FMO DATABASE

FMODB ID: JKML9

Calculation Name: 3M5H-F-Xray547

Preferred Name:

Target Type:

Ligand Name: n-acetyl-alpha-neuraminic acid | 2-acetamido-2-deoxy-beta-d-glucopyranose | beta-d-galactopyranose

Ligand 3-letter code: SIA | NAG | GAL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3M5H

Chain ID: F

ChEMBL ID:

UniProt ID: B7NY59

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	170
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1485250.503296
FMO2-HF: Nuclear repulsion	1415157.242878
FMO2-HF: Total energy	-70093.260418
FMO2-MP2: Total energy	-70294.882312

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(F:1:GLY)

Summations of interaction energy for fragment #1(F:1:GLY)

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.
-283.349	-278.083	11.223	-8.504	-7.983	-0.109

Interaction energy analysis for fragmet #1(F:1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.818 / q_NPA : 0.895

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	F	3	PHE	0	-0.042	-0.026	3.304	13.393	14.833	-0.002	-0.626	-0.812	-0.001
4	F	4	GLY	0	0.017	0.020	3.389	8.299	8.477	0.004	-0.032	-0.150	0.000
5	F	5	ALA	0	0.033	0.029	4.707	6.001	6.045	-0.001	-0.007	-0.036	0.000
6	F	6	ILE	0	-0.019	-0.027	4.544	3.413	3.453	-0.001	-0.023	-0.016	0.000
7	F	7	ALA	0	-0.043	-0.019	3.716	-10.782	-10.301	0.002	-0.152	-0.330	-0.001
105	F	105	GLN	0	-0.035	-0.012	4.014	1.746	1.836	-0.001	-0.010	-0.079	0.000
108	F	108	ILE	0	0.003	0.007	2.774	-0.909	-0.431	0.112	-0.187	-0.403	-0.002
109	F	109	ASP	-1	-0.785	-0.897	1.933	-116.575	-115.176	7.990	-5.220	-4.169	-0.074
110	F	110	LEU	0	-0.039	-0.008	3.736	3.807	3.859	0.001	-0.001	-0.052	0.000
112	F	112	ASP	-1	-0.722	-0.867	2.597	-71.972	-70.869	3.120	-2.236	-1.987	-0.031
113	F	113	SER	0	-0.032	-0.001	4.749	5.864	5.825	-0.001	-0.010	0.051	0.000
8	F	8	GLY	0	-0.029	-0.010	5.767	-3.824	-3.824	0.000	0.000	0.000	0.000
9	F	9	PHE	0	-0.039	-0.014	6.380	3.195	3.195	0.000	0.000	0.000	0.000
10	F	10	ILE	0	-0.037	-0.017	8.298	2.871	2.871	0.000	0.000	0.000	0.000
11	F	11	GLU	-1	-0.919	-0.954	8.996	-24.150	-24.150	0.000	0.000	0.000	0.000
12	F	12	ASN	0	-0.067	-0.049	10.911	-0.794	-0.794	0.000	0.000	0.000	0.000
13	F	13	GLY	0	0.020	0.019	11.826	0.333	0.333	0.000	0.000	0.000	0.000
14	F	14	TRP	0	-0.004	-0.011	12.769	1.313	1.313	0.000	0.000	0.000	0.000
15	F	15	GLU	-1	-0.890	-0.948	16.560	-16.177	-16.177	0.000	0.000	0.000	0.000
16	F	16	GLY	0	-0.019	-0.010	18.611	0.574	0.574	0.000	0.000	0.000	0.000
17	F	17	LEU	0	-0.046	-0.010	16.127	0.713	0.713	0.000	0.000	0.000	0.000
18	F	18	ILE	0	-0.003	-0.013	19.062	-0.476	-0.476	0.000	0.000	0.000	0.000
19	F	19	ASN	0	-0.066	-0.039	21.027	0.146	0.146	0.000	0.000	0.000	0.000
20	F	20	GLY	0	-0.004	-0.007	18.691	0.476	0.476	0.000	0.000	0.000	0.000
21	F	21	TRP	0	-0.013	-0.005	11.418	-0.605	-0.605	0.000	0.000	0.000	0.000
22	F	22	TYR	0	0.008	-0.003	9.018	-0.544	-0.544	0.000	0.000	0.000	0.000
23	F	23	GLY	0	-0.010	-0.016	14.563	1.350	1.350	0.000	0.000	0.000	0.000
24	F	24	PHE	0	-0.015	-0.001	16.469	-0.763	-0.763	0.000	0.000	0.000	0.000
25	F	25	ARG	1	0.924	0.954	19.169	14.816	14.816	0.000	0.000	0.000	0.000
26	F	26	HIS	0	0.038	0.026	20.814	-0.297	-0.297	0.000	0.000	0.000	0.000
27	F	27	GLN	0	0.059	0.027	22.562	0.206	0.206	0.000	0.000	0.000	0.000
28	F	28	ASN	0	0.020	-0.002	26.481	0.037	0.037	0.000	0.000	0.000	0.000
29	F	29	ALA	0	-0.052	-0.031	29.812	0.083	0.083	0.000	0.000	0.000	0.000
30	F	30	GLN	0	-0.035	-0.014	32.220	0.224	0.224	0.000	0.000	0.000	0.000
31	F	31	GLY	0	0.023	0.010	30.715	0.196	0.196	0.000	0.000	0.000	0.000
32	F	32	GLU	-1	-0.910	-0.954	23.762	-13.181	-13.181	0.000	0.000	0.000	0.000
33	F	33	GLY	0	-0.008	0.003	25.718	0.380	0.380	0.000	0.000	0.000	0.000
34	F	34	THR	0	-0.004	0.004	20.620	-0.772	-0.772	0.000	0.000	0.000	0.000
35	F	35	ALA	0	-0.006	-0.005	21.688	0.548	0.548	0.000	0.000	0.000	0.000
36	F	36	ALA	0	0.032	0.015	19.266	-0.639	-0.639	0.000	0.000	0.000	0.000
37	F	37	ASP	-1	-0.779	-0.860	17.202	-15.718	-15.718	0.000	0.000	0.000	0.000
38	F	38	TYR	0	-0.019	0.002	18.387	-0.467	-0.467	0.000	0.000	0.000	0.000
39	F	39	LYS	1	0.910	0.954	18.202	13.822	13.822	0.000	0.000	0.000	0.000
40	F	40	SER	0	0.026	-0.025	13.368	-0.329	-0.329	0.000	0.000	0.000	0.000
41	F	41	THR	0	-0.013	-0.015	14.346	-1.256	-1.256	0.000	0.000	0.000	0.000
42	F	42	GLN	0	-0.047	-0.036	16.018	-0.139	-0.139	0.000	0.000	0.000	0.000
43	F	43	SER	0	-0.006	-0.007	14.039	0.358	0.358	0.000	0.000	0.000	0.000
44	F	44	ALA	0	0.011	0.019	11.859	-0.427	-0.427	0.000	0.000	0.000	0.000
45	F	45	ILE	0	0.010	0.013	13.355	-0.087	-0.087	0.000	0.000	0.000	0.000
46	F	46	ASP	-1	-0.832	-0.896	16.448	-14.650	-14.650	0.000	0.000	0.000	0.000
47	F	47	GLN	0	-0.076	-0.056	12.674	-0.260	-0.260	0.000	0.000	0.000	0.000
48	F	48	ILE	0	-0.016	-0.007	11.113	-0.154	-0.154	0.000	0.000	0.000	0.000
49	F	49	THR	0	-0.021	-0.024	15.164	0.805	0.805	0.000	0.000	0.000	0.000
50	F	50	GLY	0	-0.007	-0.005	18.232	0.714	0.714	0.000	0.000	0.000	0.000
51	F	51	LYS	1	0.753	0.864	11.550	26.015	26.015	0.000	0.000	0.000	0.000
52	F	52	LEU	0	0.025	0.013	17.474	0.703	0.703	0.000	0.000	0.000	0.000
53	F	53	ASN	0	0.008	-0.004	20.110	0.711	0.711	0.000	0.000	0.000	0.000
54	F	54	ARG	1	0.817	0.903	17.211	17.718	17.718	0.000	0.000	0.000	0.000
55	F	55	LEU	0	-0.080	-0.042	18.049	0.371	0.371	0.000	0.000	0.000	0.000
56	F	56	ILE	0	0.006	-0.006	22.377	0.533	0.533	0.000	0.000	0.000	0.000
57	F	57	GLY	0	-0.001	-0.003	24.997	0.100	0.100	0.000	0.000	0.000	0.000
58	F	58	LYS	1	0.918	0.977	23.851	13.156	13.156	0.000	0.000	0.000	0.000
59	F	59	THR	0	0.008	0.005	29.218	0.183	0.183	0.000	0.000	0.000	0.000
60	F	60	ASN	0	-0.022	-0.012	30.395	-0.488	-0.488	0.000	0.000	0.000	0.000
61	F	61	GLN	0	-0.014	-0.009	33.124	0.022	0.022	0.000	0.000	0.000	0.000
62	F	62	GLN	0	0.000	0.008	35.835	-0.129	-0.129	0.000	0.000	0.000	0.000
63	F	63	PHE	0	-0.014	-0.014	34.763	0.004	0.004	0.000	0.000	0.000	0.000
64	F	64	GLU	-1	-0.929	-0.961	40.018	-6.970	-6.970	0.000	0.000	0.000	0.000
65	F	65	LEU	0	-0.033	-0.019	42.840	-0.132	-0.132	0.000	0.000	0.000	0.000
66	F	66	ILE	0	-0.040	-0.017	41.798	0.144	0.144	0.000	0.000	0.000	0.000
67	F	67	ASP	-1	-0.817	-0.906	43.653	-7.260	-7.260	0.000	0.000	0.000	0.000
68	F	68	ASN	0	-0.045	-0.037	46.402	0.047	0.047	0.000	0.000	0.000	0.000
69	F	69	GLU	-1	-0.883	-0.924	45.302	-7.075	-7.075	0.000	0.000	0.000	0.000
70	F	70	PHE	0	-0.059	-0.029	48.281	0.076	0.076	0.000	0.000	0.000	0.000
71	F	71	ASN	0	-0.095	-0.054	52.048	0.131	0.131	0.000	0.000	0.000	0.000
72	F	72	GLU	-1	-0.825	-0.897	50.136	-6.529	-6.529	0.000	0.000	0.000	0.000
73	F	73	ILE	0	-0.011	-0.001	47.481	0.146	0.146	0.000	0.000	0.000	0.000
74	F	74	GLU	-1	-0.904	-0.960	51.736	-6.034	-6.034	0.000	0.000	0.000	0.000
75	F	75	GLN	0	0.008	-0.021	49.679	-0.048	-0.048	0.000	0.000	0.000	0.000
76	F	76	GLN	0	-0.039	0.002	48.671	-0.254	-0.254	0.000	0.000	0.000	0.000
77	F	77	ILE	0	0.030	0.008	47.799	-0.166	-0.166	0.000	0.000	0.000	0.000
78	F	78	GLY	0	0.043	0.023	46.219	-0.163	-0.163	0.000	0.000	0.000	0.000
79	F	79	ASN	0	-0.037	-0.034	44.320	-0.306	-0.306	0.000	0.000	0.000	0.000
80	F	80	VAL	0	-0.014	0.008	42.894	-0.209	-0.209	0.000	0.000	0.000	0.000
81	F	81	ILE	0	-0.011	0.009	41.760	-0.246	-0.246	0.000	0.000	0.000	0.000
82	F	82	ASN	0	0.015	0.003	40.241	-0.286	-0.286	0.000	0.000	0.000	0.000
83	F	83	TRP	0	0.029	0.023	37.627	-0.255	-0.255	0.000	0.000	0.000	0.000
84	F	84	THR	0	-0.034	-0.032	37.122	-0.277	-0.277	0.000	0.000	0.000	0.000
85	F	85	ARG	1	0.866	0.919	35.821	7.794	7.794	0.000	0.000	0.000	0.000
86	F	86	ASP	-1	-0.890	-0.934	34.394	-9.044	-9.044	0.000	0.000	0.000	0.000
87	F	87	ALA	0	0.037	0.016	32.626	-0.388	-0.388	0.000	0.000	0.000	0.000
88	F	88	MET	0	-0.052	-0.033	31.273	-0.482	-0.482	0.000	0.000	0.000	0.000
89	F	89	THR	0	-0.013	-0.013	30.068	-0.419	-0.419	0.000	0.000	0.000	0.000
90	F	90	GLU	-1	-0.954	-0.957	28.360	-10.972	-10.972	0.000	0.000	0.000	0.000
91	F	91	ILE	0	-0.012	-0.009	26.650	-0.597	-0.597	0.000	0.000	0.000	0.000
92	F	92	TRP	0	-0.029	-0.026	25.187	-0.815	-0.815	0.000	0.000	0.000	0.000
93	F	93	SER	0	-0.014	-0.014	24.455	-0.528	-0.528	0.000	0.000	0.000	0.000
94	F	94	TYR	0	-0.011	0.001	21.114	-0.943	-0.943	0.000	0.000	0.000	0.000
95	F	95	ASN	0	-0.032	-0.031	20.739	-1.032	-1.032	0.000	0.000	0.000	0.000
96	F	96	ALA	0	-0.019	-0.007	20.175	-0.733	-0.733	0.000	0.000	0.000	0.000
97	F	97	GLU	-1	-0.922	-0.957	17.645	-17.445	-17.445	0.000	0.000	0.000	0.000
98	F	98	LEU	0	-0.014	-0.006	15.564	-1.455	-1.455	0.000	0.000	0.000	0.000
99	F	99	LEU	0	-0.024	-0.007	15.218	-1.378	-1.378	0.000	0.000	0.000	0.000
100	F	100	VAL	0	0.016	-0.001	14.779	-1.363	-1.363	0.000	0.000	0.000	0.000
101	F	101	ALA	0	0.015	0.016	12.154	-1.951	-1.951	0.000	0.000	0.000	0.000
102	F	102	MET	0	-0.025	-0.012	10.517	-2.686	-2.686	0.000	0.000	0.000	0.000
103	F	103	GLU	-1	-0.786	-0.876	10.423	-22.929	-22.929	0.000	0.000	0.000	0.000
104	F	104	ASN	0	0.016	0.007	9.881	-1.294	-1.294	0.000	0.000	0.000	0.000
106	F	106	HIS	0	0.028	0.017	5.626	-5.757	-5.757	0.000	0.000	0.000	0.000
107	F	107	THR	0	0.009	-0.011	7.568	-0.712	-0.712	0.000	0.000	0.000	0.000
111	F	111	ALA	0	0.031	0.005	6.469	2.618	2.618	0.000	0.000	0.000	0.000
114	F	114	GLU	-1	-0.820	-0.899	7.068	-19.192	-19.192	0.000	0.000	0.000	0.000
115	F	115	MET	0	0.004	0.025	7.705	2.790	2.790	0.000	0.000	0.000	0.000
116	F	116	SER	0	0.006	0.008	7.619	3.746	3.746	0.000	0.000	0.000	0.000
117	F	117	LYS	1	0.834	0.904	9.528	26.001	26.001	0.000	0.000	0.000	0.000
118	F	118	LEU	0	-0.036	-0.012	12.313	1.909	1.909	0.000	0.000	0.000	0.000
119	F	119	TYR	0	0.010	-0.015	12.090	1.199	1.199	0.000	0.000	0.000	0.000
120	F	120	GLU	-1	-0.827	-0.940	13.212	-17.682	-17.682	0.000	0.000	0.000	0.000
121	F	121	ARG	1	0.773	0.894	15.429	16.087	16.087	0.000	0.000	0.000	0.000
122	F	122	VAL	0	-0.007	-0.004	17.467	1.071	1.071	0.000	0.000	0.000	0.000
123	F	123	LYS	1	0.871	0.940	16.728	18.504	18.504	0.000	0.000	0.000	0.000
124	F	124	LYS	1	0.836	0.913	17.139	18.133	18.133	0.000	0.000	0.000	0.000
125	F	125	GLN	0	-0.042	-0.005	21.629	0.197	0.197	0.000	0.000	0.000	0.000
126	F	126	LEU	0	0.036	0.013	21.377	0.663	0.663	0.000	0.000	0.000	0.000
127	F	127	ARG	1	0.883	0.947	24.027	11.781	11.781	0.000	0.000	0.000	0.000
128	F	128	GLU	-1	-0.908	-0.952	25.153	-11.554	-11.554	0.000	0.000	0.000	0.000
129	F	129	ASN	0	-0.011	-0.035	27.146	0.395	0.395	0.000	0.000	0.000	0.000
130	F	130	ALA	0	-0.015	-0.007	23.233	0.126	0.126	0.000	0.000	0.000	0.000
131	F	131	GLU	-1	-0.855	-0.896	22.648	-11.906	-11.906	0.000	0.000	0.000	0.000
132	F	132	GLU	-1	-0.834	-0.901	16.444	-17.983	-17.983	0.000	0.000	0.000	0.000
133	F	133	ASP	-1	-0.812	-0.879	18.302	-15.843	-15.843	0.000	0.000	0.000	0.000
134	F	134	GLY	0	-0.023	-0.006	15.085	0.039	0.039	0.000	0.000	0.000	0.000
135	F	135	THR	0	-0.030	-0.041	13.502	-1.652	-1.652	0.000	0.000	0.000	0.000
136	F	136	GLY	0	-0.011	-0.013	13.077	-0.860	-0.860	0.000	0.000	0.000	0.000
137	F	137	CYS	0	-0.084	-0.030	13.706	0.671	0.671	0.000	0.000	0.000	0.000
138	F	138	PHE	0	-0.002	-0.021	16.508	-0.171	-0.171	0.000	0.000	0.000	0.000
139	F	139	GLU	-1	-0.931	-0.948	20.265	-12.224	-12.224	0.000	0.000	0.000	0.000
140	F	140	ILE	0	-0.025	-0.022	23.738	0.094	0.094	0.000	0.000	0.000	0.000
141	F	141	PHE	0	0.026	0.014	25.553	0.372	0.372	0.000	0.000	0.000	0.000
142	F	142	HIS	0	0.011	0.023	29.618	0.114	0.114	0.000	0.000	0.000	0.000
143	F	143	LYS	1	0.926	0.949	30.930	8.204	8.204	0.000	0.000	0.000	0.000
144	F	144	CYS	0	-0.034	0.017	28.811	-0.274	-0.274	0.000	0.000	0.000	0.000
145	F	145	ASP	-1	-0.810	-0.909	30.630	-9.310	-9.310	0.000	0.000	0.000	0.000
146	F	146	ASP	-1	-0.848	-0.940	30.238	-10.215	-10.215	0.000	0.000	0.000	0.000
147	F	147	GLN	0	-0.036	-0.009	30.381	-0.294	-0.294	0.000	0.000	0.000	0.000
148	F	149	MET	0	0.023	0.019	26.198	-0.545	-0.545	0.000	0.000	0.000	0.000
149	F	150	GLU	-1	-0.933	-0.968	26.054	-10.916	-10.916	0.000	0.000	0.000	0.000
150	F	151	SER	0	-0.032	-0.019	27.186	-0.274	-0.274	0.000	0.000	0.000	0.000
151	F	152	ILE	0	0.033	0.014	22.570	-0.228	-0.228	0.000	0.000	0.000	0.000
152	F	153	ARG	1	0.898	0.970	22.641	11.477	11.477	0.000	0.000	0.000	0.000
153	F	154	ASN	0	-0.034	-0.020	23.250	-0.483	-0.483	0.000	0.000	0.000	0.000
154	F	155	ASN	0	-0.084	-0.046	23.829	-0.232	-0.232	0.000	0.000	0.000	0.000
155	F	156	THR	0	-0.040	-0.041	25.780	0.318	0.318	0.000	0.000	0.000	0.000
156	F	157	TYR	0	-0.057	-0.028	27.084	0.282	0.282	0.000	0.000	0.000	0.000
157	F	158	ASP	-1	-0.795	-0.884	28.919	-9.556	-9.556	0.000	0.000	0.000	0.000
158	F	159	HIS	0	0.030	0.003	28.572	-0.009	-0.009	0.000	0.000	0.000	0.000
159	F	160	THR	0	-0.095	-0.070	30.433	0.146	0.146	0.000	0.000	0.000	0.000
160	F	161	GLN	0	-0.032	-0.008	34.130	0.029	0.029	0.000	0.000	0.000	0.000
161	F	162	TYR	0	0.044	0.020	31.782	0.246	0.246	0.000	0.000	0.000	0.000
162	F	163	ARG	1	0.924	0.996	30.412	9.733	9.733	0.000	0.000	0.000	0.000
163	F	164	THR	0	-0.040	-0.028	33.629	-0.100	-0.100	0.000	0.000	0.000	0.000
164	F	165	GLU	-1	-0.847	-0.920	35.006	-8.854	-8.854	0.000	0.000	0.000	0.000
165	F	166	SER	0	0.018	-0.007	30.353	-0.116	-0.116	0.000	0.000	0.000	0.000
166	F	167	LEU	0	-0.030	-0.015	31.427	-0.116	-0.116	0.000	0.000	0.000	0.000
167	F	168	GLN	0	-0.061	-0.036	33.541	0.061	0.061	0.000	0.000	0.000	0.000
168	F	169	ASN	0	-0.082	-0.043	33.091	0.360	0.360	0.000	0.000	0.000	0.000
169	F	170	ARG	1	0.770	0.872	27.075	10.968	10.968	0.000	0.000	0.000	0.000
170	F	171	ILE	-1	-1.000	-0.969	32.084	-8.934	-8.934	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:1:GLY)