FMO DATABASE

FMODB ID: Y1MQ2

Calculation Name: 4RDN-A-Xray547

Preferred Name: YTH domain-containing family protein 2

Target Type: SINGLE PROTEIN

Ligand Name: n-methyladenosine

Ligand 3-letter code: 6MD

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4RDN

Chain ID: A

ChEMBL ID: CHEMBL4295992

UniProt ID: Q9Y5A9

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	149
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1508400.565905
FMO2-HF: Nuclear repulsion	1447410.191975
FMO2-HF: Total energy	-60990.373931
FMO2-MP2: Total energy	-61167.616056

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:400:GLU)

Summations of interaction energy for fragment #1(A:400:GLU)

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.
-9.644	-4.355	1.94	-2.779	-4.45	0.02

Interaction energy analysis for fragmet #1(A:400:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.033 / q_NPA : -0.022

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	402	LEU	0	0.090	0.051	2.304	-5.472	-0.280	1.941	-2.767	-4.366	0.020
4	A	403	TYR	0	0.023	0.027	4.637	0.049	0.146	-0.001	-0.012	-0.084	0.000
5	A	404	PHE	0	0.029	0.011	7.856	0.272	0.272	0.000	0.000	0.000	0.000
6	A	405	GLN	0	0.026	0.008	6.914	0.673	0.673	0.000	0.000	0.000	0.000
7	A	406	HIS	0	0.046	0.020	9.380	-1.557	-1.557	0.000	0.000	0.000	0.000
8	A	407	MET	0	0.035	0.022	12.802	-0.307	-0.307	0.000	0.000	0.000	0.000
9	A	408	LYS	1	0.891	0.944	14.861	-2.420	-2.420	0.000	0.000	0.000	0.000
10	A	409	HIS	0	0.049	0.030	18.195	-0.160	-0.160	0.000	0.000	0.000	0.000
11	A	410	GLY	0	0.062	0.023	19.507	-0.081	-0.081	0.000	0.000	0.000	0.000
12	A	411	ARG	1	0.789	0.877	20.508	-0.216	-0.216	0.000	0.000	0.000	0.000
13	A	412	VAL	0	0.017	0.004	18.909	-0.109	-0.109	0.000	0.000	0.000	0.000
14	A	413	PHE	0	0.002	0.005	22.341	0.080	0.080	0.000	0.000	0.000	0.000
15	A	414	ILE	0	-0.024	-0.010	23.000	-0.091	-0.091	0.000	0.000	0.000	0.000
16	A	415	ILE	0	-0.003	0.004	26.038	0.065	0.065	0.000	0.000	0.000	0.000
17	A	416	LYS	1	0.845	0.918	28.207	0.381	0.381	0.000	0.000	0.000	0.000
18	A	417	SER	0	0.031	0.025	30.853	0.053	0.053	0.000	0.000	0.000	0.000
19	A	418	TYR	0	-0.008	-0.026	33.073	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	419	SER	0	0.006	0.022	35.212	-0.011	-0.011	0.000	0.000	0.000	0.000
21	A	420	GLU	-1	-0.756	-0.889	31.072	-0.729	-0.729	0.000	0.000	0.000	0.000
22	A	421	ASP	-1	-0.883	-0.930	34.059	-0.487	-0.487	0.000	0.000	0.000	0.000
23	A	422	ASP	-1	-0.830	-0.932	35.334	-0.384	-0.384	0.000	0.000	0.000	0.000
24	A	423	ILE	0	-0.021	-0.009	29.132	0.004	0.004	0.000	0.000	0.000	0.000
25	A	424	HIS	0	0.006	-0.006	31.225	-0.035	-0.035	0.000	0.000	0.000	0.000
26	A	425	ARG	1	0.906	0.967	33.067	0.393	0.393	0.000	0.000	0.000	0.000
27	A	426	SER	0	-0.013	-0.027	30.890	-0.006	-0.006	0.000	0.000	0.000	0.000
28	A	427	ILE	0	-0.021	-0.012	27.608	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	428	LYS	1	0.896	0.958	30.132	0.565	0.565	0.000	0.000	0.000	0.000
30	A	429	TYR	0	-0.033	-0.028	33.297	0.007	0.007	0.000	0.000	0.000	0.000
31	A	430	ASN	0	0.014	0.014	29.085	0.004	0.004	0.000	0.000	0.000	0.000
32	A	431	ILE	0	0.018	0.022	31.765	0.044	0.044	0.000	0.000	0.000	0.000
33	A	432	TRP	0	-0.010	-0.001	31.556	-0.056	-0.056	0.000	0.000	0.000	0.000
34	A	433	CYS	0	0.009	0.025	33.687	0.046	0.046	0.000	0.000	0.000	0.000
35	A	434	SER	0	-0.015	-0.006	33.777	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	435	THR	0	0.029	-0.017	35.822	0.005	0.005	0.000	0.000	0.000	0.000
37	A	436	GLU	-1	-0.839	-0.915	38.017	-0.023	-0.023	0.000	0.000	0.000	0.000
38	A	437	HIS	0	0.030	0.017	35.730	0.011	0.011	0.000	0.000	0.000	0.000
39	A	438	GLY	0	0.009	0.008	34.381	0.027	0.027	0.000	0.000	0.000	0.000
40	A	439	ASN	0	0.047	-0.009	33.950	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	440	LYS	1	0.908	0.957	35.209	0.003	0.003	0.000	0.000	0.000	0.000
42	A	441	ARG	1	0.858	0.930	31.805	0.003	0.003	0.000	0.000	0.000	0.000
43	A	442	LEU	0	0.012	0.009	28.957	0.030	0.030	0.000	0.000	0.000	0.000
44	A	443	ASP	-1	-0.738	-0.857	31.127	0.010	0.010	0.000	0.000	0.000	0.000
45	A	444	ALA	0	0.003	0.011	33.172	0.024	0.024	0.000	0.000	0.000	0.000
46	A	445	ALA	0	-0.026	0.003	27.819	0.050	0.050	0.000	0.000	0.000	0.000
47	A	446	TYR	0	0.021	-0.003	27.610	0.043	0.043	0.000	0.000	0.000	0.000
48	A	447	ARG	1	0.868	0.917	29.606	-0.015	-0.015	0.000	0.000	0.000	0.000
49	A	448	SER	0	-0.027	-0.030	29.903	0.040	0.040	0.000	0.000	0.000	0.000
50	A	449	MET	0	-0.049	-0.017	22.977	0.111	0.111	0.000	0.000	0.000	0.000
51	A	450	ASN	0	-0.051	-0.026	26.897	0.023	0.023	0.000	0.000	0.000	0.000
52	A	451	GLY	0	0.041	0.029	26.576	0.011	0.011	0.000	0.000	0.000	0.000
53	A	452	LYS	1	0.849	0.946	24.047	-0.514	-0.514	0.000	0.000	0.000	0.000
54	A	453	GLY	0	0.015	-0.014	20.974	0.136	0.136	0.000	0.000	0.000	0.000
55	A	454	PRO	0	-0.032	0.007	18.578	-0.032	-0.032	0.000	0.000	0.000	0.000
56	A	455	VAL	0	0.037	0.005	21.896	0.106	0.106	0.000	0.000	0.000	0.000
57	A	456	TYR	0	-0.025	-0.012	17.263	-0.065	-0.065	0.000	0.000	0.000	0.000
58	A	457	LEU	0	-0.002	-0.001	22.478	0.100	0.100	0.000	0.000	0.000	0.000
59	A	458	LEU	0	0.003	-0.005	19.558	-0.119	-0.119	0.000	0.000	0.000	0.000
60	A	459	PHE	0	0.064	0.023	23.136	0.095	0.095	0.000	0.000	0.000	0.000
61	A	460	SER	0	-0.032	-0.025	24.911	-0.062	-0.062	0.000	0.000	0.000	0.000
62	A	461	VAL	0	0.061	0.038	27.076	0.073	0.073	0.000	0.000	0.000	0.000
63	A	462	ASN	0	-0.039	-0.022	30.370	-0.016	-0.016	0.000	0.000	0.000	0.000
64	A	463	GLY	0	-0.002	-0.009	32.666	-0.008	-0.008	0.000	0.000	0.000	0.000
65	A	464	SER	0	-0.003	-0.007	29.079	-0.026	-0.026	0.000	0.000	0.000	0.000
66	A	465	GLY	0	0.015	0.015	28.199	-0.035	-0.035	0.000	0.000	0.000	0.000
67	A	466	HIS	0	-0.053	-0.027	24.086	-0.009	-0.009	0.000	0.000	0.000	0.000
68	A	467	PHE	0	-0.029	-0.005	21.634	0.132	0.132	0.000	0.000	0.000	0.000
69	A	468	CYS	0	0.041	0.031	23.436	-0.065	-0.065	0.000	0.000	0.000	0.000
70	A	469	GLY	0	0.052	0.017	21.674	-0.083	-0.083	0.000	0.000	0.000	0.000
71	A	470	VAL	0	-0.075	-0.029	18.623	0.106	0.106	0.000	0.000	0.000	0.000
72	A	471	ALA	0	0.071	0.045	21.850	-0.084	-0.084	0.000	0.000	0.000	0.000
73	A	472	GLU	-1	-0.878	-0.934	22.383	-0.364	-0.364	0.000	0.000	0.000	0.000
74	A	473	MET	0	-0.026	-0.002	24.111	-0.015	-0.015	0.000	0.000	0.000	0.000
75	A	474	LYS	1	0.798	0.878	23.802	0.420	0.420	0.000	0.000	0.000	0.000
76	A	475	SER	0	-0.001	0.008	29.195	0.009	0.009	0.000	0.000	0.000	0.000
77	A	476	ALA	0	0.015	0.004	32.344	0.010	0.010	0.000	0.000	0.000	0.000
78	A	477	VAL	0	-0.073	-0.031	34.559	-0.031	-0.031	0.000	0.000	0.000	0.000
79	A	478	ASP	-1	-0.817	-0.893	36.763	-0.122	-0.122	0.000	0.000	0.000	0.000
80	A	479	TYR	0	0.003	-0.037	38.647	-0.014	-0.014	0.000	0.000	0.000	0.000
81	A	480	ASN	0	-0.071	-0.020	42.219	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	481	THR	0	0.033	0.019	41.605	-0.011	-0.011	0.000	0.000	0.000	0.000
83	A	482	CYS	0	-0.052	-0.028	44.843	0.009	0.009	0.000	0.000	0.000	0.000
84	A	483	ALA	0	0.031	0.023	44.635	-0.009	-0.009	0.000	0.000	0.000	0.000
85	A	484	GLY	0	0.026	-0.002	45.925	-0.009	-0.009	0.000	0.000	0.000	0.000
86	A	485	VAL	0	-0.047	-0.015	40.740	-0.016	-0.016	0.000	0.000	0.000	0.000
87	A	486	TRP	0	-0.078	-0.041	35.225	-0.036	-0.036	0.000	0.000	0.000	0.000
88	A	487	SER	0	-0.020	-0.007	39.877	0.023	0.023	0.000	0.000	0.000	0.000
89	A	488	GLN	0	0.015	0.004	41.262	0.022	0.022	0.000	0.000	0.000	0.000
90	A	489	ASP	-1	-0.824	-0.902	42.763	-0.198	-0.198	0.000	0.000	0.000	0.000
91	A	490	LYS	1	0.858	0.918	41.534	0.213	0.213	0.000	0.000	0.000	0.000
92	A	491	TRP	0	-0.052	-0.025	38.849	0.033	0.033	0.000	0.000	0.000	0.000
93	A	492	LYS	1	0.980	0.990	41.774	0.095	0.095	0.000	0.000	0.000	0.000
94	A	493	GLY	0	0.055	0.010	40.476	0.021	0.021	0.000	0.000	0.000	0.000
95	A	494	ARG	1	0.812	0.919	37.046	0.206	0.206	0.000	0.000	0.000	0.000
96	A	495	PHE	0	-0.001	-0.006	30.189	0.031	0.031	0.000	0.000	0.000	0.000
97	A	496	ASP	-1	-0.817	-0.908	32.495	-0.327	-0.327	0.000	0.000	0.000	0.000
98	A	497	VAL	0	-0.065	-0.043	27.877	0.029	0.029	0.000	0.000	0.000	0.000
99	A	498	ARG	1	0.951	0.973	24.486	0.667	0.667	0.000	0.000	0.000	0.000
100	A	499	TRP	0	0.016	0.002	24.611	-0.053	-0.053	0.000	0.000	0.000	0.000
101	A	500	ILE	0	-0.083	-0.036	18.397	-0.017	-0.017	0.000	0.000	0.000	0.000
102	A	501	PHE	0	-0.010	-0.018	14.277	-0.234	-0.234	0.000	0.000	0.000	0.000
103	A	502	VAL	0	0.046	0.024	20.376	0.168	0.168	0.000	0.000	0.000	0.000
104	A	503	LYS	1	0.802	0.896	15.013	2.882	2.882	0.000	0.000	0.000	0.000
105	A	504	ASP	-1	-0.830	-0.906	21.672	-1.075	-1.075	0.000	0.000	0.000	0.000
106	A	505	VAL	0	-0.046	-0.026	17.705	-0.174	-0.174	0.000	0.000	0.000	0.000
107	A	506	PRO	0	0.024	0.017	20.156	0.185	0.185	0.000	0.000	0.000	0.000
108	A	507	ASN	0	0.064	0.006	20.976	-0.075	-0.075	0.000	0.000	0.000	0.000
109	A	508	SER	0	-0.071	-0.035	21.992	0.049	0.049	0.000	0.000	0.000	0.000
110	A	509	GLN	0	0.027	0.014	15.995	-0.144	-0.144	0.000	0.000	0.000	0.000
111	A	510	LEU	0	0.034	0.012	16.833	0.037	0.037	0.000	0.000	0.000	0.000
112	A	511	ARG	1	0.897	0.946	19.181	0.697	0.697	0.000	0.000	0.000	0.000
113	A	512	HIS	0	0.027	0.011	18.374	0.166	0.166	0.000	0.000	0.000	0.000
114	A	513	ILE	0	-0.008	0.014	15.232	0.173	0.173	0.000	0.000	0.000	0.000
115	A	514	ARG	1	0.901	0.948	19.167	-0.191	-0.191	0.000	0.000	0.000	0.000
116	A	515	LEU	0	0.004	-0.002	21.508	0.123	0.123	0.000	0.000	0.000	0.000
117	A	516	GLU	0	-0.018	-0.046	20.755	-0.088	-0.088	0.000	0.000	0.000	0.000
118	A	517	ASN	0	-0.017	-0.016	25.266	0.006	0.006	0.000	0.000	0.000	0.000
119	A	518	ASN	0	-0.005	-0.007	27.390	-0.035	-0.035	0.000	0.000	0.000	0.000
120	A	519	GLU	-1	-0.814	-0.902	28.824	0.099	0.099	0.000	0.000	0.000	0.000
121	A	520	ASN	0	0.004	0.004	24.516	-0.036	-0.036	0.000	0.000	0.000	0.000
122	A	521	LYS	1	0.877	0.947	26.137	-0.107	-0.107	0.000	0.000	0.000	0.000
123	A	522	PRO	0	-0.005	0.001	23.716	0.036	0.036	0.000	0.000	0.000	0.000
124	A	523	VAL	0	0.042	0.021	20.180	-0.009	-0.009	0.000	0.000	0.000	0.000
125	A	524	THR	0	-0.008	0.007	22.648	-0.023	-0.023	0.000	0.000	0.000	0.000
126	A	525	ASN	0	-0.059	-0.019	25.058	-0.070	-0.070	0.000	0.000	0.000	0.000
127	A	526	SER	0	-0.028	-0.023	25.841	0.085	0.085	0.000	0.000	0.000	0.000
128	A	527	ARG	1	0.964	0.975	28.690	0.038	0.038	0.000	0.000	0.000	0.000
129	A	528	ASP	-1	-0.708	-0.847	30.075	-0.237	-0.237	0.000	0.000	0.000	0.000
130	A	529	THR	0	-0.019	0.008	29.454	0.070	0.070	0.000	0.000	0.000	0.000
131	A	530	GLN	0	-0.080	-0.025	26.473	0.040	0.040	0.000	0.000	0.000	0.000
132	A	531	GLU	-1	-0.771	-0.849	24.743	0.252	0.252	0.000	0.000	0.000	0.000
133	A	532	VAL	0	-0.008	-0.003	19.824	0.028	0.028	0.000	0.000	0.000	0.000
134	A	533	PRO	0	-0.006	0.008	20.646	0.035	0.035	0.000	0.000	0.000	0.000
135	A	534	LEU	0	0.062	0.032	16.807	-0.008	-0.008	0.000	0.000	0.000	0.000
136	A	535	GLU	-1	-0.756	-0.863	15.014	1.044	1.044	0.000	0.000	0.000	0.000
137	A	536	LYS	1	0.828	0.914	14.530	-0.809	-0.809	0.000	0.000	0.000	0.000
138	A	537	ALA	0	0.006	0.003	16.026	-0.239	-0.239	0.000	0.000	0.000	0.000
139	A	538	LYS	1	0.843	0.910	11.726	-2.160	-2.160	0.000	0.000	0.000	0.000
140	A	539	GLN	0	-0.012	0.000	11.777	-0.572	-0.572	0.000	0.000	0.000	0.000
141	A	540	VAL	0	0.034	0.010	12.841	-0.495	-0.495	0.000	0.000	0.000	0.000
142	A	541	LEU	0	0.021	0.012	14.048	-0.314	-0.314	0.000	0.000	0.000	0.000
143	A	542	LYS	1	0.851	0.926	6.212	0.979	0.979	0.000	0.000	0.000	0.000
144	A	543	ILE	0	0.004	0.030	10.690	-0.823	-0.823	0.000	0.000	0.000	0.000
145	A	544	ILE	0	0.010	0.007	12.758	-0.259	-0.259	0.000	0.000	0.000	0.000
146	A	545	ALA	0	-0.020	-0.008	11.131	-0.145	-0.145	0.000	0.000	0.000	0.000
147	A	546	SER	0	-0.097	-0.075	9.026	-0.238	-0.238	0.000	0.000	0.000	0.000
148	A	547	TYR	0	0.020	0.013	11.104	-0.153	-0.153	0.000	0.000	0.000	0.000
149	A	548	LYS	0	0.077	0.056	14.432	0.844	0.844	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:400:GLU)