FMO DATABASE

FMODB ID: 652VZ

Calculation Name: 1KQR-A-Xray549

Preferred Name:

Target Type:

Ligand Name: 2-o-methyl-5-n-acetyl-alpha-d-neuraminic acid | glycerol

Ligand 3-letter code: MNA | GOL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1KQR

Chain ID: A

ChEMBL ID:

UniProt ID: P12473

Base Structure: X-ray

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	160
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1647273.502973
FMO2-HF: Nuclear repulsion	1583683.207925
FMO2-HF: Total energy	-63590.295048
FMO2-MP2: Total energy	-63775.539419

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:65:LEU)

Summations of interaction energy for fragment #1(A:65:LEU)

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.
-198.501	-186.412	12.131	-7.875	-16.345	-0.067

Interaction energy analysis for fragmet #1(A:65:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.812 / q_NPA : 0.908

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	67	GLY	0	0.045	0.043	3.851	1.643	3.335	-0.009	-0.676	-1.006	0.000
4	A	68	PRO	0	-0.062	-0.032	4.749	-2.564	-2.497	-0.001	-0.010	-0.056	0.000
19	A	83	LEU	0	0.010	-0.004	2.813	2.401	2.897	0.211	-0.115	-0.593	0.000
142	A	206	TYR	0	0.050	0.016	2.322	-1.964	-0.714	4.053	-1.376	-3.927	-0.012
143	A	207	ILE	0	-0.029	-0.007	3.911	4.649	5.060	0.002	-0.095	-0.318	0.000
144	A	208	ILE	0	-0.016	-0.014	2.225	-23.504	-21.128	3.676	-2.346	-3.706	-0.016
145	A	209	PRO	0	0.040	0.035	3.909	8.488	8.675	0.001	-0.049	-0.138	0.000
148	A	212	GLU	-1	-0.938	-0.973	2.669	-85.283	-82.421	0.333	-1.684	-1.511	-0.019
151	A	215	THR	0	0.023	0.011	4.335	1.597	1.720	-0.001	-0.013	-0.109	0.000
155	A	219	TYR	0	0.006	-0.005	2.319	-7.662	-5.562	3.112	-1.321	-3.891	-0.019
160	A	224	LEU	-1	-0.948	-0.968	2.476	-32.576	-32.051	0.754	-0.190	-1.090	-0.001
5	A	69	TYR	0	-0.109	-0.084	6.573	4.413	4.413	0.000	0.000	0.000	0.000
6	A	70	GLN	0	0.035	0.009	9.658	0.986	0.986	0.000	0.000	0.000	0.000
7	A	71	PRO	0	-0.009	0.007	12.685	-0.323	-0.323	0.000	0.000	0.000	0.000
8	A	72	THR	0	0.005	0.002	13.932	1.069	1.069	0.000	0.000	0.000	0.000
9	A	73	THR	0	-0.015	0.009	16.015	-0.104	-0.104	0.000	0.000	0.000	0.000
10	A	74	PHE	0	0.000	-0.005	10.755	0.329	0.329	0.000	0.000	0.000	0.000
11	A	75	ASN	0	0.019	0.006	16.837	-0.218	-0.218	0.000	0.000	0.000	0.000
12	A	76	PRO	0	0.002	0.022	11.935	-0.540	-0.540	0.000	0.000	0.000	0.000
13	A	77	PRO	0	0.018	0.014	10.967	1.551	1.551	0.000	0.000	0.000	0.000
14	A	78	VAL	0	0.006	-0.002	13.062	-0.393	-0.393	0.000	0.000	0.000	0.000
15	A	79	ASP	-1	-0.849	-0.925	12.835	-20.824	-20.824	0.000	0.000	0.000	0.000
16	A	80	TYR	0	0.009	0.007	6.172	-0.988	-0.988	0.000	0.000	0.000	0.000
17	A	81	TRP	0	-0.064	-0.048	7.106	3.669	3.669	0.000	0.000	0.000	0.000
18	A	82	MET	0	-0.030	-0.004	6.407	-3.972	-3.972	0.000	0.000	0.000	0.000
20	A	84	LEU	0	-0.021	-0.022	5.890	-0.981	-0.981	0.000	0.000	0.000	0.000
21	A	85	ALA	0	0.046	0.011	7.229	0.218	0.218	0.000	0.000	0.000	0.000
22	A	86	PRO	0	-0.005	0.003	9.148	1.000	1.000	0.000	0.000	0.000	0.000
23	A	87	THR	0	0.029	0.005	13.017	0.356	0.356	0.000	0.000	0.000	0.000
24	A	88	ALA	0	-0.018	-0.004	15.282	0.675	0.675	0.000	0.000	0.000	0.000
25	A	89	ALA	0	0.024	0.012	17.533	-0.571	-0.571	0.000	0.000	0.000	0.000
26	A	90	GLY	0	-0.001	0.003	20.080	0.197	0.197	0.000	0.000	0.000	0.000
27	A	91	VAL	0	-0.004	-0.007	19.076	-0.376	-0.376	0.000	0.000	0.000	0.000
28	A	92	VAL	0	-0.001	0.005	13.124	-0.255	-0.255	0.000	0.000	0.000	0.000
29	A	93	VAL	0	0.016	-0.007	13.589	-0.774	-0.774	0.000	0.000	0.000	0.000
30	A	94	GLU	-1	-0.826	-0.902	15.756	-12.063	-12.063	0.000	0.000	0.000	0.000
31	A	95	GLY	0	0.054	0.017	18.222	-0.601	-0.601	0.000	0.000	0.000	0.000
32	A	96	THR	0	-0.036	-0.036	19.716	0.591	0.591	0.000	0.000	0.000	0.000
33	A	97	ASN	0	-0.007	-0.015	22.848	-0.103	-0.103	0.000	0.000	0.000	0.000
34	A	98	ASN	0	-0.083	-0.041	24.913	0.516	0.516	0.000	0.000	0.000	0.000
35	A	99	THR	0	-0.017	-0.017	27.941	0.388	0.388	0.000	0.000	0.000	0.000
36	A	100	ASP	-1	-0.782	-0.851	27.421	-10.810	-10.810	0.000	0.000	0.000	0.000
37	A	101	ARG	1	0.857	0.919	22.668	11.945	11.945	0.000	0.000	0.000	0.000
38	A	102	TRP	0	0.002	0.033	24.067	-0.077	-0.077	0.000	0.000	0.000	0.000
39	A	103	LEU	0	-0.030	-0.019	17.966	0.338	0.338	0.000	0.000	0.000	0.000
40	A	104	ALA	0	0.077	0.034	19.749	-0.397	-0.397	0.000	0.000	0.000	0.000
41	A	105	THR	0	-0.027	-0.010	15.687	0.260	0.260	0.000	0.000	0.000	0.000
42	A	106	ILE	0	-0.024	-0.011	18.184	-0.159	-0.159	0.000	0.000	0.000	0.000
43	A	107	LEU	0	-0.023	-0.004	15.474	-0.094	-0.094	0.000	0.000	0.000	0.000
44	A	108	VAL	0	-0.011	-0.011	18.915	0.452	0.452	0.000	0.000	0.000	0.000
45	A	109	GLU	-1	-0.746	-0.873	21.082	-11.802	-11.802	0.000	0.000	0.000	0.000
46	A	110	PRO	0	-0.009	0.002	21.470	0.216	0.216	0.000	0.000	0.000	0.000
47	A	111	ASN	0	-0.062	-0.030	24.197	0.363	0.363	0.000	0.000	0.000	0.000
48	A	112	VAL	0	-0.016	0.023	26.290	0.250	0.250	0.000	0.000	0.000	0.000
49	A	113	THR	0	0.027	0.002	28.938	0.046	0.046	0.000	0.000	0.000	0.000
50	A	114	SER	0	-0.045	-0.030	31.693	-0.187	-0.187	0.000	0.000	0.000	0.000
51	A	115	GLU	-1	-0.778	-0.867	29.826	-9.110	-9.110	0.000	0.000	0.000	0.000
52	A	116	THR	0	-0.038	-0.022	31.678	-0.210	-0.210	0.000	0.000	0.000	0.000
53	A	117	ARG	1	0.769	0.868	25.030	10.625	10.625	0.000	0.000	0.000	0.000
54	A	118	SER	0	0.008	-0.008	30.314	0.062	0.062	0.000	0.000	0.000	0.000
55	A	119	TYR	0	0.012	-0.003	23.867	-0.361	-0.361	0.000	0.000	0.000	0.000
56	A	120	THR	0	-0.022	-0.011	25.378	0.392	0.392	0.000	0.000	0.000	0.000
57	A	121	LEU	0	0.003	0.001	23.249	-0.499	-0.499	0.000	0.000	0.000	0.000
58	A	122	PHE	0	0.010	-0.020	22.492	0.470	0.470	0.000	0.000	0.000	0.000
59	A	123	GLY	0	-0.030	-0.005	25.487	0.329	0.329	0.000	0.000	0.000	0.000
60	A	124	THR	0	-0.023	-0.008	27.333	0.461	0.461	0.000	0.000	0.000	0.000
61	A	125	GLN	0	-0.036	-0.016	28.782	-0.302	-0.302	0.000	0.000	0.000	0.000
62	A	126	GLU	-1	-0.836	-0.924	28.581	-9.317	-9.317	0.000	0.000	0.000	0.000
63	A	127	GLN	0	-0.018	-0.003	30.033	-0.206	-0.206	0.000	0.000	0.000	0.000
64	A	128	ILE	0	0.000	-0.001	27.114	0.015	0.015	0.000	0.000	0.000	0.000
65	A	129	THR	0	-0.016	-0.017	30.084	0.008	0.008	0.000	0.000	0.000	0.000
66	A	130	ILE	0	-0.050	-0.012	26.126	-0.272	-0.272	0.000	0.000	0.000	0.000
67	A	131	ALA	0	0.061	0.019	27.674	0.338	0.338	0.000	0.000	0.000	0.000
68	A	132	ASN	0	-0.087	-0.067	23.115	-0.289	-0.289	0.000	0.000	0.000	0.000
69	A	133	ALA	0	0.029	0.017	26.600	0.173	0.173	0.000	0.000	0.000	0.000
70	A	134	SER	0	0.031	0.034	23.705	0.252	0.252	0.000	0.000	0.000	0.000
71	A	135	GLN	0	-0.007	-0.009	25.929	-0.079	-0.079	0.000	0.000	0.000	0.000
72	A	136	THR	0	-0.029	-0.031	23.777	0.021	0.021	0.000	0.000	0.000	0.000
73	A	137	GLN	0	-0.026	0.002	19.074	-0.143	-0.143	0.000	0.000	0.000	0.000
74	A	138	TRP	0	0.054	0.011	17.489	0.564	0.564	0.000	0.000	0.000	0.000
75	A	139	LYS	1	0.882	0.949	19.378	11.017	11.017	0.000	0.000	0.000	0.000
76	A	140	PHE	0	0.012	0.014	13.351	0.208	0.208	0.000	0.000	0.000	0.000
77	A	141	ILE	0	-0.021	-0.021	18.406	0.312	0.312	0.000	0.000	0.000	0.000
78	A	142	ASP	-1	-0.685	-0.772	18.169	-15.835	-15.835	0.000	0.000	0.000	0.000
79	A	143	VAL	0	0.007	-0.001	20.881	0.626	0.626	0.000	0.000	0.000	0.000
80	A	144	VAL	0	0.002	-0.011	22.647	-0.258	-0.258	0.000	0.000	0.000	0.000
81	A	145	LYS	1	0.880	0.962	25.259	10.398	10.398	0.000	0.000	0.000	0.000
82	A	146	THR	0	0.001	-0.013	27.497	-0.284	-0.284	0.000	0.000	0.000	0.000
83	A	147	THR	0	0.017	0.008	29.786	0.141	0.141	0.000	0.000	0.000	0.000
84	A	148	GLN	0	0.049	0.035	31.037	0.044	0.044	0.000	0.000	0.000	0.000
85	A	149	ASN	0	-0.016	-0.019	32.097	-0.216	-0.216	0.000	0.000	0.000	0.000
86	A	150	GLY	0	-0.016	0.016	33.157	0.222	0.222	0.000	0.000	0.000	0.000
87	A	151	SER	0	0.007	-0.015	32.330	-0.104	-0.104	0.000	0.000	0.000	0.000
88	A	152	TYR	0	-0.038	-0.023	26.246	-0.220	-0.220	0.000	0.000	0.000	0.000
89	A	153	SER	0	-0.027	-0.004	28.616	0.356	0.356	0.000	0.000	0.000	0.000
90	A	154	GLN	0	-0.042	-0.033	25.624	-0.567	-0.567	0.000	0.000	0.000	0.000
91	A	155	TYR	0	0.004	-0.001	23.570	0.330	0.330	0.000	0.000	0.000	0.000
92	A	156	GLY	0	-0.021	0.011	21.168	-0.526	-0.526	0.000	0.000	0.000	0.000
93	A	157	PRO	0	-0.014	-0.018	21.209	0.532	0.532	0.000	0.000	0.000	0.000
94	A	158	LEU	0	-0.011	-0.005	13.832	-0.225	-0.225	0.000	0.000	0.000	0.000
95	A	159	GLN	0	-0.030	-0.009	18.252	0.230	0.230	0.000	0.000	0.000	0.000
96	A	160	SER	0	0.052	0.008	13.623	-0.552	-0.552	0.000	0.000	0.000	0.000
97	A	161	THR	0	0.027	0.008	16.365	0.777	0.777	0.000	0.000	0.000	0.000
98	A	162	PRO	0	0.015	0.009	11.402	0.487	0.487	0.000	0.000	0.000	0.000
99	A	163	LYS	1	0.812	0.927	11.839	14.992	14.992	0.000	0.000	0.000	0.000
100	A	164	LEU	0	0.019	0.022	6.423	-0.254	-0.254	0.000	0.000	0.000	0.000
101	A	165	TYR	0	-0.041	-0.060	9.685	1.262	1.262	0.000	0.000	0.000	0.000
102	A	166	ALA	0	0.020	0.011	8.201	-1.772	-1.772	0.000	0.000	0.000	0.000
103	A	167	VAL	0	-0.002	-0.001	10.066	1.961	1.961	0.000	0.000	0.000	0.000
104	A	168	MET	0	0.016	0.033	10.699	-2.177	-2.177	0.000	0.000	0.000	0.000
105	A	169	LYS	1	0.784	0.904	12.752	19.513	19.513	0.000	0.000	0.000	0.000
106	A	170	HIS	0	-0.018	-0.052	15.427	-0.272	-0.272	0.000	0.000	0.000	0.000
107	A	171	ASN	0	0.017	0.010	17.341	0.722	0.722	0.000	0.000	0.000	0.000
108	A	172	GLY	0	0.008	0.001	20.908	0.612	0.612	0.000	0.000	0.000	0.000
109	A	173	LYS	1	0.839	0.932	20.069	14.225	14.225	0.000	0.000	0.000	0.000
110	A	174	ILE	0	0.030	0.026	16.566	-0.675	-0.675	0.000	0.000	0.000	0.000
111	A	175	TYR	0	0.003	-0.013	15.127	1.127	1.127	0.000	0.000	0.000	0.000
112	A	176	THR	0	-0.024	-0.036	14.203	-0.739	-0.739	0.000	0.000	0.000	0.000
113	A	177	TYR	0	0.085	0.028	10.108	0.124	0.124	0.000	0.000	0.000	0.000
114	A	178	ASN	0	-0.063	-0.039	14.572	0.461	0.461	0.000	0.000	0.000	0.000
115	A	179	GLY	0	0.054	0.042	17.392	-0.422	-0.422	0.000	0.000	0.000	0.000
116	A	180	GLU	-1	-0.885	-0.950	19.116	-11.989	-11.989	0.000	0.000	0.000	0.000
117	A	181	THR	0	-0.011	0.029	14.069	-0.241	-0.241	0.000	0.000	0.000	0.000
118	A	182	PRO	0	-0.043	-0.019	15.483	0.780	0.780	0.000	0.000	0.000	0.000
119	A	183	ASN	0	-0.049	-0.045	16.444	-0.423	-0.423	0.000	0.000	0.000	0.000
120	A	184	VAL	0	-0.020	0.007	12.873	0.633	0.633	0.000	0.000	0.000	0.000
121	A	185	THR	0	-0.035	-0.030	16.339	0.100	0.100	0.000	0.000	0.000	0.000
122	A	186	THR	0	-0.002	0.004	13.714	-0.133	-0.133	0.000	0.000	0.000	0.000
123	A	187	LYS	1	0.826	0.945	16.548	16.258	16.258	0.000	0.000	0.000	0.000
124	A	188	TYR	0	0.001	-0.017	18.161	-0.703	-0.703	0.000	0.000	0.000	0.000
125	A	189	TYR	0	-0.046	-0.040	19.421	1.085	1.085	0.000	0.000	0.000	0.000
126	A	190	SER	0	-0.002	-0.004	22.319	-0.532	-0.532	0.000	0.000	0.000	0.000
127	A	191	THR	0	-0.048	-0.019	22.236	0.351	0.351	0.000	0.000	0.000	0.000
128	A	192	THR	0	0.013	-0.023	24.592	-0.280	-0.280	0.000	0.000	0.000	0.000
129	A	193	ASN	0	-0.007	0.000	25.254	-0.143	-0.143	0.000	0.000	0.000	0.000
130	A	194	TYR	0	0.039	0.035	18.432	-0.419	-0.419	0.000	0.000	0.000	0.000
131	A	195	ASP	-1	-0.867	-0.943	19.132	-14.559	-14.559	0.000	0.000	0.000	0.000
132	A	196	SER	0	-0.056	-0.032	19.316	-0.488	-0.488	0.000	0.000	0.000	0.000
133	A	197	VAL	0	-0.026	-0.004	18.587	0.126	0.126	0.000	0.000	0.000	0.000
134	A	198	ASN	0	0.023	0.011	18.064	-1.188	-1.188	0.000	0.000	0.000	0.000
135	A	199	MET	0	-0.023	-0.008	14.242	0.585	0.585	0.000	0.000	0.000	0.000
136	A	200	THR	0	-0.001	-0.019	16.399	-0.225	-0.225	0.000	0.000	0.000	0.000
137	A	201	ALA	0	-0.017	-0.004	12.554	0.098	0.098	0.000	0.000	0.000	0.000
138	A	202	PHE	0	-0.026	-0.023	14.556	0.494	0.494	0.000	0.000	0.000	0.000
139	A	203	CYS	0	-0.093	-0.034	12.285	0.326	0.326	0.000	0.000	0.000	0.000
140	A	204	ASP	-1	-0.809	-0.909	8.778	-21.831	-21.831	0.000	0.000	0.000	0.000
141	A	205	PHE	0	-0.060	-0.037	6.852	-0.150	-0.150	0.000	0.000	0.000	0.000
146	A	210	ARG	1	0.959	0.974	6.893	19.577	19.577	0.000	0.000	0.000	0.000
147	A	211	GLU	-1	-0.927	-0.968	8.910	-27.434	-27.434	0.000	0.000	0.000	0.000
149	A	213	GLU	-1	-0.819	-0.907	6.676	-25.090	-25.090	0.000	0.000	0.000	0.000
150	A	214	SER	0	-0.037	-0.012	9.175	0.155	0.155	0.000	0.000	0.000	0.000
152	A	216	CYS	0	-0.057	-0.017	5.279	-0.534	-0.534	0.000	0.000	0.000	0.000
153	A	217	THR	0	0.024	-0.003	6.259	2.688	2.688	0.000	0.000	0.000	0.000
154	A	218	GLU	-1	-0.896	-0.934	8.228	-21.392	-21.392	0.000	0.000	0.000	0.000
156	A	220	ILE	0	-0.050	-0.016	6.818	2.366	2.366	0.000	0.000	0.000	0.000
157	A	221	ASN	0	0.004	-0.018	9.550	2.593	2.593	0.000	0.000	0.000	0.000
158	A	222	ASN	0	-0.074	-0.048	10.439	2.756	2.756	0.000	0.000	0.000	0.000
159	A	223	GLY	0	-0.024	0.004	8.880	1.338	1.338	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:65:LEU)