FMO DATABASE

FMODB ID: QMN3Y

Calculation Name: 3Q0B-X-Xray547

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: 3Q0B

Chain ID: X

ChEMBL ID:

UniProt ID: O82175

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	163
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1596062.201902
FMO2-HF: Nuclear repulsion	1533528.74713
FMO2-HF: Total energy	-62533.454772
FMO2-MP2: Total energy	-62719.031879

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:362:GLN)

Summations of interaction energy for fragment #1(A:362:GLN)

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.
-42.527	-35.953	23.61	-11.25	-18.936	-0.085

Interaction energy analysis for fragmet #1(A:362:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.783 / q_NPA : 0.856

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	364	ILE	0	0.039	0.033	3.737	4.864	6.820	0.003	-0.753	-1.207	-0.002
26	A	387	ILE	0	-0.012	0.019	5.111	-1.847	-1.764	-0.001	0.000	-0.082	0.000
28	A	389	ARG	1	0.861	0.916	2.348	52.857	55.482	3.112	-1.371	-4.367	-0.002
35	A	396	ASP	-1	-0.784	-0.864	3.152	-53.527	-52.101	0.339	-0.705	-1.059	-0.004
36	A	397	TYR	0	0.029	0.014	3.172	1.940	2.867	0.051	-0.303	-0.675	-0.001
37	A	398	MET	0	-0.041	-0.003	1.989	-25.980	-25.163	10.372	-4.594	-6.596	-0.054
38	A	399	LYS	1	0.957	0.979	3.831	31.947	32.220	0.009	-0.105	-0.176	0.000
47	A	408	THR	0	-0.013	-0.001	1.883	-12.686	-14.925	9.720	-3.144	-4.338	-0.024
48	A	409	SER	0	-0.013	-0.017	4.098	1.311	1.463	-0.001	-0.044	-0.106	0.000
106	A	467	ARG	1	0.787	0.869	3.423	34.186	34.740	0.006	-0.231	-0.330	0.002
4	A	365	GLY	0	0.028	0.022	6.242	0.988	0.988	0.000	0.000	0.000	0.000
5	A	366	THR	0	0.018	0.000	8.030	-1.553	-1.553	0.000	0.000	0.000	0.000
6	A	367	VAL	0	-0.004	0.011	6.782	-2.009	-2.009	0.000	0.000	0.000	0.000
7	A	368	PRO	0	-0.021	-0.027	8.934	1.946	1.946	0.000	0.000	0.000	0.000
8	A	369	GLY	0	0.025	0.022	11.887	-0.675	-0.675	0.000	0.000	0.000	0.000
9	A	370	VAL	0	-0.043	-0.013	11.029	-0.107	-0.107	0.000	0.000	0.000	0.000
10	A	371	GLU	-1	-0.898	-0.950	13.936	-17.410	-17.410	0.000	0.000	0.000	0.000
11	A	372	VAL	0	-0.087	-0.056	16.060	-0.287	-0.287	0.000	0.000	0.000	0.000
12	A	373	GLY	0	0.013	0.001	17.406	0.748	0.748	0.000	0.000	0.000	0.000
13	A	374	ASP	-1	-0.852	-0.899	16.081	-16.200	-16.200	0.000	0.000	0.000	0.000
14	A	375	GLU	-1	-0.904	-0.957	17.321	-13.188	-13.188	0.000	0.000	0.000	0.000
15	A	376	PHE	0	0.006	-0.015	14.344	-0.319	-0.319	0.000	0.000	0.000	0.000
16	A	377	GLN	0	-0.035	-0.022	17.882	1.097	1.097	0.000	0.000	0.000	0.000
17	A	378	TYR	0	-0.011	-0.025	17.432	0.189	0.189	0.000	0.000	0.000	0.000
18	A	379	ARG	1	0.857	0.906	10.491	20.265	20.265	0.000	0.000	0.000	0.000
19	A	380	MET	0	-0.009	-0.012	12.225	-1.544	-1.544	0.000	0.000	0.000	0.000
20	A	381	GLU	-1	-0.751	-0.864	13.077	-17.277	-17.277	0.000	0.000	0.000	0.000
21	A	382	LEU	0	0.016	0.011	9.992	-1.118	-1.118	0.000	0.000	0.000	0.000
22	A	383	ASN	0	-0.098	-0.051	8.446	-2.264	-2.264	0.000	0.000	0.000	0.000
23	A	384	LEU	0	0.009	0.009	8.272	-2.965	-2.965	0.000	0.000	0.000	0.000
24	A	385	LEU	0	0.010	0.006	9.718	-1.087	-1.087	0.000	0.000	0.000	0.000
25	A	386	GLY	0	-0.025	-0.011	5.697	-1.451	-1.451	0.000	0.000	0.000	0.000
27	A	388	HIS	0	-0.001	-0.005	5.462	-2.095	-2.095	0.000	0.000	0.000	0.000
29	A	390	PRO	0	-0.043	-0.005	5.754	2.994	2.994	0.000	0.000	0.000	0.000
30	A	391	SER	0	0.048	0.027	8.916	0.954	0.954	0.000	0.000	0.000	0.000
31	A	392	GLN	0	0.016	0.002	12.444	1.158	1.158	0.000	0.000	0.000	0.000
32	A	393	SER	0	-0.027	-0.018	9.089	1.384	1.384	0.000	0.000	0.000	0.000
33	A	394	GLY	0	0.073	0.047	10.123	-1.142	-1.142	0.000	0.000	0.000	0.000
34	A	395	ILE	0	0.028	0.038	7.316	-0.553	-0.553	0.000	0.000	0.000	0.000
39	A	400	ASP	-1	-0.817	-0.915	6.136	-28.258	-28.258	0.000	0.000	0.000	0.000
40	A	401	ASP	-1	-0.949	-0.955	8.579	-21.711	-21.711	0.000	0.000	0.000	0.000
41	A	402	GLY	0	0.053	0.018	11.382	2.155	2.155	0.000	0.000	0.000	0.000
42	A	403	GLY	0	-0.083	-0.041	12.097	-1.110	-1.110	0.000	0.000	0.000	0.000
43	A	404	GLU	-1	-0.921	-0.953	12.053	-19.627	-19.627	0.000	0.000	0.000	0.000
44	A	405	LEU	0	-0.057	-0.027	7.976	-2.683	-2.683	0.000	0.000	0.000	0.000
45	A	406	VAL	0	0.076	0.027	6.473	2.252	2.252	0.000	0.000	0.000	0.000
46	A	407	ALA	0	0.025	0.008	5.544	-5.668	-5.668	0.000	0.000	0.000	0.000
49	A	410	ILE	0	-0.010	-0.008	6.042	-1.001	-1.001	0.000	0.000	0.000	0.000
50	A	411	VAL	0	0.007	0.010	9.095	0.792	0.792	0.000	0.000	0.000	0.000
51	A	412	SER	0	-0.046	-0.024	11.881	0.608	0.608	0.000	0.000	0.000	0.000
52	A	413	SER	0	0.036	-0.010	15.417	0.200	0.200	0.000	0.000	0.000	0.000
53	A	414	GLY	0	0.061	0.047	18.004	0.374	0.374	0.000	0.000	0.000	0.000
54	A	415	GLY	0	-0.067	-0.053	19.044	0.323	0.323	0.000	0.000	0.000	0.000
55	A	416	TYR	0	0.008	-0.009	17.603	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	417	ASN	0	0.007	0.018	20.766	0.118	0.118	0.000	0.000	0.000	0.000
57	A	418	ASP	-1	-0.767	-0.829	17.333	-14.721	-14.721	0.000	0.000	0.000	0.000
58	A	419	VAL	0	-0.037	-0.016	20.412	0.450	0.450	0.000	0.000	0.000	0.000
59	A	420	LEU	0	-0.003	-0.008	17.456	-0.513	-0.513	0.000	0.000	0.000	0.000
60	A	421	ASP	-1	-0.843	-0.889	21.764	-10.707	-10.707	0.000	0.000	0.000	0.000
61	A	422	ASN	0	-0.043	-0.040	23.370	-0.579	-0.579	0.000	0.000	0.000	0.000
62	A	423	SER	0	-0.040	-0.030	24.292	0.114	0.114	0.000	0.000	0.000	0.000
63	A	424	ASP	-1	-0.825	-0.905	21.750	-12.154	-12.154	0.000	0.000	0.000	0.000
64	A	425	VAL	0	-0.049	-0.029	20.413	-0.685	-0.685	0.000	0.000	0.000	0.000
65	A	426	LEU	0	0.012	0.020	15.323	0.048	0.048	0.000	0.000	0.000	0.000
66	A	427	ILE	0	-0.019	-0.013	18.456	-0.321	-0.321	0.000	0.000	0.000	0.000
67	A	428	TYR	0	0.013	-0.008	12.752	-0.274	-0.274	0.000	0.000	0.000	0.000
68	A	429	THR	0	-0.034	-0.033	16.695	0.601	0.601	0.000	0.000	0.000	0.000
69	A	430	GLY	0	0.007	0.015	15.545	-0.894	-0.894	0.000	0.000	0.000	0.000
70	A	431	GLN	0	-0.014	-0.009	11.039	-0.050	-0.050	0.000	0.000	0.000	0.000
71	A	432	GLY	0	0.024	0.005	15.697	0.175	0.175	0.000	0.000	0.000	0.000
72	A	433	GLY	0	0.069	0.016	18.204	0.385	0.385	0.000	0.000	0.000	0.000
73	A	434	ASN	0	-0.030	-0.016	21.454	0.157	0.157	0.000	0.000	0.000	0.000
74	A	435	VAL	0	0.032	0.021	21.603	0.523	0.523	0.000	0.000	0.000	0.000
75	A	436	GLY	0	0.003	-0.004	21.304	0.355	0.355	0.000	0.000	0.000	0.000
76	A	437	LYS	1	0.889	0.944	18.597	12.934	12.934	0.000	0.000	0.000	0.000
77	A	438	LYS	1	0.857	0.944	20.724	10.528	10.528	0.000	0.000	0.000	0.000
78	A	439	LYS	1	0.936	0.966	23.041	10.883	10.883	0.000	0.000	0.000	0.000
79	A	440	ASN	0	0.002	-0.005	24.613	0.218	0.218	0.000	0.000	0.000	0.000
80	A	441	ASN	0	-0.057	-0.039	28.122	0.067	0.067	0.000	0.000	0.000	0.000
81	A	442	GLU	-1	-0.825	-0.888	25.158	-11.079	-11.079	0.000	0.000	0.000	0.000
82	A	443	PRO	0	0.023	0.009	28.203	-0.106	-0.106	0.000	0.000	0.000	0.000
83	A	444	PRO	0	-0.031	-0.014	26.055	-0.319	-0.319	0.000	0.000	0.000	0.000
84	A	445	LYS	1	0.854	0.922	22.227	12.371	12.371	0.000	0.000	0.000	0.000
85	A	446	ASP	-1	-0.768	-0.883	24.205	-10.892	-10.892	0.000	0.000	0.000	0.000
86	A	447	GLN	0	-0.086	-0.054	19.051	-0.355	-0.355	0.000	0.000	0.000	0.000
87	A	448	GLN	0	0.039	0.021	18.219	0.451	0.451	0.000	0.000	0.000	0.000
88	A	449	LEU	0	0.021	0.019	16.105	-0.791	-0.791	0.000	0.000	0.000	0.000
89	A	450	VAL	0	0.009	-0.005	14.366	-0.149	-0.149	0.000	0.000	0.000	0.000
90	A	451	THR	0	-0.004	-0.015	9.736	-0.024	-0.024	0.000	0.000	0.000	0.000
91	A	452	GLY	0	0.074	0.031	8.806	-1.051	-1.051	0.000	0.000	0.000	0.000
92	A	453	ASN	0	0.005	0.007	9.765	-0.390	-0.390	0.000	0.000	0.000	0.000
93	A	454	LEU	0	-0.034	-0.010	12.169	0.506	0.506	0.000	0.000	0.000	0.000
94	A	455	ALA	0	-0.003	0.001	7.537	0.107	0.107	0.000	0.000	0.000	0.000
95	A	456	LEU	0	0.021	0.004	9.655	-0.365	-0.365	0.000	0.000	0.000	0.000
96	A	457	LYS	1	0.919	0.976	11.331	15.356	15.356	0.000	0.000	0.000	0.000
97	A	458	ASN	0	-0.027	-0.020	11.646	2.083	2.083	0.000	0.000	0.000	0.000
98	A	459	SER	0	-0.013	-0.033	9.571	0.011	0.011	0.000	0.000	0.000	0.000
99	A	460	ILE	0	-0.037	0.022	12.047	0.390	0.390	0.000	0.000	0.000	0.000
100	A	461	ASN	0	-0.031	-0.027	15.772	0.995	0.995	0.000	0.000	0.000	0.000
101	A	462	LYS	1	0.862	0.917	11.911	21.849	21.849	0.000	0.000	0.000	0.000
102	A	463	LYS	1	0.893	0.964	14.311	14.763	14.763	0.000	0.000	0.000	0.000
103	A	464	ASN	0	-0.004	0.023	7.875	0.946	0.946	0.000	0.000	0.000	0.000
104	A	465	PRO	0	0.013	-0.003	10.717	0.154	0.154	0.000	0.000	0.000	0.000
105	A	466	VAL	0	-0.027	-0.002	7.373	-2.802	-2.802	0.000	0.000	0.000	0.000
107	A	468	VAL	0	0.030	0.018	9.020	-1.038	-1.038	0.000	0.000	0.000	0.000
108	A	469	ILE	0	-0.032	-0.014	8.826	0.285	0.285	0.000	0.000	0.000	0.000
109	A	470	ARG	1	0.899	0.943	12.768	13.585	13.585	0.000	0.000	0.000	0.000
110	A	471	GLY	0	-0.018	-0.019	16.341	0.031	0.031	0.000	0.000	0.000	0.000
111	A	472	ILE	0	-0.042	-0.005	18.184	0.548	0.548	0.000	0.000	0.000	0.000
112	A	473	LYS	1	0.999	0.992	21.748	10.112	10.112	0.000	0.000	0.000	0.000
113	A	474	ASN	0	0.064	0.043	24.922	-0.008	-0.008	0.000	0.000	0.000	0.000
114	A	475	THR	0	-0.003	-0.017	25.921	0.306	0.306	0.000	0.000	0.000	0.000
115	A	476	THR	0	-0.008	-0.016	27.538	-0.292	-0.292	0.000	0.000	0.000	0.000
116	A	477	LEU	0	-0.034	-0.009	30.288	0.051	0.051	0.000	0.000	0.000	0.000
117	A	478	GLN	0	0.037	0.042	24.348	0.451	0.451	0.000	0.000	0.000	0.000
118	A	479	SER	0	-0.034	-0.028	27.269	0.234	0.234	0.000	0.000	0.000	0.000
119	A	480	SER	0	0.002	-0.011	27.063	-0.299	-0.299	0.000	0.000	0.000	0.000
120	A	481	VAL	0	0.002	0.001	23.266	-0.021	-0.021	0.000	0.000	0.000	0.000
121	A	482	VAL	0	0.002	0.011	26.008	-0.052	-0.052	0.000	0.000	0.000	0.000
122	A	483	ALA	0	-0.016	-0.005	21.095	-0.077	-0.077	0.000	0.000	0.000	0.000
123	A	484	LYS	1	0.854	0.923	21.751	11.925	11.925	0.000	0.000	0.000	0.000
124	A	485	ASN	0	-0.084	-0.051	19.895	0.473	0.473	0.000	0.000	0.000	0.000
125	A	486	TYR	0	-0.037	-0.027	14.940	-0.545	-0.545	0.000	0.000	0.000	0.000
126	A	487	VAL	0	0.088	0.062	16.828	0.153	0.153	0.000	0.000	0.000	0.000
127	A	488	TYR	0	-0.043	-0.015	11.473	-1.326	-1.326	0.000	0.000	0.000	0.000
128	A	489	ASP	-1	-0.751	-0.870	14.395	-14.017	-14.017	0.000	0.000	0.000	0.000
129	A	490	GLY	0	0.082	0.046	14.045	0.911	0.911	0.000	0.000	0.000	0.000
130	A	491	LEU	0	-0.063	-0.036	10.568	-1.224	-1.224	0.000	0.000	0.000	0.000
131	A	492	TYR	0	0.009	-0.018	12.350	1.465	1.465	0.000	0.000	0.000	0.000
132	A	493	LEU	0	-0.006	0.007	12.490	-1.466	-1.466	0.000	0.000	0.000	0.000
133	A	494	VAL	0	0.004	-0.009	12.211	0.452	0.452	0.000	0.000	0.000	0.000
134	A	495	GLU	-1	-0.855	-0.907	15.029	-12.659	-12.659	0.000	0.000	0.000	0.000
135	A	496	GLU	-1	-0.834	-0.914	18.615	-11.398	-11.398	0.000	0.000	0.000	0.000
136	A	497	TYR	0	-0.019	-0.028	17.578	-0.742	-0.742	0.000	0.000	0.000	0.000
137	A	498	TRP	0	-0.039	-0.019	19.504	0.294	0.294	0.000	0.000	0.000	0.000
138	A	499	GLU	-1	-0.884	-0.956	21.537	-12.250	-12.250	0.000	0.000	0.000	0.000
139	A	500	GLU	-1	-0.846	-0.919	23.939	-10.643	-10.643	0.000	0.000	0.000	0.000
140	A	501	THR	0	-0.023	-0.014	26.027	-0.126	-0.126	0.000	0.000	0.000	0.000
141	A	502	GLY	0	0.015	0.006	28.149	0.163	0.163	0.000	0.000	0.000	0.000
142	A	503	SER	0	0.007	-0.008	29.129	0.116	0.116	0.000	0.000	0.000	0.000
143	A	504	HIS	0	-0.020	0.002	26.333	0.450	0.450	0.000	0.000	0.000	0.000
144	A	505	GLY	0	0.006	0.002	31.772	0.061	0.061	0.000	0.000	0.000	0.000
145	A	506	LYS	1	0.864	0.939	26.698	9.401	9.401	0.000	0.000	0.000	0.000
146	A	507	LEU	0	0.033	0.022	23.067	0.015	0.015	0.000	0.000	0.000	0.000
147	A	508	VAL	0	-0.035	-0.028	21.443	-0.356	-0.356	0.000	0.000	0.000	0.000
148	A	509	PHE	0	0.000	0.002	18.029	0.075	0.075	0.000	0.000	0.000	0.000
149	A	510	LYS	1	0.891	0.952	19.089	12.046	12.046	0.000	0.000	0.000	0.000
150	A	511	PHE	0	-0.003	-0.017	15.356	-0.139	-0.139	0.000	0.000	0.000	0.000
151	A	512	LYS	1	0.858	0.937	17.395	11.918	11.918	0.000	0.000	0.000	0.000
152	A	513	LEU	0	-0.015	-0.022	12.233	-0.604	-0.604	0.000	0.000	0.000	0.000
153	A	514	ARG	1	0.784	0.859	16.772	12.866	12.866	0.000	0.000	0.000	0.000
154	A	515	ARG	1	0.809	0.904	16.917	13.463	13.463	0.000	0.000	0.000	0.000
155	A	516	ILE	0	-0.028	-0.021	14.428	0.553	0.553	0.000	0.000	0.000	0.000
156	A	517	PRO	0	0.039	0.008	18.305	0.073	0.073	0.000	0.000	0.000	0.000
157	A	518	GLY	0	-0.002	-0.001	21.067	-0.397	-0.397	0.000	0.000	0.000	0.000
158	A	519	GLN	0	-0.042	-0.015	15.989	-0.922	-0.922	0.000	0.000	0.000	0.000
159	A	520	PRO	0	0.037	0.017	19.704	0.457	0.457	0.000	0.000	0.000	0.000
160	A	521	GLU	-1	-0.918	-0.944	21.533	-11.038	-11.038	0.000	0.000	0.000	0.000
161	A	522	LEU	0	-0.023	-0.021	19.032	-0.215	-0.215	0.000	0.000	0.000	0.000
162	A	523	PRO	0	-0.033	-0.010	23.281	0.166	0.166	0.000	0.000	0.000	0.000
163	A	524	TRP	-1	-0.926	-0.932	24.419	-10.270	-10.270	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:362:GLN)