FMO DATABASE

FMODB ID: Q56MY

Calculation Name: 1JJ2-1-Xray549

Preferred Name:

Target Type:

Ligand Name: cadmium ion | potassium ion

Ligand 3-letter code: CD | K

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1JJ2

Chain ID: 1

ChEMBL ID:

UniProt ID: P60617

Base Structure: X-ray

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	48
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-222231.33772
FMO2-HF: Nuclear repulsion	201961.935499
FMO2-HF: Total energy	-20269.402221
FMO2-MP2: Total energy	-20329.00926

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(1:1:GLY)

Summations of interaction energy for fragment #1(1:1: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.
132.423	133.22	-0.008	-0.268	-0.522	-0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.930 / q_NPA : 0.954

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

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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	1	3	LYS	1	1.017	1.018	3.856	45.803	46.600	-0.008	-0.268	-0.522	-0.001
4	1	4	SER	0	0.105	0.055	6.189	3.808	3.808	0.000	0.000	0.000	0.000
5	1	5	LYS	1	1.007	0.985	9.637	17.268	17.268	0.000	0.000	0.000	0.000
6	1	6	ALA	0	0.003	0.006	12.761	1.077	1.077	0.000	0.000	0.000	0.000
7	1	7	THR	0	0.032	-0.010	7.428	0.651	0.651	0.000	0.000	0.000	0.000
8	1	8	LYS	1	0.917	0.958	10.727	25.309	25.309	0.000	0.000	0.000	0.000
9	1	9	LYS	1	0.954	0.977	11.641	17.501	17.501	0.000	0.000	0.000	0.000
10	1	10	ARG	1	0.866	0.941	11.807	23.290	23.290	0.000	0.000	0.000	0.000
11	1	11	LEU	0	0.054	0.019	8.342	0.485	0.485	0.000	0.000	0.000	0.000
12	1	12	ALA	0	0.007	0.007	12.858	0.852	0.852	0.000	0.000	0.000	0.000
13	1	13	LYS	1	0.910	0.960	15.448	15.618	15.618	0.000	0.000	0.000	0.000
14	1	14	LEU	0	0.051	0.015	13.983	0.898	0.898	0.000	0.000	0.000	0.000
15	1	15	ASP	-1	-0.957	-0.951	15.199	-17.981	-17.981	0.000	0.000	0.000	0.000
16	1	16	ASN	0	0.022	0.007	17.090	1.089	1.089	0.000	0.000	0.000	0.000
17	1	17	GLN	0	-0.046	-0.038	20.116	0.222	0.222	0.000	0.000	0.000	0.000
18	1	18	ASN	0	-0.017	-0.004	18.103	1.099	1.099	0.000	0.000	0.000	0.000
19	1	19	SER	0	0.000	0.022	21.139	0.233	0.233	0.000	0.000	0.000	0.000
20	1	20	ARG	1	0.911	0.954	24.132	10.433	10.433	0.000	0.000	0.000	0.000
21	1	21	VAL	0	0.048	0.025	27.519	-0.074	-0.074	0.000	0.000	0.000	0.000
22	1	22	PRO	0	0.013	0.011	30.425	0.097	0.097	0.000	0.000	0.000	0.000
23	1	23	ALA	0	0.059	0.010	32.379	0.196	0.196	0.000	0.000	0.000	0.000
24	1	24	TRP	0	0.075	0.030	33.701	0.274	0.274	0.000	0.000	0.000	0.000
25	1	25	VAL	0	0.018	0.012	33.977	0.181	0.181	0.000	0.000	0.000	0.000
26	1	26	MET	0	-0.034	0.006	35.398	0.046	0.046	0.000	0.000	0.000	0.000
27	1	27	LEU	0	0.071	0.032	37.935	0.158	0.158	0.000	0.000	0.000	0.000
28	1	28	LYS	1	0.912	1.000	39.739	8.084	8.084	0.000	0.000	0.000	0.000
29	1	29	THR	0	-0.068	-0.057	38.064	0.035	0.035	0.000	0.000	0.000	0.000
30	1	30	ASP	0	-0.035	-0.050	40.627	0.065	0.065	0.000	0.000	0.000	0.000
31	1	31	GLU	-1	-0.800	-0.872	40.216	-7.816	-7.816	0.000	0.000	0.000	0.000
32	1	32	VAL	0	0.018	0.022	36.860	-0.159	-0.159	0.000	0.000	0.000	0.000
33	1	33	GLN	0	-0.030	-0.026	35.740	-0.315	-0.315	0.000	0.000	0.000	0.000
34	1	35	ARG	1	0.813	0.883	31.262	8.814	8.814	0.000	0.000	0.000	0.000
35	1	36	ASN	0	0.008	0.000	24.535	0.193	0.193	0.000	0.000	0.000	0.000
36	1	37	HIS	0	0.000	-0.011	28.137	-0.356	-0.356	0.000	0.000	0.000	0.000
37	1	38	LYS	1	0.957	0.976	23.428	12.457	12.457	0.000	0.000	0.000	0.000
38	1	39	ARG	1	0.916	0.972	22.313	11.071	11.071	0.000	0.000	0.000	0.000
39	1	40	ARG	1	0.956	0.969	14.028	19.900	19.900	0.000	0.000	0.000	0.000
40	1	41	HIS	0	0.023	0.014	17.517	-0.959	-0.959	0.000	0.000	0.000	0.000
41	1	42	TRP	0	0.020	-0.012	12.505	-0.406	-0.406	0.000	0.000	0.000	0.000
42	1	43	ARG	1	0.957	0.983	13.146	17.220	17.220	0.000	0.000	0.000	0.000
43	1	44	ARG	1	0.940	0.966	15.371	14.280	14.280	0.000	0.000	0.000	0.000
44	1	45	ASN	0	-0.025	-0.006	16.836	1.006	1.006	0.000	0.000	0.000	0.000
45	1	46	ASP	-1	-0.852	-0.912	12.852	-24.514	-24.514	0.000	0.000	0.000	0.000
46	1	47	THR	0	-0.144	-0.078	11.142	0.966	0.966	0.000	0.000	0.000	0.000
47	1	48	ASP	-1	-0.873	-0.928	12.518	-19.051	-19.051	0.000	0.000	0.000	0.000
48	1	49	GLU	-2	-1.725	-1.843	9.635	-56.625	-56.625	0.000	0.000	0.000	0.000

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