FMO DATABASE

FMODB ID: 7KVYK

Calculation Name: 4AOC-B-Xray547

Preferred Name:

Target Type:

Ligand Name: methyl l-glycero-alpha-d-manno-heptopyranoside | sulfate ion | calcium ion

Ligand 3-letter code: A1Q | SO4 | CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4AOC

Chain ID: B

ChEMBL ID:

UniProt ID: A0A0H2

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	120
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-901895.539494
FMO2-HF: Nuclear repulsion	857216.542932
FMO2-HF: Total energy	-44678.996561
FMO2-MP2: Total energy	-44812.764345

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:9:ARG)

Summations of interaction energy for fragment #1(A:9:ARG)

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.
-375.051	-365.459	31.675	-17.238	-24.024	-0.235

Interaction energy analysis for fragmet #1(A:9:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.691 / q_NPA : 1.859

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	11	GLY	0	0.018	0.003	1.988	-23.129	-23.692	7.328	-2.440	-4.325	-0.061
4	A	12	GLU	-1	-0.875	-0.952	3.794	-46.279	-46.009	0.006	-0.098	-0.177	-0.001
5	A	13	PHE	0	-0.033	-0.007	4.749	-11.808	-11.724	-0.001	-0.004	-0.078	0.000
63	A	71	PHE	0	0.011	0.003	3.608	3.431	3.690	0.000	-0.053	-0.206	0.000
73	A	81	ALA	0	-0.021	0.005	3.525	-4.927	-4.781	0.001	-0.031	-0.115	0.000
74	A	82	THR	0	0.005	-0.012	3.362	0.981	2.051	0.007	-0.459	-0.618	0.000
75	A	83	ASP	-1	-0.872	-0.944	1.871	-221.840	-216.918	23.310	-12.881	-15.351	-0.154
76	A	84	ALA	0	-0.026	-0.010	2.475	15.933	17.341	0.574	-0.463	-1.519	-0.011
77	A	85	ARG	1	0.866	0.930	3.872	46.438	47.038	0.001	-0.147	-0.453	-0.001
108	A	116	TYR	0	-0.110	-0.057	2.669	-13.390	-11.994	0.449	-0.662	-1.182	-0.007
6	A	14	SER	0	0.018	0.003	7.072	5.283	5.283	0.000	0.000	0.000	0.000
7	A	15	ILE	0	-0.024	0.006	10.072	0.324	0.324	0.000	0.000	0.000	0.000
8	A	16	PRO	0	0.017	0.006	12.681	0.751	0.751	0.000	0.000	0.000	0.000
9	A	17	PRO	0	0.033	0.010	16.444	-0.319	-0.319	0.000	0.000	0.000	0.000
10	A	18	ASN	0	-0.035	-0.006	18.447	0.520	0.520	0.000	0.000	0.000	0.000
11	A	19	THR	0	-0.035	0.000	17.319	0.950	0.950	0.000	0.000	0.000	0.000
12	A	20	ASP	-1	-0.831	-0.911	18.367	-26.217	-26.217	0.000	0.000	0.000	0.000
13	A	21	PHE	0	-0.058	-0.052	14.073	-0.670	-0.670	0.000	0.000	0.000	0.000
14	A	22	ARG	1	0.903	0.956	17.887	26.112	26.112	0.000	0.000	0.000	0.000
15	A	23	ALA	0	0.005	-0.014	14.997	-2.339	-2.339	0.000	0.000	0.000	0.000
16	A	24	ILE	0	0.026	0.013	15.766	1.645	1.645	0.000	0.000	0.000	0.000
17	A	25	PHE	0	-0.010	-0.011	14.886	-2.964	-2.964	0.000	0.000	0.000	0.000
18	A	26	PHE	0	0.000	-0.021	15.682	2.449	2.449	0.000	0.000	0.000	0.000
19	A	27	ALA	0	0.015	0.008	15.255	-2.663	-2.663	0.000	0.000	0.000	0.000
20	A	28	ASN	0	-0.115	-0.058	14.200	4.002	4.002	0.000	0.000	0.000	0.000
21	A	29	ALA	0	0.090	0.068	14.468	0.303	0.303	0.000	0.000	0.000	0.000
22	A	30	ALA	0	-0.043	-0.030	16.409	1.608	1.608	0.000	0.000	0.000	0.000
23	A	31	GLU	-1	-0.854	-0.918	16.847	-27.034	-27.034	0.000	0.000	0.000	0.000
24	A	32	GLN	0	-0.048	-0.036	17.624	-0.958	-0.958	0.000	0.000	0.000	0.000
25	A	33	GLN	0	-0.006	-0.020	12.605	-3.259	-3.259	0.000	0.000	0.000	0.000
26	A	34	HIS	0	-0.033	-0.025	15.574	1.824	1.824	0.000	0.000	0.000	0.000
27	A	35	ILE	0	0.016	0.008	12.807	-2.374	-2.374	0.000	0.000	0.000	0.000
28	A	36	LYS	1	0.873	0.929	13.878	39.264	39.264	0.000	0.000	0.000	0.000
29	A	37	LEU	0	0.007	0.005	11.978	-3.873	-3.873	0.000	0.000	0.000	0.000
30	A	38	PHE	0	0.011	0.005	12.601	2.941	2.941	0.000	0.000	0.000	0.000
31	A	39	ILE	0	0.004	0.008	12.998	-2.500	-2.500	0.000	0.000	0.000	0.000
32	A	40	GLY	0	0.020	0.000	14.116	1.738	1.738	0.000	0.000	0.000	0.000
33	A	41	ASP	-1	-0.915	-0.963	14.701	-35.001	-35.001	0.000	0.000	0.000	0.000
34	A	42	SER	0	-0.073	-0.028	16.955	1.687	1.687	0.000	0.000	0.000	0.000
35	A	43	GLN	0	-0.032	-0.038	17.136	-1.648	-1.648	0.000	0.000	0.000	0.000
36	A	44	GLU	-1	-0.883	-0.931	19.024	-27.781	-27.781	0.000	0.000	0.000	0.000
37	A	45	PRO	0	-0.070	-0.019	16.880	-0.855	-0.855	0.000	0.000	0.000	0.000
38	A	46	ALA	0	-0.008	-0.011	17.078	1.613	1.613	0.000	0.000	0.000	0.000
39	A	47	ALA	0	-0.011	-0.012	16.984	1.253	1.253	0.000	0.000	0.000	0.000
40	A	48	TYR	0	-0.035	-0.026	17.039	-1.193	-1.193	0.000	0.000	0.000	0.000
41	A	49	HIS	0	0.004	0.010	18.309	2.195	2.195	0.000	0.000	0.000	0.000
42	A	50	LYS	1	0.880	0.949	18.722	25.304	25.304	0.000	0.000	0.000	0.000
43	A	51	LEU	0	-0.036	-0.009	18.190	1.387	1.387	0.000	0.000	0.000	0.000
44	A	52	THR	0	-0.007	-0.007	18.113	-1.202	-1.202	0.000	0.000	0.000	0.000
45	A	53	THR	0	0.042	0.004	19.284	-0.135	-0.135	0.000	0.000	0.000	0.000
46	A	54	ARG	1	0.911	0.953	20.481	23.816	23.816	0.000	0.000	0.000	0.000
47	A	55	ASP	-1	-0.830	-0.878	22.153	-25.131	-25.131	0.000	0.000	0.000	0.000
48	A	56	GLY	0	0.027	0.032	22.884	0.745	0.745	0.000	0.000	0.000	0.000
49	A	57	PRO	0	-0.001	-0.003	20.700	-1.000	-1.000	0.000	0.000	0.000	0.000
50	A	58	ARG	1	0.820	0.895	20.269	27.916	27.916	0.000	0.000	0.000	0.000
51	A	59	GLU	-1	-0.889	-0.950	19.803	-28.411	-28.411	0.000	0.000	0.000	0.000
52	A	60	ALA	0	-0.015	0.005	18.588	1.046	1.046	0.000	0.000	0.000	0.000
53	A	61	THR	0	-0.028	-0.021	19.578	-0.462	-0.462	0.000	0.000	0.000	0.000
54	A	62	LEU	0	-0.011	0.009	16.372	0.744	0.744	0.000	0.000	0.000	0.000
55	A	63	ASN	0	0.048	0.012	19.242	-0.755	-0.755	0.000	0.000	0.000	0.000
56	A	64	SER	0	-0.024	-0.028	15.137	-0.122	-0.122	0.000	0.000	0.000	0.000
57	A	65	GLY	0	0.045	0.036	16.288	-1.111	-1.111	0.000	0.000	0.000	0.000
58	A	66	ASN	0	0.008	-0.015	15.782	-0.294	-0.294	0.000	0.000	0.000	0.000
59	A	67	GLY	0	0.005	-0.003	14.846	-0.191	-0.191	0.000	0.000	0.000	0.000
60	A	68	LYS	1	0.852	0.936	11.195	37.926	37.926	0.000	0.000	0.000	0.000
61	A	69	ILE	0	0.033	0.018	9.989	2.373	2.373	0.000	0.000	0.000	0.000
62	A	70	ARG	1	0.871	0.947	8.403	35.873	35.873	0.000	0.000	0.000	0.000
64	A	72	GLU	-1	-0.866	-0.925	9.127	-44.887	-44.887	0.000	0.000	0.000	0.000
65	A	73	VAL	0	0.012	0.006	9.659	2.833	2.833	0.000	0.000	0.000	0.000
66	A	74	SER	0	-0.020	0.006	10.878	-1.126	-1.126	0.000	0.000	0.000	0.000
67	A	75	VAL	0	0.065	0.033	13.064	1.850	1.850	0.000	0.000	0.000	0.000
68	A	76	ASN	0	-0.070	-0.045	15.259	0.348	0.348	0.000	0.000	0.000	0.000
69	A	77	GLY	0	-0.017	-0.010	17.750	0.392	0.392	0.000	0.000	0.000	0.000
70	A	78	LYS	1	0.940	0.985	13.077	34.091	34.091	0.000	0.000	0.000	0.000
71	A	79	PRO	0	-0.008	-0.005	9.919	0.321	0.321	0.000	0.000	0.000	0.000
72	A	80	SER	0	0.047	0.011	8.407	1.249	1.249	0.000	0.000	0.000	0.000
78	A	86	LEU	0	0.056	0.030	6.405	4.929	4.929	0.000	0.000	0.000	0.000
79	A	87	ALA	0	-0.047	-0.025	9.232	-0.621	-0.621	0.000	0.000	0.000	0.000
80	A	88	PRO	0	0.015	0.022	12.694	1.988	1.988	0.000	0.000	0.000	0.000
81	A	89	ILE	0	0.026	0.017	15.485	0.491	0.491	0.000	0.000	0.000	0.000
82	A	90	ASN	0	-0.017	-0.004	17.823	1.542	1.542	0.000	0.000	0.000	0.000
83	A	91	GLY	0	0.027	0.017	21.226	0.083	0.083	0.000	0.000	0.000	0.000
84	A	92	LYS	1	0.897	0.949	24.949	20.630	20.630	0.000	0.000	0.000	0.000
85	A	93	LYS	1	0.906	0.957	28.548	19.178	19.178	0.000	0.000	0.000	0.000
86	A	94	SER	0	0.027	0.005	31.176	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	95	ASP	-1	-0.792	-0.858	33.401	-17.991	-17.991	0.000	0.000	0.000	0.000
88	A	96	GLY	0	-0.005	0.000	32.840	0.186	0.186	0.000	0.000	0.000	0.000
89	A	97	SER	0	-0.081	-0.066	30.929	-0.613	-0.613	0.000	0.000	0.000	0.000
90	A	98	PRO	0	0.019	-0.017	25.477	-0.103	-0.103	0.000	0.000	0.000	0.000
91	A	99	PHE	0	-0.020	0.001	23.614	0.532	0.532	0.000	0.000	0.000	0.000
92	A	100	THR	0	0.008	-0.013	18.661	-0.151	-0.151	0.000	0.000	0.000	0.000
93	A	101	VAL	0	-0.025	0.004	18.970	0.573	0.573	0.000	0.000	0.000	0.000
94	A	102	ASN	0	-0.033	-0.017	14.652	-2.185	-2.185	0.000	0.000	0.000	0.000
95	A	103	PHE	0	0.054	0.015	13.541	1.195	1.195	0.000	0.000	0.000	0.000
96	A	104	GLY	0	-0.013	0.002	9.484	-2.184	-2.184	0.000	0.000	0.000	0.000
97	A	105	ILE	0	-0.027	-0.006	8.405	3.713	3.713	0.000	0.000	0.000	0.000
98	A	106	VAL	0	0.002	-0.001	5.977	-9.240	-9.240	0.000	0.000	0.000	0.000
99	A	107	VAL	0	0.011	0.004	6.060	7.544	7.544	0.000	0.000	0.000	0.000
100	A	108	SER	0	-0.018	-0.046	5.775	-9.392	-9.392	0.000	0.000	0.000	0.000
101	A	109	GLU	0	0.050	0.050	5.984	5.577	5.577	0.000	0.000	0.000	0.000
102	A	110	ASP	-1	-0.875	-0.958	7.515	-43.381	-43.381	0.000	0.000	0.000	0.000
103	A	111	GLY	0	-0.041	-0.023	10.021	0.998	0.998	0.000	0.000	0.000	0.000
104	A	112	HIS	0	-0.050	-0.007	10.807	2.245	2.245	0.000	0.000	0.000	0.000
105	A	113	ASP	-1	-0.831	-0.932	11.599	-38.529	-38.529	0.000	0.000	0.000	0.000
106	A	114	SER	0	-0.102	-0.057	7.750	-2.129	-2.129	0.000	0.000	0.000	0.000
107	A	115	ASP	-1	-0.835	-0.909	8.310	-46.113	-46.113	0.000	0.000	0.000	0.000
109	A	117	ASN	0	-0.024	-0.031	7.537	-2.401	-2.401	0.000	0.000	0.000	0.000
110	A	118	ASP	-1	-0.731	-0.838	10.598	-43.436	-43.436	0.000	0.000	0.000	0.000
111	A	119	GLY	0	0.014	0.002	10.743	4.120	4.120	0.000	0.000	0.000	0.000
112	A	120	ILE	0	-0.070	-0.011	10.523	-5.675	-5.675	0.000	0.000	0.000	0.000
113	A	121	VAL	0	-0.007	-0.006	10.686	3.840	3.840	0.000	0.000	0.000	0.000
114	A	122	VAL	0	-0.027	-0.009	10.964	-3.935	-3.935	0.000	0.000	0.000	0.000
115	A	123	LEU	0	-0.013	0.000	10.009	2.487	2.487	0.000	0.000	0.000	0.000
116	A	124	GLN	0	0.000	-0.020	13.303	-0.452	-0.452	0.000	0.000	0.000	0.000
117	A	125	TRP	0	0.047	0.032	11.287	0.496	0.496	0.000	0.000	0.000	0.000
118	A	126	PRO	0	-0.010	-0.022	18.085	-0.757	-0.757	0.000	0.000	0.000	0.000
119	A	127	ILE	0	-0.019	-0.013	20.112	-0.262	-0.262	0.000	0.000	0.000	0.000
120	A	128	GLY	-1	-0.903	-0.916	22.681	-21.453	-21.453	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:9:ARG)