FMO DATABASE

FMODB ID: 9QYZ2

Calculation Name: 4X42-B-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4X42

Chain ID: B

ChEMBL ID:

UniProt ID: P09866

Base Structure: X-ray

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	99
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-695338.096584
FMO2-HF: Nuclear repulsion	656482.757958
FMO2-HF: Total energy	-38855.338626
FMO2-MP2: Total energy	-38966.44064

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:574:SER)

Summations of interaction energy for fragment #1(B:574:SER)

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.
8.024	9.466	-0.023	-0.692	-0.726	-0.002

Interaction energy analysis for fragmet #1(B:574:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.865 / q_NPA : 0.914

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	B	576	MET	0	0.029	0.032	3.840	0.891	2.333	-0.023	-0.692	-0.726	-0.002
4	B	577	SER	0	-0.011	-0.002	5.883	-1.768	-1.768	0.000	0.000	0.000	0.000
5	B	578	TYR	0	0.059	0.036	8.013	1.896	1.896	0.000	0.000	0.000	0.000
6	B	579	THR	0	0.018	0.003	11.554	-0.725	-0.725	0.000	0.000	0.000	0.000
7	B	580	MET	0	-0.017	-0.016	14.636	-0.141	-0.141	0.000	0.000	0.000	0.000
8	B	581	CYS	0	-0.078	-0.016	15.513	-0.208	-0.208	0.000	0.000	0.000	0.000
9	B	582	SER	0	0.024	0.006	20.267	0.292	0.292	0.000	0.000	0.000	0.000
10	B	583	GLY	0	-0.003	0.001	23.244	0.609	0.609	0.000	0.000	0.000	0.000
11	B	584	LYS	1	0.836	0.902	25.685	9.586	9.586	0.000	0.000	0.000	0.000
12	B	585	PHE	0	0.059	0.016	21.554	-0.350	-0.350	0.000	0.000	0.000	0.000
13	B	586	SER	0	-0.062	-0.056	27.661	0.343	0.343	0.000	0.000	0.000	0.000
14	B	587	ILE	0	0.014	0.005	29.098	-0.419	-0.419	0.000	0.000	0.000	0.000
15	B	588	ASP	-1	-0.933	-0.963	29.167	-10.483	-10.483	0.000	0.000	0.000	0.000
16	B	589	LYS	1	0.922	0.943	30.364	10.083	10.083	0.000	0.000	0.000	0.000
17	B	590	GLU	-1	-0.897	-0.954	30.553	-9.205	-9.205	0.000	0.000	0.000	0.000
18	B	591	MET	0	-0.055	-0.006	27.321	-0.179	-0.179	0.000	0.000	0.000	0.000
19	B	592	ALA	0	0.009	0.009	30.714	0.380	0.380	0.000	0.000	0.000	0.000
20	B	593	GLU	-1	-0.902	-0.956	30.576	-9.775	-9.775	0.000	0.000	0.000	0.000
21	B	594	THR	0	-0.056	-0.046	27.626	0.262	0.262	0.000	0.000	0.000	0.000
22	B	595	GLN	0	-0.046	-0.039	30.977	0.060	0.060	0.000	0.000	0.000	0.000
23	B	596	HIS	0	0.010	0.000	27.303	0.323	0.323	0.000	0.000	0.000	0.000
24	B	597	GLY	0	0.012	0.026	28.579	-0.215	-0.215	0.000	0.000	0.000	0.000
25	B	598	THR	0	-0.051	-0.025	24.402	0.052	0.052	0.000	0.000	0.000	0.000
26	B	599	THR	0	0.001	-0.022	26.719	0.304	0.304	0.000	0.000	0.000	0.000
27	B	600	VAL	0	-0.003	-0.008	25.272	-0.639	-0.639	0.000	0.000	0.000	0.000
28	B	601	VAL	0	-0.011	0.010	25.575	0.535	0.535	0.000	0.000	0.000	0.000
29	B	602	LYS	1	0.910	0.966	25.760	10.907	10.907	0.000	0.000	0.000	0.000
30	B	603	VAL	0	0.031	0.020	23.931	0.481	0.481	0.000	0.000	0.000	0.000
31	B	604	LYS	1	0.958	0.993	25.521	9.905	9.905	0.000	0.000	0.000	0.000
32	B	605	TYR	0	-0.017	-0.016	22.634	0.183	0.183	0.000	0.000	0.000	0.000
33	B	606	GLU	-1	-0.808	-0.880	25.805	-9.861	-9.861	0.000	0.000	0.000	0.000
34	B	607	GLY	0	-0.013	0.009	25.887	0.333	0.333	0.000	0.000	0.000	0.000
35	B	608	ALA	0	0.034	0.026	24.761	-0.143	-0.143	0.000	0.000	0.000	0.000
36	B	609	GLY	0	0.009	0.000	20.988	-0.198	-0.198	0.000	0.000	0.000	0.000
37	B	610	ALA	0	-0.001	0.023	18.933	-0.739	-0.739	0.000	0.000	0.000	0.000
38	B	611	PRO	0	-0.024	0.002	15.220	0.464	0.464	0.000	0.000	0.000	0.000
39	B	613	LYS	1	0.916	0.956	11.425	24.982	24.982	0.000	0.000	0.000	0.000
40	B	614	VAL	0	0.045	0.010	15.779	0.880	0.880	0.000	0.000	0.000	0.000
41	B	615	PRO	0	-0.050	-0.011	18.140	-0.602	-0.602	0.000	0.000	0.000	0.000
42	B	616	ILE	0	0.037	0.012	18.706	0.715	0.715	0.000	0.000	0.000	0.000
43	B	617	GLU	-1	-0.875	-0.909	20.241	-13.500	-13.500	0.000	0.000	0.000	0.000
44	B	618	ILE	0	0.033	0.019	22.317	0.444	0.444	0.000	0.000	0.000	0.000
45	B	619	ARG	1	0.759	0.852	24.800	11.342	11.342	0.000	0.000	0.000	0.000
46	B	620	ASP	-1	-0.741	-0.876	27.779	-10.076	-10.076	0.000	0.000	0.000	0.000
47	B	621	VAL	0	0.043	0.017	30.658	0.067	0.067	0.000	0.000	0.000	0.000
48	B	622	ASN	0	-0.042	-0.011	32.813	0.510	0.510	0.000	0.000	0.000	0.000
49	B	623	LYS	1	0.896	0.946	31.312	9.095	9.095	0.000	0.000	0.000	0.000
50	B	624	GLU	-1	-0.899	-0.932	28.729	-10.440	-10.440	0.000	0.000	0.000	0.000
51	B	625	LYS	1	0.846	0.910	20.602	14.069	14.069	0.000	0.000	0.000	0.000
52	B	626	VAL	0	0.023	0.015	24.581	-0.013	-0.013	0.000	0.000	0.000	0.000
53	B	627	VAL	0	-0.018	-0.016	18.587	-0.569	-0.569	0.000	0.000	0.000	0.000
54	B	628	GLY	0	-0.002	-0.009	18.279	0.345	0.345	0.000	0.000	0.000	0.000
55	B	629	ARG	1	0.907	0.961	19.348	12.536	12.536	0.000	0.000	0.000	0.000
56	B	630	ILE	0	-0.017	-0.010	17.626	0.546	0.546	0.000	0.000	0.000	0.000
57	B	631	ILE	0	0.018	0.015	17.946	-0.809	-0.809	0.000	0.000	0.000	0.000
58	B	632	SER	0	-0.012	0.002	17.638	-0.424	-0.424	0.000	0.000	0.000	0.000
59	B	633	SER	0	0.029	0.011	12.210	-0.400	-0.400	0.000	0.000	0.000	0.000
60	B	634	THR	0	-0.047	-0.044	10.485	0.982	0.982	0.000	0.000	0.000	0.000
61	B	635	PRO	0	0.047	0.040	13.361	-0.628	-0.628	0.000	0.000	0.000	0.000
62	B	636	LEU	0	0.036	0.026	12.706	-0.368	-0.368	0.000	0.000	0.000	0.000
63	B	637	ALA	0	0.017	0.028	16.745	1.023	1.023	0.000	0.000	0.000	0.000
64	B	638	GLU	-1	-0.855	-0.936	16.529	-19.974	-19.974	0.000	0.000	0.000	0.000
65	B	639	ASN	0	-0.042	-0.045	19.120	0.355	0.355	0.000	0.000	0.000	0.000
66	B	640	THR	0	0.011	-0.005	22.263	0.004	0.004	0.000	0.000	0.000	0.000
67	B	641	ASN	0	-0.045	-0.036	25.324	0.345	0.345	0.000	0.000	0.000	0.000
68	B	642	SER	0	-0.033	-0.006	22.803	0.041	0.041	0.000	0.000	0.000	0.000
69	B	643	VAL	0	0.023	-0.001	25.065	0.145	0.145	0.000	0.000	0.000	0.000
70	B	644	THR	0	-0.035	-0.025	19.811	-0.152	-0.152	0.000	0.000	0.000	0.000
71	B	645	ASN	0	-0.013	-0.017	22.373	1.128	1.128	0.000	0.000	0.000	0.000
72	B	646	ILE	0	-0.018	-0.019	20.718	-0.888	-0.888	0.000	0.000	0.000	0.000
73	B	647	GLU	-1	-0.853	-0.893	21.387	-12.962	-12.962	0.000	0.000	0.000	0.000
74	B	648	LEU	0	-0.026	-0.019	21.297	-0.909	-0.909	0.000	0.000	0.000	0.000
75	B	649	GLU	-1	-0.875	-0.944	23.523	-12.243	-12.243	0.000	0.000	0.000	0.000
76	B	650	PRO	0	-0.010	0.015	25.331	-0.142	-0.142	0.000	0.000	0.000	0.000
77	B	651	PRO	0	-0.001	-0.002	27.334	0.109	0.109	0.000	0.000	0.000	0.000
78	B	652	PHE	0	-0.009	-0.013	29.660	0.038	0.038	0.000	0.000	0.000	0.000
79	B	653	GLY	0	0.018	0.020	33.478	-0.008	-0.008	0.000	0.000	0.000	0.000
80	B	654	ASP	-1	-0.872	-0.930	34.519	-8.665	-8.665	0.000	0.000	0.000	0.000
81	B	655	SER	0	-0.051	-0.029	29.472	-0.311	-0.311	0.000	0.000	0.000	0.000
82	B	656	TYR	0	-0.017	-0.003	30.165	0.110	0.110	0.000	0.000	0.000	0.000
83	B	657	ILE	0	-0.002	-0.004	24.970	-0.494	-0.494	0.000	0.000	0.000	0.000
84	B	658	VAL	0	-0.027	-0.011	25.917	0.421	0.421	0.000	0.000	0.000	0.000
85	B	659	ILE	0	0.021	0.003	23.098	-0.662	-0.662	0.000	0.000	0.000	0.000
86	B	660	GLY	0	-0.003	0.002	23.373	0.516	0.516	0.000	0.000	0.000	0.000
87	B	661	VAL	0	-0.016	-0.020	23.043	-0.059	-0.059	0.000	0.000	0.000	0.000
88	B	662	GLY	0	0.029	0.014	25.900	0.272	0.272	0.000	0.000	0.000	0.000
89	B	663	ASP	-1	-0.888	-0.950	29.362	-9.427	-9.427	0.000	0.000	0.000	0.000
90	B	664	LYS	1	0.897	0.939	31.148	9.492	9.492	0.000	0.000	0.000	0.000
91	B	665	ALA	0	-0.001	0.031	27.660	-0.124	-0.124	0.000	0.000	0.000	0.000
92	B	666	LEU	0	-0.011	-0.009	27.607	0.471	0.471	0.000	0.000	0.000	0.000
93	B	667	LYS	1	0.882	0.930	28.794	9.441	9.441	0.000	0.000	0.000	0.000
94	B	668	LEU	0	0.001	0.007	28.547	0.341	0.341	0.000	0.000	0.000	0.000
95	B	669	ASN	0	-0.031	-0.038	31.298	-0.374	-0.374	0.000	0.000	0.000	0.000
96	B	670	TRP	0	0.008	0.004	31.113	0.020	0.020	0.000	0.000	0.000	0.000
97	B	671	PHE	0	0.015	0.019	33.145	-0.069	-0.069	0.000	0.000	0.000	0.000
98	B	672	ARG	1	0.845	0.933	29.088	10.382	10.382	0.000	0.000	0.000	0.000
99	B	673	LYS	0	0.124	0.054	34.808	-0.692	-0.692	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:574:SER)