FMO DATABASE

FMODB ID: G57L1

Calculation Name: 3PMK-N-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PMK

Chain ID: N

ChEMBL ID:

UniProt ID: B7UCZ3

Base Structure: X-ray

Registration Date: 2023-09-23

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	30
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-93829.797032
FMO2-HF: Nuclear repulsion	81679.323133
FMO2-HF: Total energy	-12150.473899
FMO2-MP2: Total energy	-12186.485565

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(N:6:LYS)

Summations of interaction energy for fragment #1(N:6:LYS)

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.
2.021	3.642	-0.013	-0.764	-0.843	0.001

Interaction energy analysis for fragmet #1(N:6:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.998 / q_NPA : 0.992

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

Sort

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	N	8	ARG	1	0.923	0.965	3.819	28.244	29.865	-0.013	-0.764	-0.843	0.001
4	N	9	GLU	-1	-0.884	-0.933	5.874	-20.684	-20.684	0.000	0.000	0.000	0.000
5	N	10	TYR	0	-0.041	-0.043	8.227	0.372	0.372	0.000	0.000	0.000	0.000
6	N	11	LEU	0	0.091	0.037	11.824	0.117	0.117	0.000	0.000	0.000	0.000
7	N	12	LYS	1	0.939	0.966	10.286	22.648	22.648	0.000	0.000	0.000	0.000
8	N	13	SER	0	-0.004	0.001	16.468	0.553	0.553	0.000	0.000	0.000	0.000
9	N	14	TYR	0	-0.012	0.010	18.202	0.935	0.935	0.000	0.000	0.000	0.000
10	N	15	SER	0	0.007	0.006	19.122	-0.303	-0.303	0.000	0.000	0.000	0.000
11	N	16	ARG	1	0.853	0.922	21.219	10.242	10.242	0.000	0.000	0.000	0.000
12	N	17	LEU	0	0.013	0.004	17.003	0.278	0.278	0.000	0.000	0.000	0.000
13	N	18	ASP	-1	-0.885	-0.947	18.903	-13.285	-13.285	0.000	0.000	0.000	0.000
14	N	19	GLN	0	-0.020	-0.019	21.458	-0.035	-0.035	0.000	0.000	0.000	0.000
15	N	20	ALA	0	-0.006	0.012	23.659	0.241	0.241	0.000	0.000	0.000	0.000
16	N	21	VAL	0	-0.003	-0.016	20.302	0.204	0.204	0.000	0.000	0.000	0.000
17	N	22	GLY	0	0.017	0.016	23.657	0.107	0.107	0.000	0.000	0.000	0.000
18	N	23	GLU	-1	-0.802	-0.908	26.024	-9.531	-9.531	0.000	0.000	0.000	0.000
19	N	24	ILE	0	-0.071	-0.038	24.242	0.210	0.210	0.000	0.000	0.000	0.000
20	N	25	ASP	-1	-0.914	-0.959	26.072	-10.216	-10.216	0.000	0.000	0.000	0.000
21	N	26	GLU	-1	-0.947	-0.961	27.986	-8.561	-8.561	0.000	0.000	0.000	0.000
22	N	27	ILE	0	-0.035	-0.023	31.286	0.287	0.287	0.000	0.000	0.000	0.000
23	N	28	GLU	-1	-0.916	-0.967	27.926	-9.739	-9.739	0.000	0.000	0.000	0.000
24	N	29	ALA	0	-0.004	-0.002	30.870	0.151	0.151	0.000	0.000	0.000	0.000
25	N	30	GLN	0	-0.090	-0.046	32.839	0.158	0.158	0.000	0.000	0.000	0.000
26	N	31	ARG	1	0.831	0.942	30.363	9.474	9.474	0.000	0.000	0.000	0.000
27	N	32	ALA	0	0.021	0.022	33.624	-0.090	-0.090	0.000	0.000	0.000	0.000
28	N	33	GLU	-1	-0.964	-0.974	35.272	-7.570	-7.570	0.000	0.000	0.000	0.000
29	N	34	LYS	1	0.915	0.936	37.219	7.648	7.648	0.000	0.000	0.000	0.000
30	N	35	SER	0	-0.003	0.015	40.048	0.166	0.166	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(N:6:LYS)