FMO DATABASE

FMODB ID: KVNK3

Calculation Name: 5KO4-B-Xray547

Preferred Name:

Target Type:

Ligand Name: sulfate ion

Ligand 3-letter code: SO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5KO4

Chain ID: B

ChEMBL ID:

UniProt ID: Q38AE9

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	100
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-839500.714968
FMO2-HF: Nuclear repulsion	796453.996354
FMO2-HF: Total energy	-43046.718614
FMO2-MP2: Total energy	-43169.101057

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:30:PHE)

Summations of interaction energy for fragment #1(A:30:PHE)

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.
-70.594	-57.368	15.2	-9.294	-19.134	-0.074

Interaction energy analysis for fragmet #1(A:30:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.891 / q_NPA : 0.939

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	32	LYS	1	0.889	0.955	3.388	41.335	43.832	-0.001	-1.125	-1.372	0.001
4	A	33	GLN	0	0.108	0.063	2.298	-18.356	-16.512	4.976	-3.460	-3.361	-0.035
5	A	34	CYS	0	-0.024	0.007	2.769	4.225	4.655	3.541	-1.487	-2.484	-0.017
6	A	35	ARG	1	0.932	0.961	5.234	41.028	41.189	-0.001	-0.012	-0.148	0.000
53	A	82	TYR	0	-0.057	-0.046	3.434	-0.445	-0.080	0.010	-0.060	-0.314	0.000
54	A	83	THR	0	0.030	0.014	3.163	-8.848	-6.983	0.139	-0.907	-1.097	-0.008
55	A	84	SER	0	-0.007	-0.010	2.783	-4.943	-2.806	2.096	-1.479	-2.754	-0.006
56	A	85	PRO	0	0.061	0.012	2.404	-3.987	-1.563	3.499	-0.236	-5.688	-0.001
57	A	86	SER	0	0.046	0.027	3.973	2.572	2.830	0.029	0.026	-0.313	0.000
59	A	88	PHE	0	0.025	0.005	4.601	0.823	1.002	-0.001	-0.006	-0.172	0.000
99	A	128	LEU	0	-0.149	-0.094	2.346	-13.604	-12.552	0.914	-0.544	-1.421	-0.008
100	A	129	SER	-1	-0.926	-0.935	5.366	-29.736	-29.722	-0.001	-0.004	-0.010	0.000
7	A	36	SER	0	-0.038	0.006	7.576	4.571	4.571	0.000	0.000	0.000	0.000
8	A	37	ILE	0	0.074	0.028	6.940	2.628	2.628	0.000	0.000	0.000	0.000
9	A	38	LEU	0	-0.019	-0.010	9.315	2.299	2.299	0.000	0.000	0.000	0.000
10	A	39	HIS	0	-0.079	-0.044	10.981	1.099	1.099	0.000	0.000	0.000	0.000
11	A	40	VAL	0	0.015	0.009	12.947	1.611	1.611	0.000	0.000	0.000	0.000
12	A	41	VAL	0	0.003	-0.002	13.111	1.317	1.317	0.000	0.000	0.000	0.000
13	A	42	MET	0	-0.085	-0.036	14.881	0.857	0.857	0.000	0.000	0.000	0.000
14	A	43	ASP	-1	-0.862	-0.914	17.182	-15.601	-15.601	0.000	0.000	0.000	0.000
15	A	44	LEU	0	-0.065	-0.031	17.388	0.990	0.990	0.000	0.000	0.000	0.000
16	A	45	ASP	-1	-0.788	-0.888	19.584	-12.895	-12.895	0.000	0.000	0.000	0.000
17	A	46	ARG	1	0.917	0.941	21.249	11.477	11.477	0.000	0.000	0.000	0.000
18	A	47	ASP	-1	-0.955	-0.963	24.150	-10.475	-10.475	0.000	0.000	0.000	0.000
19	A	48	GLY	0	-0.026	-0.006	21.828	0.159	0.159	0.000	0.000	0.000	0.000
20	A	49	ILE	0	-0.049	-0.019	22.870	0.033	0.033	0.000	0.000	0.000	0.000
21	A	50	PHE	0	-0.015	-0.019	19.375	0.161	0.161	0.000	0.000	0.000	0.000
22	A	51	ALA	0	0.018	0.010	18.510	-0.830	-0.830	0.000	0.000	0.000	0.000
23	A	52	ARG	1	0.953	0.963	18.984	11.765	11.765	0.000	0.000	0.000	0.000
24	A	53	ASP	-1	-0.822	-0.892	21.303	-11.930	-11.930	0.000	0.000	0.000	0.000
25	A	54	PRO	0	0.039	0.040	21.319	0.540	0.540	0.000	0.000	0.000	0.000
26	A	55	SER	0	-0.035	-0.045	23.358	0.509	0.509	0.000	0.000	0.000	0.000
27	A	56	LYS	1	0.892	0.931	25.804	10.735	10.735	0.000	0.000	0.000	0.000
28	A	57	LEU	0	0.024	0.035	26.666	0.336	0.336	0.000	0.000	0.000	0.000
29	A	58	PRO	0	0.010	-0.004	29.940	0.009	0.009	0.000	0.000	0.000	0.000
30	A	59	ASP	-1	-0.839	-0.915	31.462	-8.692	-8.692	0.000	0.000	0.000	0.000
31	A	60	TYR	0	0.037	0.023	22.651	-0.276	-0.276	0.000	0.000	0.000	0.000
32	A	61	ARG	1	0.852	0.898	26.003	9.599	9.599	0.000	0.000	0.000	0.000
33	A	62	MET	0	-0.076	-0.017	27.673	0.078	0.078	0.000	0.000	0.000	0.000
34	A	63	ILE	0	-0.015	0.002	27.608	0.050	0.050	0.000	0.000	0.000	0.000
35	A	64	ILE	0	-0.002	0.012	22.333	-0.198	-0.198	0.000	0.000	0.000	0.000
36	A	65	SER	0	-0.007	-0.011	22.935	-0.016	-0.016	0.000	0.000	0.000	0.000
37	A	66	HIS	0	-0.052	-0.027	16.326	-0.569	-0.569	0.000	0.000	0.000	0.000
38	A	67	PRO	0	0.022	0.021	19.045	-0.521	-0.521	0.000	0.000	0.000	0.000
39	A	68	MET	0	-0.004	0.009	13.901	-0.775	-0.775	0.000	0.000	0.000	0.000
40	A	69	TRP	0	0.002	0.010	16.004	0.504	0.504	0.000	0.000	0.000	0.000
41	A	70	TRP	0	0.076	0.013	13.770	-1.364	-1.364	0.000	0.000	0.000	0.000
42	A	71	ASP	-1	-0.866	-0.947	13.965	-16.980	-16.980	0.000	0.000	0.000	0.000
43	A	72	LEU	0	-0.077	-0.018	13.542	-0.446	-0.446	0.000	0.000	0.000	0.000
44	A	73	ILE	0	0.060	0.029	9.220	-1.084	-1.084	0.000	0.000	0.000	0.000
45	A	74	LYS	1	0.904	0.942	9.611	15.539	15.539	0.000	0.000	0.000	0.000
46	A	75	ALA	0	-0.017	-0.001	11.071	-1.052	-1.052	0.000	0.000	0.000	0.000
47	A	76	ARG	1	0.856	0.923	8.411	19.221	19.221	0.000	0.000	0.000	0.000
48	A	77	LEU	0	-0.020	-0.010	4.937	-2.186	-2.186	0.000	0.000	0.000	0.000
49	A	78	THR	0	-0.131	-0.080	7.650	-0.709	-0.709	0.000	0.000	0.000	0.000
50	A	79	ARG	1	0.877	0.937	10.301	18.515	18.515	0.000	0.000	0.000	0.000
51	A	80	TYR	0	-0.035	-0.012	5.900	-0.869	-0.869	0.000	0.000	0.000	0.000
52	A	81	GLU	-1	-0.821	-0.904	7.076	-19.863	-19.863	0.000	0.000	0.000	0.000
58	A	87	ALA	0	-0.001	0.006	5.287	2.175	2.175	0.000	0.000	0.000	0.000
60	A	89	ILE	0	0.012	0.006	6.384	2.335	2.335	0.000	0.000	0.000	0.000
61	A	90	ASN	0	-0.041	-0.019	8.745	2.801	2.801	0.000	0.000	0.000	0.000
62	A	91	ASP	-1	-0.754	-0.842	9.974	-19.856	-19.856	0.000	0.000	0.000	0.000
63	A	92	MET	0	-0.028	-0.018	9.129	1.595	1.595	0.000	0.000	0.000	0.000
64	A	93	ARG	1	0.812	0.852	12.018	21.643	21.643	0.000	0.000	0.000	0.000
65	A	94	LEU	0	-0.028	0.003	14.298	1.077	1.077	0.000	0.000	0.000	0.000
66	A	95	VAL	0	-0.050	-0.015	14.893	0.931	0.931	0.000	0.000	0.000	0.000
67	A	96	VAL	0	0.016	0.007	16.668	0.784	0.784	0.000	0.000	0.000	0.000
68	A	97	GLN	0	-0.016	-0.012	18.496	0.429	0.429	0.000	0.000	0.000	0.000
69	A	98	ASN	0	0.008	-0.021	19.138	0.907	0.907	0.000	0.000	0.000	0.000
70	A	99	CYS	0	-0.115	-0.036	21.457	0.668	0.668	0.000	0.000	0.000	0.000
71	A	100	TYR	0	-0.085	-0.088	21.099	0.744	0.744	0.000	0.000	0.000	0.000
72	A	101	ASP	-1	-0.842	-0.906	23.829	-11.413	-11.413	0.000	0.000	0.000	0.000
73	A	102	TYR	0	-0.095	-0.058	26.013	0.394	0.394	0.000	0.000	0.000	0.000
74	A	103	ASN	0	-0.055	-0.030	26.533	0.094	0.094	0.000	0.000	0.000	0.000
75	A	104	ARG	1	0.849	0.889	28.912	8.429	8.429	0.000	0.000	0.000	0.000
76	A	105	GLU	-1	-0.821	-0.898	29.572	-10.056	-10.056	0.000	0.000	0.000	0.000
77	A	106	GLU	-1	-0.740	-0.843	30.315	-8.957	-8.957	0.000	0.000	0.000	0.000
78	A	107	SER	0	-0.018	0.007	29.562	0.163	0.163	0.000	0.000	0.000	0.000
79	A	108	PRO	0	0.023	-0.007	29.404	-0.310	-0.310	0.000	0.000	0.000	0.000
80	A	109	PHE	0	0.005	0.013	26.099	-0.325	-0.325	0.000	0.000	0.000	0.000
81	A	110	SER	0	0.073	0.005	24.939	-0.603	-0.603	0.000	0.000	0.000	0.000
82	A	111	THR	0	-0.042	-0.019	25.104	-0.255	-0.255	0.000	0.000	0.000	0.000
83	A	112	LEU	0	-0.030	-0.017	22.439	-0.271	-0.271	0.000	0.000	0.000	0.000
84	A	113	ALA	0	0.012	0.006	20.783	-0.616	-0.616	0.000	0.000	0.000	0.000
85	A	114	ARG	1	0.924	0.959	20.125	10.414	10.414	0.000	0.000	0.000	0.000
86	A	115	ARG	1	0.858	0.934	20.821	12.656	12.656	0.000	0.000	0.000	0.000
87	A	116	ILE	0	0.021	0.005	16.357	-0.565	-0.565	0.000	0.000	0.000	0.000
88	A	117	GLU	-1	-0.849	-0.898	16.294	-15.841	-15.841	0.000	0.000	0.000	0.000
89	A	118	ILE	0	-0.031	-0.017	15.993	-0.728	-0.728	0.000	0.000	0.000	0.000
90	A	119	ALA	0	0.020	0.017	16.228	-0.663	-0.663	0.000	0.000	0.000	0.000
91	A	120	MET	0	-0.031	-0.006	11.860	-1.392	-1.392	0.000	0.000	0.000	0.000
92	A	121	GLU	-1	-0.741	-0.837	11.355	-22.487	-22.487	0.000	0.000	0.000	0.000
93	A	122	ASP	-1	-0.883	-0.939	12.461	-18.031	-18.031	0.000	0.000	0.000	0.000
94	A	123	LEU	0	-0.026	-0.008	10.248	-0.926	-0.926	0.000	0.000	0.000	0.000
95	A	124	PHE	0	-0.051	-0.041	7.822	-3.829	-3.829	0.000	0.000	0.000	0.000
96	A	125	VAL	0	0.006	0.006	8.309	-2.247	-2.247	0.000	0.000	0.000	0.000
97	A	126	THR	0	-0.067	-0.026	10.635	0.407	0.407	0.000	0.000	0.000	0.000
98	A	127	GLU	-1	-0.930	-0.991	5.684	-37.204	-37.204	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:30:PHE)