FMO DATABASE

FMODB ID: 3QKVL

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

Total energy (hartree)

FMO2-HF: Electronic energy	-98743.738931
FMO2-HF: Nuclear repulsion	86094.640426
FMO2-HF: Total energy	-12649.098505
FMO2-MP2: Total energy	-12684.588283

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.
-15.408	-7.572	7.513	-5.609	-9.74	-0.018

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 : 0.027 / q_NPA : 0.006

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	-0.852	-0.904	3.752	-2.881	-0.600	-0.017	-0.967	-1.297	0.000
4	B	5	GLN	0	0.024	0.003	2.067	-11.070	-7.933	4.379	-2.978	-4.538	-0.030
5	B	6	GLN	0	-0.022	-0.005	2.717	-0.364	1.855	3.152	-1.648	-3.723	0.012
6	B	7	LYS	1	0.996	1.004	5.290	-2.952	-2.753	-0.001	-0.016	-0.182	0.000
7	B	8	VAL	0	0.005	0.009	7.594	-0.117	-0.117	0.000	0.000	0.000	0.000
8	B	9	SER	0	-0.051	-0.041	6.261	-0.264	-0.264	0.000	0.000	0.000	0.000
9	B	10	GLU	-1	-0.955	-0.966	8.786	0.878	0.878	0.000	0.000	0.000	0.000
10	B	11	ILE	0	0.011	-0.001	10.702	0.041	0.041	0.000	0.000	0.000	0.000
11	B	12	PHE	0	-0.028	-0.033	11.564	0.014	0.014	0.000	0.000	0.000	0.000
12	B	13	GLN	0	-0.001	0.008	11.418	-0.103	-0.103	0.000	0.000	0.000	0.000
13	B	14	SER	0	0.047	0.022	14.130	0.071	0.071	0.000	0.000	0.000	0.000
14	B	15	SER	0	0.001	0.009	16.445	0.071	0.071	0.000	0.000	0.000	0.000
15	B	16	LYS	1	0.871	0.922	13.751	1.228	1.228	0.000	0.000	0.000	0.000
16	B	17	GLU	-1	-0.909	-0.940	18.817	-0.175	-0.175	0.000	0.000	0.000	0.000
17	B	18	LYS	1	0.896	0.944	20.705	0.234	0.234	0.000	0.000	0.000	0.000
18	B	19	LEU	0	-0.039	-0.021	20.607	0.021	0.021	0.000	0.000	0.000	0.000
19	B	20	GLN	0	-0.041	-0.021	21.768	0.007	0.007	0.000	0.000	0.000	0.000
20	B	21	GLY	0	0.014	0.014	24.958	0.023	0.023	0.000	0.000	0.000	0.000
21	B	22	ASP	-1	-0.834	-0.936	26.541	-0.169	-0.169	0.000	0.000	0.000	0.000
22	B	23	ALA	0	-0.001	0.001	27.946	0.015	0.015	0.000	0.000	0.000	0.000
23	B	24	LYS	1	0.831	0.908	29.715	0.161	0.161	0.000	0.000	0.000	0.000
24	B	25	VAL	0	0.007	0.020	31.313	0.015	0.015	0.000	0.000	0.000	0.000
25	B	26	VAL	0	-0.005	-0.002	32.154	0.010	0.010	0.000	0.000	0.000	0.000
26	B	27	SER	0	0.002	-0.007	33.803	0.005	0.005	0.000	0.000	0.000	0.000
27	B	28	ASP	-1	-0.868	-0.929	35.552	-0.132	-0.132	0.000	0.000	0.000	0.000
28	B	29	ALA	0	-0.051	-0.014	37.259	0.010	0.010	0.000	0.000	0.000	0.000
29	B	30	PHE	0	-0.017	-0.022	36.199	0.004	0.004	0.000	0.000	0.000	0.000
30	B	31	MET	0	-0.081	-0.014	39.300	0.004	0.004	0.000	0.000	0.000	0.000
31	B	32	MET	0	-0.034	-0.018	41.651	0.007	0.007	0.000	0.000	0.000	0.000

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