FMO DATABASE

FMODB ID: VRLV1

Calculation Name: 2NN4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NN4

Chain ID: A

ChEMBL ID:

UniProt ID: P54494

Base Structure: X-ray

Registration Date: 2023-06-20

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	62
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-396093.297941
FMO2-HF: Nuclear repulsion	369511.971603
FMO2-HF: Total energy	-26581.326338
FMO2-MP2: Total energy	-26658.27571

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:1:LEU)

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

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.
-10.715	-2.383	7.751	-7.84	-8.241	-0.037

Interaction energy analysis for fragmet #1(A:1:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.006

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	3	THR	0	-0.034	-0.028	3.124	-1.220	1.847	-0.011	-1.596	-1.461	-0.002
4	A	4	PHE	0	0.122	0.049	3.803	0.081	0.420	0.002	-0.128	-0.213	-0.001
5	A	5	TYR	0	0.043	0.028	6.400	0.083	0.083	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.753	-0.882	1.779	-7.348	-6.095	7.334	-4.829	-3.757	-0.036
7	A	7	VAL	0	0.014	0.008	3.449	-0.416	0.329	0.064	-0.209	-0.600	0.001
8	A	8	GLN	0	0.022	0.012	4.875	-0.293	-0.285	-0.001	-0.006	-0.001	0.000
9	A	9	GLN	0	-0.025	0.000	6.426	0.101	0.101	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.010	0.004	4.552	-0.009	0.095	-0.001	-0.005	-0.097	0.000
11	A	11	LEU	0	0.049	0.016	6.692	0.041	0.041	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.913	0.964	9.720	0.272	0.272	0.000	0.000	0.000	0.000
13	A	13	THR	0	-0.127	-0.064	9.533	-0.027	-0.027	0.000	0.000	0.000	0.000
14	A	14	PHE	0	-0.019	-0.015	9.750	0.005	0.005	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.005	0.008	13.984	0.020	0.020	0.000	0.000	0.000	0.000
16	A	16	HIS	0	-0.043	-0.031	12.821	-0.018	-0.018	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.066	-0.039	13.185	-0.010	-0.010	0.000	0.000	0.000	0.000
18	A	18	VAL	0	-0.020	0.004	14.759	-0.014	-0.014	0.000	0.000	0.000	0.000
19	A	19	TYR	0	-0.042	-0.030	15.202	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	20	PHE	0	-0.059	-0.037	17.535	-0.011	-0.011	0.000	0.000	0.000	0.000
21	A	21	GLY	0	-0.025	0.002	19.260	-0.011	-0.011	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.865	-0.931	19.313	0.159	0.159	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.890	0.945	11.377	-0.198	-0.198	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.888	-0.936	15.143	0.287	0.287	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.045	0.017	16.763	0.041	0.041	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.849	-0.940	14.029	0.173	0.173	0.000	0.000	0.000	0.000
27	A	27	ILE	0	-0.033	-0.021	11.296	0.070	0.070	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.932	-0.964	13.317	0.350	0.350	0.000	0.000	0.000	0.000
29	A	29	PHE	0	0.001	0.000	14.907	0.024	0.024	0.000	0.000	0.000	0.000
30	A	30	MET	0	-0.043	-0.023	8.653	-0.015	-0.015	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.011	-0.009	10.946	0.129	0.129	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.843	-0.907	12.646	0.302	0.302	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.819	-0.910	13.379	0.201	0.201	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.041	-0.020	7.442	0.033	0.033	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.747	0.872	11.553	-0.322	-0.322	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.806	-0.918	14.665	0.181	0.181	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.005	-0.001	11.494	-0.039	-0.039	0.000	0.000	0.000	0.000
38	A	38	TYR	0	-0.037	-0.020	12.733	-0.042	-0.042	0.000	0.000	0.000	0.000
39	A	39	MET	0	-0.057	-0.021	14.450	-0.043	-0.043	0.000	0.000	0.000	0.000
40	A	40	ASN	0	-0.091	-0.047	17.487	-0.051	-0.051	0.000	0.000	0.000	0.000
41	A	41	HIS	0	-0.048	-0.029	16.654	-0.023	-0.023	0.000	0.000	0.000	0.000
42	A	42	MET	0	-0.034	-0.003	14.541	-0.033	-0.033	0.000	0.000	0.000	0.000
43	A	43	ILE	0	-0.036	-0.004	9.171	-0.014	-0.014	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.860	-0.912	9.893	0.033	0.033	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.876	0.913	10.680	-0.130	-0.130	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.825	-0.902	8.573	0.380	0.380	0.000	0.000	0.000	0.000
47	A	47	GLN	0	-0.047	-0.045	6.118	0.238	0.238	0.000	0.000	0.000	0.000
48	A	48	TRP	0	0.021	0.018	6.415	0.723	0.723	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.014	0.008	8.700	0.270	0.270	0.000	0.000	0.000	0.000
50	A	50	ARG	1	0.832	0.909	2.953	-1.842	0.073	0.323	-0.761	-1.477	0.000
51	A	51	ALA	0	0.031	0.009	4.452	0.925	1.057	-0.001	-0.035	-0.096	0.000
52	A	52	ALA	0	0.055	0.024	5.389	-0.410	-0.394	-0.001	-0.001	-0.013	0.000
53	A	53	ALA	0	-0.019	-0.009	7.555	-0.228	-0.228	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.065	-0.024	3.473	-1.568	-0.815	0.043	-0.270	-0.526	0.001
55	A	55	LEU	0	0.017	0.007	6.583	-0.571	-0.571	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.856	0.909	8.854	-0.740	-0.740	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.872	0.938	7.758	-0.353	-0.353	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.878	-0.948	8.879	0.109	0.109	0.000	0.000	0.000	0.000
59	A	59	LEU	0	0.040	0.036	10.880	-0.093	-0.093	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.840	-0.891	14.134	0.285	0.285	0.000	0.000	0.000	0.000
61	A	61	GLN	0	-0.099	-0.035	10.281	-0.063	-0.063	0.000	0.000	0.000	0.000
62	A	62	THR	0	-0.098	-0.062	14.256	-0.070	-0.070	0.000	0.000	0.000	0.000

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