FMO DATABASE

FMODB ID: N3R7Q

Calculation Name: 1NVP-B-Xray315

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	45
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-203978.30597
FMO2-HF: Nuclear repulsion	185802.423911
FMO2-HF: Total energy	-18175.882058
FMO2-MP2: Total energy	-18228.374515

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:8:ACE )

Summations of interaction energy for fragment #1(B:8:ACE )

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.
2.851	4.973	0.007	-1.004	-1.125	-0.002

Interaction energy analysis for fragmet #1(B:8:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.070 / q_NPA : 0.024

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	10	VAL	0	0.058	0.048	3.753	-0.341	1.342	-0.003	-0.837	-0.843	-0.002
4	B	11	PRO	0	0.031	0.011	3.601	-0.145	0.050	0.009	-0.054	-0.150	0.000
5	B	12	LYS	1	0.921	0.957	4.047	3.160	3.404	0.001	-0.113	-0.132	0.000
6	B	13	LEU	0	0.052	0.044	7.484	0.173	0.173	0.000	0.000	0.000	0.000
7	B	14	TYR	0	0.031	0.006	9.307	0.105	0.105	0.000	0.000	0.000	0.000
8	B	15	ARG	1	0.938	0.981	9.608	0.188	0.188	0.000	0.000	0.000	0.000
9	B	16	SER	0	0.034	0.007	11.517	0.031	0.031	0.000	0.000	0.000	0.000
10	B	17	VAL	0	0.013	0.010	13.433	0.039	0.039	0.000	0.000	0.000	0.000
11	B	18	ILE	0	-0.041	-0.017	14.344	0.034	0.034	0.000	0.000	0.000	0.000
12	B	19	GLU	-1	-0.852	-0.921	15.407	-0.139	-0.139	0.000	0.000	0.000	0.000
13	B	20	ASP	-1	-0.920	-0.952	17.602	-0.227	-0.227	0.000	0.000	0.000	0.000
14	B	21	VAL	0	-0.009	-0.002	19.237	0.020	0.020	0.000	0.000	0.000	0.000
15	B	22	ILE	0	-0.033	-0.026	20.219	0.017	0.017	0.000	0.000	0.000	0.000
16	B	23	ASN	0	-0.044	-0.045	21.030	0.024	0.024	0.000	0.000	0.000	0.000
17	B	24	ASP	-1	-0.926	-0.965	23.401	-0.121	-0.121	0.000	0.000	0.000	0.000
18	B	25	VAL	0	-0.068	-0.019	25.018	0.009	0.009	0.000	0.000	0.000	0.000
19	B	26	ARG	1	0.851	0.910	24.462	0.088	0.088	0.000	0.000	0.000	0.000
20	B	27	ASP	-1	-0.854	-0.939	28.602	-0.064	-0.064	0.000	0.000	0.000	0.000
21	B	28	ILE	0	0.003	0.019	29.398	0.004	0.004	0.000	0.000	0.000	0.000
22	B	29	PHE	0	-0.020	-0.021	27.996	0.005	0.005	0.000	0.000	0.000	0.000
23	B	30	LEU	0	-0.036	-0.015	32.213	0.005	0.005	0.000	0.000	0.000	0.000
24	B	31	ASP	-1	-0.958	-0.976	34.584	-0.046	-0.046	0.000	0.000	0.000	0.000
25	B	32	ASP	-1	-0.976	-0.987	35.018	-0.036	-0.036	0.000	0.000	0.000	0.000
26	B	33	GLY	0	-0.101	-0.035	36.933	0.003	0.003	0.000	0.000	0.000	0.000
27	B	34	VAL	0	-0.089	-0.048	32.376	0.003	0.003	0.000	0.000	0.000	0.000
28	B	35	ASP	-1	-0.838	-0.913	33.645	-0.032	-0.032	0.000	0.000	0.000	0.000
29	B	36	GLU	-1	-0.776	-0.883	28.770	-0.059	-0.059	0.000	0.000	0.000	0.000
30	B	37	GLN	0	-0.085	-0.070	29.129	-0.001	-0.001	0.000	0.000	0.000	0.000
31	B	38	VAL	0	0.020	0.012	28.745	0.000	0.000	0.000	0.000	0.000	0.000
32	B	39	LEU	0	-0.009	0.023	25.438	-0.001	-0.001	0.000	0.000	0.000	0.000
33	B	40	MET	0	-0.020	-0.021	23.275	-0.007	-0.007	0.000	0.000	0.000	0.000
34	B	41	GLU	-1	-0.934	-0.958	24.013	-0.014	-0.014	0.000	0.000	0.000	0.000
35	B	42	LEU	0	-0.011	0.008	23.190	0.004	0.004	0.000	0.000	0.000	0.000
36	B	43	LYS	1	0.866	0.920	17.784	0.119	0.119	0.000	0.000	0.000	0.000
37	B	44	THR	0	0.011	0.011	19.531	0.001	0.001	0.000	0.000	0.000	0.000
38	B	45	LEU	0	-0.062	-0.042	20.279	0.011	0.011	0.000	0.000	0.000	0.000
39	B	46	TRP	0	-0.039	-0.023	17.269	0.006	0.006	0.000	0.000	0.000	0.000
40	B	47	GLU	-1	-0.911	-0.975	15.697	-0.079	-0.079	0.000	0.000	0.000	0.000
41	B	48	ASN	0	-0.018	-0.019	15.570	0.022	0.022	0.000	0.000	0.000	0.000
42	B	49	LYS	1	0.932	0.971	17.652	0.016	0.016	0.000	0.000	0.000	0.000
43	B	50	LEU	0	-0.069	-0.017	12.172	0.009	0.009	0.000	0.000	0.000	0.000
44	B	51	MET	0	-0.090	-0.025	12.989	0.041	0.041	0.000	0.000	0.000	0.000
45	B	52	NME	0	-0.017	-0.009	14.615	0.026	0.026	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:8:ACE )