FMO DATABASE

FMODB ID: YN4Q2

Calculation Name: 1NH2-C-Xray540

Preferred Name:

Target Type:

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

Ligand 3-letter code: 5IU

Ligand of Interest (LOI):

PDB ID: 1NH2

Chain ID: C

ChEMBL ID:

UniProt ID: P32774

Base Structure: X-ray

Registration Date: 2025-07-09

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

DOI:

Apendix: None

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	99
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-237529.68323
FMO2-HF: Nuclear repulsion	216209.12512
FMO2-HF: Total energy	-21320.55811
FMO2-MP2: Total energy	-21381.080386

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.
-0.153	3.267	0.006	-1.884	-1.54	0.005

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 : 0 / q_Mulliken : 0.124 / q_NPA : 0.054

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

Sort

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].
4	C	229	TYR	0	-0.115	0.063	3.929	0.345	0.922	0.021	-0.153	-0.444	-0.001
5	C	230	LEU	0	0.043	-0.077	3.771	-0.439	2.336	-0.013	-1.723	-1.039	0.006
6	C	230	LEU	0	-0.078	0.075	5.246	0.250	0.295	-0.001	-0.003	-0.041	0.000
7	C	231	ILE	0	-0.035	-0.121	4.812	-0.330	-0.307	-0.001	-0.005	-0.016	0.000
8	C	231	ILE	0	0.053	0.031	7.206	0.106	0.106	0.000	0.000	0.000	0.000
9	C	241	GLU	0	0.125	-0.016	16.611	0.027	0.027	0.000	0.000	0.000	0.000
10	C	241	GLU	-1	-1.013	-0.855	14.083	0.123	0.123	0.000	0.000	0.000	0.000
11	C	242	ASN	0	0.012	-0.079	16.392	-0.040	-0.040	0.000	0.000	0.000	0.000
12	C	242	ASN	0	-0.133	0.038	16.241	-0.035	-0.035	0.000	0.000	0.000	0.000
13	C	243	LEU	0	0.152	-0.091	16.163	0.042	0.042	0.000	0.000	0.000	0.000
14	C	243	LEU	0	-0.071	0.127	16.330	-0.005	-0.005	0.000	0.000	0.000	0.000
15	C	244	MET	0	0.099	-0.093	18.050	-0.004	-0.004	0.000	0.000	0.000	0.000
16	C	244	MET	0	-0.132	0.076	18.800	0.003	0.003	0.000	0.000	0.000	0.000
17	C	245	LEU	0	0.012	-0.115	19.230	-0.015	-0.015	0.000	0.000	0.000	0.000
18	C	245	LEU	0	-0.055	0.110	19.821	-0.004	-0.004	0.000	0.000	0.000	0.000
19	C	246	CYS	0	0.106	-0.090	21.949	0.008	0.008	0.000	0.000	0.000	0.000
20	C	246	CYS	0	-0.145	0.069	22.558	0.007	0.007	0.000	0.000	0.000	0.000
21	C	247	LEU	0	0.119	-0.083	23.435	-0.019	-0.019	0.000	0.000	0.000	0.000
22	C	247	LEU	0	-0.080	0.100	25.884	0.000	0.000	0.000	0.000	0.000	0.000
23	C	248	TYR	0	0.083	-0.088	23.197	0.020	0.020	0.000	0.000	0.000	0.000
24	C	248	TYR	0	-0.059	0.089	21.626	-0.006	-0.006	0.000	0.000	0.000	0.000
25	C	249	ASP	0	0.089	-0.100	24.575	-0.014	-0.014	0.000	0.000	0.000	0.000
26	C	249	ASP	-1	-0.914	-0.828	27.779	0.007	0.007	0.000	0.000	0.000	0.000
27	C	250	LYS	0	0.106	-0.085	25.190	-0.012	-0.012	0.000	0.000	0.000	0.000
28	C	250	LYS	1	0.829	1.056	25.059	-0.020	-0.020	0.000	0.000	0.000	0.000
29	C	251	VAL	0	0.016	-0.120	20.614	0.021	0.021	0.000	0.000	0.000	0.000
30	C	251	VAL	0	-0.021	0.140	18.475	0.000	0.000	0.000	0.000	0.000	0.000
31	C	252	THR	0	-0.020	-0.079	21.293	-0.023	-0.023	0.000	0.000	0.000	0.000
32	C	252	THR	0	-0.062	0.038	22.951	0.005	0.005	0.000	0.000	0.000	0.000
33	C	253	ARG	0	0.158	-0.071	19.435	0.021	0.021	0.000	0.000	0.000	0.000
34	C	253	ARG	1	0.836	1.065	16.758	0.028	0.028	0.000	0.000	0.000	0.000
35	C	254	THR	0	-0.037	-0.108	20.630	-0.023	-0.023	0.000	0.000	0.000	0.000
36	C	254	THR	0	-0.002	0.073	23.187	0.003	0.003	0.000	0.000	0.000	0.000
37	C	255	LYS	0	0.017	-0.049	20.445	0.018	0.018	0.000	0.000	0.000	0.000
38	C	255	LYS	1	0.865	1.026	20.391	-0.082	-0.082	0.000	0.000	0.000	0.000
39	C	256	ALA	0	0.174	-0.094	16.482	-0.057	-0.057	0.000	0.000	0.000	0.000
40	C	256	ALA	0	-0.048	0.133	15.600	0.010	0.010	0.000	0.000	0.000	0.000
41	C	257	ARG	0	0.129	-0.069	16.315	0.031	0.031	0.000	0.000	0.000	0.000
42	C	257	ARG	1	0.681	0.989	20.219	-0.200	-0.200	0.000	0.000	0.000	0.000
43	C	258	TRP	0	0.095	-0.105	17.252	-0.043	-0.043	0.000	0.000	0.000	0.000
44	C	258	TRP	0	-0.068	0.105	13.786	-0.027	-0.027	0.000	0.000	0.000	0.000
45	C	259	LYS	0	0.073	-0.105	18.496	0.035	0.035	0.000	0.000	0.000	0.000
46	C	259	LYS	1	0.749	0.994	22.458	-0.116	-0.116	0.000	0.000	0.000	0.000
47	C	260	CYS	0	0.059	-0.118	20.663	-0.029	-0.029	0.000	0.000	0.000	0.000
48	C	260	CYS	0	-0.052	0.123	19.148	-0.006	-0.006	0.000	0.000	0.000	0.000
49	C	261	SER	0	0.022	-0.066	21.907	0.023	0.023	0.000	0.000	0.000	0.000
50	C	261	SER	0	-0.080	0.017	26.314	-0.004	-0.004	0.000	0.000	0.000	0.000
51	C	262	LEU	0	0.063	-0.095	23.841	-0.022	-0.022	0.000	0.000	0.000	0.000
52	C	262	LEU	0	-0.032	0.119	20.530	0.002	0.002	0.000	0.000	0.000	0.000
53	C	263	LYS	0	0.087	-0.069	24.999	0.013	0.013	0.000	0.000	0.000	0.000
54	C	263	LYS	1	0.763	0.970	28.134	0.005	0.005	0.000	0.000	0.000	0.000
55	C	264	ASP	0	0.049	-0.076	26.883	-0.002	-0.002	0.000	0.000	0.000	0.000
56	C	264	ASP	-1	-0.904	-0.810	29.082	-0.002	-0.002	0.000	0.000	0.000	0.000
57	C	265	GLY	0	0.098	-0.084	25.819	-0.011	-0.011	0.000	0.000	0.000	0.000
58	C	266	VAL	0	0.079	-0.005	25.155	0.007	0.007	0.000	0.000	0.000	0.000
59	C	266	VAL	0	-0.068	0.117	24.649	-0.002	-0.002	0.000	0.000	0.000	0.000
60	C	267	VAL	0	0.047	-0.101	22.488	-0.011	-0.011	0.000	0.000	0.000	0.000
61	C	267	VAL	0	-0.136	0.064	20.806	0.003	0.003	0.000	0.000	0.000	0.000
62	C	268	THR	0	0.137	-0.081	22.058	0.001	0.001	0.000	0.000	0.000	0.000
63	C	268	THR	0	-0.054	0.080	21.520	-0.005	-0.005	0.000	0.000	0.000	0.000
64	C	269	ILE	0	0.070	-0.090	20.720	0.022	0.022	0.000	0.000	0.000	0.000
65	C	269	ILE	0	-0.122	0.084	19.954	0.006	0.006	0.000	0.000	0.000	0.000
66	C	270	ASN	0	0.076	-0.042	21.000	-0.017	-0.017	0.000	0.000	0.000	0.000
67	C	270	ASN	0	-0.098	0.042	21.167	0.013	0.013	0.000	0.000	0.000	0.000
68	C	271	ARG	0	0.078	-0.079	22.737	-0.006	-0.006	0.000	0.000	0.000	0.000
69	C	271	ARG	1	0.832	1.030	21.756	-0.266	-0.266	0.000	0.000	0.000	0.000
70	C	272	ASN	0	0.136	-0.077	24.842	-0.015	-0.015	0.000	0.000	0.000	0.000
71	C	272	ASN	0	-0.141	0.052	26.614	-0.011	-0.011	0.000	0.000	0.000	0.000
72	C	273	ASP	0	0.090	-0.075	25.286	0.018	0.018	0.000	0.000	0.000	0.000
73	C	273	ASP	-1	-0.892	-0.799	25.790	0.100	0.100	0.000	0.000	0.000	0.000
74	C	274	TYR	0	0.027	-0.111	26.501	-0.006	-0.006	0.000	0.000	0.000	0.000
75	C	274	TYR	0	-0.100	0.084	25.474	0.007	0.007	0.000	0.000	0.000	0.000
76	C	275	THR	0	0.041	-0.065	27.073	-0.001	-0.001	0.000	0.000	0.000	0.000
77	C	275	THR	0	-0.018	0.068	29.008	0.001	0.001	0.000	0.000	0.000	0.000
78	C	276	PHE	0	0.082	-0.095	28.210	0.005	0.005	0.000	0.000	0.000	0.000
79	C	276	PHE	0	-0.074	0.106	23.472	0.002	0.002	0.000	0.000	0.000	0.000
80	C	277	GLN	0	0.132	-0.077	29.273	-0.008	-0.008	0.000	0.000	0.000	0.000
81	C	277	GLN	0	-0.137	0.073	31.982	-0.001	-0.001	0.000	0.000	0.000	0.000
82	C	278	LYS	0	0.042	-0.101	28.724	-0.010	-0.010	0.000	0.000	0.000	0.000
83	C	278	LYS	1	0.759	0.990	28.973	-0.026	-0.026	0.000	0.000	0.000	0.000
84	C	279	ALA	0	0.085	-0.103	25.158	0.006	0.006	0.000	0.000	0.000	0.000
85	C	279	ALA	0	-0.011	0.138	24.430	0.002	0.002	0.000	0.000	0.000	0.000
86	C	280	GLN	0	-0.001	-0.124	24.428	-0.018	-0.018	0.000	0.000	0.000	0.000
87	C	280	GLN	0	-0.049	0.117	25.484	-0.005	-0.005	0.000	0.000	0.000	0.000
88	C	281	VAL	0	0.081	-0.099	20.096	0.016	0.016	0.000	0.000	0.000	0.000
89	C	281	VAL	0	-0.050	0.125	18.002	0.001	0.001	0.000	0.000	0.000	0.000
90	C	282	GLU	0	0.102	-0.103	20.355	-0.029	-0.029	0.000	0.000	0.000	0.000
91	C	282	GLU	-1	-0.815	-0.748	21.503	0.146	0.146	0.000	0.000	0.000	0.000
92	C	283	ALA	0	0.092	-0.104	16.067	0.024	0.024	0.000	0.000	0.000	0.000
93	C	283	ALA	0	-0.062	0.119	15.159	0.003	0.003	0.000	0.000	0.000	0.000
94	C	284	GLU	0	0.023	-0.112	16.263	-0.065	-0.065	0.000	0.000	0.000	0.000
95	C	284	GLU	-1	-0.895	-0.811	16.660	0.255	0.255	0.000	0.000	0.000	0.000
96	C	285	TRP	0	0.095	-0.074	12.311	0.124	0.124	0.000	0.000	0.000	0.000
97	C	285	TRP	0	-0.113	0.081	8.788	0.029	0.029	0.000	0.000	0.000	0.000
98	C	286	VAL	0	-0.042	-0.134	11.465	0.012	0.012	0.000	0.000	0.000	0.000
99	C	286	VAL	0	0.037	0.027	14.591	-0.017	-0.017	0.000	0.000	0.000	0.000

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