FMO DATABASE

FMODB ID: 5G32Z

Calculation Name: 1KJ2-B-Xray547

Preferred Name:

Target Type:

Ligand Name: n-acetyl-alpha-neuraminic acid | 2-acetamido-2-deoxy-beta-d-glucopyranose | beta-d-galactopyranose | alpha-d-mannopyranose

Ligand 3-letter code: SIA | NAG | GAL | MAN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1KJ2

Chain ID: B

ChEMBL ID:

UniProt ID: P01887

Base Structure: X-ray

Registration Date: 2025-10-06

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	116
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-997900.392178
FMO2-HF: Nuclear repulsion	950752.401724
FMO2-HF: Total energy	-47147.990454
FMO2-MP2: Total energy	-47284.489996

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:1:VAL)

Summations of interaction energy for fragment #1(B: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.
48.036	55.137	2.578	-3.8	-5.879	-0.042

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.864 / 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	B	3	LEU	0	0.041	0.026	2.495	1.728	4.421	0.372	-1.120	-1.945	-0.008
106	B	107	TYR	0	-0.014	-0.017	2.617	-16.418	-12.103	2.207	-2.674	-3.848	-0.034
108	B	109	GLY	0	0.013	0.009	4.741	-4.803	-4.710	-0.001	-0.006	-0.086	0.000
4	B	4	LEU	0	0.011	0.005	5.347	6.790	6.790	0.000	0.000	0.000	0.000
5	B	5	GLU	-1	-0.930	-0.956	6.046	-27.730	-27.730	0.000	0.000	0.000	0.000
6	B	6	GLN	0	-0.013	-0.021	8.400	0.521	0.521	0.000	0.000	0.000	0.000
7	B	7	ASN	0	-0.024	-0.001	10.088	-0.225	-0.225	0.000	0.000	0.000	0.000
8	B	8	PRO	0	0.008	0.008	12.808	0.849	0.849	0.000	0.000	0.000	0.000
9	B	9	ARG	1	1.014	1.007	8.690	24.083	24.083	0.000	0.000	0.000	0.000
10	B	10	TRP	0	-0.032	-0.021	12.696	-0.247	-0.247	0.000	0.000	0.000	0.000
11	B	11	ARG	1	0.924	0.955	16.261	13.905	13.905	0.000	0.000	0.000	0.000
12	B	12	LEU	0	0.043	0.053	19.799	-0.134	-0.134	0.000	0.000	0.000	0.000
13	B	13	VAL	0	0.006	-0.006	23.467	-0.174	-0.174	0.000	0.000	0.000	0.000
14	B	14	PRO	0	0.047	0.026	25.714	0.274	0.274	0.000	0.000	0.000	0.000
15	B	15	ARG	1	0.993	0.976	29.504	8.779	8.779	0.000	0.000	0.000	0.000
16	B	16	GLY	0	-0.021	0.015	30.504	0.103	0.103	0.000	0.000	0.000	0.000
17	B	17	GLN	0	-0.014	-0.012	29.083	0.180	0.180	0.000	0.000	0.000	0.000
18	B	18	ALA	0	0.004	0.010	26.784	-0.203	-0.203	0.000	0.000	0.000	0.000
19	B	19	VAL	0	-0.036	-0.010	20.914	-0.047	-0.047	0.000	0.000	0.000	0.000
20	B	20	ASN	0	-0.018	-0.009	22.082	-0.018	-0.018	0.000	0.000	0.000	0.000
21	B	21	LEU	0	-0.001	0.012	16.039	-0.171	-0.171	0.000	0.000	0.000	0.000
22	B	22	ARG	1	0.867	0.918	15.374	17.238	17.238	0.000	0.000	0.000	0.000
23	B	23	CYS	0	-0.059	-0.008	10.269	-0.318	-0.318	0.000	0.000	0.000	0.000
24	B	24	ILE	0	0.020	0.016	11.782	1.490	1.490	0.000	0.000	0.000	0.000
25	B	25	LEU	0	0.020	-0.008	9.673	-3.140	-3.140	0.000	0.000	0.000	0.000
26	B	26	LYS	1	0.920	0.967	7.966	36.802	36.802	0.000	0.000	0.000	0.000
27	B	27	ASN	0	-0.008	-0.025	8.837	3.677	3.677	0.000	0.000	0.000	0.000
28	B	28	SER	0	0.056	0.011	10.699	-0.209	-0.209	0.000	0.000	0.000	0.000
29	B	29	GLN	0	0.009	0.014	11.263	0.014	0.014	0.000	0.000	0.000	0.000
30	B	30	TYR	0	-0.034	-0.006	7.913	-0.349	-0.349	0.000	0.000	0.000	0.000
31	B	30	PRO	0	0.030	0.019	11.564	-0.441	-0.441	0.000	0.000	0.000	0.000
32	B	31	TRP	0	0.047	0.040	14.229	1.542	1.542	0.000	0.000	0.000	0.000
33	B	32	MET	0	-0.014	0.008	12.352	-2.334	-2.334	0.000	0.000	0.000	0.000
34	B	33	SER	0	0.013	0.013	13.304	2.319	2.319	0.000	0.000	0.000	0.000
35	B	34	TRP	0	-0.039	-0.018	13.519	-1.922	-1.922	0.000	0.000	0.000	0.000
36	B	35	TYR	0	0.050	0.018	13.843	1.081	1.081	0.000	0.000	0.000	0.000
37	B	36	GLN	0	0.062	0.055	15.869	-0.273	-0.273	0.000	0.000	0.000	0.000
38	B	37	GLN	0	-0.024	-0.004	15.364	-0.999	-0.999	0.000	0.000	0.000	0.000
39	B	38	ASP	-1	-0.785	-0.884	18.124	-12.914	-12.914	0.000	0.000	0.000	0.000
40	B	39	LEU	0	0.006	-0.011	20.610	-0.491	-0.491	0.000	0.000	0.000	0.000
41	B	40	GLN	0	-0.051	-0.012	22.615	0.147	0.147	0.000	0.000	0.000	0.000
42	B	41	LYS	1	0.887	0.942	19.248	13.857	13.857	0.000	0.000	0.000	0.000
43	B	42	GLN	0	0.035	0.009	19.472	-0.798	-0.798	0.000	0.000	0.000	0.000
44	B	43	LEU	0	-0.021	-0.009	14.502	-0.083	-0.083	0.000	0.000	0.000	0.000
45	B	44	GLN	0	0.007	-0.004	18.508	0.646	0.646	0.000	0.000	0.000	0.000
46	B	45	TRP	0	0.017	-0.004	17.390	-0.122	-0.122	0.000	0.000	0.000	0.000
47	B	46	LEU	0	-0.056	-0.017	18.541	0.848	0.848	0.000	0.000	0.000	0.000
48	B	47	PHE	0	0.032	0.000	18.907	0.764	0.764	0.000	0.000	0.000	0.000
49	B	48	THR	0	0.043	0.012	16.993	-0.892	-0.892	0.000	0.000	0.000	0.000
50	B	49	LEU	0	-0.011	0.005	18.100	0.822	0.822	0.000	0.000	0.000	0.000
51	B	50	ARG	1	0.908	0.950	17.896	14.659	14.659	0.000	0.000	0.000	0.000
52	B	51	SER	0	-0.014	-0.028	19.666	-0.518	-0.518	0.000	0.000	0.000	0.000
53	B	52	PRO	0	-0.014	-0.010	21.841	0.035	0.035	0.000	0.000	0.000	0.000
54	B	53	GLY	0	-0.001	0.007	23.624	0.499	0.499	0.000	0.000	0.000	0.000
55	B	54	ASP	-1	-0.815	-0.874	22.907	-12.975	-12.975	0.000	0.000	0.000	0.000
56	B	55	LYS	1	0.911	0.928	24.034	10.856	10.856	0.000	0.000	0.000	0.000
57	B	56	GLU	-1	-0.846	-0.912	24.200	-12.388	-12.388	0.000	0.000	0.000	0.000
58	B	57	VAL	0	-0.002	-0.006	25.315	-0.315	-0.315	0.000	0.000	0.000	0.000
59	B	58	LYS	1	0.830	0.915	23.718	12.848	12.848	0.000	0.000	0.000	0.000
60	B	59	SER	0	0.044	0.037	26.458	-0.324	-0.324	0.000	0.000	0.000	0.000
61	B	60	LEU	0	-0.002	-0.004	23.707	-0.060	-0.060	0.000	0.000	0.000	0.000
62	B	61	PRO	0	0.019	-0.004	27.552	0.141	0.141	0.000	0.000	0.000	0.000
63	B	62	GLY	0	0.016	0.020	26.864	-0.406	-0.406	0.000	0.000	0.000	0.000
64	B	63	ALA	0	-0.045	-0.031	24.468	-0.288	-0.288	0.000	0.000	0.000	0.000
65	B	64	ASP	-1	-0.797	-0.870	26.381	-10.153	-10.153	0.000	0.000	0.000	0.000
66	B	65	TYR	0	-0.038	-0.055	21.309	-0.473	-0.473	0.000	0.000	0.000	0.000
67	B	66	LEU	0	0.008	0.004	24.563	0.396	0.396	0.000	0.000	0.000	0.000
68	B	67	ALA	0	0.006	0.019	20.599	-0.435	-0.435	0.000	0.000	0.000	0.000
69	B	68	THR	0	-0.023	-0.042	21.146	0.702	0.702	0.000	0.000	0.000	0.000
70	B	69	ARG	1	0.775	0.897	16.251	17.147	17.147	0.000	0.000	0.000	0.000
71	B	70	VAL	0	-0.040	-0.023	20.450	0.690	0.690	0.000	0.000	0.000	0.000
72	B	71	THR	0	0.028	0.005	19.343	0.372	0.372	0.000	0.000	0.000	0.000
73	B	72	ASP	-1	-0.846	-0.927	18.622	-15.428	-15.428	0.000	0.000	0.000	0.000
74	B	73	THR	0	0.013	0.002	15.051	-0.921	-0.921	0.000	0.000	0.000	0.000
75	B	74	GLU	-1	-0.855	-0.886	14.862	-17.722	-17.722	0.000	0.000	0.000	0.000
76	B	75	LEU	0	0.033	0.022	14.593	1.169	1.169	0.000	0.000	0.000	0.000
77	B	76	ARG	1	0.901	0.933	16.584	13.648	13.648	0.000	0.000	0.000	0.000
78	B	77	LEU	0	0.012	0.013	18.078	0.174	0.174	0.000	0.000	0.000	0.000
79	B	78	GLN	0	-0.036	-0.017	20.115	0.210	0.210	0.000	0.000	0.000	0.000
80	B	79	VAL	0	0.007	-0.007	21.480	0.010	0.010	0.000	0.000	0.000	0.000
81	B	80	ALA	0	0.044	0.011	24.086	0.157	0.157	0.000	0.000	0.000	0.000
82	B	81	ASN	0	-0.016	-0.025	27.581	-0.094	-0.094	0.000	0.000	0.000	0.000
83	B	82	MET	0	-0.016	0.012	21.604	-0.075	-0.075	0.000	0.000	0.000	0.000
84	B	83	SER	0	-0.033	-0.007	27.253	0.013	0.013	0.000	0.000	0.000	0.000
85	B	84	GLN	0	0.022	0.006	26.173	-0.067	-0.067	0.000	0.000	0.000	0.000
86	B	85	GLY	0	0.024	0.013	23.142	-0.324	-0.324	0.000	0.000	0.000	0.000
87	B	86	ARG	1	0.810	0.895	19.991	12.963	12.963	0.000	0.000	0.000	0.000
88	B	87	THR	0	-0.056	-0.019	13.641	-0.064	-0.064	0.000	0.000	0.000	0.000
89	B	90	LEU	0	0.052	0.027	15.250	0.148	0.148	0.000	0.000	0.000	0.000
90	B	91	TYR	0	-0.017	-0.008	9.844	-1.372	-1.372	0.000	0.000	0.000	0.000
91	B	93	THR	0	-0.027	-0.019	8.822	-2.333	-2.333	0.000	0.000	0.000	0.000
92	B	94	CYS	0	-0.033	-0.023	7.521	0.717	0.717	0.000	0.000	0.000	0.000
93	B	95	SER	0	0.024	-0.001	9.093	-2.718	-2.718	0.000	0.000	0.000	0.000
94	B	96	ALA	0	-0.004	-0.010	11.289	1.122	1.122	0.000	0.000	0.000	0.000
95	B	97	ALA	0	-0.004	0.003	13.491	1.391	1.391	0.000	0.000	0.000	0.000
96	B	98	PRO	0	-0.019	-0.013	15.044	-1.166	-1.166	0.000	0.000	0.000	0.000
97	B	99	ASP	-1	-0.911	-0.946	16.637	-16.529	-16.529	0.000	0.000	0.000	0.000
98	B	100	TRP	0	0.012	0.029	12.175	0.215	0.215	0.000	0.000	0.000	0.000
99	B	101	GLY	0	0.044	0.027	9.803	-0.668	-0.668	0.000	0.000	0.000	0.000
100	B	102	ALA	0	-0.022	-0.033	6.228	0.933	0.933	0.000	0.000	0.000	0.000
101	B	103	SER	0	-0.046	-0.026	7.298	0.935	0.935	0.000	0.000	0.000	0.000
102	B	104	ALA	0	-0.038	-0.026	8.051	0.584	0.584	0.000	0.000	0.000	0.000
103	B	105	GLU	-1	-0.878	-0.929	9.827	-19.184	-19.184	0.000	0.000	0.000	0.000
104	B	105	THR	0	-0.001	0.004	9.462	1.706	1.706	0.000	0.000	0.000	0.000
105	B	106	LEU	0	0.007	0.007	9.109	-3.444	-3.444	0.000	0.000	0.000	0.000
107	B	108	PHE	0	0.035	0.012	6.875	0.984	0.984	0.000	0.000	0.000	0.000
109	B	110	SER	0	-0.045	-0.042	5.760	2.505	2.505	0.000	0.000	0.000	0.000
110	B	111	GLY	0	0.005	0.015	7.796	2.263	2.263	0.000	0.000	0.000	0.000
111	B	112	THR	0	-0.033	-0.037	10.498	-0.370	-0.370	0.000	0.000	0.000	0.000
112	B	113	ARG	1	0.947	0.980	13.635	16.071	16.071	0.000	0.000	0.000	0.000
113	B	114	LEU	0	-0.018	-0.012	16.117	0.313	0.313	0.000	0.000	0.000	0.000
114	B	115	THR	0	-0.005	-0.012	19.695	-0.031	-0.031	0.000	0.000	0.000	0.000
115	B	116	VAL	0	-0.003	-0.008	22.819	-0.004	-0.004	0.000	0.000	0.000	0.000
116	B	117	LEU	-1	-0.877	-0.936	26.408	-10.695	-10.695	0.000	0.000	0.000	0.000

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