FMO DATABASE

FMODB ID: 5YV4Z

Calculation Name: 5V6F-A-Xray547

Preferred Name:

Target Type:

Ligand Name: beta-d-mannopyranose | alpha-d-mannopyranose

Ligand 3-letter code: BMA | MAN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5V6F

Chain ID: A

ChEMBL ID:

UniProt ID: Q9KTH2

Base Structure: X-ray

Registration Date: 2025-10-04

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	137
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1208309.946937
FMO2-HF: Nuclear repulsion	1156641.829175
FMO2-HF: Total energy	-51668.117762
FMO2-MP2: Total energy	-51820.42347

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:821:MET)

Summations of interaction energy for fragment #1(A:821:MET)

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.
50.497	58.188	0.492	-3.702	-4.481	-0.022

Interaction energy analysis for fragmet #1(A:821:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.855 / q_NPA : 0.916

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	823	SER	0	-0.030	0.007	3.851	-5.181	-2.088	-0.034	-1.807	-1.252	-0.005
119	A	939	LYS	1	0.860	0.917	4.285	50.637	50.773	-0.001	-0.007	-0.129	0.000
136	A	956	VAL	0	0.002	-0.003	3.281	-7.078	-6.701	0.018	-0.098	-0.296	0.000
137	A	957	TYR	-1	-0.829	-0.922	2.489	-61.823	-57.738	0.509	-1.790	-2.804	-0.017
4	A	824	PRO	0	0.037	0.013	6.850	-1.856	-1.856	0.000	0.000	0.000	0.000
5	A	825	ILE	0	-0.029	0.009	9.263	-0.589	-0.589	0.000	0.000	0.000	0.000
6	A	826	PHE	0	0.018	0.012	11.072	0.938	0.938	0.000	0.000	0.000	0.000
7	A	827	GLY	0	0.012	0.011	14.583	0.322	0.322	0.000	0.000	0.000	0.000
8	A	828	TYR	0	-0.024	-0.036	17.363	-0.055	-0.055	0.000	0.000	0.000	0.000
9	A	829	SER	0	0.030	0.003	13.806	0.201	0.201	0.000	0.000	0.000	0.000
10	A	830	ASN	0	-0.005	-0.003	15.700	-0.464	-0.464	0.000	0.000	0.000	0.000
11	A	831	THR	0	-0.055	-0.040	18.370	0.301	0.301	0.000	0.000	0.000	0.000
12	A	832	GLN	0	0.037	0.007	17.066	-0.559	-0.559	0.000	0.000	0.000	0.000
13	A	833	GLN	0	0.015	0.025	9.381	-1.522	-1.522	0.000	0.000	0.000	0.000
14	A	834	SER	0	-0.029	-0.012	14.120	0.914	0.914	0.000	0.000	0.000	0.000
15	A	835	GLN	0	-0.006	-0.008	7.506	-0.901	-0.901	0.000	0.000	0.000	0.000
16	A	836	ARG	1	0.828	0.903	11.719	18.417	18.417	0.000	0.000	0.000	0.000
17	A	837	VAL	0	0.078	0.042	11.113	-1.591	-1.591	0.000	0.000	0.000	0.000
18	A	838	VAL	0	-0.017	0.011	12.300	1.697	1.697	0.000	0.000	0.000	0.000
19	A	839	THR	0	-0.022	-0.027	14.379	-0.700	-0.700	0.000	0.000	0.000	0.000
20	A	840	ALA	0	0.040	0.003	16.700	-0.811	-0.811	0.000	0.000	0.000	0.000
21	A	841	ASP	-1	-0.840	-0.895	18.514	-14.484	-14.484	0.000	0.000	0.000	0.000
22	A	842	ASN	0	-0.033	-0.010	15.481	-1.296	-1.296	0.000	0.000	0.000	0.000
23	A	843	LEU	0	0.029	0.026	17.021	-0.249	-0.249	0.000	0.000	0.000	0.000
24	A	844	MET	0	-0.014	0.008	15.672	-1.091	-1.091	0.000	0.000	0.000	0.000
25	A	845	TYR	0	0.022	0.010	18.239	0.949	0.949	0.000	0.000	0.000	0.000
26	A	846	LEU	0	0.026	0.000	19.688	-0.601	-0.601	0.000	0.000	0.000	0.000
27	A	847	ARG	1	0.800	0.896	22.442	12.454	12.454	0.000	0.000	0.000	0.000
28	A	848	SER	0	0.013	0.007	24.625	-0.237	-0.237	0.000	0.000	0.000	0.000
29	A	849	GLY	0	0.053	0.043	26.893	0.418	0.418	0.000	0.000	0.000	0.000
30	A	850	PHE	0	-0.042	-0.025	29.743	-0.135	-0.135	0.000	0.000	0.000	0.000
31	A	851	ALA	0	0.032	0.027	26.036	-0.108	-0.108	0.000	0.000	0.000	0.000
32	A	852	ILE	0	-0.015	-0.016	20.585	0.131	0.131	0.000	0.000	0.000	0.000
33	A	853	ASP	-1	-0.810	-0.920	23.348	-11.537	-11.537	0.000	0.000	0.000	0.000
34	A	854	ALA	0	0.001	-0.010	21.623	-0.061	-0.061	0.000	0.000	0.000	0.000
35	A	855	ILE	0	0.029	0.018	15.984	0.018	0.018	0.000	0.000	0.000	0.000
36	A	856	GLY	0	-0.001	0.003	17.507	-0.036	-0.036	0.000	0.000	0.000	0.000
37	A	857	THR	0	-0.031	-0.024	14.533	-0.060	-0.060	0.000	0.000	0.000	0.000
38	A	858	THR	0	-0.011	-0.017	17.873	0.565	0.565	0.000	0.000	0.000	0.000
39	A	859	VAL	0	0.038	0.009	21.478	-0.098	-0.098	0.000	0.000	0.000	0.000
40	A	860	ASN	0	0.026	0.016	24.141	0.361	0.361	0.000	0.000	0.000	0.000
41	A	861	ASN	0	0.000	0.014	18.050	0.048	0.048	0.000	0.000	0.000	0.000
42	A	862	LEU	0	-0.022	0.005	19.628	-0.608	-0.608	0.000	0.000	0.000	0.000
43	A	863	VAL	0	-0.013	-0.003	16.294	0.568	0.568	0.000	0.000	0.000	0.000
44	A	864	GLY	0	0.044	-0.004	19.567	-0.439	-0.439	0.000	0.000	0.000	0.000
45	A	865	GLY	0	0.004	0.034	22.100	0.292	0.292	0.000	0.000	0.000	0.000
46	A	866	PRO	0	-0.016	-0.004	25.835	-0.190	-0.190	0.000	0.000	0.000	0.000
47	A	867	VAL	0	-0.002	-0.006	28.245	0.003	0.003	0.000	0.000	0.000	0.000
48	A	868	GLN	0	0.015	0.012	31.192	0.046	0.046	0.000	0.000	0.000	0.000
49	A	869	GLY	0	0.008	0.009	33.724	0.024	0.024	0.000	0.000	0.000	0.000
50	A	870	THR	0	-0.001	-0.007	36.267	-0.009	-0.009	0.000	0.000	0.000	0.000
51	A	871	ASN	0	-0.036	-0.011	31.193	-0.223	-0.223	0.000	0.000	0.000	0.000
52	A	872	GLY	0	0.085	0.035	28.573	0.097	0.097	0.000	0.000	0.000	0.000
53	A	873	GLY	0	-0.004	0.014	28.413	-0.366	-0.366	0.000	0.000	0.000	0.000
54	A	874	VAL	0	-0.011	-0.010	29.819	0.202	0.202	0.000	0.000	0.000	0.000
55	A	875	LEU	0	-0.005	-0.013	25.579	-0.435	-0.435	0.000	0.000	0.000	0.000
56	A	876	ARG	1	0.823	0.910	25.224	11.450	11.450	0.000	0.000	0.000	0.000
57	A	877	ALA	0	0.039	0.014	25.976	-0.166	-0.166	0.000	0.000	0.000	0.000
58	A	878	PRO	0	-0.028	-0.009	21.837	-0.299	-0.299	0.000	0.000	0.000	0.000
59	A	879	ILE	0	0.007	0.001	17.793	0.218	0.218	0.000	0.000	0.000	0.000
60	A	880	ALA	0	0.037	0.026	18.674	-0.657	-0.657	0.000	0.000	0.000	0.000
61	A	881	LEU	0	0.005	-0.030	12.974	-0.510	-0.510	0.000	0.000	0.000	0.000
62	A	882	ASP	-1	-0.859	-0.924	13.729	-18.734	-18.734	0.000	0.000	0.000	0.000
63	A	883	GLN	0	-0.024	-0.031	15.538	0.331	0.331	0.000	0.000	0.000	0.000
64	A	884	LEU	0	-0.027	0.003	13.240	0.538	0.538	0.000	0.000	0.000	0.000
65	A	885	GLN	0	-0.013	-0.004	14.540	-0.645	-0.645	0.000	0.000	0.000	0.000
66	A	886	SER	0	-0.022	-0.026	13.806	-1.467	-1.467	0.000	0.000	0.000	0.000
67	A	887	VAL	0	-0.017	0.002	13.389	0.853	0.853	0.000	0.000	0.000	0.000
68	A	888	GLU	-1	-0.832	-0.910	16.156	-14.701	-14.701	0.000	0.000	0.000	0.000
69	A	889	VAL	0	-0.014	-0.004	16.029	0.838	0.838	0.000	0.000	0.000	0.000
70	A	890	THR	0	-0.001	0.009	19.049	0.328	0.328	0.000	0.000	0.000	0.000
71	A	891	SER	0	0.021	0.002	19.792	-0.132	-0.132	0.000	0.000	0.000	0.000
72	A	892	GLY	0	0.044	0.020	22.427	0.208	0.208	0.000	0.000	0.000	0.000
73	A	893	LEU	0	-0.039	0.001	25.310	-0.181	-0.181	0.000	0.000	0.000	0.000
74	A	894	TYR	0	0.037	0.010	27.738	0.294	0.294	0.000	0.000	0.000	0.000
75	A	895	ASN	0	0.002	-0.009	29.471	0.023	0.023	0.000	0.000	0.000	0.000
76	A	896	TRP	0	-0.006	0.009	32.311	0.178	0.178	0.000	0.000	0.000	0.000
77	A	897	GLY	0	0.032	0.024	31.440	0.110	0.110	0.000	0.000	0.000	0.000
78	A	898	GLY	0	0.023	0.012	27.628	-0.277	-0.277	0.000	0.000	0.000	0.000
79	A	899	TYR	0	-0.005	-0.004	23.517	0.113	0.113	0.000	0.000	0.000	0.000
80	A	900	HIS	1	0.789	0.872	22.108	12.111	12.111	0.000	0.000	0.000	0.000
81	A	901	ILE	0	0.019	0.022	16.819	0.026	0.026	0.000	0.000	0.000	0.000
82	A	902	VAL	0	-0.055	-0.031	21.461	0.448	0.448	0.000	0.000	0.000	0.000
83	A	903	ALA	0	0.018	0.001	23.550	0.493	0.493	0.000	0.000	0.000	0.000
84	A	904	ILE	0	-0.007	-0.001	18.117	-0.765	-0.765	0.000	0.000	0.000	0.000
85	A	905	LYS	1	0.870	0.949	20.943	14.319	14.319	0.000	0.000	0.000	0.000
86	A	906	PHE	0	0.014	-0.005	16.553	-1.163	-1.163	0.000	0.000	0.000	0.000
87	A	907	THR	0	0.028	0.003	18.395	1.297	1.297	0.000	0.000	0.000	0.000
88	A	908	MET	0	-0.003	0.011	17.979	-1.647	-1.647	0.000	0.000	0.000	0.000
89	A	909	LYS	1	0.860	0.925	13.834	20.871	20.871	0.000	0.000	0.000	0.000
90	A	910	ASP	-1	-0.832	-0.879	19.621	-12.994	-12.994	0.000	0.000	0.000	0.000
91	A	911	GLY	0	-0.013	0.001	22.328	0.585	0.585	0.000	0.000	0.000	0.000
92	A	912	SER	0	-0.080	-0.047	23.869	0.309	0.309	0.000	0.000	0.000	0.000
93	A	913	SER	0	-0.026	-0.035	22.785	-0.680	-0.680	0.000	0.000	0.000	0.000
94	A	914	VAL	0	0.011	0.014	22.848	0.623	0.623	0.000	0.000	0.000	0.000
95	A	915	LEU	0	0.005	0.002	23.277	-0.676	-0.676	0.000	0.000	0.000	0.000
96	A	916	LEU	0	-0.019	-0.005	22.650	0.488	0.488	0.000	0.000	0.000	0.000
97	A	917	GLY	0	0.063	0.031	24.772	-0.484	-0.484	0.000	0.000	0.000	0.000
98	A	918	SER	0	-0.030	-0.030	26.945	0.377	0.377	0.000	0.000	0.000	0.000
99	A	919	THR	0	0.034	0.012	26.325	-0.225	-0.225	0.000	0.000	0.000	0.000
100	A	920	HIS	0	-0.026	-0.019	28.541	0.105	0.105	0.000	0.000	0.000	0.000
101	A	921	TYR	0	-0.006	0.004	31.122	0.309	0.309	0.000	0.000	0.000	0.000
102	A	922	ALA	0	0.036	0.023	28.409	-0.126	-0.126	0.000	0.000	0.000	0.000
103	A	923	SER	0	-0.006	0.006	30.373	0.080	0.080	0.000	0.000	0.000	0.000
104	A	924	ASN	0	-0.015	-0.029	28.053	-0.237	-0.237	0.000	0.000	0.000	0.000
105	A	925	LYS	1	0.914	0.963	25.661	10.515	10.515	0.000	0.000	0.000	0.000
106	A	926	LYS	1	0.785	0.883	17.191	17.621	17.621	0.000	0.000	0.000	0.000
107	A	927	VAL	0	0.019	-0.003	20.681	0.007	0.007	0.000	0.000	0.000	0.000
108	A	928	GLU	-1	-0.796	-0.877	15.545	-19.106	-19.106	0.000	0.000	0.000	0.000
109	A	929	THR	0	0.008	0.004	16.311	0.108	0.108	0.000	0.000	0.000	0.000
110	A	930	TYR	0	0.017	0.007	6.348	-2.046	-2.046	0.000	0.000	0.000	0.000
111	A	931	THR	0	0.007	-0.001	11.758	1.843	1.843	0.000	0.000	0.000	0.000
112	A	932	VAL	0	-0.007	0.002	8.975	-3.045	-3.045	0.000	0.000	0.000	0.000
113	A	933	PRO	0	-0.029	-0.013	6.187	1.878	1.878	0.000	0.000	0.000	0.000
114	A	934	GLN	0	0.091	0.030	9.250	-1.145	-1.145	0.000	0.000	0.000	0.000
115	A	935	GLY	0	0.016	0.011	10.542	-0.912	-0.912	0.000	0.000	0.000	0.000
116	A	936	LYS	1	0.857	0.934	4.857	45.542	45.542	0.000	0.000	0.000	0.000
117	A	937	ARG	1	0.891	0.942	7.892	24.366	24.366	0.000	0.000	0.000	0.000
118	A	938	ILE	0	-0.012	0.002	8.215	-3.768	-3.768	0.000	0.000	0.000	0.000
120	A	940	GLN	0	-0.047	-0.026	7.474	3.079	3.079	0.000	0.000	0.000	0.000
121	A	941	ILE	0	-0.003	0.004	8.847	-2.851	-2.851	0.000	0.000	0.000	0.000
122	A	942	ASN	0	-0.021	0.000	6.063	2.319	2.319	0.000	0.000	0.000	0.000
123	A	943	VAL	0	0.028	-0.003	10.516	-0.222	-0.222	0.000	0.000	0.000	0.000
124	A	944	TRP	0	-0.015	-0.004	9.598	-0.259	-0.259	0.000	0.000	0.000	0.000
125	A	945	THR	0	-0.016	-0.032	16.126	0.595	0.595	0.000	0.000	0.000	0.000
126	A	946	GLY	0	0.045	0.026	19.806	-0.044	-0.044	0.000	0.000	0.000	0.000
127	A	947	GLY	0	-0.012	0.004	22.683	0.508	0.508	0.000	0.000	0.000	0.000
128	A	948	TRP	0	-0.056	-0.033	24.508	0.348	0.348	0.000	0.000	0.000	0.000
129	A	949	LEU	0	0.030	0.007	24.380	0.120	0.120	0.000	0.000	0.000	0.000
130	A	950	VAL	0	0.010	0.032	17.952	-0.298	-0.298	0.000	0.000	0.000	0.000
131	A	951	GLU	-1	-0.748	-0.838	19.089	-13.407	-13.407	0.000	0.000	0.000	0.000
132	A	952	GLY	0	0.059	0.022	15.873	0.033	0.033	0.000	0.000	0.000	0.000
133	A	953	PHE	0	-0.038	-0.019	12.533	0.351	0.351	0.000	0.000	0.000	0.000
134	A	954	GLN	0	-0.010	0.001	5.972	1.700	1.700	0.000	0.000	0.000	0.000
135	A	955	PHE	0	0.029	0.011	8.354	1.300	1.300	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:821:MET)