FMO DATABASE

FMODB ID: YRQZ2

Calculation Name: 1KNM-A-Xray547

Preferred Name:

Target Type:

Ligand Name: beta-d-glucopyranose | beta-d-galactopyranose

Ligand 3-letter code: BGC | GAL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1KNM

Chain ID: A

ChEMBL ID:

UniProt ID: P26514

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	126
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1039251.445306
FMO2-HF: Nuclear repulsion	990714.200666
FMO2-HF: Total energy	-48537.24464
FMO2-MP2: Total energy	-48675.383751

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:2:PRO)

Summations of interaction energy for fragment #1(A:2:PRO)

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.
-99.286	-96.41	0.543	-1.635	-1.784	-0.016

Interaction energy analysis for fragmet #1(A:2:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.828 / q_NPA : 0.899

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].
3	A	4	ALA	0	0.035	0.000	2.653	-9.781	-6.905	0.543	-1.635	-1.784	-0.016
4	A	5	ASP	-1	-0.901	-0.953	5.267	-39.534	-39.534	0.000	0.000	0.000	0.000
5	A	6	GLY	0	0.007	0.009	7.218	2.134	2.134	0.000	0.000	0.000	0.000
6	A	7	GLY	0	0.036	0.029	10.261	1.340	1.340	0.000	0.000	0.000	0.000
7	A	8	GLN	0	0.035	0.000	13.268	0.436	0.436	0.000	0.000	0.000	0.000
8	A	9	ILE	0	0.007	0.017	16.249	-0.403	-0.403	0.000	0.000	0.000	0.000
9	A	10	LYS	1	0.956	0.978	19.019	12.996	12.996	0.000	0.000	0.000	0.000
10	A	11	GLY	0	0.048	0.029	22.335	0.041	0.041	0.000	0.000	0.000	0.000
11	A	12	VAL	0	-0.050	-0.042	25.695	0.284	0.284	0.000	0.000	0.000	0.000
12	A	13	GLY	0	-0.009	-0.015	27.941	0.287	0.287	0.000	0.000	0.000	0.000
13	A	14	SER	0	-0.025	-0.011	28.182	0.227	0.227	0.000	0.000	0.000	0.000
14	A	15	GLY	0	-0.027	0.004	27.698	0.151	0.151	0.000	0.000	0.000	0.000
15	A	16	ARG	1	0.793	0.882	26.259	9.874	9.874	0.000	0.000	0.000	0.000
16	A	17	CYS	0	-0.102	-0.038	21.161	-0.544	-0.544	0.000	0.000	0.000	0.000
17	A	18	LEU	0	0.012	0.016	19.196	0.511	0.511	0.000	0.000	0.000	0.000
18	A	19	ASP	-1	-0.766	-0.869	20.316	-14.007	-14.007	0.000	0.000	0.000	0.000
19	A	20	VAL	0	0.004	0.000	19.618	0.470	0.470	0.000	0.000	0.000	0.000
20	A	21	PRO	0	0.017	0.011	22.560	-0.083	-0.083	0.000	0.000	0.000	0.000
21	A	22	ASP	-1	-0.912	-0.951	25.550	-11.136	-11.136	0.000	0.000	0.000	0.000
22	A	23	ALA	0	-0.045	-0.016	21.727	-0.130	-0.130	0.000	0.000	0.000	0.000
23	A	24	SER	0	-0.012	0.012	22.171	-0.489	-0.489	0.000	0.000	0.000	0.000
24	A	25	THR	0	0.017	-0.006	18.707	-0.264	-0.264	0.000	0.000	0.000	0.000
25	A	26	SER	0	-0.018	-0.008	20.739	-0.326	-0.326	0.000	0.000	0.000	0.000
26	A	27	ASP	-1	-0.794	-0.880	21.167	-14.930	-14.930	0.000	0.000	0.000	0.000
27	A	28	GLY	0	-0.022	-0.006	23.544	0.574	0.574	0.000	0.000	0.000	0.000
28	A	29	THR	0	-0.079	-0.052	24.095	0.664	0.664	0.000	0.000	0.000	0.000
29	A	30	GLN	0	-0.062	-0.047	24.798	-0.237	-0.237	0.000	0.000	0.000	0.000
30	A	31	LEU	0	0.007	0.004	20.863	-0.039	-0.039	0.000	0.000	0.000	0.000
31	A	32	GLN	0	-0.017	-0.034	24.973	1.020	1.020	0.000	0.000	0.000	0.000
32	A	33	LEU	0	-0.012	0.002	24.936	-0.535	-0.535	0.000	0.000	0.000	0.000
33	A	34	TRP	0	0.003	-0.007	25.207	0.511	0.511	0.000	0.000	0.000	0.000
34	A	35	ASP	-1	-0.791	-0.870	25.750	-10.604	-10.604	0.000	0.000	0.000	0.000
35	A	37	HIS	0	0.007	0.016	21.455	-0.036	-0.036	0.000	0.000	0.000	0.000
36	A	38	SER	0	0.027	0.008	17.820	-0.314	-0.314	0.000	0.000	0.000	0.000
37	A	39	GLY	0	0.036	0.027	17.109	-1.030	-1.030	0.000	0.000	0.000	0.000
38	A	40	THR	0	0.008	-0.015	14.281	0.107	0.107	0.000	0.000	0.000	0.000
39	A	41	ASN	0	-0.028	-0.018	15.956	-1.140	-1.140	0.000	0.000	0.000	0.000
40	A	42	GLN	0	-0.024	-0.027	17.859	0.373	0.373	0.000	0.000	0.000	0.000
41	A	43	GLN	0	-0.094	-0.039	12.394	-1.675	-1.675	0.000	0.000	0.000	0.000
42	A	44	TRP	0	0.016	-0.006	13.405	-1.045	-1.045	0.000	0.000	0.000	0.000
43	A	45	ALA	0	0.027	0.012	7.965	0.070	0.070	0.000	0.000	0.000	0.000
44	A	46	ALA	0	-0.027	-0.006	9.377	1.709	1.709	0.000	0.000	0.000	0.000
45	A	47	THR	0	-0.022	-0.040	7.465	-2.915	-2.915	0.000	0.000	0.000	0.000
46	A	48	ASP	-1	-0.891	-0.945	7.790	-28.395	-28.395	0.000	0.000	0.000	0.000
47	A	49	ALA	0	-0.062	-0.022	10.477	1.901	1.901	0.000	0.000	0.000	0.000
48	A	50	GLY	0	0.015	-0.001	12.505	1.645	1.645	0.000	0.000	0.000	0.000
49	A	51	GLU	-1	-0.765	-0.826	10.741	-24.891	-24.891	0.000	0.000	0.000	0.000
50	A	52	LEU	0	-0.018	-0.018	12.637	-0.755	-0.755	0.000	0.000	0.000	0.000
51	A	53	ARG	1	0.789	0.852	8.931	28.975	28.975	0.000	0.000	0.000	0.000
52	A	54	VAL	0	0.029	0.026	12.454	-0.400	-0.400	0.000	0.000	0.000	0.000
53	A	55	TYR	0	-0.007	-0.034	13.751	-0.275	-0.275	0.000	0.000	0.000	0.000
54	A	56	GLY	0	-0.012	0.016	9.527	-0.561	-0.561	0.000	0.000	0.000	0.000
55	A	57	ASP	-1	-0.904	-0.970	10.136	-22.732	-22.732	0.000	0.000	0.000	0.000
56	A	58	LYS	1	0.851	0.928	12.395	17.942	17.942	0.000	0.000	0.000	0.000
57	A	59	CYS	0	-0.087	-0.026	13.705	-1.231	-1.231	0.000	0.000	0.000	0.000
58	A	60	LEU	0	0.020	0.012	16.020	1.149	1.149	0.000	0.000	0.000	0.000
59	A	61	ASP	-1	-0.804	-0.893	18.464	-14.104	-14.104	0.000	0.000	0.000	0.000
60	A	62	ALA	0	0.005	0.010	21.240	0.483	0.483	0.000	0.000	0.000	0.000
61	A	63	ALA	0	-0.009	-0.010	24.575	0.029	0.029	0.000	0.000	0.000	0.000
62	A	64	GLY	0	-0.015	-0.014	27.549	0.424	0.424	0.000	0.000	0.000	0.000
63	A	65	THR	0	0.010	0.000	27.981	-0.247	-0.247	0.000	0.000	0.000	0.000
64	A	66	SER	0	0.015	0.017	30.012	0.058	0.058	0.000	0.000	0.000	0.000
65	A	67	ASN	0	0.052	0.027	31.813	-0.486	-0.486	0.000	0.000	0.000	0.000
66	A	68	GLY	0	0.015	0.019	33.163	0.204	0.204	0.000	0.000	0.000	0.000
67	A	69	SER	0	-0.084	-0.037	30.083	-0.135	-0.135	0.000	0.000	0.000	0.000
68	A	70	LYS	1	0.975	0.978	28.650	10.390	10.390	0.000	0.000	0.000	0.000
69	A	71	VAL	0	0.022	0.022	23.065	-0.222	-0.222	0.000	0.000	0.000	0.000
70	A	72	GLN	0	-0.049	-0.046	23.854	0.710	0.710	0.000	0.000	0.000	0.000
71	A	73	ILE	0	0.025	0.023	19.052	-0.663	-0.663	0.000	0.000	0.000	0.000
72	A	74	TYR	0	-0.009	0.001	19.827	1.023	1.023	0.000	0.000	0.000	0.000
73	A	75	SER	0	0.031	0.027	16.955	-0.604	-0.604	0.000	0.000	0.000	0.000
74	A	77	TRP	0	-0.018	-0.006	15.705	-0.322	-0.322	0.000	0.000	0.000	0.000
75	A	78	GLY	0	0.034	0.022	16.078	0.238	0.238	0.000	0.000	0.000	0.000
76	A	79	GLY	0	0.042	0.026	16.909	0.484	0.484	0.000	0.000	0.000	0.000
77	A	80	ASP	-1	-0.869	-0.939	19.188	-14.672	-14.672	0.000	0.000	0.000	0.000
78	A	81	ASN	0	-0.064	-0.038	21.396	-0.279	-0.279	0.000	0.000	0.000	0.000
79	A	82	GLN	0	-0.037	-0.019	17.302	-0.723	-0.723	0.000	0.000	0.000	0.000
80	A	83	LYS	1	0.791	0.900	16.504	15.385	15.385	0.000	0.000	0.000	0.000
81	A	84	TRP	0	-0.025	-0.028	17.126	1.479	1.479	0.000	0.000	0.000	0.000
82	A	85	ARG	1	0.919	0.960	17.367	13.153	13.153	0.000	0.000	0.000	0.000
83	A	86	LEU	0	0.016	0.029	18.221	0.548	0.548	0.000	0.000	0.000	0.000
84	A	87	ASN	0	-0.042	-0.023	20.221	-0.485	-0.485	0.000	0.000	0.000	0.000
85	A	88	SER	0	0.025	-0.005	23.087	0.003	0.003	0.000	0.000	0.000	0.000
86	A	89	ASP	-1	-0.853	-0.889	24.841	-10.970	-10.970	0.000	0.000	0.000	0.000
87	A	90	GLY	0	0.019	0.006	23.991	0.317	0.317	0.000	0.000	0.000	0.000
88	A	91	SER	0	-0.031	-0.031	24.480	-0.287	-0.287	0.000	0.000	0.000	0.000
89	A	92	VAL	0	0.005	-0.008	20.199	-0.499	-0.499	0.000	0.000	0.000	0.000
90	A	93	VAL	0	-0.022	-0.015	22.334	0.447	0.447	0.000	0.000	0.000	0.000
91	A	94	GLY	0	0.080	0.039	21.881	-0.722	-0.722	0.000	0.000	0.000	0.000
92	A	95	VAL	0	-0.059	-0.045	19.576	0.586	0.586	0.000	0.000	0.000	0.000
93	A	96	GLN	0	-0.003	-0.004	22.725	0.502	0.502	0.000	0.000	0.000	0.000
94	A	97	SER	0	-0.016	-0.010	25.117	0.354	0.354	0.000	0.000	0.000	0.000
95	A	98	GLY	0	0.009	0.015	26.460	0.427	0.427	0.000	0.000	0.000	0.000
96	A	99	LEU	0	-0.047	-0.014	27.612	0.271	0.271	0.000	0.000	0.000	0.000
97	A	100	CYS	0	-0.057	-0.013	26.299	-0.557	-0.557	0.000	0.000	0.000	0.000
98	A	101	LEU	0	0.036	0.021	21.071	0.257	0.257	0.000	0.000	0.000	0.000
99	A	102	ASP	-1	-0.796	-0.886	25.776	-9.610	-9.610	0.000	0.000	0.000	0.000
100	A	103	ALA	0	0.033	0.018	28.658	-0.078	-0.078	0.000	0.000	0.000	0.000
101	A	104	VAL	0	0.030	0.005	29.931	0.369	0.369	0.000	0.000	0.000	0.000
102	A	105	GLY	0	-0.003	-0.003	33.073	0.119	0.119	0.000	0.000	0.000	0.000
103	A	106	ASN	0	-0.057	-0.026	34.066	0.028	0.028	0.000	0.000	0.000	0.000
104	A	107	GLY	0	0.014	0.022	34.239	0.126	0.126	0.000	0.000	0.000	0.000
105	A	108	THR	0	0.018	-0.014	31.888	-0.294	-0.294	0.000	0.000	0.000	0.000
106	A	109	ALA	0	0.010	0.015	31.839	-0.182	-0.182	0.000	0.000	0.000	0.000
107	A	110	ASN	0	0.014	-0.012	29.830	-0.481	-0.481	0.000	0.000	0.000	0.000
108	A	111	GLY	0	0.042	0.031	29.848	0.335	0.335	0.000	0.000	0.000	0.000
109	A	112	THR	0	-0.117	-0.048	30.576	0.290	0.290	0.000	0.000	0.000	0.000
110	A	113	LEU	0	0.020	0.013	29.287	-0.409	-0.409	0.000	0.000	0.000	0.000
111	A	114	ILE	0	-0.003	-0.001	24.941	0.193	0.193	0.000	0.000	0.000	0.000
112	A	115	GLN	0	-0.037	-0.032	27.999	0.143	0.143	0.000	0.000	0.000	0.000
113	A	116	LEU	0	0.025	0.020	25.377	-0.331	-0.331	0.000	0.000	0.000	0.000
114	A	117	TYR	0	-0.028	-0.030	28.933	0.521	0.521	0.000	0.000	0.000	0.000
115	A	118	THR	0	0.006	-0.007	30.710	-0.175	-0.175	0.000	0.000	0.000	0.000
116	A	120	SER	0	0.004	-0.009	31.621	0.282	0.282	0.000	0.000	0.000	0.000
117	A	121	ASN	0	0.034	0.019	30.877	0.113	0.113	0.000	0.000	0.000	0.000
118	A	122	GLY	0	0.064	0.045	32.170	0.158	0.158	0.000	0.000	0.000	0.000
119	A	123	SER	0	-0.018	-0.022	31.148	-0.309	-0.309	0.000	0.000	0.000	0.000
120	A	124	ASN	0	-0.028	-0.020	29.927	-0.236	-0.236	0.000	0.000	0.000	0.000
121	A	125	GLN	0	-0.004	-0.012	28.093	-0.256	-0.256	0.000	0.000	0.000	0.000
122	A	126	ARG	1	0.851	0.949	26.513	9.655	9.655	0.000	0.000	0.000	0.000
123	A	127	TRP	0	-0.055	-0.031	22.013	-0.057	-0.057	0.000	0.000	0.000	0.000
124	A	128	THR	0	-0.039	-0.020	21.105	-0.054	-0.054	0.000	0.000	0.000	0.000
125	A	129	ARG	1	0.817	0.873	12.413	20.279	20.279	0.000	0.000	0.000	0.000
126	A	130	THR	-1	-0.927	-0.936	16.562	-16.174	-16.174	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:PRO)