FMO DATABASE

FMODB ID: 9L3L2

Calculation Name: 1Z0F-A-Xray547

Preferred Name:

Target Type:

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

Ligand 3-letter code: GDP | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1Z0F

Chain ID: A

ChEMBL ID:

UniProt ID: P61106

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	167
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1741348.116258
FMO2-HF: Nuclear repulsion	1675138.800526
FMO2-HF: Total energy	-66209.315732
FMO2-MP2: Total energy	-66403.133704

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:7:ASN)

Summations of interaction energy for fragment #1(A:7:ASN)

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.
-57.615	-53.558	0.055	-1.577	-2.534	-0.007

Interaction energy analysis for fragmet #1(A:7:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.833 / q_NPA : 0.897

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	9	SER	-1	-0.781	-0.853	3.827	-45.012	-42.097	-0.005	-1.212	-1.698	-0.005
46	A	52	ILE	0	-0.069	-0.024	3.179	-2.436	-2.031	0.021	-0.155	-0.271	-0.001
53	A	59	LYS	1	0.880	0.936	3.065	52.536	53.273	0.039	-0.210	-0.565	-0.001
4	A	10	TYR	-1	-0.910	-0.948	5.549	-20.959	-20.959	0.000	0.000	0.000	0.000
5	A	11	ILE	0	-0.104	-0.064	8.554	-3.365	-3.365	0.000	0.000	0.000	0.000
6	A	12	PHE	0	0.033	0.026	10.804	1.872	1.872	0.000	0.000	0.000	0.000
7	A	13	LYS	1	0.891	0.961	13.833	16.701	16.701	0.000	0.000	0.000	0.000
8	A	14	TYR	0	0.033	0.009	16.006	0.609	0.609	0.000	0.000	0.000	0.000
9	A	15	ILE	0	-0.026	0.006	18.571	-0.223	-0.223	0.000	0.000	0.000	0.000
10	A	16	ILE	0	-0.040	-0.004	21.809	-0.011	-0.011	0.000	0.000	0.000	0.000
11	A	17	ILE	0	-0.002	-0.001	23.616	0.248	0.248	0.000	0.000	0.000	0.000
12	A	18	GLY	0	0.098	0.047	27.401	-0.057	-0.057	0.000	0.000	0.000	0.000
13	A	19	ASP	-1	-0.785	-0.864	30.733	-8.953	-8.953	0.000	0.000	0.000	0.000
14	A	20	MET	0	-0.009	-0.016	31.836	-0.285	-0.285	0.000	0.000	0.000	0.000
15	A	21	GLY	0	0.039	0.014	32.404	0.201	0.201	0.000	0.000	0.000	0.000
16	A	22	VAL	0	-0.015	0.002	29.309	0.038	0.038	0.000	0.000	0.000	0.000
17	A	23	GLY	0	0.033	0.023	28.460	-0.142	-0.142	0.000	0.000	0.000	0.000
18	A	24	LYS	1	0.855	0.935	25.241	10.593	10.593	0.000	0.000	0.000	0.000
19	A	25	SER	0	0.049	0.006	23.098	-0.382	-0.382	0.000	0.000	0.000	0.000
20	A	26	CYS	0	-0.058	-0.018	22.601	-0.336	-0.336	0.000	0.000	0.000	0.000
21	A	27	LEU	0	0.037	0.027	22.599	-0.373	-0.373	0.000	0.000	0.000	0.000
22	A	28	LEU	0	-0.002	0.009	17.003	-0.734	-0.734	0.000	0.000	0.000	0.000
23	A	29	HIS	0	-0.060	-0.031	18.079	-0.981	-0.981	0.000	0.000	0.000	0.000
24	A	30	GLN	0	-0.038	-0.013	18.842	-1.187	-1.187	0.000	0.000	0.000	0.000
25	A	31	PHE	0	0.014	0.006	13.671	-0.845	-0.845	0.000	0.000	0.000	0.000
26	A	32	THR	0	-0.084	-0.066	13.665	-1.410	-1.410	0.000	0.000	0.000	0.000
27	A	33	GLU	-1	-0.853	-0.921	14.169	-16.736	-16.736	0.000	0.000	0.000	0.000
28	A	34	LYS	1	0.919	0.974	16.606	17.179	17.179	0.000	0.000	0.000	0.000
29	A	35	LYS	1	0.875	0.938	18.454	13.082	13.082	0.000	0.000	0.000	0.000
30	A	36	PHE	0	0.013	0.018	21.879	-0.021	-0.021	0.000	0.000	0.000	0.000
31	A	37	MET	0	-0.015	-0.017	22.552	0.467	0.467	0.000	0.000	0.000	0.000
32	A	38	ALA	0	0.001	0.009	26.103	0.146	0.146	0.000	0.000	0.000	0.000
33	A	39	ASP	-1	-0.830	-0.919	28.562	-10.555	-10.555	0.000	0.000	0.000	0.000
34	A	40	CYS	0	-0.074	-0.043	27.554	0.047	0.047	0.000	0.000	0.000	0.000
35	A	41	PRO	0	0.002	0.007	29.558	-0.194	-0.194	0.000	0.000	0.000	0.000
36	A	42	HIS	0	0.004	0.004	30.496	0.269	0.269	0.000	0.000	0.000	0.000
37	A	43	THR	0	-0.052	-0.026	27.480	-0.134	-0.134	0.000	0.000	0.000	0.000
38	A	44	ILE	0	0.004	-0.007	28.070	0.081	0.081	0.000	0.000	0.000	0.000
39	A	45	GLY	0	0.026	0.031	25.755	0.115	0.115	0.000	0.000	0.000	0.000
40	A	46	VAL	0	-0.027	-0.014	19.119	0.131	0.131	0.000	0.000	0.000	0.000
41	A	47	GLU	-1	-0.790	-0.876	22.199	-12.960	-12.960	0.000	0.000	0.000	0.000
42	A	48	PHE	0	-0.034	-0.035	14.320	-0.409	-0.409	0.000	0.000	0.000	0.000
43	A	49	GLY	0	0.042	0.022	15.051	0.124	0.124	0.000	0.000	0.000	0.000
44	A	50	THR	0	-0.081	-0.045	10.032	-0.633	-0.633	0.000	0.000	0.000	0.000
45	A	51	ARG	1	0.807	0.878	9.458	23.154	23.154	0.000	0.000	0.000	0.000
47	A	53	ILE	0	0.014	0.012	7.521	1.900	1.900	0.000	0.000	0.000	0.000
48	A	54	GLU	-1	-0.906	-0.959	7.450	-42.281	-42.281	0.000	0.000	0.000	0.000
49	A	55	VAL	0	0.036	0.017	10.226	2.635	2.635	0.000	0.000	0.000	0.000
50	A	56	SER	0	0.002	-0.003	12.244	-0.137	-0.137	0.000	0.000	0.000	0.000
51	A	57	GLY	0	-0.015	0.004	11.233	0.760	0.760	0.000	0.000	0.000	0.000
52	A	58	GLN	0	0.027	0.020	8.104	-2.102	-2.102	0.000	0.000	0.000	0.000
54	A	60	ILE	0	0.047	0.032	7.160	-2.511	-2.511	0.000	0.000	0.000	0.000
55	A	61	LYS	1	0.889	0.949	6.445	33.189	33.189	0.000	0.000	0.000	0.000
56	A	62	LEU	0	0.042	0.029	8.300	2.906	2.906	0.000	0.000	0.000	0.000
57	A	63	GLN	0	-0.042	-0.042	11.247	-0.425	-0.425	0.000	0.000	0.000	0.000
58	A	64	ILE	0	0.032	0.021	13.638	0.872	0.872	0.000	0.000	0.000	0.000
59	A	65	TRP	0	-0.049	-0.038	16.911	-0.023	-0.023	0.000	0.000	0.000	0.000
60	A	66	ASP	-1	-0.808	-0.906	20.184	-11.771	-11.771	0.000	0.000	0.000	0.000
61	A	67	THR	0	-0.022	-0.012	23.477	0.392	0.392	0.000	0.000	0.000	0.000
62	A	68	ALA	0	0.035	0.012	25.015	0.351	0.351	0.000	0.000	0.000	0.000
63	A	69	GLY	0	0.054	0.039	28.629	0.384	0.384	0.000	0.000	0.000	0.000
64	A	70	GLN	0	-0.059	-0.051	25.528	0.230	0.230	0.000	0.000	0.000	0.000
65	A	71	GLU	0	0.027	0.014	27.535	0.206	0.206	0.000	0.000	0.000	0.000
66	A	72	ARG	1	0.988	0.997	28.827	8.577	8.577	0.000	0.000	0.000	0.000
67	A	73	PHE	0	-0.037	-0.004	31.558	0.205	0.205	0.000	0.000	0.000	0.000
68	A	74	ARG	1	0.983	0.986	22.373	12.915	12.915	0.000	0.000	0.000	0.000
69	A	75	ALA	0	0.044	0.008	27.775	-0.259	-0.259	0.000	0.000	0.000	0.000
70	A	76	VAL	0	0.005	-0.003	21.928	-0.137	-0.137	0.000	0.000	0.000	0.000
71	A	77	THR	0	0.014	0.012	23.128	-0.392	-0.392	0.000	0.000	0.000	0.000
72	A	78	ARG	1	0.866	0.929	24.521	9.814	9.814	0.000	0.000	0.000	0.000
73	A	79	SER	0	-0.006	0.002	23.542	-0.060	-0.060	0.000	0.000	0.000	0.000
74	A	80	TYR	0	-0.081	-0.061	16.648	-0.745	-0.745	0.000	0.000	0.000	0.000
75	A	81	TYR	-1	-0.841	-0.938	21.272	-12.126	-12.126	0.000	0.000	0.000	0.000
76	A	82	ARG	1	0.828	0.910	23.881	10.611	10.611	0.000	0.000	0.000	0.000
77	A	83	GLY	0	-0.023	0.003	20.694	0.088	0.088	0.000	0.000	0.000	0.000
78	A	84	ALA	0	0.003	0.003	19.550	-0.944	-0.944	0.000	0.000	0.000	0.000
79	A	85	ALA	0	-0.008	0.014	17.720	0.499	0.499	0.000	0.000	0.000	0.000
80	A	86	GLY	0	0.055	0.033	19.528	0.403	0.403	0.000	0.000	0.000	0.000
81	A	87	ALA	0	-0.017	-0.031	20.743	-0.008	-0.008	0.000	0.000	0.000	0.000
82	A	88	LEU	0	0.002	0.011	20.696	0.359	0.359	0.000	0.000	0.000	0.000
83	A	89	MET	0	-0.011	0.002	24.183	0.224	0.224	0.000	0.000	0.000	0.000
84	A	90	VAL	0	-0.031	-0.020	26.193	0.139	0.139	0.000	0.000	0.000	0.000
85	A	91	TYR	0	0.027	0.012	29.087	0.329	0.329	0.000	0.000	0.000	0.000
86	A	92	ASP	-1	-0.767	-0.858	31.834	-9.435	-9.435	0.000	0.000	0.000	0.000
87	A	93	ILE	0	0.028	0.021	32.787	0.288	0.288	0.000	0.000	0.000	0.000
88	A	94	THR	0	-0.035	-0.029	36.033	0.284	0.284	0.000	0.000	0.000	0.000
89	A	95	ARG	1	0.822	0.898	34.936	8.973	8.973	0.000	0.000	0.000	0.000
90	A	96	ARG	1	0.852	0.905	38.474	7.322	7.322	0.000	0.000	0.000	0.000
91	A	97	SER	0	-0.029	-0.017	39.500	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	98	THR	0	-0.051	-0.039	34.953	-0.168	-0.168	0.000	0.000	0.000	0.000
93	A	99	TYR	0	0.011	0.002	35.798	-0.181	-0.181	0.000	0.000	0.000	0.000
94	A	100	ASN	0	0.008	-0.008	37.524	-0.077	-0.077	0.000	0.000	0.000	0.000
95	A	101	HIS	0	-0.063	-0.045	36.933	0.272	0.272	0.000	0.000	0.000	0.000
96	A	102	LEU	0	-0.015	0.006	32.838	-0.203	-0.203	0.000	0.000	0.000	0.000
97	A	103	SER	0	0.038	0.021	34.954	-0.214	-0.214	0.000	0.000	0.000	0.000
98	A	104	SER	0	0.001	0.020	36.502	0.063	0.063	0.000	0.000	0.000	0.000
99	A	105	TRP	0	-0.011	-0.021	31.241	-0.282	-0.282	0.000	0.000	0.000	0.000
100	A	106	LEU	0	0.050	0.015	31.398	-0.357	-0.357	0.000	0.000	0.000	0.000
101	A	107	THR	0	-0.043	-0.024	32.783	-0.075	-0.075	0.000	0.000	0.000	0.000
102	A	108	ASP	-1	-0.926	-0.963	32.028	-9.347	-9.347	0.000	0.000	0.000	0.000
103	A	109	ALA	0	0.049	0.018	28.283	-0.174	-0.174	0.000	0.000	0.000	0.000
104	A	110	ARG	1	0.919	0.973	29.231	10.235	10.235	0.000	0.000	0.000	0.000
105	A	111	ASN	0	-0.036	-0.002	31.422	-0.040	-0.040	0.000	0.000	0.000	0.000
106	A	112	LEU	0	-0.043	-0.022	29.707	0.009	0.009	0.000	0.000	0.000	0.000
107	A	113	THR	0	-0.055	-0.027	25.389	-0.336	-0.336	0.000	0.000	0.000	0.000
108	A	114	ASN	0	-0.031	-0.030	22.727	0.391	0.391	0.000	0.000	0.000	0.000
109	A	115	PRO	0	-0.002	-0.017	26.902	-0.079	-0.079	0.000	0.000	0.000	0.000
110	A	116	ASN	0	0.005	0.015	22.466	0.553	0.553	0.000	0.000	0.000	0.000
111	A	117	THR	0	-0.047	-0.018	22.961	-0.250	-0.250	0.000	0.000	0.000	0.000
112	A	118	VAL	0	0.006	0.000	22.086	0.729	0.729	0.000	0.000	0.000	0.000
113	A	119	ILE	0	-0.043	-0.016	23.537	-0.359	-0.359	0.000	0.000	0.000	0.000
114	A	120	ILE	0	-0.025	-0.014	23.267	0.225	0.225	0.000	0.000	0.000	0.000
115	A	121	LEU	0	-0.012	0.010	26.517	-0.041	-0.041	0.000	0.000	0.000	0.000
116	A	122	ILE	0	-0.001	-0.018	24.755	-0.200	-0.200	0.000	0.000	0.000	0.000
117	A	123	GLY	0	0.065	0.033	28.471	0.264	0.264	0.000	0.000	0.000	0.000
118	A	124	ASN	0	-0.023	-0.035	27.910	-0.355	-0.355	0.000	0.000	0.000	0.000
119	A	125	LYS	1	0.800	0.873	30.144	9.910	9.910	0.000	0.000	0.000	0.000
120	A	126	ALA	0	0.081	0.042	31.227	0.332	0.332	0.000	0.000	0.000	0.000
121	A	127	ASP	-1	-0.836	-0.896	31.810	-9.847	-9.847	0.000	0.000	0.000	0.000
122	A	128	LEU	0	-0.075	-0.030	33.813	0.242	0.242	0.000	0.000	0.000	0.000
123	A	129	GLU	-1	-0.887	-0.942	36.789	-8.352	-8.352	0.000	0.000	0.000	0.000
124	A	130	ALA	0	-0.047	-0.031	38.665	0.152	0.152	0.000	0.000	0.000	0.000
125	A	131	GLN	0	-0.071	-0.044	39.895	0.058	0.058	0.000	0.000	0.000	0.000
126	A	132	ARG	1	0.773	0.852	35.858	8.658	8.658	0.000	0.000	0.000	0.000
127	A	133	ASP	-1	-0.831	-0.913	40.168	-7.335	-7.335	0.000	0.000	0.000	0.000
128	A	134	VAL	0	-0.072	-0.029	37.772	0.117	0.117	0.000	0.000	0.000	0.000
129	A	135	THR	0	-0.012	-0.022	39.184	-0.120	-0.120	0.000	0.000	0.000	0.000
130	A	136	TYR	0	0.069	0.036	32.818	-0.095	-0.095	0.000	0.000	0.000	0.000
131	A	137	GLU	-1	-0.874	-0.958	37.232	-8.254	-8.254	0.000	0.000	0.000	0.000
132	A	138	GLU	-1	-0.732	-0.812	39.659	-7.757	-7.757	0.000	0.000	0.000	0.000
133	A	139	ALA	0	-0.008	0.002	34.945	-0.058	-0.058	0.000	0.000	0.000	0.000
134	A	140	LYS	1	0.823	0.898	34.799	9.074	9.074	0.000	0.000	0.000	0.000
135	A	141	GLN	0	-0.038	-0.014	36.159	-0.053	-0.053	0.000	0.000	0.000	0.000
136	A	142	PHE	0	0.016	0.010	34.259	-0.073	-0.073	0.000	0.000	0.000	0.000
137	A	143	ALA	0	0.012	-0.001	32.340	-0.126	-0.126	0.000	0.000	0.000	0.000
138	A	144	GLU	-1	-0.823	-0.902	33.898	-9.458	-9.458	0.000	0.000	0.000	0.000
139	A	145	GLU	-1	-0.936	-0.959	35.770	-7.898	-7.898	0.000	0.000	0.000	0.000
140	A	146	ASN	0	-0.071	-0.041	34.083	0.049	0.049	0.000	0.000	0.000	0.000
141	A	147	GLY	0	-0.015	-0.002	32.496	-0.275	-0.275	0.000	0.000	0.000	0.000
142	A	148	LEU	0	-0.089	-0.045	29.423	-0.501	-0.501	0.000	0.000	0.000	0.000
143	A	149	LEU	0	-0.001	0.004	24.349	0.128	0.128	0.000	0.000	0.000	0.000
144	A	150	PHE	0	-0.001	-0.026	28.381	0.073	0.073	0.000	0.000	0.000	0.000
145	A	151	LEU	0	-0.010	0.014	24.628	-0.067	-0.067	0.000	0.000	0.000	0.000
146	A	152	GLU	-1	-0.768	-0.838	28.738	-9.185	-9.185	0.000	0.000	0.000	0.000
147	A	153	ALA	0	0.028	0.011	26.019	-0.306	-0.306	0.000	0.000	0.000	0.000
148	A	154	SER	0	-0.013	-0.035	27.137	0.324	0.324	0.000	0.000	0.000	0.000
149	A	155	ALA	0	-0.011	-0.015	24.820	-0.393	-0.393	0.000	0.000	0.000	0.000
150	A	156	LYS	1	0.919	0.970	25.221	9.363	9.363	0.000	0.000	0.000	0.000
151	A	157	THR	0	0.024	-0.007	26.960	-0.267	-0.267	0.000	0.000	0.000	0.000
152	A	158	GLY	0	0.019	0.016	23.333	-0.274	-0.274	0.000	0.000	0.000	0.000
153	A	159	GLU	-1	-0.943	-0.968	23.321	-11.239	-11.239	0.000	0.000	0.000	0.000
154	A	160	ASN	0	0.011	-0.013	24.021	-0.077	-0.077	0.000	0.000	0.000	0.000
155	A	161	VAL	0	-0.022	-0.009	20.255	-0.238	-0.238	0.000	0.000	0.000	0.000
156	A	162	GLU	-1	-0.832	-0.892	15.171	-21.277	-21.277	0.000	0.000	0.000	0.000
157	A	163	ASP	-1	-0.852	-0.938	18.475	-15.303	-15.303	0.000	0.000	0.000	0.000
158	A	164	ALA	0	-0.012	0.002	20.968	-0.078	-0.078	0.000	0.000	0.000	0.000
159	A	165	PHE	0	-0.021	-0.016	16.484	0.031	0.031	0.000	0.000	0.000	0.000
160	A	166	LEU	0	0.031	0.021	14.831	-0.562	-0.562	0.000	0.000	0.000	0.000
161	A	167	GLU	-1	-0.810	-0.905	17.563	-14.799	-14.799	0.000	0.000	0.000	0.000
162	A	168	ALA	0	-0.030	-0.009	19.880	0.317	0.317	0.000	0.000	0.000	0.000
163	A	169	ALA	0	-0.002	-0.008	15.324	0.023	0.023	0.000	0.000	0.000	0.000
164	A	170	LYS	1	0.843	0.897	17.444	14.755	14.755	0.000	0.000	0.000	0.000
165	A	171	LYS	1	0.884	0.958	18.872	12.701	12.701	0.000	0.000	0.000	0.000
166	A	172	ILE	0	-0.072	-0.036	17.547	0.588	0.588	0.000	0.000	0.000	0.000
167	A	173	TYR	-1	-0.945	-0.953	15.156	-20.001	-20.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:ASN)