FMO DATABASE

FMODB ID: N6J5Q

Calculation Name: 2WO3-B-Xray547

Preferred Name: Ephrin-A2

Target Type: SINGLE PROTEIN

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose

Ligand 3-letter code: NAG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2WO3

Chain ID: B

ChEMBL ID: CHEMBL1795109

UniProt ID: O43921

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	140
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1339199.45407
FMO2-HF: Nuclear repulsion	1281678.429242
FMO2-HF: Total energy	-57521.024828
FMO2-MP2: Total energy	-57687.904713

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:33:ASN)

Summations of interaction energy for fragment #1(B:33:ASN)

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.
-23.968	-22.115	-0.006	-0.841	-1.006	-0.002

Interaction energy analysis for fragmet #1(B:33:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.820 / q_NPA : 0.897

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	35	ASP	-1	-0.847	-0.891	3.614	-49.082	-47.159	-0.005	-0.832	-1.086	-0.002
35	B	67	ASP	-1	-0.724	-0.820	5.133	-52.831	-52.901	-0.001	-0.009	0.080	0.000
4	B	36	ARG	1	0.820	0.893	6.260	32.725	32.725	0.000	0.000	0.000	0.000
5	B	37	TYR	0	-0.002	-0.005	8.590	3.960	3.960	0.000	0.000	0.000	0.000
6	B	38	ALA	0	-0.018	-0.005	13.256	0.837	0.837	0.000	0.000	0.000	0.000
7	B	39	VAL	0	-0.004	-0.007	16.176	0.579	0.579	0.000	0.000	0.000	0.000
8	B	40	TYR	0	0.020	0.008	19.073	0.134	0.134	0.000	0.000	0.000	0.000
9	B	41	TRP	0	0.010	0.001	21.935	0.169	0.169	0.000	0.000	0.000	0.000
10	B	42	ASN	0	0.001	-0.019	25.049	0.643	0.643	0.000	0.000	0.000	0.000
11	B	43	ARG	1	0.983	0.972	28.310	9.110	9.110	0.000	0.000	0.000	0.000
12	B	44	SER	0	-0.006	0.012	30.123	0.318	0.318	0.000	0.000	0.000	0.000
13	B	45	ASN	0	-0.050	-0.021	22.828	-0.006	-0.006	0.000	0.000	0.000	0.000
14	B	46	PRO	0	0.054	0.023	26.410	0.008	0.008	0.000	0.000	0.000	0.000
15	B	47	ARG	1	0.922	0.959	17.790	16.536	16.536	0.000	0.000	0.000	0.000
16	B	48	PHE	0	-0.029	-0.022	23.513	-0.304	-0.304	0.000	0.000	0.000	0.000
17	B	49	HIS	0	-0.054	-0.016	25.022	0.253	0.253	0.000	0.000	0.000	0.000
18	B	50	ALA	0	0.028	0.017	29.442	0.371	0.371	0.000	0.000	0.000	0.000
19	B	51	GLY	0	-0.054	-0.037	31.936	0.048	0.048	0.000	0.000	0.000	0.000
20	B	52	ALA	0	0.030	0.019	34.555	0.262	0.262	0.000	0.000	0.000	0.000
21	B	53	GLY	0	-0.053	-0.020	36.352	0.213	0.213	0.000	0.000	0.000	0.000
22	B	54	ASP	-1	-0.890	-0.952	33.907	-9.129	-9.129	0.000	0.000	0.000	0.000
23	B	55	ASP	-1	-0.780	-0.849	29.782	-10.618	-10.618	0.000	0.000	0.000	0.000
24	B	56	GLY	0	0.013	0.014	29.238	-0.427	-0.427	0.000	0.000	0.000	0.000
25	B	57	GLY	0	-0.051	-0.023	27.572	-0.188	-0.188	0.000	0.000	0.000	0.000
26	B	58	GLY	0	0.003	0.011	26.442	-0.343	-0.343	0.000	0.000	0.000	0.000
27	B	59	TYR	0	-0.013	-0.013	18.807	-0.149	-0.149	0.000	0.000	0.000	0.000
28	B	60	THR	0	0.013	0.002	19.276	0.022	0.022	0.000	0.000	0.000	0.000
29	B	61	VAL	0	-0.074	-0.034	14.401	-0.122	-0.122	0.000	0.000	0.000	0.000
30	B	62	GLU	-1	-0.832	-0.903	12.235	-19.539	-19.539	0.000	0.000	0.000	0.000
31	B	63	VAL	0	-0.045	-0.011	9.792	-1.296	-1.296	0.000	0.000	0.000	0.000
32	B	64	SER	0	0.045	0.021	5.338	3.282	3.282	0.000	0.000	0.000	0.000
33	B	65	ILE	0	0.014	0.003	7.104	-0.151	-0.151	0.000	0.000	0.000	0.000
34	B	66	ASN	0	-0.077	-0.058	4.900	-2.607	-2.607	0.000	0.000	0.000	0.000
36	B	68	TYR	0	-0.052	-0.046	6.511	5.703	5.703	0.000	0.000	0.000	0.000
37	B	69	LEU	0	0.018	0.021	10.562	0.081	0.081	0.000	0.000	0.000	0.000
38	B	70	ASP	-1	-0.819	-0.900	13.259	-24.010	-24.010	0.000	0.000	0.000	0.000
39	B	71	ILE	0	0.018	0.014	15.608	0.629	0.629	0.000	0.000	0.000	0.000
40	B	72	TYR	0	-0.011	-0.007	15.610	0.093	0.093	0.000	0.000	0.000	0.000
41	B	73	CYS	0	-0.037	-0.008	21.534	0.053	0.053	0.000	0.000	0.000	0.000
42	B	74	PRO	0	0.009	0.004	25.251	-0.102	-0.102	0.000	0.000	0.000	0.000
43	B	75	HIS	0	-0.073	-0.043	27.142	-0.169	-0.169	0.000	0.000	0.000	0.000
44	B	76	TYR	0	0.021	0.020	29.106	0.097	0.097	0.000	0.000	0.000	0.000
45	B	77	GLY	0	0.045	0.028	32.130	-0.063	-0.063	0.000	0.000	0.000	0.000
46	B	78	ALA	0	-0.023	-0.002	32.972	0.231	0.231	0.000	0.000	0.000	0.000
47	B	79	PRO	0	-0.014	-0.012	36.243	-0.082	-0.082	0.000	0.000	0.000	0.000
48	B	80	LEU	0	0.037	0.010	34.877	-0.122	-0.122	0.000	0.000	0.000	0.000
49	B	81	PRO	0	-0.021	0.001	36.435	0.237	0.237	0.000	0.000	0.000	0.000
50	B	82	PRO	0	0.020	-0.003	39.421	-0.013	-0.013	0.000	0.000	0.000	0.000
51	B	83	ALA	0	0.044	0.023	39.360	-0.174	-0.174	0.000	0.000	0.000	0.000
52	B	84	GLU	-1	-0.885	-0.962	39.085	-7.737	-7.737	0.000	0.000	0.000	0.000
53	B	85	ARG	1	0.875	0.938	38.823	7.447	7.447	0.000	0.000	0.000	0.000
54	B	86	MET	0	-0.039	0.014	34.654	-0.309	-0.309	0.000	0.000	0.000	0.000
55	B	87	GLU	-1	-0.760	-0.848	31.446	-10.427	-10.427	0.000	0.000	0.000	0.000
56	B	88	HIS	1	0.812	0.875	31.770	8.943	8.943	0.000	0.000	0.000	0.000
57	B	89	TYR	0	0.008	-0.026	29.096	0.202	0.202	0.000	0.000	0.000	0.000
58	B	90	VAL	0	-0.025	-0.006	29.737	-0.228	-0.228	0.000	0.000	0.000	0.000
59	B	91	LEU	0	0.000	-0.001	23.798	0.079	0.079	0.000	0.000	0.000	0.000
60	B	92	TYR	0	-0.001	-0.016	26.235	0.012	0.012	0.000	0.000	0.000	0.000
61	B	93	MET	0	-0.005	0.020	18.702	-0.328	-0.328	0.000	0.000	0.000	0.000
62	B	94	VAL	0	-0.050	-0.028	23.767	0.484	0.484	0.000	0.000	0.000	0.000
63	B	95	ASN	0	0.106	0.052	24.241	-0.469	-0.469	0.000	0.000	0.000	0.000
64	B	96	GLY	0	0.088	0.038	26.404	-0.026	-0.026	0.000	0.000	0.000	0.000
65	B	97	GLU	-1	-0.874	-0.942	27.150	-10.174	-10.174	0.000	0.000	0.000	0.000
66	B	98	GLY	0	0.003	0.015	29.514	0.302	0.302	0.000	0.000	0.000	0.000
67	B	99	HIS	0	-0.044	-0.027	24.562	-0.033	-0.033	0.000	0.000	0.000	0.000
68	B	100	ALA	0	-0.005	0.005	27.994	0.115	0.115	0.000	0.000	0.000	0.000
69	B	101	SER	0	-0.044	-0.055	30.973	0.233	0.233	0.000	0.000	0.000	0.000
70	B	102	CYS	0	-0.039	-0.015	30.634	0.141	0.141	0.000	0.000	0.000	0.000
71	B	103	ASP	-1	-0.764	-0.849	32.191	-8.767	-8.767	0.000	0.000	0.000	0.000
72	B	104	HIS	0	0.057	0.023	30.103	0.131	0.131	0.000	0.000	0.000	0.000
73	B	105	ARG	1	0.798	0.868	31.548	8.324	8.324	0.000	0.000	0.000	0.000
74	B	106	GLN	0	-0.020	-0.022	34.070	0.111	0.111	0.000	0.000	0.000	0.000
75	B	107	ARG	1	0.892	0.959	30.371	9.152	9.152	0.000	0.000	0.000	0.000
76	B	108	GLY	0	0.020	0.010	27.562	-0.397	-0.397	0.000	0.000	0.000	0.000
77	B	109	PHE	0	-0.005	0.008	24.964	0.382	0.382	0.000	0.000	0.000	0.000
78	B	110	LYS	1	0.881	0.927	26.376	10.162	10.162	0.000	0.000	0.000	0.000
79	B	111	ARG	1	0.753	0.852	18.633	15.675	15.675	0.000	0.000	0.000	0.000
80	B	112	TRP	0	0.011	0.006	18.925	-0.003	-0.003	0.000	0.000	0.000	0.000
81	B	113	GLU	-1	-0.823	-0.896	25.448	-9.977	-9.977	0.000	0.000	0.000	0.000
82	B	115	ASN	0	0.000	-0.022	28.559	0.269	0.269	0.000	0.000	0.000	0.000
83	B	116	ARG	1	0.900	0.942	29.435	10.368	10.368	0.000	0.000	0.000	0.000
84	B	117	PRO	0	0.057	0.037	30.103	-0.243	-0.243	0.000	0.000	0.000	0.000
85	B	118	ALA	0	0.046	0.011	31.336	-0.082	-0.082	0.000	0.000	0.000	0.000
86	B	119	ALA	0	-0.007	0.005	28.696	0.213	0.213	0.000	0.000	0.000	0.000
87	B	120	PRO	0	0.016	-0.003	29.882	-0.240	-0.240	0.000	0.000	0.000	0.000
88	B	121	GLY	0	-0.013	0.005	27.173	-0.001	-0.001	0.000	0.000	0.000	0.000
89	B	122	GLY	0	0.002	0.018	25.425	-0.496	-0.496	0.000	0.000	0.000	0.000
90	B	123	PRO	0	-0.021	-0.024	23.204	0.151	0.151	0.000	0.000	0.000	0.000
91	B	124	LEU	0	-0.010	0.008	23.469	-0.395	-0.395	0.000	0.000	0.000	0.000
92	B	125	LYS	1	0.878	0.949	14.125	21.002	21.002	0.000	0.000	0.000	0.000
93	B	126	PHE	0	0.003	-0.014	19.540	0.252	0.252	0.000	0.000	0.000	0.000
94	B	127	SER	0	-0.015	-0.029	13.962	-0.417	-0.417	0.000	0.000	0.000	0.000
95	B	128	GLU	-1	-0.743	-0.806	14.659	-16.919	-16.919	0.000	0.000	0.000	0.000
96	B	129	LYS	1	0.926	0.972	8.395	29.866	29.866	0.000	0.000	0.000	0.000
97	B	130	PHE	0	0.039	0.031	9.491	1.990	1.990	0.000	0.000	0.000	0.000
98	B	131	GLN	0	-0.030	-0.026	9.676	-3.068	-3.068	0.000	0.000	0.000	0.000
99	B	132	LEU	0	0.016	0.011	10.171	1.518	1.518	0.000	0.000	0.000	0.000
100	B	133	PHE	0	0.028	0.012	12.512	1.236	1.236	0.000	0.000	0.000	0.000
101	B	134	THR	0	-0.014	-0.019	14.782	-1.480	-1.480	0.000	0.000	0.000	0.000
102	B	135	PRO	0	-0.042	-0.010	15.696	0.658	0.658	0.000	0.000	0.000	0.000
103	B	136	PHE	0	0.003	-0.006	18.430	0.847	0.847	0.000	0.000	0.000	0.000
104	B	137	SER	0	0.042	0.025	21.532	-0.321	-0.321	0.000	0.000	0.000	0.000
105	B	138	LEU	0	-0.012	0.001	24.314	0.254	0.254	0.000	0.000	0.000	0.000
106	B	139	GLY	0	-0.031	-0.002	20.205	-0.095	-0.095	0.000	0.000	0.000	0.000
107	B	140	PHE	0	0.002	-0.014	18.098	0.481	0.481	0.000	0.000	0.000	0.000
108	B	141	GLU	-1	-0.817	-0.890	15.453	-17.642	-17.642	0.000	0.000	0.000	0.000
109	B	142	PHE	0	-0.033	-0.009	12.481	0.661	0.661	0.000	0.000	0.000	0.000
110	B	143	ARG	1	0.836	0.880	13.589	16.987	16.987	0.000	0.000	0.000	0.000
111	B	144	PRO	0	0.048	0.009	10.913	-0.012	-0.012	0.000	0.000	0.000	0.000
112	B	145	GLY	0	-0.012	0.015	12.897	1.310	1.310	0.000	0.000	0.000	0.000
113	B	146	HIS	0	-0.059	-0.026	15.226	1.664	1.664	0.000	0.000	0.000	0.000
114	B	147	GLU	-1	-0.801	-0.869	16.255	-14.214	-14.214	0.000	0.000	0.000	0.000
115	B	148	TYR	0	0.014	0.003	15.354	-0.013	-0.013	0.000	0.000	0.000	0.000
116	B	149	TYR	0	-0.028	-0.033	19.284	-0.110	-0.110	0.000	0.000	0.000	0.000
117	B	150	TYR	0	-0.036	-0.047	17.592	-0.040	-0.040	0.000	0.000	0.000	0.000
118	B	151	ILE	0	-0.005	0.001	23.249	0.160	0.160	0.000	0.000	0.000	0.000
119	B	152	SER	0	-0.044	-0.030	26.763	-0.176	-0.176	0.000	0.000	0.000	0.000
120	B	153	ALA	0	0.020	0.023	29.144	0.259	0.259	0.000	0.000	0.000	0.000
121	B	154	THR	0	-0.009	-0.033	32.641	-0.291	-0.291	0.000	0.000	0.000	0.000
122	B	155	PRO	0	-0.041	0.001	34.114	0.339	0.339	0.000	0.000	0.000	0.000
123	B	156	PRO	0	0.007	-0.003	37.280	-0.012	-0.012	0.000	0.000	0.000	0.000
124	B	157	ASN	0	-0.033	-0.023	37.819	0.294	0.294	0.000	0.000	0.000	0.000
125	B	158	ALA	0	0.015	0.002	36.210	-0.214	-0.214	0.000	0.000	0.000	0.000
126	B	159	VAL	0	-0.048	-0.034	34.977	-0.182	-0.182	0.000	0.000	0.000	0.000
127	B	160	ASP	-1	-0.788	-0.845	33.584	-9.213	-9.213	0.000	0.000	0.000	0.000
128	B	161	ARG	1	0.919	0.965	35.098	8.104	8.104	0.000	0.000	0.000	0.000
129	B	162	PRO	0	0.048	0.021	33.470	0.249	0.249	0.000	0.000	0.000	0.000
130	B	164	LEU	0	-0.015	0.015	27.474	-0.047	-0.047	0.000	0.000	0.000	0.000
131	B	165	ARG	1	0.789	0.838	26.013	10.339	10.339	0.000	0.000	0.000	0.000
132	B	166	LEU	0	-0.011	-0.003	18.644	-0.119	-0.119	0.000	0.000	0.000	0.000
133	B	167	LYS	1	0.865	0.930	19.657	13.218	13.218	0.000	0.000	0.000	0.000
134	B	168	VAL	0	-0.017	-0.021	14.328	-0.441	-0.441	0.000	0.000	0.000	0.000
135	B	169	TYR	0	-0.002	0.000	15.529	0.374	0.374	0.000	0.000	0.000	0.000
136	B	170	VAL	0	-0.006	-0.010	10.514	-1.451	-1.451	0.000	0.000	0.000	0.000
137	B	171	ARG	1	0.893	0.936	7.900	28.286	28.286	0.000	0.000	0.000	0.000
138	B	172	PRO	0	0.023	-0.001	11.405	-0.445	-0.445	0.000	0.000	0.000	0.000
139	B	173	THR	0	-0.064	-0.036	8.984	-1.183	-1.183	0.000	0.000	0.000	0.000
140	B	174	GLN	-1	-0.928	-0.945	8.418	-23.842	-23.842	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:33:ASN)