FMO DATABASE

FMODB ID: LQ2J9

Calculation Name: 2EIS-A-Xray547

Preferred Name:

Target Type:

Ligand Name: coenzyme a

Ligand 3-letter code: COA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2EIS

Chain ID: A

ChEMBL ID:

UniProt ID: Q53VX2

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	-937572.544353
FMO2-HF: Nuclear repulsion	891016.34692
FMO2-HF: Total energy	-46556.197433
FMO2-MP2: Total energy	-46692.383674

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:3:GLU)

Summations of interaction energy for fragment #1(A:3:GLU)

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.
-90.812	-100.379	43.127	-17.447	-16.115	0.159

Interaction energy analysis for fragmet #1(A:3:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.049 / q_NPA : 0.051

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	5	ARG	1	0.851	0.901	1.788	-54.348	-59.688	20.658	-7.619	-7.699	0.074
4	A	6	MET	0	-0.050	-0.009	5.306	-2.223	-2.202	-0.001	-0.003	-0.017	0.000
38	A	40	ARG	1	0.844	0.928	4.715	18.975	19.066	-0.001	-0.026	-0.064	0.000
67	A	69	VAL	0	0.004	-0.007	2.833	-1.441	-0.277	0.183	-0.480	-0.867	0.001
68	A	70	ALA	0	0.004	0.007	4.055	0.130	0.353	-0.001	-0.024	-0.199	0.000
69	A	71	ARG	1	0.810	0.878	1.791	-71.729	-77.513	22.290	-9.273	-7.233	0.084
70	A	72	LEU	0	0.016	0.013	4.364	2.286	2.344	-0.001	-0.022	-0.036	0.000
5	A	7	VAL	0	0.039	0.035	9.115	0.921	0.921	0.000	0.000	0.000	0.000
6	A	8	TYR	0	0.014	-0.006	11.856	-0.750	-0.750	0.000	0.000	0.000	0.000
7	A	9	PRO	0	-0.019	0.007	15.362	0.363	0.363	0.000	0.000	0.000	0.000
8	A	10	VAL	0	0.012	0.012	18.549	-0.218	-0.218	0.000	0.000	0.000	0.000
9	A	11	PHE	0	0.050	0.004	20.573	0.018	0.018	0.000	0.000	0.000	0.000
10	A	12	PRO	0	0.027	-0.002	23.870	-0.024	-0.024	0.000	0.000	0.000	0.000
11	A	13	GLY	0	-0.017	0.005	26.575	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	14	GLU	-1	-0.832	-0.907	20.409	0.398	0.398	0.000	0.000	0.000	0.000
13	A	15	THR	0	-0.071	-0.050	22.975	0.084	0.084	0.000	0.000	0.000	0.000
14	A	16	ASN	0	0.010	-0.001	25.184	-0.092	-0.092	0.000	0.000	0.000	0.000
15	A	17	HIS	0	0.051	0.013	27.739	0.029	0.029	0.000	0.000	0.000	0.000
16	A	18	TYR	0	-0.056	-0.028	28.481	-0.028	-0.028	0.000	0.000	0.000	0.000
17	A	19	GLY	0	0.014	0.025	28.308	0.055	0.055	0.000	0.000	0.000	0.000
18	A	20	THR	0	-0.029	-0.023	24.062	0.109	0.109	0.000	0.000	0.000	0.000
19	A	21	LEU	0	0.012	0.005	17.329	-0.141	-0.141	0.000	0.000	0.000	0.000
20	A	22	PHE	0	-0.015	-0.001	21.901	0.043	0.043	0.000	0.000	0.000	0.000
21	A	23	GLY	0	0.034	0.005	21.068	0.001	0.001	0.000	0.000	0.000	0.000
22	A	24	GLY	0	0.016	0.000	20.227	-0.020	-0.020	0.000	0.000	0.000	0.000
23	A	25	THR	0	0.003	0.003	18.740	-0.187	-0.187	0.000	0.000	0.000	0.000
24	A	26	VAL	0	0.042	0.026	15.602	-0.116	-0.116	0.000	0.000	0.000	0.000
25	A	27	LEU	0	-0.015	-0.007	15.367	-0.071	-0.071	0.000	0.000	0.000	0.000
26	A	28	ALA	0	0.005	0.013	16.144	-0.241	-0.241	0.000	0.000	0.000	0.000
27	A	29	TRP	0	0.018	0.003	13.324	-0.262	-0.262	0.000	0.000	0.000	0.000
28	A	30	MET	0	-0.024	-0.012	11.485	-0.439	-0.439	0.000	0.000	0.000	0.000
29	A	31	ASP	-1	-0.818	-0.881	11.582	-2.373	-2.373	0.000	0.000	0.000	0.000
30	A	32	GLN	0	-0.005	-0.011	12.808	-0.434	-0.434	0.000	0.000	0.000	0.000
31	A	33	ALA	0	0.014	0.007	7.799	-1.035	-1.035	0.000	0.000	0.000	0.000
32	A	34	ALA	0	0.013	-0.003	7.976	-2.241	-2.241	0.000	0.000	0.000	0.000
33	A	35	PHE	0	0.049	0.022	9.606	-1.205	-1.205	0.000	0.000	0.000	0.000
34	A	36	VAL	0	-0.004	0.005	7.682	-0.828	-0.828	0.000	0.000	0.000	0.000
35	A	37	ALA	0	-0.053	-0.028	5.464	-2.368	-2.368	0.000	0.000	0.000	0.000
36	A	38	ALA	0	0.036	0.016	6.617	-1.104	-1.104	0.000	0.000	0.000	0.000
37	A	39	THR	0	-0.023	-0.028	9.809	-0.187	-0.187	0.000	0.000	0.000	0.000
39	A	41	HIS	0	-0.025	-0.013	7.662	-1.441	-1.441	0.000	0.000	0.000	0.000
40	A	42	ALA	0	0.035	-0.005	9.115	1.101	1.101	0.000	0.000	0.000	0.000
41	A	43	ARG	1	0.850	0.937	10.101	7.806	7.806	0.000	0.000	0.000	0.000
42	A	44	LYS	1	0.842	0.921	13.764	3.666	3.666	0.000	0.000	0.000	0.000
43	A	45	LYS	1	0.862	0.915	15.352	1.763	1.763	0.000	0.000	0.000	0.000
44	A	46	VAL	0	0.009	-0.002	13.496	-0.014	-0.014	0.000	0.000	0.000	0.000
45	A	47	VAL	0	0.001	0.006	16.785	0.161	0.161	0.000	0.000	0.000	0.000
46	A	48	THR	0	-0.022	-0.037	15.718	-0.319	-0.319	0.000	0.000	0.000	0.000
47	A	49	VAL	0	-0.074	-0.028	17.312	0.179	0.179	0.000	0.000	0.000	0.000
48	A	50	HIS	0	-0.020	-0.022	18.356	0.128	0.128	0.000	0.000	0.000	0.000
49	A	51	ALA	0	0.019	0.011	17.213	-0.220	-0.220	0.000	0.000	0.000	0.000
50	A	52	ASP	-1	-0.828	-0.869	17.367	0.045	0.045	0.000	0.000	0.000	0.000
51	A	53	ALA	0	0.028	-0.001	17.409	0.085	0.085	0.000	0.000	0.000	0.000
52	A	54	VAL	0	0.016	0.012	16.499	0.242	0.242	0.000	0.000	0.000	0.000
53	A	55	ASP	-1	-0.899	-0.951	17.328	1.497	1.497	0.000	0.000	0.000	0.000
54	A	56	PHE	0	-0.008	-0.024	17.610	0.318	0.318	0.000	0.000	0.000	0.000
55	A	57	LYS	1	0.865	0.949	17.722	-2.006	-2.006	0.000	0.000	0.000	0.000
56	A	58	ARG	1	0.853	0.926	16.471	-3.062	-3.062	0.000	0.000	0.000	0.000
57	A	59	PRO	0	0.007	0.021	19.879	0.021	0.021	0.000	0.000	0.000	0.000
58	A	60	VAL	0	0.056	0.026	17.520	0.208	0.208	0.000	0.000	0.000	0.000
59	A	61	PRO	0	0.001	0.007	20.824	-0.213	-0.213	0.000	0.000	0.000	0.000
60	A	62	LEU	0	0.018	-0.009	22.406	0.058	0.058	0.000	0.000	0.000	0.000
61	A	63	GLY	0	-0.049	-0.017	23.383	0.031	0.031	0.000	0.000	0.000	0.000
62	A	64	ALA	0	-0.024	0.006	19.353	0.093	0.093	0.000	0.000	0.000	0.000
63	A	65	ILE	0	0.014	0.008	14.658	-0.284	-0.284	0.000	0.000	0.000	0.000
64	A	66	VAL	0	0.001	-0.014	13.694	0.308	0.308	0.000	0.000	0.000	0.000
65	A	67	GLU	-1	-0.816	-0.885	6.806	12.269	12.269	0.000	0.000	0.000	0.000
66	A	68	LEU	0	-0.049	-0.023	8.846	0.558	0.558	0.000	0.000	0.000	0.000
71	A	73	LYS	1	0.792	0.900	6.828	-3.505	-3.505	0.000	0.000	0.000	0.000
72	A	74	GLU	-1	-0.885	-0.944	9.909	-0.611	-0.611	0.000	0.000	0.000	0.000
73	A	75	VAL	0	-0.010	-0.014	11.920	-0.482	-0.482	0.000	0.000	0.000	0.000
74	A	76	GLY	0	0.015	0.030	14.350	0.386	0.386	0.000	0.000	0.000	0.000
75	A	77	ARG	1	0.932	0.958	17.981	1.478	1.478	0.000	0.000	0.000	0.000
76	A	78	THR	0	0.000	-0.012	18.263	-0.084	-0.084	0.000	0.000	0.000	0.000
77	A	79	SER	0	0.000	0.012	16.419	-0.166	-0.166	0.000	0.000	0.000	0.000
78	A	80	MET	0	0.008	0.015	10.957	-0.452	-0.452	0.000	0.000	0.000	0.000
79	A	81	ARG	1	0.834	0.898	12.319	0.359	0.359	0.000	0.000	0.000	0.000
80	A	82	VAL	0	-0.031	-0.020	6.792	-0.620	-0.620	0.000	0.000	0.000	0.000
81	A	83	GLU	-1	-0.812	-0.901	8.311	6.466	6.466	0.000	0.000	0.000	0.000
82	A	84	VAL	0	-0.030	-0.024	7.652	-0.361	-0.361	0.000	0.000	0.000	0.000
83	A	85	GLU	-1	-0.820	-0.892	7.535	10.345	10.345	0.000	0.000	0.000	0.000
84	A	86	MET	0	-0.008	0.005	9.111	-0.289	-0.289	0.000	0.000	0.000	0.000
85	A	87	TRP	0	0.007	-0.017	8.131	-0.482	-0.482	0.000	0.000	0.000	0.000
86	A	88	VAL	0	-0.009	-0.006	11.895	-0.637	-0.637	0.000	0.000	0.000	0.000
87	A	89	GLU	-1	-0.846	-0.933	11.451	6.670	6.670	0.000	0.000	0.000	0.000
88	A	90	PRO	0	-0.062	-0.023	15.265	-0.452	-0.452	0.000	0.000	0.000	0.000
89	A	91	VAL	0	0.011	0.000	18.170	0.129	0.129	0.000	0.000	0.000	0.000
90	A	92	LYS	1	0.874	0.948	20.414	-1.545	-1.545	0.000	0.000	0.000	0.000
91	A	93	GLU	-1	-0.836	-0.928	22.075	2.480	2.480	0.000	0.000	0.000	0.000
92	A	94	GLY	0	-0.063	-0.020	22.391	-0.176	-0.176	0.000	0.000	0.000	0.000
93	A	95	GLU	-1	-0.987	-0.997	21.381	1.991	1.991	0.000	0.000	0.000	0.000
94	A	96	GLU	-1	-0.865	-0.930	15.371	5.146	5.146	0.000	0.000	0.000	0.000
95	A	97	ALA	0	-0.027	-0.022	12.974	-0.262	-0.262	0.000	0.000	0.000	0.000
96	A	98	TYR	0	-0.070	-0.048	14.836	-0.043	-0.043	0.000	0.000	0.000	0.000
97	A	99	LEU	0	-0.016	0.013	10.748	-0.162	-0.162	0.000	0.000	0.000	0.000
98	A	100	ALA	0	0.013	0.007	13.500	-0.609	-0.609	0.000	0.000	0.000	0.000
99	A	101	ALA	0	-0.006	-0.011	14.384	-0.474	-0.474	0.000	0.000	0.000	0.000
100	A	102	ARG	1	0.876	0.931	10.705	-4.198	-4.198	0.000	0.000	0.000	0.000
101	A	103	GLY	0	0.018	0.020	12.587	-0.380	-0.380	0.000	0.000	0.000	0.000
102	A	104	GLY	0	-0.023	0.010	12.486	0.110	0.110	0.000	0.000	0.000	0.000
103	A	105	PHE	0	0.037	0.007	12.044	-0.099	-0.099	0.000	0.000	0.000	0.000
104	A	106	VAL	0	-0.019	-0.012	12.958	-0.328	-0.328	0.000	0.000	0.000	0.000
105	A	107	LEU	0	0.031	0.018	11.839	0.103	0.103	0.000	0.000	0.000	0.000
106	A	108	VAL	0	-0.018	-0.022	14.646	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	109	ALA	0	0.031	0.023	15.633	-0.088	-0.088	0.000	0.000	0.000	0.000
108	A	110	VAL	0	-0.031	-0.016	17.426	0.311	0.311	0.000	0.000	0.000	0.000
109	A	111	ASP	-1	-0.800	-0.908	20.367	-1.853	-1.853	0.000	0.000	0.000	0.000
110	A	112	GLU	-1	-0.829	-0.900	23.032	-1.968	-1.968	0.000	0.000	0.000	0.000
111	A	113	ARG	0	-0.008	0.025	25.182	0.136	0.136	0.000	0.000	0.000	0.000
112	A	114	GLY	0	0.008	0.015	24.325	0.101	0.101	0.000	0.000	0.000	0.000
113	A	115	ARG	1	0.856	0.896	24.877	1.428	1.428	0.000	0.000	0.000	0.000
114	A	116	PRO	0	-0.004	-0.010	21.839	-0.139	-0.139	0.000	0.000	0.000	0.000
115	A	117	SER	0	-0.019	-0.008	20.235	0.063	0.063	0.000	0.000	0.000	0.000
116	A	118	PRO	0	-0.032	-0.034	19.260	-0.158	-0.158	0.000	0.000	0.000	0.000
117	A	119	VAL	0	0.007	0.016	13.985	-0.109	-0.109	0.000	0.000	0.000	0.000
118	A	120	PRO	0	0.013	0.014	12.362	0.461	0.461	0.000	0.000	0.000	0.000
119	A	121	PRO	0	0.025	0.025	13.452	-0.187	-0.187	0.000	0.000	0.000	0.000
120	A	122	LEU	0	-0.031	-0.026	9.945	-0.811	-0.811	0.000	0.000	0.000	0.000
121	A	123	GLU	-2	-1.888	-1.933	9.411	-9.525	-9.525	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:3:GLU)