FMO DATABASE

FMODB ID: JK9Z9

Calculation Name: 1IG4-A-Other549

Preferred Name:

Target Type:

Ligand Name: 5-methyl-2'-deoxy-cytidine-5'-monophosphate

Ligand 3-letter code: 5CM

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1IG4

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UIS9

Base Structure: SolutionNMR

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	75
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-453195.938346
FMO2-HF: Nuclear repulsion	422675.219173
FMO2-HF: Total energy	-30520.719174
FMO2-MP2: Total energy	-30607.114877

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:MET)

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

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.
4.676	6.895	0.001	-0.968	-1.253	-0.005

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.847 / q_NPA : 0.906

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

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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	GLU	-1	-0.861	-0.930	3.850	-61.679	-59.460	0.001	-0.968	-1.253	-0.005
4	A	4	ASP	-1	-0.827	-0.918	5.865	-25.245	-25.245	0.000	0.000	0.000	0.000
5	A	5	TRP	0	-0.076	-0.035	5.999	2.619	2.619	0.000	0.000	0.000	0.000
6	A	6	LEU	0	0.065	0.046	10.407	1.265	1.265	0.000	0.000	0.000	0.000
7	A	7	ASP	-1	-0.841	-0.913	14.216	-18.572	-18.572	0.000	0.000	0.000	0.000
8	A	8	CYS	0	-0.111	-0.046	16.981	0.308	0.308	0.000	0.000	0.000	0.000
9	A	9	PRO	0	0.025	0.003	18.917	0.368	0.368	0.000	0.000	0.000	0.000
10	A	10	ALA	0	-0.042	-0.010	22.152	0.582	0.582	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.019	0.001	20.734	0.357	0.357	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.051	0.019	22.769	0.577	0.577	0.000	0.000	0.000	0.000
13	A	13	PRO	0	-0.010	-0.007	21.735	-0.670	-0.670	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.052	0.019	18.240	0.198	0.198	0.000	0.000	0.000	0.000
15	A	15	TRP	0	0.004	0.026	16.694	-1.233	-1.233	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.807	0.892	12.486	21.283	21.283	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.853	0.904	14.048	19.074	19.074	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.865	0.947	4.826	38.334	38.334	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.832	-0.891	11.485	-18.161	-18.161	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.041	-0.030	8.983	-3.029	-3.029	0.000	0.000	0.000	0.000
21	A	21	PHE	0	0.030	0.021	11.083	1.841	1.841	0.000	0.000	0.000	0.000
22	A	22	ARG	1	0.751	0.878	12.666	18.813	18.813	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.936	0.964	9.413	23.132	23.132	0.000	0.000	0.000	0.000
24	A	24	SER	0	0.063	-0.007	12.207	0.627	0.627	0.000	0.000	0.000	0.000
25	A	25	GLY	0	-0.052	-0.023	15.425	-0.414	-0.414	0.000	0.000	0.000	0.000
26	A	26	ALA	0	0.025	0.020	18.189	0.618	0.618	0.000	0.000	0.000	0.000
27	A	27	THR	0	-0.051	-0.034	17.506	0.235	0.235	0.000	0.000	0.000	0.000
28	A	28	CYS	-1	-0.759	-0.825	16.019	-19.536	-19.536	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.067	0.003	16.691	0.875	0.875	0.000	0.000	0.000	0.000
30	A	30	ARG	1	0.876	0.950	17.522	14.371	14.371	0.000	0.000	0.000	0.000
31	A	31	SER	0	0.015	0.003	15.602	-0.812	-0.812	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.862	-0.923	14.251	-16.504	-16.504	0.000	0.000	0.000	0.000
33	A	33	THR	0	-0.004	-0.011	13.767	-1.463	-1.463	0.000	0.000	0.000	0.000
34	A	34	TYR	0	-0.072	-0.029	11.788	0.724	0.724	0.000	0.000	0.000	0.000
35	A	35	TYR	0	-0.007	-0.053	13.278	-0.905	-0.905	0.000	0.000	0.000	0.000
36	A	36	GLN	0	-0.124	-0.047	11.491	-1.065	-1.065	0.000	0.000	0.000	0.000
37	A	37	SER	0	0.086	0.026	14.222	0.486	0.486	0.000	0.000	0.000	0.000
38	A	38	PRO	0	-0.062	-0.010	16.496	-0.847	-0.847	0.000	0.000	0.000	0.000
39	A	39	THR	0	0.004	-0.016	18.589	0.009	0.009	0.000	0.000	0.000	0.000
40	A	40	GLY	0	-0.033	-0.002	16.265	0.075	0.075	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.815	-0.920	16.266	-13.800	-13.800	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.865	0.927	8.586	24.264	24.264	0.000	0.000	0.000	0.000
43	A	43	ILE	0	0.080	0.067	15.111	0.134	0.134	0.000	0.000	0.000	0.000
44	A	44	ARG	1	0.934	0.949	12.288	19.342	19.342	0.000	0.000	0.000	0.000
45	A	45	SER	0	0.015	-0.001	17.071	0.186	0.186	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.960	0.983	20.412	10.655	10.655	0.000	0.000	0.000	0.000
47	A	47	VAL	0	-0.013	0.007	23.488	0.316	0.316	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.923	-0.976	18.817	-14.846	-14.846	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.004	0.011	19.967	0.132	0.132	0.000	0.000	0.000	0.000
50	A	50	THR	0	-0.015	-0.014	22.391	0.289	0.289	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.895	0.950	23.883	11.832	11.832	0.000	0.000	0.000	0.000
52	A	52	TYR	0	0.010	0.004	21.239	0.371	0.371	0.000	0.000	0.000	0.000
53	A	53	LEU	0	0.008	0.012	24.147	0.169	0.169	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.040	0.036	26.780	0.432	0.432	0.000	0.000	0.000	0.000
55	A	55	PRO	0	-0.012	-0.025	29.523	-0.037	-0.037	0.000	0.000	0.000	0.000
56	A	56	ALA	0	-0.003	0.001	31.425	0.175	0.175	0.000	0.000	0.000	0.000
57	A	57	CYS	0	-0.075	-0.028	29.297	0.245	0.245	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.802	-0.898	28.997	-10.359	-10.359	0.000	0.000	0.000	0.000
59	A	59	LEU	0	0.020	-0.011	25.002	-0.063	-0.063	0.000	0.000	0.000	0.000
60	A	60	THR	0	-0.078	-0.057	28.117	-0.392	-0.392	0.000	0.000	0.000	0.000
61	A	61	LEU	0	0.022	0.025	29.847	0.037	0.037	0.000	0.000	0.000	0.000
62	A	62	PHE	0	-0.022	0.007	19.857	-0.311	-0.311	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.846	-0.925	23.349	-12.139	-12.139	0.000	0.000	0.000	0.000
64	A	64	PHE	0	-0.028	-0.017	18.997	-0.668	-0.668	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.928	0.967	19.505	14.270	14.270	0.000	0.000	0.000	0.000
66	A	66	GLN	0	0.008	0.007	18.693	-1.179	-1.179	0.000	0.000	0.000	0.000
67	A	67	GLY	0	0.031	0.013	19.016	-0.648	-0.648	0.000	0.000	0.000	0.000
68	A	68	ILE	0	0.010	-0.004	20.031	-0.164	-0.164	0.000	0.000	0.000	0.000
69	A	69	LEU	0	0.032	0.017	23.423	0.125	0.125	0.000	0.000	0.000	0.000
70	A	70	CYS	0	-0.045	-0.007	26.982	0.228	0.228	0.000	0.000	0.000	0.000
71	A	71	TYR	0	0.022	0.003	29.098	0.271	0.271	0.000	0.000	0.000	0.000
72	A	72	PRO	0	-0.008	0.007	31.345	-0.162	-0.162	0.000	0.000	0.000	0.000
73	A	73	ALA	0	0.033	-0.002	32.486	-0.022	-0.022	0.000	0.000	0.000	0.000
74	A	74	PRO	0	-0.055	-0.021	35.860	0.043	0.043	0.000	0.000	0.000	0.000
75	A	75	LYS	0	0.057	0.037	39.193	-0.686	-0.686	0.000	0.000	0.000	0.000

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