FMO DATABASE

FMODB ID: 9RVV2

Calculation Name: 5DN6-I-Xray547

Preferred Name:

Target Type:

Ligand Name: adenosine-5'-triphosphate | adenosine-5'-diphosphate

Ligand 3-letter code: ATP | ADP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5DN6

Chain ID: I

ChEMBL ID:

UniProt ID: A1B619

Base Structure: X-ray

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	75
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-388334.321554
FMO2-HF: Nuclear repulsion	361547.639379
FMO2-HF: Total energy	-26786.682176
FMO2-MP2: Total energy	-26865.45568

3D Structure Molmil

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:9:VAL)

Summations of interaction energy for fragment #1(A:9:VAL)

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.
-183.967	-175.475	18.026	-11.832	-14.685	-0.123

Interaction energy analysis for fragmet #1(A:9:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.768 / q_NPA : 0.883

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	11	PRO	0	0.020	-0.005	2.949	-0.415	2.043	0.259	-1.166	-1.551	-0.005
4	A	12	GLU	-1	-0.861	-0.890	5.154	-23.204	-23.101	-0.001	-0.004	-0.097	0.000
5	A	13	ARG	1	0.954	0.973	4.374	34.868	35.110	-0.001	-0.061	-0.181	0.000
6	A	14	ASN	0	0.018	-0.012	1.925	-36.547	-33.079	6.637	-5.265	-4.840	-0.040
7	A	15	LEU	0	-0.025	-0.009	2.583	8.823	8.347	0.318	1.079	-0.921	-0.003
8	A	16	VAL	0	0.044	0.019	3.476	7.739	8.083	0.010	-0.089	-0.265	0.000
9	A	17	SER	0	-0.039	-0.022	4.231	-8.610	-8.403	-0.001	-0.030	-0.175	0.000
69	A	77	THR	0	-0.043	-0.015	3.889	-3.469	-3.282	0.000	-0.025	-0.162	0.000
70	A	78	LEU	0	0.013	0.012	4.050	2.740	3.359	-0.001	-0.273	-0.346	-0.001
71	A	79	LEU	0	-0.038	-0.017	1.829	-49.260	-48.346	10.780	-6.085	-5.609	-0.074
72	A	80	ALA	0	0.019	0.003	3.404	11.275	11.701	0.026	0.087	-0.538	0.000
10	A	18	VAL	0	0.003	0.009	6.940	3.636	3.636	0.000	0.000	0.000	0.000
11	A	19	PRO	0	0.032	0.014	9.858	-1.341	-1.341	0.000	0.000	0.000	0.000
12	A	20	VAL	0	-0.015	0.002	9.983	0.358	0.358	0.000	0.000	0.000	0.000
13	A	21	ARG	1	0.945	0.984	12.666	16.002	16.002	0.000	0.000	0.000	0.000
14	A	22	GLU	-1	-0.875	-0.961	14.226	-17.277	-17.277	0.000	0.000	0.000	0.000
15	A	23	VAL	0	-0.051	-0.007	8.813	-1.091	-1.091	0.000	0.000	0.000	0.000
16	A	24	ARG	1	0.875	0.904	12.018	18.253	18.253	0.000	0.000	0.000	0.000
17	A	25	LEU	0	-0.017	-0.009	8.801	-1.570	-1.570	0.000	0.000	0.000	0.000
18	A	26	PRO	0	0.010	0.009	12.591	1.309	1.309	0.000	0.000	0.000	0.000
19	A	27	GLY	0	0.050	0.015	14.269	-0.897	-0.897	0.000	0.000	0.000	0.000
20	A	28	ALA	0	-0.065	-0.038	15.208	1.027	1.027	0.000	0.000	0.000	0.000
21	A	29	ASP	-1	-0.931	-0.967	17.469	-15.739	-15.739	0.000	0.000	0.000	0.000
22	A	30	GLY	0	-0.035	-0.020	18.630	1.037	1.037	0.000	0.000	0.000	0.000
23	A	31	ASP	-1	-0.894	-0.917	17.574	-18.341	-18.341	0.000	0.000	0.000	0.000
24	A	32	LEU	0	0.009	0.014	12.858	0.595	0.595	0.000	0.000	0.000	0.000
25	A	33	THR	0	-0.004	0.003	14.848	-1.060	-1.060	0.000	0.000	0.000	0.000
26	A	34	ALA	0	-0.024	-0.009	12.529	0.699	0.699	0.000	0.000	0.000	0.000
27	A	35	MET	0	0.036	0.013	14.177	-0.697	-0.697	0.000	0.000	0.000	0.000
28	A	36	PRO	0	-0.011	-0.021	15.313	-0.069	-0.069	0.000	0.000	0.000	0.000
29	A	37	GLY	0	-0.007	0.002	16.760	1.070	1.070	0.000	0.000	0.000	0.000
30	A	38	HIS	0	-0.016	0.004	16.518	0.620	0.620	0.000	0.000	0.000	0.000
31	A	39	ALA	0	-0.024	-0.017	17.020	-0.354	-0.354	0.000	0.000	0.000	0.000
32	A	40	PRO	0	-0.040	-0.033	14.832	-0.802	-0.802	0.000	0.000	0.000	0.000
33	A	41	ALA	0	-0.025	0.001	13.695	1.210	1.210	0.000	0.000	0.000	0.000
34	A	42	ILE	0	0.009	0.002	10.422	-1.756	-1.756	0.000	0.000	0.000	0.000
35	A	43	VAL	0	-0.010	0.004	11.364	1.816	1.816	0.000	0.000	0.000	0.000
36	A	44	ASN	0	0.010	0.008	11.162	-3.728	-3.728	0.000	0.000	0.000	0.000
37	A	45	LEU	0	0.001	0.004	9.503	1.103	1.103	0.000	0.000	0.000	0.000
38	A	46	ARG	1	0.936	0.977	12.627	16.620	16.620	0.000	0.000	0.000	0.000
39	A	47	PRO	0	0.001	-0.004	13.695	-0.917	-0.917	0.000	0.000	0.000	0.000
40	A	48	GLY	0	-0.048	-0.028	13.355	1.850	1.850	0.000	0.000	0.000	0.000
41	A	49	LEU	0	-0.052	-0.005	12.818	-1.510	-1.510	0.000	0.000	0.000	0.000
42	A	50	VAL	0	-0.001	-0.002	7.684	-0.222	-0.222	0.000	0.000	0.000	0.000
43	A	51	THR	0	0.023	0.025	10.993	0.446	0.446	0.000	0.000	0.000	0.000
44	A	52	VAL	0	-0.008	-0.019	9.148	-0.849	-0.849	0.000	0.000	0.000	0.000
45	A	53	VAL	0	0.021	0.027	11.898	0.993	0.993	0.000	0.000	0.000	0.000
46	A	54	ALA	0	0.040	0.005	12.637	-0.471	-0.471	0.000	0.000	0.000	0.000
47	A	55	GLY	0	-0.013	-0.023	13.938	1.372	1.372	0.000	0.000	0.000	0.000
48	A	56	ASP	-1	-0.946	-0.966	16.428	-14.757	-14.757	0.000	0.000	0.000	0.000
49	A	57	GLY	0	-0.060	-0.036	18.597	0.700	0.700	0.000	0.000	0.000	0.000
50	A	58	SER	0	-0.036	-0.010	16.879	0.579	0.579	0.000	0.000	0.000	0.000
51	A	59	GLU	-1	-0.922	-0.965	15.808	-18.695	-18.695	0.000	0.000	0.000	0.000
52	A	60	THR	0	-0.080	-0.034	12.394	-0.209	-0.209	0.000	0.000	0.000	0.000
53	A	61	GLU	-1	-0.865	-0.948	12.809	-19.251	-19.251	0.000	0.000	0.000	0.000
54	A	62	PHE	0	-0.027	-0.015	7.384	0.139	0.139	0.000	0.000	0.000	0.000
55	A	63	ALA	0	0.002	0.011	11.273	-0.028	-0.028	0.000	0.000	0.000	0.000
56	A	64	VAL	0	-0.028	-0.016	7.370	-2.078	-2.078	0.000	0.000	0.000	0.000
57	A	65	THR	0	-0.029	-0.053	10.020	1.293	1.293	0.000	0.000	0.000	0.000
58	A	66	GLY	0	0.069	0.031	10.224	2.460	2.460	0.000	0.000	0.000	0.000
59	A	67	GLY	0	0.016	0.016	7.939	-4.249	-4.249	0.000	0.000	0.000	0.000
60	A	68	PHE	0	0.005	-0.007	7.106	3.534	3.534	0.000	0.000	0.000	0.000
61	A	69	ALA	0	0.001	0.004	6.402	-6.986	-6.986	0.000	0.000	0.000	0.000
62	A	70	GLU	-1	-0.950	-0.971	7.105	-25.052	-25.052	0.000	0.000	0.000	0.000
63	A	71	ILE	0	0.006	0.001	8.414	-2.776	-2.776	0.000	0.000	0.000	0.000
64	A	72	ASN	0	0.012	-0.012	11.041	2.932	2.932	0.000	0.000	0.000	0.000
65	A	73	ASN	0	0.014	0.008	13.276	-0.284	-0.284	0.000	0.000	0.000	0.000
66	A	74	GLU	-1	-0.951	-0.956	13.765	-20.255	-20.255	0.000	0.000	0.000	0.000
67	A	75	SER	0	-0.017	-0.003	8.997	-1.758	-1.758	0.000	0.000	0.000	0.000
68	A	76	VAL	0	0.046	0.011	8.511	1.223	1.223	0.000	0.000	0.000	0.000
73	A	81	GLU	-1	-0.940	-0.972	5.629	-28.458	-28.458	0.000	0.000	0.000	0.000
74	A	82	ARG	1	0.774	0.859	8.455	24.293	24.293	0.000	0.000	0.000	0.000
75	A	83	GLY	-1	-0.819	-0.874	10.914	-21.549	-21.549	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:9:VAL)