FMO DATABASE

FMODB ID: LGL79

Calculation Name: 2QRD-A-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: 2QRD

Chain ID: A

ChEMBL ID:

UniProt ID: P78789

Base Structure: X-ray

Registration Date: 2025-10-04

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	114
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-912248.607209
FMO2-HF: Nuclear repulsion	864790.321778
FMO2-HF: Total energy	-47458.285431
FMO2-MP2: Total energy	-47591.929395

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:450:ASN)

Summations of interaction energy for fragment #1(A:450:ASN)

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.
49.692	51.287	-0.008	-0.756	-0.829	0

Interaction energy analysis for fragmet #1(A:450:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.881 / q_NPA : 0.919

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].
3	A	452	TRP	0	0.073	0.031	3.785	-7.804	-6.268	-0.007	-0.753	-0.775
8	A	457	ARG	1	0.917	0.962	4.326	43.407	43.466	-0.001	-0.003	-0.054
4	A	453	HIS	0	-0.097	-0.058	5.032	-4.601	-4.601	0.000	0.000	0.000
5	A	454	PHE	0	0.070	0.039	8.169	0.435	0.435	0.000	0.000	0.000
6	A	455	GLY	0	0.079	0.034	10.921	-1.103	-1.103	0.000	0.000	0.000
7	A	456	VAL	0	-0.024	-0.004	11.036	-2.592	-2.592	0.000	0.000	0.000
9	A	458	CYS	0	-0.018	0.001	11.308	0.772	0.772	0.000	0.000	0.000
10	A	459	ARG	1	0.956	0.972	12.766	20.464	20.464	0.000	0.000	0.000
11	A	460	GLY	0	0.027	0.033	16.150	0.302	0.302	0.000	0.000	0.000
12	A	461	ASP	-1	-0.828	-0.919	19.861	-12.271	-12.271	0.000	0.000	0.000
13	A	462	ALA	0	0.029	0.021	21.731	-0.206	-0.206	0.000	0.000	0.000
14	A	463	PRO	0	-0.021	-0.028	22.757	-0.118	-0.118	0.000	0.000	0.000
15	A	464	GLU	-1	-0.895	-0.940	23.303	-12.310	-12.310	0.000	0.000	0.000
16	A	465	ILE	0	-0.001	-0.005	18.055	-0.203	-0.203	0.000	0.000	0.000
17	A	466	LEU	0	-0.015	-0.001	21.258	-0.157	-0.157	0.000	0.000	0.000
18	A	467	LEU	0	-0.020	-0.011	23.827	0.203	0.203	0.000	0.000	0.000
19	A	468	ALA	0	0.013	0.006	21.272	0.226	0.226	0.000	0.000	0.000
20	A	469	VAL	0	0.006	0.003	20.007	-0.117	-0.117	0.000	0.000	0.000
21	A	470	TYR	0	-0.019	-0.026	22.535	0.136	0.136	0.000	0.000	0.000
22	A	471	ARG	1	0.965	0.982	25.302	11.402	11.402	0.000	0.000	0.000
23	A	472	ALA	0	-0.002	0.008	21.256	0.214	0.214	0.000	0.000	0.000
24	A	473	LEU	0	-0.008	-0.010	23.328	0.117	0.117	0.000	0.000	0.000
25	A	474	GLN	0	0.007	0.003	25.251	0.203	0.203	0.000	0.000	0.000
26	A	475	ARG	1	0.826	0.904	22.273	13.409	13.409	0.000	0.000	0.000
27	A	476	ALA	0	-0.038	-0.015	24.119	-0.070	-0.070	0.000	0.000	0.000
28	A	477	GLY	0	-0.013	0.005	26.200	0.139	0.139	0.000	0.000	0.000
29	A	478	ALA	0	-0.037	-0.006	26.536	0.309	0.309	0.000	0.000	0.000
30	A	479	GLN	0	0.019	0.014	28.594	0.375	0.375	0.000	0.000	0.000
31	A	480	PHE	0	0.015	-0.012	28.382	-0.284	-0.284	0.000	0.000	0.000
32	A	481	THR	0	0.021	0.026	29.959	0.284	0.284	0.000	0.000	0.000
33	A	482	VAL	0	0.020	0.015	30.608	-0.324	-0.324	0.000	0.000	0.000
34	A	483	PRO	0	0.027	0.020	30.239	0.208	0.208	0.000	0.000	0.000
35	A	484	LYS	1	0.997	0.996	32.929	8.025	8.025	0.000	0.000	0.000
36	A	485	PRO	0	0.001	0.010	35.924	-0.092	-0.092	0.000	0.000	0.000
37	A	486	VAL	0	0.039	0.023	36.861	0.292	0.292	0.000	0.000	0.000
38	A	487	ASN	0	-0.003	-0.015	39.223	0.020	0.020	0.000	0.000	0.000
39	A	488	GLY	0	0.044	0.019	41.321	0.116	0.116	0.000	0.000	0.000
40	A	489	LYS	1	0.889	0.953	37.470	7.408	7.408	0.000	0.000	0.000
41	A	490	TYR	0	0.016	0.001	32.910	0.030	0.030	0.000	0.000	0.000
42	A	491	ARG	1	0.884	0.949	32.339	9.142	9.142	0.000	0.000	0.000
43	A	492	SER	0	0.072	0.024	27.468	0.002	0.002	0.000	0.000	0.000
44	A	493	ASP	-1	-0.854	-0.927	27.317	-10.149	-10.149	0.000	0.000	0.000
45	A	494	MET	0	-0.028	-0.017	27.872	0.040	0.040	0.000	0.000	0.000
46	A	495	TYR	0	-0.029	-0.020	23.383	-0.086	-0.086	0.000	0.000	0.000
47	A	496	THR	0	-0.044	-0.036	23.737	-0.506	-0.506	0.000	0.000	0.000
48	A	497	ILE	0	-0.035	-0.008	24.132	0.513	0.513	0.000	0.000	0.000
49	A	498	LYS	1	0.874	0.924	25.714	10.454	10.454	0.000	0.000	0.000
50	A	499	SER	0	0.002	-0.016	25.486	0.155	0.155	0.000	0.000	0.000
51	A	500	ARG	1	0.887	0.943	27.923	9.073	9.073	0.000	0.000	0.000
52	A	501	TRP	0	0.040	0.001	22.295	0.074	0.074	0.000	0.000	0.000
53	A	502	GLU	-1	-0.843	-0.935	28.857	-8.990	-8.990	0.000	0.000	0.000
54	A	503	ILE	0	-0.012	0.003	28.487	-0.375	-0.375	0.000	0.000	0.000
55	A	504	PRO	0	0.019	-0.001	26.871	0.331	0.331	0.000	0.000	0.000
56	A	505	HIS	0	-0.061	-0.043	28.942	-0.011	-0.011	0.000	0.000	0.000
57	A	506	CYS	0	0.028	0.035	31.696	0.311	0.311	0.000	0.000	0.000
58	A	507	LYS	1	0.965	0.995	33.137	9.393	9.393	0.000	0.000	0.000
59	A	508	ARG	1	0.899	0.943	29.357	10.343	10.343	0.000	0.000	0.000
60	A	509	GLU	-1	-0.878	-0.935	34.545	-9.031	-9.031	0.000	0.000	0.000
61	A	510	GLY	0	0.009	0.016	38.044	0.196	0.196	0.000	0.000	0.000
62	A	511	LYS	1	0.897	0.947	35.160	9.022	9.022	0.000	0.000	0.000
63	A	512	ASN	0	0.018	0.014	36.474	-0.351	-0.351	0.000	0.000	0.000
64	A	513	THR	0	0.006	-0.013	32.844	0.068	0.068	0.000	0.000	0.000
65	A	514	TYR	0	-0.062	-0.028	31.511	-0.208	-0.208	0.000	0.000	0.000
66	A	515	ALA	0	0.007	0.001	26.278	-0.021	-0.021	0.000	0.000	0.000
67	A	516	TYR	0	-0.032	-0.020	28.037	0.174	0.174	0.000	0.000	0.000
68	A	517	ILE	0	0.006	0.007	21.806	-0.291	-0.291	0.000	0.000	0.000
69	A	518	GLU	-1	-0.807	-0.876	23.748	-11.491	-11.491	0.000	0.000	0.000
70	A	519	LEU	0	-0.013	-0.005	20.164	-0.748	-0.748	0.000	0.000	0.000
71	A	520	GLN	0	0.032	0.034	20.206	1.212	1.212	0.000	0.000	0.000
72	A	521	LEU	0	-0.020	-0.001	18.080	-0.975	-0.975	0.000	0.000	0.000
73	A	522	TYR	0	0.010	0.002	16.991	0.991	0.991	0.000	0.000	0.000
74	A	523	GLU	-1	-0.901	-0.958	17.133	-15.380	-15.380	0.000	0.000	0.000
75	A	524	VAL	0	-0.084	-0.043	12.075	-0.214	-0.214	0.000	0.000	0.000
76	A	525	MET	0	0.005	-0.006	12.168	0.078	0.078	0.000	0.000	0.000
77	A	526	PRO	0	0.088	0.048	17.110	-0.361	-0.361	0.000	0.000	0.000
78	A	527	GLY	0	0.007	0.017	18.306	-0.370	-0.370	0.000	0.000	0.000
79	A	528	CYS	0	-0.107	-0.058	13.213	-1.233	-1.233	0.000	0.000	0.000
80	A	529	PHE	0	0.064	0.026	14.628	0.335	0.335	0.000	0.000	0.000
81	A	530	MET	0	-0.044	-0.015	11.509	-1.504	-1.504	0.000	0.000	0.000
82	A	531	LEU	0	0.009	0.011	14.190	1.430	1.430	0.000	0.000	0.000
83	A	532	ASP	-1	-0.865	-0.948	15.316	-18.713	-18.713	0.000	0.000	0.000
84	A	533	VAL	0	-0.037	-0.021	16.648	0.962	0.962	0.000	0.000	0.000
85	A	534	LYS	1	0.905	0.963	18.222	12.231	12.231	0.000	0.000	0.000
86	A	535	SER	0	0.004	0.009	20.974	0.725	0.725	0.000	0.000	0.000
87	A	536	ASN	0	-0.062	-0.048	23.650	-0.134	-0.134	0.000	0.000	0.000
88	A	537	GLY	0	0.030	0.021	26.636	0.478	0.478	0.000	0.000	0.000
89	A	538	TYR	0	-0.056	-0.061	24.692	-0.225	-0.225	0.000	0.000	0.000
90	A	539	LYS	1	0.880	0.934	30.531	8.660	8.660	0.000	0.000	0.000
91	A	540	ASP	-1	-0.793	-0.890	34.267	-8.469	-8.469	0.000	0.000	0.000
92	A	541	ILE	0	-0.014	-0.006	36.948	0.027	0.027	0.000	0.000	0.000
93	A	542	TYR	0	-0.056	-0.029	40.115	0.195	0.195	0.000	0.000	0.000
94	A	543	SER	-1	-0.934	-0.955	40.065	-7.753	-7.753	0.000	0.000	0.000
95	A	557	LYS	1	0.995	0.974	27.383	10.260	10.260	0.000	0.000	0.000
96	A	558	SER	0	0.006	0.012	25.128	-0.558	-0.558	0.000	0.000	0.000
97	A	559	SER	0	0.034	0.025	19.720	-0.159	-0.159	0.000	0.000	0.000
98	A	560	PHE	0	0.006	0.022	18.667	-0.506	-0.506	0.000	0.000	0.000
99	A	561	PRO	0	0.072	0.032	23.316	0.505	0.505	0.000	0.000	0.000
100	A	562	PHE	0	0.008	-0.009	18.600	-0.233	-0.233	0.000	0.000	0.000
101	A	563	LEU	0	0.041	0.018	15.853	-0.371	-0.371	0.000	0.000	0.000
102	A	564	ASP	-1	-0.848	-0.923	18.210	-14.994	-14.994	0.000	0.000	0.000
103	A	565	LEU	0	-0.033	-0.016	20.543	-0.040	-0.040	0.000	0.000	0.000
104	A	566	CYS	0	-0.020	-0.006	16.535	-0.112	-0.112	0.000	0.000	0.000
105	A	567	ALA	0	-0.006	0.003	15.938	-0.656	-0.656	0.000	0.000	0.000
106	A	568	MET	0	-0.016	0.000	16.971	0.021	0.021	0.000	0.000	0.000
107	A	569	LEU	0	0.019	-0.002	18.487	0.171	0.171	0.000	0.000	0.000
108	A	570	VAL	0	0.007	0.004	12.719	0.008	0.008	0.000	0.000	0.000
109	A	571	CYS	0	-0.035	-0.020	16.023	-0.210	-0.210	0.000	0.000	0.000
110	A	572	LYS	1	0.858	0.961	17.850	13.200	13.200	0.000	0.000	0.000
111	A	573	LEU	0	0.006	0.003	16.512	0.515	0.515	0.000	0.000	0.000
112	A	574	PHE	0	-0.059	-0.040	11.219	-0.245	-0.245	0.000	0.000	0.000
113	A	575	SER	0	-0.024	-0.021	16.785	0.234	0.234	0.000	0.000	0.000
114	A	576	ALA	-1	-0.923	-0.941	19.936	-12.408	-12.408	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:450:ASN)