FMO DATABASE

FMODB ID: 4GLRN

Calculation Name: 3J7R-b-Other547

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: 3J7R

Chain ID: b

ChEMBL ID:

UniProt ID: P63246

Base Structure: ElectronMicroscopy

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	75
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-330640.74784
FMO2-HF: Nuclear repulsion	300195.448042
FMO2-HF: Total energy	-30445.299798
FMO2-MP2: Total energy	-30533.640172

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:ALA)

Summations of interaction energy for fragment #1(A:2:ALA)

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.
136.857	138.259	-0.02	-0.643	-0.74	0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.900 / q_NPA : 0.938

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	SER	0	0.066	0.036	3.855	0.425	1.827	-0.020	-0.643	-0.740	0.001
4	A	5	LYS	1	0.938	0.975	6.730	23.064	23.064	0.000	0.000	0.000	0.000
5	A	6	ASN	0	0.011	-0.005	9.021	0.377	0.377	0.000	0.000	0.000	0.000
6	A	7	HIS	0	0.095	0.045	12.253	1.414	1.414	0.000	0.000	0.000	0.000
7	A	8	THR	0	-0.031	-0.031	15.697	-0.173	-0.173	0.000	0.000	0.000	0.000
8	A	9	THR	0	0.039	0.018	18.065	0.295	0.295	0.000	0.000	0.000	0.000
9	A	10	HIS	0	0.014	0.005	19.304	0.765	0.765	0.000	0.000	0.000	0.000
10	A	11	ASN	0	0.023	0.010	20.493	0.847	0.847	0.000	0.000	0.000	0.000
11	A	12	GLN	0	0.035	0.024	21.126	0.466	0.466	0.000	0.000	0.000	0.000
12	A	13	SER	0	0.096	0.060	24.227	0.427	0.427	0.000	0.000	0.000	0.000
13	A	14	ARG	1	0.986	0.983	26.235	11.687	11.687	0.000	0.000	0.000	0.000
14	A	15	LYS	1	0.865	0.937	21.377	13.895	13.895	0.000	0.000	0.000	0.000
15	A	16	TRP	0	0.072	0.029	25.162	0.394	0.394	0.000	0.000	0.000	0.000
16	A	17	HIS	0	-0.007	-0.013	29.765	0.496	0.496	0.000	0.000	0.000	0.000
17	A	18	ARG	1	0.899	0.964	26.895	10.972	10.972	0.000	0.000	0.000	0.000
18	A	19	ASN	0	0.018	0.008	32.194	0.069	0.069	0.000	0.000	0.000	0.000
19	A	20	GLY	0	0.023	0.011	34.481	0.285	0.285	0.000	0.000	0.000	0.000
20	A	21	ILE	0	0.005	0.019	32.839	0.037	0.037	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.899	0.947	35.723	8.026	8.026	0.000	0.000	0.000	0.000
22	A	23	LYS	1	1.007	0.999	38.636	7.353	7.353	0.000	0.000	0.000	0.000
23	A	24	PRO	0	0.028	0.009	39.709	0.122	0.122	0.000	0.000	0.000	0.000
24	A	25	ARG	1	0.934	0.955	41.893	6.874	6.874	0.000	0.000	0.000	0.000
25	A	26	SER	0	-0.010	0.008	44.783	0.016	0.016	0.000	0.000	0.000	0.000
26	A	27	GLN	0	0.054	0.036	47.187	0.064	0.064	0.000	0.000	0.000	0.000
27	A	28	ARG	1	0.980	0.997	50.480	5.412	5.412	0.000	0.000	0.000	0.000
28	A	29	TYR	0	-0.063	-0.048	53.706	0.033	0.033	0.000	0.000	0.000	0.000
29	A	30	GLU	-1	-0.877	-0.920	48.995	-6.442	-6.442	0.000	0.000	0.000	0.000
30	A	31	SER	0	-0.038	-0.024	48.444	0.073	0.073	0.000	0.000	0.000	0.000
31	A	32	LEU	0	0.072	0.021	50.263	-0.052	-0.052	0.000	0.000	0.000	0.000
32	A	33	LYS	1	0.942	0.973	44.281	7.138	7.138	0.000	0.000	0.000	0.000
33	A	34	GLY	0	0.033	0.005	48.307	-0.162	-0.162	0.000	0.000	0.000	0.000
34	A	35	VAL	0	-0.004	0.017	49.182	0.009	0.009	0.000	0.000	0.000	0.000
35	A	36	ASP	-1	-0.773	-0.879	52.733	-5.740	-5.740	0.000	0.000	0.000	0.000
36	A	37	PRO	0	0.065	-0.003	53.354	0.109	0.109	0.000	0.000	0.000	0.000
37	A	38	LYS	1	0.928	0.975	56.114	5.415	5.415	0.000	0.000	0.000	0.000
38	A	39	PHE	0	0.030	0.016	57.767	0.147	0.147	0.000	0.000	0.000	0.000
39	A	40	LEU	0	-0.005	0.005	53.753	0.114	0.114	0.000	0.000	0.000	0.000
40	A	41	ARG	1	0.961	0.965	58.447	5.193	5.193	0.000	0.000	0.000	0.000
41	A	42	ASN	0	0.015	0.015	61.248	0.130	0.130	0.000	0.000	0.000	0.000
42	A	43	MET	0	0.049	0.025	58.581	0.084	0.084	0.000	0.000	0.000	0.000
43	A	44	ARG	1	0.932	0.970	58.095	5.444	5.444	0.000	0.000	0.000	0.000
44	A	45	PHE	0	-0.018	-0.013	62.946	0.073	0.073	0.000	0.000	0.000	0.000
45	A	46	ALA	0	0.020	0.007	66.001	0.082	0.082	0.000	0.000	0.000	0.000
46	A	47	LYS	1	0.952	0.978	60.349	5.337	5.337	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.897	0.963	66.188	4.772	4.772	0.000	0.000	0.000	0.000
48	A	49	HIS	0	-0.060	-0.045	67.693	0.040	0.040	0.000	0.000	0.000	0.000
49	A	50	ASN	0	0.083	0.046	68.295	0.008	0.008	0.000	0.000	0.000	0.000
50	A	51	LYS	1	0.994	1.003	71.258	4.495	4.495	0.000	0.000	0.000	0.000
51	A	52	LYS	1	0.935	0.977	73.497	4.357	4.357	0.000	0.000	0.000	0.000
52	A	53	GLY	0	0.039	0.004	75.973	0.009	0.009	0.000	0.000	0.000	0.000
53	A	54	LEU	0	0.021	0.013	74.826	0.020	0.020	0.000	0.000	0.000	0.000
54	A	55	LYS	1	0.916	0.956	77.235	3.961	3.961	0.000	0.000	0.000	0.000
55	A	56	LYS	1	1.026	1.010	79.805	4.014	4.014	0.000	0.000	0.000	0.000
56	A	57	MET	0	0.015	0.015	72.830	0.013	0.013	0.000	0.000	0.000	0.000
57	A	58	GLN	0	0.052	0.030	78.358	-0.016	-0.016	0.000	0.000	0.000	0.000
58	A	59	ALA	0	0.031	0.017	80.036	0.021	0.021	0.000	0.000	0.000	0.000
59	A	60	ASN	0	0.006	-0.003	78.852	0.066	0.066	0.000	0.000	0.000	0.000
60	A	61	ASN	0	0.019	0.008	75.828	0.007	0.007	0.000	0.000	0.000	0.000
61	A	62	ALA	0	0.032	0.022	80.157	0.009	0.009	0.000	0.000	0.000	0.000
62	A	63	LYS	1	0.924	0.978	83.429	3.692	3.692	0.000	0.000	0.000	0.000
63	A	64	ALA	0	0.042	0.015	80.758	0.026	0.026	0.000	0.000	0.000	0.000
64	A	65	MET	0	-0.019	-0.019	78.604	0.009	0.009	0.000	0.000	0.000	0.000
65	A	66	SER	0	-0.009	-0.013	82.804	0.030	0.030	0.000	0.000	0.000	0.000
66	A	67	ALA	0	0.016	0.009	85.304	0.029	0.029	0.000	0.000	0.000	0.000
67	A	68	ARG	1	0.924	0.956	77.012	4.101	4.101	0.000	0.000	0.000	0.000
68	A	69	ALA	0	-0.007	0.012	84.426	-0.009	-0.009	0.000	0.000	0.000	0.000
69	A	70	GLU	-1	-0.863	-0.946	86.158	-3.503	-3.503	0.000	0.000	0.000	0.000
70	A	71	ALA	0	-0.074	-0.031	85.085	0.013	0.013	0.000	0.000	0.000	0.000
71	A	72	ILE	0	-0.038	-0.021	83.513	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	73	LYS	1	0.872	0.943	86.387	3.535	3.535	0.000	0.000	0.000	0.000
73	A	74	ALA	0	0.037	0.011	89.793	0.037	0.037	0.000	0.000	0.000	0.000
74	A	75	LEU	0	-0.093	-0.030	86.697	0.010	0.010	0.000	0.000	0.000	0.000
75	A	76	VAL	-1	-0.918	-0.953	88.805	-3.481	-3.481	0.000	0.000	0.000	0.000

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