FMO DATABASE

FMODB ID: 3ZLLL

Calculation Name: 5K9F-A-Xray547

Preferred Name:

Target Type:

Ligand Name: oxamic acid | acetate ion

Ligand 3-letter code: OXM | ACT

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5K9F

Chain ID: A

ChEMBL ID:

UniProt ID: Q13VQ7

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	103
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-765890.743846
FMO2-HF: Nuclear repulsion	725774.644564
FMO2-HF: Total energy	-40116.099282
FMO2-MP2: Total energy	-40234.717265

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:9:MET)

Summations of interaction energy for fragment #1(A:9:MET)

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.
-68.881	-66.242	26.298	-7.826	-21.111	-0.069

Interaction energy analysis for fragmet #1(A:9:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.826 / q_NPA : 0.947

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	11	VAL	0	0.046	0.015	2.416	-2.084	0.846	2.388	-1.496	-3.822	-0.011
4	A	12	GLU	-1	-0.748	-0.819	4.221	-19.437	-19.325	0.000	-0.032	-0.081	0.000
36	A	44	ARG	1	0.855	0.896	2.229	38.262	35.022	10.306	-2.672	-4.394	0.009
37	A	45	LEU	0	-0.017	-0.001	6.281	-1.184	-1.093	-0.001	-0.003	-0.087	0.000
38	A	46	LEU	0	-0.034	-0.028	2.974	-1.994	-1.316	1.452	-0.300	-1.831	0.000
56	A	64	GLY	0	0.060	0.016	2.819	-1.702	-3.382	5.859	-2.572	-1.606	0.005
57	A	65	PHE	0	-0.001	-0.018	2.731	5.256	2.001	0.346	4.636	-1.727	-0.008
58	A	66	ASP	-1	-0.788	-0.888	2.347	-67.733	-65.228	4.354	-3.191	-3.668	-0.043
59	A	67	SER	0	-0.025	-0.019	3.254	-10.198	-9.184	0.060	-0.593	-0.481	-0.005
96	A	104	THR	0	0.000	-0.014	4.695	-7.168	-7.105	-0.001	-0.023	-0.039	0.000
97	A	105	PRO	0	-0.006	0.004	2.644	4.481	5.710	0.855	-0.432	-1.651	-0.002
103	A	111	VAL	-1	-0.912	-0.956	2.733	-58.458	-56.266	0.680	-1.148	-1.724	-0.014
5	A	13	GLN	0	-0.005	-0.010	7.893	0.919	0.919	0.000	0.000	0.000	0.000
6	A	14	ARG	1	0.828	0.890	10.376	18.931	18.931	0.000	0.000	0.000	0.000
7	A	15	THR	0	0.038	0.024	13.691	0.270	0.270	0.000	0.000	0.000	0.000
8	A	16	TYR	0	-0.007	-0.002	17.066	-0.111	-0.111	0.000	0.000	0.000	0.000
9	A	17	TRP	0	-0.042	-0.048	20.291	-0.215	-0.215	0.000	0.000	0.000	0.000
10	A	18	LEU	0	0.001	0.000	23.005	0.051	0.051	0.000	0.000	0.000	0.000
11	A	19	LYS	1	0.924	0.966	25.951	9.329	9.329	0.000	0.000	0.000	0.000
12	A	20	PRO	0	0.012	0.009	29.407	-0.110	-0.110	0.000	0.000	0.000	0.000
13	A	21	GLY	0	0.014	0.014	29.936	0.226	0.226	0.000	0.000	0.000	0.000
14	A	22	SER	0	-0.066	-0.047	28.474	-0.109	-0.109	0.000	0.000	0.000	0.000
15	A	23	VAL	0	0.056	0.024	23.249	-0.129	-0.129	0.000	0.000	0.000	0.000
16	A	24	SER	0	0.042	0.022	24.860	-0.303	-0.303	0.000	0.000	0.000	0.000
17	A	25	THR	0	0.024	0.028	26.660	0.023	0.023	0.000	0.000	0.000	0.000
18	A	26	PHE	0	0.015	-0.017	20.262	-0.139	-0.139	0.000	0.000	0.000	0.000
19	A	27	LEU	0	0.005	-0.003	19.752	-0.291	-0.291	0.000	0.000	0.000	0.000
20	A	28	SER	0	0.018	0.003	22.760	-0.178	-0.178	0.000	0.000	0.000	0.000
21	A	29	LEU	0	-0.015	0.001	25.348	-0.018	-0.018	0.000	0.000	0.000	0.000
22	A	30	TYR	0	-0.042	-0.044	15.627	-0.297	-0.297	0.000	0.000	0.000	0.000
23	A	31	GLU	-1	-0.968	-0.983	20.641	-12.288	-12.288	0.000	0.000	0.000	0.000
24	A	32	ALA	0	-0.019	-0.001	21.701	-0.053	-0.053	0.000	0.000	0.000	0.000
25	A	33	GLU	-1	-0.832	-0.899	23.913	-10.046	-10.046	0.000	0.000	0.000	0.000
26	A	34	GLY	0	-0.028	-0.011	20.757	-0.093	-0.093	0.000	0.000	0.000	0.000
27	A	35	LEU	0	0.018	0.003	15.214	-0.678	-0.678	0.000	0.000	0.000	0.000
28	A	36	ALA	0	0.040	0.015	16.507	-0.771	-0.771	0.000	0.000	0.000	0.000
29	A	37	ILE	0	-0.016	-0.005	17.486	-0.531	-0.531	0.000	0.000	0.000	0.000
30	A	38	GLN	0	-0.002	0.003	13.771	0.006	0.006	0.000	0.000	0.000	0.000
31	A	39	ALA	0	0.017	0.002	12.495	-1.204	-1.204	0.000	0.000	0.000	0.000
32	A	40	GLY	0	0.006	0.016	12.680	-0.947	-0.947	0.000	0.000	0.000	0.000
33	A	41	ALA	0	-0.046	-0.014	14.192	-0.478	-0.478	0.000	0.000	0.000	0.000
34	A	42	LEU	0	-0.041	-0.040	9.684	-1.160	-1.160	0.000	0.000	0.000	0.000
35	A	43	GLY	0	-0.031	0.006	8.553	-2.262	-2.262	0.000	0.000	0.000	0.000
39	A	47	GLY	0	0.040	0.024	6.598	0.542	0.542	0.000	0.000	0.000	0.000
40	A	48	TYR	0	-0.022	-0.028	10.126	-0.163	-0.163	0.000	0.000	0.000	0.000
41	A	49	TYR	0	0.002	0.015	11.402	0.053	0.053	0.000	0.000	0.000	0.000
42	A	50	PHE	0	0.022	0.009	16.560	-0.095	-0.095	0.000	0.000	0.000	0.000
43	A	51	SER	0	-0.098	-0.063	19.784	-0.194	-0.194	0.000	0.000	0.000	0.000
44	A	52	GLU	-1	-0.839	-0.919	21.414	-10.628	-10.628	0.000	0.000	0.000	0.000
45	A	53	THR	0	-0.039	-0.026	22.584	0.288	0.288	0.000	0.000	0.000	0.000
46	A	54	GLY	0	0.011	0.003	23.109	-0.479	-0.479	0.000	0.000	0.000	0.000
47	A	55	ASP	-1	-0.822	-0.892	23.558	-11.160	-11.160	0.000	0.000	0.000	0.000
48	A	56	LEU	0	0.063	0.063	23.783	-0.470	-0.470	0.000	0.000	0.000	0.000
49	A	57	ASN	0	0.006	-0.007	25.345	0.214	0.214	0.000	0.000	0.000	0.000
50	A	58	ARG	1	0.881	0.945	18.909	13.198	13.198	0.000	0.000	0.000	0.000
51	A	59	VAL	0	-0.011	-0.004	18.813	0.100	0.100	0.000	0.000	0.000	0.000
52	A	60	ILE	0	-0.001	-0.004	13.328	-0.163	-0.163	0.000	0.000	0.000	0.000
53	A	61	GLN	0	0.018	0.024	12.585	-0.296	-0.296	0.000	0.000	0.000	0.000
54	A	62	LEU	0	0.027	0.017	7.138	-0.696	-0.696	0.000	0.000	0.000	0.000
55	A	63	TRP	0	-0.003	-0.013	7.083	0.482	0.482	0.000	0.000	0.000	0.000
60	A	68	PHE	0	0.041	0.013	5.472	1.866	1.866	0.000	0.000	0.000	0.000
61	A	69	GLU	-1	-0.785	-0.891	8.333	-20.908	-20.908	0.000	0.000	0.000	0.000
62	A	70	ASP	-1	-0.800	-0.862	7.626	-24.815	-24.815	0.000	0.000	0.000	0.000
63	A	71	ARG	1	0.856	0.923	7.552	26.818	26.818	0.000	0.000	0.000	0.000
64	A	72	THR	0	-0.036	-0.036	9.337	1.961	1.961	0.000	0.000	0.000	0.000
65	A	73	ARG	1	0.856	0.914	11.720	22.905	22.905	0.000	0.000	0.000	0.000
66	A	74	ARG	1	0.843	0.911	9.033	26.605	26.605	0.000	0.000	0.000	0.000
67	A	75	LYS	1	0.893	0.947	11.479	21.453	21.453	0.000	0.000	0.000	0.000
68	A	76	ALA	0	0.008	0.028	14.346	1.197	1.197	0.000	0.000	0.000	0.000
69	A	77	ILE	0	-0.010	-0.009	15.284	0.922	0.922	0.000	0.000	0.000	0.000
70	A	78	LEU	0	-0.024	-0.010	14.805	0.742	0.742	0.000	0.000	0.000	0.000
71	A	79	SER	0	-0.044	-0.038	17.543	0.825	0.825	0.000	0.000	0.000	0.000
72	A	80	GLY	0	-0.003	0.000	20.031	0.729	0.729	0.000	0.000	0.000	0.000
73	A	81	ASN	0	0.017	0.012	20.810	1.003	1.003	0.000	0.000	0.000	0.000
74	A	82	PRO	0	0.040	0.004	22.704	0.033	0.033	0.000	0.000	0.000	0.000
75	A	83	GLN	0	0.029	0.031	24.287	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	84	TRP	0	0.046	0.026	18.184	0.061	0.061	0.000	0.000	0.000	0.000
77	A	85	LYS	1	0.919	0.963	22.550	11.462	11.462	0.000	0.000	0.000	0.000
78	A	86	SER	0	-0.045	-0.028	25.140	0.366	0.366	0.000	0.000	0.000	0.000
79	A	87	PHE	0	0.023	0.026	21.017	0.122	0.122	0.000	0.000	0.000	0.000
80	A	88	VAL	0	-0.014	-0.009	21.984	0.168	0.168	0.000	0.000	0.000	0.000
81	A	89	GLY	0	-0.020	-0.010	24.784	0.164	0.164	0.000	0.000	0.000	0.000
82	A	90	ARG	1	0.803	0.882	27.695	10.219	10.219	0.000	0.000	0.000	0.000
83	A	91	ALA	0	0.027	0.002	24.709	0.179	0.179	0.000	0.000	0.000	0.000
84	A	92	GLY	0	0.019	0.003	25.373	-0.070	-0.070	0.000	0.000	0.000	0.000
85	A	93	SER	0	-0.011	0.002	26.326	0.028	0.028	0.000	0.000	0.000	0.000
86	A	94	MET	0	-0.013	0.010	26.919	0.312	0.312	0.000	0.000	0.000	0.000
87	A	95	ILE	0	-0.050	-0.014	22.180	-0.191	-0.191	0.000	0.000	0.000	0.000
88	A	96	GLU	-1	-0.894	-0.945	26.004	-9.530	-9.530	0.000	0.000	0.000	0.000
89	A	97	ARG	1	0.916	0.963	23.268	11.970	11.970	0.000	0.000	0.000	0.000
90	A	98	GLN	0	-0.024	-0.011	19.578	-0.399	-0.399	0.000	0.000	0.000	0.000
91	A	99	SER	0	-0.023	-0.012	18.144	0.163	0.163	0.000	0.000	0.000	0.000
92	A	100	THR	0	-0.077	-0.077	12.669	-0.617	-0.617	0.000	0.000	0.000	0.000
93	A	101	GLU	-1	-0.808	-0.876	11.181	-20.218	-20.218	0.000	0.000	0.000	0.000
94	A	102	LEU	0	-0.042	-0.034	8.505	-1.225	-1.225	0.000	0.000	0.000	0.000
95	A	103	LEU	0	0.014	0.016	6.843	1.013	1.013	0.000	0.000	0.000	0.000
98	A	106	ALA	0	0.035	0.024	5.454	-0.733	-0.733	0.000	0.000	0.000	0.000
99	A	107	PRO	0	-0.008	-0.025	7.664	-1.833	-1.833	0.000	0.000	0.000	0.000
100	A	108	PHE	0	0.006	0.008	8.930	0.061	0.061	0.000	0.000	0.000	0.000
101	A	109	SER	0	-0.048	-0.013	5.376	3.184	3.184	0.000	0.000	0.000	0.000
102	A	110	PRO	0	-0.041	-0.017	6.766	-0.788	-0.788	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:9:MET)