FMO DATABASE

FMODB ID: 7J8ZK

Calculation Name: 1NH2-C-Xray315

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	53
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-242429.81077
FMO2-HF: Nuclear repulsion	220777.247203
FMO2-HF: Total energy	-21652.563567
FMO2-MP2: Total energy	-21714.2874

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:227:ACE )

Summations of interaction energy for fragment #1(C:227:ACE )

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.
1.893	2.554	-0.005	-0.331	-0.324	0

Interaction energy analysis for fragmet #1(C:227:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / q_NPA : -0.019

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].
3	C	229	TYR	0	-0.031	-0.027	3.825	1.234	1.895	-0.005	-0.331	-0.324
4	C	230	LEU	0	-0.044	-0.012	6.397	0.444	0.444	0.000	0.000	0.000
5	C	231	ILE	0	0.027	0.020	6.181	-0.063	-0.063	0.000	0.000	0.000
6	C	232	NME	0	0.003	0.009	7.852	-0.053	-0.053	0.000	0.000	0.000
7	C	240	ACE	0	-0.023	-0.025	16.789	-0.012	-0.012	0.000	0.000	0.000
8	C	241	GLU	-1	-0.928	-0.972	12.690	0.500	0.500	0.000	0.000	0.000
9	C	242	ASN	0	-0.036	0.005	14.338	-0.100	-0.100	0.000	0.000	0.000
10	C	243	LEU	0	0.063	0.034	14.663	0.047	0.047	0.000	0.000	0.000
11	C	244	MET	0	-0.016	-0.017	16.812	-0.039	-0.039	0.000	0.000	0.000
12	C	245	LEU	0	-0.004	0.010	18.315	0.005	0.005	0.000	0.000	0.000
13	C	246	CYS	0	-0.041	-0.021	20.972	-0.008	-0.008	0.000	0.000	0.000
14	C	247	LEU	0	0.019	0.029	22.958	-0.004	-0.004	0.000	0.000	0.000
15	C	248	TYR	0	0.003	-0.014	21.719	0.008	0.008	0.000	0.000	0.000
16	C	249	ASP	-1	-0.880	-0.932	23.950	0.062	0.062	0.000	0.000	0.000
17	C	250	LYS	1	0.896	0.927	25.072	-0.065	-0.065	0.000	0.000	0.000
18	C	251	VAL	0	0.045	0.033	18.877	0.011	0.011	0.000	0.000	0.000
19	C	252	THR	0	-0.086	-0.036	21.615	-0.015	-0.015	0.000	0.000	0.000
20	C	253	ARG	1	0.981	0.977	17.406	0.009	0.009	0.000	0.000	0.000
21	C	254	THR	0	-0.050	-0.012	20.746	-0.013	-0.013	0.000	0.000	0.000
22	C	255	LYS	1	0.925	0.960	20.424	0.022	0.022	0.000	0.000	0.000
23	C	256	ALA	0	0.095	0.054	15.295	-0.008	-0.008	0.000	0.000	0.000
24	C	257	ARG	1	0.943	0.998	16.174	-0.053	-0.053	0.000	0.000	0.000
25	C	258	TRP	0	0.029	-0.003	14.667	-0.013	-0.013	0.000	0.000	0.000
26	C	259	LYS	1	0.941	0.968	18.262	-0.061	-0.061	0.000	0.000	0.000
27	C	260	CYS	0	-0.019	-0.008	17.730	-0.013	-0.013	0.000	0.000	0.000
28	C	261	SER	0	-0.035	-0.003	21.272	0.003	0.003	0.000	0.000	0.000
29	C	262	LEU	0	0.007	-0.013	19.572	-0.005	-0.005	0.000	0.000	0.000
30	C	263	LYS	1	0.896	0.945	24.207	-0.076	-0.076	0.000	0.000	0.000
31	C	264	ASP	-1	-0.876	-0.942	26.138	0.086	0.086	0.000	0.000	0.000
32	C	265	GLY	0	0.015	0.005	24.523	0.003	0.003	0.000	0.000	0.000
33	C	266	VAL	0	-0.020	-0.005	23.620	-0.009	-0.009	0.000	0.000	0.000
34	C	267	VAL	0	-0.035	-0.019	19.206	0.015	0.015	0.000	0.000	0.000
35	C	268	THR	0	0.013	0.008	20.174	-0.015	-0.015	0.000	0.000	0.000
36	C	269	ILE	0	-0.005	-0.027	18.397	0.038	0.038	0.000	0.000	0.000
37	C	270	ASN	0	-0.094	-0.056	18.898	0.000	0.000	0.000	0.000	0.000
38	C	271	ARG	1	0.918	0.942	20.073	-0.237	-0.237	0.000	0.000	0.000
39	C	272	ASN	0	0.019	0.042	22.741	-0.025	-0.025	0.000	0.000	0.000
40	C	273	ASP	-1	-0.801	-0.879	23.576	0.180	0.180	0.000	0.000	0.000
41	C	274	TYR	0	-0.064	-0.031	23.986	-0.011	-0.011	0.000	0.000	0.000
42	C	275	THR	0	0.024	0.015	25.580	0.007	0.007	0.000	0.000	0.000
43	C	276	PHE	0	-0.016	-0.021	22.690	-0.003	-0.003	0.000	0.000	0.000
44	C	277	GLN	0	0.062	0.044	28.224	0.001	0.001	0.000	0.000	0.000
45	C	278	LYS	1	0.914	0.933	27.730	-0.076	-0.076	0.000	0.000	0.000
46	C	279	ALA	0	0.036	0.029	22.762	0.004	0.004	0.000	0.000	0.000
47	C	280	GLN	0	-0.018	-0.006	23.616	-0.008	-0.008	0.000	0.000	0.000
48	C	281	VAL	0	0.019	0.017	16.767	0.010	0.010	0.000	0.000	0.000
49	C	282	GLU	-1	-0.926	-0.978	19.410	0.083	0.083	0.000	0.000	0.000
50	C	283	ALA	0	-0.005	-0.004	14.097	0.017	0.017	0.000	0.000	0.000
51	C	284	GLU	-1	-0.910	-0.968	15.192	0.051	0.051	0.000	0.000	0.000
52	C	285	TRP	0	-0.080	-0.031	9.062	0.020	0.020	0.000	0.000	0.000
53	C	286	VAL	-1	-0.898	-0.951	10.257	0.018	0.018	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:227:ACE )