FMO DATABASE

FMODB ID: YRJZ2

Calculation Name: 3JSR-A-Xray547

Preferred Name:

Target Type:

Ligand Name: potassium ion

Ligand 3-letter code: K

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3JSR

Chain ID: A

ChEMBL ID:

UniProt ID: Q8Z082

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	108
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-880085.943186
FMO2-HF: Nuclear repulsion	836425.780642
FMO2-HF: Total energy	-43660.162544
FMO2-MP2: Total energy	-43788.692791

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: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.
-103.921	-102.236	-0.007	-0.78	-0.898	0

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 : 1 / q_Mulliken : 0.879 / q_NPA : 0.927

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	3	MET	0	0.026	0.040	3.581	-5.382	-3.801	-0.005	-0.762	-0.814
96	A	96	PRO	0	-0.032	-0.033	4.311	-1.685	-1.598	-0.001	-0.014	-0.072
97	A	97	SER	0	-0.005	-0.002	5.067	-7.244	-7.227	-0.001	-0.004	-0.012
4	A	4	GLN	0	-0.038	-0.029	5.924	2.480	2.480	0.000	0.000	0.000
5	A	5	THR	0	0.040	0.024	9.127	-1.219	-1.219	0.000	0.000	0.000
6	A	6	TYR	0	-0.035	-0.021	9.080	-0.377	-0.377	0.000	0.000	0.000
7	A	7	TYR	0	0.038	0.015	14.188	0.371	0.371	0.000	0.000	0.000
8	A	8	TYR	0	0.021	0.004	17.967	-0.270	-0.270	0.000	0.000	0.000
9	A	9	VAL	0	0.014	0.001	20.140	0.474	0.474	0.000	0.000	0.000
10	A	10	LEU	0	-0.016	-0.007	23.114	-0.278	-0.278	0.000	0.000	0.000
11	A	11	ALA	0	0.052	0.023	24.943	0.460	0.460	0.000	0.000	0.000
12	A	12	SER	0	0.064	0.028	27.503	-0.296	-0.296	0.000	0.000	0.000
13	A	13	ARG	1	0.925	0.953	27.545	11.035	11.035	0.000	0.000	0.000
14	A	14	ARG	1	0.836	0.906	29.848	8.321	8.321	0.000	0.000	0.000
15	A	15	PHE	0	0.036	0.017	31.471	0.171	0.171	0.000	0.000	0.000
16	A	16	LEU	0	0.053	0.021	26.794	0.115	0.115	0.000	0.000	0.000
17	A	17	LEU	0	-0.031	-0.024	28.189	-0.059	-0.059	0.000	0.000	0.000
18	A	18	GLN	0	-0.081	-0.037	32.412	0.279	0.279	0.000	0.000	0.000
19	A	19	GLU	-1	-0.856	-0.910	35.808	-7.930	-7.930	0.000	0.000	0.000
20	A	20	GLU	-1	-0.835	-0.891	34.195	-8.532	-8.532	0.000	0.000	0.000
21	A	21	PRO	0	-0.025	0.000	33.232	-0.363	-0.363	0.000	0.000	0.000
22	A	22	ILE	0	0.025	-0.006	28.083	0.024	0.024	0.000	0.000	0.000
23	A	23	GLU	-1	-0.959	-0.972	30.191	-9.836	-9.836	0.000	0.000	0.000
24	A	24	GLU	-1	-0.776	-0.899	30.849	-9.149	-9.149	0.000	0.000	0.000
25	A	25	VAL	0	-0.008	0.004	29.161	-0.035	-0.035	0.000	0.000	0.000
26	A	26	LEU	0	0.011	0.004	24.767	-0.288	-0.288	0.000	0.000	0.000
27	A	27	LYS	1	0.838	0.934	27.655	8.697	8.697	0.000	0.000	0.000
28	A	28	GLU	-1	-0.798	-0.865	30.158	-9.578	-9.578	0.000	0.000	0.000
29	A	29	ARG	1	0.881	0.956	23.350	12.738	12.738	0.000	0.000	0.000
30	A	30	THR	0	-0.018	-0.033	25.603	-0.434	-0.434	0.000	0.000	0.000
31	A	31	ARG	1	0.714	0.818	27.118	9.379	9.379	0.000	0.000	0.000
32	A	32	HIS	0	-0.053	-0.037	28.742	-0.178	-0.178	0.000	0.000	0.000
33	A	33	TYR	0	-0.072	-0.101	21.450	0.103	0.103	0.000	0.000	0.000
34	A	34	HIS	0	-0.016	0.004	26.509	-0.434	-0.434	0.000	0.000	0.000
35	A	35	GLU	-1	-0.815	-0.884	28.065	-9.445	-9.445	0.000	0.000	0.000
36	A	36	GLN	0	-0.076	-0.034	27.521	0.482	0.482	0.000	0.000	0.000
37	A	37	GLU	-1	-0.975	-0.975	26.469	-11.370	-11.370	0.000	0.000	0.000
38	A	38	LYS	1	0.818	0.923	21.289	13.704	13.704	0.000	0.000	0.000
39	A	39	GLU	-1	-0.936	-0.972	15.848	-19.634	-19.634	0.000	0.000	0.000
40	A	40	ILE	0	-0.022	-0.017	19.700	0.196	0.196	0.000	0.000	0.000
41	A	41	ASP	-1	-0.766	-0.841	17.080	-16.124	-16.124	0.000	0.000	0.000
42	A	42	PHE	0	-0.025	-0.012	17.952	-0.260	-0.260	0.000	0.000	0.000
43	A	43	TRP	0	0.060	0.023	14.551	-0.190	-0.190	0.000	0.000	0.000
44	A	44	LEU	0	-0.001	0.007	19.934	0.024	0.024	0.000	0.000	0.000
45	A	45	VAL	0	-0.023	-0.011	17.816	-0.157	-0.157	0.000	0.000	0.000
46	A	46	PRO	0	-0.018	-0.019	21.207	0.231	0.231	0.000	0.000	0.000
47	A	47	GLN	0	0.060	0.030	22.206	-0.099	-0.099	0.000	0.000	0.000
48	A	48	PRO	0	-0.002	0.010	18.840	-0.443	-0.443	0.000	0.000	0.000
49	A	49	ALA	0	0.059	0.006	15.718	0.111	0.111	0.000	0.000	0.000
50	A	50	PHE	0	-0.013	-0.004	15.211	-0.146	-0.146	0.000	0.000	0.000
51	A	51	LEU	0	-0.031	-0.026	16.463	0.270	0.270	0.000	0.000	0.000
52	A	52	GLU	-1	-0.807	-0.885	18.697	-13.074	-13.074	0.000	0.000	0.000
53	A	53	ALA	0	-0.006	0.017	15.416	-0.085	-0.085	0.000	0.000	0.000
54	A	54	PRO	0	-0.001	-0.013	16.227	0.766	0.766	0.000	0.000	0.000
55	A	55	GLU	-1	-0.814	-0.886	14.110	-19.622	-19.622	0.000	0.000	0.000
56	A	56	PHE	0	-0.017	-0.015	15.923	0.392	0.392	0.000	0.000	0.000
57	A	57	ALA	0	0.018	0.028	20.304	0.653	0.653	0.000	0.000	0.000
58	A	58	ASP	-1	-0.870	-0.942	23.158	-11.337	-11.337	0.000	0.000	0.000
59	A	59	ILE	0	-0.071	-0.038	21.417	0.516	0.516	0.000	0.000	0.000
60	A	60	LYS	1	0.788	0.872	23.401	13.316	13.316	0.000	0.000	0.000
61	A	61	ALA	0	-0.021	-0.010	25.237	0.425	0.425	0.000	0.000	0.000
62	A	62	LYS	1	0.906	0.962	28.025	10.512	10.512	0.000	0.000	0.000
63	A	63	CYS	0	-0.035	-0.004	27.140	0.278	0.278	0.000	0.000	0.000
64	A	64	PRO	0	-0.009	-0.002	29.096	-0.011	-0.011	0.000	0.000	0.000
65	A	65	GLN	0	0.017	0.012	26.516	-0.566	-0.566	0.000	0.000	0.000
66	A	66	PRO	0	0.028	-0.004	28.491	0.393	0.393	0.000	0.000	0.000
67	A	67	ALA	0	0.002	0.016	25.064	0.306	0.306	0.000	0.000	0.000
68	A	68	ALA	0	-0.034	-0.021	24.585	-0.100	-0.100	0.000	0.000	0.000
69	A	69	ALA	0	0.023	0.017	21.119	0.231	0.231	0.000	0.000	0.000
70	A	70	ILE	0	-0.016	0.009	22.041	-0.024	-0.024	0.000	0.000	0.000
71	A	71	ILE	0	0.003	0.003	15.597	-0.037	-0.037	0.000	0.000	0.000
72	A	72	SER	0	-0.009	-0.035	17.559	0.453	0.453	0.000	0.000	0.000
73	A	73	THR	0	0.028	0.019	13.359	0.081	0.081	0.000	0.000	0.000
74	A	74	ASN	0	-0.010	-0.001	16.157	0.695	0.695	0.000	0.000	0.000
75	A	75	SER	0	0.059	0.020	19.909	0.793	0.793	0.000	0.000	0.000
76	A	76	GLN	0	0.010	0.010	21.312	0.199	0.199	0.000	0.000	0.000
77	A	77	PHE	0	0.011	0.006	22.596	0.624	0.624	0.000	0.000	0.000
78	A	78	ILE	0	0.018	0.015	20.499	0.473	0.473	0.000	0.000	0.000
79	A	79	THR	0	-0.046	-0.034	23.884	0.476	0.476	0.000	0.000	0.000
80	A	80	TRP	0	-0.005	-0.011	26.616	0.329	0.329	0.000	0.000	0.000
81	A	81	LEU	0	0.022	0.004	24.649	0.393	0.393	0.000	0.000	0.000
82	A	82	LYS	1	0.928	0.961	27.572	11.568	11.568	0.000	0.000	0.000
83	A	83	LEU	0	-0.060	-0.029	29.483	0.329	0.329	0.000	0.000	0.000
84	A	84	ARG	1	0.780	0.886	31.292	9.479	9.479	0.000	0.000	0.000
85	A	85	LEU	0	-0.004	0.003	28.827	0.203	0.203	0.000	0.000	0.000
86	A	86	GLU	-1	-0.907	-0.943	32.775	-8.308	-8.308	0.000	0.000	0.000
87	A	87	TYR	0	-0.058	-0.023	33.221	-0.084	-0.084	0.000	0.000	0.000
88	A	88	VAL	0	-0.059	-0.028	28.320	-0.215	-0.215	0.000	0.000	0.000
89	A	89	VAL	0	-0.021	-0.008	25.416	0.112	0.112	0.000	0.000	0.000
90	A	90	THR	0	-0.007	-0.013	23.968	-0.081	-0.081	0.000	0.000	0.000
91	A	91	GLY	0	-0.003	-0.002	21.378	0.397	0.397	0.000	0.000	0.000
92	A	92	GLU	-1	-0.932	-0.973	16.706	-18.044	-18.044	0.000	0.000	0.000
93	A	93	PHE	0	0.029	0.015	12.287	0.193	0.193	0.000	0.000	0.000
94	A	94	SER	0	-0.020	-0.002	9.547	-0.648	-0.648	0.000	0.000	0.000
95	A	95	ALA	0	0.038	0.026	8.062	0.406	0.406	0.000	0.000	0.000
98	A	98	GLU	-1	-0.957	-0.984	7.267	-24.989	-24.989	0.000	0.000	0.000
99	A	99	THR	0	-0.040	-0.046	9.184	0.678	0.678	0.000	0.000	0.000
100	A	100	ILE	0	-0.003	0.004	10.498	1.806	1.806	0.000	0.000	0.000
101	A	101	PRO	0	0.016	0.021	8.274	-3.217	-3.217	0.000	0.000	0.000
102	A	102	ASN	0	-0.026	-0.034	8.456	-2.189	-2.189	0.000	0.000	0.000
103	A	103	PRO	0	0.028	0.006	9.087	2.376	2.376	0.000	0.000	0.000
104	A	104	LEU	0	-0.017	0.000	12.006	1.504	1.504	0.000	0.000	0.000
105	A	105	ALA	0	-0.003	0.007	14.526	1.070	1.070	0.000	0.000	0.000
106	A	106	SER	0	-0.031	-0.012	16.185	0.287	0.287	0.000	0.000	0.000
107	A	107	LEU	0	-0.081	-0.037	18.476	-0.351	-0.351	0.000	0.000	0.000
108	A	108	ALA	-1	-0.839	-0.922	21.837	-11.881	-11.881	0.000	0.000	0.000

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