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	45	PRO	0	0.049	0.030	40.547	0.002	0.002	0.000	0.000	0.000	0.000
40	A	46	VAL	0	0.022	-0.004	38.854	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	47	SER	0	-0.044	-0.043	39.832	0.000	0.000	0.000	0.000	0.000	0.000
42	A	48	GLU	-1	-0.845	-0.889	40.420	0.025	0.025	0.000	0.000	0.000	0.000
43	A	49	GLN	0	-0.067	-0.029	35.775	0.004	0.004	0.000	0.000	0.000	0.000
44	A	50	ARG	1	0.786	0.887	33.713	-0.033	-0.033	0.000	0.000	0.000	0.000
45	A	51	LEU	0	0.019	0.011	29.659	0.005	0.005	0.000	0.000	0.000	0.000
46	A	52	TRP	0	-0.057	-0.035	27.109	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	53	ARG	1	0.896	0.927	20.009	-0.133	-0.133	0.000	0.000	0.000	0.000
48	A	54	GLY	0	-0.006	0.001	20.476	-0.012	-0.012	0.000	0.000	0.000	0.000
49	A	55	GLY	0	0.016	0.015	21.239	-0.022	-0.022	0.000	0.000	0.000	0.000
50	A	56	ARG	1	0.905	0.951	24.182	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	57	GLU	-1	-0.817	-0.897	26.563	0.037	0.037	0.000	0.000	0.000	0.000
52	A	58	LEU	0	-0.040	-0.022	25.495	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	59	SER	0	0.031	0.008	29.577	0.001	0.001	0.000	0.000	0.000	0.000
54	A	60	ASP	-1	-0.779	-0.881	32.457	0.047	0.047	0.000	0.000	0.000	0.000
55	A	61	TRP	0	0.056	0.014	34.210	0.008	0.008	0.000	0.000	0.000	0.000
56	A	62	ILE	0	-0.044	-0.005	27.948	0.001	0.001	0.000	0.000	0.000	0.000
57	A	63	LYS	1	0.911	0.962	29.622	-0.069	-0.069	0.000	0.000	0.000	0.000
58	A	64	ILE	0	-0.020	-0.021	27.118	0.004	0.004	0.000	0.000	0.000	0.000
59	A	65	GLY	0	0.007	-0.002	25.863	0.014	0.014	0.000	0.000	0.000	0.000
60	A	66	ASP	-1	-0.829	-0.917	24.377	0.096	0.096	0.000	0.000	0.000	0.000
61	A	67	LEU	0	-0.061	-0.005	23.163	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	68	THR	0	-0.062	-0.033	20.155	0.024	0.024	0.000	0.000	0.000	0.000
63	A	69	SER	0	0.057	0.019	17.102	0.013	0.013	0.000	0.000	0.000	0.000
64	A	70	LYS	1	0.911	0.962	13.396	-0.447	-0.447	0.000	0.000	0.000	0.000
65	A	71	ASN	0	0.014	0.006	17.485	0.032	0.032	0.000	0.000	0.000	0.000
66	A	72	CYS	0	-0.055	-0.042	17.122	0.015	0.015	0.000	0.000	0.000	0.000
67	A	73	HIS	0	0.067	0.043	18.480	-0.031	-0.031	0.000	0.000	0.000	0.000
68	A	74	LEU	0	-0.003	0.007	20.263	0.001	0.001	0.000	0.000	0.000	0.000
69	A	75	PHE	0	0.015	0.008	19.396	-0.013	-0.013	0.000	0.000	0.000	0.000
70	A	76	VAL	0	-0.020	-0.022	22.975	-0.012	-0.012	0.000	0.000	0.000	0.000
71	A	77	ASN	0	-0.018	-0.008	25.626	0.004	0.004	0.000	0.000	0.000	0.000
72	A	78	LEU	0	0.035	0.022	27.751	-0.009	-0.009	0.000	0.000	0.000	0.000
73	A	79	GLN	0	-0.029	-0.001	30.631	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	80	SER	0	0.068	0.024	32.885	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	81	LYS	1	0.959	0.994	33.963	-0.018	-0.018	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:ASN)