FMO DATABASE

FMODB ID: N869Q

Calculation Name: 4LKB-A-Xray547

Preferred Name:

Target Type:

Ligand Name: sulfate ion | glycerol

Ligand 3-letter code: SO4 | GOL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4LKB

Chain ID: A

ChEMBL ID:

UniProt ID: Q8YNJ7

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1067193.197617
FMO2-HF: Nuclear repulsion	1018228.780427
FMO2-HF: Total energy	-48964.417189
FMO2-MP2: Total energy	-49110.10744

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:0:SER)

Summations of interaction energy for fragment #1(A:0: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.
-20.414	-16.037	3.543	-3.013	-4.909	-0.034

Interaction energy analysis for fragmet #1(A:0:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.830 / q_NPA : 0.913

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	2	VAL	0	0.029	0.010	3.804	0.781	2.178	-0.008	-0.542	-0.848	-0.001
34	A	33	GLN	0	-0.038	0.004	5.006	-7.415	-7.369	-0.001	-0.002	-0.043	0.000
35	A	34	ILE	0	-0.076	-0.023	2.553	-12.283	-11.425	0.485	-0.435	-0.908	-0.005
36	A	35	SER	0	0.018	-0.001	3.917	9.805	9.928	-0.001	-0.022	-0.100	0.000
39	A	38	LYS	1	0.823	0.927	4.188	50.128	50.302	-0.001	-0.026	-0.148	0.000
70	A	69	PHE	0	0.046	0.004	2.329	-4.413	-2.725	3.071	-1.977	-2.782	-0.028
71	A	70	GLU	-1	-0.872	-0.932	4.938	-24.486	-24.466	-0.001	-0.002	-0.017	0.000
109	A	108	LYS	1	0.856	0.922	4.550	40.877	40.948	-0.001	-0.007	-0.063	0.000
4	A	3	GLN	0	-0.011	0.001	6.262	2.747	2.747	0.000	0.000	0.000	0.000
5	A	4	ILE	0	0.007	0.013	10.004	0.914	0.914	0.000	0.000	0.000	0.000
6	A	5	LYS	1	0.822	0.914	12.537	18.403	18.403	0.000	0.000	0.000	0.000
7	A	6	VAL	0	0.010	0.006	16.269	-0.127	-0.127	0.000	0.000	0.000	0.000
8	A	7	TYR	0	-0.033	-0.042	18.903	0.390	0.390	0.000	0.000	0.000	0.000
9	A	8	GLY	0	0.077	0.039	22.558	-0.154	-0.154	0.000	0.000	0.000	0.000
10	A	9	LEU	0	0.016	0.033	25.685	0.061	0.061	0.000	0.000	0.000	0.000
11	A	10	ALA	0	0.023	0.006	28.517	-0.200	-0.200	0.000	0.000	0.000	0.000
12	A	11	GLU	-1	-0.956	-0.990	29.420	-9.455	-9.455	0.000	0.000	0.000	0.000
13	A	12	LYS	1	0.858	0.928	29.042	9.831	9.831	0.000	0.000	0.000	0.000
14	A	13	LEU	0	0.011	0.001	21.853	-0.331	-0.331	0.000	0.000	0.000	0.000
15	A	14	ASN	0	-0.013	-0.017	24.915	-0.869	-0.869	0.000	0.000	0.000	0.000
16	A	15	PRO	0	-0.007	-0.003	26.419	-0.237	-0.237	0.000	0.000	0.000	0.000
17	A	16	ILE	0	0.086	0.057	23.434	-0.215	-0.215	0.000	0.000	0.000	0.000
18	A	17	LYS	1	0.877	0.951	21.075	12.131	12.131	0.000	0.000	0.000	0.000
19	A	18	ALA	0	0.001	0.000	19.636	-0.925	-0.925	0.000	0.000	0.000	0.000
20	A	19	GLU	-1	-0.842	-0.925	19.250	-13.362	-13.362	0.000	0.000	0.000	0.000
21	A	20	LEU	0	0.032	0.017	18.565	-0.848	-0.848	0.000	0.000	0.000	0.000
22	A	21	SER	0	-0.031	-0.013	14.766	-1.118	-1.118	0.000	0.000	0.000	0.000
23	A	22	ASN	0	0.041	0.009	14.441	-2.450	-2.450	0.000	0.000	0.000	0.000
24	A	23	ILE	0	0.004	0.031	15.049	-1.099	-1.099	0.000	0.000	0.000	0.000
25	A	24	LEU	0	0.036	0.012	13.358	-1.092	-1.092	0.000	0.000	0.000	0.000
26	A	25	HIS	0	-0.060	-0.048	7.886	-1.970	-1.970	0.000	0.000	0.000	0.000
27	A	26	THR	0	-0.015	-0.017	10.274	-2.130	-2.130	0.000	0.000	0.000	0.000
28	A	27	SER	0	-0.037	-0.040	11.997	-1.244	-1.244	0.000	0.000	0.000	0.000
29	A	28	LEU	0	-0.004	-0.015	7.180	-1.354	-1.354	0.000	0.000	0.000	0.000
30	A	29	ILE	0	-0.040	-0.017	7.318	-4.171	-4.171	0.000	0.000	0.000	0.000
31	A	30	GLU	-1	-0.872	-0.924	8.751	-20.442	-20.442	0.000	0.000	0.000	0.000
32	A	31	VAL	0	-0.050	-0.021	10.369	0.327	0.327	0.000	0.000	0.000	0.000
33	A	32	LEU	0	-0.063	-0.048	4.926	-0.366	-0.366	0.000	0.000	0.000	0.000
37	A	36	PRO	0	0.071	0.020	6.025	-2.142	-2.142	0.000	0.000	0.000	0.000
38	A	37	GLU	-1	-0.844	-0.908	8.793	-23.962	-23.962	0.000	0.000	0.000	0.000
40	A	39	ARG	1	0.877	0.929	6.453	18.525	18.525	0.000	0.000	0.000	0.000
41	A	40	PHE	0	-0.018	-0.019	6.081	1.653	1.653	0.000	0.000	0.000	0.000
42	A	41	HIS	0	0.039	0.037	10.398	1.347	1.347	0.000	0.000	0.000	0.000
43	A	42	ARG	1	0.888	0.941	13.439	21.893	21.893	0.000	0.000	0.000	0.000
44	A	43	PHE	0	0.043	0.009	16.847	-0.192	-0.192	0.000	0.000	0.000	0.000
45	A	44	PHE	0	-0.007	-0.006	18.588	0.190	0.190	0.000	0.000	0.000	0.000
46	A	45	PRO	0	-0.022	-0.010	23.163	0.122	0.122	0.000	0.000	0.000	0.000
47	A	46	LEU	0	0.006	0.015	25.979	0.162	0.162	0.000	0.000	0.000	0.000
48	A	47	ASP	-1	-0.817	-0.912	28.771	-9.610	-9.610	0.000	0.000	0.000	0.000
49	A	48	LYS	1	0.884	0.927	32.575	9.175	9.175	0.000	0.000	0.000	0.000
50	A	49	LEU	0	-0.030	-0.018	34.764	0.076	0.076	0.000	0.000	0.000	0.000
51	A	50	ASP	-1	-0.876	-0.928	31.307	-9.652	-9.652	0.000	0.000	0.000	0.000
52	A	51	PHE	0	-0.090	-0.044	26.728	-0.333	-0.333	0.000	0.000	0.000	0.000
53	A	52	TYR	0	-0.024	-0.005	31.156	0.352	0.352	0.000	0.000	0.000	0.000
54	A	53	TYR	0	0.001	0.005	29.849	-0.322	-0.322	0.000	0.000	0.000	0.000
55	A	54	PRO	0	0.002	-0.003	30.410	0.339	0.339	0.000	0.000	0.000	0.000
56	A	55	SER	0	0.029	0.004	33.408	-0.054	-0.054	0.000	0.000	0.000	0.000
57	A	56	ASP	-1	-0.896	-0.936	33.057	-9.452	-9.452	0.000	0.000	0.000	0.000
58	A	57	ARG	1	0.779	0.892	27.415	10.709	10.709	0.000	0.000	0.000	0.000
59	A	58	THR	0	-0.029	-0.049	31.177	0.248	0.248	0.000	0.000	0.000	0.000
60	A	59	ASP	-1	-0.875	-0.946	31.177	-9.821	-9.821	0.000	0.000	0.000	0.000
61	A	60	ASN	0	-0.055	-0.042	28.471	-0.188	-0.188	0.000	0.000	0.000	0.000
62	A	61	TYR	0	-0.092	-0.048	25.934	-0.400	-0.400	0.000	0.000	0.000	0.000
63	A	62	LEU	0	-0.014	-0.009	21.322	-0.243	-0.243	0.000	0.000	0.000	0.000
64	A	63	ILE	0	0.028	0.018	20.684	-0.090	-0.090	0.000	0.000	0.000	0.000
65	A	64	ILE	0	-0.010	-0.011	15.252	-0.520	-0.520	0.000	0.000	0.000	0.000
66	A	65	GLU	-1	-0.809	-0.875	15.609	-16.947	-16.947	0.000	0.000	0.000	0.000
67	A	66	ILE	0	-0.007	-0.011	9.491	-1.229	-1.229	0.000	0.000	0.000	0.000
68	A	67	ILE	0	0.014	0.014	9.979	0.159	0.159	0.000	0.000	0.000	0.000
69	A	68	MET	0	-0.012	-0.017	5.479	-2.707	-2.707	0.000	0.000	0.000	0.000
72	A	71	GLY	0	0.026	0.015	5.987	-3.297	-3.297	0.000	0.000	0.000	0.000
73	A	72	ARG	1	0.908	0.955	5.442	32.322	32.322	0.000	0.000	0.000	0.000
74	A	73	SER	0	0.067	0.030	8.030	1.672	1.672	0.000	0.000	0.000	0.000
75	A	74	VAL	0	0.032	-0.009	11.787	-0.609	-0.609	0.000	0.000	0.000	0.000
76	A	75	GLU	-1	-0.941	-0.957	14.371	-17.740	-17.740	0.000	0.000	0.000	0.000
77	A	76	THR	0	0.026	0.006	9.344	-0.422	-0.422	0.000	0.000	0.000	0.000
78	A	77	LYS	1	0.826	0.900	9.618	23.384	23.384	0.000	0.000	0.000	0.000
79	A	78	LYS	1	0.956	0.974	12.199	15.984	15.984	0.000	0.000	0.000	0.000
80	A	79	GLN	0	-0.011	-0.009	13.854	1.128	1.128	0.000	0.000	0.000	0.000
81	A	80	LEU	0	0.017	0.016	9.568	0.447	0.447	0.000	0.000	0.000	0.000
82	A	81	LEU	0	0.002	0.002	13.097	0.641	0.641	0.000	0.000	0.000	0.000
83	A	82	ARG	1	0.951	0.973	16.171	15.095	15.095	0.000	0.000	0.000	0.000
84	A	83	ASP	-1	-0.783	-0.844	14.720	-18.894	-18.894	0.000	0.000	0.000	0.000
85	A	84	ILE	0	0.017	0.014	12.590	0.486	0.486	0.000	0.000	0.000	0.000
86	A	85	PHE	0	-0.026	-0.020	16.754	0.526	0.526	0.000	0.000	0.000	0.000
87	A	86	LYS	1	0.839	0.901	19.761	14.376	14.376	0.000	0.000	0.000	0.000
88	A	87	LYS	1	0.818	0.867	15.341	19.661	19.661	0.000	0.000	0.000	0.000
89	A	88	VAL	0	-0.031	-0.013	18.693	0.213	0.213	0.000	0.000	0.000	0.000
90	A	89	ASP	-1	-0.852	-0.924	21.331	-11.213	-11.213	0.000	0.000	0.000	0.000
91	A	90	GLU	-1	-0.860	-0.918	23.337	-12.834	-12.834	0.000	0.000	0.000	0.000
92	A	91	LYS	1	0.789	0.912	22.047	13.302	13.302	0.000	0.000	0.000	0.000
93	A	92	PHE	0	-0.049	-0.048	21.149	0.121	0.121	0.000	0.000	0.000	0.000
94	A	93	GLY	0	0.037	0.038	26.483	0.404	0.404	0.000	0.000	0.000	0.000
95	A	94	ILE	0	-0.060	-0.026	24.582	0.307	0.307	0.000	0.000	0.000	0.000
96	A	95	SER	0	0.088	0.039	25.716	-0.486	-0.486	0.000	0.000	0.000	0.000
97	A	96	VAL	0	0.003	-0.012	23.760	-0.205	-0.205	0.000	0.000	0.000	0.000
98	A	97	TYR	0	-0.013	0.001	25.288	-0.232	-0.232	0.000	0.000	0.000	0.000
99	A	98	ASP	-1	-0.796	-0.865	27.286	-10.447	-10.447	0.000	0.000	0.000	0.000
100	A	99	ILE	0	-0.013	-0.008	20.651	-0.430	-0.430	0.000	0.000	0.000	0.000
101	A	100	GLU	-1	-0.875	-0.900	21.723	-12.870	-12.870	0.000	0.000	0.000	0.000
102	A	101	ILE	0	-0.023	-0.020	15.635	-0.776	-0.776	0.000	0.000	0.000	0.000
103	A	102	THR	0	-0.007	0.000	16.483	0.132	0.132	0.000	0.000	0.000	0.000
104	A	103	LEU	0	-0.012	-0.015	11.297	-1.315	-1.315	0.000	0.000	0.000	0.000
105	A	104	PHE	0	0.006	0.000	11.703	1.092	1.092	0.000	0.000	0.000	0.000
106	A	105	GLU	-1	-0.817	-0.896	8.454	-27.318	-27.318	0.000	0.000	0.000	0.000
107	A	106	ILE	0	-0.028	-0.013	8.360	2.342	2.342	0.000	0.000	0.000	0.000
108	A	107	PRO	0	0.038	0.022	8.086	-3.388	-3.388	0.000	0.000	0.000	0.000
110	A	109	GLN	0	0.118	0.066	7.952	-1.970	-1.970	0.000	0.000	0.000	0.000
111	A	110	ASN	0	-0.069	-0.032	11.076	1.765	1.765	0.000	0.000	0.000	0.000
112	A	111	TRP	0	-0.057	-0.030	7.491	-1.214	-1.214	0.000	0.000	0.000	0.000
113	A	112	GLY	0	0.046	0.038	9.825	-0.673	-0.673	0.000	0.000	0.000	0.000
114	A	113	ILE	0	-0.052	-0.048	5.756	-1.930	-1.930	0.000	0.000	0.000	0.000
115	A	114	ARG	1	0.879	0.926	9.453	25.803	25.803	0.000	0.000	0.000	0.000
116	A	115	GLY	0	0.021	0.016	12.011	0.826	0.826	0.000	0.000	0.000	0.000
117	A	116	ILE	0	0.025	0.042	10.382	1.388	1.388	0.000	0.000	0.000	0.000
118	A	117	PRO	0	0.043	0.023	11.629	-1.424	-1.424	0.000	0.000	0.000	0.000
119	A	118	GLY	0	-0.003	-0.001	7.280	-1.010	-1.010	0.000	0.000	0.000	0.000
120	A	119	ASP	-1	-0.988	-1.022	6.620	-28.184	-28.184	0.000	0.000	0.000	0.000
121	A	120	GLU	-2	-1.853	-1.908	9.218	-45.675	-45.675	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:SER)