FMO DATABASE

FMODB ID: 679YZ

Calculation Name: 6W4H-B-Xray547

Preferred Name:

Target Type:

Ligand Name: s-adenosylmethionine | beta-d-fructopyranose | sulfite ion | acetate ion | zinc ion

Ligand 3-letter code: SAM | BDF | SO3 | ACT | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6W4H

Chain ID: B

ChEMBL ID:

UniProt ID: P0DTD1

Base Structure: X-ray

Registration Date: 2025-10-04

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	116
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-842181.999819
FMO2-HF: Nuclear repulsion	795359.872748
FMO2-HF: Total energy	-46822.127071
FMO2-MP2: Total energy	-46946.476416

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:4271:ALA)

Summations of interaction energy for fragment #1(A:4271:ALA)

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.
-14.335	-12.449	0.008	-1.053	-0.841	-0.003

Interaction energy analysis for fragmet #1(A:4271:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.849 / q_NPA : 0.914

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	4273	ALA	0	0.040	0.018	3.360	-10.371	-8.485	0.008	-1.053	-0.841	-0.003
4	A	4274	VAL	0	0.010	0.010	5.971	2.580	2.580	0.000	0.000	0.000	0.000
5	A	4275	ASP	-1	-0.823	-0.904	9.816	-22.439	-22.439	0.000	0.000	0.000	0.000
6	A	4276	ALA	0	0.028	0.001	11.940	1.675	1.675	0.000	0.000	0.000	0.000
7	A	4277	ALA	0	-0.009	0.004	14.917	1.529	1.529	0.000	0.000	0.000	0.000
8	A	4278	LYS	1	0.836	0.895	13.996	19.995	19.995	0.000	0.000	0.000	0.000
9	A	4279	ALA	0	0.003	0.007	15.859	1.115	1.115	0.000	0.000	0.000	0.000
10	A	4280	TYR	0	0.006	-0.029	17.553	1.017	1.017	0.000	0.000	0.000	0.000
11	A	4281	LYS	1	0.899	0.947	18.702	16.902	16.902	0.000	0.000	0.000	0.000
12	A	4282	ASP	-1	-0.807	-0.885	17.976	-16.602	-16.602	0.000	0.000	0.000	0.000
13	A	4283	TYR	0	-0.070	-0.026	21.397	0.673	0.673	0.000	0.000	0.000	0.000
14	A	4284	LEU	0	-0.016	-0.015	23.410	0.605	0.605	0.000	0.000	0.000	0.000
15	A	4285	ALA	0	-0.047	-0.017	24.181	0.528	0.528	0.000	0.000	0.000	0.000
16	A	4286	SER	0	-0.069	-0.037	24.239	0.328	0.328	0.000	0.000	0.000	0.000
17	A	4287	GLY	0	-0.015	-0.001	26.896	0.296	0.296	0.000	0.000	0.000	0.000
18	A	4288	GLY	0	-0.018	-0.004	27.297	0.287	0.287	0.000	0.000	0.000	0.000
19	A	4289	GLN	0	-0.001	-0.010	28.358	0.125	0.125	0.000	0.000	0.000	0.000
20	A	4290	PRO	0	0.020	0.014	28.120	-0.429	-0.429	0.000	0.000	0.000	0.000
21	A	4291	ILE	0	-0.031	-0.005	23.164	0.188	0.188	0.000	0.000	0.000	0.000
22	A	4292	THR	0	0.050	0.031	27.815	0.126	0.126	0.000	0.000	0.000	0.000
23	A	4293	ASN	0	-0.003	-0.012	29.998	-0.146	-0.146	0.000	0.000	0.000	0.000
24	A	4294	CYS	0	-0.029	0.004	28.686	-0.222	-0.222	0.000	0.000	0.000	0.000
25	A	4295	VAL	0	0.016	-0.010	31.378	0.307	0.307	0.000	0.000	0.000	0.000
26	A	4296	LYS	1	0.878	0.930	34.112	8.018	8.018	0.000	0.000	0.000	0.000
27	A	4297	MET	0	-0.051	-0.020	36.275	0.066	0.066	0.000	0.000	0.000	0.000
28	A	4298	LEU	0	0.001	0.007	38.837	0.102	0.102	0.000	0.000	0.000	0.000
29	A	4299	CYS	0	-0.029	-0.019	40.115	-0.027	-0.027	0.000	0.000	0.000	0.000
30	A	4300	THR	0	0.032	0.005	43.076	0.023	0.023	0.000	0.000	0.000	0.000
31	A	4301	HIS	1	0.838	0.927	41.240	7.795	7.795	0.000	0.000	0.000	0.000
32	A	4302	THR	0	-0.022	-0.009	44.308	0.059	0.059	0.000	0.000	0.000	0.000
33	A	4303	GLY	0	0.003	0.022	41.809	0.095	0.095	0.000	0.000	0.000	0.000
34	A	4304	THR	0	-0.034	-0.055	39.228	-0.035	-0.035	0.000	0.000	0.000	0.000
35	A	4305	GLY	0	0.004	0.012	38.622	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	4306	GLN	0	-0.020	-0.018	34.739	-0.216	-0.216	0.000	0.000	0.000	0.000
37	A	4307	ALA	0	-0.015	0.002	30.237	0.001	0.001	0.000	0.000	0.000	0.000
38	A	4308	ILE	0	-0.015	-0.020	26.558	-0.113	-0.113	0.000	0.000	0.000	0.000
39	A	4309	THR	0	0.002	0.004	30.908	-0.032	-0.032	0.000	0.000	0.000	0.000
40	A	4310	VAL	0	0.024	-0.011	33.280	-0.200	-0.200	0.000	0.000	0.000	0.000
41	A	4311	THR	0	0.004	0.009	35.046	0.022	0.022	0.000	0.000	0.000	0.000
42	A	4312	PRO	0	-0.051	-0.028	36.877	-0.182	-0.182	0.000	0.000	0.000	0.000
43	A	4313	GLU	-1	-0.784	-0.871	37.111	-7.768	-7.768	0.000	0.000	0.000	0.000
44	A	4314	ALA	0	-0.030	-0.008	38.459	0.029	0.029	0.000	0.000	0.000	0.000
45	A	4315	ASN	0	0.064	0.035	39.552	0.134	0.134	0.000	0.000	0.000	0.000
46	A	4316	MET	0	0.020	-0.007	42.305	0.025	0.025	0.000	0.000	0.000	0.000
47	A	4317	ASP	-1	-0.862	-0.916	40.573	-7.526	-7.526	0.000	0.000	0.000	0.000
48	A	4318	GLN	0	-0.073	-0.031	36.602	-0.167	-0.167	0.000	0.000	0.000	0.000
49	A	4319	GLU	-1	-0.788	-0.894	37.028	-7.755	-7.755	0.000	0.000	0.000	0.000
50	A	4320	SER	0	-0.020	-0.018	35.803	-0.174	-0.174	0.000	0.000	0.000	0.000
51	A	4321	PHE	0	0.012	-0.004	32.256	0.151	0.151	0.000	0.000	0.000	0.000
52	A	4322	GLY	0	0.071	0.038	32.362	-0.079	-0.079	0.000	0.000	0.000	0.000
53	A	4323	GLY	0	0.026	0.024	28.751	-0.245	-0.245	0.000	0.000	0.000	0.000
54	A	4324	ALA	0	-0.004	-0.020	25.953	-0.446	-0.446	0.000	0.000	0.000	0.000
55	A	4325	SER	0	-0.068	-0.034	25.935	-0.325	-0.325	0.000	0.000	0.000	0.000
56	A	4326	CYS	0	0.019	0.016	26.982	0.128	0.128	0.000	0.000	0.000	0.000
57	A	4327	CYS	0	0.014	0.030	21.409	-0.586	-0.586	0.000	0.000	0.000	0.000
58	A	4328	LEU	0	0.063	0.027	17.635	0.063	0.063	0.000	0.000	0.000	0.000
59	A	4329	TYR	0	0.067	0.019	14.300	0.713	0.713	0.000	0.000	0.000	0.000
60	A	4330	CYS	0	-0.022	-0.017	18.593	0.011	0.011	0.000	0.000	0.000	0.000
61	A	4331	ARG	1	0.792	0.887	21.700	12.048	12.048	0.000	0.000	0.000	0.000
62	A	4332	CYS	0	-0.048	-0.020	18.742	0.474	0.474	0.000	0.000	0.000	0.000
63	A	4333	HIS	0	-0.053	-0.014	19.106	-0.631	-0.631	0.000	0.000	0.000	0.000
64	A	4334	ILE	0	-0.017	0.002	14.253	-0.672	-0.672	0.000	0.000	0.000	0.000
65	A	4335	ASP	-1	-0.872	-0.937	11.913	-22.976	-22.976	0.000	0.000	0.000	0.000
66	A	4336	HIS	0	-0.029	-0.032	13.943	-0.658	-0.658	0.000	0.000	0.000	0.000
67	A	4337	PRO	0	-0.005	0.013	12.209	-1.200	-1.200	0.000	0.000	0.000	0.000
68	A	4338	ASN	0	-0.041	-0.035	13.222	0.363	0.363	0.000	0.000	0.000	0.000
69	A	4339	PRO	0	0.051	0.015	12.848	-0.419	-0.419	0.000	0.000	0.000	0.000
70	A	4340	LYS	1	0.926	0.952	14.107	16.436	16.436	0.000	0.000	0.000	0.000
71	A	4341	GLY	0	0.035	0.043	15.174	0.721	0.721	0.000	0.000	0.000	0.000
72	A	4342	PHE	0	-0.037	-0.012	16.102	1.032	1.032	0.000	0.000	0.000	0.000
73	A	4343	CYS	0	-0.035	-0.015	18.914	-0.438	-0.438	0.000	0.000	0.000	0.000
74	A	4344	ASP	-1	-0.842	-0.925	21.539	-13.586	-13.586	0.000	0.000	0.000	0.000
75	A	4345	LEU	0	0.021	0.001	23.547	0.545	0.545	0.000	0.000	0.000	0.000
76	A	4346	LYS	1	0.965	0.966	24.258	12.690	12.690	0.000	0.000	0.000	0.000
77	A	4347	GLY	0	-0.055	-0.029	26.455	0.061	0.061	0.000	0.000	0.000	0.000
78	A	4348	LYS	1	0.912	0.983	28.307	11.224	11.224	0.000	0.000	0.000	0.000
79	A	4349	TYR	0	-0.008	0.000	31.006	-0.056	-0.056	0.000	0.000	0.000	0.000
80	A	4350	VAL	0	0.007	-0.001	28.651	-0.190	-0.190	0.000	0.000	0.000	0.000
81	A	4351	GLN	0	0.036	0.038	31.560	0.324	0.324	0.000	0.000	0.000	0.000
82	A	4352	ILE	0	-0.030	-0.004	29.935	-0.306	-0.306	0.000	0.000	0.000	0.000
83	A	4353	PRO	0	0.048	0.023	33.015	0.319	0.319	0.000	0.000	0.000	0.000
84	A	4354	THR	0	0.028	-0.010	35.692	-0.170	-0.170	0.000	0.000	0.000	0.000
85	A	4355	THR	0	-0.020	-0.024	35.924	0.031	0.031	0.000	0.000	0.000	0.000
86	A	4356	CYS	0	-0.061	-0.015	31.995	-0.058	-0.058	0.000	0.000	0.000	0.000
87	A	4357	ALA	0	-0.003	0.006	32.615	-0.328	-0.328	0.000	0.000	0.000	0.000
88	A	4358	ASN	0	0.006	0.002	33.461	0.005	0.005	0.000	0.000	0.000	0.000
89	A	4359	ASP	-1	-0.749	-0.877	27.477	-12.158	-12.158	0.000	0.000	0.000	0.000
90	A	4360	PRO	0	0.043	0.019	28.897	-0.323	-0.323	0.000	0.000	0.000	0.000
91	A	4361	VAL	0	0.004	0.017	23.088	-0.279	-0.279	0.000	0.000	0.000	0.000
92	A	4362	GLY	0	0.000	0.003	24.197	-0.555	-0.555	0.000	0.000	0.000	0.000
93	A	4363	PHE	0	-0.011	-0.016	25.055	-0.260	-0.260	0.000	0.000	0.000	0.000
94	A	4364	THR	0	-0.006	-0.018	24.838	-0.314	-0.314	0.000	0.000	0.000	0.000
95	A	4365	LEU	0	-0.021	-0.006	19.103	-0.459	-0.459	0.000	0.000	0.000	0.000
96	A	4366	LYS	1	0.828	0.930	21.369	11.589	11.589	0.000	0.000	0.000	0.000
97	A	4367	ASN	0	-0.026	0.003	23.987	0.454	0.454	0.000	0.000	0.000	0.000
98	A	4368	THR	0	-0.003	-0.016	23.658	-0.639	-0.639	0.000	0.000	0.000	0.000
99	A	4369	VAL	0	-0.022	-0.002	25.703	0.444	0.444	0.000	0.000	0.000	0.000
100	A	4370	CYS	-1	-0.779	-0.749	27.622	-10.086	-10.086	0.000	0.000	0.000	0.000
101	A	4371	THR	0	-0.035	-0.030	26.715	0.179	0.179	0.000	0.000	0.000	0.000
102	A	4372	VAL	0	0.016	0.001	29.864	0.120	0.120	0.000	0.000	0.000	0.000
103	A	4373	CYS	0	-0.039	-0.083	33.583	0.203	0.203	0.000	0.000	0.000	0.000
104	A	4374	GLY	0	0.034	0.030	32.101	0.194	0.194	0.000	0.000	0.000	0.000
105	A	4375	MET	0	0.006	0.012	32.940	-0.109	-0.109	0.000	0.000	0.000	0.000
106	A	4376	TRP	0	-0.015	-0.024	26.336	-0.497	-0.497	0.000	0.000	0.000	0.000
107	A	4377	LYS	1	0.854	0.895	28.355	10.510	10.510	0.000	0.000	0.000	0.000
108	A	4378	GLY	0	0.004	0.009	30.777	-0.202	-0.202	0.000	0.000	0.000	0.000
109	A	4379	TYR	0	-0.039	-0.033	30.822	0.191	0.191	0.000	0.000	0.000	0.000
110	A	4380	GLY	0	0.046	0.010	34.534	0.024	0.024	0.000	0.000	0.000	0.000
111	A	4381	CYS	0	-0.076	-0.046	33.257	0.176	0.176	0.000	0.000	0.000	0.000
112	A	4382	SER	0	0.046	0.025	35.343	-0.063	-0.063	0.000	0.000	0.000	0.000
113	A	4383	CYS	0	-0.025	-0.053	34.570	0.178	0.178	0.000	0.000	0.000	0.000
114	A	4384	ASP	-1	-0.854	-0.901	33.289	-9.592	-9.592	0.000	0.000	0.000	0.000
115	A	4385	GLN	0	-0.102	-0.048	36.537	0.013	0.013	0.000	0.000	0.000	0.000
116	A	4386	LEU	-1	-0.922	-0.948	40.338	-7.284	-7.284	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4271:ALA)