FMO DATABASE

FMODB ID: QM1ZY

Calculation Name: 3A0D-A-Xray547

Preferred Name:

Target Type:

Ligand Name: methyl alpha-d-mannopyranoside | sulfate ion

Ligand 3-letter code: MMA | SO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3A0D

Chain ID: A

ChEMBL ID:

UniProt ID: Q8L568

Base Structure: X-ray

Registration Date: 2025-10-04

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	109
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-809811.218472
FMO2-HF: Nuclear repulsion	767869.002401
FMO2-HF: Total energy	-41942.216071
FMO2-MP2: Total energy	-42064.886145

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(A:1:VAL)

Summations of interaction energy for fragment #1(A:1:VAL)

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.
-51.835	-43.488	2.124	-4.609	-5.861	-0.023

Interaction energy analysis for fragmet #1(A:1:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.868 / q_NPA : 0.927

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

Sort

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	A	3	SER	0	0.018	0.015	1.926	4.815	8.779	1.673	-2.581	-3.056	-0.009
4	A	4	LEU	0	0.023	0.015	2.954	-7.668	-6.023	0.236	-0.894	-0.986	-0.010
16	A	16	LEU	0	-0.077	-0.003	2.867	-10.814	-9.798	0.200	-0.302	-0.914	-0.002
17	A	17	GLU	-1	-0.811	-0.904	3.294	-40.327	-39.022	0.014	-0.512	-0.807	0.000
18	A	18	VAL	0	-0.034	-0.021	3.592	-11.895	-11.478	0.001	-0.320	-0.098	-0.002
5	A	5	SER	0	0.036	0.017	5.806	3.416	3.416	0.000	0.000	0.000	0.000
6	A	6	SER	0	-0.006	0.015	8.536	-0.395	-0.395	0.000	0.000	0.000	0.000
7	A	7	PRO	0	-0.016	-0.002	12.107	-0.073	-0.073	0.000	0.000	0.000	0.000
8	A	8	ASN	0	-0.029	-0.026	8.801	0.987	0.987	0.000	0.000	0.000	0.000
9	A	9	SER	0	0.006	-0.004	9.738	1.189	1.189	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.027	0.011	4.947	-1.749	-1.749	0.000	0.000	0.000	0.000
11	A	11	PHE	0	0.061	0.011	8.319	2.609	2.609	0.000	0.000	0.000	0.000
12	A	12	THR	0	-0.004	-0.023	10.524	-1.216	-1.216	0.000	0.000	0.000	0.000
13	A	13	GLY	0	-0.022	-0.007	11.857	0.195	0.195	0.000	0.000	0.000	0.000
14	A	14	HIS	0	-0.038	-0.004	6.477	-4.275	-4.275	0.000	0.000	0.000	0.000
15	A	15	SER	0	-0.011	-0.055	6.047	4.921	4.921	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.004	0.030	6.221	4.226	4.226	0.000	0.000	0.000	0.000
20	A	20	PRO	0	-0.016	-0.025	7.993	0.988	0.988	0.000	0.000	0.000	0.000
21	A	21	SER	0	0.013	-0.006	10.669	-0.288	-0.288	0.000	0.000	0.000	0.000
22	A	22	TYR	0	-0.035	-0.001	9.124	1.709	1.709	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.891	0.933	7.751	27.302	27.302	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.005	0.012	8.054	3.737	3.737	0.000	0.000	0.000	0.000
25	A	25	ILE	0	-0.004	-0.007	7.942	-3.549	-3.549	0.000	0.000	0.000	0.000
26	A	26	MET	0	-0.030	0.018	9.863	2.454	2.454	0.000	0.000	0.000	0.000
27	A	27	GLN	0	-0.008	-0.012	11.639	-0.672	-0.672	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.037	0.001	14.771	0.476	0.476	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.830	-0.912	17.418	-15.456	-15.456	0.000	0.000	0.000	0.000
30	A	30	CYS	0	-0.065	0.009	16.759	0.725	0.725	0.000	0.000	0.000	0.000
31	A	31	ASN	0	0.048	0.048	17.359	-0.123	-0.123	0.000	0.000	0.000	0.000
32	A	32	PHE	0	0.039	0.011	9.376	-1.047	-1.047	0.000	0.000	0.000	0.000
33	A	33	VAL	0	-0.004	0.003	13.243	1.055	1.055	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.002	0.007	11.159	-2.216	-2.216	0.000	0.000	0.000	0.000
35	A	35	TYR	0	-0.059	-0.055	12.535	2.446	2.446	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.783	-0.897	12.426	-21.764	-21.764	0.000	0.000	0.000	0.000
37	A	37	SER	0	-0.006	-0.016	13.723	1.246	1.246	0.000	0.000	0.000	0.000
38	A	38	GLY	0	-0.003	0.012	14.799	1.034	1.034	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.900	0.948	16.482	16.082	16.082	0.000	0.000	0.000	0.000
40	A	40	PRO	0	0.014	0.019	17.080	-0.943	-0.943	0.000	0.000	0.000	0.000
41	A	41	VAL	0	-0.067	-0.048	15.857	1.233	1.233	0.000	0.000	0.000	0.000
42	A	42	TRP	0	0.013	0.018	14.031	0.283	0.283	0.000	0.000	0.000	0.000
43	A	43	ALA	0	0.008	-0.002	16.469	-0.976	-0.976	0.000	0.000	0.000	0.000
44	A	44	SER	0	0.001	0.001	16.738	0.450	0.450	0.000	0.000	0.000	0.000
45	A	45	ASN	0	-0.051	-0.028	18.373	0.688	0.688	0.000	0.000	0.000	0.000
46	A	46	THR	0	0.018	-0.010	18.281	0.442	0.442	0.000	0.000	0.000	0.000
47	A	47	GLY	0	-0.003	0.005	20.650	-0.054	-0.054	0.000	0.000	0.000	0.000
48	A	48	GLY	0	-0.023	-0.011	21.387	0.587	0.587	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.056	-0.020	22.715	0.484	0.484	0.000	0.000	0.000	0.000
50	A	50	GLY	0	0.028	0.001	22.343	0.201	0.201	0.000	0.000	0.000	0.000
51	A	51	SER	0	-0.039	-0.013	20.363	-0.062	-0.062	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.049	0.016	18.306	0.207	0.207	0.000	0.000	0.000	0.000
53	A	54	ARG	1	0.873	0.949	12.863	15.565	15.565	0.000	0.000	0.000	0.000
54	A	55	LEU	0	0.039	0.020	9.244	1.180	1.180	0.000	0.000	0.000	0.000
55	A	56	THR	0	-0.028	-0.038	11.404	-0.877	-0.877	0.000	0.000	0.000	0.000
56	A	57	LEU	0	-0.011	0.013	10.611	0.841	0.841	0.000	0.000	0.000	0.000
57	A	58	HIS	0	0.036	0.011	13.154	-0.196	-0.196	0.000	0.000	0.000	0.000
58	A	59	ASN	0	0.082	0.043	15.695	-1.367	-1.367	0.000	0.000	0.000	0.000
59	A	60	ASN	0	0.026	0.021	17.172	-0.379	-0.379	0.000	0.000	0.000	0.000
60	A	61	GLY	0	0.060	0.036	16.002	0.424	0.424	0.000	0.000	0.000	0.000
61	A	62	ASN	0	-0.053	-0.007	16.815	-0.629	-0.629	0.000	0.000	0.000	0.000
62	A	63	LEU	0	0.029	0.010	11.680	-0.669	-0.669	0.000	0.000	0.000	0.000
63	A	64	VAL	0	-0.023	-0.014	15.182	0.935	0.935	0.000	0.000	0.000	0.000
64	A	65	ILE	0	0.013	0.008	14.698	-1.212	-1.212	0.000	0.000	0.000	0.000
65	A	66	TYR	0	-0.057	-0.049	16.381	1.447	1.447	0.000	0.000	0.000	0.000
66	A	67	ASP	-1	-0.755	-0.905	17.635	-13.562	-13.562	0.000	0.000	0.000	0.000
67	A	68	GLN	0	0.003	0.001	20.293	-0.496	-0.496	0.000	0.000	0.000	0.000
68	A	69	SER	0	-0.034	-0.007	21.467	0.403	0.403	0.000	0.000	0.000	0.000
69	A	70	ASN	0	-0.027	-0.003	20.607	-0.323	-0.323	0.000	0.000	0.000	0.000
70	A	71	ARG	1	0.946	0.963	22.239	11.758	11.758	0.000	0.000	0.000	0.000
71	A	72	VAL	0	-0.043	-0.013	21.010	-0.486	-0.486	0.000	0.000	0.000	0.000
72	A	73	ILE	0	0.022	0.005	19.238	0.582	0.582	0.000	0.000	0.000	0.000
73	A	74	TRP	0	0.006	0.001	15.864	0.016	0.016	0.000	0.000	0.000	0.000
74	A	75	GLN	0	0.003	-0.005	18.701	-0.474	-0.474	0.000	0.000	0.000	0.000
75	A	76	THR	0	0.021	0.003	16.774	0.423	0.423	0.000	0.000	0.000	0.000
76	A	77	LYS	1	0.927	0.971	19.766	11.995	11.995	0.000	0.000	0.000	0.000
77	A	78	THR	0	0.002	0.008	17.927	0.501	0.501	0.000	0.000	0.000	0.000
78	A	79	ASN	0	-0.059	-0.028	20.052	-0.657	-0.657	0.000	0.000	0.000	0.000
79	A	80	GLY	0	0.057	0.034	21.185	0.560	0.560	0.000	0.000	0.000	0.000
80	A	81	LYS	1	0.839	0.916	21.649	13.074	13.074	0.000	0.000	0.000	0.000
81	A	82	GLU	-1	-0.873	-0.949	20.879	-14.185	-14.185	0.000	0.000	0.000	0.000
82	A	83	ASP	-1	-0.833	-0.910	18.327	-13.992	-13.992	0.000	0.000	0.000	0.000
83	A	84	HIS	0	-0.049	-0.027	13.625	0.400	0.400	0.000	0.000	0.000	0.000
84	A	85	TYR	0	-0.019	-0.017	13.344	0.355	0.355	0.000	0.000	0.000	0.000
85	A	86	VAL	0	-0.040	-0.022	7.229	-1.326	-1.326	0.000	0.000	0.000	0.000
86	A	87	LEU	0	-0.004	0.016	8.485	1.497	1.497	0.000	0.000	0.000	0.000
87	A	88	VAL	0	-0.009	-0.023	6.755	-4.256	-4.256	0.000	0.000	0.000	0.000
88	A	89	LEU	0	-0.001	0.016	6.807	3.193	3.193	0.000	0.000	0.000	0.000
89	A	90	GLN	0	0.001	0.001	7.844	-3.461	-3.461	0.000	0.000	0.000	0.000
90	A	91	GLN	0	0.055	0.013	9.380	-0.247	-0.247	0.000	0.000	0.000	0.000
91	A	92	ASP	-1	-0.840	-0.916	11.724	-19.573	-19.573	0.000	0.000	0.000	0.000
92	A	93	ARG	1	0.845	0.915	12.704	19.790	19.790	0.000	0.000	0.000	0.000
93	A	94	ASN	0	-0.018	0.010	13.764	0.414	0.414	0.000	0.000	0.000	0.000
94	A	95	VAL	0	-0.009	-0.025	10.969	-2.567	-2.567	0.000	0.000	0.000	0.000
95	A	96	VAL	0	-0.015	0.010	11.517	1.704	1.704	0.000	0.000	0.000	0.000
96	A	97	ILE	0	-0.003	-0.008	11.278	-1.938	-1.938	0.000	0.000	0.000	0.000
97	A	98	TYR	0	-0.040	-0.036	11.221	1.815	1.815	0.000	0.000	0.000	0.000
98	A	99	GLY	0	0.046	0.021	13.449	-0.922	-0.922	0.000	0.000	0.000	0.000
99	A	100	PRO	0	-0.052	-0.023	15.959	0.594	0.594	0.000	0.000	0.000	0.000
100	A	101	VAL	0	0.000	-0.014	14.952	-0.343	-0.343	0.000	0.000	0.000	0.000
101	A	102	VAL	0	-0.024	0.001	17.217	0.752	0.752	0.000	0.000	0.000	0.000
102	A	103	TRP	0	0.005	-0.016	15.632	0.384	0.384	0.000	0.000	0.000	0.000
103	A	104	ALA	0	0.012	0.002	15.285	-1.034	-1.034	0.000	0.000	0.000	0.000
104	A	105	THR	0	0.006	0.012	14.218	0.705	0.705	0.000	0.000	0.000	0.000
105	A	106	GLY	0	0.004	0.010	16.595	0.558	0.558	0.000	0.000	0.000	0.000
106	A	107	SER	0	-0.075	-0.048	14.163	-0.092	-0.092	0.000	0.000	0.000	0.000
107	A	108	GLY	0	0.053	0.036	12.980	-0.732	-0.732	0.000	0.000	0.000	0.000
108	A	109	PRO	0	-0.094	-0.055	12.537	0.288	0.288	0.000	0.000	0.000	0.000
109	A	110	ALA	-1	-0.920	-0.943	12.880	-18.618	-18.618	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:VAL)