FMO DATABASE

FMODB ID: Y1JY2

Calculation Name: 4ZVF-A-Xray547

Preferred Name:

Target Type:

Ligand Name: guanosine-5'-rp-alpha-thio-triphosphate | calcium ion

Ligand 3-letter code: GAV | CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4ZVF

Chain ID: A

ChEMBL ID:

UniProt ID: P0AA89

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	164
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1711832.99694
FMO2-HF: Nuclear repulsion	1646907.427187
FMO2-HF: Total energy	-64925.569753
FMO2-MP2: Total energy	-65118.702021

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:297:MET)

Summations of interaction energy for fragment #1(A:297: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.
78.172	80.434	0.041	-0.916	-1.385	-0.001

Interaction energy analysis for fragmet #1(A:297:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.882 / q_NPA : 0.931

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	299	VAL	0	0.030	0.039	3.868	-7.600	-6.170	-0.011	-0.695	-0.724	0.000
5	A	301	THR	0	-0.030	-0.022	4.792	0.863	0.924	-0.001	-0.008	-0.051	0.000
6	A	302	LYS	1	0.816	0.897	2.780	66.585	67.356	0.053	-0.213	-0.610	-0.001
4	A	300	LEU	0	0.041	0.018	6.331	3.901	3.901	0.000	0.000	0.000	0.000
7	A	303	LEU	0	-0.009	0.034	7.487	3.043	3.043	0.000	0.000	0.000	0.000
8	A	304	LEU	0	0.007	0.011	11.100	-0.042	-0.042	0.000	0.000	0.000	0.000
9	A	305	ASN	0	0.036	0.001	13.818	1.662	1.662	0.000	0.000	0.000	0.000
10	A	306	ARG	1	0.986	0.986	15.902	14.329	14.329	0.000	0.000	0.000	0.000
11	A	307	ARG	1	0.940	0.966	19.122	15.390	15.390	0.000	0.000	0.000	0.000
12	A	308	PHE	0	0.003	-0.001	15.558	0.597	0.597	0.000	0.000	0.000	0.000
13	A	309	LEU	0	0.007	0.022	20.103	0.353	0.353	0.000	0.000	0.000	0.000
14	A	310	PRO	0	0.010	0.008	22.281	0.373	0.373	0.000	0.000	0.000	0.000
15	A	311	THR	0	-0.035	-0.027	22.280	0.499	0.499	0.000	0.000	0.000	0.000
16	A	312	ILE	0	-0.036	0.004	18.301	0.175	0.175	0.000	0.000	0.000	0.000
17	A	313	PHE	0	0.061	0.021	22.849	0.302	0.302	0.000	0.000	0.000	0.000
18	A	314	LYS	1	0.940	0.971	25.821	10.904	10.904	0.000	0.000	0.000	0.000
19	A	315	ARG	1	0.866	0.949	20.119	14.271	14.271	0.000	0.000	0.000	0.000
20	A	316	GLU	-1	-0.776	-0.891	23.325	-12.655	-12.655	0.000	0.000	0.000	0.000
21	A	317	ILE	0	-0.001	0.010	26.765	0.304	0.304	0.000	0.000	0.000	0.000
22	A	318	ALA	0	-0.014	-0.003	30.078	0.358	0.358	0.000	0.000	0.000	0.000
23	A	319	HIS	0	0.016	0.011	25.798	0.704	0.704	0.000	0.000	0.000	0.000
24	A	320	ALA	0	0.049	0.050	30.110	0.252	0.252	0.000	0.000	0.000	0.000
25	A	321	ASN	0	-0.001	-0.020	31.603	0.277	0.277	0.000	0.000	0.000	0.000
26	A	322	ARG	1	0.829	0.923	29.867	10.162	10.162	0.000	0.000	0.000	0.000
27	A	323	THR	0	-0.044	-0.039	31.758	0.100	0.100	0.000	0.000	0.000	0.000
28	A	324	GLY	0	0.016	0.023	34.529	0.123	0.123	0.000	0.000	0.000	0.000
29	A	325	THR	0	-0.028	-0.017	29.903	-0.038	-0.038	0.000	0.000	0.000	0.000
30	A	326	PRO	0	-0.036	-0.019	29.809	0.021	0.021	0.000	0.000	0.000	0.000
31	A	327	LEU	0	0.007	0.013	25.806	-0.383	-0.383	0.000	0.000	0.000	0.000
32	A	328	SER	0	-0.011	-0.023	26.587	0.269	0.269	0.000	0.000	0.000	0.000
33	A	329	VAL	0	-0.028	-0.013	23.904	-0.553	-0.553	0.000	0.000	0.000	0.000
34	A	330	LEU	0	-0.008	-0.001	22.046	0.466	0.466	0.000	0.000	0.000	0.000
35	A	331	ILE	0	0.014	0.012	22.708	-0.688	-0.688	0.000	0.000	0.000	0.000
36	A	332	ILE	0	-0.009	-0.012	19.505	0.444	0.444	0.000	0.000	0.000	0.000
37	A	333	ASP	-1	-0.756	-0.872	21.497	-13.292	-13.292	0.000	0.000	0.000	0.000
38	A	334	VAL	0	0.000	0.002	18.993	0.339	0.339	0.000	0.000	0.000	0.000
39	A	335	ASP	-1	-0.766	-0.847	22.302	-11.519	-11.519	0.000	0.000	0.000	0.000
40	A	336	LYS	1	0.797	0.876	24.850	10.179	10.179	0.000	0.000	0.000	0.000
41	A	337	PHE	0	0.097	0.058	17.915	0.018	0.018	0.000	0.000	0.000	0.000
42	A	338	LYS	1	0.966	0.998	23.294	10.609	10.609	0.000	0.000	0.000	0.000
43	A	339	GLU	-1	-0.765	-0.867	25.708	-10.539	-10.539	0.000	0.000	0.000	0.000
44	A	340	ILE	0	-0.003	0.017	20.451	-0.018	-0.018	0.000	0.000	0.000	0.000
45	A	341	ASN	0	-0.017	-0.033	20.227	-0.712	-0.712	0.000	0.000	0.000	0.000
46	A	342	ASP	-1	-0.937	-0.975	22.794	-11.461	-11.461	0.000	0.000	0.000	0.000
47	A	343	THR	0	-0.078	-0.037	25.358	0.446	0.446	0.000	0.000	0.000	0.000
48	A	344	TRP	0	-0.008	-0.015	21.041	-0.087	-0.087	0.000	0.000	0.000	0.000
49	A	345	GLY	0	0.021	0.032	20.768	-0.575	-0.575	0.000	0.000	0.000	0.000
50	A	346	HIS	0	-0.010	-0.015	16.496	0.399	0.399	0.000	0.000	0.000	0.000
51	A	347	ASN	0	-0.012	-0.012	14.784	-1.350	-1.350	0.000	0.000	0.000	0.000
52	A	348	THR	0	0.002	-0.011	14.535	-1.597	-1.597	0.000	0.000	0.000	0.000
53	A	349	GLY	0	0.040	0.032	16.282	-0.305	-0.305	0.000	0.000	0.000	0.000
54	A	350	ASP	-1	-0.866	-0.946	12.716	-21.215	-21.215	0.000	0.000	0.000	0.000
55	A	351	GLU	-1	-0.898	-0.960	9.559	-31.095	-31.095	0.000	0.000	0.000	0.000
56	A	352	ILE	0	-0.017	-0.007	12.344	-0.865	-0.865	0.000	0.000	0.000	0.000
57	A	353	LEU	0	-0.008	0.004	13.848	-0.262	-0.262	0.000	0.000	0.000	0.000
58	A	354	ARG	1	0.804	0.886	7.645	31.505	31.505	0.000	0.000	0.000	0.000
59	A	355	LYS	1	0.928	0.964	10.343	23.990	23.990	0.000	0.000	0.000	0.000
60	A	356	VAL	0	0.009	0.009	12.940	0.253	0.253	0.000	0.000	0.000	0.000
61	A	357	SER	0	0.007	-0.018	10.875	0.513	0.513	0.000	0.000	0.000	0.000
62	A	358	GLN	0	-0.126	-0.077	7.693	-4.603	-4.603	0.000	0.000	0.000	0.000
63	A	359	ALA	0	0.034	0.026	10.863	0.932	0.932	0.000	0.000	0.000	0.000
64	A	360	PHE	0	0.011	0.005	14.154	1.406	1.406	0.000	0.000	0.000	0.000
65	A	361	TYR	0	-0.002	-0.029	9.938	1.295	1.295	0.000	0.000	0.000	0.000
66	A	362	ASP	-1	-0.873	-0.916	11.846	-24.078	-24.078	0.000	0.000	0.000	0.000
67	A	363	ASN	0	-0.125	-0.077	14.311	2.211	2.211	0.000	0.000	0.000	0.000
68	A	364	VAL	0	-0.021	0.006	15.872	1.288	1.288	0.000	0.000	0.000	0.000
69	A	365	ARG	1	0.853	0.912	16.904	12.595	12.595	0.000	0.000	0.000	0.000
70	A	366	SER	0	-0.007	-0.013	15.302	-0.277	-0.277	0.000	0.000	0.000	0.000
71	A	367	SER	0	0.015	0.011	16.374	-0.269	-0.269	0.000	0.000	0.000	0.000
72	A	368	ASP	-1	-0.810	-0.869	18.216	-14.024	-14.024	0.000	0.000	0.000	0.000
73	A	369	TYR	0	-0.024	-0.040	16.450	-1.389	-1.389	0.000	0.000	0.000	0.000
74	A	370	VAL	0	0.039	0.023	13.513	0.875	0.875	0.000	0.000	0.000	0.000
75	A	371	PHE	0	-0.007	-0.021	14.192	-1.250	-1.250	0.000	0.000	0.000	0.000
76	A	372	ARG	1	0.853	0.928	13.415	20.893	20.893	0.000	0.000	0.000	0.000
77	A	373	TYR	0	-0.038	-0.031	15.992	0.449	0.449	0.000	0.000	0.000	0.000
78	A	374	GLY	0	0.037	0.012	19.607	0.757	0.757	0.000	0.000	0.000	0.000
79	A	375	GLY	0	-0.030	0.009	18.674	-1.034	-1.034	0.000	0.000	0.000	0.000
80	A	376	ASP	-1	-0.845	-0.936	18.263	-15.680	-15.680	0.000	0.000	0.000	0.000
81	A	377	GLU	-1	-0.797	-0.899	19.852	-13.993	-13.993	0.000	0.000	0.000	0.000
82	A	378	PHE	0	-0.045	-0.039	14.131	-1.081	-1.081	0.000	0.000	0.000	0.000
83	A	379	ILE	0	-0.009	-0.002	18.536	0.921	0.921	0.000	0.000	0.000	0.000
84	A	380	ILE	0	-0.009	-0.003	17.684	-1.113	-1.113	0.000	0.000	0.000	0.000
85	A	381	VAL	0	-0.017	0.001	19.852	0.821	0.821	0.000	0.000	0.000	0.000
86	A	382	LEU	0	-0.035	-0.012	20.812	-0.705	-0.705	0.000	0.000	0.000	0.000
87	A	383	THR	0	0.018	-0.027	22.141	0.685	0.685	0.000	0.000	0.000	0.000
88	A	384	GLU	-1	-0.920	-0.966	24.596	-11.509	-11.509	0.000	0.000	0.000	0.000
89	A	385	ALA	0	-0.005	0.021	25.436	0.258	0.258	0.000	0.000	0.000	0.000
90	A	386	SER	0	0.046	0.008	27.503	0.275	0.275	0.000	0.000	0.000	0.000
91	A	387	GLU	-1	-0.854	-0.938	29.976	-9.298	-9.298	0.000	0.000	0.000	0.000
92	A	388	ASN	0	0.023	-0.001	31.089	-0.237	-0.237	0.000	0.000	0.000	0.000
93	A	389	GLU	-1	-0.894	-0.936	26.127	-11.935	-11.935	0.000	0.000	0.000	0.000
94	A	390	THR	0	0.028	0.024	26.371	-0.640	-0.640	0.000	0.000	0.000	0.000
95	A	391	LEU	0	0.040	0.018	26.500	-0.460	-0.460	0.000	0.000	0.000	0.000
96	A	392	ARG	1	0.943	0.977	27.192	10.716	10.716	0.000	0.000	0.000	0.000
97	A	393	THR	0	-0.035	-0.031	21.845	-0.434	-0.434	0.000	0.000	0.000	0.000
98	A	394	ALA	0	0.036	0.022	23.051	-0.594	-0.594	0.000	0.000	0.000	0.000
99	A	395	GLU	-1	-0.798	-0.906	24.242	-11.413	-11.413	0.000	0.000	0.000	0.000
100	A	396	ARG	1	0.768	0.903	21.006	13.902	13.902	0.000	0.000	0.000	0.000
101	A	397	ILE	0	0.018	0.005	18.834	-0.368	-0.368	0.000	0.000	0.000	0.000
102	A	398	ARG	1	0.791	0.874	20.656	11.099	11.099	0.000	0.000	0.000	0.000
103	A	399	SER	0	-0.024	-0.004	23.068	-0.214	-0.214	0.000	0.000	0.000	0.000
104	A	400	ARG	1	0.926	0.954	18.397	14.508	14.508	0.000	0.000	0.000	0.000
105	A	401	VAL	0	0.028	0.027	17.645	-0.466	-0.466	0.000	0.000	0.000	0.000
106	A	402	GLU	-1	-0.835	-0.907	19.897	-11.445	-11.445	0.000	0.000	0.000	0.000
107	A	403	LYS	1	0.831	0.926	22.048	12.052	12.052	0.000	0.000	0.000	0.000
108	A	404	THR	0	-0.038	-0.027	16.039	-0.614	-0.614	0.000	0.000	0.000	0.000
109	A	405	LYS	1	0.838	0.912	18.931	12.702	12.702	0.000	0.000	0.000	0.000
110	A	406	LEU	0	0.000	0.005	14.848	-0.402	-0.402	0.000	0.000	0.000	0.000
111	A	407	LYS	1	0.855	0.934	17.863	13.789	13.789	0.000	0.000	0.000	0.000
112	A	408	ALA	0	0.063	0.039	18.625	-0.772	-0.772	0.000	0.000	0.000	0.000
113	A	409	ALA	0	-0.012	-0.017	20.603	0.143	0.143	0.000	0.000	0.000	0.000
114	A	410	ASN	0	-0.015	-0.018	21.661	-0.190	-0.190	0.000	0.000	0.000	0.000
115	A	411	GLY	0	-0.007	0.001	22.804	0.418	0.418	0.000	0.000	0.000	0.000
116	A	412	GLU	-1	-0.887	-0.924	23.822	-11.079	-11.079	0.000	0.000	0.000	0.000
117	A	413	ASP	-1	-0.854	-0.929	22.628	-13.326	-13.326	0.000	0.000	0.000	0.000
118	A	414	ILE	0	-0.020	-0.008	19.143	0.397	0.397	0.000	0.000	0.000	0.000
119	A	415	ALA	0	-0.031	-0.011	22.589	-0.206	-0.206	0.000	0.000	0.000	0.000
120	A	416	LEU	0	0.007	-0.002	18.384	-0.259	-0.259	0.000	0.000	0.000	0.000
121	A	417	SER	0	-0.041	-0.048	22.832	0.328	0.328	0.000	0.000	0.000	0.000
122	A	418	LEU	0	-0.028	-0.010	19.668	-0.467	-0.467	0.000	0.000	0.000	0.000
123	A	419	SER	0	-0.003	-0.025	23.666	0.643	0.643	0.000	0.000	0.000	0.000
124	A	420	ILE	0	-0.024	-0.027	22.912	-0.513	-0.513	0.000	0.000	0.000	0.000
125	A	421	GLY	0	0.026	0.032	26.132	0.519	0.519	0.000	0.000	0.000	0.000
126	A	422	ALA	0	-0.027	-0.023	26.929	-0.477	-0.477	0.000	0.000	0.000	0.000
127	A	423	ALA	0	0.037	0.016	28.602	0.464	0.464	0.000	0.000	0.000	0.000
128	A	424	MET	0	0.003	0.018	29.300	-0.495	-0.495	0.000	0.000	0.000	0.000
129	A	425	PHE	0	-0.011	-0.009	30.258	0.156	0.156	0.000	0.000	0.000	0.000
130	A	426	ASN	0	-0.006	-0.004	32.079	0.181	0.181	0.000	0.000	0.000	0.000
131	A	427	GLY	0	0.039	0.019	34.877	0.265	0.265	0.000	0.000	0.000	0.000
132	A	428	HIS	0	-0.013	-0.003	36.286	-0.056	-0.056	0.000	0.000	0.000	0.000
133	A	429	PRO	0	-0.003	-0.013	34.474	-0.255	-0.255	0.000	0.000	0.000	0.000
134	A	430	ASP	-1	-0.905	-0.949	32.750	-9.750	-9.750	0.000	0.000	0.000	0.000
135	A	431	TYR	0	-0.021	-0.032	25.987	-0.142	-0.142	0.000	0.000	0.000	0.000
136	A	432	GLU	-1	-0.869	-0.936	29.051	-10.754	-10.754	0.000	0.000	0.000	0.000
137	A	433	ARG	1	0.948	0.979	30.605	8.417	8.417	0.000	0.000	0.000	0.000
138	A	434	LEU	0	-0.023	-0.004	28.580	0.069	0.069	0.000	0.000	0.000	0.000
139	A	435	ILE	0	-0.011	-0.011	25.497	-0.213	-0.213	0.000	0.000	0.000	0.000
140	A	436	GLN	0	0.018	0.000	28.703	0.083	0.083	0.000	0.000	0.000	0.000
141	A	437	ILE	0	0.031	0.026	31.927	0.003	0.003	0.000	0.000	0.000	0.000
142	A	438	ALA	0	0.010	-0.004	27.921	0.055	0.055	0.000	0.000	0.000	0.000
143	A	439	ASP	-1	-0.952	-0.970	29.041	-10.921	-10.921	0.000	0.000	0.000	0.000
144	A	440	GLU	-1	-0.856	-0.925	30.033	-8.697	-8.697	0.000	0.000	0.000	0.000
145	A	441	ALA	0	-0.011	-0.004	31.104	0.123	0.123	0.000	0.000	0.000	0.000
146	A	442	LEU	0	-0.004	0.004	25.787	0.023	0.023	0.000	0.000	0.000	0.000
147	A	443	TYR	0	0.009	0.004	29.711	0.109	0.109	0.000	0.000	0.000	0.000
148	A	444	ILE	0	0.011	0.004	32.422	0.161	0.161	0.000	0.000	0.000	0.000
149	A	445	ALA	0	-0.019	-0.008	29.997	0.154	0.154	0.000	0.000	0.000	0.000
150	A	446	LYS	1	0.763	0.863	25.381	12.420	12.420	0.000	0.000	0.000	0.000
151	A	447	ARG	1	0.936	0.969	31.594	8.218	8.218	0.000	0.000	0.000	0.000
152	A	448	ARG	1	0.810	0.880	35.050	8.953	8.953	0.000	0.000	0.000	0.000
153	A	449	GLY	0	-0.020	-0.007	34.410	0.126	0.126	0.000	0.000	0.000	0.000
154	A	450	ARG	1	0.912	0.982	28.857	10.167	10.167	0.000	0.000	0.000	0.000
155	A	451	ASN	0	-0.040	-0.015	27.282	-0.107	-0.107	0.000	0.000	0.000	0.000
156	A	452	ARG	1	0.887	0.949	28.315	9.658	9.658	0.000	0.000	0.000	0.000
157	A	453	VAL	0	0.021	0.016	26.937	-0.446	-0.446	0.000	0.000	0.000	0.000
158	A	454	GLU	-1	-0.866	-0.910	29.448	-8.691	-8.691	0.000	0.000	0.000	0.000
159	A	455	LEU	0	-0.029	-0.013	30.931	-0.380	-0.380	0.000	0.000	0.000	0.000
160	A	456	TRP	0	-0.032	-0.023	32.716	0.326	0.326	0.000	0.000	0.000	0.000
161	A	457	LYS	1	0.957	0.966	34.655	8.406	8.406	0.000	0.000	0.000	0.000
162	A	458	ALA	0	0.013	0.000	38.275	0.027	0.027	0.000	0.000	0.000	0.000
163	A	459	SER	0	-0.075	-0.030	41.465	0.079	0.079	0.000	0.000	0.000	0.000
164	A	460	LEU	-1	-0.951	-0.951	36.363	-7.754	-7.754	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:297:MET)