FMO DATABASE

FMODB ID: 43VZN

Calculation Name: 1NVP-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NVP

Chain ID: B

ChEMBL ID:

UniProt ID: P52657

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	43
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-200884.068476
FMO2-HF: Nuclear repulsion	182878.787691
FMO2-HF: Total energy	-18005.280784
FMO2-MP2: Total energy	-18057.152879

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(B:9:THR)

Summations of interaction energy for fragment #1(B:9:THR)

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.
-10.038	-4.985	0.825	-2.085	-3.792	0.014

Interaction energy analysis for fragmet #1(B:9:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.033 / 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	B	11	PRO	0	0.037	0.008	3.236	-2.005	0.186	0.141	-0.866	-1.466	0.002
4	B	12	LYS	1	0.945	0.979	2.743	-8.848	-6.213	0.685	-1.190	-2.130	0.012
5	B	13	LEU	0	0.032	0.030	4.341	0.228	0.455	-0.001	-0.029	-0.196	0.000
6	B	14	TYR	0	0.000	-0.011	5.953	0.511	0.511	0.000	0.000	0.000	0.000
7	B	15	ARG	1	0.846	0.890	8.260	-0.214	-0.214	0.000	0.000	0.000	0.000
8	B	16	SER	0	-0.052	-0.021	8.225	0.080	0.080	0.000	0.000	0.000	0.000
9	B	17	VAL	0	0.024	0.007	9.895	0.079	0.079	0.000	0.000	0.000	0.000
10	B	18	ILE	0	-0.024	-0.007	11.937	0.088	0.088	0.000	0.000	0.000	0.000
11	B	19	GLU	-1	-0.826	-0.912	13.359	0.117	0.117	0.000	0.000	0.000	0.000
12	B	20	ASP	-1	-0.883	-0.926	12.218	-0.329	-0.329	0.000	0.000	0.000	0.000
13	B	21	VAL	0	0.003	-0.001	15.479	0.026	0.026	0.000	0.000	0.000	0.000
14	B	22	ILE	0	-0.025	-0.021	17.556	0.027	0.027	0.000	0.000	0.000	0.000
15	B	23	ASN	0	-0.051	-0.034	17.485	0.039	0.039	0.000	0.000	0.000	0.000
16	B	24	ASP	-1	-0.892	-0.936	19.312	-0.164	-0.164	0.000	0.000	0.000	0.000
17	B	25	VAL	0	-0.083	-0.043	21.558	0.006	0.006	0.000	0.000	0.000	0.000
18	B	26	ARG	1	0.821	0.884	22.121	0.012	0.012	0.000	0.000	0.000	0.000
19	B	27	ASP	-1	-0.891	-0.956	25.478	-0.033	-0.033	0.000	0.000	0.000	0.000
20	B	28	ILE	0	-0.011	0.004	25.627	0.001	0.001	0.000	0.000	0.000	0.000
21	B	29	PHE	0	0.008	-0.009	25.691	0.005	0.005	0.000	0.000	0.000	0.000
22	B	30	LEU	0	-0.044	-0.014	29.350	0.007	0.007	0.000	0.000	0.000	0.000
23	B	31	ASP	-1	-0.940	-0.960	31.686	-0.039	-0.039	0.000	0.000	0.000	0.000
24	B	32	ASP	-1	-1.006	-1.002	31.439	-0.053	-0.053	0.000	0.000	0.000	0.000
25	B	33	GLY	0	-0.069	-0.028	34.032	0.003	0.003	0.000	0.000	0.000	0.000
26	B	34	VAL	0	-0.090	-0.046	30.576	0.006	0.006	0.000	0.000	0.000	0.000
27	B	35	ASP	-1	-0.838	-0.917	31.651	0.021	0.021	0.000	0.000	0.000	0.000
28	B	36	GLU	-1	-0.770	-0.875	25.697	0.014	0.014	0.000	0.000	0.000	0.000
29	B	37	GLN	0	-0.087	-0.060	27.214	0.008	0.008	0.000	0.000	0.000	0.000
30	B	38	VAL	0	0.033	0.015	27.435	0.005	0.005	0.000	0.000	0.000	0.000
31	B	39	LEU	0	-0.001	0.029	22.926	-0.004	-0.004	0.000	0.000	0.000	0.000
32	B	40	MET	0	0.008	-0.005	21.226	-0.004	-0.004	0.000	0.000	0.000	0.000
33	B	41	GLU	-1	-0.954	-0.958	22.865	0.031	0.031	0.000	0.000	0.000	0.000
34	B	42	LEU	0	0.002	0.000	22.038	0.006	0.006	0.000	0.000	0.000	0.000
35	B	43	LYS	1	0.826	0.890	15.934	-0.097	-0.097	0.000	0.000	0.000	0.000
36	B	44	THR	0	-0.011	-0.015	18.678	0.019	0.019	0.000	0.000	0.000	0.000
37	B	45	LEU	0	-0.037	-0.021	19.903	0.019	0.019	0.000	0.000	0.000	0.000
38	B	46	TRP	0	-0.022	-0.004	15.651	0.010	0.010	0.000	0.000	0.000	0.000
39	B	47	GLU	-1	-0.769	-0.876	13.920	0.167	0.167	0.000	0.000	0.000	0.000
40	B	48	ASN	0	-0.060	-0.040	15.396	0.077	0.077	0.000	0.000	0.000	0.000
41	B	49	LYS	1	0.928	0.982	18.017	0.024	0.024	0.000	0.000	0.000	0.000
42	B	50	LEU	0	-0.053	-0.004	11.760	-0.016	-0.016	0.000	0.000	0.000	0.000
43	B	51	MET	0	-0.094	-0.033	13.432	0.132	0.132	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:9:THR)