FMO DATABASE

FMODB ID: 6NJ8Z

Calculation Name: 5EGO-B-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: 5CM

PDB ID: 5EGO

Chain ID: B

ChEMBL ID:

UniProt ID: Q92826

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	63
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-383296.970936
FMO2-HF: Nuclear repulsion	357463.67859
FMO2-HF: Total energy	-25833.292347
FMO2-MP2: Total energy	-25911.402566

3D Structure

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(B:217:ARG)

Summations of interaction energy for fragment #1(B:217:ARG)

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.
232.049	234.542	0.096	-0.954	-1.635	-0.003

Interaction energy analysis for fragmet #1(B:217:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.007 / q_NPA : 0.986

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	B	219	LYS	1	0.993	0.990	3.113	20.690	22.956	0.097	-0.943	-1.420	-0.003
4	B	220	ARG	1	0.961	0.984	4.464	35.053	35.280	-0.001	-0.011	-0.215	0.000
5	B	221	ILE	0	0.030	-0.006	5.883	2.570	2.570	0.000	0.000	0.000	0.000
6	B	222	PRO	0	-0.047	-0.008	9.620	-0.431	-0.431	0.000	0.000	0.000	0.000
7	B	223	TYR	0	0.013	0.003	10.066	-0.039	-0.039	0.000	0.000	0.000	0.000
8	B	224	SER	0	0.078	0.039	14.117	0.818	0.818	0.000	0.000	0.000	0.000
9	B	225	LYS	1	1.040	0.989	17.845	13.007	13.007	0.000	0.000	0.000	0.000
10	B	226	GLY	0	0.022	0.017	20.200	0.324	0.324	0.000	0.000	0.000	0.000
11	B	227	GLN	0	0.057	0.026	15.583	-0.234	-0.234	0.000	0.000	0.000	0.000
12	B	228	LEU	0	-0.039	-0.031	14.527	0.070	0.070	0.000	0.000	0.000	0.000
13	B	229	ARG	1	0.946	0.978	18.240	11.545	11.545	0.000	0.000	0.000	0.000
14	B	230	GLU	-1	-0.869	-0.941	21.060	-12.135	-12.135	0.000	0.000	0.000	0.000
15	B	231	LEU	0	-0.019	0.003	15.419	0.145	0.145	0.000	0.000	0.000	0.000
16	B	232	GLU	-1	-0.882	-0.948	19.149	-15.270	-15.270	0.000	0.000	0.000	0.000
17	B	233	ARG	1	0.940	0.994	21.196	11.534	11.534	0.000	0.000	0.000	0.000
18	B	234	GLU	-1	-0.861	-0.947	22.231	-12.020	-12.020	0.000	0.000	0.000	0.000
19	B	235	TYR	0	-0.093	-0.071	18.458	-0.305	-0.305	0.000	0.000	0.000	0.000
20	B	236	ALA	0	-0.044	-0.028	21.835	0.096	0.096	0.000	0.000	0.000	0.000
21	B	237	ALA	0	-0.023	0.018	24.976	0.425	0.425	0.000	0.000	0.000	0.000
22	B	238	ASN	0	-0.022	-0.023	24.436	0.619	0.619	0.000	0.000	0.000	0.000
23	B	239	LYS	1	0.974	0.985	20.941	12.418	12.418	0.000	0.000	0.000	0.000
24	B	240	PHE	0	-0.025	-0.018	19.759	-1.201	-1.201	0.000	0.000	0.000	0.000
25	B	241	ILE	0	0.021	0.038	18.530	0.558	0.558	0.000	0.000	0.000	0.000
26	B	242	THR	0	0.076	0.030	21.448	-0.212	-0.212	0.000	0.000	0.000	0.000
27	B	243	LYS	1	0.981	0.954	21.745	12.891	12.891	0.000	0.000	0.000	0.000
28	B	244	ASP	-1	-0.785	-0.886	23.503	-11.237	-11.237	0.000	0.000	0.000	0.000
29	B	245	LYS	1	0.878	0.943	24.047	11.210	11.210	0.000	0.000	0.000	0.000
30	B	246	ARG	1	0.861	0.938	17.396	16.056	16.056	0.000	0.000	0.000	0.000
31	B	247	ARG	1	0.968	0.975	19.801	13.596	13.596	0.000	0.000	0.000	0.000
32	B	248	LYS	1	0.987	0.997	22.435	10.993	10.993	0.000	0.000	0.000	0.000
33	B	249	ILE	0	0.029	0.018	18.740	-0.113	-0.113	0.000	0.000	0.000	0.000
34	B	250	SER	0	-0.087	-0.052	17.689	-0.219	-0.219	0.000	0.000	0.000	0.000
35	B	251	ALA	0	0.041	0.011	19.397	-0.215	-0.215	0.000	0.000	0.000	0.000
36	B	252	ALA	0	-0.015	0.005	22.450	0.066	0.066	0.000	0.000	0.000	0.000
37	B	253	THR	0	-0.076	-0.074	17.986	-0.451	-0.451	0.000	0.000	0.000	0.000
38	B	254	SER	0	0.060	0.039	18.130	-0.170	-0.170	0.000	0.000	0.000	0.000
39	B	255	LEU	0	-0.076	-0.017	12.900	-1.190	-1.190	0.000	0.000	0.000	0.000
40	B	256	SER	0	0.055	0.051	11.967	0.288	0.288	0.000	0.000	0.000	0.000
41	B	257	GLU	-1	-0.721	-0.897	14.168	-16.039	-16.039	0.000	0.000	0.000	0.000
42	B	258	ARG	1	0.948	0.980	7.771	29.948	29.948	0.000	0.000	0.000	0.000
43	B	259	GLN	0	0.035	0.014	9.365	0.232	0.232	0.000	0.000	0.000	0.000
44	B	260	ILE	0	0.033	0.042	11.188	-0.877	-0.877	0.000	0.000	0.000	0.000
45	B	261	THR	0	-0.033	-0.010	13.565	1.106	1.106	0.000	0.000	0.000	0.000
46	B	262	ILE	0	-0.018	-0.015	7.490	0.252	0.252	0.000	0.000	0.000	0.000
47	B	263	TRP	0	0.034	0.031	10.784	-0.468	-0.468	0.000	0.000	0.000	0.000
48	B	264	PHE	0	0.033	0.005	12.104	0.279	0.279	0.000	0.000	0.000	0.000
49	B	265	GLN	0	-0.056	-0.024	11.299	-0.893	-0.893	0.000	0.000	0.000	0.000
50	B	266	ASN	0	-0.022	-0.027	7.953	-0.862	-0.862	0.000	0.000	0.000	0.000
51	B	267	ARG	1	0.867	0.968	11.406	16.160	16.160	0.000	0.000	0.000	0.000
52	B	268	ARG	1	0.959	0.966	14.776	17.825	17.825	0.000	0.000	0.000	0.000
53	B	269	VAL	0	-0.044	-0.010	11.749	0.662	0.662	0.000	0.000	0.000	0.000
54	B	270	LYS	1	0.932	0.960	14.478	17.863	17.863	0.000	0.000	0.000	0.000
55	B	271	GLU	-1	-0.847	-0.919	15.815	-12.920	-12.920	0.000	0.000	0.000	0.000
56	B	272	LYS	1	1.003	0.994	18.065	16.574	16.574	0.000	0.000	0.000	0.000
57	B	273	LYS	1	0.910	0.964	13.261	20.695	20.695	0.000	0.000	0.000	0.000
58	B	274	VAL	0	0.017	0.014	19.295	-0.036	-0.036	0.000	0.000	0.000	0.000
59	B	275	LEU	0	-0.050	-0.011	21.777	0.709	0.709	0.000	0.000	0.000	0.000
60	B	276	ALA	0	-0.026	-0.027	23.439	-0.212	-0.212	0.000	0.000	0.000	0.000
61	B	277	LYS	1	0.967	0.987	25.249	11.043	11.043	0.000	0.000	0.000	0.000
62	B	278	VAL	0	0.028	0.012	27.646	-0.253	-0.253	0.000	0.000	0.000	0.000
63	B	279	LYS	1	0.997	1.018	24.832	11.731	11.731	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:217:ARG)