FMO DATABASE

FMODB ID: 9LKV2

Calculation Name: 1LRH-A-Xray547

Preferred Name:

Target Type:

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose | beta-d-mannopyranose | alpha-d-mannopyranose | naphthalen-1-yl-acetic acid

Ligand 3-letter code: NAG | BMA | MAN | NLA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1LRH

Chain ID: A

ChEMBL ID:

UniProt ID: P13689

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
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	159
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1587231.396342
FMO2-HF: Nuclear repulsion	1523510.818144
FMO2-HF: Total energy	-63720.578198
FMO2-MP2: Total energy	-63904.813974

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:1:SER)

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

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.
-167.713	-167.956	13.17	-6.757	-6.17	-0.091

Interaction energy analysis for fragmet #1(A:1:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.802 / q_NPA : 0.889

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	3	VAL	0	0.033	0.019	3.500	-0.970	0.703	0.025	-0.748	-0.950	-0.001
154	A	154	ASP	-1	-0.802	-0.898	1.774	-118.972	-120.888	13.145	-6.009	-5.220	-0.090
4	A	4	ARG	1	0.926	0.963	5.735	32.979	32.979	0.000	0.000	0.000	0.000
5	A	5	ASP	-1	-0.829	-0.902	9.079	-22.065	-22.065	0.000	0.000	0.000	0.000
6	A	6	ASN	0	-0.016	-0.016	11.581	0.566	0.566	0.000	0.000	0.000	0.000
7	A	7	SER	0	-0.033	-0.023	14.305	1.743	1.743	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.032	-0.014	16.602	-0.319	-0.319	0.000	0.000	0.000	0.000
9	A	9	VAL	0	-0.014	-0.010	19.531	0.221	0.221	0.000	0.000	0.000	0.000
10	A	10	ARG	1	0.868	0.924	13.780	19.134	19.134	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.798	-0.864	16.265	-16.549	-16.549	0.000	0.000	0.000	0.000
12	A	12	ILE	0	0.032	-0.007	15.088	-1.249	-1.249	0.000	0.000	0.000	0.000
13	A	13	SER	0	-0.084	-0.062	14.290	-1.096	-1.096	0.000	0.000	0.000	0.000
14	A	14	GLN	0	-0.029	-0.019	12.770	-1.003	-1.003	0.000	0.000	0.000	0.000
15	A	15	MET	0	-0.092	-0.017	10.380	-1.952	-1.952	0.000	0.000	0.000	0.000
16	A	16	PRO	0	-0.024	-0.009	6.042	1.117	1.117	0.000	0.000	0.000	0.000
17	A	17	GLN	0	0.025	0.020	7.708	-1.555	-1.555	0.000	0.000	0.000	0.000
18	A	18	SER	0	0.006	-0.005	7.011	-0.056	-0.056	0.000	0.000	0.000	0.000
19	A	19	SER	0	0.076	0.045	9.370	0.660	0.660	0.000	0.000	0.000	0.000
20	A	20	TYR	0	-0.069	-0.043	5.438	3.047	3.047	0.000	0.000	0.000	0.000
21	A	21	GLY	0	0.024	0.021	9.233	0.645	0.645	0.000	0.000	0.000	0.000
22	A	22	ILE	0	-0.050	-0.019	12.059	1.916	1.916	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.883	-0.957	14.857	-19.469	-19.469	0.000	0.000	0.000	0.000
24	A	24	GLY	0	0.043	0.028	17.202	0.902	0.902	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.087	-0.019	13.503	0.571	0.571	0.000	0.000	0.000	0.000
26	A	26	SER	0	-0.013	-0.004	13.384	-1.746	-1.746	0.000	0.000	0.000	0.000
27	A	27	HIS	1	0.843	0.897	10.560	25.972	25.972	0.000	0.000	0.000	0.000
28	A	28	ILE	0	0.067	0.025	10.974	-2.547	-2.547	0.000	0.000	0.000	0.000
29	A	29	THR	0	0.015	0.014	11.072	2.149	2.149	0.000	0.000	0.000	0.000
30	A	30	VAL	0	0.018	0.008	12.513	-0.909	-0.909	0.000	0.000	0.000	0.000
31	A	31	ALA	0	0.027	0.001	15.321	0.189	0.189	0.000	0.000	0.000	0.000
32	A	32	GLY	0	0.079	0.023	14.657	0.910	0.910	0.000	0.000	0.000	0.000
33	A	33	ALA	0	-0.020	-0.004	15.156	-0.345	-0.345	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.018	-0.018	10.562	0.306	0.306	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.039	-0.025	8.122	0.454	0.454	0.000	0.000	0.000	0.000
36	A	36	HIS	0	0.009	-0.003	11.113	0.852	0.852	0.000	0.000	0.000	0.000
37	A	37	GLY	0	0.015	0.029	14.568	1.299	1.299	0.000	0.000	0.000	0.000
38	A	38	MET	0	-0.073	-0.020	16.773	1.313	1.313	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.964	0.966	18.811	13.608	13.608	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.935	-0.957	21.599	-12.026	-12.026	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.007	-0.017	22.495	0.254	0.254	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.838	-0.900	15.063	-21.598	-21.598	0.000	0.000	0.000	0.000
43	A	43	VAL	0	-0.006	0.004	17.975	0.697	0.697	0.000	0.000	0.000	0.000
44	A	44	TRP	0	-0.039	-0.047	14.809	-1.273	-1.273	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.010	0.009	15.789	1.355	1.355	0.000	0.000	0.000	0.000
46	A	46	GLN	0	0.004	0.003	15.599	-2.511	-2.511	0.000	0.000	0.000	0.000
47	A	47	THR	0	0.000	-0.002	17.091	1.046	1.046	0.000	0.000	0.000	0.000
48	A	48	ILE	0	-0.010	0.002	17.974	-1.003	-1.003	0.000	0.000	0.000	0.000
49	A	49	SER	0	0.092	0.047	20.455	0.468	0.468	0.000	0.000	0.000	0.000
50	A	50	PRO	0	0.009	-0.006	22.318	0.021	0.021	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.025	0.027	25.450	-0.216	-0.216	0.000	0.000	0.000	0.000
52	A	52	GLN	0	-0.081	-0.031	20.679	0.606	0.606	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.899	0.934	22.549	11.382	11.382	0.000	0.000	0.000	0.000
54	A	54	THR	0	-0.006	0.012	20.065	-0.523	-0.523	0.000	0.000	0.000	0.000
55	A	55	PRO	0	0.044	0.019	18.690	0.644	0.644	0.000	0.000	0.000	0.000
56	A	56	ILE	0	0.045	0.041	21.723	0.024	0.024	0.000	0.000	0.000	0.000
57	A	57	HIS	0	-0.079	-0.042	21.926	-0.486	-0.486	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.889	0.953	23.962	11.908	11.908	0.000	0.000	0.000	0.000
59	A	59	HIS	1	0.878	0.920	20.943	13.155	13.155	0.000	0.000	0.000	0.000
60	A	60	SER	0	0.017	0.030	23.865	0.563	0.563	0.000	0.000	0.000	0.000
61	A	61	CYS	0	-0.072	-0.045	22.984	-0.171	-0.171	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.882	-0.933	25.448	-10.614	-10.614	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.827	-0.925	21.436	-14.922	-14.922	0.000	0.000	0.000	0.000
64	A	64	VAL	0	0.001	0.009	24.541	0.560	0.560	0.000	0.000	0.000	0.000
65	A	65	PHE	0	0.027	0.016	21.971	-0.737	-0.737	0.000	0.000	0.000	0.000
66	A	66	THR	0	0.009	0.001	24.958	0.601	0.601	0.000	0.000	0.000	0.000
67	A	67	VAL	0	0.008	0.012	25.310	-0.627	-0.627	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.018	-0.007	22.407	0.428	0.428	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.899	0.946	22.991	13.527	13.527	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.102	0.068	26.694	-0.296	-0.296	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.740	0.834	28.614	10.031	10.031	0.000	0.000	0.000	0.000
72	A	72	GLY	0	0.031	0.010	28.375	-0.457	-0.457	0.000	0.000	0.000	0.000
73	A	73	THR	0	-0.027	0.013	29.117	0.410	0.410	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.025	-0.005	27.798	-0.508	-0.508	0.000	0.000	0.000	0.000
75	A	75	LEU	0	-0.013	0.005	29.002	0.375	0.375	0.000	0.000	0.000	0.000
76	A	76	MET	0	0.009	-0.001	29.627	-0.565	-0.565	0.000	0.000	0.000	0.000
77	A	77	GLY	0	0.046	0.027	31.615	0.316	0.316	0.000	0.000	0.000	0.000
78	A	78	SER	0	-0.030	-0.024	33.397	0.049	0.049	0.000	0.000	0.000	0.000
79	A	79	SER	0	0.026	-0.025	33.022	-0.009	-0.009	0.000	0.000	0.000	0.000
80	A	80	SER	0	-0.069	-0.023	34.521	0.124	0.124	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.007	0.011	37.297	0.234	0.234	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.932	0.944	36.645	7.989	7.989	0.000	0.000	0.000	0.000
83	A	83	TYR	0	0.013	0.024	33.709	-0.122	-0.122	0.000	0.000	0.000	0.000
84	A	84	PRO	0	-0.032	0.007	30.407	0.211	0.211	0.000	0.000	0.000	0.000
85	A	85	GLY	0	0.041	0.016	33.334	0.202	0.202	0.000	0.000	0.000	0.000
86	A	86	GLN	0	-0.003	-0.012	34.689	-0.376	-0.376	0.000	0.000	0.000	0.000
87	A	87	PRO	0	-0.016	0.012	32.425	0.156	0.156	0.000	0.000	0.000	0.000
88	A	88	GLN	0	-0.027	-0.014	34.736	0.338	0.338	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.886	-0.962	34.046	-9.566	-9.566	0.000	0.000	0.000	0.000
90	A	90	ILE	0	-0.020	-0.012	33.418	0.282	0.282	0.000	0.000	0.000	0.000
91	A	91	PRO	0	-0.006	0.006	32.830	-0.348	-0.348	0.000	0.000	0.000	0.000
92	A	92	PHE	0	-0.022	-0.004	26.871	0.090	0.090	0.000	0.000	0.000	0.000
93	A	93	PHE	0	0.031	-0.002	31.658	-0.057	-0.057	0.000	0.000	0.000	0.000
94	A	94	GLN	0	0.002	0.004	29.093	0.141	0.141	0.000	0.000	0.000	0.000
95	A	95	ASN	0	-0.043	-0.026	30.284	0.168	0.168	0.000	0.000	0.000	0.000
96	A	96	THR	0	-0.026	-0.006	31.137	0.255	0.255	0.000	0.000	0.000	0.000
97	A	97	THR	0	-0.040	-0.047	29.093	-0.370	-0.370	0.000	0.000	0.000	0.000
98	A	98	PHE	0	0.019	0.009	26.453	0.363	0.363	0.000	0.000	0.000	0.000
99	A	99	SER	0	-0.005	0.000	28.475	-0.540	-0.540	0.000	0.000	0.000	0.000
100	A	100	ILE	0	-0.009	-0.005	25.975	0.301	0.301	0.000	0.000	0.000	0.000
101	A	101	PRO	0	0.018	0.014	28.777	-0.182	-0.182	0.000	0.000	0.000	0.000
102	A	102	VAL	0	0.003	-0.005	28.231	-0.309	-0.309	0.000	0.000	0.000	0.000
103	A	103	ASN	0	-0.084	-0.059	27.576	-0.036	-0.036	0.000	0.000	0.000	0.000
104	A	104	ASP	-1	-0.789	-0.870	28.828	-9.596	-9.596	0.000	0.000	0.000	0.000
105	A	105	PRO	0	-0.081	-0.023	27.992	-0.519	-0.519	0.000	0.000	0.000	0.000
106	A	106	HIS	1	0.889	0.936	23.817	13.018	13.018	0.000	0.000	0.000	0.000
107	A	107	GLN	0	0.010	0.007	24.607	0.032	0.032	0.000	0.000	0.000	0.000
108	A	108	VAL	0	-0.017	0.002	23.359	0.455	0.455	0.000	0.000	0.000	0.000
109	A	109	TRP	0	0.002	-0.006	24.268	-0.315	-0.315	0.000	0.000	0.000	0.000
110	A	110	ASN	0	-0.004	-0.003	24.621	0.755	0.755	0.000	0.000	0.000	0.000
111	A	111	SER	0	-0.024	-0.029	26.572	-0.049	-0.049	0.000	0.000	0.000	0.000
112	A	112	ASP	-1	-0.790	-0.886	29.334	-9.618	-9.618	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.918	-0.978	29.055	-9.787	-9.787	0.000	0.000	0.000	0.000
114	A	114	HIS	0	-0.085	-0.032	30.128	-0.071	-0.071	0.000	0.000	0.000	0.000
115	A	115	GLU	-1	-0.894	-0.944	27.761	-10.575	-10.575	0.000	0.000	0.000	0.000
116	A	116	ASP	-1	-0.868	-0.940	22.620	-14.033	-14.033	0.000	0.000	0.000	0.000
117	A	117	LEU	0	-0.055	-0.004	23.675	0.286	0.286	0.000	0.000	0.000	0.000
118	A	118	GLN	0	0.003	0.005	19.303	-0.115	-0.115	0.000	0.000	0.000	0.000
119	A	119	VAL	0	0.003	-0.011	20.622	0.719	0.719	0.000	0.000	0.000	0.000
120	A	120	LEU	0	0.014	0.013	19.908	-0.968	-0.968	0.000	0.000	0.000	0.000
121	A	121	VAL	0	-0.019	-0.015	19.464	0.634	0.634	0.000	0.000	0.000	0.000
122	A	122	ILE	0	0.011	0.010	20.204	-0.721	-0.721	0.000	0.000	0.000	0.000
123	A	123	ILE	0	0.018	0.013	18.095	0.525	0.525	0.000	0.000	0.000	0.000
124	A	124	SER	0	0.044	0.015	22.062	-0.112	-0.112	0.000	0.000	0.000	0.000
125	A	125	ARG	1	0.869	0.922	22.503	11.455	11.455	0.000	0.000	0.000	0.000
126	A	126	PRO	0	0.002	0.036	17.610	-0.194	-0.194	0.000	0.000	0.000	0.000
127	A	127	PRO	0	0.032	0.005	14.619	0.622	0.622	0.000	0.000	0.000	0.000
128	A	128	ALA	0	0.029	0.021	15.806	1.291	1.291	0.000	0.000	0.000	0.000
129	A	129	LYS	1	0.844	0.921	17.030	15.698	15.698	0.000	0.000	0.000	0.000
130	A	130	ILE	0	0.002	-0.002	16.671	1.026	1.026	0.000	0.000	0.000	0.000
131	A	131	PHE	0	-0.024	-0.010	19.935	-0.274	-0.274	0.000	0.000	0.000	0.000
132	A	132	LEU	0	-0.011	-0.014	18.104	0.131	0.131	0.000	0.000	0.000	0.000
133	A	133	TYR	0	-0.013	-0.049	22.676	0.275	0.275	0.000	0.000	0.000	0.000
134	A	134	ASP	-1	-0.905	-0.959	24.995	-11.349	-11.349	0.000	0.000	0.000	0.000
135	A	135	ASP	-1	-0.738	-0.853	26.612	-9.759	-9.759	0.000	0.000	0.000	0.000
136	A	136	TRP	0	-0.037	-0.027	29.151	-0.073	-0.073	0.000	0.000	0.000	0.000
137	A	137	SER	0	-0.070	-0.059	31.953	0.246	0.246	0.000	0.000	0.000	0.000
138	A	138	MET	0	-0.024	0.030	26.852	0.089	0.089	0.000	0.000	0.000	0.000
139	A	139	PRO	0	0.014	-0.021	31.872	-0.061	-0.061	0.000	0.000	0.000	0.000
140	A	140	HIS	0	0.056	0.042	30.524	-0.688	-0.688	0.000	0.000	0.000	0.000
141	A	141	THR	0	-0.040	-0.035	29.912	-0.357	-0.357	0.000	0.000	0.000	0.000
142	A	142	ALA	0	-0.012	0.001	29.932	-0.049	-0.049	0.000	0.000	0.000	0.000
143	A	143	ALA	0	0.024	0.019	26.222	-0.329	-0.329	0.000	0.000	0.000	0.000
144	A	144	VAL	0	0.007	0.003	21.337	-0.011	-0.011	0.000	0.000	0.000	0.000
145	A	145	LEU	0	-0.063	-0.015	20.169	-0.413	-0.413	0.000	0.000	0.000	0.000
146	A	146	LYS	1	0.853	0.923	12.498	22.701	22.701	0.000	0.000	0.000	0.000
147	A	147	PHE	0	-0.010	-0.005	15.834	-0.565	-0.565	0.000	0.000	0.000	0.000
148	A	148	PRO	0	0.027	0.018	11.501	0.791	0.791	0.000	0.000	0.000	0.000
149	A	149	PHE	0	0.039	0.005	12.942	0.567	0.567	0.000	0.000	0.000	0.000
150	A	150	VAL	0	0.048	0.016	9.757	-1.846	-1.846	0.000	0.000	0.000	0.000
151	A	151	TRP	0	-0.008	-0.001	7.610	-3.586	-3.586	0.000	0.000	0.000	0.000
152	A	152	ASP	-1	-0.922	-0.965	7.972	-27.705	-27.705	0.000	0.000	0.000	0.000
153	A	153	GLU	-1	-0.863	-0.935	7.830	-30.541	-30.541	0.000	0.000	0.000	0.000
155	A	156	PHE	0	-0.006	0.002	7.124	3.729	3.729	0.000	0.000	0.000	0.000
156	A	157	GLU	-1	-0.796	-0.895	7.114	-23.203	-23.203	0.000	0.000	0.000	0.000
157	A	158	ALA	0	-0.024	-0.008	5.715	1.646	1.646	0.000	0.000	0.000	0.000
158	A	159	ALA	0	-0.088	-0.046	7.828	1.165	1.165	0.000	0.000	0.000	0.000
159	A	160	LYS	0	-0.128	-0.051	11.212	3.336	3.336	0.000	0.000	0.000	0.000

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