FMO DATABASE

FMODB ID: MM79Z

Calculation Name: 1DP5-B-Xray309

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	33
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-100719.40815
FMO2-HF: Nuclear repulsion	87899.339259
FMO2-HF: Total energy	-12820.068891
FMO2-MP2: Total energy	-12856.097857

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:1:ACE )

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

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.
1.976	2.855	-0.004	-0.387	-0.489	0

Interaction energy analysis for fragmet #1(B:1:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.024 / q_NPA : 0.002

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	B	3	THR	0	0.046	0.001	3.834	1.374	2.253	-0.004	-0.387	-0.489
4	B	4	ASP	-1	-0.848	-0.901	5.805	-0.378	-0.378	0.000	0.000	0.000
5	B	5	GLN	0	0.031	0.007	7.122	-0.111	-0.111	0.000	0.000	0.000
6	B	6	GLN	0	-0.022	-0.003	5.317	0.341	0.341	0.000	0.000	0.000
7	B	7	LYS	1	0.996	1.003	8.836	0.388	0.388	0.000	0.000	0.000
8	B	8	VAL	0	0.006	0.010	11.516	0.075	0.075	0.000	0.000	0.000
9	B	9	SER	0	-0.049	-0.040	11.235	0.071	0.071	0.000	0.000	0.000
10	B	10	GLU	-1	-0.955	-0.966	12.987	-0.074	-0.074	0.000	0.000	0.000
11	B	11	ILE	0	0.011	-0.001	14.775	0.038	0.038	0.000	0.000	0.000
12	B	12	PHE	0	-0.028	-0.033	16.611	0.023	0.023	0.000	0.000	0.000
13	B	13	GLN	0	0.000	0.008	16.502	0.010	0.010	0.000	0.000	0.000
14	B	14	SER	0	0.046	0.022	19.071	0.018	0.018	0.000	0.000	0.000
15	B	15	SER	0	0.000	0.009	20.929	0.018	0.018	0.000	0.000	0.000
16	B	16	LYS	1	0.870	0.922	19.250	0.171	0.171	0.000	0.000	0.000
17	B	17	GLU	-1	-0.908	-0.939	23.710	-0.050	-0.050	0.000	0.000	0.000
18	B	18	LYS	1	0.897	0.944	25.335	0.083	0.083	0.000	0.000	0.000
19	B	19	LEU	0	-0.041	-0.022	25.754	0.006	0.006	0.000	0.000	0.000
20	B	20	GLN	0	-0.040	-0.020	27.027	0.003	0.003	0.000	0.000	0.000
21	B	21	GLY	0	0.016	0.014	29.808	0.006	0.006	0.000	0.000	0.000
22	B	22	ASP	-1	-0.836	-0.937	30.889	-0.060	-0.060	0.000	0.000	0.000
23	B	23	ALA	0	0.000	0.001	32.850	0.003	0.003	0.000	0.000	0.000
24	B	24	LYS	1	0.831	0.908	34.664	0.037	0.037	0.000	0.000	0.000
25	B	25	VAL	0	0.006	0.019	35.890	0.003	0.003	0.000	0.000	0.000
26	B	26	VAL	0	-0.006	-0.003	36.926	0.002	0.002	0.000	0.000	0.000
27	B	27	SER	0	0.003	-0.006	38.797	0.002	0.002	0.000	0.000	0.000
28	B	28	ASP	-1	-0.869	-0.928	40.490	-0.030	-0.030	0.000	0.000	0.000
29	B	29	ALA	0	-0.053	-0.016	42.089	0.002	0.002	0.000	0.000	0.000
30	B	30	PHE	0	-0.015	-0.022	41.508	0.001	0.001	0.000	0.000	0.000
31	B	31	MET	0	-0.077	-0.014	44.502	0.002	0.002	0.000	0.000	0.000
32	B	32	MET	0	-0.026	-0.017	46.748	0.002	0.002	0.000	0.000	0.000
33	B	33	NME	0	-0.015	-0.002	49.311	0.000	0.000	0.000	0.000	0.000

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