FMO DATABASE

FMODB ID: LG3K9

Calculation Name: 5W3X-D-Xray547

Preferred Name:

Target Type:

Ligand Name: acetyl coenzyme *a | inositol hexakisphosphate

Ligand 3-letter code: ACO | IHP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5W3X

Chain ID: D

ChEMBL ID:

UniProt ID: C4B7M5

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	77
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-495390.360345
FMO2-HF: Nuclear repulsion	463870.208562
FMO2-HF: Total energy	-31520.151783
FMO2-MP2: Total energy	-31611.857574

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:1197:LYS)

Summations of interaction energy for fragment #1(A:1197:LYS)

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.
155.408	166.67	12.302	-9.658	-13.907	-0.12

Interaction energy analysis for fragmet #1(A:1197:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.787 / q_NPA : 1.901

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

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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	1199	LYS	1	0.816	0.910	2.204	66.142	69.155	1.341	-1.327	-3.027	-0.012
4	A	1200	LYS	1	0.889	0.940	3.877	62.200	62.351	0.005	-0.052	-0.104	0.000
15	A	1211	ASP	-1	-0.824	-0.895	4.580	-103.275	-103.193	-0.001	-0.012	-0.069	0.000
66	A	1262	THR	0	-0.017	-0.009	4.622	-10.971	-10.765	-0.001	-0.033	-0.172	0.000
67	A	1263	TYR	0	-0.056	-0.063	2.112	-9.791	-3.892	5.112	-3.751	-7.261	-0.042
68	A	1264	LEU	0	0.000	-0.008	1.933	-40.204	-38.358	5.847	-4.471	-3.222	-0.066
69	A	1265	SER	0	0.053	0.024	4.529	10.078	10.143	-0.001	-0.012	-0.052	0.000
5	A	1201	VAL	0	0.029	0.031	7.576	-1.980	-1.980	0.000	0.000	0.000	0.000
6	A	1202	VAL	0	-0.012	-0.011	10.293	0.567	0.567	0.000	0.000	0.000	0.000
7	A	1203	SER	0	0.095	0.054	13.702	1.710	1.710	0.000	0.000	0.000	0.000
8	A	1204	ILE	0	0.069	0.038	15.679	-1.441	-1.441	0.000	0.000	0.000	0.000
9	A	1205	PRO	0	0.032	0.011	13.277	-0.112	-0.112	0.000	0.000	0.000	0.000
10	A	1206	ALA	0	-0.014	0.008	12.504	-2.447	-2.447	0.000	0.000	0.000	0.000
11	A	1207	ILE	0	-0.066	-0.055	13.591	0.575	0.575	0.000	0.000	0.000	0.000
12	A	1208	ASP	-1	-0.850	-0.916	8.154	-55.658	-55.658	0.000	0.000	0.000	0.000
13	A	1209	GLU	-1	-0.881	-0.951	6.941	-70.924	-70.924	0.000	0.000	0.000	0.000
14	A	1210	GLY	0	0.053	0.037	7.209	4.260	4.260	0.000	0.000	0.000	0.000
16	A	1212	LEU	0	0.009	0.013	5.468	7.171	7.171	0.000	0.000	0.000	0.000
17	A	1213	TRP	0	-0.019	-0.017	5.205	7.241	7.241	0.000	0.000	0.000	0.000
18	A	1214	THR	0	0.043	0.038	8.916	0.449	0.449	0.000	0.000	0.000	0.000
19	A	1215	TRP	0	-0.021	-0.029	5.637	0.084	0.084	0.000	0.000	0.000	0.000
20	A	1216	ARG	1	0.943	0.964	11.761	36.484	36.484	0.000	0.000	0.000	0.000
21	A	1217	LYS	1	0.868	0.935	14.258	33.967	33.967	0.000	0.000	0.000	0.000
22	A	1218	TYR	0	-0.039	-0.017	14.733	0.885	0.885	0.000	0.000	0.000	0.000
23	A	1219	GLY	0	0.072	0.031	16.530	1.842	1.842	0.000	0.000	0.000	0.000
24	A	1220	GLN	0	0.031	0.010	17.128	-3.729	-3.729	0.000	0.000	0.000	0.000
25	A	1221	LYS	1	0.952	0.989	18.673	28.014	28.014	0.000	0.000	0.000	0.000
26	A	1222	ASP	-1	-0.799	-0.888	19.184	-28.855	-28.855	0.000	0.000	0.000	0.000
27	A	1223	ILE	0	-0.085	-0.050	16.771	-0.592	-0.592	0.000	0.000	0.000	0.000
28	A	1224	LEU	0	0.037	0.012	20.085	0.647	0.647	0.000	0.000	0.000	0.000
29	A	1225	GLY	0	0.026	0.014	20.846	-1.025	-1.025	0.000	0.000	0.000	0.000
30	A	1226	SER	0	-0.078	-0.049	19.240	-0.980	-0.980	0.000	0.000	0.000	0.000
31	A	1227	ARG	1	0.874	0.913	21.234	27.428	27.428	0.000	0.000	0.000	0.000
32	A	1228	PHE	0	-0.032	-0.005	18.469	0.351	0.351	0.000	0.000	0.000	0.000
33	A	1229	PRO	0	0.045	0.040	19.219	-1.145	-1.145	0.000	0.000	0.000	0.000
34	A	1230	ARG	1	0.824	0.915	12.328	39.702	39.702	0.000	0.000	0.000	0.000
35	A	1231	GLY	0	-0.008	-0.002	14.487	2.552	2.552	0.000	0.000	0.000	0.000
36	A	1232	TYR	0	0.009	-0.010	12.058	-4.775	-4.775	0.000	0.000	0.000	0.000
37	A	1233	TYR	0	0.016	-0.005	10.456	4.433	4.433	0.000	0.000	0.000	0.000
38	A	1234	ARG	1	0.923	0.957	11.041	32.737	32.737	0.000	0.000	0.000	0.000
39	A	1235	CYS	-1	-0.807	-0.764	11.418	-46.510	-46.510	0.000	0.000	0.000	0.000
40	A	1236	ALA	0	-0.006	-0.006	12.449	3.293	3.293	0.000	0.000	0.000	0.000
41	A	1237	TYR	0	0.076	0.008	14.046	2.280	2.280	0.000	0.000	0.000	0.000
42	A	1238	LYS	1	0.891	0.948	14.414	38.530	38.530	0.000	0.000	0.000	0.000
43	A	1239	PHE	0	-0.009	0.001	16.672	0.468	0.468	0.000	0.000	0.000	0.000
44	A	1240	THR	0	0.036	-0.007	19.541	0.198	0.198	0.000	0.000	0.000	0.000
45	A	1241	HIS	0	0.090	0.063	17.402	-0.088	-0.088	0.000	0.000	0.000	0.000
46	A	1242	GLY	0	0.046	0.045	18.130	-0.875	-0.875	0.000	0.000	0.000	0.000
47	A	1243	CYS	0	-0.090	-0.054	12.335	-2.631	-2.631	0.000	0.000	0.000	0.000
48	A	1244	LYS	1	0.958	0.957	11.239	37.850	37.850	0.000	0.000	0.000	0.000
49	A	1245	ALA	0	-0.002	0.026	7.967	-1.261	-1.261	0.000	0.000	0.000	0.000
50	A	1246	THR	0	-0.036	-0.038	7.398	5.434	5.434	0.000	0.000	0.000	0.000
51	A	1247	LYS	1	0.817	0.903	5.870	61.895	61.895	0.000	0.000	0.000	0.000
52	A	1248	GLN	0	0.014	0.004	7.292	10.720	10.720	0.000	0.000	0.000	0.000
53	A	1249	VAL	0	0.000	0.001	8.668	-6.228	-6.228	0.000	0.000	0.000	0.000
54	A	1250	GLN	0	0.045	0.023	10.851	2.022	2.022	0.000	0.000	0.000	0.000
55	A	1251	ARG	1	0.948	0.999	12.544	32.586	32.586	0.000	0.000	0.000	0.000
56	A	1252	SER	0	-0.016	-0.016	14.363	0.477	0.477	0.000	0.000	0.000	0.000
57	A	1253	GLU	-1	-0.747	-0.850	15.889	-26.539	-26.539	0.000	0.000	0.000	0.000
58	A	1254	THR	0	-0.015	-0.013	18.251	0.799	0.799	0.000	0.000	0.000	0.000
59	A	1255	ASP	-1	-0.764	-0.890	17.515	-31.069	-31.069	0.000	0.000	0.000	0.000
60	A	1256	SER	0	-0.016	-0.004	17.405	-1.458	-1.458	0.000	0.000	0.000	0.000
61	A	1257	ASN	0	-0.069	-0.034	17.152	0.058	0.058	0.000	0.000	0.000	0.000
62	A	1258	MET	0	0.049	0.025	11.878	-3.113	-3.113	0.000	0.000	0.000	0.000
63	A	1259	LEU	0	-0.023	0.003	10.091	1.041	1.041	0.000	0.000	0.000	0.000
64	A	1260	ALA	0	-0.021	-0.035	8.797	-3.918	-3.918	0.000	0.000	0.000	0.000
65	A	1261	ILE	0	0.020	0.010	5.237	2.210	2.210	0.000	0.000	0.000	0.000
70	A	1266	GLU	-1	-0.866	-0.922	6.269	-74.657	-74.657	0.000	0.000	0.000	0.000
71	A	1267	HIS	1	0.789	0.842	7.115	67.728	67.728	0.000	0.000	0.000	0.000
72	A	1268	ASN	0	0.003	-0.011	10.290	-1.413	-1.413	0.000	0.000	0.000	0.000
73	A	1269	HIS	1	0.845	0.879	12.657	46.269	46.269	0.000	0.000	0.000	0.000
74	A	1270	PRO	0	0.094	0.046	12.675	-3.859	-3.859	0.000	0.000	0.000	0.000
75	A	1271	ARG	1	0.974	0.983	9.151	44.241	44.241	0.000	0.000	0.000	0.000
76	A	1272	PRO	0	-0.093	-0.036	11.186	1.844	1.844	0.000	0.000	0.000	0.000
77	A	1273	THR	-1	-0.879	-0.925	14.032	-32.531	-32.531	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1197:LYS)