FMO DATABASE

FMODB ID: 743KK

Calculation Name: 2MD7-B-Other547

Preferred Name: Nuclear body protein SP140

Target Type: SINGLE PROTEIN

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2MD7

Chain ID: B

ChEMBL ID: CHEMBL3108643

UniProt ID: Q13342

Base Structure: SolutionNMR

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	55
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-290198.270645
FMO2-HF: Nuclear repulsion	264852.120396
FMO2-HF: Total energy	-25346.150249
FMO2-MP2: Total energy	-25410.132912

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:1:GLY)

Summations of interaction energy for fragment #1(B: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.
-96.809	-94.832	7.895	-5.673	-4.199	-0.071

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.846 / q_NPA : 0.905

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	3	MET	0	0.041	0.028	3.842	5.913	6.919	-0.004	-0.445	-0.557	-0.002
4	B	4	GLY	0	0.017	-0.003	3.441	10.846	11.395	0.004	-0.233	-0.320	-0.001
5	B	5	MET	0	0.000	0.019	1.826	-52.654	-52.385	7.896	-4.968	-3.197	-0.068
6	B	6	ARG	1	1.007	0.986	3.986	46.568	46.721	-0.001	-0.027	-0.125	0.000
7	B	7	ASN	0	-0.003	0.017	5.788	-4.386	-4.386	0.000	0.000	0.000	0.000
8	B	8	LEU	0	0.025	-0.023	7.424	2.789	2.789	0.000	0.000	0.000	0.000
9	B	9	ASP	-1	-0.944	-0.956	9.347	-23.471	-23.471	0.000	0.000	0.000	0.000
10	B	10	GLU	-1	-0.887	-0.944	11.086	-18.862	-18.862	0.000	0.000	0.000	0.000
11	B	11	CYS	0	-0.073	-0.009	12.574	1.942	1.942	0.000	0.000	0.000	0.000
12	B	12	GLU	-1	-0.784	-0.869	14.247	-17.132	-17.132	0.000	0.000	0.000	0.000
13	B	13	VAL	0	0.028	0.010	16.563	0.208	0.208	0.000	0.000	0.000	0.000
14	B	14	CYS	0	-0.064	-0.031	11.568	0.055	0.055	0.000	0.000	0.000	0.000
15	B	15	ARG	1	0.734	0.832	14.572	19.241	19.241	0.000	0.000	0.000	0.000
16	B	16	ASP	-1	-0.968	-0.972	16.408	-13.625	-13.625	0.000	0.000	0.000	0.000
17	B	17	GLY	0	-0.024	0.004	17.195	0.572	0.572	0.000	0.000	0.000	0.000
18	B	18	GLY	0	-0.015	-0.009	18.031	0.511	0.511	0.000	0.000	0.000	0.000
19	B	19	GLU	-1	-0.926	-0.973	16.559	-18.857	-18.857	0.000	0.000	0.000	0.000
20	B	20	LEU	0	-0.061	-0.022	11.565	-0.562	-0.562	0.000	0.000	0.000	0.000
21	B	21	PHE	0	0.048	0.023	16.256	0.609	0.609	0.000	0.000	0.000	0.000
22	B	22	CYS	0	0.011	-0.014	14.482	1.333	1.333	0.000	0.000	0.000	0.000
23	B	23	CYS	0	-0.047	-0.073	14.692	-1.187	-1.187	0.000	0.000	0.000	0.000
24	B	24	ASP	-1	-0.806	-0.910	8.915	-32.459	-32.459	0.000	0.000	0.000	0.000
25	B	25	THR	0	-0.042	-0.033	10.349	-2.545	-2.545	0.000	0.000	0.000	0.000
26	B	26	CYS	0	0.029	-0.004	12.243	-0.331	-0.331	0.000	0.000	0.000	0.000
27	B	27	SER	0	0.037	0.019	10.749	-0.940	-0.940	0.000	0.000	0.000	0.000
28	B	28	ARG	1	0.738	0.849	6.292	34.617	34.617	0.000	0.000	0.000	0.000
29	B	29	VAL	0	-0.052	-0.017	8.510	-1.947	-1.947	0.000	0.000	0.000	0.000
30	B	30	PHE	0	0.039	0.013	11.405	0.795	0.795	0.000	0.000	0.000	0.000
31	B	31	HIS	0	0.030	0.024	10.123	1.940	1.940	0.000	0.000	0.000	0.000
32	B	32	GLU	-1	-0.880	-0.957	12.238	-21.199	-21.199	0.000	0.000	0.000	0.000
33	B	33	ASP	-1	-0.875	-0.938	15.181	-14.827	-14.827	0.000	0.000	0.000	0.000
34	B	35	HIS	1	0.792	0.887	13.213	20.801	20.801	0.000	0.000	0.000	0.000
35	B	36	ILE	0	-0.037	0.005	18.156	0.863	0.863	0.000	0.000	0.000	0.000
36	B	37	PRO	0	-0.001	0.003	21.456	0.010	0.010	0.000	0.000	0.000	0.000
37	B	38	PRO	0	0.025	-0.010	21.875	-0.134	-0.134	0.000	0.000	0.000	0.000
38	B	39	VAL	0	-0.013	0.003	23.515	0.617	0.617	0.000	0.000	0.000	0.000
39	B	40	GLU	-1	-0.853	-0.895	26.048	-11.800	-11.800	0.000	0.000	0.000	0.000
40	B	41	ALA	0	-0.017	-0.028	28.411	0.503	0.503	0.000	0.000	0.000	0.000
41	B	42	GLU	-1	-0.935	-0.951	28.756	-10.429	-10.429	0.000	0.000	0.000	0.000
42	B	43	ARG	1	0.833	0.885	23.667	12.159	12.159	0.000	0.000	0.000	0.000
43	B	44	THR	0	-0.018	-0.012	23.541	0.090	0.090	0.000	0.000	0.000	0.000
44	B	45	PRO	0	0.028	0.015	18.159	-0.109	-0.109	0.000	0.000	0.000	0.000
45	B	46	TRP	0	-0.041	-0.016	18.196	-0.895	-0.895	0.000	0.000	0.000	0.000
46	B	47	ASN	0	-0.069	-0.030	19.609	0.065	0.065	0.000	0.000	0.000	0.000
47	B	48	CYS	-1	-0.840	-0.700	17.813	-18.409	-18.409	0.000	0.000	0.000	0.000
48	B	49	ILE	0	0.102	0.029	19.528	0.689	0.689	0.000	0.000	0.000	0.000
49	B	50	PHE	0	0.032	-0.004	17.753	0.303	0.303	0.000	0.000	0.000	0.000
50	B	51	CYS	0	-0.061	-0.136	18.417	0.310	0.310	0.000	0.000	0.000	0.000
51	B	52	ARG	1	0.739	0.837	21.106	12.989	12.989	0.000	0.000	0.000	0.000
52	B	53	MET	0	-0.007	0.020	21.410	0.700	0.700	0.000	0.000	0.000	0.000
53	B	54	LYS	1	0.922	0.954	22.803	13.837	13.837	0.000	0.000	0.000	0.000
54	B	55	GLU	-1	-0.820	-0.869	24.946	-11.390	-11.390	0.000	0.000	0.000	0.000
55	B	56	SER	-1	-1.009	-0.989	28.214	-10.534	-10.534	0.000	0.000	0.000	0.000

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