FMO DATABASE

FMODB ID: RLG68

Calculation Name: 4D6Y-A-Xray547

Preferred Name:

Target Type:

Ligand Name: beryllium trifluoride ion

Ligand 3-letter code: BEF

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4D6Y

Chain ID: A

ChEMBL ID:

UniProt ID: Q2YPW6

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	121
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1018087.909722
FMO2-HF: Nuclear repulsion	972047.290122
FMO2-HF: Total energy	-46040.6196
FMO2-MP2: Total energy	-46177.828799

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:4:ASP)

Summations of interaction energy for fragment #1(A:4:ASP)

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.
-136.767	-126.251	29.131	-19.69	-19.958	0.058

Interaction energy analysis for fragmet #1(A:4:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.011

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	6	LEU	0	0.001	0.013	3.830	7.958	9.485	-0.017	-0.503	-1.007	0.000
24	A	27	HIS	1	0.767	0.874	3.706	10.948	11.119	0.000	-0.031	-0.140	0.000
25	A	28	GLU	-1	-0.915	-0.953	2.184	-16.174	-13.659	1.669	-1.915	-2.270	-0.017
26	A	29	THR	0	-0.027	-0.025	2.215	-26.174	-23.715	6.186	-5.007	-3.639	-0.060
27	A	30	ARG	1	0.839	0.923	2.407	-45.557	-40.737	1.695	-3.041	-3.475	0.046
42	A	45	ARG	1	0.894	0.924	1.721	-62.085	-67.651	18.211	-7.176	-5.468	0.086
43	A	46	ALA	0	0.043	0.045	5.298	5.044	5.126	-0.001	-0.002	-0.078	0.000
44	A	47	PRO	0	-0.024	0.008	2.947	1.336	3.352	0.316	-0.974	-1.358	0.007
45	A	48	ARG	1	0.826	0.881	2.352	10.630	12.778	1.073	-0.971	-2.251	-0.004
46	A	49	LEU	0	0.025	0.040	4.226	-0.281	-0.023	0.000	-0.047	-0.211	0.000
117	A	120	LEU	0	-0.062	-0.044	4.356	-1.200	-1.114	-0.001	-0.023	-0.061	0.000
4	A	7	VAL	0	0.022	0.008	6.056	-2.159	-2.159	0.000	0.000	0.000	0.000
5	A	8	VAL	0	-0.011	-0.009	9.646	0.933	0.933	0.000	0.000	0.000	0.000
6	A	9	ASP	-1	-0.747	-0.878	12.436	-0.544	-0.544	0.000	0.000	0.000	0.000
7	A	10	ASP	-1	-0.775	-0.883	15.739	0.775	0.775	0.000	0.000	0.000	0.000
8	A	11	GLU	-1	-0.927	-0.965	18.589	-0.050	-0.050	0.000	0.000	0.000	0.000
9	A	12	VAL	0	-0.041	-0.033	17.364	-0.004	-0.004	0.000	0.000	0.000	0.000
10	A	13	ASP	-1	-0.856	-0.923	16.839	-0.312	-0.312	0.000	0.000	0.000	0.000
11	A	14	ILE	0	-0.024	-0.010	15.935	-0.321	-0.321	0.000	0.000	0.000	0.000
12	A	15	ARG	1	0.824	0.899	12.875	-1.497	-1.497	0.000	0.000	0.000	0.000
13	A	16	ASP	-1	-0.879	-0.942	12.321	-0.255	-0.255	0.000	0.000	0.000	0.000
14	A	17	LEU	0	-0.052	-0.015	13.760	-0.528	-0.528	0.000	0.000	0.000	0.000
15	A	18	VAL	0	-0.023	-0.021	10.278	-0.548	-0.548	0.000	0.000	0.000	0.000
16	A	19	ALA	0	0.018	-0.006	8.816	-1.141	-1.141	0.000	0.000	0.000	0.000
17	A	20	GLY	0	0.014	0.028	9.140	-1.232	-1.232	0.000	0.000	0.000	0.000
18	A	21	ILE	0	0.008	0.000	11.103	-0.591	-0.591	0.000	0.000	0.000	0.000
19	A	22	LEU	0	-0.046	-0.022	6.443	-0.814	-0.814	0.000	0.000	0.000	0.000
20	A	23	SER	0	-0.036	-0.036	7.170	-2.526	-2.526	0.000	0.000	0.000	0.000
21	A	24	ASP	-1	-0.946	-0.961	8.135	-3.624	-3.624	0.000	0.000	0.000	0.000
22	A	25	GLU	-1	-0.984	-0.991	9.476	-4.775	-4.775	0.000	0.000	0.000	0.000
23	A	26	GLY	0	-0.017	-0.001	8.048	-0.937	-0.937	0.000	0.000	0.000	0.000
28	A	31	THR	0	-0.011	-0.012	5.841	-1.734	-1.734	0.000	0.000	0.000	0.000
29	A	32	ALA	0	-0.002	0.001	9.097	1.091	1.091	0.000	0.000	0.000	0.000
30	A	33	PHE	0	0.026	0.002	11.488	-0.592	-0.592	0.000	0.000	0.000	0.000
31	A	34	ASP	-1	-0.811	-0.874	14.957	2.035	2.035	0.000	0.000	0.000	0.000
32	A	35	ALA	0	0.019	-0.002	14.743	0.394	0.394	0.000	0.000	0.000	0.000
33	A	36	ASP	-1	-0.797	-0.864	15.197	2.517	2.517	0.000	0.000	0.000	0.000
34	A	37	SER	0	-0.017	-0.040	13.080	0.544	0.544	0.000	0.000	0.000	0.000
35	A	38	ALA	0	0.009	0.003	10.586	1.125	1.125	0.000	0.000	0.000	0.000
36	A	39	LEU	0	-0.001	-0.014	10.377	1.107	1.107	0.000	0.000	0.000	0.000
37	A	40	ALA	0	-0.005	0.010	12.179	0.478	0.478	0.000	0.000	0.000	0.000
38	A	41	ALA	0	0.007	0.001	7.140	0.924	0.924	0.000	0.000	0.000	0.000
39	A	42	ILE	0	-0.034	-0.027	7.048	3.855	3.855	0.000	0.000	0.000	0.000
40	A	43	ASN	0	-0.089	-0.064	8.671	-0.047	-0.047	0.000	0.000	0.000	0.000
41	A	44	ASP	-1	-0.973	-0.951	8.379	10.823	10.823	0.000	0.000	0.000	0.000
47	A	50	VAL	0	-0.026	-0.007	6.257	1.530	1.530	0.000	0.000	0.000	0.000
48	A	51	PHE	0	0.024	0.002	8.246	-0.750	-0.750	0.000	0.000	0.000	0.000
49	A	52	LEU	0	0.013	-0.006	11.360	0.850	0.850	0.000	0.000	0.000	0.000
50	A	53	ASP	-1	-0.767	-0.872	14.272	-0.304	-0.304	0.000	0.000	0.000	0.000
51	A	54	ILE	0	-0.027	-0.029	17.465	0.186	0.186	0.000	0.000	0.000	0.000
52	A	55	TRP	0	-0.075	-0.048	20.514	0.094	0.094	0.000	0.000	0.000	0.000
53	A	56	LEU	0	0.043	0.041	16.499	0.006	0.006	0.000	0.000	0.000	0.000
54	A	57	GLN	0	-0.019	-0.016	20.302	0.070	0.070	0.000	0.000	0.000	0.000
55	A	58	GLY	0	-0.041	-0.017	22.093	0.097	0.097	0.000	0.000	0.000	0.000
56	A	59	SER	0	-0.009	-0.013	19.539	0.218	0.218	0.000	0.000	0.000	0.000
57	A	60	ARG	1	0.806	0.880	18.984	-1.980	-1.980	0.000	0.000	0.000	0.000
58	A	61	LEU	0	-0.060	-0.030	18.898	-0.061	-0.061	0.000	0.000	0.000	0.000
59	A	62	ASP	-1	-0.776	-0.861	20.334	0.609	0.609	0.000	0.000	0.000	0.000
60	A	63	GLY	0	0.046	0.001	18.023	0.122	0.122	0.000	0.000	0.000	0.000
61	A	64	LEU	0	-0.050	-0.039	18.325	-0.044	-0.044	0.000	0.000	0.000	0.000
62	A	65	ALA	0	0.020	0.006	20.826	0.031	0.031	0.000	0.000	0.000	0.000
63	A	66	LEU	0	-0.036	-0.006	14.371	0.147	0.147	0.000	0.000	0.000	0.000
64	A	67	LEU	0	-0.016	-0.004	16.018	0.216	0.216	0.000	0.000	0.000	0.000
65	A	68	ASP	-1	-0.785	-0.851	17.309	0.551	0.551	0.000	0.000	0.000	0.000
66	A	69	GLU	-1	-0.833	-0.896	17.450	1.738	1.738	0.000	0.000	0.000	0.000
67	A	70	ILE	0	0.014	0.000	11.956	0.245	0.245	0.000	0.000	0.000	0.000
68	A	71	LYS	1	0.812	0.910	13.845	0.208	0.208	0.000	0.000	0.000	0.000
69	A	72	LYS	1	0.826	0.906	16.313	-1.389	-1.389	0.000	0.000	0.000	0.000
70	A	73	GLN	0	-0.089	-0.057	14.821	0.363	0.363	0.000	0.000	0.000	0.000
71	A	74	HIS	1	0.823	0.902	11.750	-3.227	-3.227	0.000	0.000	0.000	0.000
72	A	75	PRO	0	0.047	0.026	13.655	-0.297	-0.297	0.000	0.000	0.000	0.000
73	A	76	GLU	-1	-0.835	-0.907	10.922	1.609	1.609	0.000	0.000	0.000	0.000
74	A	77	LEU	0	-0.008	0.015	7.201	-0.397	-0.397	0.000	0.000	0.000	0.000
75	A	78	PRO	0	0.009	0.010	8.564	0.341	0.341	0.000	0.000	0.000	0.000
76	A	79	VAL	0	0.021	0.007	9.939	0.114	0.114	0.000	0.000	0.000	0.000
77	A	80	VAL	0	-0.021	-0.001	12.510	-0.117	-0.117	0.000	0.000	0.000	0.000
78	A	81	MET	0	-0.028	0.005	14.102	0.195	0.195	0.000	0.000	0.000	0.000
79	A	82	ILE	0	0.015	0.003	12.800	-0.286	-0.286	0.000	0.000	0.000	0.000
80	A	83	SER	0	0.047	0.019	17.108	0.278	0.278	0.000	0.000	0.000	0.000
81	A	84	GLY	0	0.020	0.023	20.773	-0.102	-0.102	0.000	0.000	0.000	0.000
82	A	85	HIS	1	0.857	0.929	23.472	0.097	0.097	0.000	0.000	0.000	0.000
83	A	86	GLY	0	0.065	0.041	25.041	0.047	0.047	0.000	0.000	0.000	0.000
84	A	87	ASN	0	0.036	0.025	25.680	0.012	0.012	0.000	0.000	0.000	0.000
85	A	88	ILE	0	0.071	0.024	27.403	-0.019	-0.019	0.000	0.000	0.000	0.000
86	A	89	GLU	-1	-0.935	-0.958	28.368	-0.124	-0.124	0.000	0.000	0.000	0.000
87	A	90	THR	0	-0.015	-0.024	24.242	0.043	0.043	0.000	0.000	0.000	0.000
88	A	91	ALA	0	0.020	0.014	23.573	0.012	0.012	0.000	0.000	0.000	0.000
89	A	92	VAL	0	-0.005	-0.008	23.917	-0.021	-0.021	0.000	0.000	0.000	0.000
90	A	93	SER	0	-0.044	-0.020	25.552	0.048	0.048	0.000	0.000	0.000	0.000
91	A	94	ALA	0	0.054	0.017	20.271	0.053	0.053	0.000	0.000	0.000	0.000
92	A	95	ILE	0	-0.002	0.006	19.899	0.029	0.029	0.000	0.000	0.000	0.000
93	A	96	ARG	1	0.897	0.942	21.815	0.198	0.198	0.000	0.000	0.000	0.000
94	A	97	ARG	1	0.769	0.861	21.255	-0.258	-0.258	0.000	0.000	0.000	0.000
95	A	98	GLY	0	0.007	0.010	18.694	0.144	0.144	0.000	0.000	0.000	0.000
96	A	99	ALA	0	-0.033	-0.022	16.281	-0.078	-0.078	0.000	0.000	0.000	0.000
97	A	100	TYR	0	-0.027	-0.017	14.226	-0.099	-0.099	0.000	0.000	0.000	0.000
98	A	101	ASP	-1	-0.789	-0.891	16.183	-2.062	-2.062	0.000	0.000	0.000	0.000
99	A	102	PHE	0	-0.033	-0.032	17.337	0.172	0.172	0.000	0.000	0.000	0.000
100	A	103	ILE	0	-0.030	-0.010	14.459	-0.087	-0.087	0.000	0.000	0.000	0.000
101	A	104	GLU	-1	-0.927	-0.964	18.642	-0.730	-0.730	0.000	0.000	0.000	0.000
102	A	105	LYS	1	0.733	0.869	18.769	0.163	0.163	0.000	0.000	0.000	0.000
103	A	106	PRO	0	-0.033	-0.015	21.761	0.103	0.103	0.000	0.000	0.000	0.000
104	A	107	PHE	0	0.080	0.028	15.750	-0.013	-0.013	0.000	0.000	0.000	0.000
105	A	108	LYS	1	0.894	0.931	19.215	1.477	1.477	0.000	0.000	0.000	0.000
106	A	109	ALA	0	0.084	0.040	15.679	-0.115	-0.115	0.000	0.000	0.000	0.000
107	A	110	ASP	-1	-0.832	-0.912	14.982	-3.059	-3.059	0.000	0.000	0.000	0.000
108	A	111	ARG	1	0.762	0.874	16.105	1.919	1.919	0.000	0.000	0.000	0.000
109	A	112	LEU	0	0.015	0.008	11.374	0.003	0.003	0.000	0.000	0.000	0.000
110	A	113	ILE	0	0.062	0.031	11.124	-0.586	-0.586	0.000	0.000	0.000	0.000
111	A	114	LEU	0	-0.016	-0.003	11.748	-0.515	-0.515	0.000	0.000	0.000	0.000
112	A	115	VAL	0	-0.036	-0.031	13.046	0.024	0.024	0.000	0.000	0.000	0.000
113	A	116	ALA	0	0.017	0.006	7.950	-0.094	-0.094	0.000	0.000	0.000	0.000
114	A	117	GLU	-1	-0.878	-0.941	8.735	-8.913	-8.913	0.000	0.000	0.000	0.000
115	A	118	ARG	1	0.920	0.965	10.134	3.033	3.033	0.000	0.000	0.000	0.000
116	A	119	ALA	0	0.020	0.012	10.003	0.267	0.267	0.000	0.000	0.000	0.000
118	A	121	GLU	-1	-0.976	-0.963	7.852	-3.683	-3.683	0.000	0.000	0.000	0.000
119	A	122	THR	0	-0.044	-0.024	11.013	0.628	0.628	0.000	0.000	0.000	0.000
120	A	123	SER	0	-0.084	-0.068	7.212	0.983	0.983	0.000	0.000	0.000	0.000
121	A	124	LYS	0	0.041	0.053	4.821	-13.445	-13.445	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:ASP)