FMO DATABASE

FMODB ID: LJ339

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

Total energy (hartree)

FMO2-HF: Electronic energy	-237206.048517
FMO2-HF: Nuclear repulsion	215875.708436
FMO2-HF: Total energy	-21330.34008
FMO2-MP2: Total energy	-21391.088525

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.
-24.711	-18.166	0.233	-3.365	-3.413	0.014

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 : -0.904 / q_NPA : -0.952

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	-0.045	-0.015	3.078	-18.696	-13.062	0.084	-3.013	-2.705	0.014
4	C	231	ILE	0	0.035	0.031	3.409	10.375	11.286	0.149	-0.352	-0.708	0.000
5	C	241	GLU	-1	-0.952	-0.991	13.897	21.158	21.158	0.000	0.000	0.000	0.000
6	C	242	ASN	0	-0.035	-0.002	16.124	-1.875	-1.875	0.000	0.000	0.000	0.000
7	C	243	LEU	0	0.058	0.031	16.220	0.927	0.927	0.000	0.000	0.000	0.000
8	C	244	MET	0	-0.017	-0.017	18.075	-0.991	-0.991	0.000	0.000	0.000	0.000
9	C	245	LEU	0	-0.003	0.010	19.207	0.604	0.604	0.000	0.000	0.000	0.000
10	C	246	CYS	0	-0.043	-0.022	21.778	-0.450	-0.450	0.000	0.000	0.000	0.000
11	C	247	LEU	0	0.023	0.031	23.302	0.289	0.289	0.000	0.000	0.000	0.000
12	C	248	TYR	0	0.001	-0.016	21.597	0.203	0.203	0.000	0.000	0.000	0.000
13	C	249	ASP	-1	-0.874	-0.930	24.030	10.234	10.234	0.000	0.000	0.000	0.000
14	C	250	LYS	1	0.898	0.928	25.070	-10.762	-10.762	0.000	0.000	0.000	0.000
15	C	251	VAL	0	0.042	0.032	18.456	0.219	0.219	0.000	0.000	0.000	0.000
16	C	252	THR	0	-0.081	-0.033	21.401	-0.403	-0.403	0.000	0.000	0.000	0.000
17	C	253	ARG	1	0.977	0.974	16.557	-14.725	-14.725	0.000	0.000	0.000	0.000
18	C	254	THR	0	-0.033	-0.002	20.231	-0.659	-0.659	0.000	0.000	0.000	0.000
19	C	255	LYS	1	0.927	0.960	19.779	-12.228	-12.228	0.000	0.000	0.000	0.000
20	C	256	ALA	0	0.080	0.044	14.989	0.328	0.328	0.000	0.000	0.000	0.000
21	C	257	ARG	1	0.944	0.997	16.060	-11.736	-11.736	0.000	0.000	0.000	0.000
22	C	258	TRP	0	0.031	-0.002	14.089	-0.743	-0.743	0.000	0.000	0.000	0.000
23	C	259	LYS	1	0.944	0.970	18.245	-11.856	-11.856	0.000	0.000	0.000	0.000
24	C	260	CYS	0	-0.020	-0.008	17.980	0.104	0.104	0.000	0.000	0.000	0.000
25	C	261	SER	0	-0.031	-0.001	21.510	-0.259	-0.259	0.000	0.000	0.000	0.000
26	C	262	LEU	0	0.004	-0.015	20.203	0.092	0.092	0.000	0.000	0.000	0.000
27	C	263	LYS	1	0.899	0.947	24.695	-10.537	-10.537	0.000	0.000	0.000	0.000
28	C	264	ASP	-1	-0.873	-0.941	26.726	10.385	10.385	0.000	0.000	0.000	0.000
29	C	265	GLY	0	0.012	0.003	25.435	0.290	0.290	0.000	0.000	0.000	0.000
30	C	266	VAL	0	-0.018	-0.003	24.768	-0.533	-0.533	0.000	0.000	0.000	0.000
31	C	267	VAL	0	-0.037	-0.021	20.704	0.629	0.629	0.000	0.000	0.000	0.000
32	C	268	THR	0	0.015	0.010	21.787	-0.491	-0.491	0.000	0.000	0.000	0.000
33	C	269	ILE	0	-0.008	-0.029	20.270	0.909	0.909	0.000	0.000	0.000	0.000
34	C	270	ASN	0	-0.097	-0.057	20.995	-0.073	-0.073	0.000	0.000	0.000	0.000
35	C	271	ARG	1	0.924	0.944	22.417	-13.588	-13.588	0.000	0.000	0.000	0.000
36	C	272	ASN	0	0.019	0.043	24.669	-0.692	-0.692	0.000	0.000	0.000	0.000
37	C	273	ASP	-1	-0.801	-0.879	25.429	12.502	12.502	0.000	0.000	0.000	0.000
38	C	274	TYR	0	-0.064	-0.031	25.763	-0.441	-0.441	0.000	0.000	0.000	0.000
39	C	275	THR	0	0.025	0.016	27.024	0.333	0.333	0.000	0.000	0.000	0.000
40	C	276	PHE	0	-0.018	-0.022	23.630	-0.199	-0.199	0.000	0.000	0.000	0.000
41	C	277	GLN	0	0.066	0.046	29.356	0.126	0.126	0.000	0.000	0.000	0.000
42	C	278	LYS	1	0.915	0.934	28.510	-9.399	-9.399	0.000	0.000	0.000	0.000
43	C	279	ALA	0	0.035	0.029	23.777	-0.027	-0.027	0.000	0.000	0.000	0.000
44	C	280	GLN	0	-0.017	-0.005	24.311	0.144	0.144	0.000	0.000	0.000	0.000
45	C	281	VAL	0	0.021	0.018	17.518	0.100	0.100	0.000	0.000	0.000	0.000
46	C	282	GLU	-1	-0.919	-0.975	20.325	11.657	11.657	0.000	0.000	0.000	0.000
47	C	283	ALA	0	-0.001	0.000	14.879	0.151	0.151	0.000	0.000	0.000	0.000
48	C	284	GLU	-1	-0.902	-0.962	15.661	14.655	14.655	0.000	0.000	0.000	0.000
49	C	285	TRP	0	-0.045	-0.010	8.330	0.016	0.016	0.000	0.000	0.000	0.000
50	C	286	VAL	0	0.026	0.007	10.648	0.222	0.222	0.000	0.000	0.000	0.000

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