FMO DATABASE

FMODB ID: 89K8Y

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	OptHSide
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	-94340.621264
FMO2-HF: Nuclear repulsion	82189.914225
FMO2-HF: Total energy	-12150.707038
FMO2-MP2: Total energy	-12186.740672

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.
3.581	5.376	-0.005	-0.832	-0.958	0

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 : 0.981 / q_NPA : 0.981

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].
3	N	8	ARG	1	0.902	0.948	3.812	31.718	33.513	-0.005	-0.832	-0.958
4	N	9	GLU	-1	-0.736	-0.859	5.888	-22.365	-22.365	0.000	0.000	0.000
5	N	10	TYR	0	-0.034	-0.020	8.239	0.459	0.459	0.000	0.000	0.000
6	N	11	LEU	0	0.092	0.033	11.838	0.161	0.161	0.000	0.000	0.000
7	N	12	LYS	1	0.819	0.900	10.745	22.619	22.619	0.000	0.000	0.000
8	N	13	SER	0	-0.005	0.004	16.483	0.601	0.601	0.000	0.000	0.000
9	N	14	TYR	0	-0.015	0.003	18.340	1.019	1.019	0.000	0.000	0.000
10	N	15	SER	0	0.005	0.006	19.133	-0.364	-0.364	0.000	0.000	0.000
11	N	16	ARG	1	0.813	0.891	21.229	10.628	10.628	0.000	0.000	0.000
12	N	17	LEU	0	0.014	0.005	17.045	0.279	0.279	0.000	0.000	0.000
13	N	18	ASP	-1	-0.892	-0.952	19.117	-13.826	-13.826	0.000	0.000	0.000
14	N	19	GLN	0	-0.001	-0.012	21.464	-0.010	-0.010	0.000	0.000	0.000
15	N	20	ALA	0	-0.010	0.010	23.654	0.271	0.271	0.000	0.000	0.000
16	N	21	VAL	0	-0.006	-0.015	20.308	0.220	0.220	0.000	0.000	0.000
17	N	22	GLY	0	0.016	0.016	23.664	0.127	0.127	0.000	0.000	0.000
18	N	23	GLU	-1	-0.778	-0.881	26.030	-9.827	-9.827	0.000	0.000	0.000
19	N	24	ILE	0	-0.067	-0.039	24.536	0.230	0.230	0.000	0.000	0.000
20	N	25	ASP	-1	-0.925	-0.962	26.027	-10.395	-10.395	0.000	0.000	0.000
21	N	26	GLU	-1	-0.928	-0.956	27.906	-8.742	-8.742	0.000	0.000	0.000
22	N	27	ILE	0	-0.048	-0.028	31.219	0.294	0.294	0.000	0.000	0.000
23	N	28	GLU	-1	-0.874	-0.923	27.739	-9.719	-9.719	0.000	0.000	0.000
24	N	29	ALA	0	-0.011	-0.004	30.799	0.165	0.165	0.000	0.000	0.000
25	N	30	GLN	0	-0.075	-0.041	32.745	0.147	0.147	0.000	0.000	0.000
26	N	31	ARG	1	0.805	0.907	30.482	9.591	9.591	0.000	0.000	0.000
27	N	32	ALA	0	0.033	0.028	33.524	-0.075	-0.075	0.000	0.000	0.000
28	N	33	GLU	-1	-0.945	-0.967	35.180	-7.558	-7.558	0.000	0.000	0.000
29	N	34	LYS	1	0.862	0.916	36.731	7.787	7.787	0.000	0.000	0.000
30	N	35	SER	0	0.009	0.018	39.936	0.146	0.146	0.000	0.000	0.000

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