FMO DATABASE

FMODB ID: G7QZ1

Calculation Name: 2E3X-B-Xray547

Preferred Name:

Target Type:

Ligand Name: 3-(n-hydroxycarboxamido)-2-isobutylpropanoyl-trp-methylamide | 2-acetamido-2-deoxy-beta-d-glucopyranose | alpha-d-mannopyranose | calcium ion

Ligand 3-letter code: GM6 | NAG | MAN | CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2E3X

Chain ID: B

ChEMBL ID:

UniProt ID: Q4PRD1

Base Structure: X-ray

Registration Date: 2025-10-06

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	130
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1227850.558744
FMO2-HF: Nuclear repulsion	1170182.85601
FMO2-HF: Total energy	-57667.702734
FMO2-MP2: Total energy	-57828.286148

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(B:1:ASP)

Summations of interaction energy for fragment #1(B:1:ASP)

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.
-15.604	-9.499	2.692	-3.736	-5.06	-0.001

Interaction energy analysis for fragmet #1(B:1:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.097 / q_NPA : -0.061

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	B	3	PRO	0	0.048	0.039	2.781	-4.514	-0.495	0.302	-1.926	-2.395	0.007
4	B	4	PRO	0	-0.009	0.020	5.272	-1.156	-1.093	-0.001	-0.003	-0.058	0.000
8	B	8	LEU	0	0.023	0.001	2.182	-1.733	-1.276	2.360	-1.175	-1.642	-0.004
128	B	131	PRO	0	-0.047	-0.033	2.883	0.537	1.036	0.030	-0.246	-0.282	-0.002
129	B	132	GLU	-1	-0.934	-0.970	4.185	0.799	1.288	-0.001	-0.063	-0.426	0.000
130	B	133	CYS	-1	-0.981	-0.981	3.562	-10.577	-9.999	0.002	-0.323	-0.257	-0.002
5	B	5	ASP	-1	-0.839	-0.926	8.745	0.744	0.744	0.000	0.000	0.000	0.000
6	B	6	SER	0	-0.038	-0.024	7.480	-0.758	-0.758	0.000	0.000	0.000	0.000
7	B	7	SER	0	-0.005	0.012	7.267	0.789	0.789	0.000	0.000	0.000	0.000
9	B	9	TYR	0	-0.076	-0.067	5.691	0.939	0.939	0.000	0.000	0.000	0.000
10	B	10	ARG	1	0.873	0.915	7.968	1.721	1.721	0.000	0.000	0.000	0.000
11	B	11	TYR	0	0.006	-0.004	6.154	0.666	0.666	0.000	0.000	0.000	0.000
12	B	12	PHE	0	0.035	0.040	7.076	-0.597	-0.597	0.000	0.000	0.000	0.000
13	B	14	TYR	0	-0.035	-0.038	7.398	0.660	0.660	0.000	0.000	0.000	0.000
14	B	15	ARG	1	0.852	0.916	10.733	0.447	0.447	0.000	0.000	0.000	0.000
15	B	16	VAL	0	0.018	0.011	12.946	-0.038	-0.038	0.000	0.000	0.000	0.000
16	B	17	PHE	0	0.034	0.013	15.978	0.230	0.230	0.000	0.000	0.000	0.000
17	B	18	LYS	1	0.878	0.921	19.306	-0.184	-0.184	0.000	0.000	0.000	0.000
18	B	19	GLU	-1	-0.857	-0.931	22.580	-0.123	-0.123	0.000	0.000	0.000	0.000
19	B	20	HIS	0	0.017	0.006	24.767	-0.053	-0.053	0.000	0.000	0.000	0.000
20	B	21	LYS	1	0.860	0.956	23.108	0.328	0.328	0.000	0.000	0.000	0.000
21	B	22	THR	0	0.052	0.033	27.361	-0.014	-0.014	0.000	0.000	0.000	0.000
22	B	23	TRP	0	0.021	-0.004	24.214	-0.006	-0.006	0.000	0.000	0.000	0.000
23	B	24	GLU	-1	-0.900	-0.951	25.525	-0.586	-0.586	0.000	0.000	0.000	0.000
24	B	25	ALA	0	-0.025	-0.017	26.205	-0.041	-0.041	0.000	0.000	0.000	0.000
25	B	26	ALA	0	-0.039	-0.021	22.643	-0.010	-0.010	0.000	0.000	0.000	0.000
26	B	27	GLU	-1	-0.744	-0.854	20.741	-1.225	-1.225	0.000	0.000	0.000	0.000
27	B	28	ARG	1	0.858	0.921	21.362	0.428	0.428	0.000	0.000	0.000	0.000
28	B	29	PHE	0	0.014	-0.008	19.206	-0.029	-0.029	0.000	0.000	0.000	0.000
29	B	30	CYS	0	-0.107	-0.025	14.777	0.013	0.013	0.000	0.000	0.000	0.000
30	B	31	MET	0	-0.038	0.006	16.888	-0.210	-0.210	0.000	0.000	0.000	0.000
31	B	32	GLU	-1	-0.833	-0.918	18.788	-0.473	-0.473	0.000	0.000	0.000	0.000
32	B	33	HIS	0	0.009	0.002	14.344	0.088	0.088	0.000	0.000	0.000	0.000
33	B	34	PRO	0	-0.076	-0.021	13.602	-0.127	-0.127	0.000	0.000	0.000	0.000
34	B	35	ASN	0	0.078	0.024	13.634	-0.118	-0.118	0.000	0.000	0.000	0.000
35	B	36	ASN	0	-0.052	-0.037	13.312	-0.240	-0.240	0.000	0.000	0.000	0.000
36	B	37	GLY	0	0.008	0.017	14.247	-0.102	-0.102	0.000	0.000	0.000	0.000
37	B	38	HIS	1	0.817	0.891	15.013	1.803	1.803	0.000	0.000	0.000	0.000
38	B	39	LEU	0	0.030	0.013	16.367	-0.092	-0.092	0.000	0.000	0.000	0.000
39	B	40	VAL	0	-0.060	-0.029	14.851	-0.117	-0.117	0.000	0.000	0.000	0.000
40	B	41	SER	0	-0.004	-0.002	16.896	0.127	0.127	0.000	0.000	0.000	0.000
41	B	42	ILE	0	-0.035	-0.030	16.599	-0.116	-0.116	0.000	0.000	0.000	0.000
42	B	43	GLU	-1	-0.832	-0.906	17.169	-1.700	-1.700	0.000	0.000	0.000	0.000
43	B	44	SER	0	0.006	0.002	16.746	0.066	0.066	0.000	0.000	0.000	0.000
44	B	45	MET	0	0.005	-0.003	19.324	0.023	0.023	0.000	0.000	0.000	0.000
45	B	46	GLU	-1	-0.759	-0.844	14.477	-1.587	-1.587	0.000	0.000	0.000	0.000
46	B	47	GLU	-1	-0.749	-0.825	14.115	-2.066	-2.066	0.000	0.000	0.000	0.000
47	B	48	ALA	0	0.008	-0.011	15.854	0.060	0.060	0.000	0.000	0.000	0.000
48	B	49	GLU	-1	-0.836	-0.911	18.026	-0.534	-0.534	0.000	0.000	0.000	0.000
49	B	50	PHE	0	-0.012	0.008	9.306	0.126	0.126	0.000	0.000	0.000	0.000
50	B	51	VAL	0	0.027	0.002	14.682	0.145	0.145	0.000	0.000	0.000	0.000
51	B	52	ALA	0	0.036	0.035	16.147	0.149	0.149	0.000	0.000	0.000	0.000
52	B	53	LYS	1	0.864	0.935	15.322	0.094	0.094	0.000	0.000	0.000	0.000
53	B	54	LEU	0	0.039	0.027	12.424	0.198	0.198	0.000	0.000	0.000	0.000
54	B	55	LEU	0	-0.013	-0.002	15.493	0.175	0.175	0.000	0.000	0.000	0.000
55	B	56	SER	0	-0.047	-0.049	18.868	0.094	0.094	0.000	0.000	0.000	0.000
56	B	57	ASN	0	-0.032	-0.014	16.037	0.020	0.020	0.000	0.000	0.000	0.000
57	B	58	THR	0	-0.009	0.001	16.447	0.158	0.158	0.000	0.000	0.000	0.000
58	B	59	THR	0	0.040	0.006	18.278	-0.043	-0.043	0.000	0.000	0.000	0.000
59	B	60	GLY	0	0.023	0.019	21.174	-0.046	-0.046	0.000	0.000	0.000	0.000
60	B	61	LYS	1	0.878	0.916	16.506	-0.293	-0.293	0.000	0.000	0.000	0.000
61	B	62	PHE	0	0.030	0.044	21.616	-0.056	-0.056	0.000	0.000	0.000	0.000
62	B	63	ILE	0	0.006	-0.007	23.330	-0.001	-0.001	0.000	0.000	0.000	0.000
63	B	64	THR	0	-0.020	-0.014	26.050	-0.003	-0.003	0.000	0.000	0.000	0.000
64	B	65	HIS	1	0.830	0.921	25.989	0.220	0.220	0.000	0.000	0.000	0.000
65	B	66	PHE	0	0.009	0.000	20.747	0.029	0.029	0.000	0.000	0.000	0.000
66	B	67	TRP	0	-0.029	-0.022	23.193	-0.038	-0.038	0.000	0.000	0.000	0.000
67	B	68	ILE	0	-0.001	0.012	21.262	-0.062	-0.062	0.000	0.000	0.000	0.000
68	B	69	GLY	0	0.031	0.004	20.758	0.041	0.041	0.000	0.000	0.000	0.000
69	B	70	LEU	0	-0.058	-0.013	21.658	-0.021	-0.021	0.000	0.000	0.000	0.000
70	B	71	MET	0	-0.006	0.005	24.858	0.036	0.036	0.000	0.000	0.000	0.000
71	B	72	ILE	0	0.007	0.005	27.751	-0.025	-0.025	0.000	0.000	0.000	0.000
72	B	73	LYS	1	0.870	0.923	27.198	0.745	0.745	0.000	0.000	0.000	0.000
73	B	74	ASP	-1	-0.758	-0.878	32.678	-0.424	-0.424	0.000	0.000	0.000	0.000
74	B	75	LYS	1	0.882	0.918	36.340	0.442	0.442	0.000	0.000	0.000	0.000
75	B	76	GLU	-1	-0.901	-0.904	39.108	-0.336	-0.336	0.000	0.000	0.000	0.000
76	B	77	GLN	0	-0.105	-0.060	39.310	-0.027	-0.027	0.000	0.000	0.000	0.000
77	B	78	GLU	-1	-0.790	-0.916	39.468	-0.319	-0.319	0.000	0.000	0.000	0.000
78	B	79	CYS	0	-0.098	-0.055	36.688	-0.010	-0.010	0.000	0.000	0.000	0.000
79	B	80	SER	0	0.018	0.005	39.357	0.003	0.003	0.000	0.000	0.000	0.000
80	B	81	SER	0	-0.056	-0.020	40.816	0.007	0.007	0.000	0.000	0.000	0.000
81	B	82	GLU	-1	-0.934	-0.977	43.163	-0.255	-0.255	0.000	0.000	0.000	0.000
82	B	83	TRP	0	-0.061	-0.019	46.981	0.003	0.003	0.000	0.000	0.000	0.000
83	B	84	SER	0	-0.026	-0.025	49.512	-0.002	-0.002	0.000	0.000	0.000	0.000
84	B	85	ASP	-1	-0.881	-0.921	50.503	-0.191	-0.191	0.000	0.000	0.000	0.000
85	B	86	GLY	0	-0.004	0.012	50.950	0.004	0.004	0.000	0.000	0.000	0.000
86	B	87	SER	0	-0.088	-0.052	52.012	-0.003	-0.003	0.000	0.000	0.000	0.000
87	B	88	SER	0	0.073	0.020	49.502	-0.003	-0.003	0.000	0.000	0.000	0.000
88	B	89	VAL	0	0.010	0.003	46.352	0.013	0.013	0.000	0.000	0.000	0.000
89	B	90	SER	0	-0.066	-0.018	49.269	-0.004	-0.004	0.000	0.000	0.000	0.000
90	B	91	TYR	0	-0.021	-0.023	51.778	0.002	0.002	0.000	0.000	0.000	0.000
91	B	92	ASP	-1	-0.756	-0.877	45.734	-0.250	-0.250	0.000	0.000	0.000	0.000
92	B	93	LYS	1	0.837	0.910	48.602	0.187	0.187	0.000	0.000	0.000	0.000
93	B	94	LEU	0	0.002	0.024	42.322	0.013	0.013	0.000	0.000	0.000	0.000
94	B	95	GLY	0	0.034	0.019	44.975	-0.004	-0.004	0.000	0.000	0.000	0.000
95	B	96	LYS	1	1.015	0.993	37.045	0.303	0.303	0.000	0.000	0.000	0.000
96	B	97	GLN	0	-0.049	-0.025	39.593	-0.012	-0.012	0.000	0.000	0.000	0.000
97	B	98	GLU	-1	-0.879	-0.939	39.919	-0.201	-0.201	0.000	0.000	0.000	0.000
98	B	99	PHE	0	-0.013	-0.002	37.410	-0.014	-0.014	0.000	0.000	0.000	0.000
99	B	100	ARG	1	0.871	0.923	34.744	0.249	0.249	0.000	0.000	0.000	0.000
100	B	101	LYS	1	0.905	0.958	33.277	0.394	0.394	0.000	0.000	0.000	0.000
101	B	102	CYS	0	-0.015	0.009	28.411	-0.038	-0.038	0.000	0.000	0.000	0.000
102	B	103	PHE	0	0.047	0.016	26.665	0.036	0.036	0.000	0.000	0.000	0.000
103	B	104	VAL	0	-0.024	-0.008	25.450	-0.039	-0.039	0.000	0.000	0.000	0.000
104	B	105	LEU	0	0.021	0.032	20.427	0.008	0.008	0.000	0.000	0.000	0.000
105	B	106	GLU	-1	-0.818	-0.943	24.680	-0.217	-0.217	0.000	0.000	0.000	0.000
106	B	107	LYS	1	0.877	0.964	25.564	-0.035	-0.035	0.000	0.000	0.000	0.000
107	B	108	GLU	-1	-0.948	-0.957	26.786	-0.139	-0.139	0.000	0.000	0.000	0.000
108	B	109	SER	0	-0.018	-0.019	27.499	-0.010	-0.010	0.000	0.000	0.000	0.000
109	B	110	GLY	0	0.039	0.013	25.768	-0.032	-0.032	0.000	0.000	0.000	0.000
110	B	111	TYR	0	-0.088	-0.062	21.990	-0.022	-0.022	0.000	0.000	0.000	0.000
111	B	112	ARG	1	0.863	0.921	22.366	0.484	0.484	0.000	0.000	0.000	0.000
112	B	113	MET	0	-0.008	0.016	24.387	-0.033	-0.033	0.000	0.000	0.000	0.000
113	B	114	TRP	0	0.006	-0.007	22.326	-0.003	-0.003	0.000	0.000	0.000	0.000
114	B	115	PHE	0	0.033	0.011	27.391	0.016	0.016	0.000	0.000	0.000	0.000
115	B	116	ASN	0	-0.010	-0.008	29.855	-0.016	-0.016	0.000	0.000	0.000	0.000
116	B	117	ARG	1	0.865	0.935	30.465	0.299	0.299	0.000	0.000	0.000	0.000
117	B	118	ASN	0	-0.004	-0.008	32.577	-0.020	-0.020	0.000	0.000	0.000	0.000
118	B	120	GLU	-1	-0.885	-0.940	30.879	-0.331	-0.331	0.000	0.000	0.000	0.000
119	B	121	GLU	-1	-0.817	-0.880	31.973	-0.232	-0.232	0.000	0.000	0.000	0.000
120	B	122	ARG	1	0.847	0.911	29.707	0.147	0.147	0.000	0.000	0.000	0.000
121	B	123	TYR	0	-0.037	-0.045	26.619	0.048	0.048	0.000	0.000	0.000	0.000
122	B	124	LEU	0	-0.013	0.014	22.993	0.004	0.004	0.000	0.000	0.000	0.000
123	B	125	PHE	0	0.017	-0.006	19.324	-0.034	-0.034	0.000	0.000	0.000	0.000
124	B	126	VAL	0	0.003	-0.004	14.969	0.093	0.093	0.000	0.000	0.000	0.000
125	B	128	LYS	1	0.807	0.900	11.879	2.315	2.315	0.000	0.000	0.000	0.000
126	B	129	VAL	0	-0.006	-0.016	9.231	0.267	0.267	0.000	0.000	0.000	0.000
127	B	130	PRO	0	0.053	0.016	8.540	-0.669	-0.669	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:1:ASP)