FMO DATABASE

FMODB ID: G4NG1

Calculation Name: 5IDB-A-Xray549

Preferred Name:

Target Type:

Ligand Name: beta-d-mannopyranose | alpha-d-mannopyranose | 2-[n-cyclohexylamino]ethane sulfonic acid

Ligand 3-letter code: BMA | MAN | NHE

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5IDB

Chain ID: A

ChEMBL ID:

UniProt ID: K1QRB6

Base Structure: X-ray

Registration Date: 2025-10-12

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	142
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1276777.928196
FMO2-HF: Nuclear repulsion	1223042.300971
FMO2-HF: Total energy	-53735.627224
FMO2-MP2: Total energy	-53893.338025

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:ALA)

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

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.
-64.379	-58.678	20.412	-11.929	-14.185	-0.13

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.751 / q_NPA : 0.878

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	4	TRP	0	0.026	0.003	3.835	2.023	3.521	-0.021	-0.731	-0.746	-0.001
16	A	17	ILE	0	-0.006	-0.015	3.020	2.089	2.434	0.109	-0.112	-0.342	0.000
67	A	68	LEU	0	-0.013	0.006	2.524	-2.797	-2.382	0.338	-0.150	-0.604	-0.001
68	A	69	VAL	0	0.014	0.002	4.376	3.324	3.623	-0.001	-0.132	-0.166	0.000
69	A	70	TYR	0	0.001	-0.046	2.139	-47.642	-45.276	18.448	-10.389	-10.425	-0.121
70	A	71	PRO	0	0.004	0.015	3.048	8.828	9.018	0.083	0.162	-0.435	-0.003
73	A	74	ALA	0	-0.025	0.003	2.933	0.132	0.496	0.070	-0.165	-0.269	-0.001
74	A	75	LEU	0	0.043	0.014	4.935	0.431	0.525	-0.001	-0.003	-0.090	0.000
75	A	76	GLY	0	-0.005	0.014	4.300	-12.347	-12.265	-0.001	-0.020	-0.061	0.000
77	A	78	LEU	0	-0.028	-0.024	2.483	-1.437	-1.389	1.388	-0.389	-1.047	-0.003
4	A	5	VAL	0	0.042	0.028	6.764	1.690	1.690	0.000	0.000	0.000	0.000
5	A	6	SER	0	-0.005	-0.002	9.332	0.851	0.851	0.000	0.000	0.000	0.000
6	A	7	THR	0	-0.016	-0.026	13.054	0.402	0.402	0.000	0.000	0.000	0.000
7	A	8	THR	0	0.007	-0.006	15.111	0.884	0.884	0.000	0.000	0.000	0.000
8	A	9	GLY	0	0.062	0.040	18.548	0.008	0.008	0.000	0.000	0.000	0.000
9	A	10	ASN	0	-0.033	-0.014	18.497	-0.707	-0.707	0.000	0.000	0.000	0.000
10	A	11	THR	0	-0.015	-0.002	16.167	-0.006	-0.006	0.000	0.000	0.000	0.000
11	A	12	ILE	0	-0.035	-0.010	12.380	-0.988	-0.988	0.000	0.000	0.000	0.000
12	A	13	PRO	0	0.008	0.017	9.783	0.949	0.949	0.000	0.000	0.000	0.000
13	A	14	ASP	-1	-0.854	-0.936	11.102	-21.776	-21.776	0.000	0.000	0.000	0.000
14	A	15	ASN	0	-0.063	-0.048	7.260	-1.577	-1.577	0.000	0.000	0.000	0.000
15	A	16	ALA	0	0.025	0.031	6.467	-5.529	-5.529	0.000	0.000	0.000	0.000
17	A	18	ARG	1	0.934	0.958	7.548	20.997	20.997	0.000	0.000	0.000	0.000
18	A	19	ALA	0	0.002	0.013	9.621	0.588	0.588	0.000	0.000	0.000	0.000
19	A	20	GLY	0	0.053	0.026	11.403	0.928	0.928	0.000	0.000	0.000	0.000
20	A	21	TYR	0	-0.049	-0.017	15.199	-0.394	-0.394	0.000	0.000	0.000	0.000
21	A	22	ASP	-1	-0.745	-0.840	18.395	-13.077	-13.077	0.000	0.000	0.000	0.000
22	A	23	ILE	0	0.004	-0.006	21.173	0.180	0.180	0.000	0.000	0.000	0.000
23	A	24	ASN	0	-0.022	-0.007	23.008	0.063	0.063	0.000	0.000	0.000	0.000
24	A	25	LYS	1	0.938	0.960	22.773	11.088	11.088	0.000	0.000	0.000	0.000
25	A	26	LYS	1	0.926	0.983	20.177	12.831	12.831	0.000	0.000	0.000	0.000
26	A	27	ALA	0	-0.024	-0.013	15.069	0.028	0.028	0.000	0.000	0.000	0.000
27	A	28	LEU	0	-0.069	-0.026	15.098	0.365	0.365	0.000	0.000	0.000	0.000
28	A	29	PHE	0	0.005	-0.011	10.241	-0.232	-0.232	0.000	0.000	0.000	0.000
29	A	30	ILE	0	0.034	0.018	7.028	1.606	1.606	0.000	0.000	0.000	0.000
30	A	31	ALA	0	-0.003	-0.004	8.958	-1.848	-1.848	0.000	0.000	0.000	0.000
31	A	32	ARG	1	0.808	0.869	9.503	27.679	27.679	0.000	0.000	0.000	0.000
32	A	33	ALA	0	0.028	0.010	12.313	0.004	0.004	0.000	0.000	0.000	0.000
33	A	34	VAL	0	0.014	0.012	15.667	0.078	0.078	0.000	0.000	0.000	0.000
34	A	35	VAL	0	-0.001	-0.001	18.515	0.621	0.621	0.000	0.000	0.000	0.000
35	A	36	SER	0	-0.024	-0.015	21.374	0.146	0.146	0.000	0.000	0.000	0.000
36	A	37	GLY	0	-0.003	0.004	22.541	0.280	0.280	0.000	0.000	0.000	0.000
37	A	38	GLU	-1	-0.894	-0.948	18.523	-14.704	-14.704	0.000	0.000	0.000	0.000
38	A	39	MET	0	-0.013	0.015	13.316	0.110	0.110	0.000	0.000	0.000	0.000
39	A	40	THR	0	0.003	0.006	15.332	-0.295	-0.295	0.000	0.000	0.000	0.000
40	A	41	PRO	0	0.020	0.005	11.487	-0.331	-0.331	0.000	0.000	0.000	0.000
41	A	42	GLY	0	0.001	-0.022	12.863	1.554	1.554	0.000	0.000	0.000	0.000
42	A	43	LYS	1	0.826	0.942	12.796	12.673	12.673	0.000	0.000	0.000	0.000
43	A	44	CYS	0	0.000	0.023	12.274	0.371	0.371	0.000	0.000	0.000	0.000
44	A	45	GLY	0	0.113	0.030	14.823	-0.589	-0.589	0.000	0.000	0.000	0.000
45	A	46	THR	0	0.000	0.008	16.761	0.850	0.850	0.000	0.000	0.000	0.000
46	A	47	HIS	0	-0.084	-0.050	19.348	0.540	0.540	0.000	0.000	0.000	0.000
47	A	48	LEU	0	-0.035	-0.007	17.938	0.525	0.525	0.000	0.000	0.000	0.000
48	A	49	GLU	-1	-0.903	-0.946	20.033	-12.120	-12.120	0.000	0.000	0.000	0.000
49	A	50	GLY	0	0.045	0.028	19.381	0.472	0.472	0.000	0.000	0.000	0.000
50	A	51	ALA	0	-0.015	0.011	15.306	0.025	0.025	0.000	0.000	0.000	0.000
51	A	52	HIS	0	-0.087	-0.047	17.184	1.288	1.288	0.000	0.000	0.000	0.000
52	A	53	ILE	0	0.002	-0.003	15.180	-0.626	-0.626	0.000	0.000	0.000	0.000
53	A	54	PRO	0	-0.027	-0.007	17.464	0.936	0.936	0.000	0.000	0.000	0.000
54	A	55	PHE	0	0.041	-0.002	20.236	-0.263	-0.263	0.000	0.000	0.000	0.000
55	A	56	ALA	0	0.043	0.044	22.947	0.413	0.413	0.000	0.000	0.000	0.000
56	A	57	GLY	0	0.016	0.004	26.213	0.397	0.397	0.000	0.000	0.000	0.000
57	A	58	LYS	1	0.875	0.945	25.994	11.000	11.000	0.000	0.000	0.000	0.000
58	A	59	GLU	-1	-0.815	-0.913	21.652	-13.363	-13.363	0.000	0.000	0.000	0.000
59	A	60	HIS	0	-0.062	-0.050	21.765	0.613	0.613	0.000	0.000	0.000	0.000
60	A	61	ILE	0	-0.008	0.009	21.029	-0.597	-0.597	0.000	0.000	0.000	0.000
61	A	62	ILE	0	-0.006	-0.005	18.868	0.501	0.501	0.000	0.000	0.000	0.000
62	A	63	GLN	0	0.006	-0.020	19.196	-0.914	-0.914	0.000	0.000	0.000	0.000
63	A	64	ASN	0	0.007	0.005	18.372	-0.380	-0.380	0.000	0.000	0.000	0.000
64	A	65	TYR	0	-0.052	-0.040	13.076	-0.141	-0.141	0.000	0.000	0.000	0.000
65	A	66	GLU	-1	-0.781	-0.858	9.825	-25.925	-25.925	0.000	0.000	0.000	0.000
66	A	67	VAL	0	0.001	-0.006	8.765	0.774	0.774	0.000	0.000	0.000	0.000
71	A	72	ILE	0	0.040	0.016	5.474	-3.921	-3.921	0.000	0.000	0.000	0.000
72	A	73	ASN	0	-0.031	-0.015	7.957	0.968	0.968	0.000	0.000	0.000	0.000
76	A	77	PHE	0	-0.021	-0.015	5.851	-1.723	-1.723	0.000	0.000	0.000	0.000
78	A	79	ASP	-1	-0.842	-0.912	5.972	-21.656	-21.656	0.000	0.000	0.000	0.000
79	A	80	TRP	0	-0.022	-0.034	9.529	-0.632	-0.632	0.000	0.000	0.000	0.000
80	A	81	GLN	0	0.003	0.005	12.358	1.716	1.716	0.000	0.000	0.000	0.000
81	A	82	GLN	0	-0.018	-0.010	15.402	0.193	0.193	0.000	0.000	0.000	0.000
82	A	83	ALA	0	0.003	0.010	18.494	0.245	0.245	0.000	0.000	0.000	0.000
83	A	84	SER	0	0.032	0.005	20.240	0.452	0.452	0.000	0.000	0.000	0.000
84	A	85	ASN	0	-0.016	-0.018	23.007	0.179	0.179	0.000	0.000	0.000	0.000
85	A	86	GLY	0	-0.007	-0.006	21.921	0.406	0.406	0.000	0.000	0.000	0.000
86	A	87	ASP	-1	-0.943	-0.942	21.112	-12.950	-12.950	0.000	0.000	0.000	0.000
87	A	88	VAL	0	-0.020	-0.018	15.556	-0.468	-0.468	0.000	0.000	0.000	0.000
88	A	89	PRO	0	-0.010	0.016	13.407	0.575	0.575	0.000	0.000	0.000	0.000
89	A	90	GLY	0	0.036	0.010	14.809	-0.311	-0.311	0.000	0.000	0.000	0.000
90	A	91	ASN	0	-0.026	-0.023	10.042	-0.030	-0.030	0.000	0.000	0.000	0.000
91	A	92	ALA	0	0.024	0.021	9.671	-2.631	-2.631	0.000	0.000	0.000	0.000
92	A	93	ILE	0	-0.025	-0.013	6.073	-0.797	-0.797	0.000	0.000	0.000	0.000
93	A	94	ASP	-1	-0.872	-0.932	9.105	-20.707	-20.707	0.000	0.000	0.000	0.000
94	A	95	THR	0	-0.103	-0.071	10.187	-2.013	-2.013	0.000	0.000	0.000	0.000
95	A	96	ALA	0	-0.008	-0.001	12.502	0.672	0.672	0.000	0.000	0.000	0.000
96	A	97	SER	0	0.008	0.002	16.241	-0.414	-0.414	0.000	0.000	0.000	0.000
97	A	98	GLY	0	0.047	0.027	17.655	0.668	0.668	0.000	0.000	0.000	0.000
98	A	99	ILE	0	-0.052	-0.019	15.364	0.392	0.392	0.000	0.000	0.000	0.000
99	A	100	TYR	0	0.045	0.006	12.432	-0.452	-0.452	0.000	0.000	0.000	0.000
100	A	101	ILE	0	-0.012	-0.012	7.698	0.874	0.874	0.000	0.000	0.000	0.000
101	A	102	GLY	0	0.049	0.011	11.554	-0.144	-0.144	0.000	0.000	0.000	0.000
102	A	103	ARG	1	0.721	0.826	13.048	19.270	19.270	0.000	0.000	0.000	0.000
103	A	104	VAL	0	0.025	0.005	15.394	0.494	0.494	0.000	0.000	0.000	0.000
104	A	105	LEU	0	0.020	0.025	19.217	-0.139	-0.139	0.000	0.000	0.000	0.000
105	A	106	TYR	0	0.006	-0.013	21.885	0.542	0.542	0.000	0.000	0.000	0.000
106	A	107	SER	0	-0.027	-0.017	24.229	-0.022	-0.022	0.000	0.000	0.000	0.000
107	A	108	GLY	0	0.013	0.011	25.913	0.173	0.173	0.000	0.000	0.000	0.000
108	A	109	SER	0	-0.077	-0.053	20.350	-0.259	-0.259	0.000	0.000	0.000	0.000
109	A	110	LEU	0	0.007	0.013	16.559	0.249	0.249	0.000	0.000	0.000	0.000
110	A	111	ILE	0	0.016	-0.010	17.422	-0.724	-0.724	0.000	0.000	0.000	0.000
111	A	112	PRO	0	0.007	-0.003	12.088	0.011	0.011	0.000	0.000	0.000	0.000
112	A	113	CYS	0	-0.114	-0.043	14.009	0.771	0.771	0.000	0.000	0.000	0.000
113	A	114	LYS	1	0.880	0.961	13.849	12.956	12.956	0.000	0.000	0.000	0.000
114	A	115	ILE	0	0.009	0.006	14.825	1.000	1.000	0.000	0.000	0.000	0.000
115	A	116	HIS	0	0.037	0.034	17.518	-0.487	-0.487	0.000	0.000	0.000	0.000
116	A	117	THR	0	0.035	0.010	18.694	0.661	0.661	0.000	0.000	0.000	0.000
117	A	118	GLY	0	-0.018	-0.002	21.429	0.513	0.513	0.000	0.000	0.000	0.000
118	A	119	PHE	0	-0.045	-0.049	24.339	0.512	0.512	0.000	0.000	0.000	0.000
119	A	120	LYS	1	0.917	0.972	24.095	11.753	11.753	0.000	0.000	0.000	0.000
120	A	121	VAL	0	-0.038	-0.011	23.227	0.247	0.247	0.000	0.000	0.000	0.000
121	A	122	ALA	0	0.041	0.041	19.080	-0.545	-0.545	0.000	0.000	0.000	0.000
122	A	123	TYR	0	-0.005	-0.016	19.454	0.838	0.838	0.000	0.000	0.000	0.000
123	A	124	MET	0	0.006	0.014	18.990	-0.801	-0.801	0.000	0.000	0.000	0.000
124	A	125	GLY	0	0.035	0.017	19.554	0.722	0.722	0.000	0.000	0.000	0.000
125	A	126	PHE	0	0.022	-0.008	21.182	-0.252	-0.252	0.000	0.000	0.000	0.000
126	A	127	ALA	0	0.049	0.040	23.956	0.412	0.412	0.000	0.000	0.000	0.000
127	A	128	GLY	0	0.036	0.019	25.788	0.432	0.432	0.000	0.000	0.000	0.000
128	A	129	LYS	1	0.911	0.955	26.425	9.657	9.657	0.000	0.000	0.000	0.000
129	A	130	GLU	-1	-0.800	-0.893	22.456	-12.986	-12.986	0.000	0.000	0.000	0.000
130	A	131	HIS	1	0.786	0.887	23.773	11.792	11.792	0.000	0.000	0.000	0.000
131	A	132	GLN	0	0.051	0.007	23.620	-0.266	-0.266	0.000	0.000	0.000	0.000
132	A	133	SER	0	-0.038	-0.031	22.358	0.589	0.589	0.000	0.000	0.000	0.000
133	A	134	LYS	1	0.973	0.984	23.566	10.028	10.028	0.000	0.000	0.000	0.000
134	A	135	GLU	-1	-0.906	-0.933	22.862	-11.684	-11.684	0.000	0.000	0.000	0.000
135	A	136	TYR	0	-0.014	-0.031	17.577	0.242	0.242	0.000	0.000	0.000	0.000
136	A	137	GLU	-1	-0.789	-0.846	14.837	-17.578	-17.578	0.000	0.000	0.000	0.000
137	A	138	ALA	0	0.019	-0.007	13.892	-0.545	-0.545	0.000	0.000	0.000	0.000
138	A	139	LEU	0	-0.038	-0.011	5.910	-0.452	-0.452	0.000	0.000	0.000	0.000
139	A	140	TYR	0	0.008	-0.008	9.108	0.542	0.542	0.000	0.000	0.000	0.000
140	A	141	LYS	1	0.833	0.910	5.082	43.175	43.175	0.000	0.000	0.000	0.000
141	A	142	VAL	0	-0.029	-0.012	7.752	2.782	2.782	0.000	0.000	0.000	0.000
142	A	143	ILE	-1	-0.799	-0.866	7.537	-38.023	-38.023	0.000	0.000	0.000	0.000

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