FMO DATABASE

FMODB ID: R4Z88

Calculation Name: 1RK8-C-Xray549

Preferred Name:

Target Type:

Ligand Name: calcium ion

Ligand 3-letter code: CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1RK8

Chain ID: C

ChEMBL ID:

UniProt ID: P49028

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	33
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-120769.368077
FMO2-HF: Nuclear repulsion	107763.777231
FMO2-HF: Total energy	-13005.590846
FMO2-MP2: Total energy	-13044.657739

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(C:3:THR)

Summations of interaction energy for fragment #1(C:3:THR)

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.
95.358	99.058	0.555	-1.465	-2.789	-0.012

Interaction energy analysis for fragmet #1(C:3:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.856 / q_NPA : 0.914

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	C	5	LEU	0	0.018	0.014	2.923	-1.834	0.953	0.383	-1.191	-1.979	-0.010
4	C	6	GLN	0	0.016	-0.006	4.665	-0.053	-0.042	-0.001	-0.010	0.001	0.000
11	C	13	ILE	0	0.020	0.014	4.037	-7.484	-7.361	-0.001	-0.027	-0.095	0.000
12	C	14	PRO	0	0.009	0.001	2.762	6.552	7.331	0.174	-0.237	-0.716	-0.002
5	C	7	SER	0	-0.031	-0.018	8.245	1.451	1.451	0.000	0.000	0.000	0.000
6	C	8	SER	0	0.006	-0.037	11.319	-0.337	-0.337	0.000	0.000	0.000	0.000
7	C	9	GLU	-1	-0.831	-0.868	14.500	-16.072	-16.072	0.000	0.000	0.000	0.000
8	C	10	GLY	0	0.057	0.041	12.745	0.013	0.013	0.000	0.000	0.000	0.000
9	C	11	LYS	1	0.846	0.929	7.672	32.508	32.508	0.000	0.000	0.000	0.000
10	C	12	PHE	0	0.007	-0.007	7.446	1.172	1.172	0.000	0.000	0.000	0.000
13	C	15	ALA	0	0.028	0.013	5.827	0.219	0.219	0.000	0.000	0.000	0.000
14	C	16	THR	0	0.002	-0.003	6.288	-0.417	-0.417	0.000	0.000	0.000	0.000
15	C	17	LYS	1	0.954	1.007	8.871	20.196	20.196	0.000	0.000	0.000	0.000
16	C	18	ARG	1	0.872	0.924	12.115	17.420	17.420	0.000	0.000	0.000	0.000
17	C	19	PRO	0	0.035	-0.002	14.844	0.286	0.286	0.000	0.000	0.000	0.000
18	C	20	ASP	-1	-0.779	-0.851	17.541	-16.034	-16.034	0.000	0.000	0.000	0.000
19	C	21	GLY	0	-0.005	-0.002	17.974	0.639	0.639	0.000	0.000	0.000	0.000
20	C	22	THR	0	-0.033	-0.025	17.473	-0.788	-0.788	0.000	0.000	0.000	0.000
21	C	23	TRP	0	0.054	0.008	9.692	-1.750	-1.750	0.000	0.000	0.000	0.000
22	C	24	ARG	1	0.831	0.913	10.004	27.793	27.793	0.000	0.000	0.000	0.000
23	C	25	LYS	1	0.985	0.986	11.300	17.869	17.869	0.000	0.000	0.000	0.000
24	C	26	ALA	0	0.043	0.024	9.227	-1.441	-1.441	0.000	0.000	0.000	0.000
25	C	27	ARG	1	0.916	0.950	9.219	28.171	28.171	0.000	0.000	0.000	0.000
26	C	28	ARG	1	0.825	0.895	9.458	17.452	17.452	0.000	0.000	0.000	0.000
27	C	29	VAL	0	-0.039	-0.011	8.064	0.238	0.238	0.000	0.000	0.000	0.000
28	C	30	LYS	1	1.004	1.005	11.380	17.775	17.775	0.000	0.000	0.000	0.000
29	C	31	ASP	-1	-0.785	-0.882	13.015	-22.031	-22.031	0.000	0.000	0.000	0.000
30	C	32	GLY	0	0.006	-0.007	14.036	0.974	0.974	0.000	0.000	0.000	0.000
31	C	33	TYR	0	-0.028	-0.002	11.330	-0.404	-0.404	0.000	0.000	0.000	0.000
32	C	34	VAL	0	-0.046	-0.032	8.352	-3.930	-3.930	0.000	0.000	0.000	0.000
33	C	35	PRO	-1	-0.890	-0.918	8.574	-22.795	-22.795	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:3:THR)