FMO DATABASE

FMODB ID: 723QK

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-907567.932329
FMO2-HF: Nuclear repulsion	862435.601939
FMO2-HF: Total energy	-45132.33039
FMO2-MP2: Total energy	-45261.775223

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.
-10.792	-5.53	13.096	-5.588	-12.77	-0.001

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 : -0.015 / q_NPA : -0.013

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	0.037	0.004	2.555	-4.150	-1.436	0.875	-1.478	-2.110	-0.010
4	A	4	ASP	-1	-0.810	-0.889	5.039	-1.038	-0.864	-0.001	-0.007	-0.166	0.000
5	A	5	GLU	-1	-0.854	-0.930	2.389	-4.588	-2.330	0.837	-1.184	-1.911	-0.007
6	A	6	PHE	0	-0.027	-0.020	3.034	-2.286	-0.165	1.394	-0.958	-2.558	0.001
7	A	7	TYR	0	-0.045	-0.035	3.841	-0.219	-0.447	0.042	0.424	-0.238	0.001
8	A	8	THR	0	0.006	0.008	6.092	0.162	0.162	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.995	1.001	1.982	1.979	-0.819	7.751	-1.618	-3.335	0.015
10	A	10	VAL	0	-0.029	-0.006	5.624	0.165	0.165	0.000	0.000	0.000	0.000
11	A	11	TYR	0	-0.069	-0.072	7.420	0.058	0.058	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.857	-0.920	8.390	-0.531	-0.531	0.000	0.000	0.000	0.000
13	A	13	ALA	0	0.009	0.000	8.555	0.065	0.065	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.058	-0.045	10.382	0.050	0.050	0.000	0.000	0.000	0.000
15	A	15	CYS	0	-0.061	-0.044	13.035	0.030	0.030	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.893	-0.931	11.912	-0.215	-0.215	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.090	-0.029	14.542	0.024	0.024	0.000	0.000	0.000	0.000
18	A	18	PRO	0	-0.006	0.010	17.211	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	19	TYR	0	0.027	-0.001	20.822	0.006	0.006	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.053	0.040	23.552	0.003	0.003	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.862	0.935	21.049	0.043	0.043	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.017	0.005	19.801	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	23	SER	0	0.044	0.009	14.519	0.009	0.009	0.000	0.000	0.000	0.000
24	A	24	THR	0	-0.014	-0.008	15.477	0.007	0.007	0.000	0.000	0.000	0.000
25	A	25	TYR	0	0.011	0.012	13.164	0.004	0.004	0.000	0.000	0.000	0.000
26	A	26	GLY	0	-0.007	-0.018	11.741	0.034	0.034	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.854	-0.937	11.879	0.061	0.061	0.000	0.000	0.000	0.000
28	A	28	ILE	0	0.048	0.031	8.660	0.004	0.004	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.007	-0.002	7.548	-0.045	-0.045	0.000	0.000	0.000	0.000
30	A	30	ARG	1	0.842	0.916	7.169	0.006	0.006	0.000	0.000	0.000	0.000
31	A	31	TYR	0	-0.049	-0.008	8.160	0.028	0.028	0.000	0.000	0.000	0.000
32	A	32	VAL	0	-0.015	-0.003	3.649	-0.265	-0.063	0.002	-0.028	-0.176	0.000
33	A	33	GLY	0	-0.018	0.004	3.580	-0.803	-0.413	0.010	-0.174	-0.226	-0.001
34	A	34	MET	0	-0.054	-0.035	3.581	1.084	1.513	2.186	-0.565	-2.050	0.000
35	A	35	PRO	0	0.051	0.009	6.439	-0.197	-0.197	0.000	0.000	0.000	0.000
36	A	36	SER	0	-0.020	-0.005	9.783	-0.044	-0.044	0.000	0.000	0.000	0.000
37	A	37	TYR	0	-0.028	-0.010	6.134	0.073	0.073	0.000	0.000	0.000	0.000
38	A	38	ALA	0	0.049	0.019	9.449	-0.032	-0.032	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.958	0.959	12.198	-0.097	-0.097	0.000	0.000	0.000	0.000
40	A	40	GLN	0	0.061	0.033	8.835	0.021	0.021	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.055	0.046	8.615	-0.047	-0.047	0.000	0.000	0.000	0.000
42	A	42	GLY	0	-0.006	-0.006	10.641	-0.066	-0.066	0.000	0.000	0.000	0.000
43	A	43	GLN	0	-0.049	-0.034	12.058	-0.030	-0.030	0.000	0.000	0.000	0.000
44	A	44	ALA	0	0.038	0.030	9.995	-0.040	-0.040	0.000	0.000	0.000	0.000
45	A	45	MET	0	0.000	0.021	11.954	-0.043	-0.043	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.920	0.961	15.000	0.034	0.034	0.000	0.000	0.000	0.000
47	A	47	HIS	0	-0.076	-0.052	13.333	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	48	LEU	0	-0.003	0.030	14.265	-0.019	-0.019	0.000	0.000	0.000	0.000
49	A	49	HIS	0	0.048	0.033	16.867	0.021	0.021	0.000	0.000	0.000	0.000
50	A	50	PRO	0	-0.025	-0.027	19.995	0.001	0.001	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.919	-0.968	22.866	-0.110	-0.110	0.000	0.000	0.000	0.000
52	A	52	THR	0	-0.054	-0.001	16.901	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	53	HIS	0	0.023	0.004	19.151	0.014	0.014	0.000	0.000	0.000	0.000
54	A	54	VAL	0	0.007	0.001	13.988	0.000	0.000	0.000	0.000	0.000	0.000
55	A	55	PRO	0	-0.008	0.014	16.216	0.015	0.015	0.000	0.000	0.000	0.000
56	A	56	TRP	0	0.037	-0.011	16.514	0.015	0.015	0.000	0.000	0.000	0.000
57	A	57	HIS	0	-0.071	-0.043	17.522	0.011	0.011	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.869	0.941	18.321	0.093	0.093	0.000	0.000	0.000	0.000
59	A	59	VAL	0	0.001	0.010	14.271	0.006	0.006	0.000	0.000	0.000	0.000
60	A	60	ILE	0	0.009	0.020	17.281	0.003	0.003	0.000	0.000	0.000	0.000
61	A	61	ASN	0	-0.017	-0.030	17.941	0.012	0.012	0.000	0.000	0.000	0.000
62	A	62	SER	0	0.042	-0.007	18.202	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	63	ARG	1	0.842	0.936	20.162	-0.014	-0.014	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.024	0.023	22.594	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	65	THR	0	-0.003	0.003	23.893	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	66	ILE	0	0.014	0.010	23.170	0.002	0.002	0.000	0.000	0.000	0.000
67	A	67	SER	0	-0.039	-0.024	19.964	0.002	0.002	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.919	0.975	23.112	0.003	0.003	0.000	0.000	0.000	0.000
69	A	69	ARG	1	0.752	0.869	21.166	0.031	0.031	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.845	-0.900	24.851	-0.031	-0.031	0.000	0.000	0.000	0.000
71	A	71	ILE	0	-0.024	-0.006	26.852	0.002	0.002	0.000	0.000	0.000	0.000
72	A	72	SER	0	0.059	0.001	28.503	0.003	0.003	0.000	0.000	0.000	0.000
73	A	73	ALA	0	0.028	0.009	28.916	0.000	0.000	0.000	0.000	0.000	0.000
74	A	74	GLY	0	-0.020	-0.015	24.940	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.836	-0.935	25.490	-0.017	-0.017	0.000	0.000	0.000	0.000
76	A	76	GLN	0	0.021	0.024	26.409	0.002	0.002	0.000	0.000	0.000	0.000
77	A	77	ARG	1	0.965	0.986	23.267	0.064	0.064	0.000	0.000	0.000	0.000
78	A	78	GLN	0	-0.040	-0.018	20.261	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	79	LYS	1	0.938	0.972	25.133	0.023	0.023	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.839	-0.916	28.024	-0.033	-0.033	0.000	0.000	0.000	0.000
81	A	81	ARG	1	0.925	0.963	22.490	0.073	0.073	0.000	0.000	0.000	0.000
82	A	82	LEU	0	-0.040	-0.023	22.829	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.874	-0.943	26.619	-0.026	-0.026	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.972	-0.977	29.466	-0.045	-0.045	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.888	-0.938	24.321	-0.067	-0.067	0.000	0.000	0.000	0.000
86	A	86	GLY	0	-0.027	-0.010	28.534	0.000	0.000	0.000	0.000	0.000	0.000
87	A	87	VAL	0	-0.060	-0.026	25.624	0.003	0.003	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.914	-0.959	29.065	-0.019	-0.019	0.000	0.000	0.000	0.000
89	A	89	ILE	0	-0.082	-0.029	27.368	0.002	0.002	0.000	0.000	0.000	0.000
90	A	90	TYR	0	0.011	0.003	31.147	0.001	0.001	0.000	0.000	0.000	0.000
91	A	91	GLN	0	-0.010	-0.011	32.332	0.002	0.002	0.000	0.000	0.000	0.000
92	A	92	THR	0	-0.023	-0.003	32.327	0.002	0.002	0.000	0.000	0.000	0.000
93	A	93	SER	0	0.072	0.025	34.961	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	94	LEU	0	-0.053	-0.027	33.744	0.000	0.000	0.000	0.000	0.000	0.000
95	A	95	GLY	0	0.027	0.019	34.311	0.000	0.000	0.000	0.000	0.000	0.000
96	A	96	GLU	-1	-0.922	-0.992	28.760	0.002	0.002	0.000	0.000	0.000	0.000
97	A	97	TYR	0	-0.020	-0.012	28.310	0.001	0.001	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.929	0.969	27.807	0.000	0.000	0.000	0.000	0.000	0.000
99	A	99	LEU	0	0.095	0.061	24.337	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	100	ASN	0	0.012	-0.005	27.949	0.003	0.003	0.000	0.000	0.000	0.000
101	A	101	LEU	0	0.042	0.011	21.249	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	102	PRO	0	-0.038	-0.034	24.413	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	103	GLU	-1	-0.918	-0.937	26.062	-0.020	-0.020	0.000	0.000	0.000	0.000
104	A	104	TYR	0	0.035	0.014	24.495	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	105	MET	0	-0.079	-0.014	17.018	-0.004	-0.004	0.000	0.000	0.000	0.000
106	A	106	TRP	0	0.006	-0.008	13.432	0.006	0.006	0.000	0.000	0.000	0.000
107	A	107	LYS	1	0.922	0.958	18.011	0.020	0.020	0.000	0.000	0.000	0.000
108	A	108	PRO	0	0.024	0.028	14.763	0.002	0.002	0.000	0.000	0.000	0.000

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Overview

Highlights

Manual

Support

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