FMO DATABASE

FMODB ID: 7Y1QK

Calculation Name: 1X1V-A-Xray547

Preferred Name:

Target Type:

Ligand Name: methyl alpha-d-mannopyranoside | hexane-1,6-diol

Ligand 3-letter code: MMA | HEZ

Ligand of Interest (LOI):

PDB ID: 1X1V

Chain ID: A

ChEMBL ID:

UniProt ID: Q8L5H4

Base Structure: X-ray

Registration Date: 2025-10-03

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	138
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1126432.542521
FMO2-HF: Nuclear repulsion	1076714.325853
FMO2-HF: Total energy	-49718.216668
FMO2-MP2: Total energy	-49865.759561

3D Structure

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:4:ALA)

Summations of interaction energy for fragment #1(A:4: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.
-9.905	-8.001	0.008	-0.708	-1.203	-0.002

Interaction energy analysis for fragmet #1(A:4:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.851 / 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	6	LYS	1	0.847	0.945	3.369	39.971	41.385	-0.008	-0.581	-0.825	-0.001
19	A	22	PRO	0	-0.021	-0.015	4.619	1.489	1.544	-0.001	-0.002	-0.051	0.000
135	A	138	TYR	0	-0.059	-0.066	3.320	-8.333	-7.925	0.018	-0.113	-0.313	-0.001
137	A	140	GLU	-1	-0.856	-0.917	4.750	-51.429	-51.402	-0.001	-0.012	-0.014	0.000
4	A	7	VAL	0	0.022	0.005	5.685	3.306	3.306	0.000	0.000	0.000	0.000
5	A	8	GLY	0	0.008	0.006	9.483	0.324	0.324	0.000	0.000	0.000	0.000
6	A	9	ALA	0	-0.031	-0.016	12.683	-0.520	-0.520	0.000	0.000	0.000	0.000
7	A	10	TRP	0	0.005	0.010	13.939	0.237	0.237	0.000	0.000	0.000	0.000
8	A	11	GLY	0	0.045	-0.002	17.512	-0.061	-0.061	0.000	0.000	0.000	0.000
9	A	12	GLY	0	0.003	0.004	20.374	0.219	0.219	0.000	0.000	0.000	0.000
10	A	13	ASN	0	-0.057	-0.049	20.277	-1.207	-1.207	0.000	0.000	0.000	0.000
11	A	14	GLY	0	0.028	0.036	21.482	0.093	0.093	0.000	0.000	0.000	0.000
12	A	15	GLY	0	0.058	0.043	21.302	-0.707	-0.707	0.000	0.000	0.000	0.000
13	A	16	SER	0	-0.066	-0.021	20.393	-0.139	-0.139	0.000	0.000	0.000	0.000
14	A	17	ALA	0	0.005	-0.010	14.744	-0.237	-0.237	0.000	0.000	0.000	0.000
15	A	18	PHE	0	0.009	0.011	13.871	0.356	0.356	0.000	0.000	0.000	0.000
16	A	19	ASP	-1	-0.790	-0.899	8.483	-37.434	-37.434	0.000	0.000	0.000	0.000
17	A	20	MET	0	-0.068	-0.003	10.479	2.343	2.343	0.000	0.000	0.000	0.000
18	A	21	GLY	0	0.004	0.017	6.742	0.331	0.331	0.000	0.000	0.000	0.000
20	A	23	ALA	0	-0.026	-0.018	7.035	2.696	2.696	0.000	0.000	0.000	0.000
21	A	24	TYR	0	-0.030	-0.009	9.934	-1.319	-1.319	0.000	0.000	0.000	0.000
22	A	25	ARG	1	0.916	0.944	12.209	16.270	16.270	0.000	0.000	0.000	0.000
23	A	26	ILE	0	-0.001	0.005	12.070	0.552	0.552	0.000	0.000	0.000	0.000
24	A	27	ILE	0	-0.027	-0.012	15.220	0.656	0.656	0.000	0.000	0.000	0.000
25	A	28	SER	0	-0.026	-0.033	18.795	0.895	0.895	0.000	0.000	0.000	0.000
26	A	29	VAL	0	0.020	0.002	16.845	-0.990	-0.990	0.000	0.000	0.000	0.000
27	A	30	LYS	1	0.839	0.921	19.659	12.843	12.843	0.000	0.000	0.000	0.000
28	A	31	ILE	0	0.026	0.016	21.145	-0.267	-0.267	0.000	0.000	0.000	0.000
29	A	32	PHE	0	-0.039	-0.019	23.536	0.648	0.648	0.000	0.000	0.000	0.000
30	A	33	SER	0	0.008	-0.006	25.875	-0.370	-0.370	0.000	0.000	0.000	0.000
31	A	34	GLY	0	0.013	0.034	28.407	0.356	0.356	0.000	0.000	0.000	0.000
32	A	35	ASP	-1	-0.846	-0.914	31.473	-9.667	-9.667	0.000	0.000	0.000	0.000
33	A	36	VAL	0	0.035	0.042	26.707	-0.186	-0.186	0.000	0.000	0.000	0.000
34	A	37	VAL	0	-0.051	-0.032	22.653	0.114	0.114	0.000	0.000	0.000	0.000
35	A	38	ASP	-1	-0.810	-0.919	24.603	-11.328	-11.328	0.000	0.000	0.000	0.000
36	A	39	ALA	0	0.058	0.032	22.742	-0.357	-0.357	0.000	0.000	0.000	0.000
37	A	40	VAL	0	-0.048	-0.028	17.736	0.018	0.018	0.000	0.000	0.000	0.000
38	A	41	ASP	-1	-0.848	-0.893	19.939	-13.997	-13.997	0.000	0.000	0.000	0.000
39	A	42	VAL	0	0.003	-0.008	14.329	-0.250	-0.250	0.000	0.000	0.000	0.000
40	A	43	THR	0	0.006	0.016	17.701	0.049	0.049	0.000	0.000	0.000	0.000
41	A	44	PHE	0	0.024	0.010	13.411	-0.488	-0.488	0.000	0.000	0.000	0.000
42	A	45	THR	0	0.043	0.022	15.566	0.658	0.658	0.000	0.000	0.000	0.000
43	A	46	TYR	0	0.025	-0.010	9.943	-0.528	-0.528	0.000	0.000	0.000	0.000
44	A	47	TYR	0	-0.014	-0.010	9.831	0.661	0.661	0.000	0.000	0.000	0.000
45	A	48	GLY	0	0.023	0.019	15.366	0.788	0.788	0.000	0.000	0.000	0.000
46	A	49	LYS	1	0.885	0.948	17.432	18.063	18.063	0.000	0.000	0.000	0.000
47	A	50	THR	0	0.017	0.006	18.186	-0.732	-0.732	0.000	0.000	0.000	0.000
48	A	51	GLU	-1	-0.827	-0.888	16.045	-16.790	-16.790	0.000	0.000	0.000	0.000
49	A	52	THR	0	0.043	0.005	18.337	-0.052	-0.052	0.000	0.000	0.000	0.000
50	A	53	ARG	1	0.746	0.864	15.220	18.250	18.250	0.000	0.000	0.000	0.000
51	A	54	HIS	1	0.869	0.925	18.705	13.913	13.913	0.000	0.000	0.000	0.000
52	A	55	PHE	0	-0.024	-0.023	14.290	-0.521	-0.521	0.000	0.000	0.000	0.000
53	A	56	GLY	0	0.042	0.011	19.571	0.259	0.259	0.000	0.000	0.000	0.000
54	A	57	GLY	0	0.071	0.061	22.187	0.212	0.212	0.000	0.000	0.000	0.000
55	A	58	SER	0	-0.040	-0.016	25.744	-0.435	-0.435	0.000	0.000	0.000	0.000
56	A	59	GLY	0	0.060	0.030	28.572	0.257	0.257	0.000	0.000	0.000	0.000
57	A	60	GLY	0	0.012	0.013	29.415	-0.265	-0.265	0.000	0.000	0.000	0.000
58	A	61	THR	0	-0.047	-0.026	30.834	0.311	0.311	0.000	0.000	0.000	0.000
59	A	62	PRO	0	-0.010	0.001	27.803	-0.346	-0.346	0.000	0.000	0.000	0.000
60	A	63	HIS	1	0.850	0.917	26.294	11.578	11.578	0.000	0.000	0.000	0.000
61	A	64	GLU	-1	-0.859	-0.922	24.461	-12.614	-12.614	0.000	0.000	0.000	0.000
62	A	65	ILE	0	-0.027	0.002	20.662	0.349	0.349	0.000	0.000	0.000	0.000
63	A	66	VAL	0	0.028	-0.001	21.965	-0.501	-0.501	0.000	0.000	0.000	0.000
64	A	67	LEU	0	-0.070	-0.022	16.793	0.230	0.230	0.000	0.000	0.000	0.000
65	A	68	GLN	0	-0.010	-0.009	21.042	0.436	0.436	0.000	0.000	0.000	0.000
66	A	69	GLU	-1	-0.887	-0.933	21.447	-14.030	-14.030	0.000	0.000	0.000	0.000
67	A	70	GLY	0	0.012	0.014	20.714	-0.592	-0.592	0.000	0.000	0.000	0.000
68	A	71	GLU	-1	-0.848	-0.914	20.433	-13.377	-13.377	0.000	0.000	0.000	0.000
69	A	72	TYR	0	0.047	0.011	15.032	-0.902	-0.902	0.000	0.000	0.000	0.000
70	A	73	LEU	0	0.017	0.001	14.290	0.887	0.887	0.000	0.000	0.000	0.000
71	A	74	VAL	0	0.054	0.020	14.103	-1.572	-1.572	0.000	0.000	0.000	0.000
72	A	75	GLY	0	0.023	0.011	16.092	0.267	0.267	0.000	0.000	0.000	0.000
73	A	76	MET	0	-0.030	0.006	15.256	-0.279	-0.279	0.000	0.000	0.000	0.000
74	A	77	LYS	1	0.939	0.960	17.407	13.554	13.554	0.000	0.000	0.000	0.000
75	A	78	GLY	0	0.071	0.029	20.509	0.001	0.001	0.000	0.000	0.000	0.000
76	A	79	GLU	-1	-0.814	-0.887	22.615	-11.124	-11.124	0.000	0.000	0.000	0.000
77	A	80	PHE	0	-0.007	0.009	21.578	-0.191	-0.191	0.000	0.000	0.000	0.000
78	A	81	GLY	0	0.049	0.024	24.305	0.269	0.269	0.000	0.000	0.000	0.000
79	A	82	ASN	0	-0.057	-0.023	27.254	-0.090	-0.090	0.000	0.000	0.000	0.000
80	A	83	TYR	0	-0.006	-0.022	29.552	0.281	0.281	0.000	0.000	0.000	0.000
81	A	84	HIS	0	-0.009	-0.010	31.164	-0.071	-0.071	0.000	0.000	0.000	0.000
82	A	85	GLY	0	0.030	0.024	32.304	0.142	0.142	0.000	0.000	0.000	0.000
83	A	86	VAL	0	-0.025	-0.005	25.944	-0.205	-0.205	0.000	0.000	0.000	0.000
84	A	87	VAL	0	-0.060	-0.023	23.992	0.116	0.116	0.000	0.000	0.000	0.000
85	A	88	VAL	0	0.028	0.016	23.460	-0.518	-0.518	0.000	0.000	0.000	0.000
86	A	89	VAL	0	-0.001	-0.015	19.835	0.067	0.067	0.000	0.000	0.000	0.000
87	A	90	GLY	0	0.024	0.013	23.108	0.350	0.350	0.000	0.000	0.000	0.000
88	A	91	LYS	1	0.833	0.891	25.059	11.234	11.234	0.000	0.000	0.000	0.000
89	A	92	LEU	0	0.000	-0.003	18.685	-0.621	-0.621	0.000	0.000	0.000	0.000
90	A	93	GLY	0	-0.007	0.003	21.680	0.654	0.654	0.000	0.000	0.000	0.000
91	A	94	PHE	0	-0.012	-0.007	15.500	-0.895	-0.895	0.000	0.000	0.000	0.000
92	A	95	SER	0	-0.006	0.003	19.107	0.981	0.981	0.000	0.000	0.000	0.000
93	A	96	THR	0	-0.007	-0.025	18.718	-0.852	-0.852	0.000	0.000	0.000	0.000
94	A	97	ASN	0	-0.031	-0.020	19.488	0.507	0.507	0.000	0.000	0.000	0.000
95	A	98	LYS	1	0.871	0.946	21.192	13.774	13.774	0.000	0.000	0.000	0.000
96	A	99	LYS	1	0.953	0.983	23.763	11.747	11.747	0.000	0.000	0.000	0.000
97	A	100	SER	0	0.041	0.021	23.413	-0.815	-0.815	0.000	0.000	0.000	0.000
98	A	101	TYR	0	-0.038	-0.027	22.646	0.744	0.744	0.000	0.000	0.000	0.000
99	A	102	GLY	0	0.024	0.038	23.993	-0.513	-0.513	0.000	0.000	0.000	0.000
100	A	103	PRO	0	-0.047	-0.055	24.958	0.075	0.075	0.000	0.000	0.000	0.000
101	A	104	PHE	0	-0.014	-0.014	24.088	0.550	0.550	0.000	0.000	0.000	0.000
102	A	105	GLY	0	0.066	0.043	26.341	-0.478	-0.478	0.000	0.000	0.000	0.000
103	A	106	ASN	0	-0.052	-0.035	28.724	-0.122	-0.122	0.000	0.000	0.000	0.000
104	A	107	THR	0	-0.007	-0.007	29.428	0.380	0.380	0.000	0.000	0.000	0.000
105	A	108	GLY	0	-0.042	-0.025	28.980	-0.401	-0.401	0.000	0.000	0.000	0.000
106	A	109	GLY	0	-0.020	-0.022	28.015	0.096	0.096	0.000	0.000	0.000	0.000
107	A	110	THR	0	-0.008	0.006	24.063	0.262	0.262	0.000	0.000	0.000	0.000
108	A	111	PRO	0	-0.007	-0.003	24.443	-0.467	-0.467	0.000	0.000	0.000	0.000
109	A	112	PHE	0	0.001	0.004	17.579	-0.339	-0.339	0.000	0.000	0.000	0.000
110	A	113	SER	0	-0.055	-0.051	19.486	0.742	0.742	0.000	0.000	0.000	0.000
111	A	114	LEU	0	0.006	0.016	11.734	-0.164	-0.164	0.000	0.000	0.000	0.000
112	A	115	PRO	0	0.008	0.006	16.299	-0.193	-0.193	0.000	0.000	0.000	0.000
113	A	116	ILE	0	-0.039	-0.021	11.928	-0.587	-0.587	0.000	0.000	0.000	0.000
114	A	117	ALA	0	-0.006	-0.007	15.200	0.486	0.486	0.000	0.000	0.000	0.000
115	A	118	ALA	0	-0.002	-0.006	14.027	0.934	0.934	0.000	0.000	0.000	0.000
116	A	119	GLY	0	0.029	0.036	10.798	-1.409	-1.409	0.000	0.000	0.000	0.000
117	A	120	LYS	1	0.768	0.873	9.603	30.767	30.767	0.000	0.000	0.000	0.000
118	A	121	ILE	0	-0.007	-0.008	9.444	-3.256	-3.256	0.000	0.000	0.000	0.000
119	A	122	SER	0	-0.070	-0.046	6.236	1.800	1.800	0.000	0.000	0.000	0.000
120	A	123	GLY	0	0.014	0.000	8.773	1.156	1.156	0.000	0.000	0.000	0.000
121	A	124	PHE	0	-0.002	-0.007	9.376	-0.897	-0.897	0.000	0.000	0.000	0.000
122	A	125	PHE	0	-0.034	-0.021	7.836	-1.518	-1.518	0.000	0.000	0.000	0.000
123	A	126	GLY	0	0.018	0.010	11.073	0.749	0.749	0.000	0.000	0.000	0.000
124	A	127	ARG	1	0.816	0.896	14.148	16.276	16.276	0.000	0.000	0.000	0.000
125	A	128	GLY	0	0.028	0.015	17.615	0.158	0.158	0.000	0.000	0.000	0.000
126	A	129	GLY	0	0.000	-0.001	20.606	-0.028	-0.028	0.000	0.000	0.000	0.000
127	A	130	ASP	-1	-0.935	-0.961	24.228	-10.658	-10.658	0.000	0.000	0.000	0.000
128	A	131	PHE	0	0.043	0.021	25.190	0.110	0.110	0.000	0.000	0.000	0.000
129	A	132	ILE	0	-0.002	0.001	18.965	-0.653	-0.653	0.000	0.000	0.000	0.000
130	A	133	ASP	-1	-0.836	-0.927	20.675	-13.407	-13.407	0.000	0.000	0.000	0.000
131	A	134	ALA	0	0.015	0.000	17.175	0.079	0.079	0.000	0.000	0.000	0.000
132	A	135	ILE	0	-0.023	-0.005	14.578	-0.506	-0.506	0.000	0.000	0.000	0.000
133	A	136	GLY	0	0.002	0.005	11.427	0.550	0.550	0.000	0.000	0.000	0.000
134	A	137	VAL	0	0.008	0.004	9.186	0.502	0.502	0.000	0.000	0.000	0.000
136	A	139	LEU	0	-0.002	-0.011	5.068	6.200	6.200	0.000	0.000	0.000	0.000
138	A	141	PRO	-1	-0.812	-0.894	6.106	-23.283	-23.283	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:ALA)