FMO DATABASE

FMODB ID: 2GN6R

Calculation Name: 4V8P-A-Xray547

Preferred Name:

Target Type:

Ligand Name: magnesium ion | zinc ion

Ligand 3-letter code: MG | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4V8P

Chain ID: A

ChEMBL ID:

UniProt ID: Q245F2

Base Structure: X-ray

Registration Date: 2025-10-06

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	126
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1021923.133515
FMO2-HF: Nuclear repulsion	972418.270456
FMO2-HF: Total energy	-49504.863059
FMO2-MP2: Total energy	-49652.00901

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:2:LYS)

Summations of interaction energy for fragment #1(A:2: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.
386.642	392.654	17.778	-10.855	-12.934	-0.123

Interaction energy analysis for fragmet #1(A:2:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.693 / q_NPA : 1.833

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

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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	4	HIS	0	0.075	0.055	3.208	-2.792	0.366	0.038	-1.404	-1.792	-0.008
4	A	5	VAL	0	0.010	0.003	2.416	-37.252	-33.590	2.204	-2.703	-3.163	-0.034
5	A	6	GLU	-1	-0.820	-0.917	3.555	-83.991	-83.114	0.014	-0.427	-0.464	-0.004
6	A	7	VAL	0	-0.038	-0.007	2.315	6.425	7.742	0.731	-0.505	-1.543	-0.002
7	A	8	SER	0	-0.018	-0.019	1.886	-35.777	-37.653	8.314	-3.446	-2.992	-0.045
8	A	9	SER	0	0.049	0.017	1.929	-13.807	-15.107	6.477	-2.290	-2.887	-0.030
9	A	10	ALA	0	0.035	0.034	4.036	8.541	8.715	0.000	-0.080	-0.093	0.000
10	A	11	ARG	1	1.038	1.001	7.323	42.056	42.056	0.000	0.000	0.000	0.000
11	A	12	ARG	1	0.993	0.998	10.504	36.675	36.675	0.000	0.000	0.000	0.000
12	A	13	LYS	1	0.994	0.997	8.263	56.207	56.207	0.000	0.000	0.000	0.000
13	A	14	GLN	0	0.048	0.029	6.701	6.596	6.596	0.000	0.000	0.000	0.000
14	A	15	ARG	1	0.982	0.986	10.981	34.461	34.461	0.000	0.000	0.000	0.000
15	A	16	LYS	1	0.964	0.990	13.983	34.640	34.640	0.000	0.000	0.000	0.000
16	A	17	ALA	0	0.021	0.009	12.700	1.989	1.989	0.000	0.000	0.000	0.000
17	A	18	HIS	0	0.048	0.029	14.652	0.397	0.397	0.000	0.000	0.000	0.000
18	A	19	PHE	0	-0.015	-0.011	16.589	1.814	1.814	0.000	0.000	0.000	0.000
19	A	20	ALA	0	-0.017	-0.005	18.443	1.671	1.671	0.000	0.000	0.000	0.000
20	A	21	SER	0	-0.013	-0.009	18.433	0.934	0.934	0.000	0.000	0.000	0.000
21	A	22	PRO	0	0.090	0.038	19.767	1.379	1.379	0.000	0.000	0.000	0.000
22	A	23	SER	0	0.023	0.006	22.589	-0.592	-0.592	0.000	0.000	0.000	0.000
23	A	24	HIS	0	0.056	0.013	20.988	0.432	0.432	0.000	0.000	0.000	0.000
24	A	25	LEU	0	0.038	0.028	17.073	-0.279	-0.279	0.000	0.000	0.000	0.000
25	A	26	ARG	1	0.845	0.920	20.381	25.211	25.211	0.000	0.000	0.000	0.000
26	A	27	GLN	0	-0.022	-0.028	22.449	-0.239	-0.239	0.000	0.000	0.000	0.000
27	A	28	THR	0	-0.010	0.003	17.960	0.323	0.323	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.015	0.005	16.011	-0.471	-0.471	0.000	0.000	0.000	0.000
29	A	30	MET	0	-0.092	-0.021	19.485	0.399	0.399	0.000	0.000	0.000	0.000
30	A	31	SER	0	-0.017	-0.020	20.032	1.012	1.012	0.000	0.000	0.000	0.000
31	A	32	ALA	0	0.001	0.006	22.440	-0.304	-0.304	0.000	0.000	0.000	0.000
32	A	33	HIS	0	-0.027	-0.024	23.111	-0.678	-0.678	0.000	0.000	0.000	0.000
33	A	34	LEU	0	0.008	-0.001	24.219	0.950	0.950	0.000	0.000	0.000	0.000
34	A	35	SER	0	0.018	0.011	26.682	-0.312	-0.312	0.000	0.000	0.000	0.000
35	A	36	LYS	0	0.078	0.039	28.138	-0.810	-0.810	0.000	0.000	0.000	0.000
36	A	37	ASP	-1	-0.804	-0.884	29.839	-18.026	-18.026	0.000	0.000	0.000	0.000
37	A	38	LEU	0	-0.060	-0.036	29.429	-0.133	-0.133	0.000	0.000	0.000	0.000
38	A	39	ARG	1	0.800	0.883	24.726	22.232	22.232	0.000	0.000	0.000	0.000
39	A	40	SER	0	0.032	0.005	26.857	-0.530	-0.530	0.000	0.000	0.000	0.000
40	A	41	LYS	1	0.905	0.970	29.198	17.639	17.639	0.000	0.000	0.000	0.000
41	A	42	TYR	0	-0.005	-0.022	27.549	0.474	0.474	0.000	0.000	0.000	0.000
42	A	43	ASN	0	0.031	0.042	22.805	-0.364	-0.364	0.000	0.000	0.000	0.000
43	A	44	VAL	0	0.020	0.001	21.986	-1.123	-1.123	0.000	0.000	0.000	0.000
44	A	45	ARG	1	0.979	0.998	18.443	29.287	29.287	0.000	0.000	0.000	0.000
45	A	46	SER	0	0.035	0.014	19.050	0.875	0.875	0.000	0.000	0.000	0.000
46	A	47	MET	0	0.029	0.033	22.096	-0.486	-0.486	0.000	0.000	0.000	0.000
47	A	48	PRO	0	0.031	0.022	22.300	0.104	0.104	0.000	0.000	0.000	0.000
48	A	49	VAL	0	0.024	0.022	24.439	0.877	0.877	0.000	0.000	0.000	0.000
49	A	50	ARG	1	0.917	0.955	27.835	17.909	17.909	0.000	0.000	0.000	0.000
50	A	51	LYS	1	0.911	0.933	31.193	17.044	17.044	0.000	0.000	0.000	0.000
51	A	52	ASP	-1	-0.781	-0.863	34.502	-16.058	-16.058	0.000	0.000	0.000	0.000
52	A	53	ASP	-1	-0.755	-0.834	30.776	-19.631	-19.631	0.000	0.000	0.000	0.000
53	A	54	GLU	-1	-0.884	-0.936	34.156	-15.851	-15.851	0.000	0.000	0.000	0.000
54	A	55	VAL	0	-0.032	-0.026	30.760	-0.555	-0.555	0.000	0.000	0.000	0.000
55	A	56	LEU	0	0.051	0.038	32.182	0.561	0.561	0.000	0.000	0.000	0.000
56	A	57	ILE	0	0.002	0.004	31.085	-0.918	-0.918	0.000	0.000	0.000	0.000
57	A	58	VAL	0	0.003	0.004	27.303	0.378	0.378	0.000	0.000	0.000	0.000
58	A	59	ARG	1	0.935	0.949	24.424	23.741	23.741	0.000	0.000	0.000	0.000
59	A	60	GLY	0	0.066	0.037	29.616	-0.124	-0.124	0.000	0.000	0.000	0.000
60	A	61	LYS	1	0.974	0.971	31.706	17.531	17.531	0.000	0.000	0.000	0.000
61	A	62	PHE	0	0.078	0.036	34.610	0.311	0.311	0.000	0.000	0.000	0.000
62	A	63	LYS	1	0.925	0.971	31.049	19.327	19.327	0.000	0.000	0.000	0.000
63	A	64	GLY	0	0.006	0.010	34.258	0.435	0.435	0.000	0.000	0.000	0.000
64	A	65	ASN	0	-0.011	0.001	36.230	0.666	0.666	0.000	0.000	0.000	0.000
65	A	66	LYS	1	0.902	0.931	35.862	15.737	15.737	0.000	0.000	0.000	0.000
66	A	67	GLY	0	0.044	0.027	36.594	0.513	0.513	0.000	0.000	0.000	0.000
67	A	68	LYS	1	0.991	1.001	36.440	14.298	14.298	0.000	0.000	0.000	0.000
68	A	69	VAL	0	-0.024	-0.005	32.073	0.025	0.025	0.000	0.000	0.000	0.000
69	A	70	THR	0	0.018	0.005	35.230	0.283	0.283	0.000	0.000	0.000	0.000
70	A	71	GLN	0	0.049	0.009	34.696	0.260	0.260	0.000	0.000	0.000	0.000
71	A	72	VAL	0	0.020	0.017	28.905	-0.328	-0.328	0.000	0.000	0.000	0.000
72	A	73	TYR	0	-0.010	-0.003	31.616	-0.192	-0.192	0.000	0.000	0.000	0.000
73	A	74	ARG	1	0.917	0.942	26.803	21.900	21.900	0.000	0.000	0.000	0.000
74	A	75	LYS	1	0.998	1.012	26.705	18.317	18.317	0.000	0.000	0.000	0.000
75	A	76	LYS	1	0.959	0.973	27.647	18.129	18.129	0.000	0.000	0.000	0.000
76	A	77	TRP	0	-0.008	-0.018	20.321	0.256	0.256	0.000	0.000	0.000	0.000
77	A	78	ALA	0	-0.007	0.013	26.907	-0.179	-0.179	0.000	0.000	0.000	0.000
78	A	79	ILE	0	-0.015	-0.005	27.324	0.294	0.294	0.000	0.000	0.000	0.000
79	A	80	HIS	0	0.021	0.010	30.982	0.271	0.271	0.000	0.000	0.000	0.000
80	A	81	VAL	0	-0.003	-0.004	33.698	-0.188	-0.188	0.000	0.000	0.000	0.000
81	A	82	GLU	-1	-0.872	-0.953	36.443	-14.362	-14.362	0.000	0.000	0.000	0.000
82	A	83	LYS	1	0.967	0.973	40.030	13.717	13.717	0.000	0.000	0.000	0.000
83	A	84	ILE	0	-0.015	0.014	35.706	-0.046	-0.046	0.000	0.000	0.000	0.000
84	A	85	SER	0	-0.026	-0.013	38.842	-0.304	-0.304	0.000	0.000	0.000	0.000
85	A	86	LYS	1	0.899	0.955	38.884	15.934	15.934	0.000	0.000	0.000	0.000
86	A	87	ASN	0	0.071	0.031	43.068	-0.048	-0.048	0.000	0.000	0.000	0.000
87	A	88	LYS	1	0.906	0.957	44.454	13.734	13.734	0.000	0.000	0.000	0.000
88	A	89	LEU	0	0.064	0.024	48.043	0.142	0.142	0.000	0.000	0.000	0.000
89	A	90	ASN	0	0.049	0.026	49.929	0.033	0.033	0.000	0.000	0.000	0.000
90	A	91	GLY	0	0.053	0.037	51.848	0.142	0.142	0.000	0.000	0.000	0.000
91	A	92	ALA	0	-0.028	-0.001	48.349	-0.065	-0.065	0.000	0.000	0.000	0.000
92	A	93	PRO	0	0.011	0.002	45.563	-0.318	-0.318	0.000	0.000	0.000	0.000
93	A	94	TYR	0	-0.020	-0.018	39.764	-0.366	-0.366	0.000	0.000	0.000	0.000
94	A	95	GLN	0	0.036	0.010	38.131	-0.090	-0.090	0.000	0.000	0.000	0.000
95	A	96	ILE	0	-0.027	-0.005	34.616	-0.204	-0.204	0.000	0.000	0.000	0.000
96	A	97	PRO	0	-0.078	-0.026	31.336	-0.179	-0.179	0.000	0.000	0.000	0.000
97	A	98	LEU	0	0.031	0.010	29.950	-0.251	-0.251	0.000	0.000	0.000	0.000
98	A	99	SER	0	0.041	0.013	23.515	-0.429	-0.429	0.000	0.000	0.000	0.000
99	A	100	ALA	0	0.029	0.008	23.809	0.227	0.227	0.000	0.000	0.000	0.000
100	A	101	SER	0	0.016	0.010	20.911	0.211	0.211	0.000	0.000	0.000	0.000
101	A	102	GLN	0	-0.033	-0.012	22.748	-0.451	-0.451	0.000	0.000	0.000	0.000
102	A	103	LEU	0	-0.025	-0.004	25.882	1.045	1.045	0.000	0.000	0.000	0.000
103	A	104	VAL	0	0.016	0.004	26.352	-0.919	-0.919	0.000	0.000	0.000	0.000
104	A	105	LEU	0	-0.027	-0.005	26.819	0.803	0.803	0.000	0.000	0.000	0.000
105	A	106	THR	0	0.003	-0.015	30.048	-0.012	-0.012	0.000	0.000	0.000	0.000
106	A	107	LYS	1	0.970	0.992	33.270	16.453	16.453	0.000	0.000	0.000	0.000
107	A	108	LEU	0	0.012	0.008	29.218	-0.194	-0.194	0.000	0.000	0.000	0.000
108	A	109	LYS	1	0.848	0.910	33.239	16.844	16.844	0.000	0.000	0.000	0.000
109	A	110	LEU	0	0.010	0.001	33.142	-0.702	-0.702	0.000	0.000	0.000	0.000
110	A	111	ASP	-1	-0.761	-0.896	33.244	-18.025	-18.025	0.000	0.000	0.000	0.000
111	A	112	LYS	1	1.049	1.036	33.743	16.675	16.675	0.000	0.000	0.000	0.000
112	A	113	SER	0	-0.005	0.001	30.618	-0.509	-0.509	0.000	0.000	0.000	0.000
113	A	114	ARG	1	0.734	0.821	28.326	19.800	19.800	0.000	0.000	0.000	0.000
114	A	115	GLN	0	0.035	0.016	28.878	-0.491	-0.491	0.000	0.000	0.000	0.000
115	A	116	SER	0	0.022	0.027	29.205	-0.593	-0.593	0.000	0.000	0.000	0.000
116	A	117	LEU	0	-0.039	-0.011	24.101	-0.794	-0.794	0.000	0.000	0.000	0.000
117	A	118	LEU	0	-0.062	-0.038	24.622	-0.904	-0.904	0.000	0.000	0.000	0.000
118	A	119	THR	0	0.040	0.012	25.507	-0.404	-0.404	0.000	0.000	0.000	0.000
119	A	120	ARG	1	0.909	0.938	22.713	23.154	23.154	0.000	0.000	0.000	0.000
120	A	121	LYS	1	0.845	0.915	20.360	26.274	26.274	0.000	0.000	0.000	0.000
121	A	122	ALA	0	0.018	0.013	21.407	-0.658	-0.658	0.000	0.000	0.000	0.000
122	A	123	ALA	0	0.027	0.011	23.550	-0.127	-0.127	0.000	0.000	0.000	0.000
123	A	124	SER	0	-0.013	-0.006	18.266	-0.508	-0.508	0.000	0.000	0.000	0.000
124	A	125	LEU	0	-0.080	-0.038	17.593	-1.048	-1.048	0.000	0.000	0.000	0.000
125	A	126	LYS	1	0.901	0.947	19.830	20.718	20.718	0.000	0.000	0.000	0.000
126	A	127	THR	-1	-0.913	-0.934	20.471	-26.059	-26.059	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:LYS)