FMO DATABASE

FMODB ID: 6G7VZ

Calculation Name: 1DP5-B-Xray540

Preferred Name: Saccharopepesin

Target Type: SINGLE PROTEIN

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose | beta-d-mannopyranose | alpha-d-mannopyranose

Ligand 3-letter code: NAG | BMA | MAN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1DP5

Chain ID: B

ChEMBL ID: CHEMBL4451

UniProt ID: P07267

Base Structure: X-ray

Registration Date: 2025-07-07

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	61
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-98737.154727
FMO2-HF: Nuclear repulsion	86094.640426
FMO2-HF: Total energy	-12642.514301
FMO2-MP2: Total energy	-12677.840465

3D Structure Molmil

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.
1.361	2.598	0.15	0.577	-1.966	-0.003

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 : 0.126 / q_NPA : 0.055

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].
4	B	3	THR	0	-0.023	0.059	4.078	0.436	0.729	0.000	-0.123	-0.170	0.000
5	B	4	ASP	0	0.216	-0.097	3.752	-2.481	-0.806	-0.002	-0.848	-0.825	0.000
6	B	4	ASP	-1	-0.962	-0.824	4.674	1.360	1.414	-0.001	-0.003	-0.050	0.000
7	B	5	GLN	0	0.112	-0.071	3.618	0.401	0.521	0.003	0.040	-0.163	0.000
8	B	5	GLN	0	-0.084	0.092	2.945	-0.436	-1.995	0.154	1.764	-0.359	-0.003
9	B	6	GLN	0	0.075	-0.108	4.165	0.356	0.668	-0.002	-0.203	-0.108	0.000
10	B	6	GLN	0	-0.047	0.110	3.855	1.028	1.293	0.000	-0.048	-0.217	0.000
11	B	7	LYS	0	0.080	-0.088	5.977	0.284	0.361	-0.002	-0.002	-0.074	0.000
12	B	7	LYS	1	0.868	1.073	7.699	-0.649	-0.649	0.000	0.000	0.000	0.000
13	B	8	VAL	0	0.101	-0.088	8.022	0.186	0.186	0.000	0.000	0.000	0.000
14	B	8	VAL	0	-0.068	0.103	8.596	0.009	0.009	0.000	0.000	0.000	0.000
15	B	9	SER	0	0.031	-0.086	8.391	0.291	0.291	0.000	0.000	0.000	0.000
16	B	9	SER	0	-0.089	0.043	7.426	-0.104	-0.104	0.000	0.000	0.000	0.000
17	B	10	GLU	0	0.100	-0.112	9.941	0.118	0.118	0.000	0.000	0.000	0.000
18	B	10	GLU	-1	-1.039	-0.846	10.981	-0.432	-0.432	0.000	0.000	0.000	0.000
19	B	11	ILE	0	0.065	-0.101	11.990	0.099	0.099	0.000	0.000	0.000	0.000
20	B	11	ILE	0	-0.078	0.090	12.316	0.016	0.016	0.000	0.000	0.000	0.000
21	B	12	PHE	0	0.052	-0.123	13.038	0.110	0.110	0.000	0.000	0.000	0.000
22	B	12	PHE	0	-0.085	0.102	12.952	-0.012	-0.012	0.000	0.000	0.000	0.000
23	B	13	GLN	0	0.004	-0.129	14.051	0.080	0.080	0.000	0.000	0.000	0.000
24	B	13	GLN	0	-0.003	0.126	13.426	-0.035	-0.035	0.000	0.000	0.000	0.000
25	B	14	SER	0	0.113	-0.055	15.902	0.038	0.038	0.000	0.000	0.000	0.000
26	B	14	SER	0	-0.045	0.097	16.494	0.027	0.027	0.000	0.000	0.000	0.000
27	B	15	SER	0	0.057	-0.059	17.634	0.052	0.052	0.000	0.000	0.000	0.000
28	B	15	SER	0	-0.060	0.049	18.094	0.012	0.012	0.000	0.000	0.000	0.000
29	B	16	LYS	0	0.066	-0.072	18.804	0.047	0.047	0.000	0.000	0.000	0.000
30	B	16	LYS	1	0.788	1.003	15.810	0.630	0.630	0.000	0.000	0.000	0.000
31	B	17	GLU	0	0.107	-0.105	20.545	0.024	0.024	0.000	0.000	0.000	0.000
32	B	17	GLU	-1	-0.984	-0.848	21.555	-0.267	-0.267	0.000	0.000	0.000	0.000
33	B	18	LYS	0	0.067	-0.073	22.188	0.025	0.025	0.000	0.000	0.000	0.000
34	B	18	LYS	1	0.808	1.025	22.824	0.155	0.155	0.000	0.000	0.000	0.000
35	B	19	LEU	0	0.056	-0.114	23.317	0.027	0.027	0.000	0.000	0.000	0.000
36	B	19	LEU	0	-0.101	0.099	21.927	0.000	0.000	0.000	0.000	0.000	0.000
37	B	20	GLN	0	0.041	-0.117	24.886	0.021	0.021	0.000	0.000	0.000	0.000
38	B	20	GLN	0	-0.106	0.092	23.789	-0.016	-0.016	0.000	0.000	0.000	0.000
39	B	21	GLY	0	-0.015	-0.098	26.611	0.015	0.015	0.000	0.000	0.000	0.000
40	B	22	ASP	0	0.148	-0.001	27.995	0.014	0.014	0.000	0.000	0.000	0.000
41	B	22	ASP	-1	-0.969	-0.826	27.543	-0.148	-0.148	0.000	0.000	0.000	0.000
42	B	23	ALA	0	0.115	-0.098	29.361	0.017	0.017	0.000	0.000	0.000	0.000
43	B	23	ALA	0	-0.058	0.112	29.681	-0.002	-0.002	0.000	0.000	0.000	0.000
44	B	24	LYS	0	0.089	-0.100	31.206	0.009	0.009	0.000	0.000	0.000	0.000
45	B	24	LYS	1	0.757	0.999	32.366	0.116	0.116	0.000	0.000	0.000	0.000
46	B	25	VAL	0	0.026	-0.077	32.901	0.007	0.007	0.000	0.000	0.000	0.000
47	B	25	VAL	0	-0.053	0.089	32.748	0.001	0.001	0.000	0.000	0.000	0.000
48	B	26	VAL	0	0.081	-0.093	33.959	0.010	0.010	0.000	0.000	0.000	0.000
49	B	26	VAL	0	-0.087	0.090	33.320	0.000	0.000	0.000	0.000	0.000	0.000
50	B	27	SER	0	0.059	-0.076	35.261	0.008	0.008	0.000	0.000	0.000	0.000
51	B	27	SER	0	-0.042	0.067	35.708	-0.003	-0.003	0.000	0.000	0.000	0.000
52	B	28	ASP	0	0.056	-0.120	37.120	0.004	0.004	0.000	0.000	0.000	0.000
53	B	28	ASP	-1	-0.954	-0.805	37.918	-0.106	-0.106	0.000	0.000	0.000	0.000
54	B	29	ALA	0	0.062	-0.093	38.654	0.006	0.006	0.000	0.000	0.000	0.000
55	B	29	ALA	0	-0.095	0.089	39.191	0.000	0.000	0.000	0.000	0.000	0.000
56	B	30	PHE	0	0.041	-0.107	39.794	0.007	0.007	0.000	0.000	0.000	0.000
57	B	30	PHE	0	-0.069	0.071	37.599	-0.001	-0.001	0.000	0.000	0.000	0.000
58	B	31	MET	0	-0.056	-0.086	41.347	0.005	0.005	0.000	0.000	0.000	0.000
59	B	31	MET	0	-0.102	0.078	40.971	0.000	0.000	0.000	0.000	0.000	0.000
60	B	32	MET	0	-0.031	-0.140	43.243	0.001	0.001	0.000	0.000	0.000	0.000
61	B	32	MET	0	0.024	0.027	43.674	0.001	0.001	0.000	0.000	0.000	0.000

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