FMO DATABASE

FMODB ID: NN6VQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-94652.883946
FMO2-HF: Nuclear repulsion	82502.082584
FMO2-HF: Total energy	-12150.801362
FMO2-MP2: Total energy	-12186.823809

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.
3.259	4.927	-0.008	-0.823	-0.837	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 : 0.995 / q_NPA : 0.987

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	N	8	ARG	1	0.907	0.947	3.879	30.711	32.379	-0.008	-0.823	-0.837	0.001
4	N	9	GLU	-1	-0.747	-0.852	6.295	-22.087	-22.087	0.000	0.000	0.000	0.000
5	N	10	TYR	0	-0.002	-0.006	8.123	0.771	0.771	0.000	0.000	0.000	0.000
6	N	11	LEU	0	0.072	0.023	11.865	-0.034	-0.034	0.000	0.000	0.000	0.000
7	N	12	LYS	1	0.803	0.889	10.978	22.395	22.395	0.000	0.000	0.000	0.000
8	N	13	SER	0	0.019	0.016	16.524	0.628	0.628	0.000	0.000	0.000	0.000
9	N	14	TYR	0	-0.003	0.008	18.035	0.977	0.977	0.000	0.000	0.000	0.000
10	N	15	SER	0	-0.034	-0.024	19.868	-0.146	-0.146	0.000	0.000	0.000	0.000
11	N	16	ARG	1	0.843	0.902	21.473	10.856	10.856	0.000	0.000	0.000	0.000
12	N	17	LEU	0	0.021	0.016	16.887	0.260	0.260	0.000	0.000	0.000	0.000
13	N	18	ASP	-1	-0.903	-0.951	18.855	-13.710	-13.710	0.000	0.000	0.000	0.000
14	N	19	GLN	0	0.006	-0.001	21.294	0.000	0.000	0.000	0.000	0.000	0.000
15	N	20	ALA	0	0.017	0.017	23.666	0.239	0.239	0.000	0.000	0.000	0.000
16	N	21	VAL	0	-0.020	-0.022	20.119	0.141	0.141	0.000	0.000	0.000	0.000
17	N	22	GLY	0	0.020	0.024	23.488	0.134	0.134	0.000	0.000	0.000	0.000
18	N	23	GLU	-1	-0.801	-0.893	26.007	-9.930	-9.930	0.000	0.000	0.000	0.000
19	N	24	ILE	0	-0.060	-0.033	24.718	0.228	0.228	0.000	0.000	0.000	0.000
20	N	25	ASP	-1	-0.932	-0.959	25.757	-10.379	-10.379	0.000	0.000	0.000	0.000
21	N	26	GLU	-1	-0.932	-0.966	27.717	-8.734	-8.734	0.000	0.000	0.000	0.000
22	N	27	ILE	0	-0.051	-0.032	31.021	0.294	0.294	0.000	0.000	0.000	0.000
23	N	28	GLU	-1	-0.869	-0.915	27.895	-9.713	-9.713	0.000	0.000	0.000	0.000
24	N	29	ALA	0	-0.005	-0.008	30.793	0.227	0.227	0.000	0.000	0.000	0.000
25	N	30	GLN	0	-0.091	-0.049	32.718	0.168	0.168	0.000	0.000	0.000	0.000
26	N	31	ARG	1	0.832	0.911	30.722	9.562	9.562	0.000	0.000	0.000	0.000
27	N	32	ALA	0	0.021	0.024	33.246	-0.005	-0.005	0.000	0.000	0.000	0.000
28	N	33	GLU	-1	-0.937	-0.956	34.860	-7.566	-7.566	0.000	0.000	0.000	0.000
29	N	34	LYS	1	0.851	0.904	36.695	7.814	7.814	0.000	0.000	0.000	0.000
30	N	35	SER	0	-0.010	0.011	39.691	0.158	0.158	0.000	0.000	0.000	0.000

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