FMO DATABASE

FMODB ID: 6439Z

Calculation Name: 1O3Y-A-Xray547

Preferred Name: ADP-ribosylation factor 1

Target Type: SINGLE PROTEIN

Ligand Name: guanosine-5'-triphosphate

Ligand 3-letter code: GTP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1O3Y

Chain ID: A

ChEMBL ID: CHEMBL1075273

UniProt ID: P84078

Base Structure: X-ray

Registration Date: 2025-10-05

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	166
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1775236.293552
FMO2-HF: Nuclear repulsion	1708729.823103
FMO2-HF: Total energy	-66506.470449
FMO2-MP2: Total energy	-66700.106798

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:GLY)

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

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.
-67.856	-66.935	-0.004	-0.377	-0.54	-0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.831 / q_NPA : 0.901

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

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	MET	0	0.009	0.020	3.833	-0.356	0.565	-0.004	-0.377	-0.540	-0.001
4	A	19	ARG	1	0.865	0.935	6.672	28.261	28.261	0.000	0.000	0.000	0.000
5	A	20	ILE	0	-0.002	0.001	8.193	2.389	2.389	0.000	0.000	0.000	0.000
6	A	21	LEU	0	0.008	0.011	11.864	0.184	0.184	0.000	0.000	0.000	0.000
7	A	22	MET	0	-0.047	-0.012	14.957	0.728	0.728	0.000	0.000	0.000	0.000
8	A	23	VAL	0	0.011	-0.007	18.017	0.412	0.412	0.000	0.000	0.000	0.000
9	A	24	GLY	0	0.080	0.046	21.236	0.119	0.119	0.000	0.000	0.000	0.000
10	A	25	LEU	0	0.010	0.012	24.938	-0.234	-0.234	0.000	0.000	0.000	0.000
11	A	26	ASP	-1	-0.855	-0.922	27.179	-10.418	-10.418	0.000	0.000	0.000	0.000
12	A	27	ALA	0	0.043	0.007	29.151	0.169	0.169	0.000	0.000	0.000	0.000
13	A	28	ALA	0	0.005	0.015	26.913	0.104	0.104	0.000	0.000	0.000	0.000
14	A	29	GLY	0	0.035	0.014	26.843	-0.083	-0.083	0.000	0.000	0.000	0.000
15	A	30	LYS	1	0.825	0.929	21.703	12.870	12.870	0.000	0.000	0.000	0.000
16	A	31	THR	0	0.007	-0.031	21.550	-0.270	-0.270	0.000	0.000	0.000	0.000
17	A	32	THR	0	-0.009	-0.006	22.208	-0.242	-0.242	0.000	0.000	0.000	0.000
18	A	33	ILE	0	0.027	0.015	20.085	-0.152	-0.152	0.000	0.000	0.000	0.000
19	A	34	LEU	0	-0.039	-0.008	15.302	-0.434	-0.434	0.000	0.000	0.000	0.000
20	A	35	TYR	0	0.028	-0.003	18.348	-0.447	-0.447	0.000	0.000	0.000	0.000
21	A	36	LYS	1	0.902	0.982	20.562	12.209	12.209	0.000	0.000	0.000	0.000
22	A	37	LEU	0	-0.040	-0.033	17.392	-0.087	-0.087	0.000	0.000	0.000	0.000
23	A	38	LYS	1	0.811	0.913	12.981	21.278	21.278	0.000	0.000	0.000	0.000
24	A	39	LEU	0	-0.031	-0.022	17.452	-0.278	-0.278	0.000	0.000	0.000	0.000
25	A	40	GLY	0	0.005	0.026	20.666	0.494	0.494	0.000	0.000	0.000	0.000
26	A	41	GLU	-1	-0.905	-0.957	23.237	-10.833	-10.833	0.000	0.000	0.000	0.000
27	A	42	ILE	0	-0.068	-0.028	24.867	-0.338	-0.338	0.000	0.000	0.000	0.000
28	A	43	VAL	0	-0.003	0.007	23.886	0.336	0.336	0.000	0.000	0.000	0.000
29	A	44	THR	0	-0.001	-0.005	26.933	0.277	0.277	0.000	0.000	0.000	0.000
30	A	45	THR	0	-0.036	-0.021	25.903	-0.198	-0.198	0.000	0.000	0.000	0.000
31	A	46	ILE	0	0.024	0.014	27.825	0.453	0.453	0.000	0.000	0.000	0.000
32	A	47	PRO	0	-0.008	-0.020	27.696	-0.394	-0.394	0.000	0.000	0.000	0.000
33	A	48	THR	0	0.005	0.014	22.065	0.257	0.257	0.000	0.000	0.000	0.000
34	A	49	ILE	0	0.011	0.003	25.518	0.023	0.023	0.000	0.000	0.000	0.000
35	A	50	GLY	0	0.020	0.010	22.645	0.112	0.112	0.000	0.000	0.000	0.000
36	A	51	PHE	0	-0.044	-0.035	14.930	-0.030	-0.030	0.000	0.000	0.000	0.000
37	A	52	ASN	0	-0.018	-0.005	18.306	0.403	0.403	0.000	0.000	0.000	0.000
38	A	53	VAL	0	-0.018	-0.022	11.732	-0.523	-0.523	0.000	0.000	0.000	0.000
39	A	54	GLU	-1	-0.815	-0.916	13.139	-19.552	-19.552	0.000	0.000	0.000	0.000
40	A	55	THR	0	-0.028	0.002	7.452	-3.007	-3.007	0.000	0.000	0.000	0.000
41	A	56	VAL	0	0.010	0.016	10.440	1.529	1.529	0.000	0.000	0.000	0.000
42	A	57	GLU	-1	-0.903	-0.949	10.162	-31.045	-31.045	0.000	0.000	0.000	0.000
43	A	58	TYR	0	-0.005	-0.017	12.403	2.464	2.464	0.000	0.000	0.000	0.000
44	A	59	LYS	1	0.899	0.959	13.669	15.098	15.098	0.000	0.000	0.000	0.000
45	A	60	ASN	0	0.030	0.017	11.464	0.201	0.201	0.000	0.000	0.000	0.000
46	A	61	ILE	0	0.021	0.031	8.648	-2.569	-2.569	0.000	0.000	0.000	0.000
47	A	62	SER	0	0.011	0.003	6.733	2.858	2.858	0.000	0.000	0.000	0.000
48	A	63	PHE	0	-0.011	-0.006	6.993	-6.104	-6.104	0.000	0.000	0.000	0.000
49	A	64	THR	0	-0.027	-0.010	6.926	-0.845	-0.845	0.000	0.000	0.000	0.000
50	A	65	VAL	0	-0.002	0.003	8.898	0.252	0.252	0.000	0.000	0.000	0.000
51	A	66	TRP	0	0.009	-0.006	9.657	1.452	1.452	0.000	0.000	0.000	0.000
52	A	67	ASP	-1	-0.758	-0.845	14.646	-13.953	-13.953	0.000	0.000	0.000	0.000
53	A	68	VAL	0	0.020	0.007	17.771	0.295	0.295	0.000	0.000	0.000	0.000
54	A	69	GLY	0	0.037	0.007	20.327	0.461	0.461	0.000	0.000	0.000	0.000
55	A	70	GLY	0	-0.029	-0.015	24.059	0.013	0.013	0.000	0.000	0.000	0.000
56	A	71	LEU	0	0.003	0.004	26.265	0.306	0.306	0.000	0.000	0.000	0.000
57	A	72	ASP	-1	-0.845	-0.926	28.766	-9.758	-9.758	0.000	0.000	0.000	0.000
58	A	73	LYS	1	0.951	0.970	29.887	8.873	8.873	0.000	0.000	0.000	0.000
59	A	74	ILE	0	-0.055	-0.017	25.648	0.031	0.031	0.000	0.000	0.000	0.000
60	A	75	ARG	1	0.834	0.913	25.273	9.821	9.821	0.000	0.000	0.000	0.000
61	A	76	PRO	0	0.001	-0.003	24.931	-0.450	-0.450	0.000	0.000	0.000	0.000
62	A	77	LEU	0	-0.041	-0.020	22.759	-0.238	-0.238	0.000	0.000	0.000	0.000
63	A	78	TRP	0	0.019	-0.011	20.581	-0.765	-0.765	0.000	0.000	0.000	0.000
64	A	79	ARG	1	0.982	0.983	19.271	11.621	11.621	0.000	0.000	0.000	0.000
65	A	80	HIS	0	-0.041	-0.015	18.767	-0.686	-0.686	0.000	0.000	0.000	0.000
66	A	81	TYR	0	-0.064	-0.024	15.056	-0.783	-0.783	0.000	0.000	0.000	0.000
67	A	82	PHE	0	0.041	0.022	14.542	-1.226	-1.226	0.000	0.000	0.000	0.000
68	A	83	GLN	0	-0.011	-0.007	12.963	0.176	0.176	0.000	0.000	0.000	0.000
69	A	84	ASN	0	-0.037	-0.025	9.142	-0.291	-0.291	0.000	0.000	0.000	0.000
70	A	85	THR	0	-0.060	-0.025	9.573	-3.624	-3.624	0.000	0.000	0.000	0.000
71	A	86	GLN	0	0.047	0.024	7.088	-1.705	-1.705	0.000	0.000	0.000	0.000
72	A	87	GLY	0	0.030	0.015	11.458	1.317	1.317	0.000	0.000	0.000	0.000
73	A	88	LEU	0	-0.008	-0.005	13.930	-0.382	-0.382	0.000	0.000	0.000	0.000
74	A	89	ILE	0	0.013	0.002	16.121	0.491	0.491	0.000	0.000	0.000	0.000
75	A	90	PHE	0	0.007	0.001	18.782	0.184	0.184	0.000	0.000	0.000	0.000
76	A	91	VAL	0	-0.024	-0.013	22.128	0.313	0.313	0.000	0.000	0.000	0.000
77	A	92	VAL	0	-0.007	-0.014	24.617	0.230	0.230	0.000	0.000	0.000	0.000
78	A	93	ASP	-1	-0.802	-0.896	28.385	-9.617	-9.617	0.000	0.000	0.000	0.000
79	A	94	SER	0	0.027	-0.009	31.301	0.145	0.145	0.000	0.000	0.000	0.000
80	A	95	ASN	0	0.001	0.002	33.428	0.399	0.399	0.000	0.000	0.000	0.000
81	A	96	ASP	-1	-0.837	-0.894	34.197	-8.690	-8.690	0.000	0.000	0.000	0.000
82	A	97	ARG	1	0.860	0.882	35.845	7.803	7.803	0.000	0.000	0.000	0.000
83	A	98	GLU	-1	-0.942	-0.961	38.301	-7.569	-7.569	0.000	0.000	0.000	0.000
84	A	99	ARG	1	0.781	0.870	32.514	9.388	9.388	0.000	0.000	0.000	0.000
85	A	100	VAL	0	0.008	0.003	32.724	-0.318	-0.318	0.000	0.000	0.000	0.000
86	A	101	ASN	0	0.009	-0.003	33.201	-0.155	-0.155	0.000	0.000	0.000	0.000
87	A	102	GLU	-1	-0.734	-0.851	32.074	-9.562	-9.562	0.000	0.000	0.000	0.000
88	A	103	ALA	0	-0.026	-0.022	29.400	-0.339	-0.339	0.000	0.000	0.000	0.000
89	A	104	ARG	1	0.909	0.959	28.842	8.915	8.915	0.000	0.000	0.000	0.000
90	A	105	GLU	-1	-0.969	-0.978	29.907	-9.165	-9.165	0.000	0.000	0.000	0.000
91	A	106	GLU	-1	-0.816	-0.906	27.015	-10.897	-10.897	0.000	0.000	0.000	0.000
92	A	107	LEU	0	-0.036	-0.004	23.992	-0.499	-0.499	0.000	0.000	0.000	0.000
93	A	108	MET	0	-0.030	-0.022	25.380	-0.472	-0.472	0.000	0.000	0.000	0.000
94	A	109	ARG	1	0.854	0.924	27.100	10.218	10.218	0.000	0.000	0.000	0.000
95	A	110	MET	0	-0.026	0.004	20.571	-0.454	-0.454	0.000	0.000	0.000	0.000
96	A	111	LEU	0	-0.042	-0.040	21.774	-0.471	-0.471	0.000	0.000	0.000	0.000
97	A	112	ALA	0	-0.025	-0.008	23.698	-0.081	-0.081	0.000	0.000	0.000	0.000
98	A	113	GLU	-1	-0.921	-0.948	21.423	-12.907	-12.907	0.000	0.000	0.000	0.000
99	A	114	ASP	-1	-0.872	-0.941	21.434	-13.102	-13.102	0.000	0.000	0.000	0.000
100	A	115	GLU	-1	-0.888	-0.934	14.626	-19.924	-19.924	0.000	0.000	0.000	0.000
101	A	116	LEU	0	-0.010	-0.006	15.986	-1.117	-1.117	0.000	0.000	0.000	0.000
102	A	117	ARG	1	0.878	0.945	18.227	15.904	15.904	0.000	0.000	0.000	0.000
103	A	118	ASP	-1	-0.888	-0.949	16.100	-16.628	-16.628	0.000	0.000	0.000	0.000
104	A	119	ALA	0	-0.060	-0.005	15.151	-0.655	-0.655	0.000	0.000	0.000	0.000
105	A	120	VAL	0	-0.025	-0.004	14.727	1.352	1.352	0.000	0.000	0.000	0.000
106	A	121	LEU	0	-0.016	-0.014	17.030	-0.476	-0.476	0.000	0.000	0.000	0.000
107	A	122	LEU	0	-0.020	-0.001	18.637	0.505	0.505	0.000	0.000	0.000	0.000
108	A	123	VAL	0	0.010	-0.004	20.551	-0.053	-0.053	0.000	0.000	0.000	0.000
109	A	124	PHE	0	0.021	-0.001	20.096	0.086	0.086	0.000	0.000	0.000	0.000
110	A	125	ALA	0	0.020	0.013	24.887	0.218	0.218	0.000	0.000	0.000	0.000
111	A	126	ASN	0	0.032	0.008	26.905	0.198	0.198	0.000	0.000	0.000	0.000
112	A	127	LYS	1	0.807	0.900	28.937	10.248	10.248	0.000	0.000	0.000	0.000
113	A	128	GLN	0	-0.054	-0.047	31.512	0.496	0.496	0.000	0.000	0.000	0.000
114	A	129	ASP	-1	-0.875	-0.936	33.411	-9.340	-9.340	0.000	0.000	0.000	0.000
115	A	130	LEU	0	-0.026	-0.009	35.577	0.313	0.313	0.000	0.000	0.000	0.000
116	A	131	PRO	0	-0.002	-0.010	37.850	-0.031	-0.031	0.000	0.000	0.000	0.000
117	A	132	ASN	0	-0.049	-0.022	40.408	0.231	0.231	0.000	0.000	0.000	0.000
118	A	133	ALA	0	-0.032	-0.003	35.405	-0.029	-0.029	0.000	0.000	0.000	0.000
119	A	134	MET	0	-0.042	0.000	35.118	0.122	0.122	0.000	0.000	0.000	0.000
120	A	135	ASN	0	0.065	0.037	34.599	-0.431	-0.431	0.000	0.000	0.000	0.000
121	A	136	ALA	0	0.072	0.014	30.710	-0.030	-0.030	0.000	0.000	0.000	0.000
122	A	137	ALA	0	-0.015	0.024	32.245	-0.174	-0.174	0.000	0.000	0.000	0.000
123	A	138	GLU	-1	-0.752	-0.863	34.788	-8.156	-8.156	0.000	0.000	0.000	0.000
124	A	139	ILE	0	0.001	-0.011	30.027	-0.008	-0.008	0.000	0.000	0.000	0.000
125	A	140	THR	0	-0.014	-0.029	30.839	-0.302	-0.302	0.000	0.000	0.000	0.000
126	A	141	ASP	-1	-0.932	-0.957	32.077	-8.842	-8.842	0.000	0.000	0.000	0.000
127	A	142	LYS	1	0.829	0.911	34.686	8.427	8.427	0.000	0.000	0.000	0.000
128	A	143	LEU	0	0.022	0.012	27.987	-0.014	-0.014	0.000	0.000	0.000	0.000
129	A	144	GLY	0	0.009	0.011	31.446	-0.077	-0.077	0.000	0.000	0.000	0.000
130	A	145	LEU	0	-0.005	0.008	26.937	-0.037	-0.037	0.000	0.000	0.000	0.000
131	A	146	HIS	0	0.051	0.014	29.515	-0.348	-0.348	0.000	0.000	0.000	0.000
132	A	147	SER	0	-0.108	-0.053	31.945	0.151	0.151	0.000	0.000	0.000	0.000
133	A	148	LEU	0	-0.030	-0.007	25.510	-0.009	-0.009	0.000	0.000	0.000	0.000
134	A	149	ARG	1	0.956	0.969	28.502	9.497	9.497	0.000	0.000	0.000	0.000
135	A	150	HIS	0	-0.026	-0.026	24.911	-0.294	-0.294	0.000	0.000	0.000	0.000
136	A	151	ARG	1	0.891	0.954	19.468	14.307	14.307	0.000	0.000	0.000	0.000
137	A	152	ASN	0	0.038	0.023	19.231	0.882	0.882	0.000	0.000	0.000	0.000
138	A	153	TRP	0	0.011	-0.009	20.746	-0.564	-0.564	0.000	0.000	0.000	0.000
139	A	154	TYR	0	0.007	0.011	22.295	0.377	0.377	0.000	0.000	0.000	0.000
140	A	155	ILE	0	-0.024	-0.006	23.851	-0.258	-0.258	0.000	0.000	0.000	0.000
141	A	156	GLN	0	-0.035	-0.015	24.164	0.060	0.060	0.000	0.000	0.000	0.000
142	A	157	ALA	0	0.023	0.011	26.452	0.003	0.003	0.000	0.000	0.000	0.000
143	A	158	THR	0	0.009	-0.004	24.772	-0.326	-0.326	0.000	0.000	0.000	0.000
144	A	159	CYS	0	-0.012	0.022	28.214	0.356	0.356	0.000	0.000	0.000	0.000
145	A	160	ALA	0	-0.007	-0.012	26.065	-0.206	-0.206	0.000	0.000	0.000	0.000
146	A	161	THR	0	0.011	-0.006	26.892	-0.286	-0.286	0.000	0.000	0.000	0.000
147	A	162	SER	0	0.005	-0.039	29.657	-0.048	-0.048	0.000	0.000	0.000	0.000
148	A	163	GLY	0	-0.017	-0.021	26.257	-0.191	-0.191	0.000	0.000	0.000	0.000
149	A	164	ASP	-1	-0.858	-0.889	26.027	-10.877	-10.877	0.000	0.000	0.000	0.000
150	A	165	GLY	0	0.030	0.004	26.393	-0.023	-0.023	0.000	0.000	0.000	0.000
151	A	166	LEU	0	-0.029	-0.017	21.922	-0.525	-0.525	0.000	0.000	0.000	0.000
152	A	167	TYR	0	-0.017	-0.010	20.614	-0.940	-0.940	0.000	0.000	0.000	0.000
153	A	168	GLU	-1	-0.837	-0.923	20.863	-13.253	-13.253	0.000	0.000	0.000	0.000
154	A	169	GLY	0	-0.002	-0.007	21.414	-0.219	-0.219	0.000	0.000	0.000	0.000
155	A	170	LEU	0	0.003	-0.006	15.395	-0.752	-0.752	0.000	0.000	0.000	0.000
156	A	171	ASP	-1	-0.854	-0.921	16.965	-16.977	-16.977	0.000	0.000	0.000	0.000
157	A	172	TRP	0	0.034	0.028	18.313	-1.043	-1.043	0.000	0.000	0.000	0.000
158	A	173	LEU	0	-0.003	-0.007	14.122	-0.488	-0.488	0.000	0.000	0.000	0.000
159	A	174	SER	0	-0.062	-0.039	13.651	-1.484	-1.484	0.000	0.000	0.000	0.000
160	A	175	ASN	0	-0.054	-0.049	14.048	-1.704	-1.704	0.000	0.000	0.000	0.000
161	A	176	GLN	0	-0.027	-0.005	16.139	-0.255	-0.255	0.000	0.000	0.000	0.000
162	A	177	LEU	0	-0.034	-0.011	10.701	-0.771	-0.771	0.000	0.000	0.000	0.000
163	A	178	ARG	1	0.735	0.871	10.505	19.821	19.821	0.000	0.000	0.000	0.000
164	A	179	ASN	0	0.018	0.001	10.696	2.937	2.937	0.000	0.000	0.000	0.000
165	A	180	GLN	0	-0.052	-0.018	10.721	1.704	1.704	0.000	0.000	0.000	0.000
166	A	181	LYS	0	0.149	0.089	13.666	-7.220	-7.220	0.000	0.000	0.000	0.000

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