FMO DATABASE

FMODB ID: 4GJ8N

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	107
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-788438.432252
FMO2-HF: Nuclear repulsion	747289.328475
FMO2-HF: Total energy	-41149.103777
FMO2-MP2: Total energy	-41272.099641

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:7:SER)

Summations of interaction energy for fragment #1(A:7:SER)

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.
196.609	199.332	0.062	-1.253	-1.532	-0.007

Interaction energy analysis for fragmet #1(A:7:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.874 / q_NPA : 0.923

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	9	VAL	0	0.031	0.014	3.076	8.341	10.032	0.009	-0.758	-0.942	-0.003
4	A	10	ALA	0	-0.034	-0.014	3.217	-9.287	-8.255	0.053	-0.495	-0.590	-0.004
5	A	11	PRO	0	0.044	0.031	5.184	1.686	1.686	0.000	0.000	0.000	0.000
6	A	12	THR	0	0.042	0.002	7.019	3.488	3.488	0.000	0.000	0.000	0.000
7	A	13	ARG	1	0.855	0.932	10.423	18.465	18.465	0.000	0.000	0.000	0.000
8	A	14	LEU	0	0.051	0.032	12.560	0.999	0.999	0.000	0.000	0.000	0.000
9	A	15	TRP	0	-0.040	-0.033	11.941	0.051	0.051	0.000	0.000	0.000	0.000
10	A	16	VAL	0	0.053	0.039	17.747	-0.695	-0.695	0.000	0.000	0.000	0.000
11	A	17	LYS	1	0.921	0.967	16.734	17.017	17.017	0.000	0.000	0.000	0.000
12	A	18	ALA	0	0.047	0.028	20.581	0.613	0.613	0.000	0.000	0.000	0.000
13	A	19	ALA	0	0.041	0.031	22.882	-0.540	-0.540	0.000	0.000	0.000	0.000
14	A	20	PHE	0	-0.036	-0.025	25.315	0.462	0.462	0.000	0.000	0.000	0.000
15	A	21	THR	0	0.054	0.023	27.376	-0.050	-0.050	0.000	0.000	0.000	0.000
16	A	22	GLY	0	0.041	0.029	30.823	0.193	0.193	0.000	0.000	0.000	0.000
17	A	23	PHE	0	-0.018	-0.011	31.881	-0.057	-0.057	0.000	0.000	0.000	0.000
18	A	24	ARG	1	0.921	0.962	34.882	7.883	7.883	0.000	0.000	0.000	0.000
19	A	25	ARG	1	0.841	0.918	37.686	8.050	8.050	0.000	0.000	0.000	0.000
20	A	26	SER	0	0.044	0.038	40.668	0.082	0.082	0.000	0.000	0.000	0.000
21	A	27	LYS	1	0.973	0.964	43.136	6.392	6.392	0.000	0.000	0.000	0.000
22	A	28	HIS	0	0.108	0.056	44.167	-0.262	-0.262	0.000	0.000	0.000	0.000
23	A	29	THR	0	0.033	0.027	44.171	0.068	0.068	0.000	0.000	0.000	0.000
24	A	30	GLN	0	-0.002	-0.006	37.031	-0.203	-0.203	0.000	0.000	0.000	0.000
25	A	31	ASN	0	0.061	0.031	39.261	-0.040	-0.040	0.000	0.000	0.000	0.000
26	A	32	SER	0	0.048	0.013	35.477	-0.125	-0.125	0.000	0.000	0.000	0.000
27	A	33	ASN	0	-0.039	-0.017	34.503	-0.367	-0.367	0.000	0.000	0.000	0.000
28	A	34	GLN	0	-0.040	-0.013	34.336	0.003	0.003	0.000	0.000	0.000	0.000
29	A	35	ALA	0	0.037	0.033	29.807	0.120	0.120	0.000	0.000	0.000	0.000
30	A	36	LEU	0	-0.033	-0.011	31.903	0.100	0.100	0.000	0.000	0.000	0.000
31	A	37	LEU	0	0.011	-0.007	25.872	-0.336	-0.336	0.000	0.000	0.000	0.000
32	A	38	LYS	1	0.934	0.973	28.184	10.862	10.862	0.000	0.000	0.000	0.000
33	A	39	LEU	0	-0.005	-0.002	25.156	-0.543	-0.543	0.000	0.000	0.000	0.000
34	A	40	GLN	0	0.023	-0.012	20.432	-0.247	-0.247	0.000	0.000	0.000	0.000
35	A	41	ASN	0	-0.016	-0.025	23.061	0.023	0.023	0.000	0.000	0.000	0.000
36	A	42	VAL	0	0.011	0.042	26.740	0.300	0.300	0.000	0.000	0.000	0.000
37	A	43	ASN	0	0.019	-0.001	29.218	-0.159	-0.159	0.000	0.000	0.000	0.000
38	A	44	THR	0	0.069	0.043	32.425	0.195	0.195	0.000	0.000	0.000	0.000
39	A	45	LYS	1	0.861	0.933	34.395	7.248	7.248	0.000	0.000	0.000	0.000
40	A	46	GLU	-1	-0.827	-0.931	35.958	-8.116	-8.116	0.000	0.000	0.000	0.000
41	A	47	ASP	-1	-0.844	-0.918	31.262	-9.475	-9.475	0.000	0.000	0.000	0.000
42	A	48	VAL	0	-0.075	-0.051	31.264	-0.324	-0.324	0.000	0.000	0.000	0.000
43	A	49	ALA	0	0.007	0.015	31.935	-0.188	-0.188	0.000	0.000	0.000	0.000
44	A	50	PHE	0	0.040	0.032	26.642	-0.091	-0.091	0.000	0.000	0.000	0.000
45	A	51	TYR	0	-0.033	-0.040	24.776	-0.535	-0.535	0.000	0.000	0.000	0.000
46	A	52	GLN	0	-0.004	0.002	29.424	-0.117	-0.117	0.000	0.000	0.000	0.000
47	A	53	GLY	0	0.028	0.023	30.868	0.139	0.139	0.000	0.000	0.000	0.000
48	A	54	LYS	1	0.837	0.924	25.400	10.974	10.974	0.000	0.000	0.000	0.000
49	A	55	ARG	1	0.922	0.967	22.814	12.596	12.596	0.000	0.000	0.000	0.000
50	A	56	VAL	0	0.000	-0.005	22.665	-0.439	-0.439	0.000	0.000	0.000	0.000
51	A	57	VAL	0	-0.031	-0.017	18.386	0.174	0.174	0.000	0.000	0.000	0.000
52	A	58	TYR	0	0.062	0.030	20.457	-0.399	-0.399	0.000	0.000	0.000	0.000
53	A	59	ILE	0	-0.011	-0.016	14.301	-0.237	-0.237	0.000	0.000	0.000	0.000
54	A	60	TYR	0	0.022	0.011	18.341	0.085	0.085	0.000	0.000	0.000	0.000
55	A	61	LYS	1	0.976	0.979	13.245	21.084	21.084	0.000	0.000	0.000	0.000
56	A	62	GLY	0	0.012	0.004	17.963	0.947	0.947	0.000	0.000	0.000	0.000
57	A	63	GLN	0	0.049	0.028	18.700	-0.641	-0.641	0.000	0.000	0.000	0.000
58	A	64	LYS	1	0.961	0.992	15.702	18.579	18.579	0.000	0.000	0.000	0.000
59	A	65	LYS	1	0.991	0.997	19.600	12.957	12.957	0.000	0.000	0.000	0.000
60	A	66	ASN	0	0.029	0.012	19.671	-0.415	-0.415	0.000	0.000	0.000	0.000
61	A	67	GLY	0	0.066	0.046	18.104	-0.352	-0.352	0.000	0.000	0.000	0.000
62	A	68	SER	0	-0.059	-0.020	15.227	-1.274	-1.274	0.000	0.000	0.000	0.000
63	A	69	ASN	0	0.071	0.015	14.385	1.472	1.472	0.000	0.000	0.000	0.000
64	A	70	TYR	0	-0.006	-0.007	11.073	0.292	0.292	0.000	0.000	0.000	0.000
65	A	71	ARG	1	0.878	0.942	16.173	14.320	14.320	0.000	0.000	0.000	0.000
66	A	72	THR	0	0.004	-0.005	18.523	-0.622	-0.622	0.000	0.000	0.000	0.000
67	A	73	ILE	0	-0.010	0.009	20.463	0.503	0.503	0.000	0.000	0.000	0.000
68	A	74	TRP	0	0.038	0.012	18.944	-0.148	-0.148	0.000	0.000	0.000	0.000
69	A	75	GLY	0	0.063	0.018	24.261	0.483	0.483	0.000	0.000	0.000	0.000
70	A	76	ARG	1	0.864	0.946	26.117	9.654	9.654	0.000	0.000	0.000	0.000
71	A	77	ILE	0	0.033	0.029	26.639	0.164	0.164	0.000	0.000	0.000	0.000
72	A	78	GLY	0	-0.017	0.002	29.787	0.061	0.061	0.000	0.000	0.000	0.000
73	A	79	LYS	1	0.950	0.966	33.523	7.913	7.913	0.000	0.000	0.000	0.000
74	A	80	ALA	0	0.067	0.045	34.476	-0.239	-0.239	0.000	0.000	0.000	0.000
75	A	81	HIS	0	-0.038	-0.029	35.744	0.296	0.296	0.000	0.000	0.000	0.000
76	A	82	GLY	0	0.030	0.019	36.842	-0.127	-0.127	0.000	0.000	0.000	0.000
77	A	83	ASN	0	0.030	-0.006	38.166	-0.130	-0.130	0.000	0.000	0.000	0.000
78	A	84	ASN	0	0.059	0.038	35.680	0.039	0.039	0.000	0.000	0.000	0.000
79	A	85	GLY	0	0.023	0.010	32.248	-0.139	-0.139	0.000	0.000	0.000	0.000
80	A	86	VAL	0	-0.024	-0.011	30.968	-0.397	-0.397	0.000	0.000	0.000	0.000
81	A	87	ALA	0	0.017	0.009	30.358	0.271	0.271	0.000	0.000	0.000	0.000
82	A	88	VAL	0	-0.030	-0.011	31.845	-0.128	-0.128	0.000	0.000	0.000	0.000
83	A	89	ALA	0	0.004	-0.003	28.769	-0.080	-0.080	0.000	0.000	0.000	0.000
84	A	90	ARG	1	0.954	0.976	30.715	8.719	8.719	0.000	0.000	0.000	0.000
85	A	91	PHE	0	0.018	-0.013	24.321	-0.311	-0.311	0.000	0.000	0.000	0.000
86	A	92	ALA	0	0.005	0.011	28.055	0.304	0.304	0.000	0.000	0.000	0.000
87	A	93	HIS	0	-0.031	-0.015	28.738	0.126	0.126	0.000	0.000	0.000	0.000
88	A	94	ASN	0	0.020	0.001	29.252	-0.420	-0.420	0.000	0.000	0.000	0.000
89	A	95	LEU	0	-0.004	0.006	25.608	-0.116	-0.116	0.000	0.000	0.000	0.000
90	A	96	PRO	0	0.040	0.023	26.379	0.332	0.332	0.000	0.000	0.000	0.000
91	A	97	PRO	0	0.066	0.009	28.647	-0.275	-0.275	0.000	0.000	0.000	0.000
92	A	98	GLN	0	0.028	0.008	27.229	-0.350	-0.350	0.000	0.000	0.000	0.000
93	A	99	ALA	0	-0.028	0.000	24.972	-0.349	-0.349	0.000	0.000	0.000	0.000
94	A	100	ILE	0	-0.005	0.021	25.580	-0.333	-0.333	0.000	0.000	0.000	0.000
95	A	101	GLY	0	0.015	0.023	26.162	0.018	0.018	0.000	0.000	0.000	0.000
96	A	102	SER	0	-0.093	-0.057	21.399	-0.669	-0.669	0.000	0.000	0.000	0.000
97	A	103	VAL	0	-0.007	-0.017	18.954	0.306	0.306	0.000	0.000	0.000	0.000
98	A	104	LEU	0	-0.031	-0.011	19.421	-0.639	-0.639	0.000	0.000	0.000	0.000
99	A	105	ARG	1	0.914	0.953	11.920	20.025	20.025	0.000	0.000	0.000	0.000
100	A	106	VAL	0	0.055	0.031	19.232	0.412	0.412	0.000	0.000	0.000	0.000
101	A	107	MET	0	-0.030	-0.016	15.872	-0.533	-0.533	0.000	0.000	0.000	0.000
102	A	108	LEU	0	0.064	0.016	20.724	0.579	0.579	0.000	0.000	0.000	0.000
103	A	109	TYR	0	-0.012	-0.013	17.670	0.434	0.434	0.000	0.000	0.000	0.000
104	A	110	PRO	0	-0.040	-0.008	23.450	0.209	0.209	0.000	0.000	0.000	0.000
105	A	111	ASN	0	0.023	0.004	26.983	0.181	0.181	0.000	0.000	0.000	0.000
106	A	112	ARG	1	0.879	0.931	28.728	9.270	9.270	0.000	0.000	0.000	0.000
107	A	113	ALA	-1	-0.817	-0.880	32.275	-8.431	-8.431	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:SER)