FMO DATABASE

FMODB ID: M311Z

Calculation Name: 1NH2-C-Xray372

Preferred Name:

Target Type:

Ligand Name: 5-iodo-2'-deoxyuridine-5'-monophosphate

ligand 3-letter code: 5IU

PDB ID: 1NH2

Chain ID: C

ChEMBL ID:

UniProt ID: P32774

Base Structure: X-ray

Registration Date: 2023-06-20

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	OptAll
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	50
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-237539.921732
FMO2-HF: Nuclear repulsion	216209.12512
FMO2-HF: Total energy	-21330.796612
FMO2-MP2: Total energy	-21391.567862

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(C:228:ASP)

Summations of interaction energy for fragment #1(C:228:ASP)

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.
-53.147	-47.106	5.388	-5.848	-5.582	0.062

Interaction energy analysis for fragmet #1(C:228:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.809 / q_NPA : -0.903

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	C	230	LEU	0	-0.041	-0.010	2.054	-31.863	-26.156	5.387	-5.783	-5.312	0.061
4	C	231	ILE	0	0.003	0.008	3.833	-1.539	-1.205	0.001	-0.065	-0.270	0.001
5	C	241	GLU	-1	-0.934	-0.983	14.083	20.119	20.119	0.000	0.000	0.000	0.000
6	C	242	ASN	0	-0.050	-0.021	16.241	-1.726	-1.726	0.000	0.000	0.000	0.000
7	C	243	LEU	0	0.041	0.033	16.163	0.837	0.837	0.000	0.000	0.000	0.000
8	C	244	MET	0	-0.035	-0.020	18.050	-0.940	-0.940	0.000	0.000	0.000	0.000
9	C	245	LEU	0	0.004	0.011	19.230	0.574	0.574	0.000	0.000	0.000	0.000
10	C	246	CYS	0	-0.040	-0.020	21.949	-0.452	-0.452	0.000	0.000	0.000	0.000
11	C	247	LEU	0	0.013	0.029	23.435	0.335	0.335	0.000	0.000	0.000	0.000
12	C	248	TYR	0	0.003	-0.017	21.626	0.253	0.253	0.000	0.000	0.000	0.000
13	C	249	ASP	-1	-0.831	-0.898	24.575	10.133	10.133	0.000	0.000	0.000	0.000
14	C	250	LYS	1	0.921	0.953	25.059	-10.815	-10.815	0.000	0.000	0.000	0.000
15	C	251	VAL	0	0.035	0.020	18.475	0.204	0.204	0.000	0.000	0.000	0.000
16	C	252	THR	0	-0.053	-0.027	21.293	-0.469	-0.469	0.000	0.000	0.000	0.000
17	C	253	ARG	1	0.957	0.968	16.758	-15.084	-15.084	0.000	0.000	0.000	0.000
18	C	254	THR	0	-0.042	-0.017	20.630	-0.740	-0.740	0.000	0.000	0.000	0.000
19	C	255	LYS	1	0.944	0.965	20.391	-12.026	-12.026	0.000	0.000	0.000	0.000
20	C	256	ALA	0	0.066	0.045	15.600	0.385	0.385	0.000	0.000	0.000	0.000
21	C	257	ARG	1	0.835	0.935	16.315	-11.757	-11.757	0.000	0.000	0.000	0.000
22	C	258	TRP	0	0.023	-0.001	13.786	-0.743	-0.743	0.000	0.000	0.000	0.000
23	C	259	LYS	1	0.813	0.885	18.496	-11.669	-11.669	0.000	0.000	0.000	0.000
24	C	260	CYS	0	-0.016	0.004	19.148	0.204	0.204	0.000	0.000	0.000	0.000
25	C	261	SER	0	-0.043	-0.044	21.907	-0.300	-0.300	0.000	0.000	0.000	0.000
26	C	262	LEU	0	0.036	0.011	20.530	0.120	0.120	0.000	0.000	0.000	0.000
27	C	263	LYS	1	0.844	0.895	24.999	-10.220	-10.220	0.000	0.000	0.000	0.000
28	C	264	ASP	-1	-0.803	-0.887	26.883	10.132	10.132	0.000	0.000	0.000	0.000
29	C	265	GLY	0	0.034	0.011	25.819	0.274	0.274	0.000	0.000	0.000	0.000
30	C	266	VAL	0	-0.007	0.000	24.649	-0.502	-0.502	0.000	0.000	0.000	0.000
31	C	267	VAL	0	-0.037	-0.034	20.806	0.563	0.563	0.000	0.000	0.000	0.000
32	C	268	THR	0	0.047	0.029	21.520	-0.406	-0.406	0.000	0.000	0.000	0.000
33	C	269	ILE	0	-0.010	-0.026	19.954	0.823	0.823	0.000	0.000	0.000	0.000
34	C	270	ASN	0	-0.019	-0.019	21.000	-0.396	-0.396	0.000	0.000	0.000	0.000
35	C	271	ARG	1	0.887	0.939	21.756	-13.344	-13.344	0.000	0.000	0.000	0.000
36	C	272	ASN	0	-0.015	0.013	24.842	-0.807	-0.807	0.000	0.000	0.000	0.000
37	C	273	ASP	-1	-0.817	-0.885	25.286	12.223	12.223	0.000	0.000	0.000	0.000
38	C	274	TYR	0	-0.037	-0.015	25.474	-0.420	-0.420	0.000	0.000	0.000	0.000
39	C	275	THR	0	0.009	-0.004	27.073	0.292	0.292	0.000	0.000	0.000	0.000
40	C	276	PHE	0	-0.006	-0.011	23.472	-0.233	-0.233	0.000	0.000	0.000	0.000
41	C	277	GLN	0	-0.010	0.003	29.273	-0.082	-0.082	0.000	0.000	0.000	0.000
42	C	278	LYS	1	0.824	0.884	28.724	-9.914	-9.914	0.000	0.000	0.000	0.000
43	C	279	ALA	0	0.043	0.044	24.430	-0.077	-0.077	0.000	0.000	0.000	0.000
44	C	280	GLN	0	-0.019	0.002	24.428	-0.034	-0.034	0.000	0.000	0.000	0.000
45	C	281	VAL	0	0.036	0.025	18.002	0.051	0.051	0.000	0.000	0.000	0.000
46	C	282	GLU	-1	-0.750	-0.857	20.355	11.529	11.529	0.000	0.000	0.000	0.000
47	C	283	ALA	0	0.018	0.010	15.159	0.127	0.127	0.000	0.000	0.000	0.000
48	C	284	GLU	-1	-0.836	-0.918	16.263	13.954	13.954	0.000	0.000	0.000	0.000
49	C	285	TRP	0	-0.033	-0.016	8.788	0.059	0.059	0.000	0.000	0.000	0.000
50	C	286	VAL	0	0.012	0.006	11.465	0.220	0.220	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:228:ASP)