FMO DATABASE

FMODB ID: 3M7QL

Calculation Name: 2A9P-A-Xray547

Preferred Name:

Target Type:

Ligand Name: beryllium trifluoride ion | manganese (ii) ion

Ligand 3-letter code: BEF | MN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2A9P

Chain ID: A

ChEMBL ID:

UniProt ID: Q9S1K0

Base Structure: X-ray

Registration Date: 2025-10-05

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	117
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1007090.323807
FMO2-HF: Nuclear repulsion	961011.548586
FMO2-HF: Total energy	-46078.77522
FMO2-MP2: Total energy	-46214.172477

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:2:LYS)

Summations of interaction energy for fragment #1(A:2:LYS)

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.
-527.262	-517.495	18.621	-13.128	-15.26	-0.149

Interaction energy analysis for fragmet #1(A:2:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.683 / q_NPA : 1.835

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	4	ILE	0	0.007	0.004	3.859	-0.144	1.517	-0.016	-0.677	-0.969	-0.003
25	A	26	TYR	0	-0.063	-0.037	2.195	-14.814	-13.835	1.235	-0.527	-1.686	-0.004
26	A	27	GLU	-1	-0.900	-0.950	3.536	-69.314	-68.638	0.000	-0.206	-0.470	0.000
46	A	47	ASP	-1	-0.812	-0.918	1.910	-202.015	-197.366	17.102	-11.323	-10.428	-0.138
47	A	48	ILE	0	-0.043	-0.027	4.414	3.195	3.402	-0.001	-0.024	-0.182	0.000
115	A	116	LEU	0	-0.009	-0.002	2.820	-7.177	-5.692	0.302	-0.364	-1.423	-0.004
116	A	117	ARG	1	0.846	0.939	4.638	40.111	40.221	-0.001	-0.007	-0.102	0.000
4	A	5	LEU	0	0.015	0.024	6.151	3.648	3.648	0.000	0.000	0.000	0.000
5	A	6	ILE	0	-0.056	-0.022	9.820	0.910	0.910	0.000	0.000	0.000	0.000
6	A	7	VAL	0	0.013	-0.003	12.253	1.295	1.295	0.000	0.000	0.000	0.000
7	A	8	ASP	-1	-0.801	-0.920	15.695	-28.922	-28.922	0.000	0.000	0.000	0.000
8	A	9	ASP	-1	-0.867	-0.924	18.625	-25.439	-25.439	0.000	0.000	0.000	0.000
9	A	10	GLU	-1	-0.893	-0.934	21.994	-23.527	-23.527	0.000	0.000	0.000	0.000
10	A	11	LYS	1	0.811	0.884	19.773	27.840	27.840	0.000	0.000	0.000	0.000
11	A	12	PRO	0	0.005	-0.010	20.388	-1.122	-1.122	0.000	0.000	0.000	0.000
12	A	13	ILE	0	0.031	0.018	18.584	-0.788	-0.788	0.000	0.000	0.000	0.000
13	A	14	SER	0	0.044	0.020	16.496	-2.395	-2.395	0.000	0.000	0.000	0.000
14	A	15	ASP	-1	-0.823	-0.892	15.661	-32.511	-32.511	0.000	0.000	0.000	0.000
15	A	16	ILE	0	-0.019	-0.007	16.292	-1.593	-1.593	0.000	0.000	0.000	0.000
16	A	17	ILE	0	0.032	0.024	12.019	-1.593	-1.593	0.000	0.000	0.000	0.000
17	A	18	LYS	1	1.014	1.012	11.796	36.711	36.711	0.000	0.000	0.000	0.000
18	A	19	PHE	0	-0.021	0.004	11.644	-3.090	-3.090	0.000	0.000	0.000	0.000
19	A	20	ASN	0	-0.050	-0.054	12.478	-1.200	-1.200	0.000	0.000	0.000	0.000
20	A	21	MET	0	0.019	0.032	7.685	-3.139	-3.139	0.000	0.000	0.000	0.000
21	A	22	THR	0	0.011	-0.013	7.683	-5.280	-5.280	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.824	0.914	9.287	36.023	36.023	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.952	-0.971	7.076	-47.927	-47.927	0.000	0.000	0.000	0.000
24	A	25	GLY	0	-0.039	-0.010	6.373	-3.570	-3.570	0.000	0.000	0.000	0.000
27	A	28	VAL	0	-0.066	-0.038	5.469	-2.957	-2.957	0.000	0.000	0.000	0.000
28	A	29	VAL	0	0.034	0.026	8.759	4.075	4.075	0.000	0.000	0.000	0.000
29	A	30	THR	0	-0.060	-0.034	11.125	-0.371	-0.371	0.000	0.000	0.000	0.000
30	A	31	ALA	0	-0.003	0.005	14.373	0.820	0.820	0.000	0.000	0.000	0.000
31	A	32	PHE	0	-0.015	-0.022	17.099	-0.452	-0.452	0.000	0.000	0.000	0.000
32	A	33	ASN	0	0.019	-0.004	20.400	1.318	1.318	0.000	0.000	0.000	0.000
33	A	34	GLY	0	0.096	0.036	20.242	-1.593	-1.593	0.000	0.000	0.000	0.000
34	A	35	ARG	1	0.777	0.890	20.965	23.060	23.060	0.000	0.000	0.000	0.000
35	A	36	GLU	-1	-0.802	-0.913	19.028	-29.737	-29.737	0.000	0.000	0.000	0.000
36	A	37	ALA	0	-0.028	-0.013	16.491	-2.101	-2.101	0.000	0.000	0.000	0.000
37	A	38	LEU	0	-0.014	0.000	15.978	-2.413	-2.413	0.000	0.000	0.000	0.000
38	A	39	GLU	-1	-0.926	-0.969	17.229	-29.083	-29.083	0.000	0.000	0.000	0.000
39	A	40	GLN	0	0.017	-0.009	13.767	-2.872	-2.872	0.000	0.000	0.000	0.000
40	A	41	PHE	0	-0.029	-0.016	10.960	-3.973	-3.973	0.000	0.000	0.000	0.000
41	A	42	GLU	-1	-0.926	-0.976	12.681	-39.848	-39.848	0.000	0.000	0.000	0.000
42	A	43	ALA	0	-0.063	-0.020	14.546	-0.796	-0.796	0.000	0.000	0.000	0.000
43	A	44	GLU	-1	-0.874	-0.936	9.753	-53.525	-53.525	0.000	0.000	0.000	0.000
44	A	45	GLN	0	-0.056	-0.008	8.846	-9.012	-9.012	0.000	0.000	0.000	0.000
45	A	46	PRO	0	-0.041	-0.007	6.374	-8.220	-8.220	0.000	0.000	0.000	0.000
48	A	49	ILE	0	0.003	0.009	6.859	-0.377	-0.377	0.000	0.000	0.000	0.000
49	A	50	ILE	0	-0.041	-0.019	9.306	1.313	1.313	0.000	0.000	0.000	0.000
50	A	51	LEU	0	-0.003	-0.006	11.953	0.562	0.562	0.000	0.000	0.000	0.000
51	A	52	ASP	-1	-0.775	-0.882	15.531	-26.218	-26.218	0.000	0.000	0.000	0.000
52	A	53	LEU	0	0.001	-0.024	18.904	-0.159	-0.159	0.000	0.000	0.000	0.000
53	A	54	MET	0	-0.087	-0.037	21.960	0.968	0.968	0.000	0.000	0.000	0.000
54	A	55	LEU	0	0.041	0.035	19.276	0.105	0.105	0.000	0.000	0.000	0.000
55	A	56	PRO	0	0.012	-0.004	23.686	0.746	0.746	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.880	-0.919	24.696	-22.972	-22.972	0.000	0.000	0.000	0.000
57	A	58	ILE	0	-0.059	-0.030	23.333	0.601	0.601	0.000	0.000	0.000	0.000
58	A	59	ASP	-1	-0.792	-0.881	23.401	-25.045	-25.045	0.000	0.000	0.000	0.000
59	A	60	GLY	0	0.054	0.001	20.247	-0.786	-0.786	0.000	0.000	0.000	0.000
60	A	61	LEU	0	-0.013	-0.008	20.135	-1.364	-1.364	0.000	0.000	0.000	0.000
61	A	62	GLU	-1	-0.797	-0.883	22.238	-24.289	-24.289	0.000	0.000	0.000	0.000
62	A	63	VAL	0	-0.020	0.004	17.389	-0.676	-0.676	0.000	0.000	0.000	0.000
63	A	64	ALA	0	0.027	0.014	17.497	-1.189	-1.189	0.000	0.000	0.000	0.000
64	A	65	LYS	1	0.850	0.907	18.284	23.004	23.004	0.000	0.000	0.000	0.000
65	A	66	THR	0	-0.111	-0.068	20.654	0.522	0.522	0.000	0.000	0.000	0.000
66	A	67	ILE	0	0.062	0.038	13.817	-0.058	-0.058	0.000	0.000	0.000	0.000
67	A	68	ARG	1	0.765	0.865	12.422	40.309	40.309	0.000	0.000	0.000	0.000
68	A	69	LYS	1	0.812	0.920	17.362	27.220	27.220	0.000	0.000	0.000	0.000
69	A	70	THR	0	-0.037	-0.016	16.462	0.599	0.599	0.000	0.000	0.000	0.000
70	A	71	SER	0	0.017	0.013	10.862	-2.089	-2.089	0.000	0.000	0.000	0.000
71	A	72	SER	0	-0.002	0.003	11.080	1.357	1.357	0.000	0.000	0.000	0.000
72	A	73	VAL	0	-0.004	0.016	7.291	-1.962	-1.962	0.000	0.000	0.000	0.000
73	A	74	PRO	0	0.037	0.022	7.009	4.780	4.780	0.000	0.000	0.000	0.000
74	A	75	ILE	0	0.005	0.000	9.872	-2.425	-2.425	0.000	0.000	0.000	0.000
75	A	76	LEU	0	-0.020	-0.004	11.676	2.231	2.231	0.000	0.000	0.000	0.000
76	A	77	MET	0	0.004	0.026	13.322	0.460	0.460	0.000	0.000	0.000	0.000
77	A	78	LEU	0	-0.048	-0.036	14.973	0.075	0.075	0.000	0.000	0.000	0.000
78	A	79	SER	0	0.077	0.044	17.516	0.781	0.781	0.000	0.000	0.000	0.000
79	A	80	ALA	0	0.013	0.008	21.198	0.277	0.277	0.000	0.000	0.000	0.000
80	A	81	LYS	1	0.812	0.914	24.383	22.027	22.027	0.000	0.000	0.000	0.000
81	A	82	ASP	-1	-0.837	-0.924	24.405	-22.239	-22.239	0.000	0.000	0.000	0.000
82	A	83	SER	0	-0.037	-0.036	26.363	0.136	0.136	0.000	0.000	0.000	0.000
83	A	84	GLU	-1	-0.928	-0.972	27.477	-19.905	-19.905	0.000	0.000	0.000	0.000
84	A	85	PHE	0	0.032	0.013	27.990	-0.607	-0.607	0.000	0.000	0.000	0.000
85	A	86	ASP	-1	-0.774	-0.862	25.791	-21.803	-21.803	0.000	0.000	0.000	0.000
86	A	87	LYS	1	0.881	0.943	23.054	23.080	23.080	0.000	0.000	0.000	0.000
87	A	88	VAL	0	-0.006	0.007	23.580	-0.996	-0.996	0.000	0.000	0.000	0.000
88	A	89	ILE	0	0.013	0.011	24.801	-0.665	-0.665	0.000	0.000	0.000	0.000
89	A	90	GLY	0	0.018	-0.005	22.040	-0.653	-0.653	0.000	0.000	0.000	0.000
90	A	91	LEU	0	-0.026	-0.017	19.051	-1.290	-1.290	0.000	0.000	0.000	0.000
91	A	92	GLU	-1	-0.966	-0.976	20.675	-23.107	-23.107	0.000	0.000	0.000	0.000
92	A	93	LEU	0	-0.086	-0.049	21.871	0.147	0.147	0.000	0.000	0.000	0.000
93	A	94	GLY	0	-0.016	0.001	18.298	-0.777	-0.777	0.000	0.000	0.000	0.000
94	A	95	ALA	0	-0.011	0.003	16.021	-2.359	-2.359	0.000	0.000	0.000	0.000
95	A	96	ASP	-1	-0.830	-0.924	13.065	-41.966	-41.966	0.000	0.000	0.000	0.000
96	A	97	ASP	-1	-0.856	-0.926	14.447	-35.309	-35.309	0.000	0.000	0.000	0.000
97	A	98	TYR	0	-0.039	-0.041	16.207	-0.375	-0.375	0.000	0.000	0.000	0.000
98	A	99	VAL	0	-0.051	-0.020	15.765	1.135	1.135	0.000	0.000	0.000	0.000
99	A	100	THR	0	0.025	0.008	18.650	0.365	0.365	0.000	0.000	0.000	0.000
100	A	101	LYS	1	0.755	0.879	20.053	27.169	27.169	0.000	0.000	0.000	0.000
101	A	102	PRO	0	-0.013	-0.011	22.408	0.848	0.848	0.000	0.000	0.000	0.000
102	A	103	PHE	0	0.058	0.025	16.883	-0.028	-0.028	0.000	0.000	0.000	0.000
103	A	104	SER	0	0.011	0.008	19.342	-0.023	-0.023	0.000	0.000	0.000	0.000
104	A	105	ASN	0	0.041	0.006	15.849	-1.559	-1.559	0.000	0.000	0.000	0.000
105	A	106	ARG	1	0.972	0.980	13.952	33.396	33.396	0.000	0.000	0.000	0.000
106	A	107	GLU	-1	-0.857	-0.908	14.768	-31.406	-31.406	0.000	0.000	0.000	0.000
107	A	108	LEU	0	0.048	0.026	11.671	-1.735	-1.735	0.000	0.000	0.000	0.000
108	A	109	GLN	0	-0.034	-0.023	10.222	-0.671	-0.671	0.000	0.000	0.000	0.000
109	A	110	ALA	0	-0.051	-0.025	10.123	-3.629	-3.629	0.000	0.000	0.000	0.000
110	A	111	ARG	1	0.787	0.866	11.645	31.738	31.738	0.000	0.000	0.000	0.000
111	A	112	VAL	0	0.057	0.029	6.220	-1.915	-1.915	0.000	0.000	0.000	0.000
112	A	113	LYS	1	0.901	0.948	6.923	45.322	45.322	0.000	0.000	0.000	0.000
113	A	114	ALA	0	-0.096	-0.056	7.997	-0.907	-0.907	0.000	0.000	0.000	0.000
114	A	115	LEU	0	0.013	0.008	9.236	0.666	0.666	0.000	0.000	0.000	0.000
117	A	118	ARG	0	0.046	0.043	7.256	-12.161	-12.161	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:LYS)