FMO DATABASE

FMODB ID: 6NLKZ

Calculation Name: 4HDV-A-Xray372

Preferred Name:

Target Type:

Ligand Name: 2,6-diaminopurine nucleotide

ligand 3-letter code: 1AP

PDB ID: 4HDV

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UTN9

Base Structure: X-ray

Registration Date: 2023-06-21

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	108
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-910890.099608
FMO2-HF: Nuclear repulsion	865756.642428
FMO2-HF: Total energy	-45133.457181
FMO2-MP2: Total energy	-45262.859973

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(A:1:MET)

Summations of interaction energy for fragment #1(A:1:MET)

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.
-19.103	-19.998	27.736	-11.275	-15.566	-0.003

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / 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

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].
3	A	3	MET	0	0.041	0.004	2.725	-3.282	-0.939	0.596	-1.266	-1.673	-0.005
4	A	4	ASP	-1	-0.799	-0.885	5.000	0.017	0.198	-0.001	-0.011	-0.168	0.000
5	A	5	GLU	-1	-0.796	-0.884	2.339	0.113	2.811	2.093	-1.688	-3.104	-0.018
6	A	6	PHE	0	-0.007	-0.003	2.435	0.381	2.505	0.924	-0.697	-2.351	-0.001
7	A	7	TYR	0	-0.009	-0.025	3.815	-0.294	-0.111	0.016	0.083	-0.282	0.000
8	A	8	THR	0	-0.029	-0.016	7.185	-0.063	-0.063	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.907	0.929	2.108	-12.608	-22.065	20.086	-6.206	-4.422	0.033
10	A	10	VAL	0	-0.019	-0.008	5.915	-0.585	-0.585	0.000	0.000	0.000	0.000
11	A	11	TYR	0	-0.059	-0.059	7.932	-0.108	-0.108	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.844	-0.916	9.303	1.130	1.130	0.000	0.000	0.000	0.000
13	A	13	ALA	0	0.012	-0.001	8.875	-0.120	-0.120	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.048	-0.046	10.833	-0.086	-0.086	0.000	0.000	0.000	0.000
15	A	15	CYS	0	-0.059	-0.044	13.377	-0.033	-0.033	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.859	-0.890	12.809	0.249	0.249	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.067	-0.007	14.765	-0.035	-0.035	0.000	0.000	0.000	0.000
18	A	18	PRO	0	-0.003	0.002	17.614	0.010	0.010	0.000	0.000	0.000	0.000
19	A	19	TYR	0	-0.002	-0.020	21.321	-0.018	-0.018	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.053	0.034	24.281	0.000	0.000	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.797	0.914	21.566	0.058	0.058	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.009	0.002	20.010	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	23	SER	0	0.054	0.013	14.434	-0.015	-0.015	0.000	0.000	0.000	0.000
24	A	24	THR	0	0.006	-0.001	15.445	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	25	TYR	0	-0.023	-0.022	12.955	-0.057	-0.057	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.000	-0.017	11.285	-0.132	-0.132	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.843	-0.890	11.367	-0.544	-0.544	0.000	0.000	0.000	0.000
28	A	28	ILE	0	0.030	0.012	8.807	-0.056	-0.056	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.001	-0.001	7.008	-0.110	-0.110	0.000	0.000	0.000	0.000
30	A	30	ARG	1	0.806	0.877	6.438	0.190	0.190	0.000	0.000	0.000	0.000
31	A	31	TYR	0	-0.070	-0.049	7.893	-0.155	-0.155	0.000	0.000	0.000	0.000
32	A	32	VAL	0	-0.024	-0.003	3.539	-0.045	0.246	0.006	-0.043	-0.254	0.000
33	A	33	GLY	0	0.011	0.014	2.920	-3.620	-2.358	0.154	-0.652	-0.765	-0.008
34	A	34	MET	0	-0.056	-0.028	2.554	-1.981	-2.501	3.862	-0.795	-2.547	-0.004
35	A	35	PRO	0	0.037	-0.003	5.437	0.442	0.442	0.000	0.000	0.000	0.000
36	A	36	SER	0	-0.002	0.007	9.045	0.120	0.120	0.000	0.000	0.000	0.000
37	A	37	TYR	0	-0.013	-0.001	5.283	0.301	0.301	0.000	0.000	0.000	0.000
38	A	38	ALA	0	0.035	0.013	8.386	0.119	0.119	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.940	0.958	11.368	0.757	0.757	0.000	0.000	0.000	0.000
40	A	40	GLN	0	0.065	0.037	7.944	0.147	0.147	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.027	0.029	8.357	0.087	0.087	0.000	0.000	0.000	0.000
42	A	42	GLY	0	0.013	0.009	10.129	0.155	0.155	0.000	0.000	0.000	0.000
43	A	43	GLN	0	-0.041	-0.030	11.521	-0.041	-0.041	0.000	0.000	0.000	0.000
44	A	44	ALA	0	0.055	0.041	9.448	0.100	0.100	0.000	0.000	0.000	0.000
45	A	45	MET	0	-0.008	0.010	11.610	0.141	0.141	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.804	0.890	14.710	0.334	0.334	0.000	0.000	0.000	0.000
47	A	47	HIS	0	-0.073	-0.049	13.861	0.002	0.002	0.000	0.000	0.000	0.000
48	A	48	LEU	0	-0.051	0.006	14.819	0.043	0.043	0.000	0.000	0.000	0.000
49	A	49	HIS	0	0.041	0.028	17.155	-0.019	-0.019	0.000	0.000	0.000	0.000
50	A	50	PRO	0	-0.052	-0.034	20.437	0.008	0.008	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.858	-0.942	23.339	-0.023	-0.023	0.000	0.000	0.000	0.000
52	A	52	THR	0	-0.062	-0.018	17.857	0.031	0.031	0.000	0.000	0.000	0.000
53	A	53	HIS	0	0.017	0.000	20.646	-0.009	-0.009	0.000	0.000	0.000	0.000
54	A	54	VAL	0	0.015	0.016	14.636	0.006	0.006	0.000	0.000	0.000	0.000
55	A	55	PRO	0	-0.007	0.012	16.691	-0.036	-0.036	0.000	0.000	0.000	0.000
56	A	56	TRP	0	0.039	-0.013	16.827	-0.043	-0.043	0.000	0.000	0.000	0.000
57	A	57	HIS	0	-0.034	-0.016	17.839	-0.047	-0.047	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.846	0.925	18.914	0.001	0.001	0.000	0.000	0.000	0.000
59	A	59	VAL	0	0.025	0.010	14.055	-0.021	-0.021	0.000	0.000	0.000	0.000
60	A	60	ILE	0	0.012	0.030	17.354	-0.008	-0.008	0.000	0.000	0.000	0.000
61	A	61	ASN	0	-0.007	-0.026	17.508	-0.053	-0.053	0.000	0.000	0.000	0.000
62	A	62	SER	0	0.045	-0.004	17.933	0.012	0.012	0.000	0.000	0.000	0.000
63	A	63	ARG	1	0.754	0.853	20.156	0.257	0.257	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.025	0.014	22.705	0.023	0.023	0.000	0.000	0.000	0.000
65	A	65	THR	0	-0.063	-0.045	23.718	0.013	0.013	0.000	0.000	0.000	0.000
66	A	66	ILE	0	0.009	0.018	22.919	-0.024	-0.024	0.000	0.000	0.000	0.000
67	A	67	SER	0	-0.007	-0.001	19.855	0.009	0.009	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.881	0.934	22.852	0.179	0.179	0.000	0.000	0.000	0.000
69	A	69	ARG	1	0.810	0.886	20.212	0.214	0.214	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.824	-0.898	23.036	-0.239	-0.239	0.000	0.000	0.000	0.000
71	A	71	ILE	0	0.027	0.018	25.885	0.017	0.017	0.000	0.000	0.000	0.000
72	A	72	SER	0	-0.008	-0.026	26.920	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	73	ALA	0	0.054	0.022	28.796	0.003	0.003	0.000	0.000	0.000	0.000
74	A	74	GLY	0	-0.016	-0.004	24.582	0.007	0.007	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.793	-0.872	24.813	-0.171	-0.171	0.000	0.000	0.000	0.000
76	A	76	GLN	0	0.005	-0.011	26.162	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	77	ARG	1	0.948	0.977	22.557	0.113	0.113	0.000	0.000	0.000	0.000
78	A	78	GLN	0	-0.038	-0.027	20.089	-0.008	-0.008	0.000	0.000	0.000	0.000
79	A	79	LYS	1	0.800	0.879	25.020	0.092	0.092	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.785	-0.873	28.054	-0.077	-0.077	0.000	0.000	0.000	0.000
81	A	81	ARG	1	0.936	0.963	22.403	0.054	0.054	0.000	0.000	0.000	0.000
82	A	82	LEU	0	-0.050	-0.022	23.075	0.006	0.006	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.804	-0.896	26.969	-0.077	-0.077	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.942	-0.964	29.336	-0.034	-0.034	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.846	-0.895	24.447	-0.022	-0.022	0.000	0.000	0.000	0.000
86	A	86	GLY	0	-0.001	0.001	28.570	0.001	0.001	0.000	0.000	0.000	0.000
87	A	87	VAL	0	-0.059	-0.030	25.877	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.906	-0.950	29.310	-0.066	-0.066	0.000	0.000	0.000	0.000
89	A	89	ILE	0	-0.097	-0.042	27.240	-0.013	-0.013	0.000	0.000	0.000	0.000
90	A	90	TYR	0	0.010	0.011	30.753	0.003	0.003	0.000	0.000	0.000	0.000
91	A	91	GLN	0	-0.031	-0.031	31.876	-0.007	-0.007	0.000	0.000	0.000	0.000
92	A	92	THR	0	-0.044	-0.017	31.621	0.004	0.004	0.000	0.000	0.000	0.000
93	A	93	SER	0	0.050	0.007	34.321	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	94	LEU	0	-0.029	-0.012	33.086	0.002	0.002	0.000	0.000	0.000	0.000
95	A	95	GLY	0	0.038	0.033	33.456	-0.006	-0.006	0.000	0.000	0.000	0.000
96	A	96	GLU	-1	-0.791	-0.843	26.629	-0.221	-0.221	0.000	0.000	0.000	0.000
97	A	97	TYR	0	0.043	0.016	28.473	0.007	0.007	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.880	0.947	27.569	0.146	0.146	0.000	0.000	0.000	0.000
99	A	99	LEU	0	0.101	0.068	24.068	0.011	0.011	0.000	0.000	0.000	0.000
100	A	100	ASN	0	-0.004	-0.024	27.871	-0.020	-0.020	0.000	0.000	0.000	0.000
101	A	101	LEU	0	0.037	0.008	20.944	0.005	0.005	0.000	0.000	0.000	0.000
102	A	102	PRO	0	-0.016	-0.013	24.233	0.000	0.000	0.000	0.000	0.000	0.000
103	A	103	GLU	-1	-0.845	-0.885	25.896	-0.075	-0.075	0.000	0.000	0.000	0.000
104	A	104	TYR	0	-0.018	-0.036	24.477	0.008	0.008	0.000	0.000	0.000	0.000
105	A	105	MET	0	-0.066	-0.001	16.430	-0.004	-0.004	0.000	0.000	0.000	0.000
106	A	106	TRP	0	0.034	0.006	13.436	-0.010	-0.010	0.000	0.000	0.000	0.000
107	A	107	LYS	1	0.855	0.918	18.269	0.078	0.078	0.000	0.000	0.000	0.000
108	A	108	PRO	0	0.019	0.032	14.605	0.025	0.025	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)