FMO DATABASE

FMODB ID: Q1G6Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-201035.094949
FMO2-HF: Nuclear repulsion	183030.207497
FMO2-HF: Total energy	-18004.887452
FMO2-MP2: Total energy	-18056.830979

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.
-7.08	-2.8	1.192	-2.088	-3.384	0.005

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 : 0.007 / q_NPA : -0.020

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	0.028	0.009	3.274	-2.010	0.930	0.177	-1.378	-1.738	0.004
4	B	12	LYS	1	0.965	0.981	2.356	-5.443	-4.335	1.016	-0.674	-1.451	0.001
5	B	13	LEU	0	0.051	0.044	4.292	-0.004	0.228	-0.001	-0.036	-0.195	0.000
6	B	14	TYR	0	0.031	0.006	5.855	0.401	0.401	0.000	0.000	0.000	0.000
7	B	15	ARG	1	0.940	0.982	8.059	-0.426	-0.426	0.000	0.000	0.000	0.000
8	B	16	SER	0	0.029	0.005	8.204	0.015	0.015	0.000	0.000	0.000	0.000
9	B	17	VAL	0	0.013	0.010	9.555	0.027	0.027	0.000	0.000	0.000	0.000
10	B	18	ILE	0	-0.041	-0.016	11.787	0.069	0.069	0.000	0.000	0.000	0.000
11	B	19	GLU	-1	-0.853	-0.922	12.838	0.225	0.225	0.000	0.000	0.000	0.000
12	B	20	ASP	-1	-0.921	-0.953	13.154	-0.104	-0.104	0.000	0.000	0.000	0.000
13	B	21	VAL	0	-0.008	-0.001	15.685	0.006	0.006	0.000	0.000	0.000	0.000
14	B	22	ILE	0	-0.031	-0.026	17.680	0.019	0.019	0.000	0.000	0.000	0.000
15	B	23	ASN	0	-0.046	-0.046	17.729	0.020	0.020	0.000	0.000	0.000	0.000
16	B	24	ASP	-1	-0.924	-0.965	18.921	-0.066	-0.066	0.000	0.000	0.000	0.000
17	B	25	VAL	0	-0.069	-0.019	21.526	-0.005	-0.005	0.000	0.000	0.000	0.000
18	B	26	ARG	1	0.852	0.911	21.820	-0.050	-0.050	0.000	0.000	0.000	0.000
19	B	27	ASP	-1	-0.855	-0.940	25.717	0.006	0.006	0.000	0.000	0.000	0.000
20	B	28	ILE	0	0.003	0.019	25.675	-0.002	-0.002	0.000	0.000	0.000	0.000
21	B	29	PHE	0	-0.018	-0.020	25.676	0.001	0.001	0.000	0.000	0.000	0.000
22	B	30	LEU	0	-0.037	-0.016	29.532	0.003	0.003	0.000	0.000	0.000	0.000
23	B	31	ASP	-1	-0.958	-0.976	31.663	-0.012	-0.012	0.000	0.000	0.000	0.000
24	B	32	ASP	-1	-0.977	-0.987	32.095	-0.034	-0.034	0.000	0.000	0.000	0.000
25	B	33	GLY	0	-0.101	-0.035	34.226	0.001	0.001	0.000	0.000	0.000	0.000
26	B	34	VAL	0	-0.087	-0.047	30.490	0.003	0.003	0.000	0.000	0.000	0.000
27	B	35	ASP	-1	-0.838	-0.912	31.858	0.038	0.038	0.000	0.000	0.000	0.000
28	B	36	GLU	-1	-0.777	-0.884	26.477	0.050	0.050	0.000	0.000	0.000	0.000
29	B	37	GLN	0	-0.085	-0.070	27.373	0.002	0.002	0.000	0.000	0.000	0.000
30	B	38	VAL	0	0.021	0.012	27.462	0.004	0.004	0.000	0.000	0.000	0.000
31	B	39	LEU	0	-0.011	0.022	23.124	-0.002	-0.002	0.000	0.000	0.000	0.000
32	B	40	MET	0	-0.020	-0.021	21.600	-0.001	-0.001	0.000	0.000	0.000	0.000
33	B	41	GLU	-1	-0.936	-0.958	22.948	0.036	0.036	0.000	0.000	0.000	0.000
34	B	42	LEU	0	-0.010	0.007	21.568	0.000	0.000	0.000	0.000	0.000	0.000
35	B	43	LYS	1	0.865	0.920	15.917	-0.185	-0.185	0.000	0.000	0.000	0.000
36	B	44	THR	0	0.012	0.011	18.625	0.020	0.020	0.000	0.000	0.000	0.000
37	B	45	LEU	0	-0.065	-0.042	20.094	0.007	0.007	0.000	0.000	0.000	0.000
38	B	46	TRP	0	-0.039	-0.023	15.245	0.004	0.004	0.000	0.000	0.000	0.000
39	B	47	GLU	-1	-0.915	-0.978	15.033	0.194	0.194	0.000	0.000	0.000	0.000
40	B	48	ASN	0	-0.033	-0.030	15.694	0.063	0.063	0.000	0.000	0.000	0.000
41	B	49	LYS	1	0.928	0.965	18.083	0.033	0.033	0.000	0.000	0.000	0.000
42	B	50	LEU	0	-0.074	-0.016	11.684	-0.018	-0.018	0.000	0.000	0.000	0.000
43	B	51	MET	0	-0.071	-0.012	13.869	0.035	0.035	0.000	0.000	0.000	0.000

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