FMO DATABASE

FMODB ID: N89QQ

Calculation Name: 3F8K-A-Xray547

Preferred Name:

Target Type:

Ligand Name: coenzyme a

Ligand 3-letter code: COA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3F8K

Chain ID: A

ChEMBL ID:

UniProt ID: Q97V23

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	131
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1243780.291711
FMO2-HF: Nuclear repulsion	1190566.167218
FMO2-HF: Total energy	-53214.124492
FMO2-MP2: Total energy	-53371.548601

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:5:ILE)

Summations of interaction energy for fragment #1(A:5:ILE)

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.
-11.113	-4.226	4.191	-3.585	-7.49	-0.026

Interaction energy analysis for fragmet #1(A:5:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.848 / q_NPA : 0.920

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	7	ILE	0	0.009	0.009	2.742	0.859	3.116	0.220	-0.618	-1.860	-0.001
4	A	8	ARG	1	0.708	0.801	5.098	28.101	28.113	-0.001	-0.003	-0.008	0.000
44	A	59	ALA	0	-0.009	-0.013	3.433	-2.800	-2.544	0.011	-0.063	-0.204	0.000
45	A	60	GLU	-1	-0.781	-0.859	4.295	-29.477	-29.283	-0.001	-0.049	-0.144	0.000
46	A	61	VAL	0	-0.031	-0.035	2.520	-26.877	-23.337	1.356	-2.306	-2.589	-0.025
47	A	62	ASP	-1	-0.855	-0.925	4.190	-32.642	-32.556	0.000	-0.034	-0.051	0.000
74	A	89	GLY	0	-0.001	0.000	4.847	-3.195	-3.097	-0.001	-0.003	-0.093	0.000
75	A	90	ILE	0	0.026	0.011	2.236	0.547	0.595	2.579	-0.456	-2.171	0.000
76	A	91	GLY	0	0.064	0.026	3.897	0.844	0.864	0.001	0.017	-0.037	0.000
78	A	93	LEU	0	0.021	0.015	3.340	0.980	1.356	0.027	-0.070	-0.333	0.000
5	A	9	LYS	1	0.867	0.940	8.847	17.732	17.732	0.000	0.000	0.000	0.000
6	A	10	ALA	0	0.003	-0.003	12.289	-0.808	-0.808	0.000	0.000	0.000	0.000
7	A	11	THR	0	0.008	-0.007	13.934	1.347	1.347	0.000	0.000	0.000	0.000
8	A	12	LYS	1	0.979	0.966	17.225	13.528	13.528	0.000	0.000	0.000	0.000
9	A	13	GLU	-1	-0.880	-0.926	18.225	-15.076	-15.076	0.000	0.000	0.000	0.000
10	A	14	ASP	-1	-0.804	-0.865	13.851	-22.214	-22.214	0.000	0.000	0.000	0.000
11	A	15	TRP	0	0.017	0.019	15.614	-0.720	-0.720	0.000	0.000	0.000	0.000
12	A	16	GLU	-1	-0.770	-0.885	17.888	-15.071	-15.071	0.000	0.000	0.000	0.000
13	A	17	LYS	1	0.864	0.928	12.071	20.781	20.781	0.000	0.000	0.000	0.000
14	A	18	ILE	0	-0.016	-0.007	13.395	-0.909	-0.909	0.000	0.000	0.000	0.000
15	A	19	TYR	0	0.007	0.025	14.815	0.100	0.100	0.000	0.000	0.000	0.000
16	A	20	GLN	0	-0.051	-0.046	15.705	-0.726	-0.726	0.000	0.000	0.000	0.000
17	A	21	LEU	0	-0.051	-0.012	10.686	-0.246	-0.246	0.000	0.000	0.000	0.000
18	A	22	TYR	0	-0.028	-0.053	13.982	0.563	0.563	0.000	0.000	0.000	0.000
19	A	23	ASN	0	0.018	0.003	16.966	0.761	0.761	0.000	0.000	0.000	0.000
20	A	24	SER	0	-0.089	-0.044	14.884	-0.082	-0.082	0.000	0.000	0.000	0.000
21	A	25	LEU	0	-0.086	-0.039	13.296	-0.673	-0.673	0.000	0.000	0.000	0.000
22	A	26	SER	0	0.000	-0.023	17.274	0.829	0.829	0.000	0.000	0.000	0.000
23	A	27	ASP	-1	-0.816	-0.927	19.901	-12.132	-12.132	0.000	0.000	0.000	0.000
24	A	28	GLU	-1	-0.831	-0.890	19.725	-13.504	-13.504	0.000	0.000	0.000	0.000
25	A	29	ASP	-1	-0.801	-0.873	15.954	-16.557	-16.557	0.000	0.000	0.000	0.000
26	A	30	LEU	0	0.011	0.001	17.431	-0.453	-0.453	0.000	0.000	0.000	0.000
27	A	31	TYR	0	0.028	0.015	19.463	0.144	0.144	0.000	0.000	0.000	0.000
28	A	32	LEU	0	-0.032	-0.025	17.868	0.087	0.087	0.000	0.000	0.000	0.000
29	A	33	ARG	1	0.790	0.868	14.279	16.453	16.453	0.000	0.000	0.000	0.000
30	A	34	PHE	0	-0.009	0.000	17.378	-0.223	-0.223	0.000	0.000	0.000	0.000
31	A	35	PHE	0	0.020	0.035	20.710	0.506	0.506	0.000	0.000	0.000	0.000
32	A	36	HIS	1	0.879	0.902	22.403	11.278	11.278	0.000	0.000	0.000	0.000
33	A	37	LEU	0	0.011	0.014	24.000	0.279	0.279	0.000	0.000	0.000	0.000
34	A	38	TYR	0	0.017	0.008	22.918	0.396	0.396	0.000	0.000	0.000	0.000
35	A	39	ARG	1	0.807	0.907	26.654	9.748	9.748	0.000	0.000	0.000	0.000
36	A	40	ILE	0	-0.098	-0.038	28.165	0.260	0.260	0.000	0.000	0.000	0.000
37	A	41	THR	-1	-0.951	-0.967	29.418	-8.783	-8.783	0.000	0.000	0.000	0.000
38	A	53	ASP	-1	-0.842	-0.913	23.668	-11.519	-11.519	0.000	0.000	0.000	0.000
39	A	54	HIS	0	-0.053	-0.027	18.621	-0.264	-0.264	0.000	0.000	0.000	0.000
40	A	55	VAL	0	-0.032	-0.013	15.671	-0.160	-0.160	0.000	0.000	0.000	0.000
41	A	56	THR	0	0.014	-0.003	13.389	0.043	0.043	0.000	0.000	0.000	0.000
42	A	57	PHE	0	-0.034	-0.032	9.348	-0.423	-0.423	0.000	0.000	0.000	0.000
43	A	58	LEU	0	-0.007	-0.001	8.556	0.620	0.620	0.000	0.000	0.000	0.000
48	A	63	GLY	0	-0.008	0.005	6.714	-0.636	-0.636	0.000	0.000	0.000	0.000
49	A	64	LYS	1	0.924	0.962	7.955	25.951	25.951	0.000	0.000	0.000	0.000
50	A	65	VAL	0	0.028	0.011	7.161	-4.640	-4.640	0.000	0.000	0.000	0.000
51	A	66	VAL	0	0.008	0.007	4.940	1.911	1.911	0.000	0.000	0.000	0.000
52	A	67	GLY	0	-0.006	-0.012	7.129	1.371	1.371	0.000	0.000	0.000	0.000
53	A	68	GLU	-1	-0.764	-0.806	7.938	-19.864	-19.864	0.000	0.000	0.000	0.000
54	A	69	ALA	0	-0.002	-0.004	9.578	0.724	0.724	0.000	0.000	0.000	0.000
55	A	70	SER	0	0.014	0.002	11.378	-0.162	-0.162	0.000	0.000	0.000	0.000
56	A	71	LEU	0	-0.023	-0.007	14.937	0.262	0.262	0.000	0.000	0.000	0.000
57	A	72	HIS	0	0.062	0.022	17.352	-0.163	-0.163	0.000	0.000	0.000	0.000
58	A	73	LYS	1	0.870	0.917	21.180	10.995	10.995	0.000	0.000	0.000	0.000
59	A	74	ASP	-1	-0.799	-0.888	24.052	-10.953	-10.953	0.000	0.000	0.000	0.000
60	A	75	GLY	0	0.015	0.015	21.695	0.232	0.232	0.000	0.000	0.000	0.000
61	A	76	GLU	-1	-0.879	-0.919	20.625	-12.094	-12.094	0.000	0.000	0.000	0.000
62	A	77	PHE	0	-0.033	-0.023	14.661	-0.584	-0.584	0.000	0.000	0.000	0.000
63	A	78	SER	0	-0.015	-0.015	15.724	0.166	0.166	0.000	0.000	0.000	0.000
64	A	79	LEU	0	-0.037	-0.022	8.994	-0.966	-0.966	0.000	0.000	0.000	0.000
65	A	80	VAL	0	0.019	0.022	11.175	0.740	0.740	0.000	0.000	0.000	0.000
66	A	81	VAL	0	-0.032	-0.015	6.606	-1.721	-1.721	0.000	0.000	0.000	0.000
67	A	82	HIS	0	0.090	0.044	9.033	0.577	0.577	0.000	0.000	0.000	0.000
68	A	83	ARG	1	0.830	0.893	10.157	13.962	13.962	0.000	0.000	0.000	0.000
69	A	84	ASN	0	0.012	0.006	11.555	0.942	0.942	0.000	0.000	0.000	0.000
70	A	85	TYR	0	0.026	0.006	5.968	-0.692	-0.692	0.000	0.000	0.000	0.000
71	A	86	ARG	1	0.777	0.880	6.503	17.336	17.336	0.000	0.000	0.000	0.000
72	A	87	THR	0	-0.044	-0.035	9.113	0.100	0.100	0.000	0.000	0.000	0.000
73	A	88	LEU	0	0.051	0.035	4.953	0.032	0.032	0.000	0.000	0.000	0.000
77	A	92	THR	0	-0.013	-0.009	7.244	2.239	2.239	0.000	0.000	0.000	0.000
79	A	94	LEU	0	0.017	0.026	5.252	1.097	1.097	0.000	0.000	0.000	0.000
80	A	95	VAL	0	0.050	0.026	7.554	1.311	1.311	0.000	0.000	0.000	0.000
81	A	96	LYS	1	0.931	0.962	9.610	22.137	22.137	0.000	0.000	0.000	0.000
82	A	97	THR	0	-0.020	-0.021	8.231	0.313	0.313	0.000	0.000	0.000	0.000
83	A	98	LEU	0	-0.002	0.005	10.835	0.934	0.934	0.000	0.000	0.000	0.000
84	A	99	ILE	0	0.003	0.004	13.519	1.027	1.027	0.000	0.000	0.000	0.000
85	A	100	GLU	-1	-0.884	-0.944	13.748	-16.039	-16.039	0.000	0.000	0.000	0.000
86	A	101	GLU	-1	-0.813	-0.913	14.945	-16.158	-16.158	0.000	0.000	0.000	0.000
87	A	102	ALA	0	0.012	0.017	16.668	0.809	0.809	0.000	0.000	0.000	0.000
88	A	103	LYS	1	0.940	0.975	18.529	14.799	14.799	0.000	0.000	0.000	0.000
89	A	104	LYS	1	0.857	0.940	15.386	17.819	17.819	0.000	0.000	0.000	0.000
90	A	105	SER	0	-0.043	-0.033	20.321	0.495	0.495	0.000	0.000	0.000	0.000
91	A	106	GLY	0	0.010	0.016	22.683	0.454	0.454	0.000	0.000	0.000	0.000
92	A	107	LEU	0	-0.032	-0.010	20.811	0.419	0.419	0.000	0.000	0.000	0.000
93	A	108	SER	0	0.067	0.026	24.045	-0.254	-0.254	0.000	0.000	0.000	0.000
94	A	109	THR	0	-0.066	-0.042	24.045	0.122	0.122	0.000	0.000	0.000	0.000
95	A	110	VAL	0	0.021	0.013	18.454	-0.276	-0.276	0.000	0.000	0.000	0.000
96	A	111	LYS	1	0.820	0.904	20.516	11.023	11.023	0.000	0.000	0.000	0.000
97	A	112	PHE	0	0.028	0.013	17.989	-0.457	-0.457	0.000	0.000	0.000	0.000
98	A	113	TYR	0	0.047	0.020	20.086	0.376	0.376	0.000	0.000	0.000	0.000
99	A	114	THR	0	-0.043	-0.014	18.922	-0.609	-0.609	0.000	0.000	0.000	0.000
100	A	115	LEU	0	0.083	0.057	21.480	0.356	0.356	0.000	0.000	0.000	0.000
101	A	116	PRO	0	0.007	0.005	22.310	-0.570	-0.570	0.000	0.000	0.000	0.000
102	A	117	GLU	-1	-0.793	-0.904	23.340	-11.047	-11.047	0.000	0.000	0.000	0.000
103	A	118	ASN	0	-0.022	-0.003	16.534	-1.009	-1.009	0.000	0.000	0.000	0.000
104	A	119	THR	0	0.006	-0.026	18.706	-0.252	-0.252	0.000	0.000	0.000	0.000
105	A	120	PRO	0	-0.053	-0.038	13.827	-0.273	-0.273	0.000	0.000	0.000	0.000
106	A	121	MET	0	0.030	0.028	14.353	-0.976	-0.976	0.000	0.000	0.000	0.000
107	A	122	ILE	0	0.048	0.039	15.666	-0.006	-0.006	0.000	0.000	0.000	0.000
108	A	123	LYS	1	0.916	0.957	16.256	14.295	14.295	0.000	0.000	0.000	0.000
109	A	124	ILE	0	-0.066	-0.035	10.764	-0.315	-0.315	0.000	0.000	0.000	0.000
110	A	125	GLY	0	0.063	0.029	14.480	-0.055	-0.055	0.000	0.000	0.000	0.000
111	A	126	ARG	1	0.961	0.970	17.442	11.662	11.662	0.000	0.000	0.000	0.000
112	A	127	LYS	1	0.850	0.930	11.247	19.453	19.453	0.000	0.000	0.000	0.000
113	A	128	LEU	0	-0.065	-0.035	12.210	-0.607	-0.607	0.000	0.000	0.000	0.000
114	A	129	GLY	0	0.040	0.032	16.831	0.086	0.086	0.000	0.000	0.000	0.000
115	A	130	PHE	0	-0.055	-0.028	16.463	0.402	0.402	0.000	0.000	0.000	0.000
116	A	131	LYS	1	0.846	0.909	21.225	10.675	10.675	0.000	0.000	0.000	0.000
117	A	132	MET	0	-0.032	0.004	21.320	-0.109	-0.109	0.000	0.000	0.000	0.000
118	A	133	ARG	1	0.806	0.894	24.814	10.259	10.259	0.000	0.000	0.000	0.000
119	A	134	PHE	0	-0.026	-0.025	23.805	-0.425	-0.425	0.000	0.000	0.000	0.000
120	A	135	TYR	0	0.016	0.013	28.380	0.267	0.267	0.000	0.000	0.000	0.000
121	A	136	GLU	-1	-0.893	-0.951	29.199	-9.022	-9.022	0.000	0.000	0.000	0.000
122	A	137	ASP	-1	-0.882	-0.929	29.830	-8.936	-8.936	0.000	0.000	0.000	0.000
123	A	138	GLU	-1	-0.897	-0.958	26.123	-10.125	-10.125	0.000	0.000	0.000	0.000
124	A	139	VAL	0	-0.063	-0.024	22.154	0.206	0.206	0.000	0.000	0.000	0.000
125	A	140	TYR	0	-0.003	-0.019	23.635	-0.382	-0.382	0.000	0.000	0.000	0.000
126	A	141	GLY	0	0.027	-0.009	21.143	0.150	0.150	0.000	0.000	0.000	0.000
127	A	142	GLU	-1	-0.760	-0.854	21.871	-10.316	-10.316	0.000	0.000	0.000	0.000
128	A	143	MET	0	-0.049	-0.009	18.110	0.344	0.344	0.000	0.000	0.000	0.000
129	A	144	ARG	1	0.889	0.930	22.685	9.666	9.666	0.000	0.000	0.000	0.000
130	A	145	LEU	0	-0.075	-0.040	20.108	-0.349	-0.349	0.000	0.000	0.000	0.000
131	A	146	THR	-1	-0.853	-0.901	24.141	-9.819	-9.819	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:ILE)