FMO DATABASE

FMODB ID: 3K5ML

Calculation Name: 2FFQ-A-Xray547

Preferred Name:

Target Type:

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

Ligand 3-letter code: GSP | MG

Ligand of Interest (LOI):

PDB ID: 2FFQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q9NRW1

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

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	-1775591.279527
FMO2-HF: Nuclear repulsion	1709748.074107
FMO2-HF: Total energy	-65843.20542
FMO2-MP2: Total energy	-66036.811558

3D Structure

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:13:LYS)

Summations of interaction energy for fragment #1(A:13:LYS)

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.
-86.717	-82.901	0.712	-1.282	-3.247	-0.008

Interaction energy analysis for fragmet #1(A:13:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.813 / q_NPA : 1.890

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	15	LYS	1	0.823	0.931	2.803	99.435	102.115	0.234	-0.805	-2.110	-0.004
4	A	16	LEU	0	0.057	0.026	5.316	2.014	2.065	-0.001	-0.003	-0.047	0.000
74	A	86	SER	0	-0.055	-0.038	5.116	-12.533	-12.424	-0.001	0.000	-0.108	0.000
75	A	87	THR	0	-0.021	-0.018	2.550	1.489	2.465	0.480	-0.474	-0.982	-0.004
5	A	17	VAL	0	0.038	0.024	8.957	2.868	2.868	0.000	0.000	0.000	0.000
6	A	18	PHE	0	-0.019	-0.006	11.285	1.819	1.819	0.000	0.000	0.000	0.000
7	A	19	LEU	0	0.008	0.017	14.626	1.018	1.018	0.000	0.000	0.000	0.000
8	A	20	GLY	0	0.096	0.042	17.347	0.521	0.521	0.000	0.000	0.000	0.000
9	A	21	GLU	-1	-0.805	-0.871	21.135	-24.238	-24.238	0.000	0.000	0.000	0.000
10	A	22	GLN	0	0.035	0.000	23.958	-0.609	-0.609	0.000	0.000	0.000	0.000
11	A	23	SER	0	-0.007	-0.005	26.092	0.400	0.400	0.000	0.000	0.000	0.000
12	A	24	VAL	0	-0.005	0.019	22.488	0.462	0.462	0.000	0.000	0.000	0.000
13	A	25	GLY	0	0.028	0.015	23.985	-0.008	-0.008	0.000	0.000	0.000	0.000
14	A	26	LYS	1	0.833	0.928	18.151	28.045	28.045	0.000	0.000	0.000	0.000
15	A	27	THR	0	0.068	0.006	19.366	-0.510	-0.510	0.000	0.000	0.000	0.000
16	A	28	SER	0	-0.024	0.007	20.684	-0.159	-0.159	0.000	0.000	0.000	0.000
17	A	29	LEU	0	-0.002	0.000	19.008	0.220	0.220	0.000	0.000	0.000	0.000
18	A	30	ILE	0	0.031	0.020	15.174	-0.543	-0.543	0.000	0.000	0.000	0.000
19	A	31	THR	0	-0.030	-0.025	17.564	-0.346	-0.346	0.000	0.000	0.000	0.000
20	A	32	ARG	1	0.804	0.902	20.512	23.100	23.100	0.000	0.000	0.000	0.000
21	A	33	PHE	0	-0.008	-0.011	12.807	0.371	0.371	0.000	0.000	0.000	0.000
22	A	34	MET	0	-0.063	-0.019	14.997	-1.340	-1.340	0.000	0.000	0.000	0.000
23	A	35	TYR	0	0.014	-0.010	17.820	-0.265	-0.265	0.000	0.000	0.000	0.000
24	A	36	ASP	-1	-0.837	-0.891	21.455	-23.301	-23.301	0.000	0.000	0.000	0.000
25	A	37	SER	0	-0.018	-0.002	23.443	0.898	0.898	0.000	0.000	0.000	0.000
26	A	38	PHE	0	0.010	-0.017	24.565	-0.748	-0.748	0.000	0.000	0.000	0.000
27	A	39	ASP	-1	-0.780	-0.869	26.966	-18.742	-18.742	0.000	0.000	0.000	0.000
28	A	40	ASN	0	-0.046	-0.042	28.953	-0.238	-0.238	0.000	0.000	0.000	0.000
29	A	41	THR	0	-0.023	-0.009	31.578	0.510	0.510	0.000	0.000	0.000	0.000
30	A	42	TYR	0	-0.032	-0.021	27.203	-0.996	-0.996	0.000	0.000	0.000	0.000
31	A	43	GLN	0	0.006	-0.005	27.857	0.550	0.550	0.000	0.000	0.000	0.000
32	A	44	ALA	0	-0.035	-0.011	26.717	-0.778	-0.778	0.000	0.000	0.000	0.000
33	A	45	THR	0	0.035	0.019	20.300	0.750	0.750	0.000	0.000	0.000	0.000
34	A	46	ILE	0	-0.048	-0.041	23.797	0.407	0.407	0.000	0.000	0.000	0.000
35	A	47	GLY	0	0.032	0.018	21.625	0.550	0.550	0.000	0.000	0.000	0.000
36	A	48	ILE	0	-0.053	-0.024	14.973	-0.092	-0.092	0.000	0.000	0.000	0.000
37	A	49	ASP	-1	-0.888	-0.920	17.051	-29.796	-29.796	0.000	0.000	0.000	0.000
38	A	50	PHE	0	-0.016	-0.027	9.283	-3.128	-3.128	0.000	0.000	0.000	0.000
39	A	51	LEU	0	-0.013	0.006	12.736	2.169	2.169	0.000	0.000	0.000	0.000
40	A	52	SER	0	-0.004	-0.012	9.733	-3.955	-3.955	0.000	0.000	0.000	0.000
41	A	53	LYS	1	0.843	0.920	10.814	36.448	36.448	0.000	0.000	0.000	0.000
42	A	54	THR	0	-0.025	-0.011	10.533	-5.046	-5.046	0.000	0.000	0.000	0.000
43	A	55	MET	0	-0.033	-0.007	10.765	2.582	2.582	0.000	0.000	0.000	0.000
44	A	56	TYR	0	-0.020	-0.019	11.806	-2.538	-2.538	0.000	0.000	0.000	0.000
45	A	57	LEU	0	-0.049	-0.024	10.079	0.568	0.568	0.000	0.000	0.000	0.000
46	A	58	GLU	-1	-0.801	-0.883	13.167	-40.970	-40.970	0.000	0.000	0.000	0.000
47	A	59	ASP	-1	-0.870	-0.922	14.556	-30.490	-30.490	0.000	0.000	0.000	0.000
48	A	60	ARG	1	0.880	0.951	6.930	55.203	55.203	0.000	0.000	0.000	0.000
49	A	61	THR	0	-0.006	-0.017	11.154	0.251	0.251	0.000	0.000	0.000	0.000
50	A	62	VAL	0	0.007	0.018	6.439	-4.477	-4.477	0.000	0.000	0.000	0.000
51	A	63	ARG	1	0.940	0.965	6.209	57.435	57.435	0.000	0.000	0.000	0.000
52	A	64	LEU	0	0.012	0.010	5.715	-10.187	-10.187	0.000	0.000	0.000	0.000
53	A	65	GLN	0	-0.017	-0.016	5.545	-2.868	-2.868	0.000	0.000	0.000	0.000
54	A	66	LEU	0	-0.024	-0.013	7.470	-2.042	-2.042	0.000	0.000	0.000	0.000
55	A	67	TRP	0	0.045	0.013	7.850	4.103	4.103	0.000	0.000	0.000	0.000
56	A	68	ASP	-1	-0.774	-0.877	12.514	-29.715	-29.715	0.000	0.000	0.000	0.000
57	A	69	THR	0	0.006	-0.022	15.478	0.510	0.510	0.000	0.000	0.000	0.000
58	A	70	ALA	0	0.002	0.007	18.036	1.207	1.207	0.000	0.000	0.000	0.000
59	A	71	GLY	0	-0.005	-0.003	21.717	-0.021	-0.021	0.000	0.000	0.000	0.000
60	A	72	GLN	0	0.002	0.003	23.047	1.612	1.612	0.000	0.000	0.000	0.000
61	A	73	GLU	-1	-0.878	-0.945	25.365	-20.767	-20.767	0.000	0.000	0.000	0.000
62	A	74	ARG	1	0.896	0.940	26.119	20.344	20.344	0.000	0.000	0.000	0.000
63	A	75	PHE	0	0.015	0.005	22.457	0.225	0.225	0.000	0.000	0.000	0.000
64	A	76	ARG	1	0.978	0.994	21.545	22.328	22.328	0.000	0.000	0.000	0.000
65	A	77	SER	0	-0.015	-0.008	20.816	-1.106	-1.106	0.000	0.000	0.000	0.000
66	A	78	LEU	0	0.003	-0.004	19.035	-0.758	-0.758	0.000	0.000	0.000	0.000
67	A	79	ILE	0	-0.001	0.005	15.959	-1.891	-1.891	0.000	0.000	0.000	0.000
68	A	80	PRO	0	0.041	0.022	14.810	-2.415	-2.415	0.000	0.000	0.000	0.000
69	A	81	SER	0	-0.008	0.000	12.952	-2.488	-2.488	0.000	0.000	0.000	0.000
70	A	82	TYR	0	-0.020	-0.016	10.738	-3.252	-3.252	0.000	0.000	0.000	0.000
71	A	83	ILE	0	-0.014	0.008	9.861	-4.160	-4.160	0.000	0.000	0.000	0.000
72	A	84	ARG	1	0.883	0.939	9.884	38.234	38.234	0.000	0.000	0.000	0.000
73	A	85	ASP	-1	-0.843	-0.905	6.542	-79.448	-79.448	0.000	0.000	0.000	0.000
76	A	88	VAL	0	0.001	0.002	5.747	5.375	5.375	0.000	0.000	0.000	0.000
77	A	89	ALA	0	0.042	0.031	8.933	0.124	0.124	0.000	0.000	0.000	0.000
78	A	90	VAL	0	-0.026	-0.018	12.160	1.731	1.731	0.000	0.000	0.000	0.000
79	A	91	VAL	0	-0.005	0.005	14.718	1.039	1.039	0.000	0.000	0.000	0.000
80	A	92	VAL	0	-0.024	-0.015	18.012	1.111	1.111	0.000	0.000	0.000	0.000
81	A	93	TYR	0	0.027	0.009	20.687	0.268	0.268	0.000	0.000	0.000	0.000
82	A	94	ASP	-1	-0.808	-0.874	24.420	-20.529	-20.529	0.000	0.000	0.000	0.000
83	A	95	ILE	0	0.030	0.017	27.562	0.398	0.398	0.000	0.000	0.000	0.000
84	A	96	THR	0	-0.026	-0.030	29.904	0.774	0.774	0.000	0.000	0.000	0.000
85	A	97	ASN	0	-0.030	-0.013	29.908	0.372	0.372	0.000	0.000	0.000	0.000
86	A	98	LEU	0	0.125	0.058	30.245	-0.742	-0.742	0.000	0.000	0.000	0.000
87	A	99	ASN	0	0.000	0.010	29.450	-0.211	-0.211	0.000	0.000	0.000	0.000
88	A	100	SER	0	-0.041	-0.037	26.310	-0.848	-0.848	0.000	0.000	0.000	0.000
89	A	101	PHE	0	0.061	0.033	25.849	-0.898	-0.898	0.000	0.000	0.000	0.000
90	A	102	GLN	0	0.027	0.041	26.636	-0.913	-0.913	0.000	0.000	0.000	0.000
91	A	103	GLN	0	0.028	0.004	25.380	-0.941	-0.941	0.000	0.000	0.000	0.000
92	A	104	THR	0	-0.054	-0.039	22.317	-1.134	-1.134	0.000	0.000	0.000	0.000
93	A	105	SER	0	-0.010	-0.016	21.722	-1.190	-1.190	0.000	0.000	0.000	0.000
94	A	106	LYS	1	0.809	0.903	22.536	24.071	24.071	0.000	0.000	0.000	0.000
95	A	107	TRP	0	0.014	-0.006	18.353	-1.108	-1.108	0.000	0.000	0.000	0.000
96	A	108	ILE	0	-0.013	-0.015	17.819	-2.002	-2.002	0.000	0.000	0.000	0.000
97	A	109	ASP	-1	-0.920	-0.946	18.445	-28.015	-28.015	0.000	0.000	0.000	0.000
98	A	110	ASP	-1	-0.883	-0.944	18.280	-29.752	-29.752	0.000	0.000	0.000	0.000
99	A	111	VAL	0	-0.014	-0.031	13.030	-1.785	-1.785	0.000	0.000	0.000	0.000
100	A	112	ARG	1	0.825	0.909	14.481	29.929	29.929	0.000	0.000	0.000	0.000
101	A	113	THR	0	-0.003	0.004	16.525	-0.206	-0.206	0.000	0.000	0.000	0.000
102	A	114	GLU	-1	-0.908	-0.966	13.531	-39.405	-39.405	0.000	0.000	0.000	0.000
103	A	115	ARG	1	0.761	0.874	5.678	66.793	66.793	0.000	0.000	0.000	0.000
104	A	116	GLY	0	0.019	0.021	11.810	-1.551	-1.551	0.000	0.000	0.000	0.000
105	A	117	SER	0	-0.026	-0.034	13.875	1.648	1.648	0.000	0.000	0.000	0.000
106	A	118	ASP	-1	-0.908	-0.933	7.158	-71.916	-71.916	0.000	0.000	0.000	0.000
107	A	119	VAL	0	-0.017	-0.017	8.790	-5.281	-5.281	0.000	0.000	0.000	0.000
108	A	120	ILE	0	0.018	0.035	8.372	3.987	3.987	0.000	0.000	0.000	0.000
109	A	121	ILE	0	0.020	0.002	11.022	-0.788	-0.788	0.000	0.000	0.000	0.000
110	A	122	MET	0	-0.031	-0.008	14.119	1.979	1.979	0.000	0.000	0.000	0.000
111	A	123	LEU	0	0.000	0.010	16.163	-0.095	-0.095	0.000	0.000	0.000	0.000
112	A	124	VAL	0	-0.006	-0.024	18.329	0.451	0.451	0.000	0.000	0.000	0.000
113	A	125	GLY	0	0.069	0.040	21.152	0.459	0.459	0.000	0.000	0.000	0.000
114	A	126	ASN	0	-0.019	-0.030	23.379	0.371	0.371	0.000	0.000	0.000	0.000
115	A	127	LYS	1	0.817	0.890	25.332	21.697	21.697	0.000	0.000	0.000	0.000
116	A	128	THR	0	0.063	0.018	27.782	0.628	0.628	0.000	0.000	0.000	0.000
117	A	129	ASP	-1	-0.866	-0.904	30.185	-19.212	-19.212	0.000	0.000	0.000	0.000
118	A	130	LEU	0	-0.051	-0.025	32.063	0.672	0.672	0.000	0.000	0.000	0.000
119	A	131	ALA	0	0.030	0.005	34.411	0.169	0.169	0.000	0.000	0.000	0.000
120	A	132	ASP	-1	-0.925	-0.959	35.761	-14.861	-14.861	0.000	0.000	0.000	0.000
121	A	133	LYS	1	0.912	0.960	36.228	16.290	16.290	0.000	0.000	0.000	0.000
122	A	134	ARG	1	0.756	0.823	30.413	19.132	19.132	0.000	0.000	0.000	0.000
123	A	135	GLN	0	-0.066	-0.035	33.907	0.476	0.476	0.000	0.000	0.000	0.000
124	A	136	ILE	0	-0.039	0.000	29.852	0.020	0.020	0.000	0.000	0.000	0.000
125	A	137	THR	0	-0.020	-0.033	32.356	-0.234	-0.234	0.000	0.000	0.000	0.000
126	A	138	ILE	0	-0.004	0.003	27.694	-0.668	-0.668	0.000	0.000	0.000	0.000
127	A	139	GLU	-1	-0.841	-0.930	28.883	-19.197	-19.197	0.000	0.000	0.000	0.000
128	A	140	GLU	-1	-0.844	-0.894	30.224	-18.582	-18.582	0.000	0.000	0.000	0.000
129	A	141	GLY	0	-0.005	-0.003	26.767	-0.508	-0.508	0.000	0.000	0.000	0.000
130	A	142	GLU	-1	-0.943	-0.980	25.396	-22.622	-22.622	0.000	0.000	0.000	0.000
131	A	143	GLN	0	-0.027	-0.016	25.937	-0.901	-0.901	0.000	0.000	0.000	0.000
132	A	144	ARG	1	0.945	0.987	24.763	21.359	21.359	0.000	0.000	0.000	0.000
133	A	145	ALA	0	-0.017	-0.018	21.723	-0.813	-0.813	0.000	0.000	0.000	0.000
134	A	146	LYS	1	0.944	0.980	22.225	20.503	20.503	0.000	0.000	0.000	0.000
135	A	147	GLU	-1	-0.920	-0.967	24.289	-21.327	-21.327	0.000	0.000	0.000	0.000
136	A	148	LEU	0	-0.021	-0.002	21.564	-0.200	-0.200	0.000	0.000	0.000	0.000
137	A	149	SER	0	0.010	0.012	20.087	-1.393	-1.393	0.000	0.000	0.000	0.000
138	A	150	VAL	0	-0.061	-0.015	17.435	-1.913	-1.913	0.000	0.000	0.000	0.000
139	A	151	MET	0	-0.009	0.002	14.737	0.653	0.653	0.000	0.000	0.000	0.000
140	A	152	PHE	0	0.091	0.037	18.084	-0.038	-0.038	0.000	0.000	0.000	0.000
141	A	153	ILE	0	-0.037	-0.016	19.453	-0.274	-0.274	0.000	0.000	0.000	0.000
142	A	154	GLU	-1	-0.702	-0.797	22.153	-21.042	-21.042	0.000	0.000	0.000	0.000
143	A	155	THR	0	-0.030	-0.037	21.011	-0.460	-0.460	0.000	0.000	0.000	0.000
144	A	156	SER	0	-0.049	-0.039	24.489	0.615	0.615	0.000	0.000	0.000	0.000
145	A	157	ALA	0	0.011	0.002	23.457	-0.094	-0.094	0.000	0.000	0.000	0.000
146	A	158	LYS	1	0.885	0.970	24.679	18.269	18.269	0.000	0.000	0.000	0.000
147	A	159	THR	0	0.034	-0.004	28.243	0.059	0.059	0.000	0.000	0.000	0.000
148	A	160	GLY	0	0.013	0.015	24.651	0.112	0.112	0.000	0.000	0.000	0.000
149	A	161	TYR	0	0.013	0.008	24.274	-0.868	-0.868	0.000	0.000	0.000	0.000
150	A	162	ASN	0	0.030	-0.009	22.655	-0.784	-0.784	0.000	0.000	0.000	0.000
151	A	163	VAL	0	-0.003	0.019	19.346	-1.389	-1.389	0.000	0.000	0.000	0.000
152	A	164	LYS	1	0.909	0.933	18.185	24.012	24.012	0.000	0.000	0.000	0.000
153	A	165	GLN	0	0.019	0.025	17.554	-2.083	-2.083	0.000	0.000	0.000	0.000
154	A	166	LEU	0	0.016	0.011	16.121	-0.848	-0.848	0.000	0.000	0.000	0.000
155	A	167	PHE	0	0.021	0.002	12.537	-1.595	-1.595	0.000	0.000	0.000	0.000
156	A	168	ARG	1	0.927	0.967	12.654	27.113	27.113	0.000	0.000	0.000	0.000
157	A	169	ARG	1	0.884	0.923	13.508	28.723	28.723	0.000	0.000	0.000	0.000
158	A	170	VAL	0	0.014	0.013	10.070	-1.006	-1.006	0.000	0.000	0.000	0.000
159	A	171	ALA	0	-0.032	-0.027	8.822	-4.106	-4.106	0.000	0.000	0.000	0.000
160	A	172	SER	0	-0.040	-0.047	9.236	-3.160	-3.160	0.000	0.000	0.000	0.000
161	A	173	ALA	0	0.026	0.005	11.120	-1.048	-1.048	0.000	0.000	0.000	0.000
162	A	174	LEU	0	-0.087	-0.048	4.960	-4.849	-4.849	0.000	0.000	0.000	0.000
163	A	175	LEU	0	-0.137	-0.072	6.569	-8.350	-8.350	0.000	0.000	0.000	0.000
164	A	176	GLU	-2	-1.886	-1.904	8.793	-86.046	-86.046	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:13:LYS)