FMO DATABASE

FMODB ID: 3M7NL

Calculation Name: 2A1I-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: 2A1I

Chain ID: A

ChEMBL ID: CHEMBL3883316

UniProt ID: P07992

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	129
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1129270.972742
FMO2-HF: Nuclear repulsion	1077673.634557
FMO2-HF: Total energy	-51597.338185
FMO2-MP2: Total energy	-51747.833156

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:99:ASN)

Summations of interaction energy for fragment #1(A:99:ASN)

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.
-26.398	-23.174	0.061	-1.229	-2.054	0

Interaction energy analysis for fragmet #1(A:99:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.852 / q_NPA : 0.912

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	101	ILE	0	-0.024	-0.002	3.793	-5.944	-4.327	-0.013	-0.814	-0.790	-0.001
21	A	119	VAL	0	-0.005	0.006	5.039	-1.597	-1.413	-0.001	-0.003	-0.179	0.000
22	A	120	PRO	0	0.018	0.016	3.504	0.828	1.898	0.073	-0.340	-0.802	0.001
115	A	213	LYS	1	0.833	0.942	3.492	56.112	56.465	0.002	-0.072	-0.283	0.000
4	A	102	ILE	0	0.020	0.016	5.498	0.772	0.772	0.000	0.000	0.000	0.000
5	A	103	VAL	0	-0.016	-0.004	8.505	2.461	2.461	0.000	0.000	0.000	0.000
6	A	104	SER	0	0.062	0.036	12.176	0.784	0.784	0.000	0.000	0.000	0.000
7	A	105	PRO	0	-0.020	-0.026	15.401	0.586	0.586	0.000	0.000	0.000	0.000
8	A	106	ARG	1	0.955	0.973	17.708	14.767	14.767	0.000	0.000	0.000	0.000
9	A	107	GLN	0	0.042	0.038	16.390	0.755	0.755	0.000	0.000	0.000	0.000
10	A	108	ARG	1	0.944	0.975	17.813	16.494	16.494	0.000	0.000	0.000	0.000
11	A	109	GLY	0	0.021	0.015	19.822	0.752	0.752	0.000	0.000	0.000	0.000
12	A	110	ASN	0	-0.011	-0.002	19.286	0.933	0.933	0.000	0.000	0.000	0.000
13	A	111	PRO	0	-0.015	-0.019	19.760	-0.628	-0.628	0.000	0.000	0.000	0.000
14	A	112	VAL	0	0.025	0.008	16.130	-0.159	-0.159	0.000	0.000	0.000	0.000
15	A	113	LEU	0	-0.013	0.000	14.467	-0.606	-0.606	0.000	0.000	0.000	0.000
16	A	114	LYS	1	0.904	0.962	14.976	12.999	12.999	0.000	0.000	0.000	0.000
17	A	115	PHE	0	-0.035	-0.024	16.063	0.380	0.380	0.000	0.000	0.000	0.000
18	A	116	VAL	0	-0.043	0.005	9.850	0.006	0.006	0.000	0.000	0.000	0.000
19	A	117	ARG	1	0.763	0.864	11.587	16.737	16.737	0.000	0.000	0.000	0.000
20	A	118	ASN	0	-0.042	-0.036	9.448	-0.341	-0.341	0.000	0.000	0.000	0.000
23	A	121	TRP	0	0.000	-0.013	6.293	-3.506	-3.506	0.000	0.000	0.000	0.000
24	A	122	GLU	-1	-0.850	-0.900	6.168	-43.093	-43.093	0.000	0.000	0.000	0.000
25	A	123	PHE	0	-0.050	-0.035	9.654	0.410	0.410	0.000	0.000	0.000	0.000
26	A	124	GLY	0	0.028	0.010	11.322	-0.745	-0.745	0.000	0.000	0.000	0.000
27	A	125	ASP	-1	-0.949	-0.974	12.276	-16.912	-16.912	0.000	0.000	0.000	0.000
28	A	126	VAL	0	-0.017	-0.004	11.129	-0.709	-0.709	0.000	0.000	0.000	0.000
29	A	127	ILE	0	0.068	0.037	14.605	0.749	0.749	0.000	0.000	0.000	0.000
30	A	128	PRO	0	-0.006	0.006	13.579	1.050	1.050	0.000	0.000	0.000	0.000
31	A	129	ASP	-1	-0.809	-0.891	15.707	-16.334	-16.334	0.000	0.000	0.000	0.000
32	A	130	TYR	0	0.012	-0.009	11.746	-0.832	-0.832	0.000	0.000	0.000	0.000
33	A	131	VAL	0	-0.001	0.004	7.813	1.434	1.434	0.000	0.000	0.000	0.000
34	A	132	LEU	0	0.013	-0.011	7.699	-4.121	-4.121	0.000	0.000	0.000	0.000
35	A	133	GLY	0	0.028	-0.002	6.541	-4.000	-4.000	0.000	0.000	0.000	0.000
36	A	134	GLN	0	0.018	0.016	7.616	1.024	1.024	0.000	0.000	0.000	0.000
37	A	135	SER	0	0.038	0.026	9.108	2.558	2.558	0.000	0.000	0.000	0.000
38	A	136	THR	0	-0.035	-0.023	10.665	1.356	1.356	0.000	0.000	0.000	0.000
39	A	137	CYS	0	-0.059	-0.007	10.841	-1.856	-1.856	0.000	0.000	0.000	0.000
40	A	138	ALA	0	0.061	0.035	13.141	1.237	1.237	0.000	0.000	0.000	0.000
41	A	139	LEU	0	-0.006	0.006	15.771	-0.491	-0.491	0.000	0.000	0.000	0.000
42	A	140	PHE	0	-0.016	-0.016	18.734	0.038	0.038	0.000	0.000	0.000	0.000
43	A	141	LEU	0	-0.019	-0.010	20.363	0.360	0.360	0.000	0.000	0.000	0.000
44	A	142	SER	0	-0.049	-0.039	24.194	0.191	0.191	0.000	0.000	0.000	0.000
45	A	143	LEU	0	0.058	0.020	26.714	0.225	0.225	0.000	0.000	0.000	0.000
46	A	144	ARG	1	0.954	0.973	28.570	10.845	10.845	0.000	0.000	0.000	0.000
47	A	145	TYR	0	-0.045	-0.024	27.457	0.208	0.208	0.000	0.000	0.000	0.000
48	A	146	HIS	0	0.000	-0.028	29.223	-0.166	-0.166	0.000	0.000	0.000	0.000
49	A	147	ASN	0	-0.027	-0.017	30.680	0.314	0.314	0.000	0.000	0.000	0.000
50	A	148	LEU	0	-0.053	-0.019	32.921	0.272	0.272	0.000	0.000	0.000	0.000
51	A	149	HIS	0	-0.071	-0.022	30.364	0.260	0.260	0.000	0.000	0.000	0.000
52	A	150	PRO	0	0.056	0.036	31.209	-0.360	-0.360	0.000	0.000	0.000	0.000
53	A	151	ASP	-1	-0.877	-0.940	32.100	-9.233	-9.233	0.000	0.000	0.000	0.000
54	A	152	TYR	0	-0.070	-0.031	22.597	-0.387	-0.387	0.000	0.000	0.000	0.000
55	A	153	ILE	0	0.010	-0.007	23.183	-0.365	-0.365	0.000	0.000	0.000	0.000
56	A	154	HIS	0	0.078	0.037	25.820	-0.530	-0.530	0.000	0.000	0.000	0.000
57	A	155	GLY	0	0.033	0.017	27.307	-0.193	-0.193	0.000	0.000	0.000	0.000
58	A	156	ARG	1	0.738	0.844	18.316	15.409	15.409	0.000	0.000	0.000	0.000
59	A	157	LEU	0	0.030	0.009	22.064	-0.599	-0.599	0.000	0.000	0.000	0.000
60	A	158	GLN	0	-0.012	-0.011	23.511	-0.469	-0.469	0.000	0.000	0.000	0.000
61	A	159	SER	0	-0.089	-0.043	22.799	-0.156	-0.156	0.000	0.000	0.000	0.000
62	A	160	LEU	0	-0.018	-0.001	16.763	-0.571	-0.571	0.000	0.000	0.000	0.000
63	A	161	GLY	0	0.021	0.016	20.067	-0.482	-0.482	0.000	0.000	0.000	0.000
64	A	162	LYS	1	0.892	0.918	21.138	12.211	12.211	0.000	0.000	0.000	0.000
65	A	163	ASN	0	-0.048	-0.010	17.158	-0.119	-0.119	0.000	0.000	0.000	0.000
66	A	164	PHE	0	0.016	0.002	11.541	-0.836	-0.836	0.000	0.000	0.000	0.000
67	A	165	ALA	0	0.032	0.010	15.746	0.925	0.925	0.000	0.000	0.000	0.000
68	A	166	LEU	0	0.008	0.019	15.029	0.918	0.918	0.000	0.000	0.000	0.000
69	A	167	ARG	1	0.768	0.866	15.478	13.461	13.461	0.000	0.000	0.000	0.000
70	A	168	VAL	0	0.008	0.005	16.298	0.712	0.712	0.000	0.000	0.000	0.000
71	A	169	LEU	0	0.010	-0.002	18.545	-0.347	-0.347	0.000	0.000	0.000	0.000
72	A	170	LEU	0	-0.031	-0.005	17.456	0.338	0.338	0.000	0.000	0.000	0.000
73	A	171	VAL	0	0.003	-0.006	20.809	0.092	0.092	0.000	0.000	0.000	0.000
74	A	172	GLN	0	-0.029	-0.031	23.813	-0.322	-0.322	0.000	0.000	0.000	0.000
75	A	173	VAL	0	-0.013	-0.016	25.329	0.399	0.399	0.000	0.000	0.000	0.000
76	A	174	ASP	-1	-0.783	-0.851	28.501	-10.860	-10.860	0.000	0.000	0.000	0.000
77	A	175	VAL	0	-0.011	-0.006	30.288	0.206	0.206	0.000	0.000	0.000	0.000
78	A	176	LYS	1	0.889	0.936	33.829	7.821	7.821	0.000	0.000	0.000	0.000
79	A	177	ASP	-1	-0.819	-0.892	37.022	-7.727	-7.727	0.000	0.000	0.000	0.000
80	A	178	PRO	0	0.022	0.023	32.921	0.031	0.031	0.000	0.000	0.000	0.000
81	A	179	GLN	0	0.010	-0.021	34.342	-0.366	-0.366	0.000	0.000	0.000	0.000
82	A	180	GLN	0	-0.013	-0.013	36.059	-0.126	-0.126	0.000	0.000	0.000	0.000
83	A	181	ALA	0	0.082	0.043	32.555	-0.077	-0.077	0.000	0.000	0.000	0.000
84	A	182	LEU	0	0.029	0.001	29.445	-0.251	-0.251	0.000	0.000	0.000	0.000
85	A	183	LYS	1	0.954	0.992	31.652	7.807	7.807	0.000	0.000	0.000	0.000
86	A	184	GLU	-1	-0.916	-0.951	32.870	-9.101	-9.101	0.000	0.000	0.000	0.000
87	A	185	LEU	0	0.036	0.011	27.607	-0.186	-0.186	0.000	0.000	0.000	0.000
88	A	186	ALA	0	0.028	0.016	28.865	-0.316	-0.316	0.000	0.000	0.000	0.000
89	A	187	LYS	1	0.926	0.963	30.148	8.316	8.316	0.000	0.000	0.000	0.000
90	A	188	MET	0	0.005	0.019	27.995	-0.191	-0.191	0.000	0.000	0.000	0.000
91	A	189	CYS	0	-0.024	-0.021	25.761	-0.380	-0.380	0.000	0.000	0.000	0.000
92	A	190	ILE	0	-0.010	0.002	26.476	-0.243	-0.243	0.000	0.000	0.000	0.000
93	A	191	LEU	0	-0.043	-0.023	28.891	-0.033	-0.033	0.000	0.000	0.000	0.000
94	A	192	ALA	0	0.011	0.010	25.130	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	193	ASP	-1	-0.850	-0.907	23.811	-13.460	-13.460	0.000	0.000	0.000	0.000
96	A	194	CYS	0	-0.039	-0.012	21.192	-0.565	-0.565	0.000	0.000	0.000	0.000
97	A	195	THR	0	0.029	0.014	20.029	0.665	0.665	0.000	0.000	0.000	0.000
98	A	196	LEU	0	-0.004	-0.003	21.494	-0.470	-0.470	0.000	0.000	0.000	0.000
99	A	197	ILE	0	-0.028	-0.008	19.500	0.108	0.108	0.000	0.000	0.000	0.000
100	A	198	LEU	0	0.002	0.005	22.742	0.023	0.023	0.000	0.000	0.000	0.000
101	A	199	ALA	0	0.002	0.002	21.634	-0.291	-0.291	0.000	0.000	0.000	0.000
102	A	200	TRP	0	0.025	-0.004	23.672	0.496	0.496	0.000	0.000	0.000	0.000
103	A	201	SER	0	0.002	0.002	23.143	0.139	0.139	0.000	0.000	0.000	0.000
104	A	202	PRO	0	0.015	-0.007	21.245	-0.435	-0.435	0.000	0.000	0.000	0.000
105	A	203	GLU	-1	-0.791	-0.883	18.533	-15.227	-15.227	0.000	0.000	0.000	0.000
106	A	204	GLU	-1	-0.819	-0.897	18.067	-13.475	-13.475	0.000	0.000	0.000	0.000
107	A	205	ALA	0	0.030	0.008	18.339	-0.572	-0.572	0.000	0.000	0.000	0.000
108	A	206	GLY	0	0.022	0.008	15.001	-0.949	-0.949	0.000	0.000	0.000	0.000
109	A	207	ARG	1	0.969	0.983	13.653	14.533	14.533	0.000	0.000	0.000	0.000
110	A	208	TYR	0	-0.012	-0.008	14.479	-0.794	-0.794	0.000	0.000	0.000	0.000
111	A	209	LEU	0	-0.019	-0.010	11.989	-0.800	-0.800	0.000	0.000	0.000	0.000
112	A	210	GLU	-1	-0.809	-0.893	9.665	-23.468	-23.468	0.000	0.000	0.000	0.000
113	A	211	THR	0	-0.040	-0.037	10.101	-0.803	-0.803	0.000	0.000	0.000	0.000
114	A	212	TYR	0	-0.009	-0.026	12.193	-0.024	-0.024	0.000	0.000	0.000	0.000
116	A	214	ALA	0	-0.018	0.002	7.113	-2.952	-2.952	0.000	0.000	0.000	0.000
117	A	215	TYR	0	-0.022	-0.002	9.093	0.617	0.617	0.000	0.000	0.000	0.000
118	A	216	GLU	-1	-0.892	-0.946	8.067	-33.335	-33.335	0.000	0.000	0.000	0.000
119	A	217	GLN	0	-0.044	-0.039	10.364	3.289	3.289	0.000	0.000	0.000	0.000
120	A	218	LYS	1	0.886	0.939	12.472	20.905	20.905	0.000	0.000	0.000	0.000
121	A	219	PRO	0	0.027	0.036	11.910	-1.428	-1.428	0.000	0.000	0.000	0.000
122	A	220	ALA	0	0.010	0.006	12.507	1.092	1.092	0.000	0.000	0.000	0.000
123	A	221	ASP	-1	-0.868	-0.935	14.129	-14.359	-14.359	0.000	0.000	0.000	0.000
124	A	222	LEU	0	0.015	-0.012	15.228	0.419	0.419	0.000	0.000	0.000	0.000
125	A	223	LEU	0	-0.050	-0.024	18.749	0.606	0.606	0.000	0.000	0.000	0.000
126	A	224	MET	0	-0.028	-0.015	21.317	0.786	0.786	0.000	0.000	0.000	0.000
127	A	225	GLU	-1	-0.992	-0.989	16.061	-18.537	-18.537	0.000	0.000	0.000	0.000
128	A	226	LYS	1	0.862	0.937	20.431	13.704	13.704	0.000	0.000	0.000	0.000
129	A	227	LEU	-1	-0.949	-0.953	23.060	-11.504	-11.504	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:99:ASN)