FMO DATABASE

FMODB ID: 7Y4VK

Calculation Name: 1FL0-A-Xray547

Preferred Name: Aminoacyl tRNA synthase complex-interacting multifunctional protein 1

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1FL0

Chain ID: A

ChEMBL ID: CHEMBL4295810

UniProt ID: Q12904

Base Structure: X-ray

Registration Date: 2025-09-02

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	-1622553.749429
FMO2-HF: Nuclear repulsion	1557788.444636
FMO2-HF: Total energy	-64765.304793
FMO2-MP2: Total energy	-64948.321924

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:150:ILE)

Summations of interaction energy for fragment #1(A:150: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.
-0.95799999999999	6.987	5.541	-3.922	-9.564	-0.027

Interaction energy analysis for fragmet #1(A:150:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.790 / q_NPA : 0.883

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	152	VAL	0	0.069	0.026	3.772	0.493	2.853	-0.029	-1.054	-1.278	-0.004
5	A	154	ARG	1	0.818	0.868	2.466	45.094	46.598	0.746	-0.450	-1.800	-0.003
121	A	270	ILE	0	0.032	0.013	2.319	-1.655	-0.681	1.906	-0.570	-2.310	0.001
122	A	271	TRP	0	0.099	0.045	3.227	-6.270	-5.295	0.072	-0.480	-0.566	-0.004
124	A	273	GLN	0	-0.051	-0.038	2.590	-6.749	-5.194	1.679	-1.027	-2.207	-0.013
125	A	274	ILE	0	-0.024	-0.003	2.477	-4.570	-4.032	1.168	-0.333	-1.373	-0.004
126	A	275	GLN	0	0.027	0.004	4.869	3.515	3.554	-0.001	-0.008	-0.030	0.000
4	A	153	SER	0	-0.038	-0.012	5.342	4.060	4.060	0.000	0.000	0.000	0.000
6	A	155	LEU	0	-0.006	-0.003	5.663	2.962	2.962	0.000	0.000	0.000	0.000
7	A	156	ASP	-1	-0.821	-0.905	8.232	-18.065	-18.065	0.000	0.000	0.000	0.000
8	A	157	LEU	0	0.021	0.010	10.438	1.275	1.275	0.000	0.000	0.000	0.000
9	A	158	ARG	1	0.798	0.862	13.588	16.370	16.370	0.000	0.000	0.000	0.000
10	A	159	ILE	0	-0.008	0.007	17.340	0.037	0.037	0.000	0.000	0.000	0.000
11	A	160	GLY	0	0.042	0.013	20.752	0.055	0.055	0.000	0.000	0.000	0.000
12	A	161	CYS	0	-0.037	-0.014	23.127	0.137	0.137	0.000	0.000	0.000	0.000
13	A	162	ILE	0	-0.023	-0.007	24.808	0.020	0.020	0.000	0.000	0.000	0.000
14	A	163	ILE	0	-0.002	0.001	27.713	0.311	0.311	0.000	0.000	0.000	0.000
15	A	164	THR	0	-0.052	-0.048	30.562	0.274	0.274	0.000	0.000	0.000	0.000
16	A	165	ALA	0	0.045	0.021	29.733	-0.405	-0.405	0.000	0.000	0.000	0.000
17	A	166	ARG	1	0.962	0.989	31.315	9.151	9.151	0.000	0.000	0.000	0.000
18	A	167	LYS	1	0.861	0.930	31.553	8.298	8.298	0.000	0.000	0.000	0.000
19	A	168	HIS	0	-0.007	-0.009	28.244	0.318	0.318	0.000	0.000	0.000	0.000
20	A	169	PRO	0	-0.044	-0.031	31.959	0.135	0.135	0.000	0.000	0.000	0.000
21	A	170	ASP	-1	-0.901	-0.944	32.697	-8.491	-8.491	0.000	0.000	0.000	0.000
22	A	171	ALA	0	-0.066	-0.048	29.853	-0.147	-0.147	0.000	0.000	0.000	0.000
23	A	172	ASP	-1	-0.792	-0.884	31.171	-8.606	-8.606	0.000	0.000	0.000	0.000
24	A	173	SER	0	0.003	0.003	29.753	0.026	0.026	0.000	0.000	0.000	0.000
25	A	174	LEU	0	-0.059	-0.033	25.490	-0.390	-0.390	0.000	0.000	0.000	0.000
26	A	175	TYR	0	-0.028	-0.035	27.560	0.567	0.567	0.000	0.000	0.000	0.000
27	A	176	VAL	0	-0.026	-0.024	27.364	-0.297	-0.297	0.000	0.000	0.000	0.000
28	A	177	GLU	-1	-0.799	-0.891	24.540	-11.301	-11.301	0.000	0.000	0.000	0.000
29	A	178	GLU	-1	-0.909	-0.923	26.851	-9.498	-9.498	0.000	0.000	0.000	0.000
30	A	179	VAL	0	-0.018	-0.023	23.403	0.182	0.182	0.000	0.000	0.000	0.000
31	A	180	ASP	-1	-0.833	-0.917	25.314	-11.143	-11.143	0.000	0.000	0.000	0.000
32	A	181	VAL	0	-0.010	-0.023	19.815	-0.353	-0.353	0.000	0.000	0.000	0.000
33	A	182	GLY	0	0.051	0.027	22.070	-0.521	-0.521	0.000	0.000	0.000	0.000
34	A	183	GLU	-1	-0.855	-0.880	20.268	-14.032	-14.032	0.000	0.000	0.000	0.000
35	A	184	ILE	0	-0.021	-0.021	24.927	0.287	0.287	0.000	0.000	0.000	0.000
36	A	185	ALA	0	-0.013	-0.002	27.183	0.419	0.419	0.000	0.000	0.000	0.000
37	A	186	PRO	0	0.011	0.007	26.358	-0.382	-0.382	0.000	0.000	0.000	0.000
38	A	187	ARG	1	0.750	0.840	17.207	14.650	14.650	0.000	0.000	0.000	0.000
39	A	188	THR	0	0.013	0.009	24.424	0.345	0.345	0.000	0.000	0.000	0.000
40	A	189	VAL	0	-0.057	-0.025	21.128	-0.615	-0.615	0.000	0.000	0.000	0.000
41	A	190	VAL	0	0.001	-0.005	22.720	0.571	0.571	0.000	0.000	0.000	0.000
42	A	191	SER	0	0.004	-0.018	22.738	-0.745	-0.745	0.000	0.000	0.000	0.000
43	A	192	GLY	0	-0.016	-0.010	23.121	0.540	0.540	0.000	0.000	0.000	0.000
44	A	193	LEU	0	0.013	-0.018	22.528	-0.041	-0.041	0.000	0.000	0.000	0.000
45	A	194	VAL	0	0.000	0.010	26.297	0.190	0.190	0.000	0.000	0.000	0.000
46	A	195	ASN	0	-0.049	-0.028	29.205	0.424	0.424	0.000	0.000	0.000	0.000
47	A	196	HIS	0	0.011	0.008	26.155	0.068	0.068	0.000	0.000	0.000	0.000
48	A	197	VAL	0	-0.006	0.005	26.886	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	198	PRO	0	0.047	0.053	29.881	0.007	0.007	0.000	0.000	0.000	0.000
50	A	199	LEU	0	0.007	-0.009	32.487	-0.112	-0.112	0.000	0.000	0.000	0.000
51	A	200	GLU	-1	-0.871	-0.945	33.767	-8.492	-8.492	0.000	0.000	0.000	0.000
52	A	201	GLN	0	0.004	0.007	31.443	-0.055	-0.055	0.000	0.000	0.000	0.000
53	A	202	MET	0	-0.036	-0.017	26.057	-0.484	-0.484	0.000	0.000	0.000	0.000
54	A	203	GLN	0	-0.048	-0.032	29.894	-0.246	-0.246	0.000	0.000	0.000	0.000
55	A	204	ASN	0	-0.015	-0.006	31.567	0.014	0.014	0.000	0.000	0.000	0.000
56	A	205	ARG	1	0.911	0.972	25.966	10.849	10.849	0.000	0.000	0.000	0.000
57	A	206	MET	0	0.009	0.011	25.396	-0.186	-0.186	0.000	0.000	0.000	0.000
58	A	207	VAL	0	-0.016	-0.018	21.615	-0.038	-0.038	0.000	0.000	0.000	0.000
59	A	208	ILE	0	0.022	0.003	16.053	-0.178	-0.178	0.000	0.000	0.000	0.000
60	A	209	LEU	0	0.015	0.004	17.507	0.105	0.105	0.000	0.000	0.000	0.000
61	A	210	LEU	0	-0.004	0.001	10.230	-0.806	-0.806	0.000	0.000	0.000	0.000
62	A	211	CYS	0	-0.033	-0.013	14.008	1.116	1.116	0.000	0.000	0.000	0.000
63	A	212	ASN	0	0.021	0.004	8.772	1.035	1.035	0.000	0.000	0.000	0.000
64	A	213	LEU	0	0.035	0.022	11.107	-0.912	-0.912	0.000	0.000	0.000	0.000
65	A	214	LYS	1	0.779	0.874	12.967	16.875	16.875	0.000	0.000	0.000	0.000
66	A	215	PRO	0	0.001	0.006	15.282	0.291	0.291	0.000	0.000	0.000	0.000
67	A	216	ALA	0	-0.001	0.008	18.521	0.214	0.214	0.000	0.000	0.000	0.000
68	A	217	LYS	1	0.919	0.955	20.442	10.783	10.783	0.000	0.000	0.000	0.000
69	A	218	MET	0	0.004	0.008	20.633	-0.068	-0.068	0.000	0.000	0.000	0.000
70	A	219	ARG	1	0.994	1.006	25.359	10.457	10.457	0.000	0.000	0.000	0.000
71	A	220	GLY	0	0.013	0.008	29.083	0.160	0.160	0.000	0.000	0.000	0.000
72	A	221	VAL	0	0.007	0.014	26.749	0.028	0.028	0.000	0.000	0.000	0.000
73	A	222	LEU	0	-0.051	-0.029	22.365	-0.242	-0.242	0.000	0.000	0.000	0.000
74	A	223	SER	0	0.044	0.026	20.333	0.345	0.345	0.000	0.000	0.000	0.000
75	A	224	GLN	0	-0.001	-0.021	20.074	-0.345	-0.345	0.000	0.000	0.000	0.000
76	A	225	ALA	0	0.024	0.027	17.221	-0.446	-0.446	0.000	0.000	0.000	0.000
77	A	226	MET	0	-0.010	0.001	14.017	0.567	0.567	0.000	0.000	0.000	0.000
78	A	227	VAL	0	0.057	0.028	17.246	-0.516	-0.516	0.000	0.000	0.000	0.000
79	A	228	MET	0	-0.014	0.008	12.072	-0.341	-0.341	0.000	0.000	0.000	0.000
80	A	229	CYS	0	-0.020	-0.016	16.796	1.057	1.057	0.000	0.000	0.000	0.000
81	A	230	ALA	0	0.050	0.033	16.979	-0.954	-0.954	0.000	0.000	0.000	0.000
82	A	231	SER	0	-0.013	-0.020	18.514	0.485	0.485	0.000	0.000	0.000	0.000
83	A	232	SER	0	-0.019	-0.005	19.558	-0.463	-0.463	0.000	0.000	0.000	0.000
84	A	233	PRO	0	-0.016	-0.019	22.102	0.029	0.029	0.000	0.000	0.000	0.000
85	A	234	GLU	-1	-0.868	-0.936	24.377	-11.202	-11.202	0.000	0.000	0.000	0.000
86	A	235	LYS	1	0.887	0.962	25.163	11.133	11.133	0.000	0.000	0.000	0.000
87	A	236	ILE	0	0.001	-0.001	21.194	-0.666	-0.666	0.000	0.000	0.000	0.000
88	A	237	GLU	-1	-0.713	-0.846	22.210	-10.985	-10.985	0.000	0.000	0.000	0.000
89	A	238	ILE	0	-0.005	-0.002	21.365	-0.636	-0.636	0.000	0.000	0.000	0.000
90	A	239	LEU	0	-0.019	-0.006	16.489	0.375	0.375	0.000	0.000	0.000	0.000
91	A	240	ALA	0	0.018	0.005	20.911	0.160	0.160	0.000	0.000	0.000	0.000
92	A	241	PRO	0	0.009	-0.007	21.821	-0.401	-0.401	0.000	0.000	0.000	0.000
93	A	242	PRO	0	-0.005	0.023	22.449	0.526	0.526	0.000	0.000	0.000	0.000
94	A	243	ASN	0	0.019	-0.002	25.462	0.038	0.038	0.000	0.000	0.000	0.000
95	A	244	GLY	0	-0.003	-0.006	28.708	-0.043	-0.043	0.000	0.000	0.000	0.000
96	A	245	SER	0	-0.019	-0.020	24.086	-0.205	-0.205	0.000	0.000	0.000	0.000
97	A	246	VAL	0	-0.024	-0.016	25.310	0.475	0.475	0.000	0.000	0.000	0.000
98	A	247	PRO	0	-0.049	-0.023	23.980	-0.593	-0.593	0.000	0.000	0.000	0.000
99	A	248	GLY	0	0.032	0.021	21.168	0.291	0.291	0.000	0.000	0.000	0.000
100	A	249	ASP	-1	-0.880	-0.929	20.482	-13.303	-13.303	0.000	0.000	0.000	0.000
101	A	250	ARG	1	0.780	0.868	13.845	18.274	18.274	0.000	0.000	0.000	0.000
102	A	251	ILE	0	-0.035	-0.009	13.887	0.183	0.183	0.000	0.000	0.000	0.000
103	A	252	THR	0	-0.046	-0.031	13.202	-1.067	-1.067	0.000	0.000	0.000	0.000
104	A	253	PHE	0	0.046	0.010	11.225	0.596	0.596	0.000	0.000	0.000	0.000
105	A	254	ASP	-1	-0.893	-0.943	12.414	-19.883	-19.883	0.000	0.000	0.000	0.000
106	A	255	ALA	0	-0.039	-0.015	11.997	-0.151	-0.151	0.000	0.000	0.000	0.000
107	A	256	PHE	0	-0.049	-0.041	6.888	-2.615	-2.615	0.000	0.000	0.000	0.000
108	A	257	PRO	0	0.012	0.020	9.112	0.122	0.122	0.000	0.000	0.000	0.000
109	A	258	GLY	0	0.010	-0.013	8.349	-2.475	-2.475	0.000	0.000	0.000	0.000
110	A	259	GLU	-1	-0.829	-0.895	9.429	-18.168	-18.168	0.000	0.000	0.000	0.000
111	A	260	PRO	0	-0.043	-0.010	8.464	-1.885	-1.885	0.000	0.000	0.000	0.000
112	A	261	ASP	-1	-0.840	-0.874	6.903	-32.317	-32.317	0.000	0.000	0.000	0.000
113	A	262	LYS	1	0.966	0.976	9.398	16.981	16.981	0.000	0.000	0.000	0.000
114	A	263	GLU	-1	-0.807	-0.898	11.837	-15.472	-15.472	0.000	0.000	0.000	0.000
115	A	264	LEU	0	-0.019	0.010	6.545	-1.392	-1.392	0.000	0.000	0.000	0.000
116	A	265	ASN	0	0.005	-0.006	8.383	2.274	2.274	0.000	0.000	0.000	0.000
117	A	266	PRO	0	0.052	0.030	9.229	-0.963	-0.963	0.000	0.000	0.000	0.000
118	A	267	LYS	1	0.943	0.965	10.912	16.532	16.532	0.000	0.000	0.000	0.000
119	A	268	LYS	1	0.955	0.957	5.978	24.708	24.708	0.000	0.000	0.000	0.000
120	A	269	LYS	1	0.876	0.974	6.419	18.738	18.738	0.000	0.000	0.000	0.000
123	A	272	GLU	-1	-0.901	-0.961	5.910	-23.183	-23.183	0.000	0.000	0.000	0.000
127	A	276	PRO	0	-0.022	-0.012	7.358	1.687	1.687	0.000	0.000	0.000	0.000
128	A	277	ASP	-1	-0.785	-0.879	7.350	-35.771	-35.771	0.000	0.000	0.000	0.000
129	A	278	LEU	0	-0.066	-0.022	8.414	0.880	0.880	0.000	0.000	0.000	0.000
130	A	279	HIS	0	-0.033	-0.014	10.868	1.975	1.975	0.000	0.000	0.000	0.000
131	A	280	THR	0	-0.005	-0.023	14.653	-0.427	-0.427	0.000	0.000	0.000	0.000
132	A	281	ASN	0	0.022	0.015	17.981	0.223	0.223	0.000	0.000	0.000	0.000
133	A	282	ASP	-1	-0.833	-0.931	19.823	-11.832	-11.832	0.000	0.000	0.000	0.000
134	A	283	GLU	-1	-0.952	-0.968	23.215	-11.790	-11.790	0.000	0.000	0.000	0.000
135	A	284	CYS	0	-0.058	-0.025	22.343	0.294	0.294	0.000	0.000	0.000	0.000
136	A	285	VAL	0	-0.016	0.000	19.147	-0.180	-0.180	0.000	0.000	0.000	0.000
137	A	286	ALA	0	0.006	0.003	16.068	-0.481	-0.481	0.000	0.000	0.000	0.000
138	A	287	THR	0	-0.041	-0.020	14.496	-0.280	-0.280	0.000	0.000	0.000	0.000
139	A	288	TYR	0	0.035	0.006	5.283	-3.268	-3.268	0.000	0.000	0.000	0.000
140	A	289	LYS	1	0.799	0.891	7.513	35.850	35.850	0.000	0.000	0.000	0.000
141	A	290	GLY	0	0.051	0.034	11.893	0.655	0.655	0.000	0.000	0.000	0.000
142	A	291	VAL	0	-0.032	-0.013	13.062	1.433	1.433	0.000	0.000	0.000	0.000
143	A	292	PRO	0	0.020	-0.007	14.269	-0.924	-0.924	0.000	0.000	0.000	0.000
144	A	293	PHE	0	-0.005	-0.008	11.914	-0.781	-0.781	0.000	0.000	0.000	0.000
145	A	294	GLU	-1	-0.914	-0.956	16.102	-13.841	-13.841	0.000	0.000	0.000	0.000
146	A	295	VAL	0	-0.002	0.000	18.284	-0.604	-0.604	0.000	0.000	0.000	0.000
147	A	296	LYS	1	0.998	0.984	17.343	17.534	17.534	0.000	0.000	0.000	0.000
148	A	297	GLY	0	0.009	0.012	22.337	0.450	0.450	0.000	0.000	0.000	0.000
149	A	298	LYS	1	0.841	0.934	24.628	11.455	11.455	0.000	0.000	0.000	0.000
150	A	299	GLY	0	0.032	0.024	24.024	0.433	0.433	0.000	0.000	0.000	0.000
151	A	300	VAL	0	0.010	-0.005	20.512	-0.461	-0.461	0.000	0.000	0.000	0.000
152	A	301	CYS	0	-0.037	0.000	18.605	0.744	0.744	0.000	0.000	0.000	0.000
153	A	302	ARG	1	0.946	0.984	20.174	11.773	11.773	0.000	0.000	0.000	0.000
154	A	303	ALA	0	0.013	0.018	21.251	0.191	0.191	0.000	0.000	0.000	0.000
155	A	304	GLN	0	-0.134	-0.074	22.894	0.446	0.446	0.000	0.000	0.000	0.000
156	A	305	THR	0	-0.066	-0.074	26.192	0.321	0.321	0.000	0.000	0.000	0.000
157	A	306	MET	0	-0.038	-0.002	22.015	0.023	0.023	0.000	0.000	0.000	0.000
158	A	307	SER	0	0.061	0.053	21.994	-0.648	-0.648	0.000	0.000	0.000	0.000
159	A	308	ASN	0	-0.084	-0.037	19.790	-0.419	-0.419	0.000	0.000	0.000	0.000
160	A	309	SER	0	0.005	0.002	19.061	0.000	0.000	0.000	0.000	0.000	0.000
161	A	310	GLY	0	-0.007	0.002	14.990	-0.587	-0.587	0.000	0.000	0.000	0.000
162	A	311	ILE	0	-0.026	-0.022	13.352	1.193	1.193	0.000	0.000	0.000	0.000
163	A	312	LYS	1	0.800	0.905	12.360	15.438	15.438	0.000	0.000	0.000	0.000
164	A	313	LEU	-1	-0.915	-0.950	7.594	-21.488	-21.488	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:150:ILE)