FMO DATABASE

FMODB ID: 65JRZ

Calculation Name: 2F01-A-Xray549

Preferred Name: Streptavidin

Target Type: SINGLE PROTEIN

Ligand Name: biotin | epi-biotin | glycerol

Ligand 3-letter code: BTN | BTQ | GOL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2F01

Chain ID: A

ChEMBL ID: CHEMBL1075026

UniProt ID: P22629

Base Structure: X-ray

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	121
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230712

Total energy (hartree)

FMO2-HF: Electronic energy	-885951.819579
FMO2-HF: Nuclear repulsion	841735.752626
FMO2-HF: Total energy	-44216.066953
FMO2-MP2: Total energy	-44348.17987

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:14:GLU)

Summations of interaction energy for fragment #1(A:14:GLU)

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.
-50.448	-42.129	21.492	-10.417	-19.396	0.018

Interaction energy analysis for fragmet #1(A:14:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : -0.002

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	16	GLY	0	0.025	0.018	3.698	1.129	2.764	0.005	-0.659	-0.982	0.000
4	A	17	ILE	0	0.011	0.015	2.408	3.043	4.621	0.513	-0.706	-1.385	-0.005
5	A	18	THR	0	0.016	0.006	3.900	3.147	3.832	0.002	-0.221	-0.466	0.000
20	A	33	ALA	0	-0.030	-0.015	2.498	-2.088	-1.282	0.985	-0.753	-1.038	-0.003
21	A	34	GLY	0	0.011	0.013	3.013	3.018	5.016	1.612	-1.490	-2.121	0.004
22	A	35	ALA	0	0.072	0.026	2.574	-7.254	-5.976	5.095	-1.410	-4.964	0.032
23	A	36	ASP	-1	-0.845	-0.919	3.141	0.976	-0.629	0.388	1.733	-0.516	0.011
24	A	37	GLY	0	0.050	0.043	4.999	-3.911	-3.882	-0.001	-0.002	-0.026	0.000
47	A	60	TYR	0	-0.025	-0.025	1.981	-40.157	-38.497	12.895	-6.885	-7.670	-0.021
49	A	62	SER	0	-0.043	-0.030	4.321	-5.839	-5.655	-0.001	-0.023	-0.160	0.000
50	A	63	ALA	0	-0.061	-0.027	5.293	1.536	1.607	-0.001	-0.001	-0.068	0.000
6	A	19	GLY	0	0.015	0.017	5.820	0.420	0.420	0.000	0.000	0.000	0.000
7	A	20	THR	0	-0.007	0.002	9.579	0.323	0.323	0.000	0.000	0.000	0.000
8	A	21	TRP	0	-0.026	-0.012	7.341	-0.246	-0.246	0.000	0.000	0.000	0.000
9	A	22	TYR	0	0.029	0.017	13.365	0.352	0.352	0.000	0.000	0.000	0.000
10	A	23	ASN	0	0.014	0.008	16.460	-0.169	-0.169	0.000	0.000	0.000	0.000
11	A	24	GLN	0	0.049	0.004	18.079	-0.033	-0.033	0.000	0.000	0.000	0.000
12	A	25	LEU	0	-0.067	-0.028	21.372	0.155	0.155	0.000	0.000	0.000	0.000
13	A	26	GLY	0	0.019	0.015	21.773	0.133	0.133	0.000	0.000	0.000	0.000
14	A	27	SER	0	-0.032	-0.001	19.573	0.149	0.149	0.000	0.000	0.000	0.000
15	A	28	THR	0	-0.010	-0.006	16.657	-0.242	-0.242	0.000	0.000	0.000	0.000
16	A	29	PHE	0	-0.007	-0.004	9.410	0.215	0.215	0.000	0.000	0.000	0.000
17	A	30	ILE	0	-0.005	-0.001	12.279	-0.429	-0.429	0.000	0.000	0.000	0.000
18	A	31	VAL	0	0.015	0.007	6.906	0.520	0.520	0.000	0.000	0.000	0.000
19	A	32	THR	0	-0.018	-0.022	6.216	-0.806	-0.806	0.000	0.000	0.000	0.000
25	A	38	ALA	0	-0.064	-0.028	6.103	-3.744	-3.744	0.000	0.000	0.000	0.000
26	A	39	LEU	0	-0.038	-0.018	5.230	-0.446	-0.446	0.000	0.000	0.000	0.000
27	A	40	THR	0	-0.019	-0.010	8.044	0.792	0.792	0.000	0.000	0.000	0.000
28	A	41	GLY	0	0.063	0.025	9.739	-0.744	-0.744	0.000	0.000	0.000	0.000
29	A	42	THR	0	-0.064	-0.039	12.384	0.299	0.299	0.000	0.000	0.000	0.000
30	A	43	TYR	0	0.044	0.020	14.859	-0.278	-0.278	0.000	0.000	0.000	0.000
31	A	44	GLU	-1	-0.911	-0.970	16.932	-0.541	-0.541	0.000	0.000	0.000	0.000
32	A	45	SER	0	-0.018	-0.026	20.260	-0.193	-0.193	0.000	0.000	0.000	0.000
33	A	46	ALA	0	0.009	0.014	22.233	0.111	0.111	0.000	0.000	0.000	0.000
34	A	47	VAL	0	-0.009	-0.001	24.408	0.079	0.079	0.000	0.000	0.000	0.000
35	A	48	GLY	0	0.034	0.027	25.748	-0.026	-0.026	0.000	0.000	0.000	0.000
36	A	49	ASN	0	-0.023	-0.011	28.183	0.044	0.044	0.000	0.000	0.000	0.000
37	A	50	ALA	0	0.013	0.000	24.743	0.036	0.036	0.000	0.000	0.000	0.000
38	A	51	GLU	-1	-0.809	-0.892	26.500	-0.323	-0.323	0.000	0.000	0.000	0.000
39	A	52	SER	0	0.015	0.018	24.695	0.041	0.041	0.000	0.000	0.000	0.000
40	A	53	ARG	1	0.946	0.975	18.636	0.528	0.528	0.000	0.000	0.000	0.000
41	A	54	TYR	0	0.007	0.022	19.853	0.136	0.136	0.000	0.000	0.000	0.000
42	A	55	VAL	0	-0.004	-0.005	16.511	-0.132	-0.132	0.000	0.000	0.000	0.000
43	A	56	LEU	0	-0.033	-0.001	10.892	-0.102	-0.102	0.000	0.000	0.000	0.000
44	A	57	THR	0	-0.022	-0.018	12.669	0.332	0.332	0.000	0.000	0.000	0.000
45	A	58	GLY	0	0.051	0.010	11.182	-0.429	-0.429	0.000	0.000	0.000	0.000
46	A	59	ARG	1	0.781	0.891	8.954	-1.920	-1.920	0.000	0.000	0.000	0.000
48	A	61	ASP	-1	-0.825	-0.908	6.902	-1.985	-1.985	0.000	0.000	0.000	0.000
51	A	64	PRO	0	-0.007	0.014	6.055	0.430	0.430	0.000	0.000	0.000	0.000
52	A	65	ALA	0	0.007	0.002	9.117	0.506	0.506	0.000	0.000	0.000	0.000
53	A	66	THR	0	-0.032	-0.026	10.990	-0.584	-0.584	0.000	0.000	0.000	0.000
54	A	67	ASP	-1	-0.861	-0.909	12.766	-2.440	-2.440	0.000	0.000	0.000	0.000
55	A	68	GLY	0	-0.013	-0.003	13.913	0.243	0.243	0.000	0.000	0.000	0.000
56	A	69	SER	0	-0.071	-0.051	13.109	-0.014	-0.014	0.000	0.000	0.000	0.000
57	A	70	GLY	0	-0.020	0.002	10.910	-0.617	-0.617	0.000	0.000	0.000	0.000
58	A	71	THR	0	-0.052	-0.028	5.005	-0.607	-0.607	0.000	0.000	0.000	0.000
59	A	72	ALA	0	0.045	0.020	8.377	-0.544	-0.544	0.000	0.000	0.000	0.000
60	A	73	LEU	0	-0.044	-0.028	6.550	-1.192	-1.192	0.000	0.000	0.000	0.000
61	A	74	GLY	0	0.030	0.020	9.394	0.553	0.553	0.000	0.000	0.000	0.000
62	A	75	TRP	0	-0.022	-0.010	10.452	-0.055	-0.055	0.000	0.000	0.000	0.000
63	A	76	THR	0	0.006	0.002	12.990	0.040	0.040	0.000	0.000	0.000	0.000
64	A	77	VAL	0	0.006	0.008	16.125	0.068	0.068	0.000	0.000	0.000	0.000
65	A	78	ALA	0	0.021	0.015	18.484	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	79	TRP	0	-0.007	-0.013	20.330	0.029	0.029	0.000	0.000	0.000	0.000
67	A	80	LYS	1	0.889	0.933	24.075	0.036	0.036	0.000	0.000	0.000	0.000
68	A	81	ASN	0	0.035	0.013	23.955	0.079	0.079	0.000	0.000	0.000	0.000
69	A	82	ASN	0	-0.064	-0.046	25.538	0.028	0.028	0.000	0.000	0.000	0.000
70	A	83	TYR	0	-0.021	0.002	25.998	0.031	0.031	0.000	0.000	0.000	0.000
71	A	84	ARG	1	0.853	0.908	28.601	0.398	0.398	0.000	0.000	0.000	0.000
72	A	85	ASN	0	-0.014	-0.021	28.201	-0.026	-0.026	0.000	0.000	0.000	0.000
73	A	86	ALA	0	0.015	0.020	27.683	0.005	0.005	0.000	0.000	0.000	0.000
74	A	87	HIS	0	-0.035	-0.014	29.602	-0.023	-0.023	0.000	0.000	0.000	0.000
75	A	88	SER	0	0.034	0.011	26.674	-0.024	-0.024	0.000	0.000	0.000	0.000
76	A	89	ALA	0	-0.011	-0.006	21.811	0.044	0.044	0.000	0.000	0.000	0.000
77	A	90	THR	0	0.021	0.033	19.106	0.065	0.065	0.000	0.000	0.000	0.000
78	A	91	THR	0	-0.035	-0.005	17.535	-0.025	-0.025	0.000	0.000	0.000	0.000
79	A	92	TRP	0	0.012	-0.020	14.292	0.048	0.048	0.000	0.000	0.000	0.000
80	A	93	SER	0	-0.014	-0.017	13.956	-0.240	-0.240	0.000	0.000	0.000	0.000
81	A	94	GLY	0	0.034	0.007	13.067	0.286	0.286	0.000	0.000	0.000	0.000
82	A	95	GLN	0	-0.009	-0.001	10.419	-0.328	-0.328	0.000	0.000	0.000	0.000
83	A	96	TYR	0	0.008	0.005	6.194	-0.786	-0.786	0.000	0.000	0.000	0.000
84	A	97	VAL	0	0.017	0.012	8.750	0.221	0.221	0.000	0.000	0.000	0.000
85	A	98	GLY	0	0.039	0.015	8.919	-0.386	-0.386	0.000	0.000	0.000	0.000
86	A	99	GLY	0	0.022	0.006	9.498	1.065	1.065	0.000	0.000	0.000	0.000
87	A	100	ALA	0	-0.024	-0.025	11.637	-0.462	-0.462	0.000	0.000	0.000	0.000
88	A	101	GLU	-1	-0.948	-0.970	14.239	-2.404	-2.404	0.000	0.000	0.000	0.000
89	A	102	ALA	0	-0.022	0.002	9.692	-0.036	-0.036	0.000	0.000	0.000	0.000
90	A	103	ARG	1	0.906	0.945	11.369	4.106	4.106	0.000	0.000	0.000	0.000
91	A	104	ILE	0	-0.004	0.008	7.266	-1.272	-1.272	0.000	0.000	0.000	0.000
92	A	105	ASN	0	0.008	0.015	11.347	0.688	0.688	0.000	0.000	0.000	0.000
93	A	106	THR	0	-0.035	-0.042	13.236	-0.169	-0.169	0.000	0.000	0.000	0.000
94	A	107	GLN	0	0.048	0.022	15.803	0.322	0.322	0.000	0.000	0.000	0.000
95	A	108	TRP	0	-0.030	-0.031	17.652	-0.081	-0.081	0.000	0.000	0.000	0.000
96	A	109	LEU	0	0.008	0.003	19.763	0.132	0.132	0.000	0.000	0.000	0.000
97	A	110	LEU	0	-0.005	0.007	21.839	-0.012	-0.012	0.000	0.000	0.000	0.000
98	A	111	THR	0	0.010	-0.004	24.191	0.031	0.031	0.000	0.000	0.000	0.000
99	A	112	SER	0	-0.010	-0.023	26.517	0.018	0.018	0.000	0.000	0.000	0.000
100	A	113	GLY	0	-0.007	0.000	29.359	0.014	0.014	0.000	0.000	0.000	0.000
101	A	114	THR	0	-0.034	-0.023	31.757	-0.012	-0.012	0.000	0.000	0.000	0.000
102	A	115	THR	0	0.028	0.011	35.136	0.013	0.013	0.000	0.000	0.000	0.000
103	A	116	GLU	-1	-0.857	-0.934	37.722	-0.176	-0.176	0.000	0.000	0.000	0.000
104	A	117	ALA	0	-0.001	-0.001	38.723	-0.022	-0.022	0.000	0.000	0.000	0.000
105	A	118	ASN	0	-0.060	-0.049	37.550	-0.026	-0.026	0.000	0.000	0.000	0.000
106	A	119	ALA	0	0.059	0.035	34.509	-0.032	-0.032	0.000	0.000	0.000	0.000
107	A	120	TRP	0	0.012	0.010	33.695	-0.046	-0.046	0.000	0.000	0.000	0.000
108	A	121	LYS	1	0.891	0.964	33.856	0.326	0.326	0.000	0.000	0.000	0.000
109	A	122	SER	0	-0.028	-0.016	30.984	-0.025	-0.025	0.000	0.000	0.000	0.000
110	A	123	THR	0	-0.023	-0.004	26.345	-0.019	-0.019	0.000	0.000	0.000	0.000
111	A	124	LEU	0	-0.005	0.011	27.017	0.010	0.010	0.000	0.000	0.000	0.000
112	A	125	VAL	0	0.002	-0.004	23.896	-0.040	-0.040	0.000	0.000	0.000	0.000
113	A	126	GLY	0	0.008	0.003	23.301	0.078	0.078	0.000	0.000	0.000	0.000
114	A	127	HIS	0	-0.025	-0.002	20.148	-0.179	-0.179	0.000	0.000	0.000	0.000
115	A	128	ASP	-1	-0.771	-0.845	17.265	-1.829	-1.829	0.000	0.000	0.000	0.000
116	A	129	THR	0	-0.030	-0.009	16.341	-0.312	-0.312	0.000	0.000	0.000	0.000
117	A	130	PHE	0	-0.016	-0.014	12.715	0.237	0.237	0.000	0.000	0.000	0.000
118	A	131	THR	0	0.007	-0.013	13.718	-0.461	-0.461	0.000	0.000	0.000	0.000
119	A	132	LYS	1	0.794	0.906	7.083	9.483	9.483	0.000	0.000	0.000	0.000
120	A	133	VAL	0	-0.012	-0.013	12.660	0.432	0.432	0.000	0.000	0.000	0.000
121	A	134	LYS	0	0.037	0.025	13.235	-0.483	-0.483	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:14:GLU)