FMO DATABASE

FMODB ID: 6486Z

Calculation Name: 3J80-W-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: 3J80

Chain ID: W

ChEMBL ID:

UniProt ID: P38912

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-05

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	129
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1118718.764765
FMO2-HF: Nuclear repulsion	1068525.587891
FMO2-HF: Total energy	-50193.176874
FMO2-MP2: Total energy	-50341.439354

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:THR)

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

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.
109.19	111.835	0.39	-1.076	-1.96	0.002

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.903 / 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

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	4	THR	0	0.027	0.019	2.918	1.459	3.959	0.391	-1.064	-1.828	0.002
4	A	5	SER	0	0.029	0.015	4.459	5.140	5.285	-0.001	-0.012	-0.132	0.000
5	A	6	VAL	0	0.052	0.007	7.779	0.292	0.292	0.000	0.000	0.000	0.000
6	A	7	LEU	0	-0.039	-0.017	9.624	1.199	1.199	0.000	0.000	0.000	0.000
7	A	8	ALA	0	0.046	0.022	10.531	1.185	1.185	0.000	0.000	0.000	0.000
8	A	9	ASP	-1	-0.807	-0.890	8.187	-35.714	-35.714	0.000	0.000	0.000	0.000
9	A	10	ALA	0	-0.048	-0.020	11.578	1.298	1.298	0.000	0.000	0.000	0.000
10	A	11	LEU	0	0.047	0.018	14.734	1.092	1.092	0.000	0.000	0.000	0.000
11	A	12	ASN	0	-0.015	0.005	12.200	2.252	2.252	0.000	0.000	0.000	0.000
12	A	13	ALA	0	0.038	0.020	14.671	0.954	0.954	0.000	0.000	0.000	0.000
13	A	14	ILE	0	0.027	0.012	16.301	0.951	0.951	0.000	0.000	0.000	0.000
14	A	15	ASN	0	0.023	0.017	18.584	1.661	1.661	0.000	0.000	0.000	0.000
15	A	16	ASN	0	-0.047	-0.032	16.012	-0.215	-0.215	0.000	0.000	0.000	0.000
16	A	17	ALA	0	0.013	0.009	19.567	0.649	0.649	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.744	-0.887	21.731	-11.168	-11.168	0.000	0.000	0.000	0.000
18	A	19	LYS	1	0.808	0.905	22.178	13.956	13.956	0.000	0.000	0.000	0.000
19	A	20	THR	0	-0.077	-0.042	22.626	0.316	0.316	0.000	0.000	0.000	0.000
20	A	21	GLY	0	0.047	0.045	25.387	0.398	0.398	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.862	0.933	23.143	12.942	12.942	0.000	0.000	0.000	0.000
22	A	23	ARG	1	0.955	0.962	26.300	10.011	10.011	0.000	0.000	0.000	0.000
23	A	24	GLN	0	0.029	0.032	24.672	0.369	0.369	0.000	0.000	0.000	0.000
24	A	25	VAL	0	-0.032	-0.021	18.789	-0.422	-0.422	0.000	0.000	0.000	0.000
25	A	26	LEU	0	0.007	0.015	16.243	0.130	0.130	0.000	0.000	0.000	0.000
26	A	27	ILE	0	-0.014	-0.016	14.593	-1.486	-1.486	0.000	0.000	0.000	0.000
27	A	28	ARG	1	0.947	0.964	10.237	24.322	24.322	0.000	0.000	0.000	0.000
28	A	29	PRO	0	0.000	0.001	9.955	0.163	0.163	0.000	0.000	0.000	0.000
29	A	30	SER	0	0.036	0.020	12.353	1.507	1.507	0.000	0.000	0.000	0.000
30	A	31	SER	0	0.090	0.030	13.677	0.202	0.202	0.000	0.000	0.000	0.000
31	A	32	LYS	1	1.041	1.007	15.793	15.088	15.088	0.000	0.000	0.000	0.000
32	A	33	VAL	0	-0.009	-0.004	15.432	0.581	0.581	0.000	0.000	0.000	0.000
33	A	34	ILE	0	0.005	0.011	13.440	0.466	0.466	0.000	0.000	0.000	0.000
34	A	35	ILE	0	0.036	0.033	17.611	0.636	0.636	0.000	0.000	0.000	0.000
35	A	36	LYS	1	0.874	0.936	20.759	13.291	13.291	0.000	0.000	0.000	0.000
36	A	37	PHE	0	0.029	0.010	19.331	0.415	0.415	0.000	0.000	0.000	0.000
37	A	38	LEU	0	0.022	0.011	20.086	0.406	0.406	0.000	0.000	0.000	0.000
38	A	39	GLN	0	0.084	0.035	23.081	0.203	0.203	0.000	0.000	0.000	0.000
39	A	40	VAL	0	-0.056	-0.028	24.677	0.588	0.588	0.000	0.000	0.000	0.000
40	A	41	MET	0	0.008	0.009	22.814	0.121	0.121	0.000	0.000	0.000	0.000
41	A	42	GLN	0	-0.038	-0.020	26.566	0.303	0.303	0.000	0.000	0.000	0.000
42	A	43	LYS	1	0.930	0.965	28.066	11.057	11.057	0.000	0.000	0.000	0.000
43	A	44	HIS	1	0.816	0.910	28.859	10.430	10.430	0.000	0.000	0.000	0.000
44	A	45	GLY	0	0.033	0.039	31.544	0.113	0.113	0.000	0.000	0.000	0.000
45	A	46	TYR	0	0.003	-0.003	27.850	0.167	0.167	0.000	0.000	0.000	0.000
46	A	47	ILE	0	-0.075	-0.034	24.463	-0.218	-0.218	0.000	0.000	0.000	0.000
47	A	48	GLY	0	0.023	0.016	28.080	0.409	0.409	0.000	0.000	0.000	0.000
48	A	49	GLU	-1	-0.878	-0.931	29.263	-10.024	-10.024	0.000	0.000	0.000	0.000
49	A	50	PHE	0	-0.045	-0.051	22.723	-0.537	-0.537	0.000	0.000	0.000	0.000
50	A	51	GLU	-1	-0.830	-0.907	24.556	-11.638	-11.638	0.000	0.000	0.000	0.000
51	A	52	TYR	0	-0.071	-0.049	18.305	-0.614	-0.614	0.000	0.000	0.000	0.000
52	A	53	ILE	0	0.005	-0.003	20.531	0.574	0.574	0.000	0.000	0.000	0.000
53	A	54	ASP	-1	-0.875	-0.948	20.427	-13.986	-13.986	0.000	0.000	0.000	0.000
54	A	55	ASP	-1	-0.860	-0.916	17.751	-16.598	-16.598	0.000	0.000	0.000	0.000
55	A	56	HIS	0	0.053	0.042	19.411	-0.766	-0.766	0.000	0.000	0.000	0.000
56	A	57	ARG	1	0.886	0.913	14.101	17.030	17.030	0.000	0.000	0.000	0.000
57	A	58	SER	0	-0.071	-0.019	12.759	-0.402	-0.402	0.000	0.000	0.000	0.000
58	A	59	GLY	0	0.042	0.023	14.821	0.280	0.280	0.000	0.000	0.000	0.000
59	A	60	LYS	1	0.783	0.881	15.417	16.454	16.454	0.000	0.000	0.000	0.000
60	A	61	ILE	0	-0.013	0.003	17.327	0.643	0.643	0.000	0.000	0.000	0.000
61	A	62	VAL	0	0.001	0.022	19.182	-0.805	-0.805	0.000	0.000	0.000	0.000
62	A	63	VAL	0	-0.004	-0.009	20.767	0.165	0.165	0.000	0.000	0.000	0.000
63	A	64	GLN	0	0.065	0.034	23.603	-0.405	-0.405	0.000	0.000	0.000	0.000
64	A	65	LEU	0	-0.051	-0.028	23.401	-0.045	-0.045	0.000	0.000	0.000	0.000
65	A	66	ASN	0	-0.005	-0.025	27.284	0.594	0.594	0.000	0.000	0.000	0.000
66	A	67	GLY	0	0.044	0.036	29.173	0.396	0.396	0.000	0.000	0.000	0.000
67	A	68	ARG	1	0.851	0.932	30.253	9.537	9.537	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.033	-0.010	23.972	-0.124	-0.124	0.000	0.000	0.000	0.000
69	A	70	ASN	0	0.080	0.051	26.848	-0.233	-0.233	0.000	0.000	0.000	0.000
70	A	71	LYS	1	0.912	0.934	21.283	13.898	13.898	0.000	0.000	0.000	0.000
71	A	72	CYS	0	-0.013	0.033	20.460	0.329	0.329	0.000	0.000	0.000	0.000
72	A	73	GLY	0	-0.008	-0.005	18.904	-0.701	-0.701	0.000	0.000	0.000	0.000
73	A	74	VAL	0	-0.045	-0.033	14.309	0.270	0.270	0.000	0.000	0.000	0.000
74	A	75	ILE	0	-0.008	0.004	16.581	-0.531	-0.531	0.000	0.000	0.000	0.000
75	A	76	SER	0	0.005	-0.002	12.477	-0.081	-0.081	0.000	0.000	0.000	0.000
76	A	77	PRO	0	0.000	0.019	12.769	-1.394	-1.394	0.000	0.000	0.000	0.000
77	A	78	ARG	1	0.977	0.989	12.737	21.028	21.028	0.000	0.000	0.000	0.000
78	A	79	PHE	0	0.083	0.028	16.895	0.282	0.282	0.000	0.000	0.000	0.000
79	A	80	ASN	0	-0.004	-0.015	19.895	-0.347	-0.347	0.000	0.000	0.000	0.000
80	A	81	VAL	0	0.007	0.014	22.598	0.163	0.163	0.000	0.000	0.000	0.000
81	A	82	LYS	1	0.975	0.987	25.778	10.279	10.279	0.000	0.000	0.000	0.000
82	A	83	ILE	0	0.025	0.017	29.424	0.208	0.208	0.000	0.000	0.000	0.000
83	A	84	ALA	0	0.098	0.047	31.870	0.055	0.055	0.000	0.000	0.000	0.000
84	A	85	ASP	-1	-0.881	-0.952	27.858	-10.540	-10.540	0.000	0.000	0.000	0.000
85	A	86	VAL	0	-0.020	-0.007	28.553	-0.351	-0.351	0.000	0.000	0.000	0.000
86	A	87	GLU	-1	-0.867	-0.932	29.792	-9.275	-9.275	0.000	0.000	0.000	0.000
87	A	88	LYS	1	0.868	0.933	29.574	9.772	9.772	0.000	0.000	0.000	0.000
88	A	89	TRP	0	-0.008	-0.018	21.627	-0.345	-0.345	0.000	0.000	0.000	0.000
89	A	90	THR	0	-0.014	-0.010	27.511	-0.323	-0.323	0.000	0.000	0.000	0.000
90	A	91	ALA	0	0.000	0.002	29.688	-0.029	-0.029	0.000	0.000	0.000	0.000
91	A	92	ASN	0	-0.030	-0.005	27.014	0.312	0.312	0.000	0.000	0.000	0.000
92	A	93	LEU	0	-0.068	-0.037	22.852	-0.341	-0.341	0.000	0.000	0.000	0.000
93	A	94	LEU	0	-0.020	-0.002	26.707	-0.309	-0.309	0.000	0.000	0.000	0.000
94	A	95	PRO	0	-0.022	-0.008	28.990	0.286	0.286	0.000	0.000	0.000	0.000
95	A	96	ALA	0	-0.007	0.002	32.089	0.353	0.353	0.000	0.000	0.000	0.000
96	A	97	ARG	1	0.937	0.967	33.869	7.873	7.873	0.000	0.000	0.000	0.000
97	A	98	GLN	0	-0.004	-0.001	35.926	0.128	0.128	0.000	0.000	0.000	0.000
98	A	99	PHE	0	0.048	0.032	34.444	-0.110	-0.110	0.000	0.000	0.000	0.000
99	A	100	GLY	0	0.047	0.021	30.385	-0.127	-0.127	0.000	0.000	0.000	0.000
100	A	101	TYR	0	-0.050	-0.050	27.759	0.063	0.063	0.000	0.000	0.000	0.000
101	A	102	VAL	0	0.014	0.012	24.262	-0.572	-0.572	0.000	0.000	0.000	0.000
102	A	103	ILE	0	-0.052	-0.029	22.105	0.288	0.288	0.000	0.000	0.000	0.000
103	A	104	LEU	0	0.003	-0.003	22.021	-0.781	-0.781	0.000	0.000	0.000	0.000
104	A	105	THR	0	-0.034	-0.014	19.370	0.449	0.449	0.000	0.000	0.000	0.000
105	A	106	THR	0	0.035	0.001	22.465	-0.034	-0.034	0.000	0.000	0.000	0.000
106	A	107	SER	0	0.023	0.013	25.445	-0.197	-0.197	0.000	0.000	0.000	0.000
107	A	108	ALA	0	0.023	0.018	27.203	0.100	0.100	0.000	0.000	0.000	0.000
108	A	109	GLY	0	0.011	0.006	25.628	0.173	0.173	0.000	0.000	0.000	0.000
109	A	110	ILE	0	-0.069	-0.051	19.668	-0.278	-0.278	0.000	0.000	0.000	0.000
110	A	111	MET	0	-0.038	-0.004	23.925	0.250	0.250	0.000	0.000	0.000	0.000
111	A	112	ASP	-1	-0.761	-0.869	25.385	-10.832	-10.832	0.000	0.000	0.000	0.000
112	A	113	HIS	0	0.089	0.031	27.687	-0.243	-0.243	0.000	0.000	0.000	0.000
113	A	114	GLU	-1	-0.825	-0.899	29.628	-8.936	-8.936	0.000	0.000	0.000	0.000
114	A	115	GLU	-1	-0.859	-0.924	30.561	-9.081	-9.081	0.000	0.000	0.000	0.000
115	A	116	ALA	0	-0.038	-0.023	28.895	0.164	0.164	0.000	0.000	0.000	0.000
116	A	117	HIS	0	-0.006	0.006	31.025	0.121	0.121	0.000	0.000	0.000	0.000
117	A	118	ARG	1	0.923	0.934	34.180	8.913	8.913	0.000	0.000	0.000	0.000
118	A	119	LYS	1	0.838	0.920	31.199	9.787	9.787	0.000	0.000	0.000	0.000
119	A	120	HIS	0	0.013	0.016	34.970	0.107	0.107	0.000	0.000	0.000	0.000
120	A	121	VAL	0	-0.029	-0.010	29.802	-0.028	-0.028	0.000	0.000	0.000	0.000
121	A	122	SER	0	-0.015	-0.011	27.907	-0.082	-0.082	0.000	0.000	0.000	0.000
122	A	123	GLY	0	0.032	0.004	24.865	0.118	0.118	0.000	0.000	0.000	0.000
123	A	124	LYS	1	0.809	0.914	17.619	15.781	15.781	0.000	0.000	0.000	0.000
124	A	125	ILE	0	0.027	0.026	20.634	0.048	0.048	0.000	0.000	0.000	0.000
125	A	126	LEU	0	-0.110	-0.058	16.824	-1.026	-1.026	0.000	0.000	0.000	0.000
126	A	127	GLY	0	0.031	-0.014	17.971	-0.978	-0.978	0.000	0.000	0.000	0.000
127	A	128	PHE	0	0.000	0.015	20.116	0.410	0.410	0.000	0.000	0.000	0.000
128	A	129	VAL	0	-0.029	-0.033	22.629	-0.686	-0.686	0.000	0.000	0.000	0.000
129	A	130	TYR	-1	-0.837	-0.885	25.277	-11.255	-11.255	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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