FMO DATABASE

FMODB ID: Y1222

Calculation Name: 1F9A-A-Xray547

Preferred Name:

Target Type:

Ligand Name: adenosine-5'-triphosphate | magnesium ion

Ligand 3-letter code: ATP | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1F9A

Chain ID: A

ChEMBL ID:

UniProt ID: Q57961

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	164
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1769313.073706
FMO2-HF: Nuclear repulsion	1703445.870768
FMO2-HF: Total energy	-65867.202937
FMO2-MP2: Total energy	-66063.148806

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:1:LEU)

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

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.
-250.384	-241.38	22.359	-15.649	-15.714	-0.176

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.763 / q_NPA : 0.871

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	GLY	0	0.058	0.039	3.868	2.919	4.461	-0.017	-0.679	-0.846	0.000
26	A	26	GLU	-1	-0.902	-0.918	4.321	-28.922	-28.796	-0.001	-0.014	-0.111	0.000
27	A	27	VAL	0	-0.071	-0.038	2.573	-10.800	-8.100	1.233	-1.200	-2.734	-0.012
28	A	28	ASP	-1	-0.797	-0.871	1.709	-111.964	-112.173	15.186	-9.205	-5.772	-0.113
29	A	29	GLU	-1	-0.811	-0.880	4.474	-34.312	-33.974	-0.001	-0.042	-0.294	0.000
93	A	93	ASP	-1	-0.826	-0.903	2.251	-76.629	-72.871	5.814	-4.378	-5.194	-0.051
94	A	94	ILE	0	0.001	0.007	2.802	4.604	5.353	0.145	-0.131	-0.763	0.000
4	A	4	PHE	0	-0.010	-0.005	6.039	2.755	2.755	0.000	0.000	0.000	0.000
5	A	5	ILE	0	0.010	0.008	9.421	1.496	1.496	0.000	0.000	0.000	0.000
6	A	6	ILE	0	-0.019	0.000	12.605	0.459	0.459	0.000	0.000	0.000	0.000
7	A	7	GLY	0	-0.027	-0.013	16.120	0.545	0.545	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.814	0.903	19.563	11.338	11.338	0.000	0.000	0.000	0.000
9	A	9	PHE	0	0.012	0.006	17.113	0.448	0.448	0.000	0.000	0.000	0.000
10	A	10	GLN	0	-0.035	0.017	23.318	0.107	0.107	0.000	0.000	0.000	0.000
11	A	11	PRO	0	-0.003	-0.012	26.897	0.358	0.358	0.000	0.000	0.000	0.000
12	A	12	PHE	0	0.047	0.017	18.197	-0.024	-0.024	0.000	0.000	0.000	0.000
13	A	13	HIS	0	0.030	0.003	22.437	0.496	0.496	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.919	0.939	21.826	10.739	10.739	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.003	0.007	20.868	-0.427	-0.427	0.000	0.000	0.000	0.000
16	A	16	HIS	0	-0.013	-0.007	18.453	-0.469	-0.469	0.000	0.000	0.000	0.000
17	A	17	LEU	0	0.042	0.015	17.000	-0.871	-0.871	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.871	-0.919	16.553	-16.256	-16.256	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.034	-0.014	13.535	-0.713	-0.713	0.000	0.000	0.000	0.000
20	A	20	ILE	0	-0.011	-0.008	12.536	-1.180	-1.180	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.883	0.927	11.631	14.330	14.330	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.905	0.950	11.744	17.309	17.309	0.000	0.000	0.000	0.000
23	A	23	ILE	0	-0.018	-0.012	7.500	-0.614	-0.614	0.000	0.000	0.000	0.000
24	A	24	ALA	0	0.005	0.006	7.059	-3.680	-3.680	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.972	-0.974	8.213	-21.776	-21.776	0.000	0.000	0.000	0.000
30	A	30	ILE	0	-0.014	-0.009	6.367	-2.855	-2.855	0.000	0.000	0.000	0.000
31	A	31	ILE	0	-0.016	-0.004	8.171	3.332	3.332	0.000	0.000	0.000	0.000
32	A	32	ILE	0	-0.019	-0.010	11.134	0.719	0.719	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.069	0.016	14.485	1.014	1.014	0.000	0.000	0.000	0.000
34	A	34	ILE	0	-0.038	-0.028	16.363	0.814	0.814	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.055	0.030	20.044	0.343	0.343	0.000	0.000	0.000	0.000
36	A	36	SER	0	-0.030	-0.059	21.427	0.458	0.458	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.046	-0.002	23.548	0.497	0.497	0.000	0.000	0.000	0.000
38	A	38	GLN	0	0.019	-0.005	25.438	-0.126	-0.126	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.848	0.932	28.354	11.157	11.157	0.000	0.000	0.000	0.000
40	A	40	SER	0	0.008	0.006	29.530	-0.215	-0.215	0.000	0.000	0.000	0.000
41	A	41	HIS	0	-0.018	-0.026	32.258	0.323	0.323	0.000	0.000	0.000	0.000
42	A	42	THR	0	0.053	0.034	33.389	0.269	0.269	0.000	0.000	0.000	0.000
43	A	43	LEU	0	0.070	0.031	34.110	-0.317	-0.317	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.853	-0.935	30.112	-10.414	-10.414	0.000	0.000	0.000	0.000
45	A	45	ASN	0	-0.060	-0.028	28.162	-0.815	-0.815	0.000	0.000	0.000	0.000
46	A	46	PRO	0	0.042	0.044	30.690	0.082	0.082	0.000	0.000	0.000	0.000
47	A	47	PHE	0	0.017	-0.001	28.639	0.167	0.167	0.000	0.000	0.000	0.000
48	A	48	THR	0	0.076	0.028	28.974	-0.275	-0.275	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.016	0.016	24.528	-0.208	-0.208	0.000	0.000	0.000	0.000
50	A	50	GLY	0	0.054	0.025	24.875	-0.434	-0.434	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.702	-0.827	26.310	-10.295	-10.295	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.736	0.859	23.625	12.231	12.231	0.000	0.000	0.000	0.000
53	A	53	ILE	0	0.041	0.023	21.059	-0.379	-0.379	0.000	0.000	0.000	0.000
54	A	54	LEU	0	0.006	0.032	22.307	-0.569	-0.569	0.000	0.000	0.000	0.000
55	A	55	MET	0	-0.037	-0.016	24.383	-0.011	-0.011	0.000	0.000	0.000	0.000
56	A	56	ILE	0	-0.007	0.013	17.990	-0.045	-0.045	0.000	0.000	0.000	0.000
57	A	57	THR	0	0.036	-0.003	19.676	-0.644	-0.644	0.000	0.000	0.000	0.000
58	A	58	GLN	0	-0.029	-0.029	20.743	-0.114	-0.114	0.000	0.000	0.000	0.000
59	A	59	SER	0	-0.071	-0.058	20.838	0.468	0.468	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.018	-0.008	15.234	0.009	0.009	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.868	0.956	17.361	12.735	12.735	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-1.008	-0.995	19.282	-14.235	-14.235	0.000	0.000	0.000	0.000
63	A	63	TYR	0	-0.003	-0.001	12.613	0.207	0.207	0.000	0.000	0.000	0.000
64	A	64	ASP	-1	-0.931	-0.952	13.364	-23.106	-23.106	0.000	0.000	0.000	0.000
65	A	65	LEU	0	0.004	0.002	10.062	-1.485	-1.485	0.000	0.000	0.000	0.000
66	A	66	THR	0	0.034	0.026	8.493	2.833	2.833	0.000	0.000	0.000	0.000
67	A	67	TYR	0	0.007	-0.021	9.771	-1.795	-1.795	0.000	0.000	0.000	0.000
68	A	68	TYR	0	-0.019	-0.038	8.579	3.613	3.613	0.000	0.000	0.000	0.000
69	A	69	PRO	0	-0.022	-0.006	13.789	0.086	0.086	0.000	0.000	0.000	0.000
70	A	70	ILE	0	0.037	0.022	13.902	0.984	0.984	0.000	0.000	0.000	0.000
71	A	71	PRO	0	-0.062	-0.028	17.863	0.277	0.277	0.000	0.000	0.000	0.000
72	A	72	ILE	0	0.021	0.032	16.366	0.212	0.212	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.928	0.952	20.955	12.680	12.680	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.774	-0.865	23.685	-12.147	-12.147	0.000	0.000	0.000	0.000
75	A	75	ILE	0	0.016	-0.002	23.388	0.316	0.316	0.000	0.000	0.000	0.000
76	A	76	GLU	-1	-0.913	-0.945	26.170	-10.542	-10.542	0.000	0.000	0.000	0.000
77	A	77	PHE	0	-0.011	-0.018	26.317	0.276	0.276	0.000	0.000	0.000	0.000
78	A	78	ASN	0	0.055	0.012	23.545	-0.567	-0.567	0.000	0.000	0.000	0.000
79	A	79	SER	0	0.027	0.014	22.460	-0.425	-0.425	0.000	0.000	0.000	0.000
80	A	80	ILE	0	-0.010	-0.003	22.204	-0.292	-0.292	0.000	0.000	0.000	0.000
81	A	81	TRP	0	-0.022	0.001	16.691	-0.675	-0.675	0.000	0.000	0.000	0.000
82	A	82	VAL	0	0.036	0.018	14.771	-0.224	-0.224	0.000	0.000	0.000	0.000
83	A	83	SER	0	0.044	0.033	16.391	-0.574	-0.574	0.000	0.000	0.000	0.000
84	A	84	TYR	0	-0.037	-0.007	18.289	-0.045	-0.045	0.000	0.000	0.000	0.000
85	A	85	VAL	0	0.021	-0.002	14.019	-0.122	-0.122	0.000	0.000	0.000	0.000
86	A	86	GLU	-1	-0.836	-0.884	12.944	-20.638	-20.638	0.000	0.000	0.000	0.000
87	A	87	SER	0	-0.056	-0.039	14.601	-0.275	-0.275	0.000	0.000	0.000	0.000
88	A	88	LEU	0	-0.096	-0.042	16.710	0.511	0.511	0.000	0.000	0.000	0.000
89	A	89	THR	0	-0.064	-0.052	11.738	-0.584	-0.584	0.000	0.000	0.000	0.000
90	A	90	PRO	0	0.017	0.015	8.699	0.207	0.207	0.000	0.000	0.000	0.000
91	A	91	PRO	0	0.012	0.003	7.502	-0.979	-0.979	0.000	0.000	0.000	0.000
92	A	92	PHE	0	-0.004	-0.004	5.045	-5.289	-5.289	0.000	0.000	0.000	0.000
95	A	95	VAL	0	-0.010	0.000	5.783	-0.177	-0.177	0.000	0.000	0.000	0.000
96	A	96	TYR	0	-0.023	-0.039	5.762	1.100	1.100	0.000	0.000	0.000	0.000
97	A	97	SER	0	-0.009	-0.026	11.359	1.490	1.490	0.000	0.000	0.000	0.000
98	A	98	GLY	0	-0.009	-0.008	14.964	0.186	0.186	0.000	0.000	0.000	0.000
99	A	99	ASN	0	-0.047	-0.022	18.249	0.676	0.676	0.000	0.000	0.000	0.000
100	A	100	PRO	0	0.056	0.009	19.028	-0.507	-0.507	0.000	0.000	0.000	0.000
101	A	101	LEU	0	0.021	0.030	20.699	-0.112	-0.112	0.000	0.000	0.000	0.000
102	A	102	VAL	0	-0.007	-0.012	15.469	-0.249	-0.249	0.000	0.000	0.000	0.000
103	A	103	ARG	1	0.837	0.922	14.607	16.057	16.057	0.000	0.000	0.000	0.000
104	A	104	VAL	0	0.029	0.019	16.532	-0.533	-0.533	0.000	0.000	0.000	0.000
105	A	105	LEU	0	0.005	0.000	18.467	-0.141	-0.141	0.000	0.000	0.000	0.000
106	A	106	PHE	0	0.009	-0.004	12.697	-0.216	-0.216	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.822	-0.912	13.866	-17.296	-17.296	0.000	0.000	0.000	0.000
108	A	108	GLU	-1	-0.966	-0.985	15.118	-13.126	-13.126	0.000	0.000	0.000	0.000
109	A	109	ARG	1	0.842	0.921	14.960	15.580	15.580	0.000	0.000	0.000	0.000
110	A	110	GLY	0	0.010	0.016	12.907	-0.661	-0.661	0.000	0.000	0.000	0.000
111	A	111	TYR	0	-0.065	-0.056	8.548	-1.546	-1.546	0.000	0.000	0.000	0.000
112	A	112	GLU	-1	-0.894	-0.949	6.208	-26.282	-26.282	0.000	0.000	0.000	0.000
113	A	113	VAL	0	-0.041	-0.020	9.146	-1.082	-1.082	0.000	0.000	0.000	0.000
114	A	114	LYS	1	0.909	0.963	6.206	30.434	30.434	0.000	0.000	0.000	0.000
115	A	115	ARG	1	0.897	0.940	11.401	14.706	14.706	0.000	0.000	0.000	0.000
116	A	116	PRO	0	0.019	0.017	13.357	-0.550	-0.550	0.000	0.000	0.000	0.000
117	A	117	GLU	-1	-0.822	-0.902	14.355	-15.963	-15.963	0.000	0.000	0.000	0.000
118	A	118	MET	0	-0.067	-0.038	16.506	0.015	0.015	0.000	0.000	0.000	0.000
119	A	119	PHE	0	0.089	0.045	16.047	0.800	0.800	0.000	0.000	0.000	0.000
120	A	120	ASN	0	-0.040	-0.040	21.508	0.333	0.333	0.000	0.000	0.000	0.000
121	A	121	ARG	1	0.968	0.975	23.321	12.377	12.377	0.000	0.000	0.000	0.000
122	A	122	LYS	1	0.957	0.984	25.604	9.576	9.576	0.000	0.000	0.000	0.000
123	A	123	GLU	-1	-0.786	-0.890	28.418	-9.440	-9.440	0.000	0.000	0.000	0.000
124	A	124	TYR	0	0.012	0.003	23.174	0.170	0.170	0.000	0.000	0.000	0.000
125	A	125	SER	0	-0.029	-0.030	24.947	-0.353	-0.353	0.000	0.000	0.000	0.000
126	A	126	GLY	0	0.071	0.039	26.391	0.242	0.242	0.000	0.000	0.000	0.000
127	A	127	THR	0	0.014	-0.004	27.999	0.153	0.153	0.000	0.000	0.000	0.000
128	A	128	GLU	-1	-0.792	-0.848	30.521	-8.733	-8.733	0.000	0.000	0.000	0.000
129	A	129	ILE	0	-0.005	-0.006	27.709	0.265	0.265	0.000	0.000	0.000	0.000
130	A	130	ARG	1	0.889	0.943	28.635	10.513	10.513	0.000	0.000	0.000	0.000
131	A	131	ARG	1	0.919	0.953	33.560	8.941	8.941	0.000	0.000	0.000	0.000
132	A	132	ARG	1	0.804	0.904	33.483	9.364	9.364	0.000	0.000	0.000	0.000
133	A	133	MET	0	-0.022	-0.006	33.327	0.114	0.114	0.000	0.000	0.000	0.000
134	A	134	LEU	0	-0.031	-0.005	36.882	0.211	0.211	0.000	0.000	0.000	0.000
135	A	135	ASN	0	-0.004	-0.015	39.369	0.348	0.348	0.000	0.000	0.000	0.000
136	A	136	GLY	0	-0.029	-0.003	40.299	0.188	0.188	0.000	0.000	0.000	0.000
137	A	137	GLU	-1	-0.939	-0.954	38.413	-7.996	-7.996	0.000	0.000	0.000	0.000
138	A	138	LYS	1	0.940	0.950	36.669	7.701	7.701	0.000	0.000	0.000	0.000
139	A	139	TRP	0	0.107	0.030	30.943	-0.232	-0.232	0.000	0.000	0.000	0.000
140	A	140	GLU	-1	-0.910	-0.953	31.487	-9.315	-9.315	0.000	0.000	0.000	0.000
141	A	141	HIS	0	-0.038	-0.011	30.642	-0.254	-0.254	0.000	0.000	0.000	0.000
142	A	142	LEU	0	-0.023	-0.001	28.396	-0.299	-0.299	0.000	0.000	0.000	0.000
143	A	143	VAL	0	-0.004	0.001	25.952	-0.522	-0.522	0.000	0.000	0.000	0.000
144	A	144	PRO	0	0.061	0.026	22.808	0.311	0.311	0.000	0.000	0.000	0.000
145	A	145	LYS	1	0.976	0.979	25.654	10.018	10.018	0.000	0.000	0.000	0.000
146	A	146	ALA	0	0.106	0.065	25.150	0.291	0.291	0.000	0.000	0.000	0.000
147	A	147	VAL	0	-0.024	-0.014	25.004	0.137	0.137	0.000	0.000	0.000	0.000
148	A	148	VAL	0	-0.046	-0.021	27.686	0.299	0.299	0.000	0.000	0.000	0.000
149	A	149	ASP	-1	-0.916	-0.953	30.375	-9.932	-9.932	0.000	0.000	0.000	0.000
150	A	150	VAL	0	0.040	0.019	27.589	0.278	0.278	0.000	0.000	0.000	0.000
151	A	151	ILE	0	-0.047	-0.024	29.617	0.264	0.264	0.000	0.000	0.000	0.000
152	A	152	LYS	1	0.937	0.957	32.662	8.899	8.899	0.000	0.000	0.000	0.000
153	A	153	GLU	-1	-0.936	-0.951	31.941	-9.890	-9.890	0.000	0.000	0.000	0.000
154	A	154	ILE	0	-0.049	-0.029	30.973	0.229	0.229	0.000	0.000	0.000	0.000
155	A	155	LYS	1	0.859	0.924	34.912	7.991	7.991	0.000	0.000	0.000	0.000
156	A	156	GLY	0	0.013	0.004	34.259	0.134	0.134	0.000	0.000	0.000	0.000
157	A	157	VAL	0	0.000	-0.020	35.285	0.031	0.031	0.000	0.000	0.000	0.000
158	A	158	GLU	-1	-0.870	-0.928	37.592	-7.529	-7.529	0.000	0.000	0.000	0.000
159	A	159	ARG	1	0.780	0.859	33.143	9.527	9.527	0.000	0.000	0.000	0.000
160	A	160	LEU	0	-0.009	-0.015	34.464	0.060	0.060	0.000	0.000	0.000	0.000
161	A	161	ARG	1	0.882	0.923	37.967	7.848	7.848	0.000	0.000	0.000	0.000
162	A	162	LYS	1	0.928	0.979	41.547	7.505	7.505	0.000	0.000	0.000	0.000
163	A	163	LEU	0	-0.075	-0.023	37.369	0.045	0.045	0.000	0.000	0.000	0.000
164	A	164	ALA	-1	-0.927	-0.941	41.063	-7.226	-7.226	0.000	0.000	0.000	0.000

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