FMO DATABASE

FMODB ID: 2G9QR

Calculation Name: 1CMC-A-Xray549

Preferred Name:

Target Type:

Ligand Name: s-adenosylmethionine | magnesium ion

Ligand 3-letter code: SAM | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1CMC

Chain ID: A

ChEMBL ID:

UniProt ID: P0A8U6

Base Structure: X-ray

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	104
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-794554.069492
FMO2-HF: Nuclear repulsion	752428.897368
FMO2-HF: Total energy	-42125.172124
FMO2-MP2: Total energy	-42248.180221

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:1:ALA)

Summations of interaction energy for fragment #1(A:1: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.
-85.998	-83.603	0.294	-1.249	-1.44	-0.009

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.781 / q_NPA : 0.880

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	3	TRP	0	0.008	0.007	2.895	-4.330	-1.935	0.294	-1.249	-1.440	-0.009
4	A	4	SER	0	0.007	-0.010	5.422	2.050	2.050	0.000	0.000	0.000	0.000
5	A	5	GLY	0	0.056	0.029	7.059	2.509	2.509	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.937	-0.979	9.848	-20.998	-20.998	0.000	0.000	0.000	0.000
7	A	7	TYR	0	-0.033	-0.015	11.723	-0.250	-0.250	0.000	0.000	0.000	0.000
8	A	8	ILE	0	0.031	0.017	12.377	1.505	1.505	0.000	0.000	0.000	0.000
9	A	9	SER	0	0.050	0.025	15.213	-0.411	-0.411	0.000	0.000	0.000	0.000
10	A	10	PRO	0	-0.046	-0.023	16.284	0.054	0.054	0.000	0.000	0.000	0.000
11	A	11	TYR	0	-0.095	-0.085	18.507	0.602	0.602	0.000	0.000	0.000	0.000
12	A	12	ALA	0	0.013	0.003	22.262	0.083	0.083	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.916	-0.955	25.116	-9.743	-9.743	0.000	0.000	0.000	0.000
14	A	14	HIS	1	0.832	0.910	22.759	13.104	13.104	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.035	0.017	25.139	0.139	0.139	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.896	0.942	27.603	9.378	9.378	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.858	0.931	23.554	12.791	12.791	0.000	0.000	0.000	0.000
18	A	18	SER	0	-0.012	-0.009	27.161	-0.130	-0.130	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.853	-0.923	21.761	-13.725	-13.725	0.000	0.000	0.000	0.000
20	A	20	GLN	0	-0.063	-0.039	26.189	0.298	0.298	0.000	0.000	0.000	0.000
21	A	21	VAL	0	0.049	0.026	25.455	-0.388	-0.388	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.943	0.964	26.049	11.055	11.055	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.945	0.972	26.619	9.217	9.217	0.000	0.000	0.000	0.000
24	A	24	ILE	0	0.041	0.020	23.493	0.160	0.160	0.000	0.000	0.000	0.000
25	A	25	THR	0	-0.009	-0.004	27.939	0.194	0.194	0.000	0.000	0.000	0.000
26	A	26	VAL	0	0.018	0.007	24.082	-0.158	-0.158	0.000	0.000	0.000	0.000
27	A	27	SER	0	0.003	0.006	27.275	0.441	0.441	0.000	0.000	0.000	0.000
28	A	28	ILE	0	0.016	0.007	24.907	-0.430	-0.430	0.000	0.000	0.000	0.000
29	A	29	PRO	0	0.035	0.015	25.411	0.459	0.459	0.000	0.000	0.000	0.000
30	A	30	LEU	0	0.070	0.027	27.713	-0.286	-0.286	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.960	0.975	27.041	11.408	11.408	0.000	0.000	0.000	0.000
32	A	32	VAL	0	0.034	0.020	22.564	-0.138	-0.138	0.000	0.000	0.000	0.000
33	A	33	LEU	0	0.024	0.010	25.219	-0.187	-0.187	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.846	0.920	27.771	10.382	10.382	0.000	0.000	0.000	0.000
35	A	35	ILE	0	0.042	0.023	22.614	0.088	0.088	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.002	0.008	22.631	-0.069	-0.069	0.000	0.000	0.000	0.000
37	A	37	THR	0	-0.047	-0.046	25.152	0.188	0.188	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.800	-0.863	27.692	-10.290	-10.290	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.773	-0.853	22.386	-13.202	-13.202	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.898	0.962	25.852	10.387	10.387	0.000	0.000	0.000	0.000
41	A	41	THR	0	-0.048	-0.044	27.359	0.345	0.345	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.725	0.803	23.664	13.184	13.184	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.859	0.894	20.171	14.617	14.617	0.000	0.000	0.000	0.000
44	A	44	GLN	0	-0.056	-0.025	28.128	0.397	0.397	0.000	0.000	0.000	0.000
45	A	45	VAL	0	-0.024	-0.017	31.597	0.237	0.237	0.000	0.000	0.000	0.000
46	A	46	ASN	0	-0.064	-0.029	29.571	0.311	0.311	0.000	0.000	0.000	0.000
47	A	47	ASN	0	-0.002	0.008	31.447	-0.114	-0.114	0.000	0.000	0.000	0.000
48	A	48	LEU	0	0.024	0.024	25.852	0.051	0.051	0.000	0.000	0.000	0.000
49	A	49	ARG	1	0.826	0.901	25.965	11.379	11.379	0.000	0.000	0.000	0.000
50	A	50	HIS	1	0.810	0.880	23.375	12.530	12.530	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.052	0.048	24.611	-0.412	-0.412	0.000	0.000	0.000	0.000
52	A	52	THR	0	-0.047	-0.073	25.944	0.431	0.431	0.000	0.000	0.000	0.000
53	A	53	ASN	0	0.033	-0.005	24.811	-0.412	-0.412	0.000	0.000	0.000	0.000
54	A	54	SER	0	0.009	-0.003	23.349	-0.444	-0.444	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.737	-0.817	21.841	-12.656	-12.656	0.000	0.000	0.000	0.000
56	A	56	LEU	0	0.027	0.026	20.073	-0.700	-0.700	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.042	-0.026	18.757	-0.810	-0.810	0.000	0.000	0.000	0.000
58	A	58	CYS	0	-0.038	-0.011	17.577	-0.676	-0.676	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.724	-0.816	15.887	-16.571	-16.571	0.000	0.000	0.000	0.000
60	A	60	ALA	0	-0.001	-0.004	14.102	-1.512	-1.512	0.000	0.000	0.000	0.000
61	A	61	PHE	0	-0.033	-0.013	13.175	-1.586	-1.586	0.000	0.000	0.000	0.000
62	A	62	LEU	0	0.039	0.018	11.939	-1.514	-1.514	0.000	0.000	0.000	0.000
63	A	63	HIS	0	-0.060	-0.009	9.684	-1.841	-1.841	0.000	0.000	0.000	0.000
64	A	64	ALA	0	-0.032	-0.028	8.375	-3.577	-3.577	0.000	0.000	0.000	0.000
65	A	65	PHE	0	-0.075	-0.031	8.304	-2.297	-2.297	0.000	0.000	0.000	0.000
66	A	66	THR	0	-0.026	-0.028	6.088	-1.605	-1.605	0.000	0.000	0.000	0.000
67	A	67	GLY	0	0.032	0.016	5.181	-5.532	-5.532	0.000	0.000	0.000	0.000
68	A	68	GLN	0	-0.022	0.001	6.106	1.012	1.012	0.000	0.000	0.000	0.000
69	A	69	PRO	0	-0.003	-0.005	9.350	1.023	1.023	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.022	-0.007	11.843	1.440	1.440	0.000	0.000	0.000	0.000
71	A	71	PRO	0	-0.020	0.000	14.888	-0.154	-0.154	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.818	-0.900	18.254	-15.139	-15.139	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.806	-0.904	20.397	-12.545	-12.545	0.000	0.000	0.000	0.000
74	A	74	ALA	0	-0.076	-0.039	23.514	0.708	0.708	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.763	-0.885	19.457	-15.617	-15.617	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.025	-0.007	21.939	0.415	0.415	0.000	0.000	0.000	0.000
77	A	77	ARG	1	0.839	0.902	24.808	10.970	10.970	0.000	0.000	0.000	0.000
78	A	78	LYS	1	0.843	0.907	28.274	9.849	9.849	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.827	-0.894	30.870	-9.755	-9.755	0.000	0.000	0.000	0.000
80	A	80	ARG	1	0.762	0.887	21.426	14.103	14.103	0.000	0.000	0.000	0.000
81	A	81	SER	0	0.010	0.004	27.259	0.328	0.328	0.000	0.000	0.000	0.000
82	A	82	ASP	-1	-0.865	-0.919	25.143	-12.835	-12.835	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.864	-0.921	22.597	-12.504	-12.504	0.000	0.000	0.000	0.000
84	A	84	ILE	0	0.024	0.017	16.442	-0.180	-0.180	0.000	0.000	0.000	0.000
85	A	85	PRO	0	0.022	0.023	16.102	0.575	0.575	0.000	0.000	0.000	0.000
86	A	86	GLU	-1	-0.785	-0.885	17.326	-15.265	-15.265	0.000	0.000	0.000	0.000
87	A	87	ALA	0	-0.004	-0.006	14.883	-0.422	-0.422	0.000	0.000	0.000	0.000
88	A	88	ALA	0	-0.025	-0.009	13.096	-1.615	-1.615	0.000	0.000	0.000	0.000
89	A	89	LYS	1	0.809	0.881	13.965	13.417	13.417	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.883	-0.930	15.919	-17.152	-17.152	0.000	0.000	0.000	0.000
91	A	91	ILE	0	0.028	0.015	9.189	-0.344	-0.344	0.000	0.000	0.000	0.000
92	A	92	MET	0	-0.090	-0.016	11.862	-0.455	-0.455	0.000	0.000	0.000	0.000
93	A	93	ARG	1	0.824	0.895	13.554	16.101	16.101	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.974	-0.976	11.286	-27.414	-27.414	0.000	0.000	0.000	0.000
95	A	95	MET	0	-0.062	-0.026	7.316	-0.349	-0.349	0.000	0.000	0.000	0.000
96	A	96	GLY	0	-0.025	-0.007	11.992	0.542	0.542	0.000	0.000	0.000	0.000
97	A	97	ILE	0	-0.050	-0.010	12.015	1.426	1.426	0.000	0.000	0.000	0.000
98	A	98	ASN	0	0.019	-0.004	15.755	-0.131	-0.131	0.000	0.000	0.000	0.000
99	A	99	PRO	0	0.008	0.000	17.256	0.264	0.264	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.834	-0.926	18.810	-13.872	-13.872	0.000	0.000	0.000	0.000
101	A	101	THR	0	-0.120	-0.066	21.423	0.636	0.636	0.000	0.000	0.000	0.000
102	A	102	TRP	0	0.021	0.017	14.739	0.085	0.085	0.000	0.000	0.000	0.000
103	A	103	GLU	-1	-0.993	-0.995	19.616	-12.156	-12.156	0.000	0.000	0.000	0.000
104	A	104	TYR	-1	-0.798	-0.876	18.314	-13.968	-13.968	0.000	0.000	0.000	0.000

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