FMO DATABASE

FMODB ID: 676VZ

Calculation Name: 3ACD-A-Xray547

Preferred Name:

Target Type:

Ligand Name: inosinic acid | 1,4-diethylene dioxide

Ligand 3-letter code: IMP | DIO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3ACD

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SLS3

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	164
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1651464.178125
FMO2-HF: Nuclear repulsion	1587733.424498
FMO2-HF: Total energy	-63730.753628
FMO2-MP2: Total energy	-63918.814467

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:4:MET)

Summations of interaction energy for fragment #1(A:4: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.
-49.7	-48.248	-0.015	-0.541	-0.897	-0.001

Interaction energy analysis for fragmet #1(A:4:MET)

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 : 0.908

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	6	THR	0	0.024	0.014	3.828	3.151	4.603	-0.015	-0.541	-0.897	-0.001
4	A	7	PRO	0	-0.002	-0.001	6.250	1.170	1.170	0.000	0.000	0.000	0.000
5	A	8	GLY	0	0.031	0.030	9.819	-0.912	-0.912	0.000	0.000	0.000	0.000
6	A	9	ASN	0	-0.029	-0.032	12.325	0.384	0.384	0.000	0.000	0.000	0.000
7	A	10	GLY	0	0.040	0.033	15.167	1.300	1.300	0.000	0.000	0.000	0.000
8	A	11	PRO	0	-0.001	0.014	17.673	-0.836	-0.836	0.000	0.000	0.000	0.000
9	A	12	VAL	0	0.018	0.019	18.627	-0.036	-0.036	0.000	0.000	0.000	0.000
10	A	13	GLN	0	0.015	0.025	13.916	-2.723	-2.723	0.000	0.000	0.000	0.000
11	A	14	ILE	0	0.005	0.008	15.206	0.975	0.975	0.000	0.000	0.000	0.000
12	A	15	SER	0	0.029	0.010	13.023	-1.117	-1.117	0.000	0.000	0.000	0.000
13	A	16	ALA	0	0.066	0.020	11.012	1.002	1.002	0.000	0.000	0.000	0.000
14	A	17	GLU	-1	-0.968	-0.977	13.148	-18.675	-18.675	0.000	0.000	0.000	0.000
15	A	18	ALA	0	0.006	0.005	16.031	1.147	1.147	0.000	0.000	0.000	0.000
16	A	19	ILE	0	0.016	0.013	14.353	0.878	0.878	0.000	0.000	0.000	0.000
17	A	20	LYS	1	0.926	0.975	16.644	16.958	16.958	0.000	0.000	0.000	0.000
18	A	21	LYS	1	0.942	0.970	18.383	14.620	14.620	0.000	0.000	0.000	0.000
19	A	22	ARG	1	0.828	0.925	21.136	12.312	12.312	0.000	0.000	0.000	0.000
20	A	23	VAL	0	0.012	0.006	19.807	0.605	0.605	0.000	0.000	0.000	0.000
21	A	24	GLU	-1	-0.911	-0.981	21.824	-13.701	-13.701	0.000	0.000	0.000	0.000
22	A	25	GLU	-1	-0.934	-0.952	24.271	-11.418	-11.418	0.000	0.000	0.000	0.000
23	A	26	LEU	0	-0.023	-0.005	24.712	0.472	0.472	0.000	0.000	0.000	0.000
24	A	27	GLY	0	0.020	0.005	26.380	0.376	0.376	0.000	0.000	0.000	0.000
25	A	28	GLY	0	0.009	0.003	27.806	0.427	0.427	0.000	0.000	0.000	0.000
26	A	29	GLU	-1	-0.945	-0.985	30.245	-9.925	-9.925	0.000	0.000	0.000	0.000
27	A	30	ILE	0	0.011	0.004	28.815	0.377	0.377	0.000	0.000	0.000	0.000
28	A	31	ALA	0	-0.008	-0.015	31.830	0.323	0.323	0.000	0.000	0.000	0.000
29	A	32	ARG	1	0.923	0.969	33.547	9.108	9.108	0.000	0.000	0.000	0.000
30	A	33	ASP	-1	-0.816	-0.890	35.696	-8.426	-8.426	0.000	0.000	0.000	0.000
31	A	34	TYR	0	-0.030	-0.021	35.181	0.213	0.213	0.000	0.000	0.000	0.000
32	A	35	GLN	0	-0.016	-0.003	37.512	0.168	0.168	0.000	0.000	0.000	0.000
33	A	36	GLY	0	-0.034	-0.023	39.238	0.175	0.175	0.000	0.000	0.000	0.000
34	A	37	LYS	1	0.830	0.925	38.825	7.824	7.824	0.000	0.000	0.000	0.000
35	A	38	THR	0	0.007	0.001	37.754	-0.071	-0.071	0.000	0.000	0.000	0.000
36	A	39	PRO	0	0.016	0.029	33.913	0.117	0.117	0.000	0.000	0.000	0.000
37	A	40	HIS	0	0.000	0.027	34.162	-0.063	-0.063	0.000	0.000	0.000	0.000
38	A	41	LEU	0	0.035	0.013	28.032	0.019	0.019	0.000	0.000	0.000	0.000
39	A	42	ILE	0	-0.022	-0.014	30.081	-0.121	-0.121	0.000	0.000	0.000	0.000
40	A	43	CYS	0	0.010	0.006	24.158	-0.343	-0.343	0.000	0.000	0.000	0.000
41	A	44	VAL	0	0.016	0.018	25.906	0.195	0.195	0.000	0.000	0.000	0.000
42	A	45	LEU	0	-0.077	-0.022	22.168	-0.733	-0.733	0.000	0.000	0.000	0.000
43	A	46	ASN	0	0.005	-0.035	19.776	0.870	0.870	0.000	0.000	0.000	0.000
44	A	47	GLY	0	0.021	0.021	19.314	-0.612	-0.612	0.000	0.000	0.000	0.000
45	A	48	ALA	0	0.022	0.015	19.142	-0.838	-0.838	0.000	0.000	0.000	0.000
46	A	49	PHE	0	0.004	-0.009	14.763	-0.124	-0.124	0.000	0.000	0.000	0.000
47	A	50	ILE	0	-0.037	-0.008	13.378	0.124	0.124	0.000	0.000	0.000	0.000
48	A	51	PHE	0	0.054	0.029	17.501	0.202	0.202	0.000	0.000	0.000	0.000
49	A	52	MET	0	0.017	0.013	19.903	0.558	0.558	0.000	0.000	0.000	0.000
50	A	53	ALA	0	-0.016	-0.007	18.822	0.448	0.448	0.000	0.000	0.000	0.000
51	A	54	ASP	-1	-0.834	-0.876	16.927	-17.696	-17.696	0.000	0.000	0.000	0.000
52	A	55	LEU	0	0.030	0.016	20.320	0.520	0.520	0.000	0.000	0.000	0.000
53	A	56	VAL	0	-0.026	-0.031	23.707	0.542	0.542	0.000	0.000	0.000	0.000
54	A	57	ARG	1	0.765	0.865	17.182	16.369	16.369	0.000	0.000	0.000	0.000
55	A	58	ALA	0	0.000	0.018	23.823	0.088	0.088	0.000	0.000	0.000	0.000
56	A	59	ILE	0	-0.011	0.006	25.638	0.395	0.395	0.000	0.000	0.000	0.000
57	A	60	PRO	0	-0.040	-0.007	29.139	0.093	0.093	0.000	0.000	0.000	0.000
58	A	61	LEU	0	-0.004	-0.007	31.498	0.367	0.367	0.000	0.000	0.000	0.000
59	A	62	PRO	0	-0.041	-0.008	33.172	-0.211	-0.211	0.000	0.000	0.000	0.000
60	A	63	LEU	0	0.025	0.009	29.855	0.183	0.183	0.000	0.000	0.000	0.000
61	A	64	THR	0	-0.039	-0.035	33.377	0.069	0.069	0.000	0.000	0.000	0.000
62	A	65	MET	0	0.021	0.012	27.106	-0.267	-0.267	0.000	0.000	0.000	0.000
63	A	66	ASP	-1	-0.800	-0.897	30.362	-9.325	-9.325	0.000	0.000	0.000	0.000
64	A	67	PHE	0	-0.029	-0.011	23.927	-0.290	-0.290	0.000	0.000	0.000	0.000
65	A	68	ILE	0	0.021	0.019	28.261	0.338	0.338	0.000	0.000	0.000	0.000
66	A	69	ALA	0	0.020	0.018	26.968	-0.487	-0.487	0.000	0.000	0.000	0.000
67	A	70	ILE	0	0.000	0.005	27.948	0.505	0.505	0.000	0.000	0.000	0.000
68	A	71	SER	-1	-0.894	-0.940	28.182	-10.477	-10.477	0.000	0.000	0.000	0.000
69	A	84	GLU	0	-0.086	-0.044	34.114	0.779	0.779	0.000	0.000	0.000	0.000
70	A	85	LEU	0	0.032	0.019	32.564	-0.332	-0.332	0.000	0.000	0.000	0.000
71	A	86	LEU	0	-0.009	-0.005	28.193	0.173	0.173	0.000	0.000	0.000	0.000
72	A	87	LYS	1	0.784	0.881	29.011	10.106	10.106	0.000	0.000	0.000	0.000
73	A	88	ASP	-1	-0.828	-0.915	31.594	-8.828	-8.828	0.000	0.000	0.000	0.000
74	A	89	LEU	0	-0.009	0.001	33.381	-0.233	-0.233	0.000	0.000	0.000	0.000
75	A	90	ARG	1	0.882	0.926	31.370	9.750	9.750	0.000	0.000	0.000	0.000
76	A	91	LEU	0	-0.019	-0.007	34.232	0.245	0.245	0.000	0.000	0.000	0.000
77	A	92	PRO	0	-0.040	-0.023	37.267	0.016	0.016	0.000	0.000	0.000	0.000
78	A	93	ILE	0	0.033	0.009	36.986	-0.081	-0.081	0.000	0.000	0.000	0.000
79	A	94	HIS	0	-0.052	-0.020	40.019	0.147	0.147	0.000	0.000	0.000	0.000
80	A	95	GLY	0	0.016	0.004	43.787	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	96	ARG	1	0.782	0.887	36.884	8.321	8.321	0.000	0.000	0.000	0.000
82	A	97	ASP	-1	-0.806	-0.880	38.693	-7.700	-7.700	0.000	0.000	0.000	0.000
83	A	98	VAL	0	-0.013	-0.021	34.779	-0.208	-0.208	0.000	0.000	0.000	0.000
84	A	99	ILE	0	-0.009	-0.001	30.300	0.053	0.053	0.000	0.000	0.000	0.000
85	A	100	VAL	0	0.023	0.011	30.039	-0.195	-0.195	0.000	0.000	0.000	0.000
86	A	101	VAL	0	-0.034	-0.018	24.646	-0.099	-0.099	0.000	0.000	0.000	0.000
87	A	102	GLU	-1	-0.814	-0.929	25.796	-11.777	-11.777	0.000	0.000	0.000	0.000
88	A	103	ASP	-1	-0.839	-0.934	20.684	-14.669	-14.669	0.000	0.000	0.000	0.000
89	A	104	ILE	0	-0.044	-0.041	22.083	-0.136	-0.136	0.000	0.000	0.000	0.000
90	A	105	VAL	0	0.024	0.021	24.101	0.296	0.296	0.000	0.000	0.000	0.000
91	A	106	ASP	-1	-0.747	-0.860	26.450	-11.539	-11.539	0.000	0.000	0.000	0.000
92	A	107	THR	0	0.040	0.022	28.327	0.269	0.269	0.000	0.000	0.000	0.000
93	A	108	GLY	0	0.042	0.021	31.075	0.355	0.355	0.000	0.000	0.000	0.000
94	A	109	LEU	0	-0.001	-0.008	32.796	0.142	0.142	0.000	0.000	0.000	0.000
95	A	110	THR	0	0.032	0.012	29.020	0.257	0.257	0.000	0.000	0.000	0.000
96	A	111	LEU	0	0.035	0.018	30.905	0.117	0.117	0.000	0.000	0.000	0.000
97	A	112	SER	0	0.002	0.003	32.802	0.230	0.230	0.000	0.000	0.000	0.000
98	A	113	TYR	0	0.003	0.010	35.204	0.100	0.100	0.000	0.000	0.000	0.000
99	A	114	LEU	0	-0.017	-0.007	31.059	0.159	0.159	0.000	0.000	0.000	0.000
100	A	115	LEU	0	0.006	-0.006	35.056	0.129	0.129	0.000	0.000	0.000	0.000
101	A	116	ASP	-1	-0.862	-0.937	37.398	-7.735	-7.735	0.000	0.000	0.000	0.000
102	A	117	TYR	0	-0.038	-0.015	37.434	0.218	0.218	0.000	0.000	0.000	0.000
103	A	118	LEU	0	-0.053	-0.036	34.361	0.128	0.128	0.000	0.000	0.000	0.000
104	A	119	GLU	-1	-0.818	-0.930	39.002	-7.569	-7.569	0.000	0.000	0.000	0.000
105	A	120	ALA	0	-0.018	0.013	42.122	0.240	0.240	0.000	0.000	0.000	0.000
106	A	121	ARG	1	0.860	0.919	39.792	8.199	8.199	0.000	0.000	0.000	0.000
107	A	122	LYS	1	0.869	0.941	43.799	6.810	6.810	0.000	0.000	0.000	0.000
108	A	123	PRO	0	0.024	0.034	40.350	0.094	0.094	0.000	0.000	0.000	0.000
109	A	124	ALA	0	-0.034	-0.021	42.520	0.169	0.169	0.000	0.000	0.000	0.000
110	A	125	SER	0	-0.065	-0.048	40.390	0.018	0.018	0.000	0.000	0.000	0.000
111	A	126	VAL	0	0.038	0.024	36.167	-0.165	-0.165	0.000	0.000	0.000	0.000
112	A	127	ARG	1	0.813	0.917	34.551	8.626	8.626	0.000	0.000	0.000	0.000
113	A	128	VAL	0	0.027	0.014	30.029	-0.117	-0.117	0.000	0.000	0.000	0.000
114	A	129	ALA	0	-0.004	0.004	27.153	0.058	0.058	0.000	0.000	0.000	0.000
115	A	130	ALA	0	0.010	0.002	25.474	-0.077	-0.077	0.000	0.000	0.000	0.000
116	A	131	LEU	0	0.018	0.031	17.937	0.024	0.024	0.000	0.000	0.000	0.000
117	A	132	LEU	0	0.008	-0.009	19.119	-0.114	-0.114	0.000	0.000	0.000	0.000
118	A	133	SER	0	0.030	0.025	23.591	0.438	0.438	0.000	0.000	0.000	0.000
119	A	134	LYS	1	0.843	0.938	24.028	12.691	12.691	0.000	0.000	0.000	0.000
120	A	135	PRO	0	0.040	0.030	27.915	0.258	0.258	0.000	0.000	0.000	0.000
121	A	136	SER	0	-0.023	-0.019	29.649	0.245	0.245	0.000	0.000	0.000	0.000
122	A	137	ARG	1	0.806	0.875	28.204	11.318	11.318	0.000	0.000	0.000	0.000
123	A	138	ARG	1	0.806	0.915	30.060	10.232	10.232	0.000	0.000	0.000	0.000
124	A	139	GLN	0	-0.043	-0.033	33.971	0.144	0.144	0.000	0.000	0.000	0.000
125	A	140	VAL	0	-0.026	-0.002	36.028	0.307	0.307	0.000	0.000	0.000	0.000
126	A	141	GLU	-1	-0.900	-0.956	36.128	-9.132	-9.132	0.000	0.000	0.000	0.000
127	A	142	VAL	0	-0.031	-0.020	33.352	0.117	0.117	0.000	0.000	0.000	0.000
128	A	143	PRO	0	-0.029	0.003	34.683	-0.171	-0.171	0.000	0.000	0.000	0.000
129	A	144	ILE	0	0.036	-0.004	29.122	-0.224	-0.224	0.000	0.000	0.000	0.000
130	A	145	HIS	0	-0.026	0.002	32.474	-0.051	-0.051	0.000	0.000	0.000	0.000
131	A	146	TYR	0	-0.019	-0.038	28.950	0.119	0.119	0.000	0.000	0.000	0.000
132	A	147	LEU	0	0.033	0.019	26.298	-0.355	-0.355	0.000	0.000	0.000	0.000
133	A	148	GLY	0	0.001	0.002	23.544	0.065	0.065	0.000	0.000	0.000	0.000
134	A	149	PHE	0	-0.024	-0.033	19.980	0.036	0.036	0.000	0.000	0.000	0.000
135	A	150	GLU	-1	-0.924	-0.959	24.477	-10.410	-10.410	0.000	0.000	0.000	0.000
136	A	151	ILE	0	-0.059	-0.034	21.670	-0.419	-0.419	0.000	0.000	0.000	0.000
137	A	152	GLU	-1	-0.870	-0.951	24.067	-12.650	-12.650	0.000	0.000	0.000	0.000
138	A	153	ASP	-1	-0.885	-0.960	25.177	-12.181	-12.181	0.000	0.000	0.000	0.000
139	A	154	ALA	0	0.046	0.029	20.972	-0.131	-0.131	0.000	0.000	0.000	0.000
140	A	155	TYR	0	-0.052	-0.033	17.903	0.596	0.596	0.000	0.000	0.000	0.000
141	A	156	VAL	0	0.009	-0.010	17.546	-0.747	-0.747	0.000	0.000	0.000	0.000
142	A	157	TYR	0	-0.012	-0.021	10.593	0.954	0.954	0.000	0.000	0.000	0.000
143	A	158	GLY	0	0.017	0.012	11.643	-0.996	-0.996	0.000	0.000	0.000	0.000
144	A	159	TYR	0	-0.050	-0.075	11.720	2.256	2.256	0.000	0.000	0.000	0.000
145	A	160	GLY	0	0.005	0.009	13.565	1.556	1.556	0.000	0.000	0.000	0.000
146	A	161	LEU	0	0.038	0.026	15.661	0.699	0.699	0.000	0.000	0.000	0.000
147	A	162	ASP	-1	-0.829	-0.898	14.618	-18.376	-18.376	0.000	0.000	0.000	0.000
148	A	163	ARG	1	0.874	0.925	9.988	26.653	26.653	0.000	0.000	0.000	0.000
149	A	164	ALA	0	0.017	0.008	15.278	-0.567	-0.567	0.000	0.000	0.000	0.000
150	A	165	GLN	0	0.019	-0.004	16.760	-0.692	-0.692	0.000	0.000	0.000	0.000
151	A	166	PHE	0	-0.027	-0.004	11.299	-1.049	-1.049	0.000	0.000	0.000	0.000
152	A	167	ASP	-1	-0.814	-0.901	9.348	-28.868	-28.868	0.000	0.000	0.000	0.000
153	A	168	ARG	1	0.832	0.906	10.537	16.795	16.795	0.000	0.000	0.000	0.000
154	A	169	ASN	0	-0.004	-0.006	6.673	1.977	1.977	0.000	0.000	0.000	0.000
155	A	170	LEU	0	-0.018	0.007	6.760	-4.505	-4.505	0.000	0.000	0.000	0.000
156	A	171	PRO	0	-0.029	-0.012	6.518	3.466	3.466	0.000	0.000	0.000	0.000
157	A	172	PHE	0	-0.015	-0.020	6.802	1.344	1.344	0.000	0.000	0.000	0.000
158	A	173	ILE	0	0.015	0.027	11.451	-0.786	-0.786	0.000	0.000	0.000	0.000
159	A	174	THR	0	-0.037	-0.041	10.983	-0.590	-0.590	0.000	0.000	0.000	0.000
160	A	175	SER	0	0.027	0.000	14.084	1.237	1.237	0.000	0.000	0.000	0.000
161	A	176	ILE	0	-0.037	-0.009	15.121	-1.271	-1.271	0.000	0.000	0.000	0.000
162	A	177	ARG	1	0.901	0.934	17.111	16.241	16.241	0.000	0.000	0.000	0.000
163	A	178	PRO	0	-0.027	-0.015	20.110	-0.314	-0.314	0.000	0.000	0.000	0.000
164	A	179	GLU	-2	-1.893	-1.926	21.215	-26.150	-26.150	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:MET)