FMO DATABASE

FMODB ID: LJQ39

Calculation Name: 1DP5-B-Xray372

Preferred Name: Saccharopepesin

Target Type: SINGLE PROTEIN

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose

ligand 3-letter code: NAG

PDB ID: 1DP5

Chain ID: B

ChEMBL ID: CHEMBL4451

UniProt ID: P07267

Base Structure: X-ray

Registration Date: 2023-03-13

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	31
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-98732.98665
FMO2-HF: Nuclear repulsion	86083.749202
FMO2-HF: Total energy	-12649.237448
FMO2-MP2: Total energy	-12684.711224

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:2:ASN)

Summations of interaction energy for fragment #1(B:2:ASN)

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.
-26.891	-26.012	17.253	-7.713	-10.42	-0.017

Interaction energy analysis for fragmet #1(B:2:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : -0.013

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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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	4	ASP	-1	-0.845	-0.899	3.745	-2.977	-0.663	-0.017	-0.990	-1.308	-0.001
4	B	5	GLN	0	0.035	0.016	1.852	-15.397	-17.000	10.790	-4.116	-5.071	-0.043
5	B	6	GLN	0	-0.010	-0.002	2.011	-8.688	-8.520	6.480	-2.607	-4.041	0.027
6	B	7	LYS	1	0.975	0.998	5.460	-1.688	-1.688	0.000	0.000	0.000	0.000
7	B	8	VAL	0	-0.006	0.001	7.703	0.013	0.013	0.000	0.000	0.000	0.000
8	B	9	SER	0	-0.047	-0.033	6.110	-0.088	-0.088	0.000	0.000	0.000	0.000
9	B	10	GLU	-1	-0.947	-0.967	8.687	0.804	0.804	0.000	0.000	0.000	0.000
10	B	11	ILE	0	0.009	-0.001	10.819	0.049	0.049	0.000	0.000	0.000	0.000
11	B	12	PHE	0	-0.025	-0.030	11.182	0.013	0.013	0.000	0.000	0.000	0.000
12	B	13	GLN	0	-0.017	-0.006	11.475	-0.066	-0.066	0.000	0.000	0.000	0.000
13	B	14	SER	0	0.053	0.025	14.105	0.055	0.055	0.000	0.000	0.000	0.000
14	B	15	SER	0	-0.001	0.004	16.414	0.063	0.063	0.000	0.000	0.000	0.000
15	B	16	LYS	1	0.884	0.939	13.781	0.976	0.976	0.000	0.000	0.000	0.000
16	B	17	GLU	-1	-0.911	-0.943	18.788	-0.106	-0.106	0.000	0.000	0.000	0.000
17	B	18	LYS	1	0.828	0.893	20.696	0.209	0.209	0.000	0.000	0.000	0.000
18	B	19	LEU	0	-0.008	-0.005	20.362	0.015	0.015	0.000	0.000	0.000	0.000
19	B	20	GLN	0	-0.046	-0.022	21.477	-0.005	-0.005	0.000	0.000	0.000	0.000
20	B	21	GLY	0	0.017	0.014	24.922	0.021	0.021	0.000	0.000	0.000	0.000
21	B	22	ASP	-1	-0.810	-0.906	26.298	-0.171	-0.171	0.000	0.000	0.000	0.000
22	B	23	ALA	0	0.005	0.003	27.845	0.011	0.011	0.000	0.000	0.000	0.000
23	B	24	LYS	1	0.818	0.897	29.637	0.126	0.126	0.000	0.000	0.000	0.000
24	B	25	VAL	0	0.011	0.019	31.145	0.013	0.013	0.000	0.000	0.000	0.000
25	B	26	VAL	0	-0.004	-0.001	32.052	0.008	0.008	0.000	0.000	0.000	0.000
26	B	27	SER	0	0.004	-0.001	33.684	0.004	0.004	0.000	0.000	0.000	0.000
27	B	28	ASP	-1	-0.863	-0.923	35.469	-0.106	-0.106	0.000	0.000	0.000	0.000
28	B	29	ALA	0	-0.047	-0.013	37.171	0.009	0.009	0.000	0.000	0.000	0.000
29	B	30	PHE	0	-0.016	-0.023	35.852	0.002	0.002	0.000	0.000	0.000	0.000
30	B	31	MET	0	-0.079	-0.010	39.011	0.002	0.002	0.000	0.000	0.000	0.000
31	B	32	MET	0	-0.030	-0.016	41.528	0.008	0.008	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:2:ASN)