FMO DATABASE

FMODB ID: KK1Q3

Calculation Name: 2J9C-A-Xray547

Preferred Name:

Target Type:

Ligand Name: adenosine-5'-triphosphate | acetate ion | 1,2-ethanediol | magnesium ion | chloride ion

Ligand 3-letter code: ATP | ACT | EDO | MG | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2J9C

Chain ID: A

ChEMBL ID:

UniProt ID: Q60381

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	117
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-876493.41116
FMO2-HF: Nuclear repulsion	831191.03335
FMO2-HF: Total energy	-45302.37781
FMO2-MP2: Total energy	-45435.236824

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:GLY)

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

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.
-203.767	-195.506	12.05	-11.099	-9.213	-0.13

Interaction energy analysis for fragmet #1(A:-1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.814 / q_NPA : 0.903

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	1	MET	0	0.057	0.039	3.841	-5.572	-4.716	-0.010	-0.479	-0.367	0.001
68	A	66	LYS	1	0.858	0.900	3.330	44.112	44.323	0.004	-0.059	-0.156	0.000
69	A	67	GLU	-1	-0.926	-0.968	2.045	-98.000	-93.360	5.589	-5.636	-4.594	-0.073
70	A	68	GLU	-1	-0.788	-0.912	2.168	-111.738	-109.220	6.468	-4.924	-4.062	-0.058
71	A	69	ASP	-1	-0.791	-0.881	5.134	-33.325	-33.289	-0.001	-0.001	-0.034	0.000
4	A	2	LYS	1	0.877	0.938	6.714	43.050	43.050	0.000	0.000	0.000	0.000
5	A	3	LYS	1	0.818	0.912	9.041	18.456	18.456	0.000	0.000	0.000	0.000
6	A	4	VAL	0	0.019	0.016	11.700	0.374	0.374	0.000	0.000	0.000	0.000
7	A	5	GLU	-1	-0.804	-0.900	14.156	-14.896	-14.896	0.000	0.000	0.000	0.000
8	A	6	ALA	0	0.017	0.013	17.895	0.284	0.284	0.000	0.000	0.000	0.000
9	A	7	ILE	0	-0.032	-0.016	20.370	0.479	0.479	0.000	0.000	0.000	0.000
10	A	8	ILE	0	0.045	0.016	23.346	0.072	0.072	0.000	0.000	0.000	0.000
11	A	9	ARG	1	0.823	0.897	26.163	10.338	10.338	0.000	0.000	0.000	0.000
12	A	10	PRO	0	0.013	0.009	28.940	-0.218	-0.218	0.000	0.000	0.000	0.000
13	A	11	GLU	-1	-0.902	-0.968	30.638	-9.807	-9.807	0.000	0.000	0.000	0.000
14	A	12	LYS	1	0.783	0.889	27.272	11.092	11.092	0.000	0.000	0.000	0.000
15	A	13	LEU	0	0.022	0.025	25.184	-0.400	-0.400	0.000	0.000	0.000	0.000
16	A	14	GLU	-1	-0.850	-0.923	25.872	-11.606	-11.606	0.000	0.000	0.000	0.000
17	A	15	ILE	0	0.017	0.004	26.485	-0.248	-0.248	0.000	0.000	0.000	0.000
18	A	16	VAL	0	0.017	0.015	21.524	-0.396	-0.396	0.000	0.000	0.000	0.000
19	A	17	LYS	1	0.897	0.939	21.763	11.271	11.271	0.000	0.000	0.000	0.000
20	A	18	LYS	1	0.760	0.885	22.073	12.181	12.181	0.000	0.000	0.000	0.000
21	A	19	ALA	0	0.056	0.027	22.271	-0.297	-0.297	0.000	0.000	0.000	0.000
22	A	20	LEU	0	-0.012	-0.008	16.440	-0.638	-0.638	0.000	0.000	0.000	0.000
23	A	21	SER	0	-0.052	-0.046	17.854	-0.602	-0.602	0.000	0.000	0.000	0.000
24	A	22	ASP	-1	-0.807	-0.882	19.596	-13.400	-13.400	0.000	0.000	0.000	0.000
25	A	23	ALA	0	-0.045	-0.011	16.724	-0.081	-0.081	0.000	0.000	0.000	0.000
26	A	24	GLY	0	0.032	0.020	15.582	-1.302	-1.302	0.000	0.000	0.000	0.000
27	A	25	TYR	0	-0.025	0.000	10.865	-0.218	-0.218	0.000	0.000	0.000	0.000
28	A	26	VAL	0	0.006	-0.020	15.149	0.919	0.919	0.000	0.000	0.000	0.000
29	A	27	GLY	0	-0.021	0.010	15.257	0.872	0.872	0.000	0.000	0.000	0.000
30	A	28	MET	0	-0.031	-0.015	15.535	-0.570	-0.570	0.000	0.000	0.000	0.000
31	A	29	THR	0	-0.044	-0.020	18.156	0.763	0.763	0.000	0.000	0.000	0.000
32	A	30	VAL	0	0.032	0.016	20.900	-0.248	-0.248	0.000	0.000	0.000	0.000
33	A	31	SER	0	-0.052	-0.029	23.989	0.232	0.232	0.000	0.000	0.000	0.000
34	A	32	GLU	-1	-0.883	-0.928	26.801	-10.776	-10.776	0.000	0.000	0.000	0.000
35	A	33	VAL	0	-0.028	-0.017	27.102	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	34	LYS	1	0.947	0.969	30.210	9.152	9.152	0.000	0.000	0.000	0.000
37	A	35	GLY	0	0.015	0.008	30.567	-0.206	-0.206	0.000	0.000	0.000	0.000
38	A	36	ARG	1	0.882	0.939	31.354	9.234	9.234	0.000	0.000	0.000	0.000
39	A	37	GLY	0	0.031	0.023	30.118	-0.354	-0.354	0.000	0.000	0.000	0.000
40	A	38	VAL	0	-0.013	-0.007	29.978	0.030	0.030	0.000	0.000	0.000	0.000
41	A	39	GLN	0	0.004	0.004	32.625	0.080	0.080	0.000	0.000	0.000	0.000
42	A	40	GLY	0	0.012	0.004	35.889	-0.099	-0.099	0.000	0.000	0.000	0.000
43	A	41	GLY	0	0.007	0.004	37.081	-0.184	-0.184	0.000	0.000	0.000	0.000
44	A	42	ILE	0	-0.021	-0.009	37.699	0.213	0.213	0.000	0.000	0.000	0.000
45	A	43	VAL	0	0.028	0.013	37.679	-0.253	-0.253	0.000	0.000	0.000	0.000
46	A	44	GLU	-1	-0.795	-0.892	33.490	-9.731	-9.731	0.000	0.000	0.000	0.000
47	A	45	ARG	1	0.914	0.950	37.516	7.611	7.611	0.000	0.000	0.000	0.000
48	A	46	TYR	0	0.016	0.005	35.417	-0.097	-0.097	0.000	0.000	0.000	0.000
49	A	47	ARG	1	0.946	0.959	38.381	8.567	8.567	0.000	0.000	0.000	0.000
50	A	48	GLY	0	0.042	0.035	41.928	0.141	0.141	0.000	0.000	0.000	0.000
51	A	49	ARG	1	0.767	0.871	42.761	7.715	7.715	0.000	0.000	0.000	0.000
52	A	50	GLU	-1	-0.854	-0.934	41.761	-7.471	-7.471	0.000	0.000	0.000	0.000
53	A	51	TYR	0	-0.037	-0.018	38.400	0.132	0.132	0.000	0.000	0.000	0.000
54	A	52	ILE	0	0.052	0.028	39.225	-0.107	-0.107	0.000	0.000	0.000	0.000
55	A	53	VAL	0	0.013	0.013	38.926	-0.214	-0.214	0.000	0.000	0.000	0.000
56	A	54	ASP	-1	-0.813	-0.886	39.538	-7.783	-7.783	0.000	0.000	0.000	0.000
57	A	55	LEU	0	-0.072	-0.036	33.688	-0.124	-0.124	0.000	0.000	0.000	0.000
58	A	56	ILE	0	0.010	0.006	33.871	0.204	0.204	0.000	0.000	0.000	0.000
59	A	57	PRO	0	-0.029	-0.021	33.285	-0.288	-0.288	0.000	0.000	0.000	0.000
60	A	58	LYS	1	0.777	0.863	28.399	10.248	10.248	0.000	0.000	0.000	0.000
61	A	59	VAL	0	0.054	0.042	25.455	0.126	0.126	0.000	0.000	0.000	0.000
62	A	60	LYS	1	0.832	0.910	21.723	13.806	13.806	0.000	0.000	0.000	0.000
63	A	61	ILE	0	0.023	0.001	19.418	0.344	0.344	0.000	0.000	0.000	0.000
64	A	62	GLU	-1	-0.869	-0.925	17.760	-16.586	-16.586	0.000	0.000	0.000	0.000
65	A	63	LEU	0	0.053	0.021	14.016	0.528	0.528	0.000	0.000	0.000	0.000
66	A	64	VAL	0	-0.039	-0.015	10.566	-0.737	-0.737	0.000	0.000	0.000	0.000
67	A	65	VAL	0	0.007	0.012	8.611	0.854	0.854	0.000	0.000	0.000	0.000
72	A	70	VAL	0	-0.039	-0.023	7.786	4.794	4.794	0.000	0.000	0.000	0.000
73	A	71	ASP	-1	-0.889	-0.953	9.797	-24.250	-24.250	0.000	0.000	0.000	0.000
74	A	72	ASN	0	0.019	0.002	11.708	3.163	3.163	0.000	0.000	0.000	0.000
75	A	73	VAL	0	-0.012	-0.004	12.022	1.780	1.780	0.000	0.000	0.000	0.000
76	A	74	ILE	0	-0.019	-0.020	13.529	1.761	1.761	0.000	0.000	0.000	0.000
77	A	75	ASP	-1	-0.893	-0.930	15.999	-15.015	-15.015	0.000	0.000	0.000	0.000
78	A	76	ILE	0	0.056	0.037	16.389	1.241	1.241	0.000	0.000	0.000	0.000
79	A	77	ILE	0	-0.022	-0.014	17.238	1.211	1.211	0.000	0.000	0.000	0.000
80	A	78	CYS	0	-0.092	-0.055	19.438	1.031	1.031	0.000	0.000	0.000	0.000
81	A	79	GLU	-1	-0.947	-0.969	21.946	-12.386	-12.386	0.000	0.000	0.000	0.000
82	A	80	ASN	0	-0.032	-0.026	22.446	1.160	1.160	0.000	0.000	0.000	0.000
83	A	81	ALA	0	0.031	0.006	24.173	0.661	0.661	0.000	0.000	0.000	0.000
84	A	82	ARG	1	0.912	0.980	25.900	11.662	11.662	0.000	0.000	0.000	0.000
85	A	83	THR	0	-0.105	-0.096	27.959	0.368	0.368	0.000	0.000	0.000	0.000
86	A	84	GLY	0	-0.051	-0.032	31.090	0.218	0.218	0.000	0.000	0.000	0.000
87	A	85	ASN	0	-0.039	-0.005	32.480	0.379	0.379	0.000	0.000	0.000	0.000
88	A	86	PRO	0	0.042	0.006	32.395	-0.361	-0.361	0.000	0.000	0.000	0.000
89	A	87	GLY	0	0.048	0.030	31.233	0.156	0.156	0.000	0.000	0.000	0.000
90	A	88	ASP	-1	-0.702	-0.798	27.878	-10.610	-10.610	0.000	0.000	0.000	0.000
91	A	89	GLY	0	0.037	0.009	25.521	-0.179	-0.179	0.000	0.000	0.000	0.000
92	A	90	LYS	1	0.862	0.939	22.384	12.732	12.732	0.000	0.000	0.000	0.000
93	A	91	ILE	0	0.046	0.027	16.825	0.066	0.066	0.000	0.000	0.000	0.000
94	A	92	PHE	0	-0.038	-0.015	17.758	0.491	0.491	0.000	0.000	0.000	0.000
95	A	93	VAL	0	0.046	0.025	11.052	-0.494	-0.494	0.000	0.000	0.000	0.000
96	A	94	ILE	0	-0.020	-0.004	13.328	0.783	0.783	0.000	0.000	0.000	0.000
97	A	95	PRO	0	-0.014	-0.005	10.691	-2.305	-2.305	0.000	0.000	0.000	0.000
98	A	96	VAL	0	0.009	-0.002	10.109	2.318	2.318	0.000	0.000	0.000	0.000
99	A	97	GLU	-1	-0.958	-0.972	9.236	-26.009	-26.009	0.000	0.000	0.000	0.000
100	A	98	ARG	1	0.804	0.853	9.933	18.862	18.862	0.000	0.000	0.000	0.000
101	A	99	VAL	0	0.032	0.013	10.688	1.002	1.002	0.000	0.000	0.000	0.000
102	A	100	VAL	0	0.017	0.014	12.933	-0.448	-0.448	0.000	0.000	0.000	0.000
103	A	101	ARG	1	0.822	0.917	14.962	20.503	20.503	0.000	0.000	0.000	0.000
104	A	102	VAL	0	-0.003	-0.014	17.651	0.672	0.672	0.000	0.000	0.000	0.000
105	A	103	ARG	1	0.860	0.934	20.728	14.802	14.802	0.000	0.000	0.000	0.000
106	A	104	THR	0	-0.051	-0.070	18.811	0.687	0.687	0.000	0.000	0.000	0.000
107	A	105	LYS	1	0.905	0.949	19.487	13.544	13.544	0.000	0.000	0.000	0.000
108	A	106	GLU	-1	-0.697	-0.788	15.140	-18.367	-18.367	0.000	0.000	0.000	0.000
109	A	107	GLU	-1	-0.792	-0.871	12.342	-21.515	-21.515	0.000	0.000	0.000	0.000
110	A	108	GLY	0	-0.012	0.004	9.545	-0.985	-0.985	0.000	0.000	0.000	0.000
111	A	109	LYS	0	-0.032	-0.025	6.527	-1.089	-1.089	0.000	0.000	0.000	0.000
112	A	110	GLU	-1	-0.833	-0.925	8.257	-21.246	-21.246	0.000	0.000	0.000	0.000
113	A	111	ALA	0	-0.065	-0.028	11.837	1.630	1.630	0.000	0.000	0.000	0.000
114	A	112	LEU	0	-0.058	-0.037	7.855	1.239	1.239	0.000	0.000	0.000	0.000
115	A	113	LEU	0	-0.045	-0.007	9.471	-0.343	-0.343	0.000	0.000	0.000	0.000
116	A	114	GLU	-1	-0.969	-0.980	12.808	-14.854	-14.854	0.000	0.000	0.000	0.000
117	A	115	HIS	-1	-0.898	-0.947	15.765	-17.132	-17.132	0.000	0.000	0.000	0.000

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