FMO DATABASE

FMODB ID: 1V2KZ

Calculation Name: 5KNH-I-Xray547

Preferred Name:

Target Type:

Ligand Name: acetate ion

Ligand 3-letter code: ACT

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5KNH

Chain ID: I

ChEMBL ID:

UniProt ID: Q0PW92

Base Structure: X-ray

Registration Date: 2025-10-06

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	108
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-845467.987637
FMO2-HF: Nuclear repulsion	802349.655175
FMO2-HF: Total energy	-43118.332462
FMO2-MP2: Total energy	-43241.687771

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(I:4:VAL)

Summations of interaction energy for fragment #1(I:4:VAL)

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.
-6.784	-0.335	5.713	-4.363	-7.796	-0.033

Interaction energy analysis for fragmet #1(I:4:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.851 / q_NPA : 0.922

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	I	6	PRO	0	0.086	0.035	2.687	-4.188	-1.436	0.593	-1.413	-1.931	-0.012
4	I	7	SER	0	0.054	0.032	5.307	0.730	0.878	-0.001	-0.010	-0.137	0.000
5	I	8	THR	0	-0.013	-0.010	2.140	2.544	1.426	4.121	-0.803	-2.199	0.001
6	I	9	ALA	0	0.036	0.022	2.726	1.176	2.423	0.438	-0.452	-1.233	-0.004
7	I	10	LEU	0	-0.010	0.004	3.852	4.622	4.748	0.011	-0.019	-0.118	0.000
9	I	12	GLU	-1	-0.883	-0.960	2.911	-51.098	-48.562	0.206	-1.440	-1.302	-0.016
66	I	70	PHE	0	-0.060	-0.039	2.459	-5.020	-4.262	0.345	-0.226	-0.876	-0.002
8	I	11	LYS	1	0.830	0.902	6.552	25.791	25.791	0.000	0.000	0.000	0.000
10	I	13	LEU	0	0.005	0.005	7.034	2.587	2.587	0.000	0.000	0.000	0.000
11	I	14	ILE	0	-0.010	-0.009	8.983	2.549	2.549	0.000	0.000	0.000	0.000
12	I	15	GLU	-1	-0.830	-0.902	10.196	-20.673	-20.673	0.000	0.000	0.000	0.000
13	I	16	GLU	-1	-0.812	-0.886	10.661	-18.072	-18.072	0.000	0.000	0.000	0.000
14	I	17	LEU	0	-0.005	-0.009	12.422	1.398	1.398	0.000	0.000	0.000	0.000
15	I	18	VAL	0	-0.014	-0.009	14.725	1.248	1.248	0.000	0.000	0.000	0.000
16	I	19	ASN	0	-0.014	-0.004	15.128	1.755	1.755	0.000	0.000	0.000	0.000
17	I	20	ILE	0	-0.018	-0.007	15.494	0.909	0.909	0.000	0.000	0.000	0.000
18	I	21	THR	0	-0.083	-0.050	18.508	0.830	0.830	0.000	0.000	0.000	0.000
19	I	22	GLN	0	-0.062	-0.026	20.300	0.971	0.971	0.000	0.000	0.000	0.000
20	I	23	ASN	0	-0.023	-0.019	18.989	1.006	1.006	0.000	0.000	0.000	0.000
21	I	24	GLN	0	-0.052	-0.016	20.220	0.553	0.553	0.000	0.000	0.000	0.000
22	I	25	LYS	1	0.954	0.980	23.001	9.982	9.982	0.000	0.000	0.000	0.000
23	I	26	ALA	0	0.010	0.017	26.362	-0.175	-0.175	0.000	0.000	0.000	0.000
24	I	27	PRO	0	0.024	0.006	27.599	0.252	0.252	0.000	0.000	0.000	0.000
25	I	28	LEU	0	0.025	0.013	20.959	-0.067	-0.067	0.000	0.000	0.000	0.000
26	I	29	CYS	0	-0.060	-0.019	20.622	0.280	0.280	0.000	0.000	0.000	0.000
27	I	30	ASN	0	0.014	0.014	24.732	0.152	0.152	0.000	0.000	0.000	0.000
28	I	31	GLY	0	0.066	0.043	27.762	0.321	0.321	0.000	0.000	0.000	0.000
29	I	32	SER	0	-0.048	-0.027	24.776	0.105	0.105	0.000	0.000	0.000	0.000
30	I	33	MET	0	-0.007	0.005	26.058	-0.289	-0.289	0.000	0.000	0.000	0.000
31	I	34	VAL	0	0.033	0.026	21.367	0.016	0.016	0.000	0.000	0.000	0.000
32	I	35	TRP	0	0.002	-0.016	23.411	0.590	0.590	0.000	0.000	0.000	0.000
33	I	36	SER	0	0.063	0.032	22.391	-0.537	-0.537	0.000	0.000	0.000	0.000
34	I	37	ILE	0	-0.003	-0.006	16.175	-0.093	-0.093	0.000	0.000	0.000	0.000
35	I	38	ASN	0	0.080	0.062	20.383	0.661	0.661	0.000	0.000	0.000	0.000
36	I	39	LEU	0	-0.012	-0.011	19.766	-0.700	-0.700	0.000	0.000	0.000	0.000
37	I	40	THR	0	-0.042	-0.033	21.185	-0.075	-0.075	0.000	0.000	0.000	0.000
38	I	41	ALA	0	0.000	0.010	18.138	-0.105	-0.105	0.000	0.000	0.000	0.000
39	I	42	GLY	0	0.018	0.010	14.426	-0.277	-0.277	0.000	0.000	0.000	0.000
40	I	43	VAL	0	0.036	0.011	11.752	-0.287	-0.287	0.000	0.000	0.000	0.000
41	I	44	TYR	0	0.044	0.004	7.570	-0.021	-0.021	0.000	0.000	0.000	0.000
42	I	45	CYS	0	-0.054	-0.033	6.120	1.933	1.933	0.000	0.000	0.000	0.000
43	I	46	ALA	0	0.047	0.036	13.680	0.968	0.968	0.000	0.000	0.000	0.000
44	I	47	ALA	0	-0.019	-0.016	13.265	0.781	0.781	0.000	0.000	0.000	0.000
45	I	48	LEU	0	-0.022	-0.014	11.675	0.693	0.693	0.000	0.000	0.000	0.000
46	I	49	GLU	-1	-0.764	-0.885	14.459	-14.180	-14.180	0.000	0.000	0.000	0.000
47	I	50	SER	0	-0.054	-0.031	18.088	0.533	0.533	0.000	0.000	0.000	0.000
48	I	51	LEU	0	-0.030	-0.024	14.921	0.667	0.667	0.000	0.000	0.000	0.000
49	I	52	ILE	0	-0.010	0.012	16.586	0.094	0.094	0.000	0.000	0.000	0.000
50	I	53	ASN	0	-0.022	-0.014	18.930	0.321	0.321	0.000	0.000	0.000	0.000
51	I	54	VAL	0	-0.039	-0.007	20.190	0.543	0.543	0.000	0.000	0.000	0.000
52	I	55	SER	0	0.040	0.025	20.084	-0.581	-0.581	0.000	0.000	0.000	0.000
53	I	56	GLY	0	0.022	0.004	21.172	0.369	0.369	0.000	0.000	0.000	0.000
54	I	58	SER	0	0.082	0.022	19.034	-0.437	-0.437	0.000	0.000	0.000	0.000
55	I	59	ALA	0	-0.028	-0.008	18.128	-0.619	-0.619	0.000	0.000	0.000	0.000
56	I	60	ILE	0	0.016	-0.009	16.269	-0.375	-0.375	0.000	0.000	0.000	0.000
57	I	61	GLU	-1	-0.931	-0.942	14.754	-17.928	-17.928	0.000	0.000	0.000	0.000
58	I	62	LYS	1	0.897	0.936	9.940	21.081	21.081	0.000	0.000	0.000	0.000
59	I	63	THR	0	0.051	0.015	10.318	-2.417	-2.417	0.000	0.000	0.000	0.000
60	I	64	GLN	0	0.001	-0.017	10.674	-1.497	-1.497	0.000	0.000	0.000	0.000
61	I	65	ARG	1	0.941	0.982	9.122	22.511	22.511	0.000	0.000	0.000	0.000
62	I	66	MET	0	-0.040	-0.012	6.268	-1.175	-1.175	0.000	0.000	0.000	0.000
63	I	67	LEU	0	0.001	0.002	6.349	-2.764	-2.764	0.000	0.000	0.000	0.000
64	I	68	ASN	0	-0.036	-0.033	8.936	0.100	0.100	0.000	0.000	0.000	0.000
65	I	69	GLY	0	-0.013	0.003	5.308	-0.215	-0.215	0.000	0.000	0.000	0.000
67	I	72	PRO	0	0.079	0.062	7.809	2.374	2.374	0.000	0.000	0.000	0.000
68	I	73	HIS	0	-0.004	0.001	9.608	1.537	1.537	0.000	0.000	0.000	0.000
69	I	74	LYS	1	0.783	0.887	13.222	18.178	18.178	0.000	0.000	0.000	0.000
70	I	75	VAL	0	0.031	0.014	15.898	0.897	0.897	0.000	0.000	0.000	0.000
71	I	76	SER	0	0.045	0.015	18.937	0.123	0.123	0.000	0.000	0.000	0.000
72	I	77	ALA	0	0.049	0.033	22.157	0.164	0.164	0.000	0.000	0.000	0.000
73	I	78	GLY	0	0.013	0.010	18.670	0.273	0.273	0.000	0.000	0.000	0.000
74	I	79	GLN	0	-0.072	-0.038	18.617	-0.671	-0.671	0.000	0.000	0.000	0.000
75	I	80	PHE	0	0.030	0.001	20.804	0.271	0.271	0.000	0.000	0.000	0.000
76	I	81	SER	0	-0.023	-0.013	22.307	0.507	0.507	0.000	0.000	0.000	0.000
77	I	82	SER	0	-0.047	-0.035	18.993	-0.737	-0.737	0.000	0.000	0.000	0.000
78	I	83	LEU	0	-0.001	0.006	21.253	-0.011	-0.011	0.000	0.000	0.000	0.000
79	I	84	ARG	1	0.914	0.959	23.439	10.026	10.026	0.000	0.000	0.000	0.000
80	I	85	VAL	0	-0.023	0.011	23.481	0.406	0.406	0.000	0.000	0.000	0.000
81	I	86	ARG	0	-0.091	-0.072	24.091	-0.710	-0.710	0.000	0.000	0.000	0.000
82	I	87	ASP	-1	-0.809	-0.877	26.620	-10.336	-10.336	0.000	0.000	0.000	0.000
83	I	88	THR	0	-0.027	-0.011	27.541	0.348	0.348	0.000	0.000	0.000	0.000
84	I	89	LYS	1	0.807	0.899	26.499	10.476	10.476	0.000	0.000	0.000	0.000
85	I	90	ILE	0	-0.008	0.001	23.499	0.307	0.307	0.000	0.000	0.000	0.000
86	I	91	GLU	-1	-0.828	-0.929	25.970	-10.327	-10.327	0.000	0.000	0.000	0.000
87	I	92	VAL	0	-0.005	-0.012	20.305	-0.319	-0.319	0.000	0.000	0.000	0.000
88	I	93	ALA	0	0.006	-0.002	21.621	-0.501	-0.501	0.000	0.000	0.000	0.000
89	I	94	GLN	0	-0.046	-0.025	23.060	-0.021	-0.021	0.000	0.000	0.000	0.000
90	I	95	PHE	0	0.015	0.000	16.745	-0.301	-0.301	0.000	0.000	0.000	0.000
91	I	96	VAL	0	0.009	0.003	17.454	-0.626	-0.626	0.000	0.000	0.000	0.000
92	I	97	LYS	1	0.976	0.995	18.411	10.660	10.660	0.000	0.000	0.000	0.000
93	I	98	ASP	-1	-0.857	-0.923	20.401	-12.405	-12.405	0.000	0.000	0.000	0.000
94	I	99	LEU	0	-0.003	0.002	13.670	-0.278	-0.278	0.000	0.000	0.000	0.000
95	I	100	LEU	0	0.013	0.014	15.294	-0.730	-0.730	0.000	0.000	0.000	0.000
96	I	101	VAL	0	-0.061	-0.045	17.025	-0.099	-0.099	0.000	0.000	0.000	0.000
97	I	102	HIS	0	0.006	0.002	17.219	0.319	0.319	0.000	0.000	0.000	0.000
98	I	103	LEU	0	0.027	0.011	11.839	-0.297	-0.297	0.000	0.000	0.000	0.000
99	I	104	LYS	1	0.951	0.962	15.031	14.182	14.182	0.000	0.000	0.000	0.000
100	I	105	LYS	1	0.871	0.956	16.912	12.790	12.790	0.000	0.000	0.000	0.000
101	I	106	LEU	0	0.089	0.038	14.923	0.016	0.016	0.000	0.000	0.000	0.000
102	I	107	PHE	0	-0.049	-0.012	12.767	0.023	0.023	0.000	0.000	0.000	0.000
103	I	108	ARG	1	0.921	0.956	15.698	13.884	13.884	0.000	0.000	0.000	0.000
104	I	109	GLU	-1	-0.947	-0.971	19.134	-13.176	-13.176	0.000	0.000	0.000	0.000
105	I	110	GLY	0	0.029	0.036	17.836	0.250	0.250	0.000	0.000	0.000	0.000
106	I	111	GLN	0	-0.096	-0.059	15.933	-0.367	-0.367	0.000	0.000	0.000	0.000
107	I	112	PHE	0	-0.054	-0.045	10.148	-1.284	-1.284	0.000	0.000	0.000	0.000
108	I	113	ASN	-1	-0.928	-0.945	12.299	-19.356	-19.356	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(I:4:VAL)