FMO DATABASE

FMODB ID: 9R7Y2

Calculation Name: 2I2S-A-Xray547

Preferred Name:

Target Type:

Ligand Name: 2-o-methyl-5-n-acetyl-alpha-d-neuraminic acid | sulfate ion | (4s)-2-methyl-2,4-pentanediol | glycerol

Ligand 3-letter code: MNA | SO4 | MPD | GOL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2I2S

Chain ID: A

ChEMBL ID:

UniProt ID: P0C6Y8

Base Structure: X-ray

Registration Date: 2025-10-05

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	163
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1698446.74572
FMO2-HF: Nuclear repulsion	1633943.879778
FMO2-HF: Total energy	-64502.865942
FMO2-MP2: Total energy	-64692.228417

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:62:GLY)

Summations of interaction energy for fragment #1(A:62:GLY)

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.
-85.036	-82.01	0	-1.526	-1.499	-0.009

Interaction energy analysis for fragmet #1(A:62:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.879 / q_NPA : 0.920

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	64	LEU	0	-0.007	0.014	3.580	7.240	9.038	-0.006	-0.831	-0.961	-0.004
4	A	65	LEU	0	-0.032	-0.012	3.848	8.314	8.606	-0.001	-0.072	-0.219	0.000
5	A	66	ASP	-1	-0.872	-0.923	3.301	-60.748	-59.812	0.007	-0.623	-0.319	-0.005
6	A	67	GLY	0	-0.012	0.006	5.816	5.597	5.597	0.000	0.000	0.000	0.000
7	A	68	PRO	0	-0.044	-0.032	5.634	-7.455	-7.455	0.000	0.000	0.000	0.000
8	A	69	TYR	0	-0.053	-0.028	8.746	0.066	0.066	0.000	0.000	0.000	0.000
9	A	70	GLN	0	0.037	0.018	12.064	1.576	1.576	0.000	0.000	0.000	0.000
10	A	71	PRO	0	-0.015	0.001	15.475	0.134	0.134	0.000	0.000	0.000	0.000
11	A	72	THR	0	0.024	0.015	17.456	0.666	0.666	0.000	0.000	0.000	0.000
12	A	73	THR	0	-0.029	-0.027	20.082	0.035	0.035	0.000	0.000	0.000	0.000
13	A	74	PHE	0	-0.021	-0.020	17.011	-0.327	-0.327	0.000	0.000	0.000	0.000
14	A	75	ASN	0	-0.028	-0.039	20.900	0.122	0.122	0.000	0.000	0.000	0.000
15	A	76	PRO	0	0.006	0.027	17.359	-0.280	-0.280	0.000	0.000	0.000	0.000
16	A	77	PRO	0	0.035	0.018	16.284	0.973	0.973	0.000	0.000	0.000	0.000
17	A	78	THR	0	-0.009	-0.010	18.944	-0.299	-0.299	0.000	0.000	0.000	0.000
18	A	79	SER	0	-0.049	-0.039	18.983	-0.269	-0.269	0.000	0.000	0.000	0.000
19	A	80	TYR	0	0.004	-0.002	11.989	-0.357	-0.357	0.000	0.000	0.000	0.000
20	A	81	TRP	0	-0.065	-0.042	13.885	1.390	1.390	0.000	0.000	0.000	0.000
21	A	82	ILE	0	-0.008	-0.004	12.962	-1.844	-1.844	0.000	0.000	0.000	0.000
22	A	83	LEU	0	0.012	0.000	9.869	1.408	1.408	0.000	0.000	0.000	0.000
23	A	84	LEU	0	-0.007	-0.014	12.355	-1.299	-1.299	0.000	0.000	0.000	0.000
24	A	85	ALA	0	0.051	0.013	13.105	0.203	0.203	0.000	0.000	0.000	0.000
25	A	86	PRO	0	0.007	0.011	15.213	0.350	0.350	0.000	0.000	0.000	0.000
26	A	87	THR	0	0.016	0.007	18.858	0.207	0.207	0.000	0.000	0.000	0.000
27	A	88	VAL	0	-0.007	-0.006	20.856	0.324	0.324	0.000	0.000	0.000	0.000
28	A	89	GLU	-1	-0.869	-0.919	24.148	-10.828	-10.828	0.000	0.000	0.000	0.000
29	A	90	GLY	0	0.043	0.029	26.903	0.013	0.013	0.000	0.000	0.000	0.000
30	A	91	VAL	0	-0.042	-0.036	25.471	-0.066	-0.066	0.000	0.000	0.000	0.000
31	A	92	VAL	0	0.010	0.011	20.001	-0.309	-0.309	0.000	0.000	0.000	0.000
32	A	93	ILE	0	-0.004	-0.010	19.017	-0.651	-0.651	0.000	0.000	0.000	0.000
33	A	94	GLN	0	0.035	0.028	22.404	0.877	0.877	0.000	0.000	0.000	0.000
34	A	95	GLY	0	0.020	-0.001	24.185	-0.553	-0.553	0.000	0.000	0.000	0.000
35	A	96	THR	0	-0.032	-0.034	26.053	0.481	0.481	0.000	0.000	0.000	0.000
36	A	97	ASN	0	0.009	-0.020	28.659	-0.196	-0.196	0.000	0.000	0.000	0.000
37	A	98	ASN	0	-0.074	-0.036	31.027	0.254	0.254	0.000	0.000	0.000	0.000
38	A	99	ILE	0	-0.010	-0.002	34.010	0.301	0.301	0.000	0.000	0.000	0.000
39	A	100	ASP	-1	-0.794	-0.866	34.620	-9.002	-9.002	0.000	0.000	0.000	0.000
40	A	101	ARG	1	0.857	0.923	30.087	9.955	9.955	0.000	0.000	0.000	0.000
41	A	102	TRP	0	-0.013	0.027	31.121	-0.204	-0.204	0.000	0.000	0.000	0.000
42	A	103	LEU	0	-0.014	-0.010	26.536	0.277	0.277	0.000	0.000	0.000	0.000
43	A	104	ALA	0	0.015	-0.002	26.096	-0.309	-0.309	0.000	0.000	0.000	0.000
44	A	105	THR	0	-0.002	0.009	23.212	0.101	0.101	0.000	0.000	0.000	0.000
45	A	106	ILE	0	-0.039	-0.011	25.149	-0.223	-0.223	0.000	0.000	0.000	0.000
46	A	107	LEU	0	0.010	-0.004	22.211	-0.195	-0.195	0.000	0.000	0.000	0.000
47	A	108	ILE	0	-0.003	0.004	26.056	0.282	0.282	0.000	0.000	0.000	0.000
48	A	109	GLU	-1	-0.697	-0.820	27.828	-10.639	-10.639	0.000	0.000	0.000	0.000
49	A	110	PRO	0	-0.017	-0.014	27.875	0.292	0.292	0.000	0.000	0.000	0.000
50	A	111	ASN	0	-0.033	-0.024	30.829	0.372	0.372	0.000	0.000	0.000	0.000
51	A	112	VAL	0	-0.056	0.012	32.627	0.267	0.267	0.000	0.000	0.000	0.000
52	A	113	GLN	0	0.038	0.004	35.275	0.090	0.090	0.000	0.000	0.000	0.000
53	A	114	THR	0	-0.023	-0.030	38.287	-0.048	-0.048	0.000	0.000	0.000	0.000
54	A	115	THR	0	-0.006	0.002	37.175	0.292	0.292	0.000	0.000	0.000	0.000
55	A	116	ASN	0	-0.026	-0.013	38.190	-0.242	-0.242	0.000	0.000	0.000	0.000
56	A	117	ARG	1	0.784	0.851	31.357	9.821	9.821	0.000	0.000	0.000	0.000
57	A	118	ILE	0	-0.007	-0.002	35.967	0.054	0.054	0.000	0.000	0.000	0.000
58	A	119	TYR	0	0.054	0.023	29.976	-0.321	-0.321	0.000	0.000	0.000	0.000
59	A	120	ASN	0	-0.014	-0.017	30.689	0.501	0.501	0.000	0.000	0.000	0.000
60	A	121	LEU	0	0.031	0.012	29.296	-0.439	-0.439	0.000	0.000	0.000	0.000
61	A	122	PHE	0	-0.034	-0.046	28.909	0.343	0.343	0.000	0.000	0.000	0.000
62	A	123	GLY	0	0.016	0.020	31.542	0.194	0.194	0.000	0.000	0.000	0.000
63	A	124	GLN	0	-0.033	-0.008	33.271	0.217	0.217	0.000	0.000	0.000	0.000
64	A	125	GLN	0	0.021	0.008	34.636	-0.082	-0.082	0.000	0.000	0.000	0.000
65	A	126	VAL	0	-0.019	-0.009	35.000	0.243	0.243	0.000	0.000	0.000	0.000
66	A	127	THR	0	-0.008	0.003	36.145	-0.136	-0.136	0.000	0.000	0.000	0.000
67	A	128	LEU	0	-0.030	-0.014	33.206	0.086	0.086	0.000	0.000	0.000	0.000
68	A	129	SER	0	0.025	0.018	37.144	-0.078	-0.078	0.000	0.000	0.000	0.000
69	A	130	VAL	0	-0.038	-0.016	33.286	-0.191	-0.191	0.000	0.000	0.000	0.000
70	A	131	GLU	-1	-0.842	-0.910	34.814	-8.189	-8.189	0.000	0.000	0.000	0.000
71	A	132	ASN	0	-0.064	-0.071	29.609	-0.162	-0.162	0.000	0.000	0.000	0.000
72	A	133	THR	0	0.038	0.018	33.206	-0.056	-0.056	0.000	0.000	0.000	0.000
73	A	134	SER	0	0.003	0.015	30.058	0.193	0.193	0.000	0.000	0.000	0.000
74	A	135	GLN	0	0.031	0.005	32.496	-0.130	-0.130	0.000	0.000	0.000	0.000
75	A	136	THR	0	-0.030	-0.018	29.209	-0.043	-0.043	0.000	0.000	0.000	0.000
76	A	137	GLN	0	-0.060	-0.018	25.363	-0.080	-0.080	0.000	0.000	0.000	0.000
77	A	138	TRP	0	0.068	0.026	24.274	0.403	0.403	0.000	0.000	0.000	0.000
78	A	139	LYS	1	0.862	0.945	26.168	9.736	9.736	0.000	0.000	0.000	0.000
79	A	140	PHE	0	0.009	0.008	20.246	0.081	0.081	0.000	0.000	0.000	0.000
80	A	141	ILE	0	-0.005	-0.017	25.784	0.371	0.371	0.000	0.000	0.000	0.000
81	A	142	ASP	-1	-0.723	-0.782	25.393	-12.802	-12.802	0.000	0.000	0.000	0.000
82	A	143	VAL	0	0.004	-0.010	28.106	0.527	0.527	0.000	0.000	0.000	0.000
83	A	144	SER	0	0.051	0.009	30.310	-0.309	-0.309	0.000	0.000	0.000	0.000
84	A	145	LYS	1	0.849	0.965	32.601	9.029	9.029	0.000	0.000	0.000	0.000
85	A	146	THR	0	0.001	-0.013	34.810	-0.175	-0.175	0.000	0.000	0.000	0.000
86	A	147	THR	0	0.041	0.019	36.995	0.147	0.147	0.000	0.000	0.000	0.000
87	A	148	PRO	0	0.026	0.025	37.703	-0.085	-0.085	0.000	0.000	0.000	0.000
88	A	149	THR	0	-0.016	-0.022	38.768	-0.115	-0.115	0.000	0.000	0.000	0.000
89	A	150	GLY	0	-0.001	0.026	40.213	0.152	0.152	0.000	0.000	0.000	0.000
90	A	151	ASN	0	0.008	-0.011	39.407	-0.163	-0.163	0.000	0.000	0.000	0.000
91	A	152	TYR	0	-0.001	-0.015	32.327	0.019	0.019	0.000	0.000	0.000	0.000
92	A	153	THR	0	-0.036	-0.027	35.565	0.210	0.210	0.000	0.000	0.000	0.000
93	A	154	GLN	0	-0.023	-0.024	32.956	-0.398	-0.398	0.000	0.000	0.000	0.000
94	A	155	HIS	0	-0.007	0.002	30.759	0.336	0.336	0.000	0.000	0.000	0.000
95	A	156	GLY	0	0.045	0.023	28.003	-0.154	-0.154	0.000	0.000	0.000	0.000
96	A	157	SER	0	-0.028	-0.010	27.039	-0.232	-0.232	0.000	0.000	0.000	0.000
97	A	158	LEU	0	-0.015	0.014	21.145	0.018	0.018	0.000	0.000	0.000	0.000
98	A	159	PHE	0	-0.034	-0.008	25.654	-0.016	-0.016	0.000	0.000	0.000	0.000
99	A	160	SER	0	0.058	0.009	20.656	-0.405	-0.405	0.000	0.000	0.000	0.000
100	A	161	THR	0	0.023	0.008	22.240	0.525	0.525	0.000	0.000	0.000	0.000
101	A	162	PRO	0	0.001	-0.001	17.018	0.068	0.068	0.000	0.000	0.000	0.000
102	A	163	LYS	1	0.820	0.922	17.899	14.434	14.434	0.000	0.000	0.000	0.000
103	A	164	LEU	0	0.013	0.022	13.064	-0.294	-0.294	0.000	0.000	0.000	0.000
104	A	165	TYR	0	-0.035	-0.045	16.715	0.871	0.871	0.000	0.000	0.000	0.000
105	A	166	ALA	0	0.025	0.004	15.521	-1.372	-1.372	0.000	0.000	0.000	0.000
106	A	167	VAL	0	0.006	0.005	17.262	1.165	1.165	0.000	0.000	0.000	0.000
107	A	168	MET	0	0.002	0.028	17.609	-1.207	-1.207	0.000	0.000	0.000	0.000
108	A	169	LYS	1	0.817	0.934	19.440	15.035	15.035	0.000	0.000	0.000	0.000
109	A	170	PHE	0	0.011	-0.031	21.531	-0.501	-0.501	0.000	0.000	0.000	0.000
110	A	171	SER	0	0.007	-0.003	23.589	0.339	0.339	0.000	0.000	0.000	0.000
111	A	172	GLY	0	0.046	0.031	27.108	0.324	0.324	0.000	0.000	0.000	0.000
112	A	173	ARG	1	0.865	0.938	26.693	11.355	11.355	0.000	0.000	0.000	0.000
113	A	174	ILE	0	0.018	0.015	23.397	-0.489	-0.489	0.000	0.000	0.000	0.000
114	A	175	TYR	0	-0.005	-0.003	21.865	0.727	0.727	0.000	0.000	0.000	0.000
115	A	176	THR	0	-0.022	-0.030	21.447	-0.546	-0.546	0.000	0.000	0.000	0.000
116	A	177	TYR	0	0.046	0.001	17.642	-0.265	-0.265	0.000	0.000	0.000	0.000
117	A	178	ASN	0	-0.044	-0.020	22.313	0.547	0.547	0.000	0.000	0.000	0.000
118	A	179	GLY	0	0.021	0.010	25.328	-0.188	-0.188	0.000	0.000	0.000	0.000
119	A	180	THR	0	0.014	-0.003	26.503	0.126	0.126	0.000	0.000	0.000	0.000
120	A	181	THR	0	-0.015	0.033	21.072	-0.086	-0.086	0.000	0.000	0.000	0.000
121	A	182	PRO	0	-0.041	-0.021	21.788	0.500	0.500	0.000	0.000	0.000	0.000
122	A	183	ASN	0	-0.034	-0.031	22.279	-0.397	-0.397	0.000	0.000	0.000	0.000
123	A	184	ALA	0	-0.028	-0.004	21.732	0.481	0.481	0.000	0.000	0.000	0.000
124	A	185	THR	0	0.015	-0.002	22.379	-0.373	-0.373	0.000	0.000	0.000	0.000
125	A	186	THR	0	0.032	0.014	20.866	0.114	0.114	0.000	0.000	0.000	0.000
126	A	187	GLY	0	0.035	0.031	23.466	0.617	0.617	0.000	0.000	0.000	0.000
127	A	188	TYR	0	-0.064	-0.051	24.980	-0.383	-0.383	0.000	0.000	0.000	0.000
128	A	189	TYR	0	-0.024	-0.027	26.601	0.745	0.745	0.000	0.000	0.000	0.000
129	A	190	SER	0	0.002	-0.004	29.056	-0.374	-0.374	0.000	0.000	0.000	0.000
130	A	191	THR	0	-0.046	-0.025	29.165	0.265	0.265	0.000	0.000	0.000	0.000
131	A	192	THR	0	0.008	-0.016	31.089	-0.214	-0.214	0.000	0.000	0.000	0.000
132	A	193	ASN	0	0.022	0.013	31.298	-0.099	-0.099	0.000	0.000	0.000	0.000
133	A	194	TYR	0	0.033	0.042	24.558	-0.411	-0.411	0.000	0.000	0.000	0.000
134	A	195	ASP	-1	-0.880	-0.947	25.109	-11.794	-11.794	0.000	0.000	0.000	0.000
135	A	196	THR	0	-0.019	-0.021	25.122	-0.375	-0.375	0.000	0.000	0.000	0.000
136	A	197	VAL	0	-0.034	0.007	24.872	-0.030	-0.030	0.000	0.000	0.000	0.000
137	A	198	ASN	0	0.025	0.022	24.136	-0.446	-0.446	0.000	0.000	0.000	0.000
138	A	199	MET	0	-0.017	-0.015	20.744	0.084	0.084	0.000	0.000	0.000	0.000
139	A	200	THR	0	-0.020	-0.012	21.849	0.175	0.175	0.000	0.000	0.000	0.000
140	A	201	SER	0	0.000	0.007	17.322	0.569	0.569	0.000	0.000	0.000	0.000
141	A	202	PHE	0	-0.012	-0.017	19.974	0.147	0.147	0.000	0.000	0.000	0.000
142	A	203	CYS	0	-0.055	-0.008	17.694	0.115	0.115	0.000	0.000	0.000	0.000
143	A	204	ASP	-1	-0.805	-0.907	12.825	-21.102	-21.102	0.000	0.000	0.000	0.000
144	A	205	PHE	0	-0.067	-0.039	12.501	0.380	0.380	0.000	0.000	0.000	0.000
145	A	206	TYR	0	0.036	0.015	6.184	-2.031	-2.031	0.000	0.000	0.000	0.000
146	A	207	ILE	0	-0.028	-0.007	8.408	3.823	3.823	0.000	0.000	0.000	0.000
147	A	208	ILE	0	0.031	0.014	8.173	-4.651	-4.651	0.000	0.000	0.000	0.000
148	A	209	PRO	0	0.030	0.012	9.874	2.824	2.824	0.000	0.000	0.000	0.000
149	A	210	ARG	1	1.001	1.001	13.012	15.051	15.051	0.000	0.000	0.000	0.000
150	A	211	ASN	0	-0.077	-0.042	13.283	0.237	0.237	0.000	0.000	0.000	0.000
151	A	212	GLN	0	0.026	0.009	10.049	0.661	0.661	0.000	0.000	0.000	0.000
152	A	213	GLU	-1	-0.821	-0.906	12.986	-17.076	-17.076	0.000	0.000	0.000	0.000
153	A	214	GLU	-1	-0.940	-0.951	15.465	-17.186	-17.186	0.000	0.000	0.000	0.000
154	A	215	LYS	1	0.879	0.920	8.959	28.072	28.072	0.000	0.000	0.000	0.000
155	A	216	CYS	0	-0.045	-0.010	12.438	-0.814	-0.814	0.000	0.000	0.000	0.000
156	A	217	THR	0	0.030	0.005	13.546	0.775	0.775	0.000	0.000	0.000	0.000
157	A	218	GLU	-1	-0.856	-0.899	12.217	-23.331	-23.331	0.000	0.000	0.000	0.000
158	A	219	TYR	0	0.053	0.012	6.801	0.298	0.298	0.000	0.000	0.000	0.000
159	A	220	ILE	0	-0.030	-0.007	13.629	0.825	0.825	0.000	0.000	0.000	0.000
160	A	221	ASN	0	-0.054	-0.036	16.814	1.705	1.705	0.000	0.000	0.000	0.000
161	A	222	HIS	0	-0.019	-0.024	15.689	1.108	1.108	0.000	0.000	0.000	0.000
162	A	223	GLY	0	-0.035	0.004	14.854	0.543	0.543	0.000	0.000	0.000	0.000
163	A	224	LEU	-1	-0.948	-0.971	8.341	-28.667	-28.667	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:62:GLY)