FMO DATABASE

FMODB ID: 5Y8QZ

Calculation Name: 5CK3-A-Xray547

Preferred Name:

Target Type:

Ligand Name: guanosine-5'-triphosphate | sulfate ion | glycerol | magnesium ion

Ligand 3-letter code: GTP | SO4 | GOL | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5CK3

Chain ID: A

ChEMBL ID:

UniProt ID: G0S1R8

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	135
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1225675.051561
FMO2-HF: Nuclear repulsion	1172514.317343
FMO2-HF: Total energy	-53160.734218
FMO2-MP2: Total energy	-53318.67428

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:1:MET)

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

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.
-182.346	-171.226	2.929	-4.887	-9.16	-0.068

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.856 / q_NPA : 0.943

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	3	LEU	0	-0.018	0.010	3.772	6.494	6.556	0.154	1.573	-1.789	0.003
21	A	21	TYR	0	-0.005	-0.009	2.355	-3.660	-0.762	0.912	-1.307	-2.502	-0.014
22	A	22	ALA	0	-0.024	-0.004	4.254	0.869	0.958	-0.001	-0.004	-0.084	0.000
90	A	90	TRP	0	0.038	0.024	2.322	1.225	2.975	0.813	-1.148	-1.415	-0.015
131	A	131	LEU	0	-0.032	-0.019	2.941	-3.749	-3.165	0.028	-0.180	-0.432	-0.002
132	A	132	GLN	0	-0.010	-0.005	5.108	-4.667	-4.597	-0.001	-0.002	-0.067	0.000
135	A	135	GLU	-2	-1.877	-1.918	2.705	-141.166	-135.499	1.024	-3.819	-2.871	-0.040
4	A	4	ASP	-1	-0.836	-0.908	5.830	-27.897	-27.897	0.000	0.000	0.000	0.000
5	A	5	ALA	0	0.036	0.019	6.147	-1.665	-1.665	0.000	0.000	0.000	0.000
6	A	6	PHE	0	0.016	0.006	8.669	0.462	0.462	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.876	-0.917	10.387	-18.058	-18.058	0.000	0.000	0.000	0.000
8	A	8	ILE	0	-0.025	-0.007	14.081	0.006	0.006	0.000	0.000	0.000	0.000
9	A	9	LEU	0	0.008	0.012	16.983	0.420	0.420	0.000	0.000	0.000	0.000
10	A	10	THR	0	0.000	-0.008	20.339	0.383	0.383	0.000	0.000	0.000	0.000
11	A	11	THR	0	-0.002	-0.029	24.028	-0.001	-0.001	0.000	0.000	0.000	0.000
12	A	12	SER	0	-0.051	-0.024	26.520	0.376	0.376	0.000	0.000	0.000	0.000
13	A	13	GLY	0	0.018	0.016	24.103	0.253	0.253	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.031	-0.007	22.876	-0.391	-0.391	0.000	0.000	0.000	0.000
15	A	15	VAL	0	0.040	0.010	16.716	-0.053	-0.053	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.047	-0.015	19.794	0.253	0.253	0.000	0.000	0.000	0.000
17	A	17	TRP	0	-0.035	-0.046	9.864	-0.342	-0.342	0.000	0.000	0.000	0.000
18	A	18	SER	0	-0.032	-0.037	12.913	-0.508	-0.508	0.000	0.000	0.000	0.000
19	A	19	ARG	1	0.833	0.931	6.392	32.762	32.762	0.000	0.000	0.000	0.000
20	A	20	THR	0	0.015	0.001	7.713	-1.013	-1.013	0.000	0.000	0.000	0.000
23	A	23	PRO	0	-0.007	-0.007	7.162	0.446	0.446	0.000	0.000	0.000	0.000
24	A	24	VAL	0	0.017	0.014	10.100	0.596	0.596	0.000	0.000	0.000	0.000
25	A	25	ASN	0	0.025	0.024	12.564	0.914	0.914	0.000	0.000	0.000	0.000
26	A	26	PRO	0	0.073	0.024	16.339	-0.150	-0.150	0.000	0.000	0.000	0.000
27	A	27	SER	0	-0.039	-0.035	18.026	0.106	0.106	0.000	0.000	0.000	0.000
28	A	28	VAL	0	0.003	0.012	15.930	0.257	0.257	0.000	0.000	0.000	0.000
29	A	29	VAL	0	0.027	0.013	15.829	-0.009	-0.009	0.000	0.000	0.000	0.000
30	A	30	ASN	0	-0.049	-0.029	18.790	0.803	0.803	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.805	-0.895	22.168	-11.966	-11.966	0.000	0.000	0.000	0.000
32	A	32	PHE	0	0.069	0.032	19.751	0.235	0.235	0.000	0.000	0.000	0.000
33	A	33	ILE	0	-0.016	-0.019	21.726	0.348	0.348	0.000	0.000	0.000	0.000
34	A	34	THR	0	-0.002	-0.008	24.070	0.586	0.586	0.000	0.000	0.000	0.000
35	A	35	ASP	0	-0.030	-0.062	24.669	0.546	0.546	0.000	0.000	0.000	0.000
36	A	36	VAL	0	-0.073	-0.028	22.944	0.262	0.262	0.000	0.000	0.000	0.000
37	A	37	PHE	0	-0.052	-0.027	22.631	0.104	0.104	0.000	0.000	0.000	0.000
38	A	38	ILE	0	-0.035	0.003	28.146	0.323	0.323	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.904	-0.979	30.541	-9.465	-9.465	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-1.014	-0.992	29.665	-9.775	-9.775	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.892	0.953	30.259	9.431	9.431	0.000	0.000	0.000	0.000
42	A	42	SER	0	-0.026	-0.024	27.049	0.343	0.343	0.000	0.000	0.000	0.000
43	A	43	ALA	0	0.021	0.021	26.336	-0.556	-0.556	0.000	0.000	0.000	0.000
44	A	44	VAL	0	0.011	0.004	26.273	0.466	0.466	0.000	0.000	0.000	0.000
45	A	45	ALA	0	0.001	0.009	25.329	-0.545	-0.545	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.008	-0.006	24.025	0.420	0.420	0.000	0.000	0.000	0.000
47	A	47	SER	0	-0.047	-0.022	20.338	-0.201	-0.201	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.944	0.970	15.961	18.788	18.788	0.000	0.000	0.000	0.000
49	A	49	ASN	0	-0.015	0.005	18.393	-0.368	-0.368	0.000	0.000	0.000	0.000
50	A	50	GLY	0	0.043	0.010	19.832	-0.580	-0.580	0.000	0.000	0.000	0.000
51	A	51	GLY	0	-0.011	0.020	19.279	-0.336	-0.336	0.000	0.000	0.000	0.000
52	A	52	SER	0	-0.009	-0.026	19.641	-0.621	-0.621	0.000	0.000	0.000	0.000
53	A	53	ALA	0	0.001	-0.001	22.320	0.551	0.551	0.000	0.000	0.000	0.000
54	A	54	ALA	0	0.046	0.025	23.750	-0.559	-0.559	0.000	0.000	0.000	0.000
55	A	55	SER	0	-0.012	0.001	26.209	0.565	0.565	0.000	0.000	0.000	0.000
56	A	56	ASN	0	-0.026	-0.009	28.301	0.054	0.054	0.000	0.000	0.000	0.000
57	A	57	PRO	0	0.020	-0.019	31.116	-0.096	-0.096	0.000	0.000	0.000	0.000
58	A	58	PRO	0	-0.040	0.003	32.898	0.063	0.063	0.000	0.000	0.000	0.000
59	A	59	TYR	0	0.025	0.005	28.723	0.169	0.169	0.000	0.000	0.000	0.000
60	A	60	LYS	1	0.818	0.912	25.454	10.936	10.936	0.000	0.000	0.000	0.000
61	A	61	HIS	0	0.065	0.019	25.527	-0.055	-0.055	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.807	-0.875	23.183	-13.201	-13.201	0.000	0.000	0.000	0.000
63	A	63	GLN	0	-0.087	-0.024	18.682	-0.140	-0.140	0.000	0.000	0.000	0.000
64	A	64	HIS	0	0.030	-0.001	18.805	0.744	0.744	0.000	0.000	0.000	0.000
65	A	65	SER	0	0.003	0.018	18.951	-0.936	-0.936	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.048	-0.013	14.715	-0.233	-0.233	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.836	0.915	13.857	18.454	18.454	0.000	0.000	0.000	0.000
68	A	68	TRP	0	-0.018	-0.001	15.092	-0.698	-0.698	0.000	0.000	0.000	0.000
69	A	69	THR	0	-0.006	-0.007	17.494	0.194	0.194	0.000	0.000	0.000	0.000
70	A	70	PHE	0	-0.015	-0.013	19.579	0.069	0.069	0.000	0.000	0.000	0.000
71	A	71	VAL	0	-0.039	-0.014	21.912	0.282	0.282	0.000	0.000	0.000	0.000
72	A	72	LYS	1	0.949	0.965	24.533	10.375	10.375	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.943	-0.964	28.107	-9.727	-9.727	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.001	-0.004	24.701	0.134	0.134	0.000	0.000	0.000	0.000
75	A	75	GLY	0	0.040	0.039	26.556	-0.128	-0.128	0.000	0.000	0.000	0.000
76	A	76	ILE	0	-0.032	-0.006	20.853	-0.087	-0.087	0.000	0.000	0.000	0.000
77	A	77	ILE	0	0.015	0.009	19.321	-0.048	-0.048	0.000	0.000	0.000	0.000
78	A	78	PHE	0	0.011	0.004	15.455	-0.287	-0.287	0.000	0.000	0.000	0.000
79	A	79	VAL	0	-0.001	-0.002	14.367	0.469	0.469	0.000	0.000	0.000	0.000
80	A	80	ALA	0	0.030	0.015	10.053	-1.450	-1.450	0.000	0.000	0.000	0.000
81	A	81	VAL	0	-0.036	-0.022	10.611	1.463	1.463	0.000	0.000	0.000	0.000
82	A	82	TYR	0	0.008	0.005	9.702	-2.856	-2.856	0.000	0.000	0.000	0.000
83	A	83	ARG	1	0.894	0.924	9.327	24.992	24.992	0.000	0.000	0.000	0.000
84	A	84	SER	0	-0.005	-0.009	12.666	0.606	0.606	0.000	0.000	0.000	0.000
85	A	85	LEU	0	-0.003	-0.005	15.687	0.707	0.707	0.000	0.000	0.000	0.000
86	A	86	LEU	0	-0.020	0.021	9.983	0.168	0.168	0.000	0.000	0.000	0.000
87	A	87	HIS	0	-0.029	-0.034	10.310	-1.874	-1.874	0.000	0.000	0.000	0.000
88	A	88	LEU	0	0.077	0.027	6.932	0.596	0.596	0.000	0.000	0.000	0.000
89	A	89	PRO	0	-0.009	-0.001	8.973	-1.409	-1.409	0.000	0.000	0.000	0.000
91	A	91	VAL	0	0.017	0.007	7.657	0.786	0.786	0.000	0.000	0.000	0.000
92	A	92	ASP	-1	-0.826	-0.907	9.760	-19.671	-19.671	0.000	0.000	0.000	0.000
93	A	93	LYS	1	0.905	0.960	11.280	25.196	25.196	0.000	0.000	0.000	0.000
94	A	94	LEU	0	0.025	0.033	7.404	1.552	1.552	0.000	0.000	0.000	0.000
95	A	95	VAL	0	-0.007	-0.013	11.146	1.318	1.318	0.000	0.000	0.000	0.000
96	A	96	ASP	-1	-0.744	-0.882	13.616	-15.801	-15.801	0.000	0.000	0.000	0.000
97	A	97	ASN	0	-0.109	-0.073	12.078	1.431	1.431	0.000	0.000	0.000	0.000
98	A	98	ILE	0	0.040	0.032	10.776	1.015	1.015	0.000	0.000	0.000	0.000
99	A	99	ARG	1	0.903	0.966	14.635	15.927	15.927	0.000	0.000	0.000	0.000
100	A	100	ALA	0	-0.033	-0.013	17.954	0.942	0.942	0.000	0.000	0.000	0.000
101	A	101	ILE	0	0.003	0.006	14.377	0.813	0.813	0.000	0.000	0.000	0.000
102	A	102	PHE	0	0.028	0.004	16.787	0.909	0.909	0.000	0.000	0.000	0.000
103	A	103	VAL	0	-0.008	-0.014	18.745	0.817	0.817	0.000	0.000	0.000	0.000
104	A	104	SER	0	-0.052	-0.014	21.430	0.925	0.925	0.000	0.000	0.000	0.000
105	A	105	LEU	0	-0.019	-0.009	18.809	0.452	0.452	0.000	0.000	0.000	0.000
106	A	106	TYR	0	-0.021	-0.016	18.493	0.646	0.646	0.000	0.000	0.000	0.000
107	A	107	SER	0	-0.014	-0.007	23.880	0.552	0.552	0.000	0.000	0.000	0.000
108	A	108	GLU	-1	-0.890	-0.955	26.207	-9.865	-9.865	0.000	0.000	0.000	0.000
109	A	109	GLN	0	-0.072	-0.041	24.780	0.646	0.646	0.000	0.000	0.000	0.000
110	A	110	PHE	0	0.029	0.004	23.115	0.207	0.207	0.000	0.000	0.000	0.000
111	A	111	LYS	1	0.958	0.992	29.094	9.553	9.553	0.000	0.000	0.000	0.000
112	A	112	ARG	1	0.850	0.938	28.327	10.951	10.951	0.000	0.000	0.000	0.000
113	A	113	PRO	0	0.025	0.018	32.561	-0.182	-0.182	0.000	0.000	0.000	0.000
114	A	114	ASN	0	-0.024	-0.020	34.951	-0.084	-0.084	0.000	0.000	0.000	0.000
115	A	115	THR	0	-0.010	-0.015	30.773	-0.013	-0.013	0.000	0.000	0.000	0.000
116	A	116	THR	0	0.048	0.031	27.056	0.017	0.017	0.000	0.000	0.000	0.000
117	A	117	ILE	0	-0.043	-0.013	26.300	-0.502	-0.502	0.000	0.000	0.000	0.000
118	A	118	ILE	0	0.018	0.009	23.177	0.306	0.306	0.000	0.000	0.000	0.000
119	A	119	GLU	-1	-0.945	-0.962	23.024	-12.658	-12.658	0.000	0.000	0.000	0.000
120	A	120	CYS	0	0.007	0.000	19.002	-0.145	-0.145	0.000	0.000	0.000	0.000
121	A	121	ILE	0	0.046	0.018	18.001	-0.991	-0.991	0.000	0.000	0.000	0.000
122	A	122	ASN	0	0.008	0.002	17.699	-1.123	-1.123	0.000	0.000	0.000	0.000
123	A	123	PHE	0	0.019	0.012	13.516	-0.590	-0.590	0.000	0.000	0.000	0.000
124	A	124	ASP	-1	-0.769	-0.879	12.113	-23.620	-23.620	0.000	0.000	0.000	0.000
125	A	125	LYS	1	0.886	0.938	11.575	15.718	15.718	0.000	0.000	0.000	0.000
126	A	126	TYR	0	0.027	0.016	12.851	-0.626	-0.626	0.000	0.000	0.000	0.000
127	A	127	PHE	0	-0.029	-0.009	6.172	-1.318	-1.318	0.000	0.000	0.000	0.000
128	A	128	ASP	-1	-0.879	-0.950	7.421	-41.596	-41.596	0.000	0.000	0.000	0.000
129	A	129	GLN	0	-0.007	-0.005	7.990	-1.758	-1.758	0.000	0.000	0.000	0.000
130	A	130	GLN	0	0.006	-0.004	9.612	-2.180	-2.180	0.000	0.000	0.000	0.000
133	A	133	GLU	-1	-0.957	-0.969	6.565	-23.491	-23.491	0.000	0.000	0.000	0.000
134	A	134	LEU	0	-0.117	-0.068	6.392	4.647	4.647	0.000	0.000	0.000	0.000

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