FMO DATABASE

FMODB ID: 241VR

Calculation Name: 2GJS-A-Xray547

Preferred Name:

Target Type:

Ligand Name: guanosine-5'-diphosphate

Ligand 3-letter code: GDP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2GJS

Chain ID: A

ChEMBL ID:

UniProt ID: P55042

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	168
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1685818.624749
FMO2-HF: Nuclear repulsion	1620812.846686
FMO2-HF: Total energy	-65005.778063
FMO2-MP2: Total energy	-65194.811163

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:91:VAL)

Summations of interaction energy for fragment #1(A:91:VAL)

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.
-177.988	-172.288	7.256	-6.126	-6.83	-0.056

Interaction energy analysis for fragmet #1(A:91:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.796 / q_NPA : 0.891

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	93	LYS	1	0.934	0.980	3.821	33.309	35.217	-0.028	-0.753	-1.127	-0.001
38	A	128	ASP	-1	-0.860	-0.931	3.944	-48.029	-47.659	0.002	-0.106	-0.267	-0.001
48	A	138	ALA	0	-0.001	-0.005	3.809	-6.690	-6.501	0.000	-0.044	-0.144	0.000
49	A	139	SER	0	-0.009	-0.011	2.220	6.829	7.813	1.761	-0.862	-1.883	-0.007
50	A	140	LEU	0	-0.046	-0.011	2.142	-23.398	-21.439	5.519	-4.326	-3.153	-0.047
51	A	141	MET	0	0.067	0.050	3.814	3.573	3.863	0.002	-0.035	-0.256	0.000
4	A	94	VAL	0	0.028	0.016	5.824	2.374	2.374	0.000	0.000	0.000	0.000
5	A	95	LEU	0	-0.019	-0.002	9.138	0.863	0.863	0.000	0.000	0.000	0.000
6	A	96	LEU	0	-0.045	-0.012	12.324	0.623	0.623	0.000	0.000	0.000	0.000
7	A	97	LEU	0	0.014	0.005	15.390	0.638	0.638	0.000	0.000	0.000	0.000
8	A	98	GLY	0	0.078	0.025	18.621	0.011	0.011	0.000	0.000	0.000	0.000
9	A	99	ALA	0	-0.015	0.010	22.182	0.043	0.043	0.000	0.000	0.000	0.000
10	A	100	PRO	0	0.046	0.015	24.575	-0.294	-0.294	0.000	0.000	0.000	0.000
11	A	101	GLY	0	0.014	0.014	25.887	0.233	0.233	0.000	0.000	0.000	0.000
12	A	102	VAL	0	-0.018	0.003	22.659	0.181	0.181	0.000	0.000	0.000	0.000
13	A	103	GLY	0	-0.001	-0.001	23.080	-0.112	-0.112	0.000	0.000	0.000	0.000
14	A	104	LYS	1	0.826	0.908	18.168	13.603	13.603	0.000	0.000	0.000	0.000
15	A	105	SER	0	0.064	-0.008	17.922	-0.360	-0.360	0.000	0.000	0.000	0.000
16	A	106	ALA	0	-0.101	-0.033	18.490	-0.141	-0.141	0.000	0.000	0.000	0.000
17	A	107	LEU	0	0.011	0.003	17.295	-0.190	-0.190	0.000	0.000	0.000	0.000
18	A	108	ALA	0	0.018	0.013	14.076	-0.808	-0.808	0.000	0.000	0.000	0.000
19	A	109	ARG	1	0.947	0.985	14.165	13.038	13.038	0.000	0.000	0.000	0.000
20	A	110	ILE	0	-0.045	-0.010	16.351	-0.163	-0.163	0.000	0.000	0.000	0.000
21	A	111	PHE	0	-0.014	0.002	7.705	0.175	0.175	0.000	0.000	0.000	0.000
22	A	112	GLY	0	0.017	0.011	11.601	-0.794	-0.794	0.000	0.000	0.000	0.000
23	A	113	GLY	0	-0.055	-0.033	12.638	-0.256	-0.256	0.000	0.000	0.000	0.000
24	A	114	VAL	0	-0.047	-0.029	15.898	0.968	0.968	0.000	0.000	0.000	0.000
25	A	115	GLU	-1	-0.910	-0.961	17.540	-13.830	-13.830	0.000	0.000	0.000	0.000
26	A	116	ASP	-1	-0.794	-0.874	14.319	-18.087	-18.087	0.000	0.000	0.000	0.000
27	A	117	GLY	0	-0.008	-0.010	15.521	1.130	1.130	0.000	0.000	0.000	0.000
28	A	118	PRO	0	-0.052	0.009	15.175	-0.953	-0.953	0.000	0.000	0.000	0.000
29	A	119	GLU	-1	-0.850	-0.925	14.512	-15.474	-15.474	0.000	0.000	0.000	0.000
30	A	120	ALA	0	-0.041	-0.023	16.461	0.259	0.259	0.000	0.000	0.000	0.000
31	A	121	GLU	-1	-0.909	-0.956	19.504	-11.985	-11.985	0.000	0.000	0.000	0.000
32	A	122	ALA	0	-0.002	0.004	19.813	-0.519	-0.519	0.000	0.000	0.000	0.000
33	A	123	ALA	0	0.003	0.004	17.083	0.259	0.259	0.000	0.000	0.000	0.000
34	A	124	GLY	0	-0.016	-0.018	16.485	-0.918	-0.918	0.000	0.000	0.000	0.000
35	A	125	HIS	1	0.803	0.874	15.889	16.104	16.104	0.000	0.000	0.000	0.000
36	A	126	THR	0	-0.017	-0.005	10.923	-0.398	-0.398	0.000	0.000	0.000	0.000
37	A	127	TYR	0	-0.021	-0.021	10.075	0.562	0.562	0.000	0.000	0.000	0.000
39	A	129	ARG	1	0.866	0.935	6.164	25.877	25.877	0.000	0.000	0.000	0.000
40	A	130	SER	0	0.004	0.013	5.436	-2.792	-2.792	0.000	0.000	0.000	0.000
41	A	131	ILE	0	-0.008	-0.010	7.032	4.855	4.855	0.000	0.000	0.000	0.000
42	A	132	VAL	0	0.016	0.006	8.390	-3.065	-3.065	0.000	0.000	0.000	0.000
43	A	133	VAL	0	-0.007	0.003	9.323	2.068	2.068	0.000	0.000	0.000	0.000
44	A	134	ASP	-1	-0.808	-0.882	10.982	-22.508	-22.508	0.000	0.000	0.000	0.000
45	A	135	GLY	0	-0.020	-0.005	13.585	0.555	0.555	0.000	0.000	0.000	0.000
46	A	136	GLU	-1	-0.852	-0.909	7.095	-37.000	-37.000	0.000	0.000	0.000	0.000
47	A	137	GLU	-1	-0.960	-0.980	6.253	-33.630	-33.630	0.000	0.000	0.000	0.000
52	A	142	VAL	0	-0.022	-0.006	5.454	0.775	0.775	0.000	0.000	0.000	0.000
53	A	143	TYR	0	-0.005	-0.036	6.673	2.422	2.422	0.000	0.000	0.000	0.000
54	A	144	ASP	-1	-0.827	-0.914	11.301	-15.782	-15.782	0.000	0.000	0.000	0.000
55	A	145	ILE	0	0.070	0.018	13.550	0.781	0.781	0.000	0.000	0.000	0.000
56	A	146	TRP	0	0.002	0.013	16.378	1.073	1.073	0.000	0.000	0.000	0.000
57	A	147	GLU	-1	-0.806	-0.901	18.351	-12.125	-12.125	0.000	0.000	0.000	0.000
58	A	148	GLN	0	-0.006	-0.006	19.973	0.929	0.929	0.000	0.000	0.000	0.000
59	A	149	ASP	-1	-0.751	-0.876	18.684	-14.512	-14.512	0.000	0.000	0.000	0.000
60	A	150	GLY	0	0.001	0.010	20.733	0.340	0.340	0.000	0.000	0.000	0.000
61	A	151	GLY	0	-0.042	-0.025	22.971	0.526	0.526	0.000	0.000	0.000	0.000
62	A	152	ARG	1	0.698	0.823	19.777	13.788	13.788	0.000	0.000	0.000	0.000
63	A	153	TRP	0	-0.043	-0.017	24.926	0.025	0.025	0.000	0.000	0.000	0.000
64	A	154	LEU	0	0.039	0.022	20.110	0.041	0.041	0.000	0.000	0.000	0.000
65	A	155	PRO	0	0.012	0.006	19.930	-0.749	-0.749	0.000	0.000	0.000	0.000
66	A	156	GLY	0	0.003	-0.007	19.796	-0.523	-0.523	0.000	0.000	0.000	0.000
67	A	157	HIS	0	0.025	0.004	17.660	-0.513	-0.513	0.000	0.000	0.000	0.000
68	A	158	CYS	0	-0.056	-0.022	15.281	-1.004	-1.004	0.000	0.000	0.000	0.000
69	A	159	MET	0	-0.050	-0.023	14.921	-0.818	-0.818	0.000	0.000	0.000	0.000
70	A	160	ALA	0	0.025	0.023	15.908	0.036	0.036	0.000	0.000	0.000	0.000
71	A	161	MET	0	-0.076	-0.015	9.407	-0.449	-0.449	0.000	0.000	0.000	0.000
72	A	162	GLY	0	0.009	-0.007	9.221	-2.220	-2.220	0.000	0.000	0.000	0.000
73	A	163	ASP	-1	-0.798	-0.877	6.211	-45.713	-45.713	0.000	0.000	0.000	0.000
74	A	164	ALA	0	0.008	-0.009	9.425	1.178	1.178	0.000	0.000	0.000	0.000
75	A	165	TYR	0	-0.012	-0.035	11.753	-0.149	-0.149	0.000	0.000	0.000	0.000
76	A	166	VAL	0	0.004	-0.003	13.453	0.503	0.503	0.000	0.000	0.000	0.000
77	A	167	ILE	0	-0.013	0.007	16.180	0.402	0.402	0.000	0.000	0.000	0.000
78	A	168	VAL	0	-0.030	-0.020	18.849	0.408	0.408	0.000	0.000	0.000	0.000
79	A	169	TYR	0	0.038	0.008	21.538	0.346	0.346	0.000	0.000	0.000	0.000
80	A	170	SER	0	-0.010	-0.025	25.291	-0.348	-0.348	0.000	0.000	0.000	0.000
81	A	171	VAL	0	0.004	-0.001	27.780	0.321	0.321	0.000	0.000	0.000	0.000
82	A	172	THR	0	-0.056	-0.020	30.037	0.215	0.215	0.000	0.000	0.000	0.000
83	A	173	ASP	-1	-0.841	-0.909	30.537	-9.810	-9.810	0.000	0.000	0.000	0.000
84	A	174	LYS	1	0.864	0.914	31.164	8.602	8.602	0.000	0.000	0.000	0.000
85	A	175	GLY	0	0.087	0.058	32.240	-0.149	-0.149	0.000	0.000	0.000	0.000
86	A	176	SER	0	-0.091	-0.069	27.326	-0.453	-0.453	0.000	0.000	0.000	0.000
87	A	177	PHE	0	-0.003	-0.008	27.299	-0.461	-0.461	0.000	0.000	0.000	0.000
88	A	178	GLU	-1	-0.905	-0.957	28.753	-9.392	-9.392	0.000	0.000	0.000	0.000
89	A	179	LYS	1	0.920	0.962	25.942	10.991	10.991	0.000	0.000	0.000	0.000
90	A	180	ALA	0	0.011	-0.006	24.484	-0.394	-0.394	0.000	0.000	0.000	0.000
91	A	181	SER	0	0.023	0.010	24.796	-0.404	-0.404	0.000	0.000	0.000	0.000
92	A	182	GLU	-1	-0.991	-0.991	27.025	-10.722	-10.722	0.000	0.000	0.000	0.000
93	A	183	LEU	0	-0.017	-0.018	21.547	-0.183	-0.183	0.000	0.000	0.000	0.000
94	A	184	ARG	0	0.014	0.016	21.660	-0.312	-0.312	0.000	0.000	0.000	0.000
95	A	185	VAL	0	0.059	0.022	23.521	-0.156	-0.156	0.000	0.000	0.000	0.000
96	A	186	GLN	0	-0.115	-0.064	23.488	0.240	0.240	0.000	0.000	0.000	0.000
97	A	187	LEU	0	0.058	0.027	17.539	0.120	0.120	0.000	0.000	0.000	0.000
98	A	188	ARG	0	-0.009	0.007	21.221	-0.579	-0.579	0.000	0.000	0.000	0.000
99	A	189	ARG	1	0.815	0.901	23.784	11.657	11.657	0.000	0.000	0.000	0.000
100	A	190	ALA	0	-0.025	-0.015	19.932	0.267	0.267	0.000	0.000	0.000	0.000
101	A	191	ARG	0	-0.010	0.003	12.793	-0.555	-0.555	0.000	0.000	0.000	0.000
102	A	192	GLN	0	0.001	0.007	18.218	-1.131	-1.131	0.000	0.000	0.000	0.000
103	A	193	THR	0	-0.031	-0.018	20.293	0.819	0.819	0.000	0.000	0.000	0.000
104	A	194	ASP	-1	-0.957	-0.957	18.677	-14.800	-14.800	0.000	0.000	0.000	0.000
105	A	195	ASP	-1	-0.854	-0.922	13.518	-22.792	-22.792	0.000	0.000	0.000	0.000
106	A	196	VAL	0	-0.036	0.005	13.176	-0.622	-0.622	0.000	0.000	0.000	0.000
107	A	197	PRO	0	-0.026	-0.015	11.898	1.189	1.189	0.000	0.000	0.000	0.000
108	A	198	ILE	0	0.005	-0.005	15.173	0.215	0.215	0.000	0.000	0.000	0.000
109	A	199	ILE	0	-0.056	-0.020	14.496	-0.164	-0.164	0.000	0.000	0.000	0.000
110	A	200	LEU	0	0.027	0.031	17.601	0.060	0.060	0.000	0.000	0.000	0.000
111	A	201	VAL	0	-0.018	-0.032	18.265	0.040	0.040	0.000	0.000	0.000	0.000
112	A	202	GLY	0	0.048	0.028	21.513	0.377	0.377	0.000	0.000	0.000	0.000
113	A	203	ASN	0	-0.010	-0.015	22.853	0.021	0.021	0.000	0.000	0.000	0.000
114	A	204	LYS	1	0.860	0.925	24.674	11.466	11.466	0.000	0.000	0.000	0.000
115	A	205	SER	0	0.012	-0.015	26.383	0.479	0.479	0.000	0.000	0.000	0.000
116	A	206	ASP	-1	-0.829	-0.891	28.469	-10.583	-10.583	0.000	0.000	0.000	0.000
117	A	207	LEU	0	-0.026	-0.001	30.796	0.417	0.417	0.000	0.000	0.000	0.000
118	A	208	VAL	0	0.000	-0.022	33.026	0.193	0.193	0.000	0.000	0.000	0.000
119	A	209	ARG	1	0.915	0.958	35.025	7.581	7.581	0.000	0.000	0.000	0.000
120	A	210	SER	0	-0.021	-0.005	34.859	0.242	0.242	0.000	0.000	0.000	0.000
121	A	211	ARG	1	0.739	0.819	29.991	10.072	10.072	0.000	0.000	0.000	0.000
122	A	212	GLU	-1	-0.854	-0.917	34.346	-8.596	-8.596	0.000	0.000	0.000	0.000
123	A	213	VAL	0	-0.049	-0.004	30.457	0.134	0.134	0.000	0.000	0.000	0.000
124	A	214	SER	0	-0.012	-0.026	32.529	-0.176	-0.176	0.000	0.000	0.000	0.000
125	A	215	VAL	0	0.026	-0.008	29.108	-0.216	-0.216	0.000	0.000	0.000	0.000
126	A	216	ASP	-1	-0.872	-0.932	30.017	-9.888	-9.888	0.000	0.000	0.000	0.000
127	A	217	GLU	-1	-0.772	-0.833	31.878	-9.253	-9.253	0.000	0.000	0.000	0.000
128	A	218	GLY	0	0.047	0.028	28.050	-0.178	-0.178	0.000	0.000	0.000	0.000
129	A	219	ARG	1	0.856	0.913	27.096	10.198	10.198	0.000	0.000	0.000	0.000
130	A	220	ALA	0	0.003	0.000	28.031	-0.182	-0.182	0.000	0.000	0.000	0.000
131	A	221	CYS	0	-0.022	-0.008	26.398	0.011	0.011	0.000	0.000	0.000	0.000
132	A	222	ALA	0	0.045	0.013	23.699	-0.148	-0.148	0.000	0.000	0.000	0.000
133	A	223	VAL	0	-0.050	-0.027	24.818	-0.213	-0.213	0.000	0.000	0.000	0.000
134	A	224	VAL	0	-0.069	-0.029	27.417	0.129	0.129	0.000	0.000	0.000	0.000
135	A	225	PHE	0	-0.042	-0.046	22.361	0.078	0.078	0.000	0.000	0.000	0.000
136	A	226	ASP	-1	-0.953	-0.955	22.740	-14.179	-14.179	0.000	0.000	0.000	0.000
137	A	227	CYS	-1	-0.860	-0.896	19.427	-15.644	-15.644	0.000	0.000	0.000	0.000
138	A	228	LYS	1	0.851	0.925	17.640	16.069	16.069	0.000	0.000	0.000	0.000
139	A	229	PHE	0	0.040	0.015	19.983	-0.181	-0.181	0.000	0.000	0.000	0.000
140	A	230	ILE	0	-0.048	-0.020	18.761	0.016	0.016	0.000	0.000	0.000	0.000
141	A	231	GLU	-1	-0.750	-0.832	22.103	-10.881	-10.881	0.000	0.000	0.000	0.000
142	A	232	THR	0	0.032	-0.002	19.761	-0.287	-0.287	0.000	0.000	0.000	0.000
143	A	233	SER	0	-0.079	-0.049	23.166	0.594	0.594	0.000	0.000	0.000	0.000
144	A	234	ALA	0	0.043	0.018	22.202	-0.277	-0.277	0.000	0.000	0.000	0.000
145	A	235	ALA	0	-0.022	-0.004	23.233	-0.060	-0.060	0.000	0.000	0.000	0.000
146	A	236	LEU	0	0.000	-0.011	26.458	0.195	0.195	0.000	0.000	0.000	0.000
147	A	237	HIS	0	-0.037	-0.023	21.503	-0.293	-0.293	0.000	0.000	0.000	0.000
148	A	238	HIS	0	0.037	0.035	21.710	-0.701	-0.701	0.000	0.000	0.000	0.000
149	A	239	ASN	0	-0.008	-0.033	20.651	-0.306	-0.306	0.000	0.000	0.000	0.000
150	A	240	VAL	0	0.001	0.010	16.563	-0.735	-0.735	0.000	0.000	0.000	0.000
151	A	241	GLN	0	0.043	0.017	13.436	-1.741	-1.741	0.000	0.000	0.000	0.000
152	A	242	ALA	0	0.026	0.014	14.503	-1.247	-1.247	0.000	0.000	0.000	0.000
153	A	243	LEU	0	0.005	0.013	14.812	-0.428	-0.428	0.000	0.000	0.000	0.000
154	A	244	PHE	0	0.018	0.005	10.639	-0.860	-0.860	0.000	0.000	0.000	0.000
155	A	245	GLU	-1	-0.848	-0.934	10.501	-22.744	-22.744	0.000	0.000	0.000	0.000
156	A	246	GLY	0	-0.008	-0.002	11.594	-0.985	-0.985	0.000	0.000	0.000	0.000
157	A	247	VAL	0	-0.013	-0.005	8.875	-0.231	-0.231	0.000	0.000	0.000	0.000
158	A	248	VAL	0	0.018	0.008	6.403	-1.878	-1.878	0.000	0.000	0.000	0.000
159	A	249	ARG	1	0.767	0.860	8.331	20.136	20.136	0.000	0.000	0.000	0.000
160	A	250	GLN	0	0.002	-0.014	11.314	1.086	1.086	0.000	0.000	0.000	0.000
161	A	251	ILE	0	0.004	0.010	6.013	0.208	0.208	0.000	0.000	0.000	0.000
162	A	252	ARG	1	0.774	0.859	6.826	35.050	35.050	0.000	0.000	0.000	0.000
163	A	253	LEU	0	0.031	0.019	9.271	1.438	1.438	0.000	0.000	0.000	0.000
164	A	254	ARG	1	0.853	0.926	11.920	20.920	20.920	0.000	0.000	0.000	0.000
165	A	255	ARG	1	0.809	0.914	5.490	42.213	42.213	0.000	0.000	0.000	0.000
166	A	256	ASP	-1	-0.919	-0.965	10.990	-24.871	-24.871	0.000	0.000	0.000	0.000
167	A	257	SER	0	-0.119	-0.083	13.541	1.562	1.562	0.000	0.000	0.000	0.000
168	A	258	LYS	0	0.103	0.091	14.978	3.028	3.028	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:91:VAL)