FMO DATABASE

FMODB ID: YR5Z2

Calculation Name: 4PC0-C-Xray547

Preferred Name:

Target Type:

Ligand Name: calcium ion

Ligand 3-letter code: CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4PC0

Chain ID: C

ChEMBL ID:

UniProt ID: Q13330

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	20
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-55367.533274
FMO2-HF: Nuclear repulsion	47694.507275
FMO2-HF: Total energy	-7673.025999
FMO2-MP2: Total energy	-7696.033409

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:671:LEU)

Summations of interaction energy for fragment #1(A:671: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.
42.883	45.51	0.146	-1.495	-1.279	-0.009

Interaction energy analysis for fragmet #1(A:671:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.860 / q_NPA : 0.919

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	A	673	SER	0	0.078	0.037	2.866	-13.707	-11.312	0.145	-1.447	-1.094	-0.009
7	A	677	THR	0	-0.015	-0.019	4.033	2.465	2.697	0.001	-0.048	-0.185	0.000
4	A	674	SER	0	0.073	0.028	5.669	-1.553	-1.553	0.000	0.000	0.000	0.000
5	A	675	SER	0	-0.049	-0.013	7.385	3.232	3.232	0.000	0.000	0.000	0.000
6	A	676	GLU	-1	-0.790	-0.903	7.120	-26.079	-26.079	0.000	0.000	0.000	0.000
8	A	678	LYS	1	0.979	0.996	6.700	23.512	23.512	0.000	0.000	0.000	0.000
9	A	679	ARG	1	0.828	0.902	10.309	25.739	25.739	0.000	0.000	0.000	0.000
10	A	680	ALA	0	0.044	0.019	7.934	2.023	2.023	0.000	0.000	0.000	0.000
11	A	681	ALA	0	0.000	0.003	9.655	1.845	1.845	0.000	0.000	0.000	0.000
12	A	682	ARG	1	0.892	0.950	11.051	19.713	19.713	0.000	0.000	0.000	0.000
13	A	683	ARG	1	0.884	0.944	13.358	20.502	20.502	0.000	0.000	0.000	0.000
14	A	684	PRO	0	0.074	0.041	13.152	-0.526	-0.526	0.000	0.000	0.000	0.000
15	A	685	TYR	0	0.020	0.013	14.234	-0.077	-0.077	0.000	0.000	0.000	0.000
16	A	686	LYS	1	0.905	0.953	14.660	16.732	16.732	0.000	0.000	0.000	0.000
17	A	687	PRO	0	0.029	0.027	12.751	-0.939	-0.939	0.000	0.000	0.000	0.000
18	A	688	ILE	0	-0.022	-0.022	6.348	-0.360	-0.360	0.000	0.000	0.000	0.000
19	A	689	ALA	0	-0.019	-0.009	9.215	1.085	1.085	0.000	0.000	0.000	0.000
20	A	690	LEU	-1	-0.929	-0.954	4.808	-30.724	-30.724	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:671:LEU)