FMO DATABASE

FMODB ID: J41N9

Calculation Name: 2A1J-A-Xray547

Preferred Name: DNA excision repair protein ERCC-1/DNA repair endonuclease XPF

Target Type: PROTEIN COMPLEX

Ligand Name: mercury (ii) ion

Ligand 3-letter code: HG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2A1J

Chain ID: A

ChEMBL ID: CHEMBL3883316

UniProt ID: P07992

Base Structure: X-ray

Registration Date: 2025-10-03

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	62
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-324997.962944
FMO2-HF: Nuclear repulsion	300792.508331
FMO2-HF: Total energy	-24205.454613
FMO2-MP2: Total energy	-24274.955526

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:837:PRO)

Summations of interaction energy for fragment #1(A:837:PRO)

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.
-3.307	1.545	0.058	-1.958	-2.951	-0.009

Interaction energy analysis for fragmet #1(A:837:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.899 / q_NPA : 0.923

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

Sort

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	839	ASP	-1	-0.899	-0.946	3.176	-60.380	-56.478	0.047	-1.798	-2.151	-0.009
4	A	840	PHE	0	-0.001	-0.004	3.619	7.117	7.628	0.010	-0.085	-0.436	0.000
5	A	841	LEU	0	0.046	0.015	4.754	6.201	6.361	-0.001	-0.021	-0.137	0.000
20	A	856	MET	0	-0.052	-0.042	4.561	-1.532	-1.458	-0.001	-0.008	-0.065	0.000
26	A	862	ILE	0	0.036	0.005	3.746	1.260	1.465	0.003	-0.046	-0.162	0.000
6	A	842	LEU	0	-0.015	-0.029	6.736	5.141	5.141	0.000	0.000	0.000	0.000
7	A	843	LYS	1	0.905	0.967	8.355	32.682	32.682	0.000	0.000	0.000	0.000
8	A	844	MET	0	-0.003	0.027	8.666	0.879	0.879	0.000	0.000	0.000	0.000
9	A	845	PRO	0	0.015	0.005	11.320	0.489	0.489	0.000	0.000	0.000	0.000
10	A	846	GLY	0	0.048	0.031	15.131	0.118	0.118	0.000	0.000	0.000	0.000
11	A	847	VAL	0	-0.013	0.010	10.073	0.614	0.614	0.000	0.000	0.000	0.000
12	A	848	ASN	0	0.009	-0.008	13.374	0.921	0.921	0.000	0.000	0.000	0.000
13	A	849	ALA	0	0.044	0.010	12.266	-0.791	-0.791	0.000	0.000	0.000	0.000
14	A	850	LYS	1	0.912	0.962	13.338	15.481	15.481	0.000	0.000	0.000	0.000
15	A	851	ASN	0	-0.002	-0.008	14.318	-0.841	-0.841	0.000	0.000	0.000	0.000
16	A	852	CYS	0	0.009	0.023	8.140	-1.015	-1.015	0.000	0.000	0.000	0.000
17	A	853	ARG	1	0.976	0.978	9.915	18.981	18.981	0.000	0.000	0.000	0.000
18	A	854	SER	0	-0.010	-0.010	12.079	-0.309	-0.309	0.000	0.000	0.000	0.000
19	A	855	LEU	0	0.033	0.013	9.585	0.341	0.341	0.000	0.000	0.000	0.000
21	A	857	HIS	0	-0.017	0.011	8.864	-0.771	-0.771	0.000	0.000	0.000	0.000
22	A	858	HIS	0	0.018	0.014	12.164	0.505	0.505	0.000	0.000	0.000	0.000
23	A	859	VAL	0	-0.034	-0.012	9.184	1.065	1.065	0.000	0.000	0.000	0.000
24	A	860	LYS	1	0.872	0.943	9.334	17.789	17.789	0.000	0.000	0.000	0.000
25	A	861	ASN	0	0.000	-0.011	5.953	-1.810	-1.810	0.000	0.000	0.000	0.000
27	A	863	ALA	0	-0.010	-0.001	7.223	2.326	2.326	0.000	0.000	0.000	0.000
28	A	864	GLU	-1	-0.824	-0.912	10.082	-17.562	-17.562	0.000	0.000	0.000	0.000
29	A	865	LEU	0	-0.003	-0.008	9.078	1.172	1.172	0.000	0.000	0.000	0.000
30	A	866	ALA	0	-0.005	-0.002	12.049	1.066	1.066	0.000	0.000	0.000	0.000
31	A	867	ALA	0	-0.037	-0.018	14.336	1.220	1.220	0.000	0.000	0.000	0.000
32	A	868	LEU	0	-0.011	0.021	13.759	0.708	0.708	0.000	0.000	0.000	0.000
33	A	869	SER	0	0.034	0.004	17.413	0.046	0.046	0.000	0.000	0.000	0.000
34	A	870	GLN	0	0.002	-0.007	19.719	-0.280	-0.280	0.000	0.000	0.000	0.000
35	A	871	ASP	-1	-0.855	-0.922	21.380	-12.170	-12.170	0.000	0.000	0.000	0.000
36	A	872	GLU	-1	-0.867	-0.925	19.180	-14.504	-14.504	0.000	0.000	0.000	0.000
37	A	873	LEU	0	0.021	0.006	14.588	-0.530	-0.530	0.000	0.000	0.000	0.000
38	A	874	THR	0	-0.018	-0.035	17.970	-0.284	-0.284	0.000	0.000	0.000	0.000
39	A	875	SER	0	-0.095	-0.049	20.293	0.063	0.063	0.000	0.000	0.000	0.000
40	A	876	ILE	0	-0.003	0.007	14.172	-0.196	-0.196	0.000	0.000	0.000	0.000
41	A	877	LEU	0	-0.051	-0.025	14.042	-0.840	-0.840	0.000	0.000	0.000	0.000
42	A	878	GLY	0	-0.011	0.008	17.587	0.157	0.157	0.000	0.000	0.000	0.000
43	A	879	ASN	0	-0.041	-0.027	20.715	0.688	0.688	0.000	0.000	0.000	0.000
44	A	880	ALA	0	0.111	0.053	21.149	-0.568	-0.568	0.000	0.000	0.000	0.000
45	A	881	ALA	0	0.014	0.017	23.055	-0.109	-0.109	0.000	0.000	0.000	0.000
46	A	882	ASN	0	-0.088	-0.058	17.722	0.343	0.343	0.000	0.000	0.000	0.000
47	A	883	ALA	0	0.032	0.023	18.212	-0.861	-0.861	0.000	0.000	0.000	0.000
48	A	884	LYS	1	0.888	0.942	19.233	12.098	12.098	0.000	0.000	0.000	0.000
49	A	885	GLN	0	-0.026	-0.018	18.531	0.216	0.216	0.000	0.000	0.000	0.000
50	A	886	LEU	0	0.007	0.006	12.070	-0.494	-0.494	0.000	0.000	0.000	0.000
51	A	887	TYR	0	0.017	0.002	15.830	-0.457	-0.457	0.000	0.000	0.000	0.000
52	A	888	ASP	-1	-0.771	-0.879	18.180	-13.365	-13.365	0.000	0.000	0.000	0.000
53	A	889	PHE	0	-0.049	-0.015	11.628	-0.080	-0.080	0.000	0.000	0.000	0.000
54	A	890	ILE	0	-0.045	-0.021	12.659	-0.452	-0.452	0.000	0.000	0.000	0.000
55	A	891	HIS	1	0.825	0.907	15.701	16.345	16.345	0.000	0.000	0.000	0.000
56	A	892	THR	0	-0.031	-0.011	19.247	1.001	1.001	0.000	0.000	0.000	0.000
57	A	893	SER	0	-0.025	-0.016	19.725	-0.778	-0.778	0.000	0.000	0.000	0.000
58	A	894	PHE	0	-0.049	-0.015	20.186	0.324	0.324	0.000	0.000	0.000	0.000
59	A	895	ALA	0	-0.035	-0.033	24.141	-0.274	-0.274	0.000	0.000	0.000	0.000
60	A	896	GLU	-1	-0.850	-0.925	26.983	-10.944	-10.944	0.000	0.000	0.000	0.000
61	A	897	VAL	0	-0.084	-0.047	29.694	0.058	0.058	0.000	0.000	0.000	0.000
62	A	898	VAL	-1	-0.964	-0.955	32.255	-8.525	-8.525	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:837:PRO)