FMO DATABASE

FMODB ID: JK659

Calculation Name: 1EDM-B-Xray547

Preferred Name: Coagulation factor IX

Target Type: SINGLE PROTEIN

Ligand Name: calcium ion

Ligand 3-letter code: CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1EDM

Chain ID: B

ChEMBL ID: CHEMBL2016

UniProt ID: P00740

Base Structure: X-ray

Registration Date: 2025-10-06

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	36
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-152659.641555
FMO2-HF: Nuclear repulsion	136002.541055
FMO2-HF: Total energy	-16657.1005
FMO2-MP2: Total energy	-16700.069338

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(B:46:VAL)

Summations of interaction energy for fragment #1(B:46:VAL)

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.
-129.535	-124.73	0.196	-2.795	-2.206	-0.027

Interaction energy analysis for fragmet #1(B:46:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.776 / q_NPA : 0.865

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	B	48	GLY	0	-0.020	-0.004	2.795	-23.552	-18.747	0.196	-2.795	-2.206	-0.027
4	B	49	ASP	-1	-0.854	-0.911	5.446	-26.953	-26.953	0.000	0.000	0.000	0.000
5	B	50	GLN	0	-0.047	-0.043	7.179	0.569	0.569	0.000	0.000	0.000	0.000
6	B	51	CYS	0	-0.004	-0.020	11.241	2.641	2.641	0.000	0.000	0.000	0.000
7	B	52	GLU	-1	-0.885	-0.947	11.609	-19.849	-19.849	0.000	0.000	0.000	0.000
8	B	53	SER	0	-0.067	-0.042	13.614	1.221	1.221	0.000	0.000	0.000	0.000
9	B	54	ASN	0	-0.109	-0.037	16.677	0.890	0.890	0.000	0.000	0.000	0.000
10	B	55	PRO	0	0.029	0.026	16.389	1.048	1.048	0.000	0.000	0.000	0.000
11	B	56	CYS	0	-0.084	-0.007	17.147	0.063	0.063	0.000	0.000	0.000	0.000
12	B	57	LEU	0	0.038	0.015	21.676	0.250	0.250	0.000	0.000	0.000	0.000
13	B	58	ASN	0	-0.053	-0.037	25.360	0.095	0.095	0.000	0.000	0.000	0.000
14	B	59	GLY	0	-0.009	-0.005	26.835	0.301	0.301	0.000	0.000	0.000	0.000
15	B	60	GLY	0	-0.004	-0.008	24.015	0.074	0.074	0.000	0.000	0.000	0.000
16	B	61	SER	0	-0.100	-0.036	20.575	-0.578	-0.578	0.000	0.000	0.000	0.000
17	B	63	LYS	1	0.847	0.924	12.690	21.265	21.265	0.000	0.000	0.000	0.000
18	B	64	ASP	-1	-0.780	-0.895	8.169	-32.676	-32.676	0.000	0.000	0.000	0.000
19	B	65	ASP	-1	-0.907	-0.941	9.722	-22.826	-22.826	0.000	0.000	0.000	0.000
20	B	66	ILE	0	-0.035	-0.027	6.120	-2.935	-2.935	0.000	0.000	0.000	0.000
21	B	67	ASN	0	-0.078	-0.037	7.300	3.006	3.006	0.000	0.000	0.000	0.000
22	B	68	SER	0	-0.091	-0.052	9.093	3.359	3.359	0.000	0.000	0.000	0.000
23	B	69	TYR	0	0.031	-0.009	11.234	-1.390	-1.390	0.000	0.000	0.000	0.000
24	B	70	GLU	-1	-0.937	-0.973	13.914	-17.776	-17.776	0.000	0.000	0.000	0.000
25	B	72	TRP	0	-0.042	-0.011	20.191	0.487	0.487	0.000	0.000	0.000	0.000
26	B	73	CYS	0	0.016	0.025	22.669	-0.321	-0.321	0.000	0.000	0.000	0.000
27	B	74	PRO	0	-0.001	-0.002	25.991	0.252	0.252	0.000	0.000	0.000	0.000
28	B	75	PHE	0	-0.036	-0.031	29.274	0.089	0.089	0.000	0.000	0.000	0.000
29	B	76	GLY	0	-0.019	-0.016	32.170	0.191	0.191	0.000	0.000	0.000	0.000
30	B	77	PHE	0	-0.021	0.014	29.124	0.170	0.170	0.000	0.000	0.000	0.000
31	B	78	GLU	-1	-0.967	-0.991	28.131	-10.045	-10.045	0.000	0.000	0.000	0.000
32	B	79	GLY	0	0.026	0.014	26.801	-0.115	-0.115	0.000	0.000	0.000	0.000
33	B	80	LYS	1	0.798	0.901	17.045	16.795	16.795	0.000	0.000	0.000	0.000
34	B	81	ASN	0	0.024	0.000	20.899	-1.421	-1.421	0.000	0.000	0.000	0.000
35	B	83	GLU	-1	-0.811	-0.920	25.724	-12.120	-12.120	0.000	0.000	0.000	0.000
36	B	84	LEU	-1	-0.901	-0.928	28.107	-9.744	-9.744	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:46:VAL)