FMO DATABASE

FMODB ID: 9GVV2

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	OptHSide
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	-237933.272149
FMO2-HF: Nuclear repulsion	216602.580852
FMO2-HF: Total energy	-21330.691297
FMO2-MP2: Total energy	-21391.451229

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.
-47.28	-40.509	6.715	-7.112	-6.375	0.066

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 : -0.845 / q_NPA : -0.926

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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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	-0.065	-0.023	1.934	-36.059	-30.274	6.599	-6.722	-5.663	0.065
4	C	231	ILE	0	0.022	0.022	3.566	7.228	8.214	0.116	-0.390	-0.712	0.001
5	C	241	GLU	-1	-0.956	-0.990	13.771	20.557	20.557	0.000	0.000	0.000	0.000
6	C	242	ASN	0	-0.035	-0.009	16.168	-1.773	-1.773	0.000	0.000	0.000	0.000
7	C	243	LEU	0	0.047	0.027	16.131	0.856	0.856	0.000	0.000	0.000	0.000
8	C	244	MET	0	-0.014	-0.012	18.053	-0.932	-0.932	0.000	0.000	0.000	0.000
9	C	245	LEU	0	0.001	0.012	19.186	0.580	0.580	0.000	0.000	0.000	0.000
10	C	246	CYS	0	-0.040	-0.025	21.756	-0.445	-0.445	0.000	0.000	0.000	0.000
11	C	247	LEU	0	0.013	0.033	23.281	0.294	0.294	0.000	0.000	0.000	0.000
12	C	248	TYR	0	0.000	-0.016	21.536	0.171	0.171	0.000	0.000	0.000	0.000
13	C	249	ASP	-1	-0.848	-0.916	24.014	10.151	10.151	0.000	0.000	0.000	0.000
14	C	250	LYS	1	0.922	0.941	25.047	-10.718	-10.718	0.000	0.000	0.000	0.000
15	C	251	VAL	0	0.039	0.026	18.418	0.172	0.172	0.000	0.000	0.000	0.000
16	C	252	THR	0	-0.070	-0.030	21.400	-0.389	-0.389	0.000	0.000	0.000	0.000
17	C	253	ARG	1	0.968	0.970	16.444	-14.971	-14.971	0.000	0.000	0.000	0.000
18	C	254	THR	0	-0.024	0.005	20.232	-0.605	-0.605	0.000	0.000	0.000	0.000
19	C	255	LYS	1	0.937	0.962	19.782	-12.173	-12.173	0.000	0.000	0.000	0.000
20	C	256	ALA	0	0.058	0.037	15.082	0.359	0.359	0.000	0.000	0.000	0.000
21	C	257	ARG	1	0.905	0.969	16.068	-11.700	-11.700	0.000	0.000	0.000	0.000
22	C	258	TRP	0	0.017	-0.008	13.654	-0.738	-0.738	0.000	0.000	0.000	0.000
23	C	259	LYS	1	0.822	0.896	18.246	-11.717	-11.717	0.000	0.000	0.000	0.000
24	C	260	CYS	0	-0.016	0.000	18.725	0.251	0.251	0.000	0.000	0.000	0.000
25	C	261	SER	0	-0.037	-0.025	21.502	-0.263	-0.263	0.000	0.000	0.000	0.000
26	C	262	LEU	0	0.007	-0.014	20.116	0.086	0.086	0.000	0.000	0.000	0.000
27	C	263	LYS	1	0.829	0.891	24.682	-10.390	-10.390	0.000	0.000	0.000	0.000
28	C	264	ASP	-1	-0.796	-0.894	26.708	10.219	10.219	0.000	0.000	0.000	0.000
29	C	265	GLY	0	0.041	0.015	25.411	0.276	0.276	0.000	0.000	0.000	0.000
30	C	266	VAL	0	-0.021	-0.004	24.916	-0.514	-0.514	0.000	0.000	0.000	0.000
31	C	267	VAL	0	-0.036	-0.022	20.714	0.604	0.604	0.000	0.000	0.000	0.000
32	C	268	THR	0	0.033	0.019	21.757	-0.431	-0.431	0.000	0.000	0.000	0.000
33	C	269	ILE	0	-0.023	-0.031	20.000	0.846	0.846	0.000	0.000	0.000	0.000
34	C	270	ASN	0	-0.068	-0.046	21.016	-0.243	-0.243	0.000	0.000	0.000	0.000
35	C	271	ARG	1	0.926	0.947	22.079	-13.347	-13.347	0.000	0.000	0.000	0.000
36	C	272	ASN	0	-0.003	0.033	24.688	-0.753	-0.753	0.000	0.000	0.000	0.000
37	C	273	ASP	-1	-0.809	-0.881	25.461	12.170	12.170	0.000	0.000	0.000	0.000
38	C	274	TYR	0	-0.050	-0.026	25.469	-0.401	-0.401	0.000	0.000	0.000	0.000
39	C	275	THR	0	0.031	0.019	27.006	0.321	0.321	0.000	0.000	0.000	0.000
40	C	276	PHE	0	-0.015	-0.016	23.486	-0.192	-0.192	0.000	0.000	0.000	0.000
41	C	277	GLN	0	-0.007	0.006	29.339	-0.111	-0.111	0.000	0.000	0.000	0.000
42	C	278	LYS	1	0.878	0.915	28.433	-9.886	-9.886	0.000	0.000	0.000	0.000
43	C	279	ALA	0	0.033	0.034	23.845	-0.021	-0.021	0.000	0.000	0.000	0.000
44	C	280	GLN	0	-0.014	0.009	24.260	0.115	0.115	0.000	0.000	0.000	0.000
45	C	281	VAL	0	0.026	0.021	17.553	0.075	0.075	0.000	0.000	0.000	0.000
46	C	282	GLU	-1	-0.760	-0.868	20.290	11.512	11.512	0.000	0.000	0.000	0.000
47	C	283	ALA	0	-0.003	0.001	14.896	0.108	0.108	0.000	0.000	0.000	0.000
48	C	284	GLU	-1	-0.866	-0.948	15.669	14.332	14.332	0.000	0.000	0.000	0.000
49	C	285	TRP	0	-0.049	-0.016	8.230	0.013	0.013	0.000	0.000	0.000	0.000
50	C	286	VAL	0	0.026	0.009	10.666	0.196	0.196	0.000	0.000	0.000	0.000

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