FMO DATABASE

FMODB ID: N6N7Q

Calculation Name: 3JCS-L-Other547

Preferred Name:

Target Type:

Ligand Name: o2'-methylguanosine-5'-monophosphate | 5,6-dihydrouridine-5'-monophosphate | o2'-methylycytidine-5'-monophosphate | o2'-methyluridine 5'-monophosphate | 2'-o-methyladenosine 5'-(dihydrogen phosphate)

Ligand 3-letter code: OMG | H2U | OMC | OMU | A2M

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3JCS

Chain ID: L

ChEMBL ID:

UniProt ID: P62885

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-06

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	143
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-971724.881064
FMO2-HF: Nuclear repulsion	915558.818492
FMO2-HF: Total energy	-56166.062572
FMO2-MP2: Total energy	-56328.955772

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:2:PRO)

Summations of interaction energy for fragment #1(A:2:PRO)

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.
301.746	306.862	1.566	-2.206	-4.477	-0.013

Interaction energy analysis for fragmet #1(A:2:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.930 / q_NPA : 0.944

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	4	ARG	1	0.990	0.998	3.040	47.326	50.201	0.159	-1.188	-1.847	-0.005
4	A	5	PHE	0	0.064	0.036	2.453	-0.102	1.860	1.408	-0.949	-2.420	-0.008
5	A	6	LYS	1	0.990	0.984	4.034	51.068	51.347	-0.001	-0.069	-0.210	0.000
6	A	7	LYS	1	1.075	1.038	6.939	22.199	22.199	0.000	0.000	0.000	0.000
7	A	8	CYS	0	-0.058	-0.023	10.674	0.986	0.986	0.000	0.000	0.000	0.000
8	A	9	ARG	1	0.893	0.945	7.905	28.671	28.671	0.000	0.000	0.000	0.000
9	A	10	HIS	0	0.052	0.027	9.813	0.666	0.666	0.000	0.000	0.000	0.000
10	A	11	GLN	0	0.045	0.025	11.316	1.354	1.354	0.000	0.000	0.000	0.000
11	A	12	ARG	1	0.915	0.968	13.388	21.990	21.990	0.000	0.000	0.000	0.000
12	A	13	GLY	0	0.082	0.039	15.902	0.391	0.391	0.000	0.000	0.000	0.000
13	A	14	SER	0	-0.016	-0.030	17.254	0.762	0.762	0.000	0.000	0.000	0.000
14	A	15	THR	0	-0.006	0.005	19.910	0.550	0.550	0.000	0.000	0.000	0.000
15	A	16	PHE	0	0.023	0.000	20.759	0.197	0.197	0.000	0.000	0.000	0.000
16	A	18	GLY	0	0.007	0.005	16.749	-0.777	-0.777	0.000	0.000	0.000	0.000
17	A	19	TYR	0	-0.017	-0.001	16.106	-0.254	-0.254	0.000	0.000	0.000	0.000
18	A	20	GLY	0	0.021	0.031	21.116	0.545	0.545	0.000	0.000	0.000	0.000
19	A	21	ARG	1	0.965	0.973	24.326	11.002	11.002	0.000	0.000	0.000	0.000
20	A	22	VAL	0	0.053	0.032	27.455	0.182	0.182	0.000	0.000	0.000	0.000
21	A	23	GLY	0	0.035	0.014	28.222	0.181	0.181	0.000	0.000	0.000	0.000
22	A	24	LYS	1	0.864	0.943	25.690	10.198	10.198	0.000	0.000	0.000	0.000
23	A	25	HIS	0	0.068	0.023	17.752	0.762	0.762	0.000	0.000	0.000	0.000
24	A	26	ARG	1	0.928	0.978	22.940	11.687	11.687	0.000	0.000	0.000	0.000
25	A	27	LYS	1	0.953	0.973	22.126	11.530	11.530	0.000	0.000	0.000	0.000
26	A	28	HIS	0	0.028	-0.006	20.927	0.777	0.777	0.000	0.000	0.000	0.000
27	A	29	GLU	-1	-0.846	-0.913	24.469	-12.528	-12.528	0.000	0.000	0.000	0.000
28	A	30	SER	0	-0.001	0.019	25.944	0.277	0.277	0.000	0.000	0.000	0.000
29	A	31	GLY	0	0.040	0.028	28.034	0.193	0.193	0.000	0.000	0.000	0.000
30	A	32	ARG	1	0.894	0.915	24.461	11.391	11.391	0.000	0.000	0.000	0.000
31	A	33	GLY	0	0.015	0.019	24.150	0.299	0.299	0.000	0.000	0.000	0.000
32	A	34	ASN	0	0.005	-0.004	25.160	-0.314	-0.314	0.000	0.000	0.000	0.000
33	A	35	ALA	0	0.001	0.003	27.668	0.437	0.437	0.000	0.000	0.000	0.000
34	A	36	GLY	0	0.067	0.020	30.258	-0.123	-0.123	0.000	0.000	0.000	0.000
35	A	37	GLY	0	-0.014	-0.010	32.200	0.066	0.066	0.000	0.000	0.000	0.000
36	A	38	MET	0	0.032	0.016	32.885	-0.016	-0.016	0.000	0.000	0.000	0.000
37	A	39	HIS	0	-0.008	-0.011	35.559	0.036	0.036	0.000	0.000	0.000	0.000
38	A	40	HIS	0	0.010	0.005	30.122	0.431	0.431	0.000	0.000	0.000	0.000
39	A	41	HIS	0	-0.031	-0.023	27.565	-0.232	-0.232	0.000	0.000	0.000	0.000
40	A	42	ARG	1	0.892	0.953	31.922	7.850	7.850	0.000	0.000	0.000	0.000
41	A	43	ILE	0	0.032	0.012	33.276	-0.012	-0.012	0.000	0.000	0.000	0.000
42	A	44	ASN	0	-0.041	-0.018	26.178	-0.082	-0.082	0.000	0.000	0.000	0.000
43	A	45	PHE	0	0.027	0.005	28.432	-0.112	-0.112	0.000	0.000	0.000	0.000
44	A	46	ASP	-1	-0.784	-0.885	32.105	-8.472	-8.472	0.000	0.000	0.000	0.000
45	A	47	LYS	1	0.893	0.966	30.902	9.978	9.978	0.000	0.000	0.000	0.000
46	A	48	TYR	0	-0.041	-0.032	28.108	-0.022	-0.022	0.000	0.000	0.000	0.000
47	A	49	HIS	0	-0.060	-0.019	26.055	-0.093	-0.093	0.000	0.000	0.000	0.000
48	A	50	PRO	0	0.046	0.020	31.284	0.144	0.144	0.000	0.000	0.000	0.000
49	A	51	GLY	0	-0.004	0.005	34.431	0.254	0.254	0.000	0.000	0.000	0.000
50	A	52	TYR	0	-0.068	-0.026	30.809	-0.046	-0.046	0.000	0.000	0.000	0.000
51	A	53	PHE	0	-0.032	-0.023	33.011	0.128	0.128	0.000	0.000	0.000	0.000
52	A	54	GLY	0	0.075	0.040	36.844	0.228	0.228	0.000	0.000	0.000	0.000
53	A	55	LYS	1	0.921	0.958	39.121	7.255	7.255	0.000	0.000	0.000	0.000
54	A	56	LEU	0	0.035	0.014	40.231	0.125	0.125	0.000	0.000	0.000	0.000
55	A	57	GLY	0	-0.016	0.005	41.841	-0.123	-0.123	0.000	0.000	0.000	0.000
56	A	58	MET	0	-0.003	-0.005	44.124	0.106	0.106	0.000	0.000	0.000	0.000
57	A	59	ASP	-1	-0.910	-0.946	42.642	-7.578	-7.578	0.000	0.000	0.000	0.000
58	A	60	HIS	0	-0.024	-0.018	41.623	0.063	0.063	0.000	0.000	0.000	0.000
59	A	61	TYR	0	0.061	0.022	41.420	-0.183	-0.183	0.000	0.000	0.000	0.000
60	A	62	HIS	0	0.063	0.032	41.339	-0.088	-0.088	0.000	0.000	0.000	0.000
61	A	63	ARG	1	0.948	0.978	34.274	8.857	8.857	0.000	0.000	0.000	0.000
62	A	64	LYS	1	0.925	0.968	38.315	7.048	7.048	0.000	0.000	0.000	0.000
63	A	65	LYS	1	0.935	0.952	34.367	8.763	8.763	0.000	0.000	0.000	0.000
64	A	66	ASN	0	0.047	0.027	37.403	-0.117	-0.117	0.000	0.000	0.000	0.000
65	A	67	PRO	0	0.028	0.015	39.467	0.056	0.056	0.000	0.000	0.000	0.000
66	A	68	MET	0	-0.046	-0.019	39.689	0.083	0.083	0.000	0.000	0.000	0.000
67	A	69	TRP	0	0.034	0.015	35.621	-0.163	-0.163	0.000	0.000	0.000	0.000
68	A	70	LYS	1	0.924	0.957	38.906	7.273	7.273	0.000	0.000	0.000	0.000
69	A	71	PRO	0	0.007	0.022	36.114	0.005	0.005	0.000	0.000	0.000	0.000
70	A	72	THR	0	-0.006	-0.007	37.729	0.201	0.201	0.000	0.000	0.000	0.000
71	A	73	ILE	0	-0.018	0.013	38.064	-0.261	-0.261	0.000	0.000	0.000	0.000
72	A	74	ASN	0	-0.017	-0.015	38.731	0.360	0.360	0.000	0.000	0.000	0.000
73	A	75	LEU	0	0.057	0.018	41.971	-0.018	-0.018	0.000	0.000	0.000	0.000
74	A	76	ASN	0	0.006	0.010	41.065	-0.021	-0.021	0.000	0.000	0.000	0.000
75	A	77	ASN	0	-0.052	-0.028	37.576	-0.211	-0.211	0.000	0.000	0.000	0.000
76	A	78	LEU	0	0.037	0.017	39.978	-0.127	-0.127	0.000	0.000	0.000	0.000
77	A	79	SER	0	0.042	0.022	41.445	-0.057	-0.057	0.000	0.000	0.000	0.000
78	A	80	ARG	1	0.909	0.965	34.192	8.746	8.746	0.000	0.000	0.000	0.000
79	A	81	LEU	0	-0.030	-0.024	38.333	-0.180	-0.180	0.000	0.000	0.000	0.000
80	A	82	ILE	0	-0.010	0.022	40.913	0.088	0.088	0.000	0.000	0.000	0.000
81	A	83	ALA	0	0.040	0.026	41.551	-0.083	-0.083	0.000	0.000	0.000	0.000
82	A	84	ALA	0	0.034	0.000	42.273	0.176	0.176	0.000	0.000	0.000	0.000
83	A	85	GLU	-1	-0.832	-0.904	44.226	-6.602	-6.602	0.000	0.000	0.000	0.000
84	A	86	GLU	-1	-0.934	-0.974	45.836	-6.711	-6.711	0.000	0.000	0.000	0.000
85	A	87	ALA	0	0.012	-0.008	46.268	0.141	0.141	0.000	0.000	0.000	0.000
86	A	88	ALA	0	0.007	0.013	48.102	0.136	0.136	0.000	0.000	0.000	0.000
87	A	89	LYS	1	0.862	0.916	48.503	6.628	6.628	0.000	0.000	0.000	0.000
88	A	90	ALA	0	0.016	0.028	50.680	0.098	0.098	0.000	0.000	0.000	0.000
89	A	91	THR	0	-0.104	-0.045	51.424	0.073	0.073	0.000	0.000	0.000	0.000
90	A	92	LYS	1	0.979	0.982	54.135	5.565	5.565	0.000	0.000	0.000	0.000
91	A	93	GLY	0	0.001	-0.009	56.703	-0.037	-0.037	0.000	0.000	0.000	0.000
92	A	94	GLY	0	0.015	0.020	57.990	0.072	0.072	0.000	0.000	0.000	0.000
93	A	95	THR	0	-0.029	-0.021	55.171	0.049	0.049	0.000	0.000	0.000	0.000
94	A	96	LEU	0	-0.023	-0.005	53.514	-0.122	-0.122	0.000	0.000	0.000	0.000
95	A	97	PRO	0	0.027	0.012	48.357	-0.007	-0.007	0.000	0.000	0.000	0.000
96	A	98	VAL	0	0.010	0.008	49.931	0.034	0.034	0.000	0.000	0.000	0.000
97	A	99	VAL	0	0.049	0.027	44.407	-0.095	-0.095	0.000	0.000	0.000	0.000
98	A	100	ASP	-1	-0.811	-0.918	45.446	-6.626	-6.626	0.000	0.000	0.000	0.000
99	A	101	LEU	0	-0.022	-0.010	42.859	-0.164	-0.164	0.000	0.000	0.000	0.000
100	A	102	GLN	0	-0.052	-0.044	41.449	-0.243	-0.243	0.000	0.000	0.000	0.000
101	A	103	SER	0	-0.012	0.001	40.962	-0.113	-0.113	0.000	0.000	0.000	0.000
102	A	104	SER	0	-0.008	-0.001	38.190	-0.183	-0.183	0.000	0.000	0.000	0.000
103	A	105	GLY	0	-0.038	-0.010	37.083	-0.254	-0.254	0.000	0.000	0.000	0.000
104	A	106	TYR	0	-0.030	-0.042	34.279	0.153	0.153	0.000	0.000	0.000	0.000
105	A	107	ALA	0	0.084	0.045	39.541	0.173	0.173	0.000	0.000	0.000	0.000
106	A	108	LYS	1	0.878	0.951	41.983	7.182	7.182	0.000	0.000	0.000	0.000
107	A	109	LEU	0	0.080	0.049	42.584	-0.179	-0.179	0.000	0.000	0.000	0.000
108	A	110	LEU	0	-0.014	-0.035	41.856	0.186	0.186	0.000	0.000	0.000	0.000
109	A	111	GLY	0	0.030	0.002	44.503	0.010	0.010	0.000	0.000	0.000	0.000
110	A	112	ASN	0	0.006	0.009	40.515	0.248	0.248	0.000	0.000	0.000	0.000
111	A	113	GLY	0	0.062	0.033	44.307	-0.014	-0.014	0.000	0.000	0.000	0.000
112	A	114	HIS	0	0.020	0.018	45.250	0.087	0.087	0.000	0.000	0.000	0.000
113	A	115	ILE	0	-0.002	-0.009	46.509	-0.159	-0.159	0.000	0.000	0.000	0.000
114	A	116	GLN	0	0.003	-0.006	44.525	0.036	0.036	0.000	0.000	0.000	0.000
115	A	117	VAL	0	0.041	0.023	46.046	0.079	0.079	0.000	0.000	0.000	0.000
116	A	118	PRO	0	0.005	0.012	48.855	-0.063	-0.063	0.000	0.000	0.000	0.000
117	A	119	CYS	0	-0.022	-0.009	48.572	-0.075	-0.075	0.000	0.000	0.000	0.000
118	A	120	ILE	0	-0.007	0.007	51.112	0.062	0.062	0.000	0.000	0.000	0.000
119	A	121	VAL	0	-0.025	-0.009	47.175	-0.126	-0.126	0.000	0.000	0.000	0.000
120	A	122	LYS	1	0.858	0.926	48.327	6.579	6.579	0.000	0.000	0.000	0.000
121	A	123	ALA	0	0.040	0.015	46.299	-0.193	-0.193	0.000	0.000	0.000	0.000
122	A	124	ARG	1	0.993	1.018	43.758	7.187	7.187	0.000	0.000	0.000	0.000
123	A	125	TYR	0	-0.010	-0.016	45.239	0.019	0.019	0.000	0.000	0.000	0.000
124	A	126	VAL	0	0.066	0.038	47.164	-0.129	-0.129	0.000	0.000	0.000	0.000
125	A	127	SER	0	-0.047	-0.028	46.430	0.072	0.072	0.000	0.000	0.000	0.000
126	A	128	LYS	1	1.039	1.010	49.173	5.967	5.967	0.000	0.000	0.000	0.000
127	A	129	LEU	0	-0.017	-0.010	48.705	0.110	0.110	0.000	0.000	0.000	0.000
128	A	130	ALA	0	0.025	0.004	47.933	0.021	0.021	0.000	0.000	0.000	0.000
129	A	131	ASP	-1	-0.824	-0.908	49.790	-5.767	-5.767	0.000	0.000	0.000	0.000
130	A	132	LYS	1	0.910	0.956	52.822	5.856	5.856	0.000	0.000	0.000	0.000
131	A	133	LYS	1	0.822	0.894	48.105	6.630	6.630	0.000	0.000	0.000	0.000
132	A	134	ILE	0	0.042	0.027	48.469	0.043	0.043	0.000	0.000	0.000	0.000
133	A	135	ARG	1	0.896	0.962	52.660	5.621	5.621	0.000	0.000	0.000	0.000
134	A	136	LYS	1	0.914	0.971	55.698	5.537	5.537	0.000	0.000	0.000	0.000
135	A	137	ALA	0	-0.048	-0.034	52.933	0.037	0.037	0.000	0.000	0.000	0.000
136	A	138	GLY	0	0.037	0.024	54.090	-0.068	-0.068	0.000	0.000	0.000	0.000
137	A	139	GLY	0	0.062	0.032	53.544	-0.045	-0.045	0.000	0.000	0.000	0.000
138	A	140	ALA	0	-0.004	-0.017	53.717	0.117	0.117	0.000	0.000	0.000	0.000
139	A	141	VAL	0	-0.030	-0.022	50.665	-0.149	-0.149	0.000	0.000	0.000	0.000
140	A	142	VAL	0	0.006	0.009	52.024	0.121	0.121	0.000	0.000	0.000	0.000
141	A	143	LEU	0	-0.005	-0.007	51.409	-0.136	-0.136	0.000	0.000	0.000	0.000
142	A	144	GLN	0	-0.015	-0.005	48.998	0.001	0.001	0.000	0.000	0.000	0.000
143	A	145	ALA	-1	-0.897	-0.944	48.383	-6.470	-6.470	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:PRO)