FMO DATABASE

FMODB ID: ZLVZN

Calculation Name: 3ID5-C-Xray547

Preferred Name:

Target Type:

Ligand Name: s-adenosylmethionine

Ligand 3-letter code: SAM

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3ID5

Chain ID: C

ChEMBL ID:

UniProt ID: P58032

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	120
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-960453.43827
FMO2-HF: Nuclear repulsion	915476.68486
FMO2-HF: Total energy	-44976.75341
FMO2-MP2: Total energy	-45109.576503

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:7:ALA)

Summations of interaction energy for fragment #1(A:7: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.
-124.692	-116.109	7.645	-8.107	-8.122	-0.084

Interaction energy analysis for fragmet #1(A:7:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.813 / q_NPA : 0.907

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	9	TYR	0	-0.043	-0.049	2.764	4.247	7.453	1.543	-1.897	-2.852	-0.015
4	A	10	VAL	0	0.000	-0.004	2.592	6.009	6.453	0.760	-0.308	-0.896	-0.003
5	A	11	LYS	1	0.944	0.965	5.031	29.617	29.576	-0.001	-0.005	0.048	0.000
52	A	58	GLU	-1	-0.869	-0.928	4.000	-41.322	-41.213	0.000	-0.024	-0.086	0.000
53	A	59	ASP	-1	-0.795	-0.875	3.010	-41.065	-39.965	0.142	-0.476	-0.766	-0.005
57	A	63	GLU	-1	-0.769	-0.874	2.174	-90.189	-86.424	5.201	-5.397	-3.570	-0.061
6	A	12	PHE	0	0.002	0.012	8.305	1.584	1.584	0.000	0.000	0.000	0.000
7	A	13	GLU	-1	-0.903	-0.944	8.375	-35.104	-35.104	0.000	0.000	0.000	0.000
8	A	14	VAL	0	-0.013	-0.019	9.031	2.580	2.580	0.000	0.000	0.000	0.000
9	A	15	PRO	0	0.014	0.009	10.987	-0.247	-0.247	0.000	0.000	0.000	0.000
10	A	16	GLN	0	0.040	0.011	12.910	1.131	1.131	0.000	0.000	0.000	0.000
11	A	17	ASP	-1	-0.861	-0.928	14.873	-15.223	-15.223	0.000	0.000	0.000	0.000
12	A	18	LEU	0	-0.060	-0.035	15.011	0.885	0.885	0.000	0.000	0.000	0.000
13	A	19	ALA	0	0.021	0.012	12.393	0.179	0.179	0.000	0.000	0.000	0.000
14	A	20	ASP	-1	-0.877	-0.945	14.214	-17.093	-17.093	0.000	0.000	0.000	0.000
15	A	21	LYS	1	0.892	0.936	17.429	13.694	13.694	0.000	0.000	0.000	0.000
16	A	22	VAL	0	0.000	-0.001	14.498	0.668	0.668	0.000	0.000	0.000	0.000
17	A	23	LEU	0	-0.046	-0.023	14.831	0.621	0.621	0.000	0.000	0.000	0.000
18	A	24	GLU	-1	-0.980	-0.993	18.011	-12.250	-12.250	0.000	0.000	0.000	0.000
19	A	25	ALA	0	-0.017	-0.009	20.161	0.644	0.644	0.000	0.000	0.000	0.000
20	A	26	VAL	0	-0.005	-0.021	17.640	0.525	0.525	0.000	0.000	0.000	0.000
21	A	27	ARG	1	0.905	0.969	19.504	14.706	14.706	0.000	0.000	0.000	0.000
22	A	28	LYS	1	1.047	1.025	23.318	11.246	11.246	0.000	0.000	0.000	0.000
23	A	29	ALA	0	-0.024	0.000	23.989	0.429	0.429	0.000	0.000	0.000	0.000
24	A	30	LYS	1	0.786	0.861	20.263	13.887	13.887	0.000	0.000	0.000	0.000
25	A	31	GLU	-1	-0.937	-0.954	26.721	-9.957	-9.957	0.000	0.000	0.000	0.000
26	A	32	SER	0	0.001	0.007	29.384	0.295	0.295	0.000	0.000	0.000	0.000
27	A	33	GLY	0	-0.032	-0.022	28.672	0.181	0.181	0.000	0.000	0.000	0.000
28	A	34	LYS	1	0.951	0.992	27.036	10.088	10.088	0.000	0.000	0.000	0.000
29	A	35	ILE	0	0.002	0.004	21.442	-0.294	-0.294	0.000	0.000	0.000	0.000
30	A	36	LYS	1	0.868	0.947	20.883	12.508	12.508	0.000	0.000	0.000	0.000
31	A	37	LYS	1	0.934	0.966	18.347	11.967	11.967	0.000	0.000	0.000	0.000
32	A	38	GLY	0	0.079	0.046	16.003	0.498	0.498	0.000	0.000	0.000	0.000
33	A	39	THR	0	0.030	0.015	12.683	0.721	0.721	0.000	0.000	0.000	0.000
34	A	40	ASN	0	-0.028	0.011	15.286	0.497	0.497	0.000	0.000	0.000	0.000
35	A	41	GLU	-1	-0.805	-0.920	18.809	-12.554	-12.554	0.000	0.000	0.000	0.000
36	A	42	THR	0	-0.004	-0.010	14.590	0.442	0.442	0.000	0.000	0.000	0.000
37	A	43	THR	0	0.048	0.010	16.193	-0.085	-0.085	0.000	0.000	0.000	0.000
38	A	44	LYS	1	0.822	0.885	17.878	12.708	12.708	0.000	0.000	0.000	0.000
39	A	45	ALA	0	-0.050	-0.016	19.992	0.705	0.705	0.000	0.000	0.000	0.000
40	A	46	VAL	0	0.036	0.019	16.669	0.534	0.534	0.000	0.000	0.000	0.000
41	A	47	GLU	-1	-0.849	-0.902	20.128	-11.860	-11.860	0.000	0.000	0.000	0.000
42	A	48	ARG	1	0.903	0.937	22.286	11.454	11.454	0.000	0.000	0.000	0.000
43	A	49	GLY	0	0.042	0.041	23.701	0.428	0.428	0.000	0.000	0.000	0.000
44	A	50	GLN	0	-0.055	-0.035	24.401	0.021	0.021	0.000	0.000	0.000	0.000
45	A	51	ALA	0	-0.018	-0.010	19.963	0.138	0.138	0.000	0.000	0.000	0.000
46	A	52	LYS	1	0.901	0.961	21.986	11.402	11.402	0.000	0.000	0.000	0.000
47	A	53	LEU	0	0.047	0.029	17.078	-0.065	-0.065	0.000	0.000	0.000	0.000
48	A	54	VAL	0	-0.028	-0.013	13.114	0.392	0.392	0.000	0.000	0.000	0.000
49	A	55	ILE	0	0.004	0.006	12.859	-0.491	-0.491	0.000	0.000	0.000	0.000
50	A	56	ILE	0	-0.018	-0.014	7.451	0.828	0.828	0.000	0.000	0.000	0.000
51	A	57	ALA	0	0.020	0.017	8.336	-0.654	-0.654	0.000	0.000	0.000	0.000
54	A	60	VAL	0	-0.049	-0.023	4.937	6.605	6.605	0.000	0.000	0.000	0.000
55	A	61	GLN	0	-0.001	0.007	5.384	-1.498	-1.498	0.000	0.000	0.000	0.000
56	A	62	PRO	0	0.020	-0.008	7.939	2.876	2.876	0.000	0.000	0.000	0.000
58	A	64	GLU	-1	-0.874	-0.959	5.914	-30.123	-30.123	0.000	0.000	0.000	0.000
59	A	65	ILE	0	-0.066	-0.018	8.842	2.291	2.291	0.000	0.000	0.000	0.000
60	A	66	VAL	0	-0.008	-0.024	6.410	2.479	2.479	0.000	0.000	0.000	0.000
61	A	67	ALA	0	0.010	0.015	7.161	0.050	0.050	0.000	0.000	0.000	0.000
62	A	68	HIS	0	-0.004	-0.007	8.245	-0.198	-0.198	0.000	0.000	0.000	0.000
63	A	69	LEU	0	-0.021	-0.003	10.660	1.284	1.284	0.000	0.000	0.000	0.000
64	A	70	PRO	0	0.033	0.016	8.402	1.564	1.564	0.000	0.000	0.000	0.000
65	A	71	LEU	0	0.048	0.022	11.708	1.103	1.103	0.000	0.000	0.000	0.000
66	A	72	LEU	0	-0.022	-0.004	14.202	1.328	1.328	0.000	0.000	0.000	0.000
67	A	73	CYS	0	-0.081	-0.049	14.620	1.146	1.146	0.000	0.000	0.000	0.000
68	A	74	ASP	-1	-0.780	-0.869	14.746	-18.387	-18.387	0.000	0.000	0.000	0.000
69	A	75	GLU	-1	-0.951	-0.955	17.553	-13.033	-13.033	0.000	0.000	0.000	0.000
70	A	76	LYS	1	0.835	0.904	19.782	13.315	13.315	0.000	0.000	0.000	0.000
71	A	77	LYS	1	0.931	0.972	20.671	12.343	12.343	0.000	0.000	0.000	0.000
72	A	78	ILE	0	-0.032	-0.005	18.626	0.437	0.437	0.000	0.000	0.000	0.000
73	A	79	PRO	0	0.028	0.017	17.258	-0.882	-0.882	0.000	0.000	0.000	0.000
74	A	80	TYR	0	-0.069	-0.077	10.835	-0.206	-0.206	0.000	0.000	0.000	0.000
75	A	81	VAL	0	0.026	0.006	11.850	-0.122	-0.122	0.000	0.000	0.000	0.000
76	A	82	TYR	0	-0.015	0.003	6.416	0.125	0.125	0.000	0.000	0.000	0.000
77	A	83	VAL	0	0.034	0.007	8.696	2.158	2.158	0.000	0.000	0.000	0.000
78	A	84	SER	0	0.076	0.033	7.629	-1.123	-1.123	0.000	0.000	0.000	0.000
79	A	85	SER	0	-0.006	-0.004	8.688	0.051	0.051	0.000	0.000	0.000	0.000
80	A	86	LYS	1	0.868	0.906	9.047	29.731	29.731	0.000	0.000	0.000	0.000
81	A	87	LYS	1	0.769	0.870	11.372	17.587	17.587	0.000	0.000	0.000	0.000
82	A	88	ALA	0	0.061	0.036	13.869	1.175	1.175	0.000	0.000	0.000	0.000
83	A	89	LEU	0	0.025	0.012	12.367	1.197	1.197	0.000	0.000	0.000	0.000
84	A	90	GLY	0	-0.006	-0.002	15.026	0.931	0.931	0.000	0.000	0.000	0.000
85	A	91	GLU	-1	-0.793	-0.871	17.148	-14.111	-14.111	0.000	0.000	0.000	0.000
86	A	92	ALA	0	-0.016	0.006	18.131	0.808	0.808	0.000	0.000	0.000	0.000
87	A	93	CYS	0	-0.110	-0.051	17.890	0.545	0.545	0.000	0.000	0.000	0.000
88	A	94	GLY	0	0.040	0.034	20.793	0.411	0.411	0.000	0.000	0.000	0.000
89	A	95	LEU	0	-0.076	-0.033	18.881	0.430	0.430	0.000	0.000	0.000	0.000
90	A	96	GLN	0	0.044	0.014	21.216	-0.318	-0.318	0.000	0.000	0.000	0.000
91	A	97	VAL	0	-0.029	-0.012	17.563	-0.371	-0.371	0.000	0.000	0.000	0.000
92	A	98	ALA	0	0.013	0.002	13.534	-0.010	-0.010	0.000	0.000	0.000	0.000
93	A	99	THR	0	-0.017	-0.018	14.352	0.363	0.363	0.000	0.000	0.000	0.000
94	A	100	ALA	0	0.037	0.016	10.074	-0.942	-0.942	0.000	0.000	0.000	0.000
95	A	101	SER	0	0.001	0.000	10.227	-1.184	-1.184	0.000	0.000	0.000	0.000
96	A	102	ALA	0	0.017	0.011	12.775	1.213	1.213	0.000	0.000	0.000	0.000
97	A	103	ALA	0	0.005	0.009	15.758	-0.592	-0.592	0.000	0.000	0.000	0.000
98	A	104	ILE	0	0.042	0.028	18.514	0.625	0.625	0.000	0.000	0.000	0.000
99	A	105	LEU	0	-0.047	-0.026	21.602	-0.029	-0.029	0.000	0.000	0.000	0.000
100	A	106	GLU	-1	-0.940	-0.983	24.876	-9.650	-9.650	0.000	0.000	0.000	0.000
101	A	107	PRO	0	0.015	-0.012	25.335	0.004	0.004	0.000	0.000	0.000	0.000
102	A	108	GLY	0	0.052	0.044	26.655	-0.100	-0.100	0.000	0.000	0.000	0.000
103	A	109	GLU	-1	-0.940	-0.986	29.793	-9.442	-9.442	0.000	0.000	0.000	0.000
104	A	110	ALA	0	-0.034	-0.016	24.438	-0.080	-0.080	0.000	0.000	0.000	0.000
105	A	111	LYS	1	0.911	0.956	25.642	9.128	9.128	0.000	0.000	0.000	0.000
106	A	112	ASP	-1	-0.816	-0.913	26.729	-10.213	-10.213	0.000	0.000	0.000	0.000
107	A	113	LEU	0	-0.031	-0.002	22.661	-0.166	-0.166	0.000	0.000	0.000	0.000
108	A	114	VAL	0	0.003	-0.012	21.630	-0.620	-0.620	0.000	0.000	0.000	0.000
109	A	115	ASP	-1	-0.841	-0.918	22.334	-11.588	-11.588	0.000	0.000	0.000	0.000
110	A	116	GLU	-1	-0.844	-0.903	22.650	-12.661	-12.661	0.000	0.000	0.000	0.000
111	A	117	ILE	0	-0.022	-0.010	17.371	-0.478	-0.478	0.000	0.000	0.000	0.000
112	A	118	ILE	0	-0.042	-0.029	19.110	-0.650	-0.650	0.000	0.000	0.000	0.000
113	A	119	LYS	1	0.831	0.904	20.523	11.049	11.049	0.000	0.000	0.000	0.000
114	A	120	ARG	1	0.895	0.953	18.842	13.862	13.862	0.000	0.000	0.000	0.000
115	A	121	VAL	0	-0.003	-0.014	14.957	-0.443	-0.443	0.000	0.000	0.000	0.000
116	A	122	ASN	0	-0.047	-0.025	16.321	-1.221	-1.221	0.000	0.000	0.000	0.000
117	A	123	GLU	-1	-0.916	-0.956	18.977	-13.536	-13.536	0.000	0.000	0.000	0.000
118	A	124	ILE	0	-0.048	-0.009	13.155	-0.025	-0.025	0.000	0.000	0.000	0.000
119	A	125	LYS	1	0.792	0.902	14.220	17.322	17.322	0.000	0.000	0.000	0.000
120	A	126	GLY	-1	-0.948	-0.949	15.938	-16.232	-16.232	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:ALA)