FMO DATABASE

FMODB ID: 8NNVY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-449736.816837
FMO2-HF: Nuclear repulsion	419574.708587
FMO2-HF: Total energy	-30162.10825
FMO2-MP2: Total energy	-30249.734582

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.
-1.358	0.278	-0.009	-0.856	-0.772	0.004

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 : 0.067 / 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	A	8	TRP	0	0.026	0.005	3.824	-1.153	0.483	-0.009	-0.856	-0.772	0.004
4	A	9	VAL	0	-0.019	-0.021	5.611	0.344	0.344	0.000	0.000	0.000	0.000
5	A	10	PRO	0	-0.006	0.009	8.098	0.025	0.025	0.000	0.000	0.000	0.000
6	A	11	VAL	0	0.030	0.014	10.493	0.052	0.052	0.000	0.000	0.000	0.000
7	A	12	THR	0	-0.025	-0.010	13.184	-0.054	-0.054	0.000	0.000	0.000	0.000
8	A	13	VAL	0	0.017	0.009	16.744	0.025	0.025	0.000	0.000	0.000	0.000
9	A	14	LEU	0	-0.004	-0.012	18.948	-0.036	-0.036	0.000	0.000	0.000	0.000
10	A	15	PRO	0	0.012	0.014	22.571	0.016	0.016	0.000	0.000	0.000	0.000
11	A	16	GLY	0	0.035	0.006	25.186	-0.019	-0.019	0.000	0.000	0.000	0.000
12	A	17	CYS	0	-0.151	-0.053	25.465	-0.002	-0.002	0.000	0.000	0.000	0.000
13	A	18	VAL	0	0.077	0.026	27.439	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	19	GLY	0	0.014	0.009	31.203	-0.007	-0.007	0.000	0.000	0.000	0.000
15	A	21	ARG	1	0.952	0.981	29.973	-0.122	-0.122	0.000	0.000	0.000	0.000
16	A	22	THR	0	-0.002	-0.003	27.278	0.010	0.010	0.000	0.000	0.000	0.000
17	A	23	VAL	0	0.010	0.008	29.443	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	24	ALA	0	-0.009	-0.004	29.439	0.010	0.010	0.000	0.000	0.000	0.000
19	A	25	ALA	0	0.002	0.012	29.265	-0.011	-0.011	0.000	0.000	0.000	0.000
20	A	26	LEU	0	0.004	0.002	30.131	0.008	0.008	0.000	0.000	0.000	0.000
21	A	27	ALA	0	0.024	-0.002	27.965	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	28	SER	0	-0.007	-0.012	29.344	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	29	TRP	0	0.045	0.026	31.669	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	30	THR	0	-0.006	-0.006	31.701	0.001	0.001	0.000	0.000	0.000	0.000
25	A	31	VAL	0	0.008	-0.004	29.648	0.006	0.006	0.000	0.000	0.000	0.000
26	A	32	ARG	1	0.908	0.935	32.257	-0.051	-0.051	0.000	0.000	0.000	0.000
27	A	33	ASP	-1	-0.791	-0.883	34.737	0.076	0.076	0.000	0.000	0.000	0.000
28	A	34	VAL	0	-0.040	-0.018	30.299	0.004	0.004	0.000	0.000	0.000	0.000
29	A	35	LYS	1	0.868	0.938	33.669	-0.060	-0.060	0.000	0.000	0.000	0.000
30	A	36	GLU	-1	-0.840	-0.914	35.878	0.061	0.061	0.000	0.000	0.000	0.000
31	A	37	ARG	1	0.893	0.964	35.269	-0.106	-0.106	0.000	0.000	0.000	0.000
32	A	38	ILE	0	0.019	0.002	32.436	0.003	0.003	0.000	0.000	0.000	0.000
33	A	39	PHE	0	-0.022	0.018	36.684	0.000	0.000	0.000	0.000	0.000	0.000
34	A	40	ALA	0	-0.014	-0.006	40.273	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	41	GLU	-1	-0.930	-0.973	35.987	0.121	0.121	0.000	0.000	0.000	0.000
36	A	42	THR	0	-0.085	-0.058	37.095	0.000	0.000	0.000	0.000	0.000	0.000
37	A	43	GLY	0	0.017	0.021	40.467	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	44	PHE	0	-0.029	-0.030	38.413	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	45	PRO	0	0.067	0.034	40.276	0.002	0.002	0.000	0.000	0.000	0.000
40	A	46	VAL	0	0.034	0.009	38.837	0.000	0.000	0.000	0.000	0.000	0.000
41	A	47	SER	0	-0.054	-0.035	39.451	0.001	0.001	0.000	0.000	0.000	0.000
42	A	48	GLU	-1	-0.861	-0.903	40.266	0.043	0.043	0.000	0.000	0.000	0.000
43	A	49	GLN	0	-0.065	-0.032	35.537	0.007	0.007	0.000	0.000	0.000	0.000
44	A	50	ARG	1	0.849	0.921	33.681	-0.050	-0.050	0.000	0.000	0.000	0.000
45	A	51	LEU	0	0.021	0.016	29.662	0.007	0.007	0.000	0.000	0.000	0.000
46	A	52	TRP	0	-0.005	0.010	26.931	-0.009	-0.009	0.000	0.000	0.000	0.000
47	A	53	ARG	1	0.927	0.938	18.966	-0.158	-0.158	0.000	0.000	0.000	0.000
48	A	54	GLY	0	-0.008	0.001	20.756	-0.011	-0.011	0.000	0.000	0.000	0.000
49	A	55	GLY	0	0.010	0.003	21.405	-0.019	-0.019	0.000	0.000	0.000	0.000
50	A	56	ARG	1	0.983	0.983	24.246	-0.019	-0.019	0.000	0.000	0.000	0.000
51	A	57	GLU	-1	-0.915	-0.948	26.289	0.055	0.055	0.000	0.000	0.000	0.000
52	A	58	LEU	0	-0.075	-0.037	25.743	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	59	SER	0	0.029	0.006	29.586	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	60	ASP	-1	-0.778	-0.900	32.159	0.058	0.058	0.000	0.000	0.000	0.000
55	A	61	TRP	0	0.025	0.003	34.019	0.007	0.007	0.000	0.000	0.000	0.000
56	A	62	ILE	0	-0.048	-0.010	28.038	0.000	0.000	0.000	0.000	0.000	0.000
57	A	63	LYS	1	0.976	0.994	29.612	-0.058	-0.058	0.000	0.000	0.000	0.000
58	A	64	ILE	0	0.020	-0.007	26.861	0.004	0.004	0.000	0.000	0.000	0.000
59	A	65	GLY	0	-0.020	-0.021	25.859	0.014	0.014	0.000	0.000	0.000	0.000
60	A	66	ASP	-1	-0.904	-0.942	24.942	0.083	0.083	0.000	0.000	0.000	0.000
61	A	67	LEU	0	-0.079	-0.025	23.355	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	68	THR	0	-0.019	0.011	20.269	0.025	0.025	0.000	0.000	0.000	0.000
63	A	69	SER	0	0.023	-0.004	16.752	0.013	0.013	0.000	0.000	0.000	0.000
64	A	70	LYS	1	0.881	0.931	13.403	-0.400	-0.400	0.000	0.000	0.000	0.000
65	A	71	ASN	0	0.045	0.037	17.738	0.010	0.010	0.000	0.000	0.000	0.000
66	A	72	CYS	0	-0.058	-0.034	17.489	0.028	0.028	0.000	0.000	0.000	0.000
67	A	73	HIS	0	0.050	0.032	18.591	-0.031	-0.031	0.000	0.000	0.000	0.000
68	A	74	LEU	0	-0.012	-0.005	20.013	0.008	0.008	0.000	0.000	0.000	0.000
69	A	75	PHE	0	0.017	0.014	20.134	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	76	VAL	0	-0.029	-0.020	23.014	-0.010	-0.010	0.000	0.000	0.000	0.000
71	A	77	ASN	0	-0.009	-0.013	25.768	0.008	0.008	0.000	0.000	0.000	0.000
72	A	78	LEU	0	0.031	0.019	27.474	-0.011	-0.011	0.000	0.000	0.000	0.000
73	A	79	GLN	0	-0.025	-0.005	30.573	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	80	SER	0	0.060	0.012	32.578	-0.004	-0.004	0.000	0.000	0.000	0.000
75	A	81	LYS	1	0.950	0.985	34.113	-0.045	-0.045	0.000	0.000	0.000	0.000

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