FMO DATABASE

FMODB ID: ZL1KN

Calculation Name: 5DKF-B-Xray547

Preferred Name:

Target Type:

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

Ligand 3-letter code: IMD | BEF | GOL | MN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5DKF

Chain ID: B

ChEMBL ID:

UniProt ID: P0AE67

Base Structure: X-ray

Registration Date: 2025-10-04

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	128
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1097263.249011
FMO2-HF: Nuclear repulsion	1047745.222748
FMO2-HF: Total energy	-49518.026263
FMO2-MP2: Total energy	-49660.640105

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:ALA)

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

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.
-169.254	-164.438	27.097	-16.567	-15.347	-0.169

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.788 / q_NPA : 0.888

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	LYS	1	0.847	0.924	3.393	56.602	58.410	0.024	-0.856	-0.977	0.000
5	A	6	LEU	0	-0.050	-0.001	2.912	2.607	3.042	0.124	-0.118	-0.441	-0.001
7	A	8	PHE	0	0.019	-0.005	4.602	0.582	0.634	-0.001	-0.005	-0.047	0.000
29	A	30	PHE	0	-0.048	-0.027	2.408	-1.115	-0.737	1.058	-0.362	-1.074	-0.002
120	A	121	ASN	0	0.072	0.026	5.103	-9.205	-9.079	-0.001	-0.005	-0.120	0.000
123	A	124	PHE	0	0.005	-0.011	2.678	-4.336	-2.595	3.532	-1.585	-3.687	-0.017
124	A	125	GLU	-1	-0.892	-0.947	4.488	-46.261	-46.223	-0.001	-0.015	-0.022	0.000
128	A	129	MET	-1	-0.840	-0.903	1.865	-141.318	-141.080	22.362	-13.621	-8.979	-0.149
4	A	5	GLU	-1	-0.896	-0.944	5.990	-22.391	-22.391	0.000	0.000	0.000	0.000
6	A	7	LYS	1	0.922	0.985	6.257	19.738	19.738	0.000	0.000	0.000	0.000
8	A	9	LEU	0	-0.013	0.002	9.870	1.537	1.537	0.000	0.000	0.000	0.000
9	A	10	VAL	0	-0.039	-0.019	12.876	-0.387	-0.387	0.000	0.000	0.000	0.000
10	A	11	VAL	0	0.018	0.003	14.931	0.894	0.894	0.000	0.000	0.000	0.000
11	A	12	ASP	-1	-0.752	-0.893	18.166	-13.680	-13.680	0.000	0.000	0.000	0.000
12	A	13	ASP	-1	-0.799	-0.886	20.973	-11.147	-11.147	0.000	0.000	0.000	0.000
13	A	14	GLN	0	-0.053	-0.020	23.941	0.163	0.163	0.000	0.000	0.000	0.000
14	A	15	SER	0	0.009	0.000	22.736	-0.678	-0.678	0.000	0.000	0.000	0.000
15	A	16	THR	0	-0.001	-0.016	22.002	-0.430	-0.430	0.000	0.000	0.000	0.000
16	A	17	MET	0	0.018	0.016	18.856	-0.590	-0.590	0.000	0.000	0.000	0.000
17	A	18	ARG	1	0.880	0.939	17.707	12.334	12.334	0.000	0.000	0.000	0.000
18	A	19	ARG	1	0.978	0.992	17.143	11.635	11.635	0.000	0.000	0.000	0.000
19	A	20	ILE	0	0.004	0.010	17.290	-0.450	-0.450	0.000	0.000	0.000	0.000
20	A	21	VAL	0	0.034	0.008	12.812	-0.783	-0.783	0.000	0.000	0.000	0.000
21	A	22	ARG	1	0.830	0.901	12.970	15.487	15.487	0.000	0.000	0.000	0.000
22	A	23	ASN	0	-0.096	-0.066	13.454	-0.789	-0.789	0.000	0.000	0.000	0.000
23	A	24	LEU	0	0.001	0.003	12.417	-0.379	-0.379	0.000	0.000	0.000	0.000
24	A	25	LEU	0	-0.004	0.004	7.593	-1.355	-1.355	0.000	0.000	0.000	0.000
25	A	26	LYS	1	0.966	0.987	9.203	15.151	15.151	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.969	-0.971	11.507	-19.798	-19.798	0.000	0.000	0.000	0.000
27	A	28	LEU	0	-0.044	-0.015	6.574	-0.927	-0.927	0.000	0.000	0.000	0.000
28	A	29	GLY	0	0.007	-0.001	6.668	-4.662	-4.662	0.000	0.000	0.000	0.000
30	A	31	ASN	0	-0.002	-0.019	7.796	3.989	3.989	0.000	0.000	0.000	0.000
31	A	32	ASN	0	-0.007	0.010	9.453	3.609	3.609	0.000	0.000	0.000	0.000
32	A	33	VAL	0	-0.014	-0.006	9.935	-1.049	-1.049	0.000	0.000	0.000	0.000
33	A	34	GLU	-1	-0.918	-0.952	12.183	-14.809	-14.809	0.000	0.000	0.000	0.000
34	A	35	GLU	-1	-0.838	-0.898	14.867	-15.279	-15.279	0.000	0.000	0.000	0.000
35	A	36	ALA	0	-0.013	-0.005	17.652	0.342	0.342	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.971	-0.992	20.133	-11.241	-11.241	0.000	0.000	0.000	0.000
37	A	38	ASP	-1	-0.771	-0.881	23.195	-10.997	-10.997	0.000	0.000	0.000	0.000
38	A	39	GLY	0	0.045	0.006	22.016	-0.513	-0.513	0.000	0.000	0.000	0.000
39	A	40	VAL	0	0.011	-0.002	23.002	-0.194	-0.194	0.000	0.000	0.000	0.000
40	A	41	ASP	-1	-0.837	-0.922	22.777	-12.852	-12.852	0.000	0.000	0.000	0.000
41	A	42	ALA	0	-0.029	-0.023	18.805	-0.454	-0.454	0.000	0.000	0.000	0.000
42	A	43	LEU	0	0.015	0.001	19.608	-0.564	-0.564	0.000	0.000	0.000	0.000
43	A	44	ASN	0	0.000	0.000	21.694	-0.064	-0.064	0.000	0.000	0.000	0.000
44	A	45	LYS	1	0.839	0.920	18.480	13.654	13.654	0.000	0.000	0.000	0.000
45	A	46	LEU	0	-0.025	-0.019	14.919	-0.601	-0.601	0.000	0.000	0.000	0.000
46	A	47	GLN	0	-0.043	-0.021	18.099	-0.100	-0.100	0.000	0.000	0.000	0.000
47	A	48	ALA	0	-0.027	0.003	20.098	0.399	0.399	0.000	0.000	0.000	0.000
48	A	49	GLY	0	-0.011	0.002	17.512	-0.061	-0.061	0.000	0.000	0.000	0.000
49	A	50	GLY	0	-0.038	-0.033	14.482	-0.111	-0.111	0.000	0.000	0.000	0.000
50	A	51	TYR	0	-0.006	-0.015	11.814	-1.075	-1.075	0.000	0.000	0.000	0.000
51	A	52	GLY	0	0.034	0.009	8.447	0.337	0.337	0.000	0.000	0.000	0.000
52	A	53	PHE	0	-0.009	-0.021	5.972	-2.280	-2.280	0.000	0.000	0.000	0.000
53	A	54	VAL	0	0.016	0.022	8.878	1.633	1.633	0.000	0.000	0.000	0.000
54	A	55	ILE	0	-0.029	-0.011	9.485	-0.722	-0.722	0.000	0.000	0.000	0.000
55	A	56	SER	0	0.019	-0.004	13.146	0.882	0.882	0.000	0.000	0.000	0.000
56	A	57	ASP	-1	-0.779	-0.883	16.970	-12.870	-12.870	0.000	0.000	0.000	0.000
57	A	58	TRP	0	-0.031	-0.019	20.199	-0.238	-0.238	0.000	0.000	0.000	0.000
58	A	59	LYS	1	0.906	0.958	23.097	10.131	10.131	0.000	0.000	0.000	0.000
59	A	60	MET	0	0.027	0.051	21.215	-0.019	-0.019	0.000	0.000	0.000	0.000
60	A	61	PRO	0	-0.004	-0.001	26.409	0.223	0.223	0.000	0.000	0.000	0.000
61	A	62	ASN	0	-0.044	-0.033	27.791	-0.013	-0.013	0.000	0.000	0.000	0.000
62	A	63	MET	0	-0.024	-0.007	24.975	0.006	0.006	0.000	0.000	0.000	0.000
63	A	64	ASP	-1	-0.808	-0.887	25.398	-11.682	-11.682	0.000	0.000	0.000	0.000
64	A	65	GLY	0	0.043	-0.008	21.583	-0.245	-0.245	0.000	0.000	0.000	0.000
65	A	66	LEU	0	-0.070	-0.030	21.143	-0.572	-0.572	0.000	0.000	0.000	0.000
66	A	67	GLU	-1	-0.845	-0.930	23.421	-11.002	-11.002	0.000	0.000	0.000	0.000
67	A	68	LEU	0	0.006	0.025	18.602	-0.109	-0.109	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.048	-0.015	17.293	-0.333	-0.333	0.000	0.000	0.000	0.000
69	A	70	LYS	1	0.868	0.922	20.079	10.926	10.926	0.000	0.000	0.000	0.000
70	A	71	THR	0	-0.011	-0.013	22.912	0.193	0.193	0.000	0.000	0.000	0.000
71	A	72	ILE	0	-0.027	-0.025	16.211	-0.069	-0.069	0.000	0.000	0.000	0.000
72	A	73	ARG	1	0.723	0.848	14.186	18.181	18.181	0.000	0.000	0.000	0.000
73	A	74	ALA	0	-0.025	-0.010	20.215	0.075	0.075	0.000	0.000	0.000	0.000
74	A	75	ASP	-1	-0.846	-0.917	21.444	-12.897	-12.897	0.000	0.000	0.000	0.000
75	A	76	GLY	0	0.019	-0.005	20.994	-0.702	-0.702	0.000	0.000	0.000	0.000
76	A	77	ALA	0	-0.038	-0.018	19.996	-0.513	-0.513	0.000	0.000	0.000	0.000
77	A	78	MET	0	-0.069	-0.029	16.648	-1.113	-1.113	0.000	0.000	0.000	0.000
78	A	79	SER	0	0.019	0.036	16.608	-1.114	-1.114	0.000	0.000	0.000	0.000
79	A	80	ALA	0	-0.013	-0.011	14.250	-0.095	-0.095	0.000	0.000	0.000	0.000
80	A	81	LEU	0	-0.020	0.016	11.316	-1.895	-1.895	0.000	0.000	0.000	0.000
81	A	82	PRO	0	0.026	0.008	7.945	1.467	1.467	0.000	0.000	0.000	0.000
82	A	83	VAL	0	0.019	0.009	10.783	0.553	0.553	0.000	0.000	0.000	0.000
83	A	84	LEU	0	-0.055	-0.012	10.275	0.549	0.549	0.000	0.000	0.000	0.000
84	A	85	MET	0	0.023	0.012	13.014	0.466	0.466	0.000	0.000	0.000	0.000
85	A	86	VAL	0	-0.019	-0.028	14.872	-0.240	-0.240	0.000	0.000	0.000	0.000
86	A	87	THR	0	0.073	0.039	17.847	0.734	0.734	0.000	0.000	0.000	0.000
87	A	88	ALA	0	0.023	0.021	21.675	-0.034	-0.034	0.000	0.000	0.000	0.000
88	A	89	TYR	0	-0.044	-0.013	24.638	0.565	0.565	0.000	0.000	0.000	0.000
89	A	90	ALA	0	0.067	0.035	24.467	-0.429	-0.429	0.000	0.000	0.000	0.000
90	A	91	LYS	1	0.897	0.967	25.933	9.404	9.404	0.000	0.000	0.000	0.000
91	A	92	LYS	1	1.015	0.990	26.485	9.436	9.436	0.000	0.000	0.000	0.000
92	A	93	GLU	-1	-0.893	-0.948	26.915	-9.659	-9.659	0.000	0.000	0.000	0.000
93	A	94	ASN	0	0.007	0.002	25.242	0.114	0.114	0.000	0.000	0.000	0.000
94	A	95	ILE	0	0.024	0.015	21.362	-0.327	-0.327	0.000	0.000	0.000	0.000
95	A	96	ILE	0	-0.022	-0.011	22.449	-0.432	-0.432	0.000	0.000	0.000	0.000
96	A	97	ALA	0	0.017	0.011	24.362	-0.194	-0.194	0.000	0.000	0.000	0.000
97	A	98	ALA	0	0.033	0.012	20.171	-0.151	-0.151	0.000	0.000	0.000	0.000
98	A	99	ALA	0	-0.019	-0.009	19.642	-0.550	-0.550	0.000	0.000	0.000	0.000
99	A	100	GLN	0	-0.047	-0.033	20.727	-0.088	-0.088	0.000	0.000	0.000	0.000
100	A	101	ALA	0	-0.013	0.008	22.031	0.156	0.156	0.000	0.000	0.000	0.000
101	A	102	GLY	0	0.047	0.029	18.900	-0.240	-0.240	0.000	0.000	0.000	0.000
102	A	103	ALA	0	-0.002	-0.003	16.353	-0.949	-0.949	0.000	0.000	0.000	0.000
103	A	104	SER	0	-0.015	-0.004	11.066	0.003	0.003	0.000	0.000	0.000	0.000
104	A	105	GLY	0	-0.002	-0.005	12.543	-1.053	-1.053	0.000	0.000	0.000	0.000
105	A	106	TYR	0	-0.010	-0.023	13.973	0.578	0.578	0.000	0.000	0.000	0.000
106	A	107	VAL	0	-0.026	-0.010	14.527	-0.203	-0.203	0.000	0.000	0.000	0.000
107	A	108	VAL	0	0.005	0.007	17.594	0.428	0.428	0.000	0.000	0.000	0.000
108	A	109	LYS	1	0.739	0.864	20.625	13.018	13.018	0.000	0.000	0.000	0.000
109	A	110	PRO	0	-0.029	-0.023	22.234	0.477	0.477	0.000	0.000	0.000	0.000
110	A	111	PHE	0	0.037	0.002	15.806	0.051	0.051	0.000	0.000	0.000	0.000
111	A	112	THR	0	0.011	0.012	17.921	-0.129	-0.129	0.000	0.000	0.000	0.000
112	A	113	ALA	0	0.049	0.009	14.787	-0.601	-0.601	0.000	0.000	0.000	0.000
113	A	114	ALA	0	0.067	0.041	13.239	-1.223	-1.223	0.000	0.000	0.000	0.000
114	A	115	THR	0	0.009	0.003	13.135	-0.838	-0.838	0.000	0.000	0.000	0.000
115	A	116	LEU	0	-0.020	-0.018	10.908	-0.582	-0.582	0.000	0.000	0.000	0.000
116	A	117	GLU	-1	-0.876	-0.937	8.182	-29.367	-29.367	0.000	0.000	0.000	0.000
117	A	118	GLU	-1	-0.939	-0.976	8.586	-22.402	-22.402	0.000	0.000	0.000	0.000
118	A	119	LYS	1	0.802	0.890	10.236	17.223	17.223	0.000	0.000	0.000	0.000
119	A	120	LEU	0	0.004	0.010	6.120	-0.045	-0.045	0.000	0.000	0.000	0.000
121	A	122	LYS	1	0.909	0.962	6.346	20.403	20.403	0.000	0.000	0.000	0.000
122	A	123	ILE	0	-0.038	-0.020	6.808	1.711	1.711	0.000	0.000	0.000	0.000
125	A	126	LYS	1	0.833	0.930	6.851	25.278	25.278	0.000	0.000	0.000	0.000
126	A	127	LEU	0	-0.039	-0.034	7.093	3.583	3.583	0.000	0.000	0.000	0.000
127	A	128	GLY	0	-0.015	0.018	6.455	2.103	2.103	0.000	0.000	0.000	0.000

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