FMO DATABASE

FMODB ID: NZ4YQ

Calculation Name: 2AL7-A-Xray547

Preferred Name: ADP-ribosylation factor-like protein 8B

Target Type: SINGLE PROTEIN

Ligand Name: guanosine-5'-diphosphate | magnesium ion

Ligand 3-letter code: GDP | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2AL7

Chain ID: A

ChEMBL ID: CHEMBL4295962

UniProt ID: Q9NVJ2

Base Structure: X-ray

Registration Date: 2025-10-03

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	155
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1622408.274004
FMO2-HF: Nuclear repulsion	1558934.56207
FMO2-HF: Total energy	-63473.711934
FMO2-MP2: Total energy	-63655.12174

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:16:SER)

Summations of interaction energy for fragment #1(A:16:SER)

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.
-136.933	-133.361	10.946	-8.309	-6.209	-0.099

Interaction energy analysis for fragmet #1(A:16:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.789 / q_NPA : 0.886

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	18	GLU	-1	-0.819	-0.884	1.780	-123.381	-120.672	10.900	-7.993	-5.616	-0.097
4	A	19	GLU	-1	-0.887	-0.940	5.101	-21.010	-20.953	-0.001	-0.004	-0.052	0.000
37	A	63	ASN	0	-0.064	-0.035	3.492	-3.309	-2.503	0.047	-0.312	-0.541	-0.002
5	A	20	MET	0	-0.014	0.017	8.834	-0.938	-0.938	0.000	0.000	0.000	0.000
6	A	21	GLU	-1	-0.821	-0.895	10.909	-16.381	-16.381	0.000	0.000	0.000	0.000
7	A	22	LEU	0	0.016	0.016	14.634	0.067	0.067	0.000	0.000	0.000	0.000
8	A	23	THR	0	-0.014	-0.034	17.080	0.502	0.502	0.000	0.000	0.000	0.000
9	A	24	LEU	0	-0.039	0.003	20.882	0.028	0.028	0.000	0.000	0.000	0.000
10	A	25	VAL	0	0.022	0.001	22.886	0.526	0.526	0.000	0.000	0.000	0.000
11	A	26	GLY	0	0.113	0.059	26.417	-0.147	-0.147	0.000	0.000	0.000	0.000
12	A	27	LEU	0	0.002	0.008	29.414	0.072	0.072	0.000	0.000	0.000	0.000
13	A	28	GLN	0	0.013	-0.002	31.806	-0.485	-0.485	0.000	0.000	0.000	0.000
14	A	29	TYR	0	0.030	-0.003	34.016	0.069	0.069	0.000	0.000	0.000	0.000
15	A	30	SER	0	0.009	0.011	29.815	-0.112	-0.112	0.000	0.000	0.000	0.000
16	A	31	GLY	0	0.048	0.024	29.246	-0.176	-0.176	0.000	0.000	0.000	0.000
17	A	32	LYS	1	0.827	0.938	25.579	10.897	10.897	0.000	0.000	0.000	0.000
18	A	33	THR	0	0.043	-0.012	24.915	-0.316	-0.316	0.000	0.000	0.000	0.000
19	A	34	THR	0	-0.075	-0.034	25.920	-0.102	-0.102	0.000	0.000	0.000	0.000
20	A	35	PHE	0	0.083	0.023	18.870	-0.143	-0.143	0.000	0.000	0.000	0.000
21	A	36	VAL	0	-0.005	-0.008	20.828	-0.533	-0.533	0.000	0.000	0.000	0.000
22	A	37	ASN	0	-0.030	-0.026	21.400	-0.664	-0.664	0.000	0.000	0.000	0.000
23	A	38	VAL	0	-0.048	-0.006	22.079	0.131	0.131	0.000	0.000	0.000	0.000
24	A	39	ILE	0	-0.036	-0.009	16.417	-0.481	-0.481	0.000	0.000	0.000	0.000
25	A	40	ALA	-1	-0.926	-0.956	17.386	-17.393	-17.393	0.000	0.000	0.000	0.000
26	A	52	VAL	0	-0.005	-0.019	30.468	0.179	0.179	0.000	0.000	0.000	0.000
27	A	53	GLY	0	0.005	-0.001	31.799	-0.136	-0.136	0.000	0.000	0.000	0.000
28	A	54	PHE	0	0.015	0.006	26.912	-0.190	-0.190	0.000	0.000	0.000	0.000
29	A	55	ASN	0	-0.032	-0.015	25.352	-0.062	-0.062	0.000	0.000	0.000	0.000
30	A	56	MET	0	0.010	0.027	20.435	-0.423	-0.423	0.000	0.000	0.000	0.000
31	A	57	ARG	1	0.904	0.952	20.350	14.489	14.489	0.000	0.000	0.000	0.000
32	A	58	LYS	1	0.896	0.939	13.692	21.170	21.170	0.000	0.000	0.000	0.000
33	A	59	VAL	0	0.010	0.018	14.674	0.892	0.892	0.000	0.000	0.000	0.000
34	A	60	THR	0	-0.004	0.003	9.890	-1.862	-1.862	0.000	0.000	0.000	0.000
35	A	61	LYS	1	0.918	0.956	10.215	21.641	21.641	0.000	0.000	0.000	0.000
36	A	62	GLY	0	0.044	0.027	7.519	-1.916	-1.916	0.000	0.000	0.000	0.000
38	A	64	VAL	0	0.074	0.046	5.258	-5.198	-5.198	0.000	0.000	0.000	0.000
39	A	65	THR	0	-0.049	-0.032	7.032	5.948	5.948	0.000	0.000	0.000	0.000
40	A	66	ILE	0	0.030	0.006	10.267	-0.107	-0.107	0.000	0.000	0.000	0.000
41	A	67	LYS	1	0.821	0.898	12.540	19.811	19.811	0.000	0.000	0.000	0.000
42	A	68	ILE	0	0.011	0.002	15.688	-0.088	-0.088	0.000	0.000	0.000	0.000
43	A	69	TRP	0	-0.024	-0.030	18.526	1.241	1.241	0.000	0.000	0.000	0.000
44	A	70	ASP	-1	-0.816	-0.896	21.955	-12.193	-12.193	0.000	0.000	0.000	0.000
45	A	71	ILE	0	0.005	-0.003	24.613	0.459	0.459	0.000	0.000	0.000	0.000
46	A	72	GLY	0	0.024	0.013	27.401	0.164	0.164	0.000	0.000	0.000	0.000
47	A	73	GLY	0	0.022	0.006	31.082	0.021	0.021	0.000	0.000	0.000	0.000
48	A	74	GLN	0	0.011	0.006	32.374	0.434	0.434	0.000	0.000	0.000	0.000
49	A	75	PRO	0	0.054	0.018	35.508	-0.161	-0.161	0.000	0.000	0.000	0.000
50	A	76	ARG	1	0.916	0.953	36.970	8.309	8.309	0.000	0.000	0.000	0.000
51	A	77	PHE	0	0.002	0.006	32.452	0.035	0.035	0.000	0.000	0.000	0.000
52	A	78	ARG	1	0.875	0.934	32.344	8.844	8.844	0.000	0.000	0.000	0.000
53	A	79	SER	0	0.009	0.011	32.497	-0.283	-0.283	0.000	0.000	0.000	0.000
54	A	80	MET	0	-0.020	-0.027	30.417	-0.011	-0.011	0.000	0.000	0.000	0.000
55	A	81	TRP	0	0.023	0.013	28.078	-0.402	-0.402	0.000	0.000	0.000	0.000
56	A	82	GLU	-1	-0.791	-0.911	26.751	-11.144	-11.144	0.000	0.000	0.000	0.000
57	A	83	ARG	1	0.846	0.917	26.357	9.451	9.451	0.000	0.000	0.000	0.000
58	A	84	TYR	0	0.024	0.016	24.066	0.000	0.000	0.000	0.000	0.000	0.000
59	A	85	CYS	0	-0.012	0.020	22.450	-0.707	-0.707	0.000	0.000	0.000	0.000
60	A	86	ARG	1	0.880	0.928	21.916	11.306	11.306	0.000	0.000	0.000	0.000
61	A	87	GLY	0	0.006	0.010	19.732	-0.034	-0.034	0.000	0.000	0.000	0.000
62	A	88	VAL	0	-0.055	-0.001	17.074	-1.008	-1.008	0.000	0.000	0.000	0.000
63	A	89	ASN	0	-0.038	-0.024	11.166	1.464	1.464	0.000	0.000	0.000	0.000
64	A	90	ALA	0	0.051	0.014	14.499	-0.161	-0.161	0.000	0.000	0.000	0.000
65	A	91	ILE	0	-0.004	0.000	16.891	0.210	0.210	0.000	0.000	0.000	0.000
66	A	92	VAL	0	-0.006	-0.005	18.781	-0.099	-0.099	0.000	0.000	0.000	0.000
67	A	93	TYR	0	-0.033	-0.031	21.461	0.518	0.518	0.000	0.000	0.000	0.000
68	A	94	MET	0	-0.028	0.003	23.574	0.135	0.135	0.000	0.000	0.000	0.000
69	A	95	ILE	0	-0.033	-0.030	26.892	0.494	0.494	0.000	0.000	0.000	0.000
70	A	96	ASP	-1	-0.824	-0.903	30.091	-9.537	-9.537	0.000	0.000	0.000	0.000
71	A	97	ALA	0	0.038	0.013	31.428	0.192	0.192	0.000	0.000	0.000	0.000
72	A	98	ALA	0	0.020	0.014	33.403	0.193	0.193	0.000	0.000	0.000	0.000
73	A	99	ASP	-1	-0.827	-0.889	36.379	-8.052	-8.052	0.000	0.000	0.000	0.000
74	A	100	ARG	1	0.844	0.886	38.021	8.228	8.228	0.000	0.000	0.000	0.000
75	A	101	GLU	-1	-0.933	-0.945	39.472	-7.385	-7.385	0.000	0.000	0.000	0.000
76	A	102	LYS	1	0.803	0.878	37.271	8.194	8.194	0.000	0.000	0.000	0.000
77	A	103	ILE	0	0.012	0.009	34.610	-0.223	-0.223	0.000	0.000	0.000	0.000
78	A	104	GLU	-1	-0.896	-0.936	36.232	-7.861	-7.861	0.000	0.000	0.000	0.000
79	A	105	ALA	0	0.018	0.002	37.730	-0.111	-0.111	0.000	0.000	0.000	0.000
80	A	106	SER	0	-0.014	-0.016	32.296	-0.283	-0.283	0.000	0.000	0.000	0.000
81	A	107	ARG	1	1.004	1.004	32.738	8.274	8.274	0.000	0.000	0.000	0.000
82	A	108	ASN	0	0.006	-0.005	33.820	-0.247	-0.247	0.000	0.000	0.000	0.000
83	A	109	GLU	-1	-0.842	-0.917	33.117	-9.138	-9.138	0.000	0.000	0.000	0.000
84	A	110	LEU	0	-0.037	-0.004	27.114	-0.274	-0.274	0.000	0.000	0.000	0.000
85	A	111	HIS	0	-0.024	-0.017	30.060	-0.173	-0.173	0.000	0.000	0.000	0.000
86	A	112	ASN	0	0.036	0.021	32.147	-0.083	-0.083	0.000	0.000	0.000	0.000
87	A	113	LEU	0	-0.073	-0.038	26.286	-0.023	-0.023	0.000	0.000	0.000	0.000
88	A	114	LEU	0	-0.015	-0.027	25.312	-0.275	-0.275	0.000	0.000	0.000	0.000
89	A	115	ASP	-1	-0.876	-0.916	28.667	-9.747	-9.747	0.000	0.000	0.000	0.000
90	A	116	LYS	1	0.800	0.915	29.157	10.055	10.055	0.000	0.000	0.000	0.000
91	A	117	PRO	0	0.062	0.027	28.620	-0.455	-0.455	0.000	0.000	0.000	0.000
92	A	118	GLN	0	-0.024	-0.009	26.829	-0.570	-0.570	0.000	0.000	0.000	0.000
93	A	119	LEU	0	-0.025	-0.015	24.092	-0.554	-0.554	0.000	0.000	0.000	0.000
94	A	120	GLN	0	-0.004	0.011	23.973	0.041	0.041	0.000	0.000	0.000	0.000
95	A	121	GLY	0	-0.022	-0.008	21.920	-0.477	-0.477	0.000	0.000	0.000	0.000
96	A	122	ILE	0	-0.075	-0.021	18.671	-0.837	-0.837	0.000	0.000	0.000	0.000
97	A	123	PRO	0	0.014	0.015	15.914	0.676	0.676	0.000	0.000	0.000	0.000
98	A	124	VAL	0	-0.012	-0.004	19.002	-0.095	-0.095	0.000	0.000	0.000	0.000
99	A	125	LEU	0	-0.004	0.006	17.964	0.021	0.021	0.000	0.000	0.000	0.000
100	A	126	VAL	0	0.012	-0.004	21.009	0.316	0.316	0.000	0.000	0.000	0.000
101	A	127	LEU	0	0.004	-0.006	20.998	-0.170	-0.170	0.000	0.000	0.000	0.000
102	A	128	GLY	0	0.026	0.008	25.282	0.415	0.415	0.000	0.000	0.000	0.000
103	A	129	ASN	0	0.014	0.000	27.536	-0.163	-0.163	0.000	0.000	0.000	0.000
104	A	130	LYS	1	0.805	0.878	28.747	9.963	9.963	0.000	0.000	0.000	0.000
105	A	131	ARG	1	0.884	0.938	28.399	11.468	11.468	0.000	0.000	0.000	0.000
106	A	132	ASP	-1	-0.808	-0.875	31.519	-9.765	-9.765	0.000	0.000	0.000	0.000
107	A	133	LEU	0	-0.037	-0.010	33.441	0.328	0.328	0.000	0.000	0.000	0.000
108	A	134	PRO	0	0.033	0.012	36.450	-0.044	-0.044	0.000	0.000	0.000	0.000
109	A	135	ASN	0	0.003	-0.020	39.412	0.002	0.002	0.000	0.000	0.000	0.000
110	A	136	ALA	0	0.030	0.036	33.760	-0.012	-0.012	0.000	0.000	0.000	0.000
111	A	137	LEU	0	-0.068	-0.028	33.896	0.193	0.193	0.000	0.000	0.000	0.000
112	A	138	ASP	-1	-0.816	-0.903	31.895	-9.777	-9.777	0.000	0.000	0.000	0.000
113	A	139	GLU	-1	-0.749	-0.910	26.718	-11.593	-11.593	0.000	0.000	0.000	0.000
114	A	140	LYS	1	0.936	0.979	29.832	9.391	9.391	0.000	0.000	0.000	0.000
115	A	141	GLN	0	0.021	-0.002	32.651	0.045	0.045	0.000	0.000	0.000	0.000
116	A	142	LEU	0	-0.023	-0.008	29.320	0.147	0.147	0.000	0.000	0.000	0.000
117	A	143	ILE	0	0.013	-0.008	27.902	0.031	0.031	0.000	0.000	0.000	0.000
118	A	144	GLU	-1	-0.950	-0.963	31.215	-8.456	-8.456	0.000	0.000	0.000	0.000
119	A	145	LYS	1	0.932	0.967	34.968	8.459	8.459	0.000	0.000	0.000	0.000
120	A	146	MET	0	-0.050	-0.016	30.336	0.260	0.260	0.000	0.000	0.000	0.000
121	A	147	ASN	0	-0.029	-0.016	32.631	-0.084	-0.084	0.000	0.000	0.000	0.000
122	A	148	LEU	0	0.024	0.003	27.133	-0.097	-0.097	0.000	0.000	0.000	0.000
123	A	149	SER	0	-0.001	-0.008	29.530	-0.335	-0.335	0.000	0.000	0.000	0.000
124	A	150	ALA	0	-0.017	0.008	31.373	0.083	0.083	0.000	0.000	0.000	0.000
125	A	151	ILE	0	-0.045	-0.017	26.767	0.018	0.018	0.000	0.000	0.000	0.000
126	A	152	GLN	0	0.020	0.003	27.795	-0.329	-0.329	0.000	0.000	0.000	0.000
127	A	153	ASP	-1	-0.825	-0.885	25.568	-12.663	-12.663	0.000	0.000	0.000	0.000
128	A	154	ARG	1	0.797	0.872	22.166	12.643	12.643	0.000	0.000	0.000	0.000
129	A	155	GLU	-1	-0.811	-0.877	17.191	-18.504	-18.504	0.000	0.000	0.000	0.000
130	A	156	ILE	0	0.006	-0.010	21.225	-0.213	-0.213	0.000	0.000	0.000	0.000
131	A	157	CYS	0	-0.052	0.000	19.575	0.383	0.383	0.000	0.000	0.000	0.000
132	A	158	CYS	0	-0.028	-0.021	22.307	0.335	0.335	0.000	0.000	0.000	0.000
133	A	159	TYR	0	0.034	0.019	18.751	-0.371	-0.371	0.000	0.000	0.000	0.000
134	A	160	SER	0	-0.032	0.008	24.621	0.235	0.235	0.000	0.000	0.000	0.000
135	A	161	ILE	0	0.012	-0.003	22.952	-0.225	-0.225	0.000	0.000	0.000	0.000
136	A	162	SER	0	-0.016	-0.037	26.124	0.462	0.462	0.000	0.000	0.000	0.000
137	A	163	CYS	0	-0.028	-0.010	25.143	-0.432	-0.432	0.000	0.000	0.000	0.000
138	A	164	LYS	1	0.880	0.954	26.178	9.228	9.228	0.000	0.000	0.000	0.000
139	A	165	GLU	-1	-0.886	-0.973	28.784	-9.918	-9.918	0.000	0.000	0.000	0.000
140	A	166	LYS	1	0.830	0.921	23.377	11.958	11.958	0.000	0.000	0.000	0.000
141	A	167	ASP	-1	-0.792	-0.882	23.717	-12.231	-12.231	0.000	0.000	0.000	0.000
142	A	168	ASN	0	0.007	-0.017	22.464	-0.336	-0.336	0.000	0.000	0.000	0.000
143	A	169	ILE	0	-0.020	0.002	19.056	-0.546	-0.546	0.000	0.000	0.000	0.000
144	A	170	ASP	-1	-0.863	-0.931	16.932	-17.858	-17.858	0.000	0.000	0.000	0.000
145	A	171	ILE	0	0.016	0.002	15.951	-1.318	-1.318	0.000	0.000	0.000	0.000
146	A	172	THR	0	-0.018	-0.014	16.847	-0.570	-0.570	0.000	0.000	0.000	0.000
147	A	173	LEU	0	-0.014	-0.013	13.167	-0.771	-0.771	0.000	0.000	0.000	0.000
148	A	174	GLN	0	-0.014	0.000	12.085	-1.039	-1.039	0.000	0.000	0.000	0.000
149	A	175	TRP	0	0.012	0.005	12.152	-2.246	-2.246	0.000	0.000	0.000	0.000
150	A	176	LEU	0	-0.014	-0.005	13.444	-0.622	-0.622	0.000	0.000	0.000	0.000
151	A	177	ILE	0	0.028	0.007	7.262	-1.359	-1.359	0.000	0.000	0.000	0.000
152	A	178	GLN	0	-0.040	-0.020	8.372	-3.208	-3.208	0.000	0.000	0.000	0.000
153	A	179	HIS	1	0.766	0.857	10.183	23.008	23.008	0.000	0.000	0.000	0.000
154	A	180	SER	0	-0.028	-0.042	5.374	4.898	4.898	0.000	0.000	0.000	0.000
155	A	181	LYS	0	-0.003	0.026	7.543	-13.172	-13.172	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:16:SER)