FMO DATABASE

FMODB ID: N6MMQ

Calculation Name: 2BOP-A-Xray549

Preferred Name:

Target Type:

Ligand Name: ytterbium (iii) ion

Ligand 3-letter code: YB

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2BOP

Chain ID: A

ChEMBL ID:

UniProt ID: P03122

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	85
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-559314.621582
FMO2-HF: Nuclear repulsion	525268.560804
FMO2-HF: Total energy	-34046.060778
FMO2-MP2: Total energy	-34144.176872

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:326:SER)

Summations of interaction energy for fragment #1(A:326: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.
41.636	48.952	4.32	-6.036	-5.601	-0.051

Interaction energy analysis for fragmet #1(A:326:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.914 / q_NPA : 0.956

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

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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	328	PHE	0	0.028	0.005	3.875	-0.685	0.915	-0.010	-0.723	-0.868	0.002
54	A	379	THR	0	0.047	0.015	4.624	-1.364	-1.301	-0.001	-0.009	-0.053	0.000
56	A	381	GLY	0	0.074	0.046	4.781	-7.449	-7.513	-0.001	-0.009	0.074	0.000
80	A	405	THR	0	-0.020	-0.031	2.961	-5.376	-5.026	0.068	-0.162	-0.255	-0.001
81	A	406	ALA	0	-0.002	0.013	2.703	6.821	7.605	0.126	-0.296	-0.615	-0.001
82	A	407	SER	0	0.017	-0.007	2.246	-32.278	-27.682	4.139	-4.824	-3.911	-0.051
83	A	408	LEU	0	-0.045	-0.013	4.877	-0.741	-0.754	-0.001	-0.013	0.027	0.000
4	A	329	ALA	0	0.017	0.010	5.881	3.335	3.335	0.000	0.000	0.000	0.000
5	A	330	LEU	0	0.026	0.033	9.544	-0.755	-0.755	0.000	0.000	0.000	0.000
6	A	331	ILE	0	-0.013	-0.012	12.238	0.978	0.978	0.000	0.000	0.000	0.000
7	A	332	SER	0	-0.032	-0.014	15.409	0.400	0.400	0.000	0.000	0.000	0.000
8	A	333	GLY	0	0.071	0.031	18.513	0.373	0.373	0.000	0.000	0.000	0.000
9	A	334	THR	0	0.047	0.015	22.288	0.028	0.028	0.000	0.000	0.000	0.000
10	A	335	ALA	0	0.060	0.017	22.742	-0.335	-0.335	0.000	0.000	0.000	0.000
11	A	336	ASN	0	0.039	0.005	23.321	-0.511	-0.511	0.000	0.000	0.000	0.000
12	A	337	GLN	0	0.076	0.053	23.924	-0.130	-0.130	0.000	0.000	0.000	0.000
13	A	338	VAL	0	0.052	0.029	18.342	-0.153	-0.153	0.000	0.000	0.000	0.000
14	A	339	LYS	1	0.878	0.942	20.190	11.345	11.345	0.000	0.000	0.000	0.000
15	A	340	CYS	0	-0.047	-0.034	22.006	-0.016	-0.016	0.000	0.000	0.000	0.000
16	A	341	TYR	0	0.010	0.008	16.368	-0.030	-0.030	0.000	0.000	0.000	0.000
17	A	342	ARG	1	0.908	0.945	16.717	16.459	16.459	0.000	0.000	0.000	0.000
18	A	343	PHE	0	-0.039	-0.013	18.993	-0.237	-0.237	0.000	0.000	0.000	0.000
19	A	344	ARG	1	0.956	0.976	22.143	12.983	12.983	0.000	0.000	0.000	0.000
20	A	345	VAL	0	0.024	0.014	15.845	0.166	0.166	0.000	0.000	0.000	0.000
21	A	346	LYS	1	0.947	0.971	18.117	15.508	15.508	0.000	0.000	0.000	0.000
22	A	347	LYS	1	0.872	0.940	19.072	11.977	11.977	0.000	0.000	0.000	0.000
23	A	348	ASN	0	0.020	0.017	21.907	0.582	0.582	0.000	0.000	0.000	0.000
24	A	349	HIS	0	0.045	0.028	18.089	-0.074	-0.074	0.000	0.000	0.000	0.000
25	A	350	ARG	1	0.864	0.931	12.705	20.508	20.508	0.000	0.000	0.000	0.000
26	A	351	HIS	0	0.072	0.041	15.140	-1.484	-1.484	0.000	0.000	0.000	0.000
27	A	352	ARG	1	0.839	0.901	14.432	15.107	15.107	0.000	0.000	0.000	0.000
28	A	353	TYR	0	-0.013	-0.021	10.667	-0.161	-0.161	0.000	0.000	0.000	0.000
29	A	354	GLU	-1	-0.901	-0.925	6.621	-29.249	-29.249	0.000	0.000	0.000	0.000
30	A	355	ASN	0	-0.008	-0.014	8.798	5.355	5.355	0.000	0.000	0.000	0.000
31	A	356	CYS	0	-0.017	-0.011	9.800	-1.005	-1.005	0.000	0.000	0.000	0.000
32	A	357	THR	0	0.010	0.028	10.853	0.812	0.812	0.000	0.000	0.000	0.000
33	A	358	THR	0	0.057	0.013	13.377	0.748	0.748	0.000	0.000	0.000	0.000
34	A	359	THR	0	-0.018	-0.005	16.004	-0.939	-0.939	0.000	0.000	0.000	0.000
35	A	360	TRP	0	0.015	0.022	12.346	0.983	0.983	0.000	0.000	0.000	0.000
36	A	361	PHE	0	0.047	-0.004	18.189	0.307	0.307	0.000	0.000	0.000	0.000
37	A	362	THR	0	0.033	0.035	18.841	-0.785	-0.785	0.000	0.000	0.000	0.000
38	A	363	VAL	0	-0.019	-0.018	20.364	0.614	0.614	0.000	0.000	0.000	0.000
39	A	364	ALA	0	0.031	0.004	23.488	-0.231	-0.231	0.000	0.000	0.000	0.000
40	A	365	ASP	-1	-0.823	-0.899	26.642	-10.259	-10.259	0.000	0.000	0.000	0.000
41	A	366	ASN	0	-0.028	-0.017	29.624	0.409	0.409	0.000	0.000	0.000	0.000
42	A	367	GLY	0	0.029	0.012	31.361	-0.054	-0.054	0.000	0.000	0.000	0.000
43	A	368	ALA	0	-0.029	-0.020	28.947	-0.377	-0.377	0.000	0.000	0.000	0.000
44	A	369	GLU	0	-0.016	0.006	28.526	-0.217	-0.217	0.000	0.000	0.000	0.000
45	A	370	ARG	1	0.855	0.924	23.564	11.712	11.712	0.000	0.000	0.000	0.000
46	A	371	GLN	0	0.043	0.026	23.152	0.705	0.705	0.000	0.000	0.000	0.000
47	A	372	GLY	0	0.015	0.009	22.462	-0.684	-0.684	0.000	0.000	0.000	0.000
48	A	373	GLN	0	-0.023	-0.012	21.120	0.748	0.748	0.000	0.000	0.000	0.000
49	A	374	ALA	0	-0.012	0.003	20.342	-0.574	-0.574	0.000	0.000	0.000	0.000
50	A	375	GLN	0	0.014	-0.002	15.146	-0.995	-0.995	0.000	0.000	0.000	0.000
51	A	376	ILE	0	-0.064	-0.043	14.101	0.783	0.783	0.000	0.000	0.000	0.000
52	A	377	LEU	0	0.027	0.030	6.495	-0.109	-0.109	0.000	0.000	0.000	0.000
53	A	378	ILE	0	-0.004	-0.011	9.628	1.342	1.342	0.000	0.000	0.000	0.000
55	A	380	PHE	0	0.018	-0.014	5.306	6.348	6.348	0.000	0.000	0.000	0.000
57	A	382	SER	0	0.006	-0.005	6.077	-1.191	-1.191	0.000	0.000	0.000	0.000
58	A	383	PRO	0	0.050	-0.001	5.803	0.273	0.273	0.000	0.000	0.000	0.000
59	A	384	SER	0	0.056	0.039	8.488	0.993	0.993	0.000	0.000	0.000	0.000
60	A	385	GLN	0	0.014	0.011	9.566	-1.163	-1.163	0.000	0.000	0.000	0.000
61	A	386	ARG	1	0.881	0.944	7.196	37.304	37.304	0.000	0.000	0.000	0.000
62	A	387	GLN	0	-0.016	-0.019	11.389	1.069	1.069	0.000	0.000	0.000	0.000
63	A	388	ASP	-1	-0.766	-0.851	14.314	-15.949	-15.949	0.000	0.000	0.000	0.000
64	A	389	PHE	0	0.023	-0.001	13.631	1.040	1.040	0.000	0.000	0.000	0.000
65	A	390	LEU	0	-0.047	-0.037	13.852	0.968	0.968	0.000	0.000	0.000	0.000
66	A	391	LYS	1	0.858	0.944	17.029	17.864	17.864	0.000	0.000	0.000	0.000
67	A	392	HIS	0	-0.044	-0.024	19.172	1.414	1.414	0.000	0.000	0.000	0.000
68	A	393	VAL	0	-0.066	-0.019	17.094	0.665	0.665	0.000	0.000	0.000	0.000
69	A	394	PRO	0	-0.006	0.010	19.963	-0.233	-0.233	0.000	0.000	0.000	0.000
70	A	395	LEU	0	0.018	-0.001	18.820	-0.315	-0.315	0.000	0.000	0.000	0.000
71	A	396	PRO	0	-0.056	-0.039	21.828	0.538	0.538	0.000	0.000	0.000	0.000
72	A	397	PRO	0	0.084	0.042	24.400	-0.367	-0.367	0.000	0.000	0.000	0.000
73	A	398	GLY	0	0.010	-0.007	26.229	0.134	0.134	0.000	0.000	0.000	0.000
74	A	399	MET	0	-0.081	-0.011	19.870	-0.073	-0.073	0.000	0.000	0.000	0.000
75	A	400	ASN	0	0.001	-0.004	18.373	-0.539	-0.539	0.000	0.000	0.000	0.000
76	A	401	ILE	0	-0.009	-0.007	13.460	-0.511	-0.511	0.000	0.000	0.000	0.000
77	A	402	SER	0	0.031	0.028	13.755	0.883	0.883	0.000	0.000	0.000	0.000
78	A	403	GLY	0	-0.020	-0.010	10.425	-1.446	-1.446	0.000	0.000	0.000	0.000
79	A	404	PHE	0	0.035	0.013	7.288	1.704	1.704	0.000	0.000	0.000	0.000
84	A	409	ASP	-1	-0.919	-0.957	7.063	-27.372	-27.372	0.000	0.000	0.000	0.000
85	A	410	PHE	-1	-0.958	-0.970	10.595	-24.233	-24.233	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:326:SER)