FMO DATABASE

FMODB ID: 6Z9JZ

Calculation Name: 2E1F-A-Xray547

Preferred Name: Werner syndrome ATP-dependent helicase

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2E1F

Chain ID: A

ChEMBL ID: CHEMBL2146312

UniProt ID: Q14191

Base Structure: X-ray

Registration Date: 2025-10-04

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	94
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-658006.286191
FMO2-HF: Nuclear repulsion	621115.816837
FMO2-HF: Total energy	-36890.469354
FMO2-MP2: Total energy	-36996.021687

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:1142:GLN)

Summations of interaction energy for fragment #1(A:1142:GLN)

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.
-5.611	-3.554	0.032	-1.143	-0.946	-0.005

Interaction energy analysis for fragmet #1(A:1142:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.853 / q_NPA : 0.916

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	1144	VAL	0	0.034	0.016	3.136	-12.294	-10.237	0.032	-1.143	-0.946	-0.005
4	A	1145	ILE	0	0.003	0.026	5.706	5.006	5.006	0.000	0.000	0.000	0.000
5	A	1146	SER	0	0.029	0.008	7.930	-2.845	-2.845	0.000	0.000	0.000	0.000
6	A	1147	ALA	0	0.037	0.003	10.326	0.609	0.609	0.000	0.000	0.000	0.000
7	A	1148	GLN	0	0.087	0.042	11.921	1.113	1.113	0.000	0.000	0.000	0.000
8	A	1149	GLU	-1	-0.778	-0.818	12.522	-18.813	-18.813	0.000	0.000	0.000	0.000
9	A	1150	GLN	0	0.018	-0.004	10.726	0.507	0.507	0.000	0.000	0.000	0.000
10	A	1151	GLU	-1	-0.951	-0.976	13.349	-15.478	-15.478	0.000	0.000	0.000	0.000
11	A	1152	THR	0	0.004	-0.010	16.682	1.408	1.408	0.000	0.000	0.000	0.000
12	A	1153	GLN	0	-0.063	-0.052	13.124	1.010	1.010	0.000	0.000	0.000	0.000
13	A	1154	ILE	0	-0.017	-0.005	14.326	0.996	0.996	0.000	0.000	0.000	0.000
14	A	1155	VAL	0	0.000	-0.003	18.160	0.982	0.982	0.000	0.000	0.000	0.000
15	A	1156	LEU	0	-0.007	0.004	20.886	0.808	0.808	0.000	0.000	0.000	0.000
16	A	1157	TYR	0	0.005	-0.001	19.594	0.724	0.724	0.000	0.000	0.000	0.000
17	A	1158	GLY	0	0.018	0.008	21.630	0.565	0.565	0.000	0.000	0.000	0.000
18	A	1159	LYS	1	0.982	0.991	23.954	11.921	11.921	0.000	0.000	0.000	0.000
19	A	1160	LEU	0	-0.010	-0.003	23.099	0.550	0.550	0.000	0.000	0.000	0.000
20	A	1161	VAL	0	-0.010	-0.005	24.095	0.444	0.444	0.000	0.000	0.000	0.000
21	A	1162	GLU	-1	-0.935	-0.960	26.836	-9.802	-9.802	0.000	0.000	0.000	0.000
22	A	1163	ALA	0	-0.026	-0.012	29.589	0.423	0.423	0.000	0.000	0.000	0.000
23	A	1164	ARG	1	0.842	0.905	25.691	11.556	11.556	0.000	0.000	0.000	0.000
24	A	1165	GLN	0	-0.022	-0.016	30.819	0.066	0.066	0.000	0.000	0.000	0.000
25	A	1166	LYS	1	0.952	0.972	32.650	8.876	8.876	0.000	0.000	0.000	0.000
26	A	1167	HIS	0	-0.049	-0.021	34.322	0.491	0.491	0.000	0.000	0.000	0.000
27	A	1168	ALA	0	0.031	0.007	33.736	0.225	0.225	0.000	0.000	0.000	0.000
28	A	1169	ASN	0	0.036	0.012	35.786	0.094	0.094	0.000	0.000	0.000	0.000
29	A	1170	LYS	1	0.897	0.952	38.361	7.995	7.995	0.000	0.000	0.000	0.000
30	A	1171	MET	0	-0.069	-0.031	36.834	0.064	0.064	0.000	0.000	0.000	0.000
31	A	1172	ASP	-1	-0.907	-0.925	40.257	-7.212	-7.212	0.000	0.000	0.000	0.000
32	A	1173	VAL	0	-0.014	-0.001	35.487	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	1174	PRO	0	0.040	0.010	34.081	-0.179	-0.179	0.000	0.000	0.000	0.000
34	A	1175	PRO	0	0.038	0.006	30.203	-0.116	-0.116	0.000	0.000	0.000	0.000
35	A	1176	ALA	0	-0.019	-0.012	29.024	-0.213	-0.213	0.000	0.000	0.000	0.000
36	A	1177	ILE	0	-0.001	0.007	29.990	-0.169	-0.169	0.000	0.000	0.000	0.000
37	A	1178	LEU	0	-0.015	0.013	31.178	-0.011	-0.011	0.000	0.000	0.000	0.000
38	A	1179	ALA	0	0.033	-0.001	26.872	-0.150	-0.150	0.000	0.000	0.000	0.000
39	A	1180	THR	0	0.035	0.033	24.112	-0.176	-0.176	0.000	0.000	0.000	0.000
40	A	1181	ASN	0	0.085	0.033	21.509	0.187	0.187	0.000	0.000	0.000	0.000
41	A	1182	LYS	1	0.877	0.939	19.094	14.275	14.275	0.000	0.000	0.000	0.000
42	A	1183	ILE	0	0.070	0.039	20.356	-0.449	-0.449	0.000	0.000	0.000	0.000
43	A	1184	LEU	0	0.017	0.013	22.625	-0.142	-0.142	0.000	0.000	0.000	0.000
44	A	1185	VAL	0	-0.004	-0.002	15.975	-0.334	-0.334	0.000	0.000	0.000	0.000
45	A	1186	ASP	-1	-0.853	-0.915	17.676	-17.388	-17.388	0.000	0.000	0.000	0.000
46	A	1187	MET	0	-0.015	-0.011	19.355	-0.099	-0.099	0.000	0.000	0.000	0.000
47	A	1188	ALA	0	-0.015	-0.010	19.042	0.045	0.045	0.000	0.000	0.000	0.000
48	A	1189	LYS	1	0.853	0.940	13.456	19.404	19.404	0.000	0.000	0.000	0.000
49	A	1190	MET	0	0.019	0.007	17.548	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	1191	ARG	1	0.738	0.850	16.915	17.681	17.681	0.000	0.000	0.000	0.000
51	A	1192	PRO	0	-0.003	0.013	22.783	0.302	0.302	0.000	0.000	0.000	0.000
52	A	1193	THR	0	-0.001	-0.042	25.732	0.445	0.445	0.000	0.000	0.000	0.000
53	A	1194	THR	0	-0.027	-0.016	28.679	0.496	0.496	0.000	0.000	0.000	0.000
54	A	1195	VAL	0	0.026	-0.003	30.098	-0.292	-0.292	0.000	0.000	0.000	0.000
55	A	1196	GLU	-1	-0.849	-0.936	31.399	-9.439	-9.439	0.000	0.000	0.000	0.000
56	A	1197	ASN	0	0.000	-0.020	26.424	-0.236	-0.236	0.000	0.000	0.000	0.000
57	A	1198	VAL	0	-0.019	-0.009	26.389	-0.420	-0.420	0.000	0.000	0.000	0.000
58	A	1199	LYS	1	0.821	0.906	27.302	9.004	9.004	0.000	0.000	0.000	0.000
59	A	1200	ARG	1	0.827	0.927	24.547	12.683	12.683	0.000	0.000	0.000	0.000
60	A	1201	ILE	0	-0.007	0.006	22.373	-0.545	-0.545	0.000	0.000	0.000	0.000
61	A	1202	ASP	-1	-0.863	-0.931	21.097	-13.675	-13.675	0.000	0.000	0.000	0.000
62	A	1203	GLY	0	-0.020	-0.020	24.467	-0.051	-0.051	0.000	0.000	0.000	0.000
63	A	1204	VAL	0	-0.076	-0.038	26.608	0.452	0.452	0.000	0.000	0.000	0.000
64	A	1205	SER	0	0.036	0.025	29.196	0.053	0.053	0.000	0.000	0.000	0.000
65	A	1206	GLU	-1	-0.843	-0.932	32.664	-8.470	-8.470	0.000	0.000	0.000	0.000
66	A	1207	GLY	0	0.036	0.015	35.157	0.046	0.046	0.000	0.000	0.000	0.000
67	A	1208	LYS	1	0.843	0.923	29.456	9.982	9.982	0.000	0.000	0.000	0.000
68	A	1209	ALA	0	0.043	0.008	31.789	-0.107	-0.107	0.000	0.000	0.000	0.000
69	A	1210	ALA	0	-0.009	0.007	32.756	-0.016	-0.016	0.000	0.000	0.000	0.000
70	A	1211	MET	0	-0.021	-0.015	34.535	0.107	0.107	0.000	0.000	0.000	0.000
71	A	1212	LEU	0	0.000	-0.007	28.444	-0.068	-0.068	0.000	0.000	0.000	0.000
72	A	1213	ALA	0	0.052	0.039	31.638	-0.247	-0.247	0.000	0.000	0.000	0.000
73	A	1214	PRO	0	0.000	-0.014	33.543	-0.116	-0.116	0.000	0.000	0.000	0.000
74	A	1215	LEU	0	-0.034	-0.020	27.284	-0.103	-0.103	0.000	0.000	0.000	0.000
75	A	1216	LEU	0	0.021	0.014	28.749	-0.350	-0.350	0.000	0.000	0.000	0.000
76	A	1217	GLU	-1	-0.872	-0.912	30.262	-9.314	-9.314	0.000	0.000	0.000	0.000
77	A	1218	VAL	0	-0.034	-0.022	27.654	-0.079	-0.079	0.000	0.000	0.000	0.000
78	A	1219	ILE	0	0.006	0.005	25.000	-0.254	-0.254	0.000	0.000	0.000	0.000
79	A	1220	LYS	1	0.899	0.941	27.056	9.253	9.253	0.000	0.000	0.000	0.000
80	A	1221	HIS	0	0.013	0.020	29.281	-0.236	-0.236	0.000	0.000	0.000	0.000
81	A	1222	PHE	0	0.006	-0.003	22.342	0.069	0.069	0.000	0.000	0.000	0.000
82	A	1223	CYS	0	-0.047	-0.029	24.244	-0.430	-0.430	0.000	0.000	0.000	0.000
83	A	1224	GLN	0	-0.012	0.024	25.913	-0.040	-0.040	0.000	0.000	0.000	0.000
84	A	1225	THR	0	-0.082	-0.053	29.034	0.233	0.233	0.000	0.000	0.000	0.000
85	A	1226	ASN	0	-0.059	-0.034	24.048	-0.046	-0.046	0.000	0.000	0.000	0.000
86	A	1227	SER	0	0.005	0.006	24.127	-0.043	-0.043	0.000	0.000	0.000	0.000
87	A	1228	VAL	0	-0.027	-0.014	20.160	-0.617	-0.617	0.000	0.000	0.000	0.000
88	A	1229	GLN	0	0.004	0.000	17.787	0.355	0.355	0.000	0.000	0.000	0.000
89	A	1230	THR	0	0.003	-0.029	20.783	-0.393	-0.393	0.000	0.000	0.000	0.000
90	A	1231	ASP	-1	-0.775	-0.852	22.348	-12.209	-12.209	0.000	0.000	0.000	0.000
91	A	1232	LEU	0	-0.008	0.014	16.188	-0.070	-0.070	0.000	0.000	0.000	0.000
92	A	1233	PHE	0	-0.024	-0.026	19.181	-0.321	-0.321	0.000	0.000	0.000	0.000
93	A	1234	SER	0	-0.027	-0.019	16.644	0.157	0.157	0.000	0.000	0.000	0.000
94	A	1235	SER	-1	-0.867	-0.898	18.716	-13.200	-13.200	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1142:GLN)