FMO DATABASE

FMODB ID: 6Z7MZ

Calculation Name: 2HQX-A-Xray547

Preferred Name: Staphylococcal nuclease domain-containing protein 1

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2HQX

Chain ID: A

ChEMBL ID: CHEMBL3879865

UniProt ID: Q7KZF4

Base Structure: X-ray

Registration Date: 2025-09-02

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	90
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-650764.144395
FMO2-HF: Nuclear repulsion	614868.150591
FMO2-HF: Total energy	-35895.993804
FMO2-MP2: Total energy	-36000.814037

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:8:THR)

Summations of interaction energy for fragment #1(A:8:THR)

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.
4.26	5.261	18.175	-8.535	-10.64	-0.089

Interaction energy analysis for fragmet #1(A:8:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.840 / q_NPA : 0.908

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	10	PHE	0	0.099	0.041	2.218	-0.708	1.076	2.364	-1.403	-2.744	-0.010
4	A	11	GLN	0	0.073	0.032	1.827	-37.991	-39.374	15.788	-7.060	-7.344	-0.078
5	A	12	LYS	1	1.025	1.020	3.361	68.479	69.079	0.023	-0.072	-0.552	-0.001
6	A	13	LEU	0	-0.014	0.018	5.955	5.863	5.863	0.000	0.000	0.000	0.000
7	A	14	MET	0	-0.015	0.000	6.637	4.360	4.360	0.000	0.000	0.000	0.000
8	A	15	GLU	-1	-0.937	-0.956	7.634	-32.695	-32.695	0.000	0.000	0.000	0.000
9	A	16	ASN	0	-0.048	-0.040	9.540	4.585	4.585	0.000	0.000	0.000	0.000
10	A	17	MET	0	-0.008	0.008	11.093	2.132	2.132	0.000	0.000	0.000	0.000
11	A	18	ARG	1	0.852	0.922	9.952	26.509	26.509	0.000	0.000	0.000	0.000
12	A	19	ASN	0	0.032	0.016	13.016	2.083	2.083	0.000	0.000	0.000	0.000
13	A	20	ASP	-1	-0.876	-0.919	15.444	-15.281	-15.281	0.000	0.000	0.000	0.000
14	A	21	ILE	0	-0.006	-0.014	15.270	1.029	1.029	0.000	0.000	0.000	0.000
15	A	22	ALA	0	-0.043	-0.022	17.841	0.850	0.850	0.000	0.000	0.000	0.000
16	A	23	SER	0	-0.057	-0.030	19.521	0.866	0.866	0.000	0.000	0.000	0.000
17	A	24	HIS	0	-0.065	-0.030	21.182	0.893	0.893	0.000	0.000	0.000	0.000
18	A	25	PRO	0	0.017	0.015	22.082	-0.293	-0.293	0.000	0.000	0.000	0.000
19	A	26	PRO	0	-0.044	-0.026	21.328	0.511	0.511	0.000	0.000	0.000	0.000
20	A	27	VAL	0	0.020	0.020	24.195	0.210	0.210	0.000	0.000	0.000	0.000
21	A	28	GLU	-1	-0.854	-0.927	28.020	-9.895	-9.895	0.000	0.000	0.000	0.000
22	A	29	GLY	0	-0.023	-0.014	29.716	0.245	0.245	0.000	0.000	0.000	0.000
23	A	30	SER	0	-0.041	-0.007	28.434	0.124	0.124	0.000	0.000	0.000	0.000
24	A	31	TYR	0	-0.006	0.005	23.093	-0.060	-0.060	0.000	0.000	0.000	0.000
25	A	32	ALA	0	0.025	0.012	27.270	0.200	0.200	0.000	0.000	0.000	0.000
26	A	33	PRO	0	-0.017	-0.010	26.051	-0.131	-0.131	0.000	0.000	0.000	0.000
27	A	34	ARG	1	0.976	0.984	26.296	10.169	10.169	0.000	0.000	0.000	0.000
28	A	35	ARG	1	0.932	0.965	25.835	9.790	9.790	0.000	0.000	0.000	0.000
29	A	36	GLY	0	-0.031	-0.021	24.073	0.312	0.312	0.000	0.000	0.000	0.000
30	A	37	GLU	-1	-0.873	-0.926	22.355	-13.196	-13.196	0.000	0.000	0.000	0.000
31	A	38	PHE	0	-0.022	-0.031	16.340	-0.368	-0.368	0.000	0.000	0.000	0.000
32	A	39	CYS	0	-0.066	-0.015	18.476	0.474	0.474	0.000	0.000	0.000	0.000
33	A	40	ILE	0	0.010	0.013	15.427	-1.094	-1.094	0.000	0.000	0.000	0.000
34	A	41	ALA	0	0.029	-0.004	16.881	1.055	1.055	0.000	0.000	0.000	0.000
35	A	42	LYS	1	0.932	0.981	16.903	13.359	13.359	0.000	0.000	0.000	0.000
36	A	43	PHE	0	0.051	0.048	15.376	1.065	1.065	0.000	0.000	0.000	0.000
37	A	44	VAL	0	0.009	-0.013	18.240	0.424	0.424	0.000	0.000	0.000	0.000
38	A	45	ASP	-1	-0.792	-0.870	14.679	-18.726	-18.726	0.000	0.000	0.000	0.000
39	A	46	GLY	0	-0.052	-0.017	18.358	0.126	0.126	0.000	0.000	0.000	0.000
40	A	47	GLU	-1	-0.899	-0.963	13.587	-20.409	-20.409	0.000	0.000	0.000	0.000
41	A	48	TRP	0	-0.014	-0.010	14.875	0.718	0.718	0.000	0.000	0.000	0.000
42	A	49	TYR	0	-0.068	-0.068	10.563	-3.016	-3.016	0.000	0.000	0.000	0.000
43	A	50	ARG	1	0.730	0.825	9.599	25.720	25.720	0.000	0.000	0.000	0.000
44	A	51	ALA	0	-0.025	-0.015	13.807	-0.371	-0.371	0.000	0.000	0.000	0.000
45	A	52	ARG	1	0.899	0.965	16.478	14.318	14.318	0.000	0.000	0.000	0.000
46	A	53	VAL	0	0.048	0.035	19.349	0.119	0.119	0.000	0.000	0.000	0.000
47	A	54	GLU	-1	-0.821	-0.882	21.720	-12.824	-12.824	0.000	0.000	0.000	0.000
48	A	55	LYS	1	0.873	0.927	24.701	10.088	10.088	0.000	0.000	0.000	0.000
49	A	56	VAL	0	0.026	0.026	27.575	-0.282	-0.282	0.000	0.000	0.000	0.000
50	A	57	GLU	-1	-0.905	-0.943	30.154	-9.130	-9.130	0.000	0.000	0.000	0.000
51	A	58	SER	0	0.005	-0.009	31.920	0.333	0.333	0.000	0.000	0.000	0.000
52	A	59	PRO	0	0.052	0.018	31.560	-0.307	-0.307	0.000	0.000	0.000	0.000
53	A	60	ALA	0	0.028	0.015	30.782	-0.292	-0.292	0.000	0.000	0.000	0.000
54	A	61	LYS	1	0.866	0.946	28.923	9.007	9.007	0.000	0.000	0.000	0.000
55	A	62	ILE	0	0.029	0.015	25.099	0.284	0.284	0.000	0.000	0.000	0.000
56	A	63	HIS	0	-0.034	-0.032	25.124	-0.442	-0.442	0.000	0.000	0.000	0.000
57	A	64	VAL	0	0.016	-0.002	20.130	0.085	0.085	0.000	0.000	0.000	0.000
58	A	65	PHE	0	0.012	0.013	15.888	-0.094	-0.094	0.000	0.000	0.000	0.000
59	A	66	TYR	0	0.011	-0.028	13.692	-0.383	-0.383	0.000	0.000	0.000	0.000
60	A	67	ILE	0	-0.032	-0.029	12.258	-0.480	-0.480	0.000	0.000	0.000	0.000
61	A	68	ASP	-1	-0.758	-0.854	8.224	-25.893	-25.893	0.000	0.000	0.000	0.000
62	A	69	TYR	0	0.013	0.000	7.359	-2.885	-2.885	0.000	0.000	0.000	0.000
63	A	70	GLY	0	0.022	0.027	11.147	0.616	0.616	0.000	0.000	0.000	0.000
64	A	71	ASN	0	-0.005	0.001	14.488	0.419	0.419	0.000	0.000	0.000	0.000
65	A	72	ARG	1	0.820	0.858	16.723	13.596	13.596	0.000	0.000	0.000	0.000
66	A	73	GLU	-1	-0.824	-0.893	19.821	-14.359	-14.359	0.000	0.000	0.000	0.000
67	A	74	VAL	0	-0.030	-0.018	21.956	0.202	0.202	0.000	0.000	0.000	0.000
68	A	75	LEU	0	0.019	0.017	21.082	0.191	0.191	0.000	0.000	0.000	0.000
69	A	76	PRO	0	0.031	0.017	25.747	0.178	0.178	0.000	0.000	0.000	0.000
70	A	77	SER	0	0.017	-0.006	26.209	-0.530	-0.530	0.000	0.000	0.000	0.000
71	A	78	THR	0	-0.012	-0.018	26.249	-0.323	-0.323	0.000	0.000	0.000	0.000
72	A	79	ARG	1	0.800	0.903	21.126	13.065	13.065	0.000	0.000	0.000	0.000
73	A	80	LEU	0	-0.030	-0.017	21.498	-0.742	-0.742	0.000	0.000	0.000	0.000
74	A	81	GLY	0	0.061	0.024	21.419	0.400	0.400	0.000	0.000	0.000	0.000
75	A	82	THR	0	0.001	-0.008	21.127	-0.287	-0.287	0.000	0.000	0.000	0.000
76	A	83	LEU	0	-0.013	0.018	14.377	-0.369	-0.369	0.000	0.000	0.000	0.000
77	A	84	SER	0	0.035	0.012	17.841	0.255	0.255	0.000	0.000	0.000	0.000
78	A	85	PRO	0	0.007	-0.023	17.073	-0.897	-0.897	0.000	0.000	0.000	0.000
79	A	86	ALA	0	0.007	0.021	15.896	-0.342	-0.342	0.000	0.000	0.000	0.000
80	A	87	PHE	0	0.048	0.021	11.884	-1.674	-1.674	0.000	0.000	0.000	0.000
81	A	88	SER	0	-0.006	-0.007	12.995	-0.316	-0.316	0.000	0.000	0.000	0.000
82	A	89	THR	0	0.007	-0.012	13.094	-0.778	-0.778	0.000	0.000	0.000	0.000
83	A	90	ARG	1	0.929	0.963	14.117	14.655	14.655	0.000	0.000	0.000	0.000
84	A	91	VAL	0	-0.032	0.012	11.628	0.255	0.255	0.000	0.000	0.000	0.000
85	A	92	LEU	0	0.021	0.010	5.469	-1.774	-1.774	0.000	0.000	0.000	0.000
86	A	93	PRO	0	0.032	0.020	10.058	0.717	0.717	0.000	0.000	0.000	0.000
87	A	94	ALA	0	-0.014	-0.004	9.536	-1.808	-1.808	0.000	0.000	0.000	0.000
88	A	95	GLN	0	-0.061	-0.051	5.418	-3.677	-3.677	0.000	0.000	0.000	0.000
89	A	96	ALA	0	-0.058	-0.008	8.148	-1.433	-1.433	0.000	0.000	0.000	0.000
90	A	97	THR	-1	-0.935	-0.950	8.674	-20.119	-20.119	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:8:THR)